The complex body and mind and how we function.

Probiotics are important for our Health

2012-02-10T12:58:00.000-08:00

We have trillions of bacteria in our bowels. These have evolved to help us. The bacteria do many things but regulating the immune system is one of the most important. (see previous blogs on bacteria). These bacteria are in communication with the immune system (70% in the gut area) and tell it many important things.

One method they use is to promote the chemical messengers of the immune system,cytokines that regulate and control many activities. They are small chemicals that pass through out the body to communicate with the far reaching immune system. Certain bacteria are more capable to do this then others. S.Therophilus, B. breve and L. Lactis were particularly good at this. Also,certain bacteria produce specific types of cytokines that may be helpful with certain specific infections. By finding out these types therapies could be created. S.Thermophilus and leuconstoc types were effective in different types of cytokines stimulation.

Use of probiotics has been shown to reduce inflammatory markers such as CRP and to increase anti inflammatory cytokines .

Our overall health is very much related to what is going on in the large intestine. It is just not the type of bacteria oresent but also the diet we eat that can harm or protect the "good' bacteria. Barley,beans and other fibers that arrive in the large bowel undigested are good sources of food for our bacteria helpers. Blueberry fiber has been shown to be important. The combination of blueberrie and probiotics was a boost to good guys and reduction of the bad bacteria. The levels of two important chemicals,butyric acid and propionic acid increased in the blood when this was eaten. Both of these are important in anti inflammatory actions. Rye bran is also helpful but not as much as the blueberry- probiotics. Blueberries are also helpful to protect the liver from damages. Scarring of the liver is reduced by this diet.(Green tea has also shown to be protective to liver scarring).

Use of antibiotics often kills off many helpful bacteria. Probiotics restore these colonies of important bacteria. At least a pill with 10 billion bacteria should be taken each day.

Fooling the Immune system

2011-12-31T11:43:00.000-08:00

Our Immune system is one of the most important things that evolution has done. It allows us to stay healthy in a sea of possible diseases. It lines the skin,gut and has sentries posted all over the body to prevent invaders from harming us. However,it was not developed to allow other helpful things to enter.
We are now working out ways to fool the system to allow friends but not foes into the body.

Transplanting foreign tissues into new hosts is an important medical advance. New hearts,kidneys,livers,lungs and other vital organs are now able to be transplanted. The body still recognizes these new tissues as invaders so many dangerous and uncomfortable drugs are used to stop the immune cells from doing their job.

The body T cells are at the heart of this rejection process. The T cells must receive a message from an antigen -presenting cell that offers the proteins from the invader to the cell surface of the T cell for recognition. This process depends on a connection between the two cells (a cellular handshake). If this handshake is stopped the T cells will not attack the new tissues. They researchers developed antibody molecules to the specific areas on the T cell surface that blocks the ability to complete the handshake and the T cell is not alerted to the new tissue. It worked. The T cells were unable to attack new tissues protected this way. Also, it is found that only that specific handshake area was compromised and the T cell retained its ability to act against other invaders. A specific protection.

When we get Arthritis or other foreign invaders we use our first line of defense in the Immune system to start the protection process. These are the large macrophages that are patrolling at all times to stop foreign (or sometimes even our own tissues) invaders. The engulf and trap particle and wall them off. They release chemicals (cytokines) to alert other immune cells to help. These same chemicals cause swelling,increase blood and pain sensations. if these are continuous then a chronic inflammation such as arthritis occurs. if there was a way to block the release of these cytokines then the resultant effects of inflammation (including pain) could be stopped.

It was discovered that the chemical for botulism will block this pathway in the macrophage. By wrapping the dangerous molecule in a shield of antigen like substance the macrophage engulfs it and the chemical is released and the cytokine release stopped. The inflammatory reaction is stopped and the pain is stopped.

By attaching certain chemicals to antibodies that can get through the blood Brain barrier these chemicals are allowed to pass where normally they do not. By using nano like sizes certain drugs can pass through these same small holes and enter the brain.

There have been reports of significant results in various cancers by creating vaccines. Cancer cells have many cell wall proteins that often help the cancer cell survive. Some of these cause the immune system to not recognize the rogue cell and it escapes destruction. By making antibodies to these specific cancer cell wall proteins the body is alerted and the immune system now sees these as foreign dangers, and the whole system goes into action. The cells are targeted and then destroyed. Also,the message remains and when a recurrence happens the immune system again does its job.

This same ability of the immune cells to recognize foreign invaders can also lead to serious disease. If a virus or other particle triggers off a T cell immune response to its peptide or protein structure the T cell may also find a similar type on the surface of a normal body cell. It will then attack this cell thinking it is a invader. This is shown to happen with the surface of Beta cells in the pancreas where a small part of the insulin molecule is similar to a foreign invader to the T cell and it will kill the body cell. Diabetes 1 can result.

There are Killer T cells and also similar Regulatory T cells. The Regulatory cells can block the ability of the Killer T cells to destroy a tumor. The cells are affected by a protein,OX40, that is on the cells surface. This protein can turn off the regulatory cells and activate the Killer ones. The tumor will then be attacked. By increasing this protein the T cells can be allowed to fight and kill the tumor.

Tumor cells excrete a reactive Nitrogen radical groups (NRG). This material blocks a protein (CCL20) whose action is to signal to the killer T cells there is a tumor and it needs to be destroyed. By stopping the NRG from deactivating the CCL2 the Killer T cells will be attracted to and kill he tumor cells.

Another immune cell that is a killer cell are the very large macrophages that continually patrol our body looking for abnormal cells. If found the macrophage actually engulfs the tumor cell and sends out messages for more killer cells to help. A protein,IKK is the switch that activates the macrophage inflammatory actions. However, when a cancer is present this same protein blocks any signal to the quiet, inactive genes that are the antitumor apoptosis genes, If this protein is inactvated the macrophage is allowed to act and the antitumor process starts.

It is obvious that the body has many ways to stop tumors but the tumors have developed many ways to avoid this. As we learn the ways we will be able to fool the tumor cells and allow our immune system to do its job.

The Immune system is our best friend but we sometimes need to fool it to get well.

A Theory of Everything

2011-12-05T21:01:00.001-08:00

The idea of one math equation that would explain everything is the quest of theoretical physics and then to prove this in a laboratory setting.

Newton came up with some amazing ideas that began modern physics. Then Einstein studied
light and began to open up another layer of discovery. Neils Bohr then began studying the atom and electrons which suddenly lead to a new level, quantum mechanics, to explain the behavior of these subatomic particles. The more we discover the more we don't know.

The last 20 years has been devoted to the idea of one single thing that would explain the whole universe (or maybe multiple ones). This is called the string theory.

It was thought that electrons, protons , neutrons were small particle like discreet things inside the atom. It is now thought that these, as well as all ,other subatomic matter, are actually irregular vibrating stands of energy called strings, These are the building blocks of everything in the universe including the space of the universe itself. Small vibrating strings of energy.

Hadrons are particles that react thru one of the four forces of nature known as the strong nuclear force.
Protons (which are made of even smaller particles called quarks) accelerated to the speed of light can collide and a hadron particle produced. When they collide they turn from a particle into energy. This energy is then capable of turning into new particles, perhaps never seen before. The change from energy to a particle requires the acquiring of mass.

The Higgs-boson is evidence that there really was such a charge of energy to begin with. This is what the scientists are looking for to prove this idea.

Quarks, electrons, muons, neutrinos and other very small particles make up the actual structure of electrons and protons and neutrons. 50 years ago a mathematical formula tied all of these together as a perfect symmetry. All experiments have agreed with this idea.

A key question is how these fundamental particle acquire mass. (Mass is the resistance we feel when picking up or pushing an object). It is thought that all space (including a vacuum) has a "syrup" like substance that sticks onto things passing through it. Some things are more "sticky" and acquire more syrup and have more mass. This area that things pass through is called the Higgs Field (a English Physicist who thought of this). The process by which the mass is acquired called the Higgs mechanism.

The search for particles that would prove this idea is being done with a collider where high speed crashes of protons are done and it is hoped that a fragment of these very elementary particles will be identified.

Our space in the universe is like a fabric that can be folded,warped and even torn. If the space is torn perhaps tunnels are formed that could allow us to go from one time or space area to another in an instant. These are called "worm holes".

This fabric of space is made of random moving, chaotic strings , sub microscopic energy and particles. However there is also a rhythm of the strings vibrations and these changes allow strings to make up everything in the universe. (The theory of everything)!)

Before the string idea it was thought we had 10 dimensions, 3 we could see and 6 that are so small they are hidden from us. The 3 we note are left-right,up-down and back and forth. It is now thought that there is another one so a total of 11. Strings need to move in more dimensions. The more degree of freedom the more strings can change shapes and changing into a complete membrane that can be very small or as large as our universe.

Space may be similar to a loaf of bread that is sliced into many pieces. Each piece has a string membrane surrounding it and our slice may be surrounded by many other slices,each a large membrane allowing multiple universes next to each other. Some of these may be very close,within inches of our membrane. We cannot see them.

It may be that a fingerprint of strings is a force called a graviton which is a gravity force that leaks off of the strings and can penetrate our membrane and could be incorporated into atoms. This would be a proof of the string idea. The work on the particle accelerators is to try and identify this force. The strings in our universe are tied to the membrane and cannot move but the gravity force (also in a string form) is not bound and can move to other dimensions.

Of course a goal is to explain the "Big Bang". Why, how, did it happen? The idea now is that our universe expanded from a hyper dense "blob" no bigger then an orange. Space has a grainy and quantized nature that is on a scale much smaller then atoms and the particles making up atoms. The quest is to find all of the particles and energy forces that was produced from this. We need to combine the macro universe with the micro elements to understand why the big bang and why the universe continues to expand.

It maybe that all of these universes, surrounded by many strings attache to the membranes, are moving around and these are each called a Brane. If the branes were to collide it could cause a big bang to occur. This may have happened many times.

Until there is proof of this it is a wild guess. The proof may be that the various forces produced by strings that are in all atoms ,even from other universes ,will be discovered when we crash protons into hydrogen atoms at high speeds. The physics guys are looking!

The Age of Anxiety

2011-12-01T16:58:00.000-08:00

Anxiety has been recognized for hundreds of years. Many ideas as to its cause from black humors to unfulfilled sex to a pineal glad abnormality have been suggested. It actually is part of a physiological process to protect us from danger. However,it can become a danger to our health.

A good part of how we respond to stress and whether a situation causes stress is due to genes.

The hypothalamic-pituitary -adrenal axis (HPA) is always on with anxiety. Keeping this on is related to a region of the brain known as the stria terminalis (BNST) which controls the autonomic nervous system ) heart rate ,breathing), This is activated by adrenaline. (Cortisol also involved does not effect the BNST). Since one system to create stress is adrenal driven and another cortisol controlled they can create different reactions. There is a feeling of challenge stress (example a musician or actor before going on stage) and there is threat type, (a dark alley with a scary stranger). It is our reaction to these feelings that is important.

Genes have changes that effect our reaction and sensitivity to stress. The way parents responded to stress will often change their epigene structure and activate certain genes that are passed on to the offspring. There is a 5X chance of anxiety syndrome if one parent had this. When male mice, exposed to anxiety situations, they then passed on this anxiety tendency much more then when they mated before the stress event.

Environment also plays a role. Being in a car accident will make you more anxious then before. Babies removed from their mothers are more anxious. However environment alone is not the complete explanation. Soldiers exposed to war and only 15% have the stress syndrome.

The stress path involves the HPA axis but also the prefrontal cortex. This allow us to take over and reason with ourselves when we become anxious. this ability to understand a real threat and a unreal one is important. A loud noise will create anxiety but when we realize it is thunder and will not hurt us our anxiety goes away. Performers learn that the alert keyed up feeling before a show can help them perform better if they control it.

People with abnormal anxiety need certain drugs and coping mechanisms to control this good-bad feeling.

The Forgotten K Super Vitamins

2011-10-25T15:44:00.000-07:00

Vitamin K is well known but it is really a group of vitamins each with a slightly different chemical structure and each doing very different things for our body. K1 is the best known and is related to blood clotting and is found in green leafed vegetables and some vegetable oils.

The other K vitamin,K2, is made by bacteria and found in very small amounts in food such as meat and eggs. The two have different side groups coming off the ring structure and this causes very different effects for us.

K1 goes to the liver and is used mainly to help with blood coagulation. K2 is transported all over the body and has significant effects on our health.

The richest source of K2 is made by the natto bacillus (rice bacteria) and is produced by fermentation. Some intestinal bacteria can also make K2.

Vitamin K activates certain proteins. It is a cofactor for an enzyme that converts inactive proteins to an active form. If these proteins are not activated they are unable to cause important reactions for our well being.

The list of effects that these have include, blood coagulation,bone metabolism,vascular injury repair,prevention of calcification in blood vessels,cell division,myelin production,and glucose metabolism. They are a key player in preventing and healing many different diseases of aging. The ingestion of enough meat and eggs to allow a functional level of K2 is probably not realistic and supplements are necessary. K2 (MK-7 form) is found in high amounts in natto a japanese fermented food. It is also available in capsule form from the natto bacteria.

Suggested dose of 100-100mcg. a day for K2 and 5 0-90mcg per day of K1. If you eat lots of green vegs then you are probably getting enough K1. You probably need supplements of K2.

K2 in treatment of osteoporosis is an important addition. A recent 7 year study showed women taking calcium for osteoporesis had a 24% increase in cardiac disease. Also,use of Vit D and calcium had an increased incidence of kidney stones.

Vitamin D boosts Ca absorbtion from the intestine and its reabsorbtion from the kidneys. Vit D also boosts the need for more active GLA proteins which need Vit K2 for activation. The Vit D dose causes a worse relative deficiency in the K2 levels and less active proteins to manage the increased calcium. The result is non delivery to the bones and increased delivery to the vessels (calcification) and to the kidney (stones).

When coumadin is given (a vitamin K antagonist) the patients get increased vessel and soft tissue calcifications. Also,Vit D and coumadin together cause this hypervitamin D effect. Again,a relative decrease in K2 and less activation of the proteins to store calcium properly.

If osteoclastin not activated it cannot store calcium in the bone regardless of the amount of calcium available. K2 activates osteoclastin.

The neuroprotective properties of K1 and 2 are shown in dementia. Products for brain repair and maintenance are reduced with subnormal K levels. Myelin repair requires these vitamins.

It has been shown that bone is related to glucose metabolism. It acts like an endocrine organ through osteocalcin. It is thought that the low Ph conditions created by the osteoclastic (resorption) activates osteoclastin within the bone that then goes to the pancreas to stimulate insulin production. Again,the K vitamins are vital to activate the osteoclastin activity.

Certain cancers have been found to be related to low k levels.

Patients with osteoporosis often with higher incidence of heart disease. Higher levels of K vitamins and they have less cardiac disease and less fractures.

It seems that the K vitamins have many effects and are very important for all of us. Although a lot of work has been done showing the help K2 gives in osteoporosis it is also clear the many other areas of the body (Heart,brain,immune etc.) are helped. if you have a good diet of green leafy food you probably need no K1. However,it does appear that 100-200 mcg of K2 supplement is important. These are available in capsule form and have no side effects (you may need to be careful if taking coumadin and a low dose may be indicated to prevent vessel calcification).

Happy people Live Longer

2011-04-27T15:23:00.000-07:00

This is an idea that has been thought to be true for years. However,no real evidence was available to show this to be true. A recent meta analysis of 24 studies has come to some conclusions. Happy people live 14 % longer then those reporting themselves as unhappy. Happy people enjoy about 7-10 years of longer life. They are less like;y to commit suicide and are less often victims of accidents.

The measurements were done with longitudinal studies where individuals are followed for many years.

The way in which happiness interacts with disease such as cancer is less clear. The effect of happiness on the outcome of disease has not been established. The effect on patients with metastatic cancer is "unclear and unconvincing".

Recent studies show that a certain percentage of our happiness (?30%) is inherited. The ability to transport serotonin is measured by a protein molecule and these are controlled by genes. if you have a long version rather then a short version of the gene you make more serotonin transport and you have more positive reactions to life. You are happier. People with 2 long genes are often most happy,people with a short and long gene in the middle and two short genes more unhappy. Asians average happiness quotient is 0.69,Blacks 1.47 and whites 1.12 and the distribution of long and short genes correlate with this.

Life is often a pursuit of happiness and now it seems that this pursuit can also give a longer life. Many countries are now including a "happiness" measurement in their statistics to judge how well the policies actually add to a persons happiness. it may also be they will find that the longer life from being happy is due to better health. However,it could be that healthy people are happier ones.

The environment is always testing our minds and bodies and the ability of the body to react is related to our genes. If you have two short genes or a mutation where one long gene is not functioning then you may react to a circumstance in a unhappy way whereas if you are blessed with two long genes it may seem a minor life disturbance.

Human Microbiome is the new Frontier

2011-04-21T14:32:00.000-07:00

100 trillion bacteria and only 10 trillion actually "human cells" make up our bodies. Evolution began with bacteria like cells and these have evolved to make their living in our bodies. The good news is that they mostly want us healthy and are able to create thousands of special chemicals that we cannot make. These allow making of vital vitamins and even antibiotics to fight off dangerous bacteria. They are important in alerting our immune system to take actions to fight disease and inflammation.

Every part of our body has various bacteria, Hundreds of different types live on our skin,hair,ears,nose, etc. Every square cm. of our healthy lungs have 2000 bacteria! bacteria in the nose make antibodies to fight infection. Mice born with sterile guts cannot make a key molecule to signal the immune system to stop inflammation. Once they are given a normal flora the immune system is signaled and the inflammation is stopped. Patients with intractable colon inflammation from "bad' bacteria have complete cures when normal bacteria flora added to their colons. Before had mostly pathologic bacteria,after normal bacteria added a normal flora found. Patients with asthma have different flora in gut then normals. Obese patients also have a different flora then normals. 124 stool samples revealed 3 million different genes.

A group of mice with weak immune systems developed fatty livers and soon became obese. The bacteria in their guts had 1000X more abnormal (bad) bacteria then normals. Healthy, normal weight mice, put in the same cage, also developed the same problems. (Mice eat each others feces). It was found these mice also had acquired the same abnormal bacteria. The mice had been "infected " with obesity.

Recent gene studies show that there are one of three major distinct bacteria floras found in all humans regardless of sex,race,weight, height etc. Each one has a different type of bacteria as the majority of the bacteria in their guts.

Autism has been shown to have a high incidence of bowel inflammation. We know that the guts bacteria are important in the function of the total body immune system and the ability to fight disease ,decrease inflammation and even produce antibodies against our own cells is related to these bacteria. It maybe that changes in Autism will be found to be related to these bacteria abnormalities.

The "little brain" is found lining the gut. It is part of the autonomic nervous system and is connected with the brain. It has 90% of the neurotransmitter serotonin and a decrease or increase of this can cause diarrhea or constipation. The vagus system also connects the gut to the brain. It has been shown that inflammation in the gut can signal parts of the brains immune system and actual structural changes can result.

Obese patients have a bacterial imbalance with an overgrowth of Firmicutes and less bacteroides. If the amount of Firmicutes is replaced with Bacteroides then the weight decreases.

We are massively outnumbered by bacteria, 10 trillion to 1 trillion. 90% of the encoding protein cells in our body are bacteria. 99% of the functional genes in our body are microbial! These are constantly exchanging information with our cells and their DNA. The DNA depends on messenger RNA to make the proteins the body needs. however,their are small segments of RNA ( microRNA) that can attach to the main mRNA and either stop its message or alter the message. 98% of the DNA is made of nonfunctioning genes but many of these are actually older genes that may have had a purpose at one time but are now not active. (Section of DNA called "junk" and makes up 90% of the DNA). These genes have no coherent message or are quiet.

It is now thought that these genes produce mRNAs that actually can combine with the regular RNA from the active genes. Each bacteria in our mouth,stomach and bowel has its own set of genes which can interact with any cell in the body. They are constantly communicating. Different people in different areas have acquired different bacteria (in Japan some have a gene for digesting seaweed). These different bacteria may be related to the different types of certain cancers in different areas of the world.

In esophageal cancer it has been found that different bacteria are associated with esophagus cancer.

We are partners with our bacteria and they are an important part of our ability to be healthy or sick.

Mutations come in many types

2011-03-31T17:29:00.000-07:00

It is well accepted that mutations are at the basis of cancer. These mutations are usually thought of as an external factor such as radiation,or toxins or chemicals actually causing a change in the nucleotides forming the various genes. This changes the transcription of the proteins produced and can cause a cancer. If these occur in a sperm/egg cell the change is passed on.

However ,a very common cause of mutations is due to a change in the methylation or acetytalation of the proteins in the histones surrounding the actual genes. There are enzymes in the histone that can add or subtract these groups. If methyl groups added or if they are subtracted the gene adjacent can be turned "on " or "off". By giving certain chemicals, phenylbutyric acid or valproic acid this process can be inhibited. The histone proteins can cause the DNA to be condensed (tightly wound) or loose. If condensed it is not available for transcription of proteins and is off. If open it is available and is on. If there is less methylation then normal the genes are suppressed. In normal cells there is usually much less methylation then in cancer cells. If the genes that suppress cancer changes and allow repair of the cell are hyper methylated (suppressed) than the cell is susceptable to cancer. If drugs such as 5-azacytodine or deoxycytidine are incorporated into the cytosine nucleotide then it blocks the enzyme to add methyl groups and preserves the gene function.

The Axoloti Salamander is a long distant relative of we humans. It has been discovered that in the oocytes of these salamanders powerful proteins exist that can modify epigenetic proteins and allow them to cause genes to be activated. Tumor suppressor genes in breast cancers have been shown to be turned on by these proteins and the cancer divisions stopped.

Our epigenetics changes can be passed on to other generations (if they occur in sex cells) and they change during our lives. The changes are different areas of the chromatin for different families(including twins) but usually have either a increased or decrease in the methylation pattern among these related groups.

Cancer may be a 3 step process.

1- epigenetic disruption of progenitor cells in an organ altered by abnormal oncogene function (tumor suppressor blocked or dividing gene left on). This sets the cell up for promoted growth.

2- Due to the increased proliferation of cells there is a higher chance of mutation due to chromosome division mistakes.

3- Passive genes that allow for unusual metabolism,blood vessel production and mobility are activated.

The epigenes are very important in the activity of our genes. They are modified during life by many external factors and are probably key to many cell changes that lead to cancer. (See the discussion on epigenes and diet).

Follow the Cancer Pathways.

2011-03-29T14:34:00.000-07:00

There are numerous proteins that are produced in the cell called kinases. These proteins are created when signals from the genes are released. These then add phosphates to other proteins and a path of activity begins. When a gene is mutated it no longer starts or stops activity normally but is out of control. The pathway is wide open at all times.

These proteins have very irregular surfaces with the active regions often the most irregular. These keys on the surface fit into a lock on another protein and the signals are passed on. If the active surface could be blocked by another chemical then the path would be interrupted and the uncontrolled activities stopped.

An example is Chronic Myelogenous Leukemia which is caused by a translocation of two chromosomes and a hybrid oncogene is formed. This gene causes uncontrolled division and cancer. A special protein blocker was discovered that covered the active part of the abnormal oncogene and the disease was stopped. This drug is called Gleevec. This idea of a specific drug to block a specific activity without side effects was a great discovery.

One of the problems with the treating of cancer by creating drugs to inactivate the abnormal oncogenes is that cancers may have a significant number of these mutations. Which ones,and how many,need to be stopped? The same type cancer in different patients may have different mutations causing the same end result of cancer. These would need individualized treatment. One drug will probably not fit all.

As of 2009 a majority of the cancer genome for all cancers had been discovered. These are genes that were mutated in tumors but not normals. In most cancers 40-50 mutations seen. In Leukemias there are usually 5-10 and this may be the reason drug treatment in these have more success. Also,cancers show individual variations of mutations with some having 140 mutations and others 40. Many of these mutations occur on genes that have little effect on the division of the cell and are probably not important for cancer control. The important pathways (the "drivers") are probably 10-15 in each cancer. These create pathways that accelerate cell division or fail to stop it. Recently, polypeptides are being developed that react with the surface of proteins in the pathways created by the mutant oncogenes ,and these are then blocked. This has the same result as if the oncogene itself was blocked.

Cervical cancer is associated with a virus (HPL) and only a few of those infected will get cancer. Those who develop cancer appear to have a gene pathway (Wnt) that is turned on and one of the proteins Beta Catenin oncogene is found in the cells. This pathway appears to be affected by external carcinogens including tobacco use. It maybe that drugs can be developed to block this protein. This turned on pathway is also found in other cancers.

Genome study in 50 breast cancer patients showed a total of 1700 mutations. Only a few (2) had a % of 25 to 40 % prevalence in the cases. The rest showed a low incidence of 3-5%. Cancer is an individual disease and a genome of mutations is important to know what the causes of the cancer are.

An enzyme phospholipase is found in a high number of the metastatic cancer cells. It appears this is an important substance to allow spread (metastases) of the cancer. If this can be blocked then it maybe that the metastases could be stopped.

Stem cells are present through out our body. All organs have a reserve of sleeping stem cells. When there is an accident and we lose a lot of blood the stem cells are alerted and soon the entire blood supply is restored. When this occurs there is a signal for the divisions to stop and the stem cells go back to sleep. It may be that cancer has its own altered stem cells and when chemotherapy kills a large number of cancer cells the stem cells go into action and produce new cancer cells (relapse). The problem is they do not stop producing and ignore any signals. Complete treatment may mean long term therapy and the cancer will be considered a chronic disease like arthritis or hypertension or diabetes.

It has been found that a gene,the Notch gene. is necessary for some cancer stem cells to grow, by stopping the function of the notch gene cancer can be stopped. There are drugs that will do this.

Now that we at last understand the basis of cancer we are developing ways to specifically target these causes and stop cancer. One discovery is that the plant autumn crocus contains a very toxic chemical called colchicine and if this can be delivered to a cancer cell it will stop its growth. A research team in England has devised a way to keep the colchicine bound to another chemical and therefore harmless until it is inside a cancer cell. The Cancer cell has a unique enzyme that will unbind the colchicine from its protection and the chemical will be toxic. It appears to destroy the blood supply feeding the cancer and the tumor dies.

Another drug,Imumab,blocks a cancer causing protein and prevents cancer from spreading. This actually is a molecule from certain bacteria that is used by the bacteria to fight off hostile bacteria. It appears to switch off certain cancer forming genes in Breast cancer.

Recently a group has taken a protein found in most breast cancers , and developed a antibody against this protein and has made a vaccine that when injected allows the immune system to develop antibodies against the protein and inactivate it (like a virus or bacteria is killed). The hope is to inject women against breast cancer!

A successful use of epigenitic treatment was recently discovered. Use of a drug, Azacvitidine and entinostat has shown great success in lung cancer patients. The first drug removes methyl groups and the second inhibits deacetylation. This restores the activity of certain genes that were inactive. he silent anticancer genes are reactivated and cause the tumor to be killed. Methyl groups on key anticancer genes indicate that the cell is unable to stop the cancer process. By allowing these genes to be active the process is stopped. The doses of these drugs were used at such a level that no side effects seen.

It is impossible for us to escape mutations to our genes since all life processes put us at risk. There will be some habits that will lower the mutation risk but early detection and specific treatment of the genetic injury will be the key.

The cause of cancer is a distorted version of ourselves

2011-03-28T15:50:00.000-07:00

The quest for what is cancer is a long and difficult one that has caused moments of hope and more periods of despair. The answer is in our genes.

Chromosomes carry vital information for normal cell development,growth and division. These controls are all in the cell itself. These are the genes that express themselves through proteins that cause the various processes in the cell to take place.

Genes that when signaled (by adding a phosphate group) begin to cause a series of reactions by making special proteins that eventually tell the cell to divide. There are also genes that act the same way after being signaled that tell the cell to stop dividing. The accelerator division genes and the suppressor genes are called oncogenes. There are hundreds of these types in each cell.

When a gene receives a mutation it changes its function. Since there are two genes it often takes two separate mutations to both to cause a significant change in action. However,if a mutated gene is inherited and the cell only has one gene that is "safe" then this can happen more often. When these oncogenes are mutated they can become a signal that causes uncontrollable growth (the gas pedal is stuck) or they do not stop the divisions (no brakes).

The suppresser oncogene encodes a protein with a deep molecular pocket in which tightly bound proteins are deposited. They are prevented from acting in the cell. When a cell divides and needs to stop the suppressor gene is inactivated and the trapped proteins released to signal the cell to stop dividing.

These oncogenes are also very closely involved with stopping and starting a number of cell functions. They can create new blood supplies near the cell,arrange a alternate metabolic path,and even allow the cell to become mobile and pass into the blood stream and travel to other sites. (Remember white and Red cells travel throughout the body and the "mobility" genes that allow this are found in all cells of the body. They are just inactivated under normal conditions). These many functions explain the ability of cancer cells to take over the body.

As an example imagine a 40 yo man exposed to a small amount of asbestosis. This sliver causes a local inflammation with cell proliferation,increased blood supply and other signs of inflammation. A small proliferation of new cells and one has a mutation of an oncogene. It divides even more then the other cells. At a later time (years) another carcinogen such as tobacco causes another mutation and now two mutated oncogenes are present. Later,another mutation (perhaps more tobacco or even Xray) to two suppressor genes is added. This cell has enough damage that uncontrolled divisions occur. As the cells divide wildly even more mutations or chromosome damages occur and perhaps more mutant oncogenes in the cell. The cells develop their own blood supply,use a different form of metabolism then normal (for hypoxic conditions) and can now travel to distant areas of the body. At these sites the cells nest and continue their uncontrolled growth. (Metastasis).

Cancer is caused by distortions of our cells activities and seem to occur over a period of time and progress from a precancerous to a overt cancer form. An example would be a colon polyp that has many proliferating cells but may eventually develop into an active cancer. It seems to be a process whereby the cells acquire mutations and the more mutations the more out of control the cell becomes. Exogenous carcinogens, chronic inflammation,perhaps abnormal diet ,certain hormone exposure all may help the cell be distorted and cause cancer.

Inherited cancers are probably due to a single gene (of the pair) being mutated but it usually takes an acquired event to cause enough damage to cause cancer. It seems that chemicals suh as hormones may slow a cancer down but will not stop it. Also, certain cells (breast) that are somewhat hormone dependent may have there growth enhanced by exposure. The real factor for the cancer is the change in the oncogenes as described.

The research now is looking for things that will block the damage to the oncogenes or shut them off (accelerators) or turn them on (suppressors). Recent discoveries include transretinoic acid that reacts with a mutant oncogene in certain leukemias and causes this to become inactive and allows stopping of the divisions. Treatment with this in certain leukemias has resulted in a 80% survival. Her-2, an oncogene in certain aggressive breast cancers, can be inactivated with a specific antibody (Herceptin) and has reduced deaths 33%.

The ability to interrupt the various proteins that are necessary to carry out the signal from the oncogene are also possible therapeutic targets. Special designed protein peptides are created and they target these various proteins. These proteins,once stopped,will stop the uncontrolled divisions.

Let us hope that soon the terrible chemotherapy will go the way of Radical mastectomy and other brutal guesses as to how to cure cancer.

Cell Cannibalism is important

2011-03-02T14:35:00.000-08:00

The ability of a cell to actually capture all or parts of itself and then reuse these products for new energy and products is very important for cell health. This process is known as autophagy. As a cell produces energy and rebuilds the thousands of proteins it creates substances called free radicals that can combine with important parts of the cell and create less efficient energy production,decreased proteins or even a disease state including cancer.

This is a old way nature evolved to protect against scarcity of nutrients. Being able to recycle parts is a help in survival. It also seems to be involved with limiting inflammatory disease. Starvation creates a increased autophagy state and so does exercise.

There are many ways the cell monitors itself. Nutrient availability,growth factors,insulin,hormone activity,energy levels,toxic products all can trigger signaling that something is wrong. When this happens certain Genes reduce cell growth and begin a selective "cleanup" to correct the problem. The area is encapsulated and delivered to a lysosome which digests the damaged material and then allows the breakdown products to be recycled by the cell. This is important for the regulation of damaged mitochondria since a damaged mitochondria would go on to divide and create a large number of inefficient energy providers that would lead to disease. Getting rid of damaged mitochondria allows less free radical changes and is antiaging.

In starvation the ability to autophage is the process that keeps the organism alive. It provides materials for energy and protein production especially to the vital organs.

This process is one of the most important in keeping our cells healthy. However,once a cancer cell is created and it thrives in a hypoxic state the signal for autophage may actually promote the cancer. The cell now has a process to recycle its metabolites to keep reproducing even though it may be distant from a blood supply.

Mitochondria are appearing to be very key to aging and chronic diseases. As they age they become less efficient and actually may be toxic to normal cell functions. When these are abnormal the cell usually begins a series of reactions to remove the damaged mitochondria, As we age this ability is compromised and can cause chronic disease and promote aging. Mitochondria are signalers to the immune system to stop various inflammatory changes. if these are damaged the inflammatory reactions are allowed to proceed.

At this time only exercise and fasting appear to increase mitochondria health.

Exercise promotes autophagy. Autophagosomes, form around structures that are marked for recycling, are increased with exercise. The more the exercise, the more structures marked for recycling. The less autophagy the less endurance and use of glucose.

Selective activation and inhibiting of the autophage process may be important in treatment of disease.

Exercise may be the fountain of youth

2011-03-02T12:14:00.000-08:00

It seems that better health is associated with aerobic exercise. As we age we see gray hair,wrinkled thin skin,atrophy of muscles,loss of sex drive and generalized frailty. These things occur at different times for individuals but do have a strong association with life styles.

Identical twins are a great example of the effect of genes and environment. By age 20 there is often a marked difference in the activity of the twins identical genome. Genes are activated or shut down with significant effect on appearance as well as health. Many identical twins die decades apart. Some get cancers, some don't. It seems the environment does effect our genes which in turn transcribe or don't transcribe important chemicals for our body maintenance.

The ability of our trillions of cells to maintain their health is very dependent on the ability to create energy to make and repair molecules. Our cells have hundreds of small packets called mitochondria in the cytoplasm. Actually, 10% of our weight is mitochondria. These power factories are very efficient producers of ATP which is the energy packet that allows all chemical activities to occur. These factories are susceptable to damage due to the by products produced during the making of ATP. These "Free Radicals" damage the protein DNA in the mitochondria and cause them to malfunction. If these are not repaired or removed the new cells will have this damaged mitochondria and their ability to function will be decreased.

There are built in systems to assure the mitochondria are repaired or destroyed when they suffer this damage. However,as we age the damage overcomes the repair ability. (See blogs on Mitochondria,Cell Death,Aging).

Genetic altered mice with damage to the genes that affect mitochondria repair will age quickly,and die at about 8 months. This rapid aging is seen with the usual signs and is analogous to a human dying at age 60. These animals have many damaged mitochondria and are unable to have the usual mechanism of repair.

If some of the same animals are exercised from age 3 mos. on a tread mill they do not show the signs of aging,are sexually active,and are strong at over 1 year. These animals have more mitochondria and fewer damaged mitochondria then the control old mice. The exercise is analogous to us running 6 miles in 55 minutes 3X each week. This exercise routine protects the mitochondria and seems to promote new normal mitochondria. This effect is seen not just in the muscles and heart but in all organs of the body.

A recent study showed a definite decrease in symptoms of Parkinsons disease when patients put on a vigorous exercise program. The effects lasted after the exercise stopped but then came back. The forced vigorous exercise seems to alter the disease.

The bone marrow has stem cells that can differentiate into bone or fat cells. Once formed they stay bone or fat. High fat and sugar solutions direct these stem cells to form fat cells. Exercise promotes bone cells. After exercise the bone density increases and with low exercise the marrow is more fatty. (low aspirin doses are also stimulants to osteoblastic activity).

There is a protein called noggin that is produced by the muscles during aerobic exercise. This material appears to activate muscle stem cells to produce more cells. it is also able to affect stem cells in the brain where it causes brain stem cells to form new neurons.

People who sit during the day have increased obesity. The muscles show decreased electrical activity (perhaps reflecting decrease mitochondria action), they burn 1/3 of the calories of moving muscle ,Insulin activity decreased and glucose increase and lipids increase in the blood. It is estimated that sitting increases chances of death by 11% per hour. Sitting is a lethal activity.

A new hormone, irisin , has been discovered which explains many of the benefits of exercise. This hormone is released from the cell walls of muscle cells and travels throughout the body to do many important metabolic things. Better glucose use, decrease in "bad' fat cells, used more calories per time. causes weight loss . The exercise activity activates a protein that causes the irisin to be released. The level of hormone remains high hours later.

There are adult stem cells in muscle (MSC) that are stimulated by exercise and release a growth factor chemical that stimulates other cells in the muscle to fuse and generate new muscle. The movement of the muscle is the stimulus. It maybe with aerobic exercise, this same chemical is released into the blood, and effects other organs as well.

It may be that exercise is another activator of the epigenetic system (see blog on epigenes) and some chemicals are produced that cause these beneficial affects.

Bacteria and our Immune system health

2011-02-26T18:13:00.000-08:00

Almost every surface of the human body has millions of bacteria. We have 10 times as many bacteria cells as our total body cells. Bacteria populated the earth 2 billion years before eukaryotic life. Mitochondria are results of captured bacteria. Our original cells descended from bacteria. As we became more complex bacteria found more places to cohabitat with these new complex cellular structures. To promote their own health and reproduction they needed a healthy host.

There are many pathogenic bacteria that can cause disease. It was important to be able to differentiate between the good and bad. The various bacteria often shared the same molecular patterns and it was important that our immune system could choose the good ones and destroy the bad.

The gut has a large number of collections of lymph cells called peyers patches. These are often in intimate contact with bacteria in the gut. A certain benign bacteria (fragilis) has developed a way to signal the lymph tissues and turn off pro inflammatory cells (T cells) so they will not attack the bacteria and they can live in our gut. With stress bacteria are able to move from the gut to the lining of the bowel and cause disease. By giving probiotics this is reduced. The more benign bacteria the more helpful molecules are absorbed into the blood stream and taken to the liver to promote better health.

The CD4 T cells are important in this function. They develop in the thymus but involve the total body. They sense and decide the good and the bad. The commensal (good) bacteria are important in programming the instructions of these immune cells. The most important area for this is the gut lining area. This harbors a large number (trillions) and a variety (hundreds) of species of bacteria. The aggregate human microbiota likely contains over 1000 species with any one person having at least 150 different types. Each of us has a relatively distinct microbiota. Samples from stool and the gut have found 395 different strains of bacteria ,2/3's are new types. Analyzing millions of genomes from these and other bacteria it is found that there are many metabolic genes that complemented the human genome. These genes produce metabolic products to digest food,and even produce vitamins. We seem to be a microbe-human superorganism with a vast genetic storehouse. Some bacteria are important in absorbing energy from food. Too much and obesity,too little , and malnutrition.

These bacteria are important in the development and upkeep of the lymphoid tissue lining the gut. Germ free animals have a much reduced immune system and less ability to respond to disease. The multiple populations of immune cells depend on the actions of these good bacteria to develop. The absence of these bacteria cause reduction in cells and lymph tissue and reduced antibody levels, This includes the spleen. The bacteria are essential in the systemic immune system. The good bacteria help protect us and allow them to have less competition and a healthy host. This appears to be an evolutionary process.

T cells are made in the thymus and then enter the periphery. Here,they are given environmental signals from the host as well as the good bacteria that instructs their development and functions. They can be induced to pro and anti inflammatory subsets. Some commensal bacteria include Bifido and Bacteroides. These secrete a molecule which is a polyschride (PSA) that directs the development of the T cells. In experimental colitis this PSA protects against almost all symptoms of the disease. Another bacteria ,SFB, adhere to the intestinal mucosa and to the lymph nodes and induce the development of helper T cells in the lining and nodes. This activity is very much reduced if these bacteria not present. They produce cytokines,peptides,chemokines, which all support T cell differentiation. These bacteria protected against different strains of bad guys.

Altered diets,antibiotics fatty diets all may change the bacteria balance and predispose to inflammation including cancer. This condition is caused dysbiosis. This condition alters the balance and may lead to both inflammation due to infection and may be related to autoimmune changes. There is evidence that the gut bacteria can affect the adaptive immune system and cause certain autoimmune diseases.

It is now thought that the same idea may hold true for viruses. In mice dormant herpesviruses seem to enhance and maintain an alert immune system an protect from infections.

The use of diet and adding probiotics to the diet will support a healthy intestinal bacteria growth and a healthy immune system. (see blog "what is a Healthy diet").

Milk Protein may be dangerous.

2010-12-19T16:45:00.000-08:00

Milk products have high levels of protein (Casein) as well as fat. There is a belief that the higher fat levels cause heart disease. The trend is towards low fat or even non fat milk.

However,it may be the protein not the fat that causes increased risk of disease. Casein has two different components,A1 and A2. Different cows produce different amounts of these components. The difference is due to a gene change of only one amino acid between A1 and A2. This change allows a peptide BCM7 to be produced by the A1 gene. Gurnsey cows produce only 10% of their casein as A1 and Holsteins 50% as A1. Goats have no A1. It is noted that countries that have cows with high levels of A1 have significantly higher heart disease,diabetes and other problems. These changes are much less in countries that have cows with little A1 in the milk.

If the BCM7 peptide is absorbed into the blood stream it is broken down to a opioid like structure that can pass into the brain and lodges in areas that may be associated with autism. It has been show that autism can be significantly reduced with a milk product without A1.

The BCM7 peptide is similar to certain normal proteins in our body and antibodies form against them . These peptides are similar as insulin producing cells of the pancreas. The antibodies attack the insulin cells (autoimmune) and higher incidence of Diabetes 1 is found in these populations.

The BCM7 seems to oxidize LDL cholesterol and this causes the LDL to become part of the inflammation reaction causing heart disease.

It seems that certain milk is not healthy and can cause serious disease. Unfortunately,most milk in the USA is that containing high A1 casein levels.

Malignant Eating Habits

2010-12-15T21:45:00.000-08:00

Overweight folks are shown to be more prone to cancer,especially breast and ovary. The gene BRCA1 is a gene that encodes (activates) a tumor suppression gene. If this gene is mutated there is a definite increase chance of cancer.

A substance called C-terminal binding protein (CtBP) helps regulate BRCA1. The activity of CtBP is regulated by the processing of calorie rich molecules. The more rich molecules the greater chance of cancer changes. CtBP works by binding to a small product of the mitochondria energy producing system,NADH. As more metabolism is required the ratio of NAD+ to NADH falls, the excess NADH combines with the CtBP and the actual shape of the CtBP changes which allows it to combine with different proteins then usual. One of the new functions is to change the epigenetic areas that control cancer suppression genes. Since BRCA1 is responsible for DNA repair and with the change in CtBP the repair function is diminished. Over time the chance of cancer increases.

Another problem is the increase in fat causing an increase in Estrogen and estrogen promotes more cell proliferation in the ovaries and breast. Now you have lots of proliferation and loss of the DNA repair system.

However avoiding being fat is very complicated. It has been shown that people who are fat for a long period of time (? years) have a different metabolic system then normal weight people. After dieting their hunger proteins increase and the suppressant ones decrease. Their muscle cells use less energy and there are other mechanisms that the body now uses to regain the weight lost. It is very difficult for these folks to lose and maintain a normal weight.

The not so good Old Immune System

2010-12-14T15:18:00.000-08:00

As we age all of our organs and cells acquire changes that often predispose to disease and eventually death. There are many important systems but our immune system is one of the most important. This system not only protects us from outside invaders but is also very important in cell regulation and the ability to cause damaged cells to die. The immune system has many important components and all are affected in varying degrees.

As cells age they lose the ability to divide (loss of telomeres) . These cells accumulate in larger numbers and in certain areas (cartilage) they can cause damage, Due to their abnormal metabolic state they secrete large amounts of damaging proteins that are harmful to neighboring cells. They can cause them to lose function and even develop cancer. These senescent cells normally secrete cytokines that alert the immune system to remove them. They also secrete growth factors to encourage the surrounding cells to divide and take their place. This is the way these cells are normally handled by the body. However,the aging immune cells lose their ability to perform these functions and the senescent cells increase. The T cells are born in the bone marrow but mature in the Thymus. As we age the thymus gets smaller and less T cell maturation. These T cells are also responsible for the large number of cytokines that are the message centers for the immune system.

It has been noted that one measure of having good health as we age is the level of cytokines in our blood. These are a group of chemicals that are an important part of the immune defense. If your level of cytokines are at a level at age 65 that they were at 25 you can expect to live longer and have good health. If below this ,the opposite. Healthy 70 year olds had levels the same as 25 year olds. Rather then talk about age span we need to consider the concept of health span. A healthy immune system increases the health span.

By giving a drug,Lenalidomide, at very low dosages once a week ,the levels of the cytokines in older people with low levels were increased. Some were increased 120 times the level before the drug given. The activity of T cells and other immune components were also increased. This may be an important way to increase health and avoid some of the damages of aging.

The gastrointestinal system contains trillions of bacteria and 70% of the immune system is related to this area. It is known that the bacteria in this area can produce many helpful chemicals and have an important effect on the immune system. If the bacteria are out of balance with certain less desirable types overgrowing we lose these benefits and even have production of damaging chemicals that cause disease and weaken the immune system. It appears that eating complex carbohydrates (Fiber),that are not digested, and adding various probiotics we can promote the "good guys" and eliminate the "bad guys".

By giving one slice of a probiotic cheeses each day to seniors there was a significant increase in the health of their immune systems. There are different types of good bacteria in probiotics, S.Thermophilus,leuconostoc,E.fecalis,L.acidophilus,C.butyricum,B. adolesentis are a few of the more common. It seems each has different effects on production of components of the immune system. However,all increase the measurements for improvement of the aging immune systems.

This help also seems to effect younger people with immune problems and inflammation. The use of these in Ulcerative Colitis improves recurrence and degree of symptoms. Certain probiotics reduce the inflammatory marker CRP.

A Conjugate Linoleic Acid is associated with reducing fat cells as well as inhibiting colon cancer. This CLA is found in a skin bacteria. The genes for this were put into a lactobacillus and it was ingested and a significant decrease in the fat cells with an increase in the CLA in the cells resulted. It is thought that making these probiotics may offer a way to reduce weight as well as prevent some cancers.

A bacteria produced peptide has been discovered that will stimulate the activity of NKT cells. These are cells that are a type of immune T cell that are important in regulating many disease processes. By giving this peptide many inflammatory diseases were suppressed. The suppression included autoimmune diseases.

We appear to have evolved and maintain trillions of bacteria living in our bowels. These small chemical factories produce enzymes and other chemicals important to our health. Diet is a key factor whether these help or hurt us. The body has evolved a way to protect us from aging cell damage but it seems to be dependent on the immune system that,unfortunately, ages and loses its ability to do this vital job.

Nutrigenetics

2010-11-12T13:49:00.000-08:00

When it was discovered that food has many different molecules that are called polyphenols, secondary metabolites, that can activate genes that will allow proteins to be made that can prolong life and stop disease the study of Nutrigenetics was created.

This was first noted years ago when caloric restriction allowed animals to live longer and more healthy lives. Since , it is now known this is due to the activation of a set of genes called the Sirutins. When these genes are activated a series of enzymes (7) are produced that regulates Insulin,glucose,fatty acids,reduces DNA damage,allows damaged cells to be removed before they can "settle in", and lowers the amount of inflammation in the body. These factors allow the increased lifespan seen with caloric reduction.

Reservatrol,is a polyphenol,that when ingested allows the Sirutins to be activated. This is produced in plants when they are stressed(drought,cold,disease).Grapes,peanuts,rasberries,blueberries,pomegrante, dark chocolate) all have this substance. The stressed plants produce secondary metabolites to increase their cellular defenses. These molecules are called xenohormetic and are able to transmit signals to receptors in the cell which activates the complex for protection. It may be that these polyphenols warn the cellular system that difficult times are coming and the cells go into a survival mode. They are a warning system to our DNA to begin methods to protect themselves. It is not certain what amount of these are necessary to activate the Sir genes but 40 mgm has been shown to do this in some experiments.

The flavinoids epicatechin gallate(found in red grapes, red wine and green tea) and ellagic acid found in the oak casts fermenting wine,has a very positive effect on glucose metabolism. it binds with the receptors on fat cells to enhance the use of glucose.

The actual methods of how these signals are transmitted and how the cell is activated is very complex and interesting. Review the blogs on mitochondria and epigenes and methylation.

Cancer and the silencing of our Genes.

2010-10-18T12:43:00.000-07:00

The many genes in each cell are not all active at anyone time. Some are selected and are active making RNA that is then sent to the cell Ribosomes and produce proteins that allow all the vital functions of life. Many genes are not active and are only called upon to produce proteins at certain times. Very precise chemical controls determine whether a gene is active or inactive. This process is called Epigenetic Regulation.

When a methyl group is placed in a selective area of the gene it shuts the gene down or inactivates it. This is a reversible situation. Enzymes called, methyl transferase , attaches methyl groups to specific letters of the gene and inactivate it. Over 50% of our genetic material is noncoding RNA. These are sequences of certain amino acids that can cause reactions to occur but do not transcribe proteins. Those RNA sequences that can cause proteins to be produced are called coding RNA. The noncoding RNA amino acids that exactly match a section of the genes in the DNA of a coding area attaches to it and the usual double helix configuration is changed to a triple helix in this region. The methyl transferase then deposits a methyl group in this area. When this occurs the genes function is inactivated and its ability to form proteins stops. If this is a gene that is important to allow the cell to stop abnormal growth the cell is now open to cancer changes. It has been shown that these methylation changes may involve a neighborhood of genes on the DNA and may begin years before the actual cancer is seen.

There are drugs that cause demethylation (Trichostatin A) and may be important is cancer treatment. By activating the genes that produce proteins to suppress cancer, the cell may undergo apoptosis and die. There are many things in our diet that may be related to methylation. Unlike gene mutations, epigenetic changes are reversible.

(See earlier epigenetic discussions).

Cancer is ultimately a disease of abnormal DNA

2010-08-13T16:14:00.000-07:00

Cancer is a disease that kills about 1/3 of humans . It is due to abnormalities in cell function that is a result of abnormalities in the genomes DNA. In order to have cell growth and division we need special genes to encode proteins to allow this. These genes fall into 3 categories.

Oncogenes are usually tightly controlled and their actions well regulated. They signal for cell growth.If these genes are changed they can become stuck on a "on" position and allow unregulated out of control cell growth (Cancer). An oncogene,RAS,with only one letter mutation, is associated with cancer changes.

Another category is tumor suppressor genes. These are the brake pedals for growth and tell the cells to stop . P53 is a well known suppressor gene and is activated when any damage is done to the DNA. If this gene is not active abnormal cells are allowed to divide,grow and spread.

The last group are genes that constantly scan the DNA of cells to detect abnormalities. If abnormal copies of DNA are found they correct them. Damage to one or more of these groups sets up the spread of cancer cells.

Micro RNA structures (less then 30 base pairs) are important for cancer control. P53 appears to work by alerting a micro RNA when a cancer is detected. This allows the cell to self destruct. If the p53 is inactive this will not occur even though the RNA is present. Recently, a micro RNA has been developed that is similar to those in the cell,when a DNA abnormality is found this mRNA triggers a reaction that allows this mRNA to begin a new long chained RNA . This RNA mimics a viral infection and triggers the cell to self destruct.

The body can protect itself against cancer changes in the cells by recognizing abnormalities and then activating cell destruction or apoptosis. Certain genes are necessary for this. P53 is the main one. P53 has the ability to trigger off apoptosis and the ability to cause cell senescence(maintain its metabolism but stops any division). Many aged cells have abnormal (short) telomeres and these promote cell divisions and increased cancer changes. It is possible to separate the apoptosis function from the senescence function of the P53. This allows the cells to live but stops any tumor changes. 50% of cancers have mutations to the P53 gene.

Another gene,P63, has properties that can replace the function of the P53 gene and also promote senescence of the cell and protect from tumor changes. If DNA replication is stopped then the chances of abnormal changes are greatly reduced and no cancer.

The good news,cancer is a multistep process.We have 6 billion base pairs in our DNA and 400 trillion cells and there is damage to many areas yet we do not get cancer 2/3 of the time. You can inherit a damaged gene that predisposes to cancer but most often the multiple mutations needed are due to environmental changes.

Most mutations are not passed on at birth but are acquired during life. However,having abnormal genes at birth creates a greater chance of cancer due to acquired mutations. As mutations occur over a life time it allows certain cells to out grow others. As these cells grow they are recognized as abnormal and the body has a sophisticated system to destroy these potential cancer cells.

Due to the many divisions of each of the 6 billion DNA letters in each cell some mistakes will always be made,even with the systems to try and limit these. However, environment is of great importance. Smoking alters the DNA in many organs. Smoking is the highest factor in many cancers of the body. Ultraviolet light,radiation,pesticides,some toxins such as aflatoxin (produced by fungus),perhaps a high meat diet, oncogenic viruses (HPV,Epstein-Barr, Hepatitis C) ll are shown to cause the DNA changes and promote cancer.

There are two types of DNA replication and repair. The standard type is with nonprotein producing DNA and is less energy demanding then the "elite" type. The standard type allows a moderate number of errors to be passed but the more elite way reduces these considerably. The key "policeman" determining which way the DNA will go is an acetylation process. If the control of this is discovered it may be possible to harness the bodies own way of protecting the dividing DNA from errors and reducing disease.

Tumors distort healthy tissue and set off the immune system. Cell proliferation,blood vessel growth due to this action can enhance the cancer. This inflammation does help cancer grow even tho the body is trying to repair itself. Many cancers are associated with inflammatory markers.

The ability to avoid many of these cancer causing agents is important. The ability to do a proper diet and supplement schedule to help avoid the damage to DNA is important. Many things can be done to limit the growth of cancer cells. Many of the factors that predispose to cancer are also involved with aging and chronic disease.

Using our Immune System to stop Cancer.

2010-08-11T12:01:00.000-07:00

The immune system can be our best friend or sometimes an enemy. This system has evolved to protect our cells from foreign invaders. It is also key to police our bodies to get rid of dysfunctional cells that can turn into cancer. The cancer cells have developed ways to hide and evade the immune system. Also, the immune system can be tricked into thinking our own healthy body cells are foreign. They will then attack and kill vital cells and create autoimmune diseases. As we get older the immune system loses some abilities to respond to cell injuries and leave us with less protection.

There is a new area of immunotherapies that can aid our system to fight cancer. In the very early stages of cancer patrolling immune cells can recognize cancer cells and destroy them. This process relies on a protein, connexin 43 that forms tiny communication channels between different types of cells. Fragments of tumor proteins called peptides escape through these channels and acts as signals triggering a immune response to them. But as cancer cells grow and divide not enough connexin 43 is produced and the cancer cells are not recognized by the patrolling cells.

By injecting Samonella bacteria (in a non disease form) into mice with melanoma cancer, and in human cancer cells, more communication channels were formed and the connexin 43 was increased to a level that the immune system now recognized the cancer cells and removed them. The technique also stopped cancer from spreading to other parts of the body.

The cell membranes contain 1/3 of the 7000 proteins in the body. These cell membrane proteins function to allow passage in and out of the cell,attract antibodies from the immune system and can transmit signals to the cell. A new technique using a laser light and studying its backscatter after it is shined thru a solution of various cell membrane proteins allows identification of what chemicals,hormones,antibodies these proteins react to. This technique promises to allow the ability to see what type and quantity of materials it takes to interact with the valuable cell membrane proteins.

Other work is producing aids to our body defense immune system to allow destruction of early cancer.

Regeneration of Tissues

2010-08-08T16:13:00.000-07:00

Certain animal forms have the ability to actually grow a new extremity when one is lost. Salamanders,Zebra fish and newts of different types. Why not us? Evolution does favor these species with the ability to create or regenerate new tissue but chose to trade this ability in other species for the protection from cancer.

There are two genes,Rb and Arf that appear to be involved. These genes are able to activate adult cells at the injury site to stem cells that can repair, grow and divide tissue. It allows regeneration to occur. One of the genes ,RB,is found in the Zebra fish and Newt and when it is inactivated allows regeneration to occur.

Humans have both the Rb and the Arf gene. The genes are made to actually cause cell death when a abnormal cell is found. This allows us a "supressor' ability for cancer cells. The second gene,Arf ,probably evolved after the amphibians. By using a silencer chemical (silencing RNA) the action of both genes can be stopped. In mice, by doing this,regeneration of muscle tissue took place after injury rather then just healing with scar tissue.

It maybe possible that these genes could be inactivated for a short time and allow regeneration to occur after injuries.

The other approach to regeneration is using stem cells. Adult cells can be converted into stem cells with the addition of certain proteins into the cell. These cells can then be injected into an area of the body after injury (heart attack) and new heart muscle cells could form.

The possibility of repairing and regenerating our tissues is possible. Evolution already has developed ways for this to happen.

Exercise the Body and build new Brain Neurons

2010-07-07T13:59:00.000-07:00

When we exert ourselves with a aerobic exercise (running,swimming,biking) we create a growth stimulus for our many body cells. We also create a increase in the blood flow throughout the body and the brain is included. The Brain has many adult stem cells waiting around to stimulate and divide to new neurons. Exercise is a significant stimulus. The stem cells respond to a protein called Noggin, which is increased with aerobic exercise and causes the stem cells to divide and create a whole new group of neurons. As we age, the level of stem cell activity decreases ,but exercise ramps this up to a higher level.

As usual, it is a more complicated process then we would think. There is a protein BMP,(Bone Morphogenic protein) that is created throughout the body and it moderates cell growth. High levels of BMP in the brain slow down the ability of the stem cells to divide,whereas the noggin speeds this process up. It is a balance but exercise favors the noggin and therefore more stem cell division. Inactivity the BMP and less stem cell activity. In vitro studies show unopposed noggin activity can eventually exhaust stem cells so they cannot divide. However,so far,it does not appear that even strenuous exercise can cause this.

Non aerobic exercise such as weight lifting,isometric,yoga etc. stimulates the local muscles but does not obtain the blood flow to involve the brain. Aerobic exercise that causes a heart rate increase is necessary.

Exercise also affects the stem cells of the bone marrow. When there is stimuli from jogging or other forces to stimulate the bone marrow cells certain genes send out signals for the bone stem cells to produce new bone forming cells. If these stem cells do not get this stimulus and have exposure to high levels of insulin then they produce fat cells. This is particularly important for younger children since how any bone cells is related to development of osteoporesis.

With the new neurons it appears that more complex functions are easier to learn.

The Discovery of Memory in the Brain

2010-05-16T12:53:00.000-07:00

The search for where and how memory occurs in our brain has been sought after for years. The source of memory has been thought to be in the heart,pineal glad,the soul etc. More recently the genes and their proteins were the area of interest.

In the early 1970's a neuro group noticed that when a electrical stimulus was passed into a living slice of hippocampus tissue a Lasting potentiation of this was formed and this stayed for hours. This was labeled the lasting long term potentiation. (LTP). Later, this observation became the life work on Neuroscientist Gary Lynch.

The normal resting brain has continuous electrical activity (Theta) of 70 cycles per second. The activity to stimulate LTP was 5 cps. When we see,hear,touch,smell the environment these 5 cps theta waves are relayed to the hippocampus. Certain patterns of cells (depending on the pattern of the stimulus) are activated by these signals. The electrical signal passes to the end of the neurons axon (which may have thousands of connections with other neurons via their dendrites) . A group of chemicals called neurotransmitters are released from the Axon and pass across a very small gap to act on the surface of the associated dendrite. There are 1000 or more of different neurotransmitters at these junctions. The important transmitter for this memory storage is glutamine. It must activate two separate receptors on the dendrite surface in a 1-2 step in a short time. These receptors are called AMPA and NMDA. In this same area are high concentrations of Calcium. When the receptors are opened, Na+ enters the dendrite, depolarizes it and allows Ca++ to enter. This happens in a few millisecs. The Ca++ activates a special protease enzyme (Calpain) that will depolarize actin fibers. When these are changed the actual shape and size of the dendrite is changed. It increases in size by 30%. small projections called "spines" are formed. This takes 2 to 10 minutes. Next small protein molecules called integrins stabilize these changes (7 to 60 minutes). The increase in size allows up to 30% more receptors to be available to transfer information in the future.

The number of gamma waves that are associated with each theta cycle allows storage of short term memory. If you have an increase in the number of electrical gamma waves for each theta wave, more bits of memory are stored.

Learning has been shown to produce the same changes as the electrical stimulus. The learning-memory does not just stay in the hippocampus but is shown to soon be in many different parts of the brain.

At least three things can stop the LTP activity and therefore stop learning and memory. Sharp waves, produced in the dentate gyrus of the hippocampus,which are weak Theta waves (less then 4Hz), if applied before the third or consolidation phase , can wipe out the LTP message. This activity is usually found when the brain is on "cruise control" and not focusing on any one thing. Walking down the street relaxed. You see a lot but later can' t remember all the details. Some things not important and not stored. A chemical ,adenosine, also can wipe out and block LTP action. A third is the blocking of integrins and the memory not fixed.

As we experience many things that are similar it takes less and less new neuron connections. A first experience may excite and recruit 15,000 connections,a second similar experience may only excite a few hundred. Each experience reenforces the earlier connections. As we experience new things our brain wants to put these into already stored categories and the new experience will be influenced by the previous memories. We are limited by our brain memories on how we actually interpret new experiences. Much of the memory process is not 100% efficient and only parts of the actual information occurring actually is stored. This is due to the slow theta waves, the only 30% of glutamine reaching the receptors and the co mingling of memories with others. Remember the variable eye witness studies?

We take the information, as imperfect as it is, and want to create a narrative or story that will satisfy our brain. We want to create a comfortable story for ourselves.

LTP is at the basis of many neuro diseases. As we age our learning ability decreases in a linear fashion. This same curve is also how LTP decreases as we age. A group of chemicals called Ampakines increases the AMPA receptors opening time by 30%. This allows much more time for the Ca++ to work and more information to be passed on. Brain Neurotrophic Growth Factor,(BDNF) found at the synapses is vital to promoting the LTP activity. This material enhances both LTP and the actions of ampakines. People who have a high diet of the spice tumeric appear to have less dementia and memory loss. This spice contains chemicals similar to BDNF. As we age the adenosine increases (which stops LTP) and decreases BDNF. Forced exercise has been shown to increase the amount of BDNF especially in the memory organ of the Hippocampus. The slowing of learning due to age is modified by ampkaine.

Many researchers have shown that Ampakine improves many neuro related diseases. This may be due to the fact that LTP is at the basis of almost all learning processes of the brain (including muscle movement,breathing,intelligence etc.) and that disruption triggers off various diseases.

The above is a long tested explanation of how memories and learning is transferred and stored in the brain. This is not a perfect system but one that has evolved over millions of years. There are many earlier parts remaining that may be of little use or even damaging . It is a complicated one and subject to many errors. It was originally developed for somewhat simple learning,where the animals are.what is dangerous,who can you trust etc. We now live in a complicated and changing world and rely more and more on this system. This storage of outside information is far from perfect yet we build all of our perceptions and consciousness on it.

Dysbiosis can be a serious problem.

2010-05-10T15:25:00.000-07:00

We have up to 100 trillion bacteria living in our intestines. over 1000 species and 300 to 500 of these are considered to be helpful and most others are neutral to us. These live in a state of harmony called symbiosis. However,due to diet changes,stress,antibiotics,ingestion of spoiled food we can change many of these to disease causing agents. This process is called dysbiosis.

The importance of our bacteria lined intestine begins at birth. The mothers milk contains a large amount of indigestable protein that is a complex lactose sugar. This allows coating of the intestine and a barrier to noxious dangerous bacteria and viruses. It also allows a friendly bacteria,bifidio longum,to thrive. This bacteria has the ability to make enzymes that can digest the complex sugars. This bacteria, and the complex coating of the mothers milk, protects the infant while it develops its own immune system.

When mothers kiss their baby they are sampling the bacteria on the face and lips. These are then sent to the tonsils and other local lymph areas and the antibodies specific to protect from these are developed. These antibodies are then transferred ,via the mothers milk,to the infant and protection is offered.

The balance is maintained by many chemical messengers between the bacteria and the host intestinal cells. If the immune system thinks the bacteria are dangerous it will attack and severe inflammation will occur. This "secretion system" of communication is vital for the intestines health and well being. When this system is stopped the number of bacteria increase,and the host loses its neutrality and the immune system is activated and inflammation occurs.

The Intestine is lined with an abundant lymphoid system. These collections of naive lymph cells are called Payers patches. The M cells between the lymph collection and the intestine mucosa have receptors that recognize the many harmless protein products and digestion debris and do not allow them to be absorbed. However,abnormal products are recognized and are let into the lymph system so antibodies and other immune defenses can be created. Antigens from the intestine are sampled and if these are abnormal the inflammatory reactions can begin.

A high fat diet can change the bacterial flora and cause production of toxins that allow leakage into the body. These toxins stimulate the immune system to react and create an inflammatory response that produces damaging cytokine enzymes. Eventually these interfere with the metabolism and insulin resistance is created. This change in bacteria growth can lead to obesity.

One type of bacteria,associated with inflammation and cancer , can be activated by stress to release chemicals which cause the bacteria to enter the cells and even pass through to the lymphatic system. The body responds with a severe inflammatory response. The whole process triggered by stress. Probiotics appear to lessen this response,probably by blocking some of the receptors and allowing "good' bacteria to compete for space. A chemical in apples,quercetin,seems to also lower the inflammatory reactions and protect the cells. Complex carbohydrates such as barley,beans are useful to promote good bacteria.

A form of E.Coli ,causing severe diarrhea,is activated by a combination of chemicals produced in the colon by neutral bacteria and also the hormones epinephrine and norepinephrine, to increase in numbers and activate "quiet" genes to produce deadly toxins. The bacteria has a special receptor on its wall (QseC) senses the chemical signals and causes the changes to occur. By giving a anti adrenergic drug (Phentolamine)the receptor is blocked and the bacteria is harmless. Stress is associated with high levels of these damaging chemicals.

The above shows the very important processes that bacteria are involved in. We all evolved together over the many years and are usually in symbiosis. However, there are many ways to cause dysbosis and have disease. These disease states often involve many other areas of the body besides the gut itself.

Calcitrol, maybe the super metabolic-immune system master

2010-03-30T14:27:00.000-07:00

Vitamin D3 ,naturally formed in the skin by sunlight, converts in the liver and kidney into a super hormone Calcitrol. Deficiency of this vital hormone is associated with at least 17 different varieties of cancer as well as heart disease,diabetes,arthritis,gum disease and possibly many muscle disorders.

Although sunlight exposure is essential for D production most of us do not get enough to really supply the D3 needed. It is thought we should have between 50 and 70 micrograms in our blood system. Many older adults (60%) have 20 or less. Due to this supplements are now thought to be necessary. It may take 2000-5000 IU per day to achieve a reasonable level. The best way to know is to get your 25-hydroxyvitamin D level and then began to replace the D3 you need to achieve the desired levels. Some will need 5000 IU per day for 2-3 months then level off at 2000-4000 per day. It is also important to have reasonable intakes of the D3 activating co factors. These include magnesium(very important),zinc,Vitamin K2,A and boron.

Since magnesium and zinc and Boron are important a good source for these are various nuts. Mixed nuts of about 1 oz. per day (sunflower seeds,pumpkin seeds and sesame seeds are best) should be part of the diet. The other factors are found in green leafy vegtables. Vitamin K2,associated with Vit D activity and bone metabolism, is found in high amounts in a japanese fermented soy product called natto. This vitamin has been shown to be very protective of fractures and is probably related to its action with D3.

Breast cancer patients with low levels of D3 had a 73% higher risk of death then those with normal levels. The tumors were of a more aggressive type with low D3. The risk of breast cancer is reduced 50% at a level of 50 nanograms and even more reduction when 70. The average person has levels below 30 ng. Calcitrol limits the production of new vessels to nourish tumor cells,it also enhances the immune system to destroy cancer cells. Breast cancer patients need testing and probably 4000-6000 IU each day of D3. It is uncertain as to the highest permissable dose but up to 10,000 units per day is thought to be safe.

Patients with heart disease and low vitamin D3 levels were 3 times more likely to die from heart disease then those patients with normal levels. Women with low D3 levels had a higher risk of high blood pressure then those with normal levels.

It has been shown that normal levels of D in the blood(25-50) are necessary for the proper function of key components of our immune system.

Some interesting facts. Optimal blood levels of Vitamin D would reduce cancer by 35%,type 2 diabetes by 33% and overall mortality by 7%. Influenza infections would be reduced by 42%.

The real unknown is how much D does one need to reach the optimal blood levels? This is probably best determined by a blood test and then starting a high dose for a few weeks and then retest to see if the levels are adequate. It maybe that as individuals we also have different doses of D needed.

Sleep is a potent weapon against disease

2010-03-19T17:37:00.000-07:00

We all know a good nights sleep is supposed to be good for us. How good? Well,maybe it is a life or death situation.

Even young healthy people with good life styles can suffer diabetes,heart attack and other serious diseases. One of the main factors appears to be a lack of sleep. Fewer then 6 hours can cause a 300 to 500 percent risk of high blood pressure. Young people have a 50% greater chance of developing blood pressure problems if they sleep less. There is a 3X increase in heart attacks with those who sleep less then 5 hours per night.

It is a metabolic fact that the body needs a certain amount of "down time' to be able to do the many important maintenance functions to assure our cells are healthy (see the mitochondria and Leptin discussions).. This time is at night when the damage of free radicals,inflammatory chemicals,extra fat and glucose are all controlled. Just one night of sleep loss causes an increase in the toxic markers in our body. C reactive protein,an important marker of inflammation is increased as well as other substances.

Sleeping 5 hours or less had a 39% increase in chance of heart attack,and 6 hours or less a 18% increased chance. At least 7 hours and preferably 8 hours is needed. This should occur with at least 4 hours after any food intake. Extra late calories can confuse the proteins that do the maintenance.

What can be done to regulate Leptin levels?

2010-03-16T14:16:00.000-07:00

The previous post discussed the importance of Leptin as the master regulator of many metabolic processes in our body. is such an important hormone that maybe at the basis of many chronic diseases and aging. Too much and the system is disrupted and bad things happen.

Too much is associated with excess caloric intake. Once we have increased our adipose tissue and we have allowed increased levels of Leptin then we have Leptin resistance and the natural protective cycle is lost. By reducing calories we can lower Leptin. however this is much harder to do if one is very overweight. The Leptin levels are stubborn and the resistance remains compared to normal weight people.

Leptin has a natural cycle of release with higher levels in the AM and less at night. The higher levels release cortisol and allow the morning wake up energy. The lower levels at night allow many repair processes to go on as well as burning of fats. One of the things to do is to eat your last meal at least 3-4 hours before sleep. If not the Leptin levels will remain up and the important repair processes and oxidation of fats will not occur. Since melatonin is related to the AM-PM cycle and it has been shown to be related to lowering levels of Leptin this may be a helpful supplement.

Eat a breakfast with a good amount of protein. This will increase your metabolism by 30%! A strong carbohydrate one is only a 4% increase. Eat meals at least 5 hours apart. Do not snack between meals. Triglycerides are formed after meals and if they are not metabolized they will elevate Leptin and also interfere with the message to tell the brain to not eat. Snacks interfere with this process.

Eat smaller portions at each meal and eat slowly so you can recognize when full. STOP when 3/4 full. Lower the amount of carbohydrates eaten and try to make these fruits and veges.

At least 30 minutes of exercise each day seems to allow the leptin to function better. Try for at least 8 hours of sleep. This is when all the vital cellular repairs are happening and the fasting time is needed.

It has been found that alpha 3 omega acids appear to play a role in lowering leptin levels. People with high levels of this have 1/4 the levels of Leptin. Other supplements tried in rat experiments to have success in lower Leptin levels include LCarnitine,and Conjugated Linoleic acids.

Regardless of the lowering of Leptin levels the above dietary ideas are the wise thing to do. (See previous blog on a healthy diet).

The Thin Hormone that prevents serious disease

2010-03-14T17:01:00.000-07:00

Leptin (thin) hormone is becoming a key chemical in the evaluation of the deadly metabolic syndrome. This includes high glucose,insulin resistance,hypertension and high cholesterol and other fatty levels in the plasma. Almost all of these patients are overweight or obese.

Attempts at lowering the blood pressure,glucose,cholesterol etc. have not been shown to be effective in preventing serious damages to the body. Billions of dollars are spent on drugs to lower these to "normal' levels with minimum results. These appear to be the results of a much more basic abnormality.

The production of lipids by the body is a normal result of our energy metabolism. Lipids are toxic and at higher levels can attack the cells (heart,pancreas) and actually destroy them. It is thought that the actual cause of damage by the metabolic syndrome is due to increased lipid levels destroying important cells. After absorption from the gut the fat is sent via the lymph and blood to the liver, Various types of fats are made (chylomicrons,VLDL,LDL,HDL) and then sent to the cells of the body. At the cell level they are transferred into the mitochondria and through a oxidative metabolism are made into ATP (energy). This allows energy production and gets rid of the potentially toxic fat.

With an excess of carbohydrates the body will spare the use of fat as a energy source and use the excess glucose. This allows the fat to be selectively spared and stored as triglycerides. The high CHO allows the accumulation of too much glucose and the cells begin to actually form fatty acids out of the glucose. This occurs in the cytoplasm and endothelial reticulum bodies. These fats are then stored in the fatty tissues. This "de Nova" fatty production from excess carbohydrates is very minimal in normal weight people.However excessively high levels of calories over time will led to fat metabolism sparing and storage of fat in the adipose tissue. The normal oxidation of fatty acids is done in the mitochondria and this is promoted by leptin.

The mitochondria also have a connection to our immune system. A protein in the mitochondria (UPI1) allows fatty cells to burn off the energy as heat rather then store this as fat. This is more prevalent in brown fat but can be found in white fat cells as well. A gene (IKKe) is one of a group involved in inflammatory changes in the body. Low level inflammation is produced by obesity and this gene is involved. This gene limits production of UPI1 (involved in releasing heat) and when it is absent the mitochondria release more UPI1 and the fatty cells burn off energy as heat and do not store fat. The finding of the TOR gene and its relationship to longer life and less disease may be due to its immuno restricting effect allowing restriction of the inflammatory immune response. Diabetes and other disease is associated with these low levels of inflammation.

Diabetes II is associated with a change in the methylation of DNA . This is an epigentic change which changes the function of a gene,PGC-1a . This gene in the muscle cells controls glucose metabolism. The methylation change is promoted by increased fatty acids and cytokinase. The increase in fat also effects the function of the important endoplasm reticulum in the cells. This structure assembles and folds vital proteins for the cell.With increase fat levels its function is decreased and the complex of proteins that protect it are lowered. The ER becomes stressed,the proteins are not produced and vital cell functions are lost. This has been shown as an important factor for Diabetes 2.

Leptin has a very strong effect on the bone cells (osteoblasts).It increases the activity and also causes more calcitonin to be produced. This calcitonin is a hormone that increases the production of insulin,increases the production of adiponectin ,which increases insulin sensitivity. It also increases the production of testosterone.

It is actually adipose tissue (white and brown) that produces most of the leptin in our bodies. Other organs including the liver,muscle,stomach also can produce this hormone. A second hormone,adiponectin, is also produced. The leptin actually affects the cells ability to oxidize fatty acids (lipids) and the adiponectin causes lipids to be stored in fatty cells (increases insulin sensitivity). These two mechanisms control the level of lipids and protects the body cells from damage. Leptin also plays an important role in our sensation of hunger by acting on the hypothalmus to let us know when we have eaten enough.

As we gain weight and increase our food intake above what we need the fatty cells are increased in size as they absorb more fatty acids and also produce more leptin. The idea that our fat cells are actually an active metabolic organ that produces a hormone is a somewhat new idea, Unfortunately,as the leptin levels increase the body has a tendency to quickly become resistant to its action. The cells should be taking in the fatty acids and metabolizing in the mitochondria are reduced nd the fatty acids accumalate in the cells and cause a toxicity to the cells. This leads to an inflammatory reaction seen in most chronic diseases. An actual lipotoxicity results.The ability of the fat cells to absorb lipids is also decreased. The result is lots of dangerous fatty acid lipids now in the body. At a lower rate of weight increase the fatty cells actually work to try and regulate the metabolic process and protect the cells from toxicity. But soon the amount of new fats overwhelm the ability and the process of resistance and toxicity begins.

This high level of Leptin, due to the increased fat cells size and the development of resistance, actually stops the leptin from reaching the hypothalmus and the message of "stop eating" is not given. The normal mechanism to stop eating since the fat stores are adequate is lost and the person continues to eat and even more fat is stored. Normally the brain will stop excess food intake if Leptin levels normal. Leptin levels actually increase as we age and this is one reason older people have tendency to gain weight more easily then younger folks. This is especially true for women with loss of estrogen.

It is thought that the insulin resistance seen in diabetes 2 is a protective mechanism where the cells slow down the intake of glucose to stop the production of even more fatty acids,which are produced by the excess glucose . We see increased levels of insulin and glucose. But these are reactions to the real cause of the problem, the changes in Leptin activity.

Fructose is an even greater problem since it promotes all of these bad things at a greater rate 20 times that of glucose. Much of our processed foods contain fructose.

As the lipids cause their toxicity in the cells the cells react with a generalized inflammatory reaction. This is an attempt to minimize the damage. Many of the "markers' seen in the various diseases are due to these inflammatory reactions. Again they are responses,not the cause, of this problem.

Leptin regulates parts of our immune system,blood pressure,blood clotting,heart function,insulin levels and even artery constriction. It is indeed the master regulator of our metabolism.

Microdoses of leptin can be given and it effects a gene in the liver that lowers glucose and increases insulins ability to act.

Proper leptin levels controls our food intake, metabolizes and stores lipids,allows normal glucose metabolism,and allows proper action of insulin.

What is a really healthy diet?

2010-02-04T16:35:00.000-08:00

With all the previous information about how things effect our epigenes and the fact these changes can cause serious diseases as well as premature aging what are some things a person could do to try and help the epigenes? How about other diet changes?

Feeding mice three different diets caused thousands of genes in the liver to have different expressions and functions. This change quickly followed the diet changes.

Yes,what we eat certainly does tell the body to produce different chemicals that control our health.

Don't smoke.

Control your calories. It is well known that caloric restriction is the only thing that has been shown to statistically increase animals life spans. The idea of reducing calories by 30% is not practical except for lab animals or prisoners. Recent work has shown that fasting one day a week or reducing your daily calories by 500 calories (a 20% reduction if on a 2000 per day diet) may produce good healthy results.

It seems there is a very important enzyme, peroxiredoxin (perox) that is a key in destroying hydrogen peroxide in our cells. Hydrogen peroxide is formed as we create free radicals in our normal cell activities. These then destroy genes and vital proteins and leave us with aging and chronic diseases. This enzyme decreases as we age. The caloric restriction produces another enzyme, Srx1, which repairs the damaged perox enzyme and allows it to function more normally and prevents oxidation damage to our cells.

A moderate amount of alcohol (1-2 drinks per day) has been shown to inhibit a chemical called notch, which is involved with smooth muscle changes in our arteries. When notch is active there is an overgrowth of muscle cells and narrowing of the arteries. Alcohol inhibits this action and the blood vessels are less narrow. Less chance of heart disease. At higher levels of consumption alcohol can stimulate acetaldehydrase, a by product of alcohol, which may block enzymes that methylates DNA and the protein epigenomes. This may change the methylation and change the functions of significant genes activity and predispose to disease. This effect seems to be associated with folate deficiency in the diet. Certain people may have a DNA change in a gene that predisposes them to these changes. (MTHFR gene). People with high alcohol intake and low folate levels have 5X the rate of colon cancer.

A small amount of alcohol is probably safe and may be beneficial.

A good methylation diet includes choline,methionine,folic acid,B12 and B6, and zinc. Foods that include these are the following:Green tea,cauliflower,broccoli,kale,box choy,cabbage,turnips,spinach,peas,beans,sunflower seeds,eggs,lettuce,peanuts,garlic,Brazil nuts,tofu,fish and liver.

A recent study shows a significant decrease in dementia when people eat a diet high in the B vitamins. The doses were 1200 IU of folic,and 50 mg of B6 and higher levels of B12. Again,supplements might be a wise choice.

Polyphenols in the diet (from plants mentioned above) can signal the genome in the nucleus to do vital functions to keep the cell healthy. In order to allow this the cell must have a ongoing supply of a key coenzyme, NAD+. This is constantly being used to furnish energy to our life processes. The substrate for this enzyme is Nicotinic acid and Nicotinamide. These are not made in the body but must be ingested. Tuna,salmon,halibut,sardines,chicken,turkey,crimini mushrooms,peanuts,lentils, whole wheat and whey protein are all good sources.

It seems polyphenols in cocoa attach to genes in the liver and promote an increase in HDL cholesterol (good) and decrease LDL (bad) and lower total cholesterol. This is probably the way that these important polyphenols work. Activating genes that produce good metabolites for the cells. (You can eat chocolate-but not too much).

Olive oil is being shown to be an amazing food. It seems to have a variety of chemicals that offer protection for inflammation of the bowel,reduces the chance of cancer and actually is anti bacterial. It also protects against damage to our red blood cells. 2-3 tablespoons is suggested each day.

By eating these foods the chemicals thought to be important for methylation of the epigenes will be ingested. This may offer a very important protection to your body.

Vitamin D is being investigated as an important methylation agent. It has been shown to affect certain genes that can suppress cancer division. This is especially true in colon and breast. Many people have low Vitamin D levels and may need supplements (need 50 to 60 micrograms in the blood). The bodies immune system use T cells to protect. The T cells must have an adequate amount of D in the blood so they can be activated to attack pathogens. Without D they are not active. The immune system is 3-5 times more effective when D is at a optimal levels. It is thought that adults need 4000-6000 IU's of D each day. Vit D is important to bone metabolism and seems to reduce osteoporosis by inhibiting the action of the bone destroying cells,osteoclasts. Recent studies show significant decreases in many types of cancer if blood levels at 60 micrograms. It takes about 2-4000 IU supplements to achieve this.

The eating of all types of animal proteins,including casein in milk, is associated with increased incidence of all types of diseases including cancer. It may be that these proteins are similar to our own,are partially broken down and then absorbed by the gut. Once in the body these partial proteins are recognized as foreign and the immune system develops antibodies against them. Many of these "foreigners" are similar to our own proteins and perhaps the bodies own immune system begins to attack and destroy our own cells. (Auto immune disease). Most diseases are associated with the release of inflammatory signals that occur with this type of response.

As we age our immune system changes. Our reserve of lymphocytes available to fight off new antigens and diseases shrinks. This is probably due to many of these cells programmed to fight off chronic,sub clinical infections such as cytomegalic viruses. By having these chronic infections (40-100% of people acquire this virus at birth) we eventually "tie up" our immune system with needless lymphocytes and limit the number available to act on new challenges. As we age it appears that the immune system gets confused and will lose the ability to recognize "self" cells. If the immune system suspects a cell surface of being a foreigner it will create antibodies against this and a autoimmune process will develop. Free radicals,glaciation and various bacteria and viruses can fool the immune system into self destruction. Many older people have high levels of auto antibodies .

At this time no dietary changes are known that would directly influence this process. However,by reducing the amount of free radicals,and glaciation changes it could reduce this problem. Antioxidants in foods may prevent some of this damage. It seems our intestinal bacteria are also involved and the diet and probiotics to promote these are important.

Mushrooms,white button and other types,have 12 X the antioxidant power of wheat germ and more then many green vegetables. They also promote important bone marrow cells (Dendritic) that produce T cells to fight disease and cancer.

What single drug can benefit you by:

1) supporting and strengthening your immune system?
2) providing anti-inflammatory properties?
3) providing anti-oxidant properties?
4) restricting blood vessel growth feeding tumors ("anti-angiogenesis")?
5) causing programmed cell death of cancer cells ("apoptosis")?
6) providing antiviral effects?
7) restricting the growth of pathogenic bacteria?
8) assisting conventional anti-cancer drugs to work more effectively at lower doses?

NONE. Mushrooms provide all these benefits, and they are not drugs. These are 'functional foods' and/or 'dietary ingredients,' which help support the immune system on a fundamental, multi-factorial level. Nature is a numbers game. We need all the support we can get as our immune systems and health are under assault from pollution, stress, contaminated food and age-related diseases as our lifespans increase.

Mushrooms are miniature pharmaceutical factories, and of the thousands of mushroom species in nature, our ancestors and modern scientists have identified several dozen that have a unique combination of talents that improve our health. Culinary mushrooms available in many grocery stores such as Shiitake, Maitake, Oyster, Enoki, Shimeji, and Pioppinos -- to name a few -- are not only delicious but are very low in fat, have no cholesterol, are rich in vitamins, and when exposed to sunlight, are one of the best sources of vitamin D (provitamin D2) on the planet.

Moreover, the mycelium -- the filamentous cobweb-like cells that give rise to the mushrooms (the mushrooms are the 'fruit' of the mycelium) -- have uniquely amplified properties, especially against viruses and bacteria. My team and I have discovered, over decades of study, that mushroom mycelium is a rich resource of new antimicrobial compounds, which work in concert, helping protecting the mushrooms -- and us -- from microbial pathogens.

Various nuts are related to important minerals,antioxidants,omega acids all important for our cellular health. Almonds,walnuts and pastachio nuts are a few. Pecans have a special form of vitamin E (gamma tocopherol) that decreases the oxidation of the bad cholesterol by 33% after 3 oz, meal. It also lowers total cholesterol by 11%. They all contain increased phenols related to antioxidant activity.

Berries of all types are shown to have antioxidants that maybe protective. Cherries are shown to have high levels of both antioxidants and antinflammatory chemicals. Taking about 20 cherries for 28 days reduced the inflammation marker .CRP, by 25%. The reduction of pain after ingesting cherries or cherrie juice was equivalent to Ibuprofin and seems to block the inflammatory enzymes Cox 1 and 2.

Certain types of hypertension are related to damaged mitochondria function and antioxidants may be important to correct this .

One of the most important antioxidants is glutathione-perhaps the "mother of all antioxidants". This is a naturally made molecule in the body. However,due to the tremendous amount of toxins and other free radical producers in our modern life,the glutathione is often depleted and low levels are associated with almost all diseases and aging. This maybe replaced by adding a supplement,N-acetyl cystine to your diet. About 600 mgm each day. Recently it has been shown that the actual glutathione itself can be absorbed fter oral intake. About 300 mgm per day was suggested. This is the building block of glutathione. Along with this another very potent natural antioxidant is alpha lipoic acid . This substance has been shown to lower the risk of atherosclerotic lesions in mice by 50% and lower body weight and lower triglyceride levels. About 200 mgm each day. All of the above mentioned methylation foods are important sources to rebuild these antioxidants.

Alpha Carotene has been shown to be very protective against oxidation damage. Interestingly, Beta Carotene was not. 1 microgrm. blood level alpha type gave a 23% lower death rate and a 6-9 microgrm. blood level a 35-40% lower death rate. The more the better. Yellow, orange and dark green foods are best. Squash,pumpkins,sweet potatoes,broccli,green beans,peas,spinach,turnip greens and leaf lettuce are all good sources.

A very important consideration is the glycation of proteins. Sugar,especially fructose, can bind to vital proteins and they are then recognized as foreign substances and attacked by the immune system. This is a cause of inflammation and aging. It is thought we should have less then 15 grams of fructose per day. Most processed foods contain corn syrup filled with fructose. However,natural fruits also have significant amounts with many having 5 to 15 grams per serving! It is wise to eat only a 1/3 of a cup or a 1/3 of an apple or banana. The total intake,regardless of source ,must be kept low. Glucose,in its natural form, is the best choice. Table sugar is sucrose and not as good. Brown Rice sugar may be the best choice. Uric acid levels are associated with abnormal fructose and if elevated indicate too much sugar and fructose.

Our colons contain millions of various bacteria. These are important in many aspects of our health. They produce by products that allow healthy maintenance of the colon cells (butyric acid) phenols,anti glucose chemicals,and signals that keep our immune system in a steady alert. There are foods that promote the good bacteria. Beans,barley,oats,apples and some other fibers have complex sugars not absorbed by the small bowel. These are food (substrates) for the good bacteria and promote their health and growth. Probiotics (Yogurt,Kiefer etc.) promote growth and addition of good strains of bacteria. There are 10 trillion bacteria and the addition of probiotic is important for their health. need as many different types of lactbacillus as possible. Most yogurt contains 9 to 12 types. Use the plain types to avoid lots of added sugar. Capsaicin, found in Red peppers,has the ability to increase enzymes that promote the cell death of abnormal (cancer) cells.

Since we have trillions of bacteria and they are very important to our health we need to consider them as a key element to prevent disease. Many things,including aging,weaken the good bacteria and predispose to disease. The immune system is 70% located along our gut, Bacteria are key in alerting this system and keeping it functional. besides a good diet we need supplements. Probiotic supplements should contain at least 50 billion total bacteria per serving, at least 10 different strains, should be slow release so they are not destroyed in the upper gut, and at time of the expiration date maintain the activity of all 50 billion bacteria,

At least 1% of our population has a genetic problem with gluten, a substance found in many grains such as oats,Barley. Rye and wheat. Gluten has a protein, gliadin , that causes antibodies to be formed against it. If Gluten is ingested this protein and antibody reaction trigger genes into action that produce damaging inflammatory changes. These changes can affect the gastric system (Celiac disease) and the brain. The brain is compromised by severe inflammatory enzymes and the antibodies may actually attack some of the brains proteins that are similar to gliadin. The result may be headaches,learning disorders or behavioral changes. More and more people are using gluten free products. There is a test for gluten antibodies that can determine if you are gluten sensitive.

There is a lot of work showing that alpha 3 omega acids are very helpful in our health. Heart rhythm, cell wall maintenance,atherosclerotic plaques all seem influenced by this chemical. Carotid artery atherosclerotic lesions that were unstable had 1/3 the amount of omega 3 acids as did the asymptomatic stable ones. Omega acids reduced the amount of inflammatory prostaglandins by a significant amount. Neuron health and function appears to be increased with this substance. There is evidence that inflammatory reactions are decreased. It is thought at least 1 gram (4 tablets of fish oil) are needed daily. The alpha 3 in fish actually come from green algae which is another source especially for those with fish allergies (Neuromin supplement). Certain grass fed cows and beef produce alpha 3 acids in their meat and milk. Walnuts and flax seed also allow production of this acid in our bodies (although only 15% or so is converted). Some eggs from special fed diets have this.

This substance (DHA in fish oil) is important for the function of our trillions of synapases. It has been shown low levels are associated with depression and suicide. Also,violent behavior. The development of fetal brains in utero are very dependent on this. There is a alpha acid,alpha omega 6, found in linoleic acid ,that has replaced the more expensive alpha 3 omega in our diets. This is associated with production of endocannabinoids that trigger appetite and cause obesity. DHA and EPA in fish oil contain powerful anti inflammatory compounds called Resolvins. These are shown to be protectors from the damaging inflammatory changes that occur.

There is evidence that a diet that promotes an acidic pH (less then 7) will cause many dysfunctional body processes. Conversely, a diet that promotes an alkaline pH is protective. It is thought that at least 60% of foods should be those that promote an alkaline response. These foods includes mostly fruits and vegetables. Animal proteins (meat,fish and milk products)promote an acid response.

A lot of work over many years shows that decreasing the amount of calories ingested (30%)will decrease aging. (See previous discussions). However,it is not proven this works in humans. It is known that excess calories, forming fat, will increase aging and chronic disease. One of the chemicals associated with this antiaging is Reservatrol which causes a number of positive effects. It appears the the starving releases this material. It is also found in certain foods. It appears to offer a number of ways to help our health including blocking the division of some cancer cells. Older people with less calorie intake appear to have less memory loss, then those with more caloric intake.

Recent studies show that the primary mechanism that decrease calories (and vigorous exercise!) work is to trigger off signals to increase autophagy. This is an important way the body actually destroys various things that are malfunctioning. Without this cleanup the cells will divide and spread the malfunction so that various diseases and aging occur. It appears a certain amount of physical stress is important to make sure our body is healthy.

It is also shown that intake of the spice Tumeric decreases loss of memory in older people. This spice appears to have chemicals similar to BDNF an important substance for brain cell health. The brains microglia cells are very important in the inflammatory control in our brain. As we age the microglia production of cytokine enzymes increase. These are related to inflammation and probably memory loss. There is an important chemical, Luteolin, found in red peppers,celery,olive oil,rosemary and carrots that protect neurons from the damage of these enzymes. This has been shown to reduce memory loss.

There are pill supplements that contain Reservatrol equal to 100 glasses of Red Wine. This would be a consideration as a supplement to your diet. The dosage is uncertain, but a dose of 200-500 mgms. is suggested daily. (actual dosage is not agreed upon).

As we age our cells become prone to DNA damage with each cell division and if our protective mechanisms are not working cancer will develop. The protective mechanisms are genes (P53,RAS) and these are often suppressed by environmental effects. 50% of tumors have inactive P53 suppressor gene. These genes action cause apoptosis or death to abnormal cells and can stop older cells from reproducing reducing chance for cancer (senescence). A drug, PEITC, a member of the isothiocynate group, can restore the protective function of the P53 gene. Foods that have this include watercress,broccoli, and cabbage. Apigenin another chemical found in fruits and vegetables, also can activate a damaged P53 and other suppressed genes. Apples,cherries,artichokes,tea and wine are sources.

There is a so called "super fiber" that may help control our intake of food. It is thought that the more fiber in the diet the better. A 30 gram amount (or more) is suggested. Most folks get less then 10 grams. Fiber has soluble (in water) and insoluble types. Insoluble adds bulk and helps with bowel function but does not add as much benefit as soluble fibers. Soluble fibers supply special nutrients to the trillions of bowel bacteria,which can then produce many vital chemicals to help fight cancer,heart disease and diabetes. Barley is one of the good choices for this (see earlier blog). Another fiber is glucomannan (GM) that comes from the root of the elephant yam. This water soluble fiber is native to Asia. It can absorb up to 50 X its weight in water. 2-4 grams of this is well tolerated per day and is associated with significant weight loss.It creates a sense of fullness (you eat less) it "pushes" food thru the colon so less calories absorbed. This has a very low weight-calorie ratio and is good for weight loss. It causes slower absorption of food and less insulin swings. Other sources of good fiber -flaxseeds,beans,grains(Barley,oats) rice bran,nuts,fruit and most vegetables.

Bitter melon extract is shown to lower blood sugar and may be protective against cancer.

An extract of white beans prevents many carbohydrates from being digested and there is less caloric absorption and weight loss results. Eating this along with meals may allow weight loss.

Spices are important. Ginseng has a number of chemicals shown to help fight inflammation. Pomegranate juice at about 175 mls. elevates antioxidant levels in the blood. Tumeric appears to lower inflammatory proteins and may relieve pain in arthritis.

We are what we eat, and there is no doubt diet plays an important role in our health and cellular functions. It maybe that we do need extra supplements ,besides a healthy diet, to get the best protection for our cells. We have evolved from bacteria and all of our metabolism has many things in common with bacteria,plants and other living things.

Crazy Genes

2010-01-08T17:08:00.000-08:00

The mental illness of Schizophrenia effects many millions of people. The disease usually shows up later in life, age 20 plus. Some cases can be found in young children. 80% of the cases have a family history but some do not. Different cases respond to different medications. Research is showing some important answers to all of these observations.

There are different genes that are responsible for signaling the development of our neurons and axons. If these are disrupted the brain does not develop properly and the disorganization shows up with disturbed thinking,attention defects,memory and learning loss. These are many of the symptoms of the schizophrenic patient.

Patients with schizophrenia have rare deletions and duplications of genes then normals. 15-20% of schizophrenia patients with these vs. 5% of normals. Patients who had no family history had 8X the spontaneous mutations (parents did not have these mutations)as normals. Different patients had different genes mutations but all had one common end point-abnormal brain development.

One of the genes involved in many cases is D1SC1. This gene has many functions in the signaling of formation of the brain. It needs other proteins to work with to make the proper development happen. It seems a combination of genes work to signal the development. Much of the development is in the hippocampus axon development. Abnormal development in this area

leads to many of the symptoms of mental illness.

Since depression is also involved with changes in the hippocampus certain changes in the gene can cause symptoms of depression while another mutation in the gene can cause symptoms of schizophrenia.

Mice with the mutant gene have symptoms of mental illness vs. those with the normal gene. It is possible to turn off the mutant gene by feeding the mice a diet with small amounts of the antibiotic doxycline. Withdrawing the drug allowed the gene to turn on. The normal gene not effected by the diet. When the mutant gene was turned off during pregnancy (feeding mother the antibiotic) the resulting brain development was different then that when the gene was allowed to express itself. The changes were similar to those found in Schizophrenic patients. The mice also exhibited the same symptoms.

There appear to be a group of genes that work to allow development of certain areas of the brain. When these genes are mutated they allow abnormal ,disorganized development and mental illness results. Many of these genes work together and a change in one can limit the expression of another. Different patients will have different gene changes. It does appear that specific molecules can be found to block some of these changes. It maybe that these will need to be given during the gestation of the infant to allow normal brain development.

Genes have expression

2009-12-26T15:30:00.000-08:00

Our cells are controlled by the Genes making up the chromosomes. But what controls the chromosomes? The ability of a gene to act (making a protein) is enabled by some signal that tells this gene to produce or in some cases to stop producing. This process is called "Gene expression". The epigenetic "software" overlying the genes is signaled and then the genes(s) it is related to are signaled. All of the external and internal factors that the living cells come in contact with appear to be involved in signaling.

There are over 3,600 molecular "switches" in our body controlling over 1,750 proteins. These switches regulate when and if a gene will function. A small molecule of RNA or protein will act as the signal to activate or suppress a gene function. The actual mechanism is a methyl or acetyl change on the protein of the gene. If the gene is changed it can cause significant damage. In over 50% of cancer cells the P53 cancer suppressor gene is altered. In Identical twins where one has rheumatoid arthritis and the other does not they share the same genes but in the RA twin 3 genes are over expressed but not in the healthy twin. The cause of the over expression is probably due to oxidative stress and free radical formation that caused a switch to be turned on over expressing the genes. (See discussion on free radicals). When a switch is "on" the protein changes shape due to a signaling molecule binding to it. There are often many switches for the same function so the final outcome is related to the fraction of the switches turned on. Some gene mutations make the gene more sensitive to being switched on.

There are 25,000 genes and the number of possible epigenetic patterns is estimated to be 50 to 100 times as large. The number is probably in the millions and there is an effort at this time to map them out,the Epigenetic genome project. This activity is perhaps the most important discovery project in science of heredity since the discovery of the gene.

Two epigenetic enzymes are key to the gene expression. HAT and HDAC are both histone enzymes that switch genes activity on and off. When base pairs of the DNA are unmethylated RNA can combine and transcription occurs. If the same base pairs are methylated then the RNA cannot combine and the gene expression is silenced. If certain epigenes are not methylated-acetylated then their function is changed and they cannot signal or over signal genes ,which changes their function. All cells use these enzymes and when they get out of balance they predispose to aging and cancer. Cancer cells are sensitive to inhibitors of these enzymes and drugs to inhibit them in cancer are far along in clinical studies.

In cases of severe trauma ,with significant blood loss, it has been discovered 6-7% of the genes change their expression in response to this shock. This is caused by removal of acetyl groups from the epigenes activating these genes. Valporic acid,which is a histone diacetylase, can prevent the loss of the acetyl groups so the genes stay "on". In experiments, the loss of 80% of blood causes 80% of the test animals to die in a short time. By giving Valporic acid 85% of the animals survived for 4 hours or longer.

A very important factor in our health is the idea of developmental plasticity. This is the fact that the diet of the mother is key to allowing various gene expressions during the fetus development. The genes and epigenetic proteins are changed by the nutrient environment. The lack of certain nutrients and the excess of others (glucose,fats) will alter the way a gene expresses itself. Many disease later in life,diabetes,heart,cancer etc. are effected by these changes.

One of the most important factors for our health and disease states is the diet we have. It seems that the many nutrients in plants are of particular importance. Proteins,fats,sugars,vitamins,minerals,fatty acids,amino acids,phytosterols and many other molecules are contained in these plants. All of these are of vital importance in the metabolism of the cells of our body . Once these are introduced the cells decide which they need,how much,and repair vital enzymes to survive. It seems that the whole complex of nutrients in the whole food are necessary to allow this function.

Studies have shown that types of diets (eg. high in animal proteins) can allow cancer to occur whereas the diet low in animal proteins stops the same cancer . Many markers of cancer can be eliminated by a specific diet and can be increased by another. It is the change in gene expression that causes this. The change in expression is from the various signals received from the nutrients bathing the cells. People with the same genetic background can suddenly have an increase in cancer when they move and change their dietary habits. The people remaining ,with the same dietary habits as before, avoid this. Identical twins begin life with the same genes but as they progress in life the number of genes turned on and off due to life style differences. These differences allow a difference in disease in identical twins.

A methylation diet that promotes methylation in the epigenetic histones appears to effect cancer. Exposure to smoke and other toxins will change the epigenetic functions. These changes can be passed on to the next generation. The effect most noted in females is related to the environmental habit during the formation of the eggs of the ovaries. This occurs while the female is in the uterus. With a male it is related to the time of sperm formation at puberty.

If a high fat diet is ingested by a mother in generation 1 the babies born will often be fatter,larger,have diabetes and obesity then the same mother on a different diet. These babies affected will be females and not the males. Probably the gene expression change on a X chromosome. These diseased female babies will then pass on the same problems to their offspring. This can occur for 2 generations. The epigenic switch changes are inherited. What your grandmother ate affects your health. (Developmental Plasticity).

Special overweight ,diabetic strain of lab Rats that are fed a high fat diet and those with identical genes fed a high folate,methionine,betaine,Vit.B12 and choline diet will vary significantly in their off spring. The regular diet group will have the same overweight diabetic offspring. The ones fed the other diet (thought to be one that promotes methyl and acetyl changes in the switch proteins) will have thin,normal healthy pups. This change will be passed on for at least 2 generations even though the mothers put on a regular diet. It appears a single gene expression allows this change.

It is thought that genetics play a role in disease but probably a minor one. The key appears to be whether the genes express themselves in a healthy or disease way. This expression is related to things we do,eat or come in contact with. It has been shown that older people who do stretching exercises and have the ability to be flexible also have more elastic arteries. This may be due to the exercises alerting the genes for muscles to produce more elastin to allow the muscles to respond to this stimulus. Since the artery muscles have the same chemistry this also effects them. When young,prepuberty boys, smoke they can effect the sperm being produced at that time of their life. Followup shows their male offspring has a shorter life span,more obesity and diabetes etc. The formation of the male sperm was affected by environmental factors and these were passed on to the next generation. This is an example of an activity perhaps causing a change in gene expression. Mice pups raised by a nurturing mother vs. those raised by a non nurturing mother have less hypertension,diabetes etc. By switching the pups at birth the same results happen. The nurturing mother,even after birth, is able to turn on switches by her actions, that benefit the health of the pups.

A transcription factor (turn genes off and on) ,CBP, helps to control the aging process in mammals. 80% variation in mammals life span affected by this molecule. A low calorie diet (30% decrease) in worms,fruit flies and mice increase its production and increases life span by 50%. A high calorie diet blocks this and life span decreases. A chemical,histone acetyl transference, duplicates the effect of CBP and allows a longer life span.

Perhaps one of the most significant gene switches occurs during the embryo stage of all living creatures. The change from a few undefined cells to a complex creature is controlled by a few powerful genes that are found in all animals,including humans. These were inherited from a common ancestor 500 million years ago that was a fish like creature that left the water for land. These genes have been used by evolution to allow all the different types of animals to develop. Each structure is controlled by a single gene. The difference is in the gene switches and timing of these switches.

It is noted that a decrease in calories allows a longer life span in many animals. This appears due to the caloric restriction switching on at least two important genes related to aging and cell maintenance. Another example of how an environmental process changes our gene expression.

These two genes are Sir1 and 2 (Silent Information Regulators). These are important in condensing chromosomes at time of division so less errors occur. They also protect cells from free radicals,improve mitochondria metabolism,protect from insulin which promotes cell health. When Sir levels are low the cells have more chromosome damages at division. A protein,trans Resveratrol, found in foods (grape skins) activates these genes.

However,it is not always the epigene causing actions,the genes themselves are subject to mutations. The sonar ability in Dolphins and most Bats is due to a long process of gene mutation in a gene responsible for the ability to hear high frequency sounds. Many animals have this gene but only a few can use sonar as part of their hearing. This is due to the production of a special protein,prestin, in the hair cells of the cochlea. It changes shape when exposed to high frequency sounds in the sonar range and transmits signals to the brain. Only the mutated gene makes this protein.

It appears we are not stuck in a rut where our genes are concerned. We do have some control in choosing the expression of our genes for our good or bad. Recent advances have developed small molecules that when given to bacteria will allow them to act as switches and turn genes on and off. Other products that will inhibit or promote functions are developing. This is promising for the future.

Plants are very evolved organisms

2009-12-21T16:35:00.000-08:00

Plants are much more then a static collection of leaves and stems and flowers. They are a living, changing organism feeling and smelling and reacting to their environment. Like all evolved creatures they want to survive. They are constantly foraging for nutrients and avoiding predators. In order to do this they have evolved complex systems that allow senses to hear,feel,smell and immune systems and chemical factories to react to changes.

Plant cells have receptors on their membranes and when the cell is invaded by foreign bacteria/viruses the receptors are attached to. This triggers a signal for the cell to respond by alerting the genes to make resistance protein antibodies. The more pathogens exposed to the more variety of antibodies produced. This is how our immune system also developed. Even though plants and animals divided 1 billion years ago the basic immune systems are similar.

By analyzing the ratio of red-green light waves on their leaves they can sense other competitors for the vital photons and grow in a opposite direction. Their roots are on a underground search for nutrients and helpful microbes that they can sense and move towards. By producing special chemicals they can create signals to other plants and insects.

When a invader takes a small "nip" off a leaf the bite leaves chemicals that alert the plant. When this happens a whole system is activated. The DNA is suddenly alerted and phenolics,alkaloids and other chemicals are produced that will irritate,trap or even kill the insect. It is the plants immune system suddenly alerted to action. These reactions often occur within 20 minutes. Some of the chemicals are volatile and can signal certain insects who will then come and kill the invader or parasites will be attracted to the area and infest the invader. When eggs are attached to certain plants the chemical that attaches the eggs signals a volatile chemical to be produced that signals a certain wasp to come and lay its eggs in the invaders eggs and kills the invading insect eggs.

A parasitic weed can actually "smell" a host tomato plant and will grow towards this signal. Once it makes contact it will eventually kill the plant and then move towards another smell. It can actually tell if one tomato plant is more healthy then another and will choose the healthy one.

A fungus that causes a "wilt" in tomatoes releases a protein that suppresses the genes that produce resistance immune proteins. If the plant has a gene that is resistant to this then the antibodies are produced that stop the disease.

The DNA in plants is very complicated and has evolved over time to help the plant survive and reproduce. There appears to be some awareness in plants since they can receive signals from the external environment,distingish if they are of danger and react to them.

SEX is more then XX or XY

2009-12-19T15:11:00.000-08:00

There are many animals with unusual sexual manifestations. Some XX females are actually males with testes and increased testosterone,some are infertile females due to poor ovarian development, and there are those many unfortunates who have characteristics of both male and females. These changes are not predicted by the expected sex chromosomes.

There is a Gene called SRY on the male Y chromosome and it allows expression of another gene Sox2 that can cause an ovary to become a testosterone producing testes. If this were allowed to express itself the females would soon be unable to reproduce due to the faulty ovaries.

The control of Sox2 is done by another gene called FOXL2. This prevents the Sox2 gene from acting. It keeps the Sox2 gene turned off. The drug,Tamoxifen (anti estrogen) ,can block the FOXL2 gene and the ovaries will turn into testes in 3 weeks. They produce testosterone but not sperm. Estrogen receptors on FOXL2 are involved in its activity. Low estrogen levels cause a repression of the FOXL2 gene and ovaries will turn into testes with testosterone. (Perhaps this is related to the masculine changes post menopausal).

The sex of all animals is a lot more complicated then a XX or XY chromosome. The other genes and the hormone levels allow many important changes. It may be possible that we will be able to correct sexual change problems with the use of gene therapy rather then surgery.

Powerful Molecular Motors to move DNA and RNA

2009-12-09T21:19:00.000-08:00

It is easy to imagine certain molecules in a cell. But imagine small powerful motors made of molecules that actually move and can propel large molecules like DNA into different areas. These engines are from our distant evolutionary ancestors and human cells,bacteria and viruses have different ones.

A recent discovery,using a special method, has show the Rho motor protein in the human cell. These are members of a class of proteins called Hexameric helicans,which are ring shaped, and are involved in moving the large DNA and RNA nucleic acid chains around. There are 6 nucleic acid bases in a ring shape,and when ATP is released at the binding sites of each of these ,they will fire in a sequence ,and actually spin in a certain direction, depending on the firing sequence. They surround 6 bases of RNA and the ATP driven engine rotates or spins the RNA bases.

This motion allows the Rho motor to actually walk along the strands of RNA and selectively terminate transcription of the RNA on the DNA at a certain point. This allows specificity of the transcription process.

Another motor,in a virus,is a series of disc like structures and they sit upon each other. Parts of the lower disc attaches to a strand of DNA and then it triggers the upper discs to tense and the DNA is pulled into the head part of the virus. The force is 20X as powerful as the force created with a muscle cell contraction and is due to electrostatic force caused by opposite charged discs.

Another protein motor exists in the mitochondria wall and draws H +into the mitochondria.

The process of oxidative phosphorylation is the key to ATP synthesis. There is a proton pump in the membrane of the mitochondria. Chemosmotic coupling is the pushing of H+ protons across the membrane against an concentration gradient . They are stored and released at certain times to create energy. There is an actual protein motor that has a mushroom shape with a protein shaft and a round head. The shaft passes through the wall of the mitochondria and the head is in the mitochondria itself. The head turns and protons pass from the cell through the shaft into the mitochondria and as the head turns it places phosphorous onto the ADP to form ATP. If there is less demand it reverses and pumps H+ back into the cell.

Kinesin, is a protein in the cell ,that can "walk" along the many microtubules (the skeleton of the cell) The protein attaches to the tubule,captures an ATP and it begins a see saw like movement along the tubule. It can also carry another molecule and deposit it at different sites. It also is crucial to move the DNA chromosomes around for cell division. Taxol,a chemotherapeutic agent, can block this and cause cell death.

Microtubules, very thin skinny straw like structures,are responsible for cell shape and 3D appearance. They also help cells divide,act as a scaffold to give cells shape,and move chromosomes and mitochondria inside the cell. As they grow they collect into bundles of 200-300 tubules. As these tubules create energy they also create physical forces that cause them to fold and bend into certain shapes and patterns (often looking like zebra stripes) and then they buckle to relieve the compression stresses created by their activity.

There are probably many more motors in our cells.

Depression and the Reward Centers

2009-12-03T13:44:00.000-08:00

It has been said depression is like a house on fire and the present drugs are water to put out the fire. Most research has been focused on the drugs that seem to help depression symptoms. So far,only limited success.

A Research group at Harvard is focusing on the house (Brain) rather then the water. What causes depression in the Brain? Their work is focused on the reward centers of the brain. These are the Nucleus Accumbiens (NA) and the prefrontal cortex. By testing rats with stress,cocaine dosages, alternating stress and pleasure,drug withdrawal etc. they were able to cause depression. The rats lost ability to have a reward sensation,were anxious and had signs of despair.

By measuring chemicals in the areas of the brain they showed a increase in a chemical ,CREB,that was elevated after the symptoms of depression were created. By using a virus, whose DNA were replaced with genes to make CREB,and transferring this into the NA to give elevated levels of CREB, they created depression in normal rats.

CREB transmits signals to increase the production from genes, of a brain opioid ,dynorphin. This is one of at least 3 brain opiates that reduce the sensation of pain. Each opiate has a certain receptor. Endorphin and Enkyorphin give a reduction of pain sensation and can give a sensation of pleasure. Dynorphin affects a kappa opioid receptor . Dynorphin blocks glutamate synthesis and this reduces the ability to experience joy or positive feelings. It also decreases serotonin production. Stress increases dynorphin production and depression can occur. Blocking the Kappa receptor from Dynorphin stops this depression. Injecting a stress hormone,Corticoid releasing factor, causes a increase in dynorphin levels and the signs of stress and depression. Blocking the gene to produce dynorphin stops this action of CRF.

The Kappa receptor is also involved in the total body metabolism. A diet high in fat and sugar stimulates the kappa receptor and tells it to store fat rather then metabolize it. Stress can also trigger this action. This mechanism promotes fat storage above what would be expected from the calories themselves. Obesity results. The brain is involved with body metabolism since a protein,SH2B1,which is produced by a gene regulates the body weight by recognizing signals from leptin and insulin that will tell the body to stop eating. If this gene is absent then no recognizing the signals of over eating. This protein is found mainly in the hypothalmus.

It appears that depressed people have high levels of the stress hormone cortisol,especially when they are put in positions to have stress. This hormone is known to reduce the number of active cells in the hippocampus. The lowering of cell numbers is associated with depression. The longer the depressed state the more cells reduced. The use of Electric Convulsive Treatment has been shown to be the most effective for severe depression. A number of treatments is sometimes necessary. After treatment,the number of new cells in the hippocampus is markedly increased. The mechanism is not known.

People who are abused as children have 40% less cortisol stress hormone receptors as do normals. This means they do not inactivate the stress hormone as well so it continues to activate the stress response after the actual stimulus is gone. This makes these people very sensitive to stress and perhaps depression. The modification of these genes occurs after birth and is related to environmental changes controlling the activity of genes.

Receptor density is important in much of our behavior. Genes that form receptors can change a behavior. Besides the cortisol receptors, there is also a receptor system for vasopressin. Animals with a few vasopressin receptors have solitary lives, and are sexually unfaithful . Animals with large numbers of receptors are monogamous,faithful,loving and attentive to their

family. Putting these vasopressin genes into animals can totally change their behavior.

Cytokines are signals for the immune system to act on cells. In the brain it is known that stress and depression activate these chemicals and prevent the neurogenesis in the hippocampus to occur. Normally the birth rate of new neurons is 10,000 but with stress and depression this is reduced by 50%. By giving a cytokine inhibitor before stress this can be reversed with no blocking of the formation of new neurons.

A gene in the Nucleus Accumbens of the brain (reward center) p 11,has been shown to be at low levels in patients with depression. This gene regulates serotonin in this area of the brain. By increasing the amount of p 11 gene in the N.Accumbens the depression was removed. The gene was transferred by a viral vector.

Our cells are constantly sending chemical signals for their actions and changes in these signals cause significant changes in the functions of these cells. Both mutations and changes in the epigenetic histones alter our mentation. We are discovering there are many factors causing depression and the effects of stress on our brains. It will be a challenge to discover in each individual patient ,which one or ones are the cause, and therefore choose the right medications.

The fear of Gene Engineering

2009-11-30T14:19:00.000-08:00

It is important to recognize that all plants and animals have been created and changed by genetic changes. Over 80% of our genes are acquired from bacteria and viruses at random. The gene pool is constantly having mutations and other changes by being exposed to the environment. Genetic Modification is part of nature and is the main tool of nature to create diversity. The ability of a cow to digest cellulose came from a bacteria in the gut and the gene incorporated into the cows genetic make up. The placenta in mammals came from a viral gene. The chloroplast in the leaves of all plants was originally a bacteria. Our mitochondria were originally bacteria. 98% of all white rice was derived from a wild type, Japonica, that had a single gene mutation that changed the color from red to white. This was selected by generations of farmers and spread throughout the world. We are now following up by taking some desirable genes (insect resistance,drought resistance) and adding those to the white rice to make it a better product. After 10 years the original corn field genes are significantly modified by natural pollenization and many of the genes are new.

About 10,000 years ago we humans began tinkering with the genes of plants (and later animals) and we would remove those we thought weak and keep the better ones. This was done by simply keeping some and destroying others.We were selecting those we liked. These plants would change because of their adding or modifying genes from pollenization and mutations. The environment would also promote certain qualities and cause new gene expression. We then learned we could place various plants near one another and get a hybrid. We even learned we could cross different types , like a cauliflower and a turnip to get a rutagaga. Brococli and Brussel sprouts came from a common ancestor. Crossing wheat with Rye etc. Many edible plants have been modified . One of the leading Organic farmers has said we have been creating weird crops for years. We select the ones we like and get rid of the others, we cross pollinate different types, and now we use chemicals and radiation to change chromosomes and genes and we select the changes we like. These are called hybrids and account for almost all seeds in all areas of farming. This has gone on for years.

The last "natural" plant,that is before man and not just nature got involved, was 10,000 years ago. In 2007 a study of "organic rice seeds" was done and showed that it had many nontarget chromosome damages and changes,and unexpected consequences in growth when compared to a rice that had been Genetically Modified by transgenetic methods.The Organic farmers can use the "bred' seed but not the transgenetic one. Actually,they are both transgeneticly changed but one was done in a crude "shotgun" type method that dragged other unwanted changes in the genes into the new product versus one done with a" rifle "that only targeted the gene of desired change. There are 10's of thousands of genes and modifying,1,2 or even a thousand only changes certain proteins that allow certain functions.. These will have no effect on the changing of the actual structural type of plant or animal. There is no way to create a "Frankenstein" by these techniques. With hybrid breeding that has gone on for years,certain characteristics are changed but corn remains corn and rice is rice. Some rice is drought resistance,some needs lots of water,some fungus resistant some susceptible. All of these are related to gene changes due to mixing and mutations.These have developed long before GM techniques. Certain wild rice is drought resistant but has a low yield. Adding the gene for drought resistance to a highly yield rice will created a valuable crop for billions of hungry people.

Cottonseed contains a natural insecticide ,Gossypol,that lowers potassium and is deadly to most animals. This allows the cotton plant to resist insects but is poisonous to humans. A recent GM process has removed the toxin from the cottonseed,but left it in the leaves and ball of cotton. This was not an addition of a gene but a subtraction of the gene responsible for the toxin. The result is a seed that can be eaten by animals including humans and it contains 22% protein and may meet the protein requirements (at the present crop level) of 500 million people each year. The shell left over would feed cattle.

A species of Dandelion has a high concentration of natural rubber in its roots. This "weed" grows easily with little water or fertilizer. By blocking an enzyme that coagulates the rubber (the purpose of this molecule is to "gum" up the mouth of insects.) By blocking this a good yield could be obtained. This could be the source of an easily harvested crop and replace the need for petroleum in the making of rubber.

A gene removed from a wild rice in Thailand has the ability to promote deep root systems that allow the rice to provide a 100% yield in drought conditions. This will allow a significant increase in the areas where rice can be grown.A gene has been placed in a common variety of rice which produces a protection against a common allergy in Japan to Cedar trees. After testing the eaters of this rice suffered no allergies and showed no other health problems. These researchers think that vitamins and other important health items can be safely added to the rice providing a "complete food" for the worlds large number of rice eaters.

Since 1997 70% of processed foods in the USA,most beer and cheeses, have been GM products. Millions have eaten these and all studies show no harmful changes.Peter Ravan,a well known environmentalist ,winner of almost all environmental awards and Time Magazines "hero of the planet", says GM modified foods have been shown to be safe for humans,animals and the environment. UN agricultural committees have reviewed all the studies for the past 15 years and over 50 of their scientists report the same findings.The European Union reviewed over 80 studies and found no risk with GM foods.(2007 Prospect magazine). The FDA,NIH,and Environmental protection agencies have to study all GM foods before they are released. Foods done with hybrid techniques (radiation and chemical seed changes) do not need to be reviewed, The KIWI fruit,a genetic hybrid of the Chinese gooseberry,causes severe attacks of allergies, and deaths have been reported. Same with "natural" peanuts. If they had been produced by GM they would not have made it to the market. Organic coffee has over 19 chemicals shown to cause cancer. All potatoes and starchy foods have a cancer producing agent(also found in tobacco products) that is released when cooked at temps above 200 F. Over 5000 carcinogens have been found in the non GM foods we eat.

Now for the "scare stories" to create fear among consumers. The monarch butterfly is killed by GM corn pollen. A Nature article 1999 mentioned a "preliminary study" that showed 44%of Butterfly catapillars killed by eating the pollen. This spread all over the world and is still quoted by environmentalists. follow up studies 3 and 5 years later showed at the most 3 butterflies out of 10,000 were possibly killed. This 30 page report (including 2 authors of the original "preliminary "study )got no media coverage. Peter Raven commented that since most butterfly deaths are due to pesticides that the decrease use of these in GM corn would probably save lives vs. the same "natural' corn crops.

GM corn will destroy the natural maize crops of Mexico. Nature paper 2001, noted that gene fragments from GM corn appeared in native maize. This created a media frenzy and Environmental groups went wild. Greenpeace demanding all GM crops be stopped. A ban was demanded. 3 years later a complete study was published in Nature,where 150,000 seeds were evaluated from almost all the maize areas in the GM region,and no changes were found, no contamination after three years of crops. Another follow up 2 years later showed less then 1% of GM genes were present in the maize crops. Environmentalists still refer to the first observation. It was found that the local farmers had been cross pollenizing their crops for years since the crops get weak and need new genetic vigor. The "natural"maize is an ongoing field of genetic modification with the farmers choosing those plants they think will grow best. Years of GM modification at work.

Terminator Gene. This started out with some truth. Monsanto did want to control the market. Within 2 years they dropped this due to pressures. All of the early law suits Monsanto were involved in helped cause this. At this time there is no "Terminator Gene" in GM plants. However, many environmentalists still quote this as a danger to the whole world of plants and even animals. Actually the farmers around the world always buy new seed each year since they want new vigor and crop yield. The saving of old seed produces low yields with disease. The "natural" hybrid seed companies make lots of money with their irradiated seeds. At this time The gates foundation and the other Institutes. are developing GM seed companies in the developing countries using their own scientists and selling to their own farmers, 65-90% of corn and rice in the world is GM crops. China is a leading researcher in this area and is rapidly converting to GM rices and cotton. Almost all Universities have ongoing GM seed discoveries. There is no one "Master Controller" of GM food.

The European ban on GM foods may be somewhat political. It seems that this ban,regardless of the studies, is a good way to protect Farmers from competition. Since more and more foods are using GM methods it allows the banning of these foods in Europe. Even so,recently a number of farmers in France ,protested against the ban. Farmers realize the safety and benefits of GM foods. As these foods produce better crops with cheaper methods they will demand to use them.

12 million farmers around the world use GM crops. This is increasing at 20% each year. Measure M in Sonoma county (an attempt to ban GM food) failed due to the large number of farmers. Farmers and scientists who understand the GM system embrace it as an answer to hunger and less pesticide and less water use. It is the wealthy nations and mainly urban who are fearful. They have been give scary tales of GM crops. This is in large part due to uninformed Environmental groups. Once a position is taken it is hard to change regardless of new information. In India GM modified cotton is now the majority and the yield has increased 50%,pesticides down 50% less water needed and the yield from 840 million to 1.7 Billion dollars. With the discovery of the new cottonseed,free of toxins,this will increase greatly.

There continue to be scare tactics used. A Congress Bill,875,called the food and safety act, has motivated both liberal environmentalists and the Beck-Limbaugh FOX news group to claim that this will tell Farmers which seeds to use and when and how much. If there is contamination they can be sued. It will put farmers and organic growers out of business. It may even stop home gardens.It is sponsored by antifood politicians and large corporations such as Monsanto. "Experts' are interviewed claiming all the above. The act has none of the above. No regulations on seeds or planting or contamination is mentioned. it is designed to assure food transported across state lines or imported from other countries pass safety inspections. No large Corporations have been lobbying or sponsoring this act. Again,don't give me the facts my mind is made up!

There is no doubt in my mind that the technological advances we now have can reduce hunger,decrease the killing of many species from insecticides,reduce water use,lower the tilling of the land and release of trapped CO2. A win win for mankind. Remember the arguments and scare tactics used against stem cell research by certain groups is very similar to the fear of GM crops.

The danger is not the actual process to do these things.It is the use of these processes by large and controlling corporations to use these methods for control and profit at the expense of the worlds farmers. This is the area that needs laws and controls.

Molecular clocks show our time line.

2009-11-14T14:21:00.000-08:00

Paleoanthropologists were the keeper of the evolutionary time until the discovery of DNA and their proteins. The new bio molecular studies showed the original clocks were all wrong.

Mutations are changes in the DNA sequence that arise at random but at a steady and slow rate. They accumulate over time and any two populations or species differ in their DNA sequence roughly in proportion to the amount of time they have been separated. This is the basis of the new clock.

The length of DNA that encodes a particular protein is called a gene. Each amino acid in the protein is transcribed by 3 base pairs (a triplet). The stopping of the transcription is done with a triplet that encodes nothing, This is the period on the protein sentence. Many amino acids have very similar chemical properties so a change in a few amino acids due to mutations would not change the function of the protein.

Looks can be deceiving,and all the anatomical changes seen by the fossil hunters , came from molecularly similar and recently divergent species.

The new clocks show that humans separated from apes about 2-3 million years ago,not 30 million.

By using mitochondrial DNA as a clock(abundant,easy to get out,has many more mutations over shorter times,only passed by mother so no recombination) it is concluded that the modern human came from Africa and lived about 140,000-290,000 years ago. All present day humans have descended from this ancestor.

There were various bipedal human like species living side by side. One,the Neanderthal man, separated from the H. Sapiens about 300,000 years ago. The common ancestor of the Neanderthal and the human like species arose 700,000 years ago. The Neanderthal man migrated to Europe and Asia 300,000 years ago and became extinct 30,000 years ago. The reason is not known. H. Sapiens migrated from Africa to the rest of the world about 60,000 years ago.

The molecular clock has allowed us to get our evolutionary time correct.

Green Genes

2009-11-05T14:30:00.000-08:00

The controversy over Genetic Modified plants (GM) is an ongoing one that has very serious outcomes to our planet. This technique is selectively removing certain genes from one plant and adding it to the genes of another. This is done to select certain favorable traits without having to include a whole collection of not so favorable or even unwanted genes. This technique has been done in nature for tens of thousands of years and by farmers for thousands of years.

Dogs,mules,cattle species,pigs, almost all used fruits and vegetables, flowers, etc. have all been significantly genetically modified to choose certain characteristics. This is done by breeding,radiation to seeds,chemical alterations to seeds etc. The result is an entirely new genetic configuration. Since 1927 radiation and chemicals have been used to change plants to hybrids to add better growth,insect resistance etc. to them. Because of the lack of technique control in these methods often undesirable changes were caused and the result was close to but not exactly what was wanted. A slower method is allowing the pollens of various species to pollinate others. Again,an example of genetic engineering done in a crude way. Many of these new combinations occur naturally in nature since millions of plants are in close proximity to one another.

A certain domestic potato was crossed with a wild type to try and have insect resistance. This did work but along with the desirable gene a gene for a toxic alkaloid was also bred and the potato caused nausea. Working with the total gene pool is not as precise as selecting just the gene desired.

We humans have 90% of our chromosomes as unused,non protein producing genes. Most are from various viruses and bacteria. Bacteria are constantly exchanging genes and modifying their own to meet new environment demands. All living things are undergoing genetic modification at all times. Exchanging and mutating genes is the basis for evolution.

At this time 70 % of processed food contains GM foods. Hundreds of millions of people for many years have eaten these foods. Thousands of studies have been done with no adverse findings. There are many who do not recognize the studies and believe that GM foods are dangerous and refuse to eat them. (A belief is based on feelings,not facts). Over 130 GM drugs in the USA and 90 plus in Europe have been used for years. Many new important drugs are done by GM. The most sensitive test for finding carcinogenic chemicals is using a GM salmonella bacteria.

"Natural" foods have been shown to contain many chemicals that are potentially harmful and can cause cancer. Many can cause severe allergic reactions . 8 chemicals in "organic" coffee causes cancer in rats. People are not questioning these natural foods because they are used to them. If these same findings had been discovered in GM foods there would be demands to get rid of them. Thousands of studies have shown no danger due to GM foods.

40% of the earth surface is used for agriculture. 5.8 million sq. miles for crops,13.5 for pasture,31 ecological. All crops are ecologically harmful for the earths homeostasis. GM crops are significantly less harmful then "Natural"crops. 40% of the crops are lost to weeds and pests each year. The present farming requires tilling the land each crop season and using fertilizers and insecticides. GM crops are engineered to have pesticide prevention into the plant itself, more drought resistance and better growth with less fertilization. This allows no tilling,the crops are left in the ground and new plants planted into them,less water needed and more compost so less water runoff. Less pesticide use so more of the natural pest fighters can survive in the fields. Billions of tons of CO2 is lost into the atmosphere each year due to the plowing and tilling of the crop lands. Billions of tons of topsoil erode each year due to these practices. There is no tilling with GM crops. All of this is prevented. It acts more like the natural eco friendly parts of the earths surface.

The inbred insect resistance allows butterflies, bees,and other friendly arthropods to survive due to no insecticides. In the developing countries over 80% of the small farmers use GM crops. The reasons are obvious. Increase yields by 50% and decrease pesticides by 50%. Their money yield per acre has risen significantly.

When a plant faces stress (drought,cold) new metabolites are formed that act as signals to the plants cells. These bind to receptor proteins that allow a cascade of reactions that end with production of abscisic acid which stops the building of ATP action of the chloroplast. The cell goes into a low metabolic state where it can last out drought conditions. Other maintenance processes are also initiated. By inserting the genes that make these stress resistance proteins the plant can now have a better ability to withstand drought and other stresses. Taking a gene from a certain wild rice allows the new transgenic plant to be able to grow in very wet conditions. An example would be rice grown during the very wet monsoon seasons. By changing the genes a new and hardy plant can be developed to grow under adverse conditions.

To prevent any genetic change to the environment (which is a normal evolutionary process going on at all times) the seeds have a built in 1 year life span. Less then 20% of the worlds farmers save their seeds and hybrid seeds are much less viable their second year. Farmers have bought new seeds routinely at each crop planting for years.

If we want to save our earth and slow down climate change we must depend on our technology. Genetic Engineering is an important technology to do this. Research people and farmers who are most familiar with GM have no reservations. Urban people, who have the least information are fearful. Education may be the key.

Life and death with our cells

2009-10-29T18:37:00.000-07:00

There are over 10 trillion of them and they can produce 10,000 X more energy per second then the sun. The mitochondria in these cells are minute structures that number in the thousands per cell and each have thousands of enzymes to produce energy. The mitochondria make up 10% of our body weight. The energy packets ,ATP, are produced at the rate of 9X10(20) or 65 Kgms. per day. It is thought a 180 lb. man needs 80-90 lbs. of ATP each day.

The process of oxidative phosphorylation is the key to ATP production. This is achieved through a proton pump process in the membrane of the mitochondria. Chemosmotic coupling is the pushing of H+ protons across this membrane against a concentration gradient. They are stored and then released ,a little at a time, to create energy. The electrons are free and are passed down a series of special proteins that function as an electric wire. The membrane potential produced is 150 millivolts and is necessary to allow this process. The final energy molecule is done with the use of ATPase enzyme. This is an actual protein motor that has a shaft and a round head. It passes its shaft through the membrane and the head is in the innerspace and protons pass through the shaft and as the head turns it places phosphorous onto the ADP to form ATP. If less demand it can pump protons back out.

With a normal functioning respiration the electrons are passed rapidly down through the chain and few free electrons left. With starvation,low demand and the chain is closed down so few electrons. With a damaged cell the mitochondria are trapped and little demand for growth so the ATP slows down but the chain still functions and excess electrons pile up. These form free radicals that can cause oxidation of the lipids in mitochondrial membrane and release the cytochrome C and other respiratory proteins and open pores so they can leak into the cell itself. Once the proteins leak out the respiratory chain is stopped. The membrane potential is lost. This signals the cell to begin the process of apoptosis. The damaged mitochondria is removed.

It appears that a low level of oxidative stress is actually good and promotes a longer lived cell. The production of free radicals (oxygen ions, peroxides)acts as a stimulus for the cell to adapt to the radicals. These cells live longer. However,when acute large doses of radicals produced the cells do not adapt and have a shorter life span. It may be that low calorie diets allow a continuous low level of free radical production and no acute overload , and may explain why the life span is increased.

When the radicals are produced , and they are leaked out of the mitochondria into the cell itself, they activate a protein, MST, which then activates proteins in the periphery of the cell,FOXO. These then go to the cell nucleus and activate the FOXO genes to begin the process of apoptosis or cell death. This way the cell rids itself of damaged cells so they cannot reproduce and repeat the damage in new generations.

However,if the damage is to the mitochondria chromosomes and they are unable to replace the damaged proteins then the process of the respiration stops. This can happen because the mDNA is immediately adjacent to the cell membrane at the first step of the chain. The free radicals concentrate in this region. If there is no repair then a retrograde signal is sent to the cells nucleus. The cell begins using glycolysis as an energy source. This is much less efficient and does not produce free radicals (No signaling). It allows the damaged cell to live and reproduce causing a new generation of damaged mitochondria.

Damaged mitochondria maybe the basis for almost all disease and aging. The mitochondria produce the energy that allows all cellular reactions to take place. As these factories are slowed down or stopped all the cells functions slow or stop. The damage can be due to genetic mutations and damage. Each mitochondria has its own set of genes ,different from those of the cell nucleus. These are passed from the mother and if her mitochondria genes are damaged (eg. diabetes 2) then the infants genes will also be damaged. Up to 50% of the mitochondria function maybe compromised at birth! Other things can damage the mitochondria such as toxins,oxidative changes,nutritional deficiencies,infections,allergies etc. The end result is poorly functioning cells. In the brain the neurons may not be able to act and dementia,autism etc. may result.

When a cell is exposed to caloric restriction the proteins Sirt3 and Sirt5 are activated , these are in the mitochondria in the intermembrane space. They effect cytochrome c, which is important in the apoptosis process of the mitochondria. Also,enhances NADPH system and allows more efficient respiration by the mitochondria. Both of these are triggered by the stress of low calorie intake. The more effective the apoptosis cleanup by the cell the less chance of cancer and,it appears,slower aging changes.

C.Elegans is a worm that has a long life span. It contains a gene,Lin 4,that affects patterns of cellular regulation that is related to aging and organ functions. A micro RNA activates this gene. When over expressed the life span increases and decreases with under expression. The genes regulate developmental programs for these affects through Insulin signaling . Metabolism linked to genetic control of aging. The genes daf 2 and daf 16 are also related to the expression of a number of genes that seem to reduce tumor growth (cancer suppress) and decrease aging changes. These genes show the strong relationship to cancer,aging and the effects of the environment.

Mitochondria divide every few weeks and there are thousands in each cell. A few damaged mitochondria are of no concern but when many are damaged or have been removed the cell is under stress. The cell has switched from normal clean up and maintenance to inflammatory functions. The cell is at a low grade of function and has inflammatory changes and is stressed to produce enough energy. The body has less energy,less muscle strength and slower recovery from illness. As this process continues and the mitochondria are removed there are not enough to maintain the cell. The remaining cells in the organ,are now under stress to produce enough energy. All of this occurs with aging. But these changes are associated with the rate of free radical production. The cell can not meet its energy requirements and apoptosis results. The organ gets smaller. Metabolically active organs like the brain,muscle and heart are most likely to loss by apoptosis.

At age 60 you have 100X more chance to develop cancer then at age 35! This is probably related to the continuing build up of damaged cells.

A group of Japanese centenarians have one gene variant in the subunit of complex 1 of the mitochondria DNA. This is the first step in the respiration chain in the mitochondria. This change slows down the electron loss,free radicals and damage to the adjacent mDNA. It gives a 50% greater chance of living to 100 years and little chronic disease. The free radical formation only reduced by a small amount but it was significant over a lifetime.

Oxidative stress,with the free radical formation,causes a protein ,MST, to be activated and this triggers a group of proteins,FOXO, to move into the nucleus of the cell where they activate genes that promote cell death.

Birds have a much longer life span compared to comparable mammals. They have an excess of mitochondria in their cells. many more respiratory chains and faster more complete passing of the electrons. Less Free radical production. Starvation increases the life span in many animals. This is probably due to the slowing down of ATP and less electrons formed and less free radicals. The triggering of dormant genes that produce proteins such as Sirutins that promote more efficient mitochondria use and metabolism and suppress of cell damage.

When you eat appears to be an important protection to our mitochondria. There is a daily waxing and waning of thousands of genes in the Liver associated with metabolism. When food is anticipated the genes are turned on. The stomach releases a hormone,ghrelin,that tells the brain you are hungry and time to eat. This release is associated with the routine of meals. Genes that breakdown sugars are released immediately after eating and those that encode fat metabolism during fasting. The molecular reason appears to give a clear separation between the process of metabolism and free radical production from the "maintenance time" of repair and separation of free radicals from DNA and other protein repair. A good separation of eating times from fasting is key. Allowing 12-16 hours of fasting and eating at a regular interval is important to maintain cellular health.

When mice with genetic altered mechanism to repair mitochondria are exercise on a regular basis their whole life they are able to repair and create mitochondria that are functional. The unexercised mice age quickly and die whereas the exercised mice do well and live a normal life span. Exercise may activate some transcription process that allows repair .

Another important aspect of cell survival is the ability to maintain the chromosomes. Each body cell has 6 feet of tightly wound chromosomes which must be kept intact with each division. Damage by radiation,chemicals,free radicals etc. is always occurring. When a DNA is damaged it must be repaired quickly. Many cancers are associated with DNA damage,especially translocation of a part of the chromosome to another. The cell has a very complicated system of repair.

The chromatin is a combination of a outer protein covering called the histone (epigene) and a tightly coiled inner area,the DNA. When there is damage an acetylation of the protein in the histone immediately adjacent to the damaged DNA occurs. This is a signal to call in the repair process.However,the DNA is often very tightly coiled and needs to be unwound so the proteins needed can do the job. A group of proteins called INO80 does this. If the gene to make this is damaged then it will not be able to expose the break for repair. The next step is a group of proteins, Hst3p, associated with the gene siritun that adds an acetyl group to the protein of the histone. This is the signal. Next, a proliferating cell nuclear antigen protein(PCNA)that forms a cuff like structure around the DNA and traps the polymerase enzyme to help with the repair. Once the repair is done another set of molecules remove the acetyl groups and stop the signal for repair. This is an important step and if these are not available further damage to the DNA will result.

This damage and repair balance is an ongoing process and can result in cell health or cancer and cell death.

When Glia is not really glue.

2009-10-25T09:15:00.000-07:00

Glia is a greek word meaning glue. This is the word given to all of the brain that was not neurons. It was thought to be an inert substance that held the neurons together. The brain is 90% Glia cells. There are three major types of glia cells,Astrocytes,Microglial and oligodendrocytes. These three cell types each turn on a different set of genes to express themselves.

All of these cells have very important and different functions besides being the stuff the neurons are surrounded by.

Astrocytes make up about half of the brain cells. They look like stars with long thin projections. One job is to clean up after the messy neurons. When an electrical signal jolts a neuron synapse region neurotransmitter chemicals are released. This very important function is monitored by the Astrocytes. They supply nutrients to allow the synapse to work and rebuild the chemicals at the synapse. They "clean up" the area to be sure no residual chemicals left after a reaction to assure a new clean reaction. Perhaps most important they determine where and when synapses will occur. One astrocyte can cover thousands of synapses at a time. The production of new synapses appears to be due to a protein,thrombospondin, secreted by the astrocyte. This protein is produced during brain development and when maturation is complete it stops production. The exception is the astrocytes in the hippocampus where current memories are stored. This structure forms new synapses every day and the thrombospondin is necessary to allow this. With a brain injury the astrocytes in the area begin production of thrombospodin. The gene for thrombospodin is found in humans and primates.

It is now known that calcium reactions ("flares") occur from astrocyte to astrocyte in the cerebellum. When this occurs ( with motion) the blood vessels nearby expand in size. This did not occur with rest. It appears the astrocytes monitor the neurons electrical activity levels by generating calcium flares and cause local blood vessels to supply more nutrients.

Synapse death is an important part of a normal brain. The developing brain develops many more synapses then it uses. These require nutrition and maintenance. The astrocytes cause some synapses to be covered with a protein,Clq that marks the synapse for destruction. This protein production is shut off in the adult brain but is abnormally active in many neurodegenerative diseases. Alzheimers disease has loss of 80-89% of synapses. Astrocytes appear to be the key in neuron health and maintenance. Protect the astroctye function and the neuron will survive. Astrocytes differ from one region of the brain to another,just like neurons.

Besides scavenging debris and forming scar tissue the astrocytes have many cell membrane reactive sites. One of these signals the production of a special protein ,MT, which grabs up dangerous free radicals and metal ions that destroy cells .This protects the surrounding neurons from further damage. The astrocytes also respond to the presence of drugs like morphine and cannabis to cause secretions of chemicals that affect the neurons function.

Microglia constitutes 10% of the brain cell mass, serve as the immune function in the brain. They are of immune cell origin and probably reach the brain before the blood brain barrier is developed. These cells also have long ,slender projections that extend to the surfaces of neurons,blood vessels and astrocytes. these extensions are constantly moving, probing various areas of the above cells as if monitoring their well being. They make a complete sweep of the total brain every few hours. If a damaged area discovered numerous microglia converge and clean up the debris. These cells are very active in building and destroying synapses. They produce enzymes,cytokines, that are related to stress and inflammation. If these enzymes are overproduced normal neurons can be destroyed. This may happen in older individuals and loss of neurons in the hippocampus causes memory loss. ( see blog on memory ) .More and more diseases of the brain are being tied to the activity of these cells and the enzymes they produce. It does appear that a chemical, luteolin,found in certain foods (red peppers,celery,carrots) protect the neurons from the overactivity of the cytokines.

Astrogila function as stem cells for neurons during early brain development. At a later more mature time,they can revert back to stem cell function, if they are exposed to regulating proteins found in neonatal brain tissue.

It is now known that vigorous exercise causes release of a chemical (noggin) that causes stem cells in the brain to turn into new neurons.

Oligodendrocytes account for 40% of the cell mass. They extrude a fatty material,myelin, that coats the surface of the neurons and insulates and promotes the electrical signals.

Other products in the "glue' are also important. Palmitate is a saturated fat and is important to join with certain proteins such as NMDA that are receptors for various synapses. Glutamate,a neural stimulater, promotes the production of these proteins but palmitate is necessary to mark and direct them to the proper positions on the surfaces of neurons to create synapses. This is necessary to allow new learning and memory paths to be created.

Using a new Diffusion Tension imaging technique which tracks microscopic water molecule movement, allows the following of changes in the White Matter. Children, 8-10 years old,with reading problems showed defects in various areas of their white matter. After intense training for 100 hours, the reading skills improved and the defects in the white matter were corrected. Reading, like many skills, involves various areas of the brain and these areas are dependent on the connections and communications done by the white matter.

In the "normal" aging brain it is shown that the important connections between the frontal and posterior areas, related to memory and learning, decay and have less ability to communicate. This is associated with loss of cognitive ability. These pathways are made of the "white matter".

Certain proteins in the brain can completely change an injury such as stroke. Transforming Growth factor (TGF) is important in the development and formation of new brain tissue. Injecting this material into the brain can restore 100% of the function of damaged tissue. Nasal spray administration gave a 70% restoration. (Vs. 30% in controls). This protein stimulates new neuron growth and the new cells migrate to the area of injury and replace the lost neurons. Another protein GCSF, that helps form and protect neurons,reduces the size of the damaged area and increases function return when injected after a stroke occurs. This illustrates the capacity for regeneration of the various parts of the brain. A protein NOGO-A, is produced when the brain does not want any new neurons or axons produced. An example would be excess pain or uncontrolled motion and less neurons are better. However, an antibody against this protein stops its inhibitory action and the neurons do increase and develop new axons. When this antibody is given with strokes and other injuries new neurons and axons develop in the injured area.

Recently,skin cells were changed from skin to neurons by activating 3 specific transcription factors(genes that tell other genes what to do). It may be possible to activate transcription factors in the glial or astrocytes cells to turn them into neurons in cases of injury to the brain.

Elephants have 97% Glial cells and only 3% neurons. Glia is definitely more then support and glue.

There may be clumps of amyloid in the brain that can actually store information. Prion proteins are usually associated with neuro degenerative disease. However, prion proteins can change shape and form clumps of amyloid like deposits that are not abnormal. These prion proteins are found in almost all healthy brain cells. This normal position maybe for insulation so the electrical communications will work. Certain proteins,CPEB, is activated by serotonin and causes other proteins to change shape. It is very short acting normally but the change in shape and the passing on of this to other proteins causes clumping and amyloid to deposit. This may strengthen the synapses between neurons. This allows a long term memory of the event to occur. If this shape change is blocked then the long term memory does not occur. Serotonin is important to allow this shape change and the long term storage of information. Prions may not all be infective but some may actually store information.

Beta amyloid is a protein produced in the brain at synapses and acts as a moderator of signal strength. Too strong a signal and the amyloid molecule is produced to reduce the intensity. Beta amyloid has a precursor,Leucine, and amyloid production is constantly going on and the molecule normally remains in the brain for about 8 hours. It is then disposed of and new amyloid produced. As we age the disposal decreases and this also happens in Alzhiemers Disease (AD). A current theory is that this decreased disposal allows the abnormal build up in AD.

Like all organs, the brain has a continuous supply of undifferentiated stem cells. It has been shown that when a aerobic exercise is done,so that a chemical,noggin, is produced and carried to the brain ,these stem cells can be induced to form new neurons. This is one of the few things that has been shown to form new neurons from stem cells. Exercise also increases the amount of an important brain chemical.BDNF, which is found in the hippocampus and related to building memory.

The neurons are a whole and separate area of the brain. There are over 200 billion of them,trillions of synapses between them (about 1/1000th. mm apart) and over 125 trillion synapses in the cerebral cortex. Each synapse is like a microprocessor with memory storage and information processing elements with micro switches to recall and use information.

It seems all tissue in the brain has important functions and interact with each other continuously.

What about the Free radicals?

2009-10-24T09:52:00.000-07:00

Radicals can cause political damage to society and free radicals can also cause aging and death to most of us. The free radicals that are in the cells of our body are often destructive, and perhaps at the basis of much disease and suffering. They also are an important signal for cell survival.

The formation of many free radicals are at the heart of our cells metabolism. The mitochondria have two very important areas,the DNA and the double cell membrane. The mitochondria are the energy factories in the cell. They maintain the oxidative processes that assure that all cell functions have enough energy to survive and grow. They do this by producing large amounts of energy packets (ATP) and in the process form free radicals.

The energy process involves exchanging electrons along the mitochondrial membrane. These electrons are produced in the mitochondria and most of their reactions occur there. A free electron wants to combine with another atom (usually O2) and this creates a Reactive Oxygen Species (ROS) which is very active in attaching to other molecules,usually a protein. This reaction often results in damage to the protein and loss of its function. The Mitochondria cell membrane is very good at containing the free radicals and protecting them from damaging the main cell. However,the mitochondrial DNA is a target and it is often damaged and loses its functions.

There are "death genes" in the cells. Mutations of these genes can cause loss of suppression of mechanisms that cause a damaged cell to die. Immortal Cancer cells are often the result. The actual executioners are enzymes called caspases. These are always present in the cell but need signals to be activated. Once activated they destroy the cells proteins and DNA. This is called apoptosis. These enzymes can be activated by a extrinsic or a intrinsic method. The extrinsic way is for the immune system to mark the cell membranes of abnormal (cancer) cells with

signal proteins. These signals activate the caspases to destroy the cell. The intrinsic method is more common and can be triggered by many insults to the cell. UV light,toxins,pollutants,drugs,viruses and bacteria,inflammation and oxidative stress,heat and cold,heart attack or stroke. The key pathway to turning on the caspase switch is the mitochondria.

Caloric restriction may prolong life by triggering genes that produce the enzyme catalase. This enzyme degrades hydrogen peroxide a highly reactive free radical. Caloric restriction may cause a change in the epigenetic area near the gene and activate its production of the enzyme. In some species the mothers caloric restriction causing increased catalase production was passed on to the next generation.

The inner mitochondrial membrane potential is the key to our cell metabolism. If this is lost then the cell cannot make adequate ATP and the membrane is attacked with numerous free radicals which cause the lipids to be oxidized in the membrane which causes various proteins,such as cytochrome c to be free and migrate into the main cell. It also,allows other mitochondrial proteins to be lost into the cell by triggering off large porous openings in the mitochondrial membrane. This process signals the caspases into action and cell death will result.

Unfortunately, often the mDNA is damaged before the cell membrane and the energy production goes from oxidation-phosphorus to glycolysis. This is a much less efficient method and does not produce free radicals (no electron transfers) no free cytochrome and no free radical leak. No apoptosis. At this point the mitochondrial cell membrane ,damaged or not,has no ROS to pass into the cell. No warning signal and no normal repair. When the cell divides the damaged mitochondria is now passed on to make more damaged energy factories.

The damaged mDNA gycolysis process leaves a build up of a substance called NADH,which is toxic to the cell itself. The cell needs to rid itself of this NADH and does this by removing an electron creating NAD+. This process helps protect the cell but also leaves a buildup of free electrons on the surface of the membrane. These electrons are also free radicals and produce ROS with oxygen.

These are now in the main cell itself and react with many proteins to cause damage. Low Density cholesterol is very common and is often damaged in the cell. It then passes out and into many areas of the body where it can damage the other cells it enters.

The proteins are programmed in the DNA, and this plan is passed out into the cell by various RNA proteins and are carried to the Ribosomes for production. Ribosomes are very large structures that are careful to avoid any production errors. Any error in a product is destroyed and this saves the cell from abnormal function. However, it has been discovered that when a cell is exposed to free radicals,toxins,virus and bacteria the ribosome is signaled to change the original DNA message. A amino acid called methionine is added at various places on the protein molecule. Methionine has a sulfur atom and this is a good receptor for the dangerous free electrons in the free radicals. They reduce the radicals. The methionine is placed near the most important areas of the protein and will protect these areas from damage.

It is now thought that free radicals may be an important stimulus to the immune system. Macrophages seem to need a certain amount of free radicals in order to produce. It is known that even in the cell itself free radical stimulation is necessary to allow the normal maintenance process. Again, its the large amount that may be the factor between normal and abnormal function.

Our normal body process is to have repairs to the damaged parts of the cell. This is usually done at night when the insulin system is quiet. During the day the Insulin system is busy handling glucose and amino acids and shuts down the repair process. ROS buildup can trigger off the Insulin system and interfere with the repair system so this process is very limited at any time. This may be the major cause of aging and disease.

Perhaps the most important molecule our body needs to help prevent the free radical damage is glutathione. Although our body makes glutathione the constant number of toxins etc. overwhelm our system. The liver and other organs lose the ability to detoxify and correct the damage. Low levels are found in almost all diseases and associated with many of the inflammatory markers of disease. It is a molecule of cystine,glycine and glutamine. There are genes responsible for the production of this molecule. These genes are usually impaired perhaps due to the great number of toxins and other radical formers we encounter in modern life. All toxins stick to the sulfur part of glutathione and are removed from the body. Levels are highest in healthy young people but decrease with age and especially illness. The addition of glutathione is discussed in the healthy diet essay.

The light in our cells

2009-09-24T17:27:00.000-07:00

Photorepair is the process that allows a living cell to repair damage. A severely damaged cell can be repaired with a weak light wave at 380 nanometres. Special photomultipliers have shown light waves emitted from living cells. Protons and electrons combine to form atoms. These atoms compose the periodic table and these combine to form chemically all the substances in the world. These atoms and molecules have various amounts of energy they absorb and release which is in the form of photons. Photosynthesis uses photons of light and when we digest these plants we use their glucose to produce CO2 and H2O and the photon ,which is a electromagnetic wave ,may be stored in the cells and is distributed throughout the body as a electromagnetic waves of various frequencies.

Molecules in our cells respond to a range of wavelengths and frequencies. Our nervous system communicates by a electrochemical process whereby information from a stimulus is converted into a electrical event. The information carried is determined by the number of fibers carrying the electrical changes and the frequency of the nerve "firing". This is the same process used by computers in a off-on principle. These emissions allow instantaneous communication of our cells. These travel at the speed of light. When DNA is "unwound" it releases light and the more unwinding the more light released. (Biophoton effect).The DNA light has a wide range of frequencies and these could be the stimuli to cause cells to do certain functions.

An experiment with the ability of rats to "map" their environment shows they synch their internal brain waves (Theta) with those of an external source to record the map they need to get around a new environment.

It is known that each cell undergoes about 100,000 chemical reaction a second! We have billions of cells. Many reactions are the same in many different cells. What is the process that c the DNA uses to allow all of this instantaneous action? It appears that this communication is due to the weak light emissions of low intensity released by DNA. Weak wave radiation can stimulate neighboring cell growth in an organism. The seeds of plants have been shown to have a electrical field surrounding them that is a blueprint of the adult plant. This blueprint for an adult is also present in a unfertilized egg of the salamander.

Once energy reaches a certain threshold molecules begin to vibrate in unison,until they are in synch (coherence) and when this happens they act like particle and waves in the universal field. The fluids in cells hold wave patterns that correspond to patterns seen in EEC's. All living cells (plants and animals) emit a permanent current of photons . The number emitted appears to be related to its position in evolution. The more complex, the fewer photons emitted. Humans 10 photons per square cm. Less evolved creatures 100. The wavelengths were 200 t0 800 nanometeres.

Bacteria use light to repair DNA. This seems to be due to detoxifying free radicals and toxins when cells subject to stress. Cancer cells have different emissions then healthy cells. In a stressed state the rate of biophoton emissions increases. Emissions have been related to natural biological rhythms as if the cells were in synch with the outer worlds rhythm. In Cancer patients this is lost and the internal communication is scrambled and they lose their connection with the outside world. We are ill when our waves go out of synch.

Normal and diseased cells have different wave patterns. A normal cell has a target like pattern and a diseased one a spiral pattern. ECG,using electrical signal reception, has shown this in the heart.

Molecules can change their shape and motion when exposed to light waves. The changes are related to the brightness of the light source,wave length and time of exposure. This idea is being used in recent cancer research. Putting chemotheurapeutic drugs into a molecule (azobenzene) adding this to a gold nanoparticle, and having it enter a cancer cell,then adding a light source to the cells, the azobenzene changes shapes and motion and releases the killer drug.

Every system likes to achieve a minimum of free energy. In a Zero Field of energy there are constant ongoing changes in the energy levels that could disturb the cells homeostasis. Emitting photons is a compensatory gesture to stop or minimize this disturbance. An attempt at energy equilibrium. If we were a candle we want a very low flame. When free range chicken eggs are examined they have a much more coherent photon pattern then those eggs produced by stressed hens in a cage. Limb repair in Salamanders can be altered by passing different electric signals in the region.

An isolated heart can be controlled (rate,output) by using electromagnetic signals that have the same frequencies as pharma molecules. Each molecule has its own signal and the signal is the activator. The molecule is the messenger. Imagine a cell ,which has 10,000 water molecules for each protein molecule. It is like a few tennis balls in a large pool. It is unlikely that they would find each other in a millisecond and cause an action. However,waves signals travel at the speed of light and will be in synch with its corresponding wave in this short time. Telescopes have measured certain specific frequencies from chemicals (molecules and their bonds) billions of light years away. Two resonating molecules create a wave that is passed on to others like a instantaneous chain reaction. Tiny changes in a molecules structure would alter this signal. This would change the action of the molecule.

Water is the largest part of living cells. It is known that water molecules can retain the memory of a specific signal after exposure and the source removed. It is like a tape recorder. Water is the medium through which the various signals are passed.

The quantum process that occur throughout the universe appears to be the same process that directs the construction and maintenance of all living beings.

A Universe of Energy

2009-09-24T15:49:00.000-07:00

Quantum Physics is a very complicated idea. Matter cannot be divided into independent units and subatomic particle and are not like billiard balls, but are vibrating and indeterminate packets of energy. They are sometimes waves , spread out over a large area,and some times particles,confined to a particular space. Sometimes they are a wave and a particle at the same time. Electrons want to be everywhere at once and it is only a probability that they are in a certain place at any time. The Quantum world is not a solid and predictable one, but uncertain and unpredictable, a state of potential possibilities. Quantum particles , once in contact, retain their ability to influence each other regardless of how far apart. There are particles that actually travel faster then the speed of light. It is our consciousness that brings the observed particle into being. Nothing in the Universe exists as an actual "thing" without our perception of it.

The "Zero point" field (called Zero because energy can be detected at temperatures of absolute zero) is all the space in the universe. It is a subatomic beehive of activity. No particle is ever at rest since it is always reacting with all other energies in the "Field'. Every exchange radiates energy. This dance of energy creates a tremendous storehouse of energy throughout the whole universe. (It is said that 1 cubic meter has enough energy to boil all of earths oceans!).

The Zero Point Field (ZPF) interconnects all matter by waves that connects all parts of the universe to every other part. It is self sustaining,all the motion of the subatomic particles create the energy in the field ,and this energy drives the particles motion.

The energy in the field is often in a wave form. Waves are encoders and carriers of information. These waves can be in synch with others and vibrate as one wave. When this happens information from one wave can be passed to the other. If out of synch, they can cancel each out,and no information is available. These patterns amount to a constant accumulation of information and waves have tremendous storage ability. All of this information is in the waves of energy in the field and is a history of the entire universe, from the beginning.

Neurons in our brain are shown to create energy signals which can alert other neurons which respond by creating energy fields to further alert many others.

Einstein related mass to energy. Everything in our world no matter how dense or large,in its most fundamental level, boils down to a collection of electric charges interacting in a sea of electromagnetic and other energy fields. Mass is energy. There is no mass,only charge.

The field causes particles to accelerate to high speeds which causes them to agglutinate into concentrated energy we call matter. The machinery of the universe is an exchange of energy.

All energy came from the Big bang and all energy past,present and future are present in the universe. Matter is made of Energy. An average man contains more energy then 1000 atomic bombs. A cupcake contains more energy then 1 million tons of TNT. An astroid hit the earth 65 million years ago. It was only 6-14 Kilometeres in size but traveled at 50,000 mph. It heated the air in front of it hotter then the suns surface, and created a explosion of rocks and dust that traveled half way to the moon. The dust and debris covered the skies for years and destroyed all the life on earth. The dinosaur extinction. The energy was 100 million times more then the original atomic bomb. It is the rate of release of the energy that creates the explosion.

In a linear accelerator a proton and a antiproton (negatively charged) collides at high speed and a annihilation reaction occurs. Tremendous energy is released and a "new" energy particle, the "Z" is produced. The amount of energy released and the temp produced is similar to the Big Bang.

There are many different forms of energy and they can be transformed. Neutrinos are almost without mass but travel at the speed of light so have great energy. There are millions of them released from star deaths,Dark holes and space matter that shower on us every second. They pass through the earth and out the other side. Cosmic rays are high energy particles that have lots of kinetic energy and can destroy DNA and life. We are protected by the large magnetic fields surrounding the earth. They do get through and can create disturbances in our electric devices. Solar flares have a release of energy at various times of millions of atomic bombs and send deadly particles towards the earth.

There are at least 4 kinds of energy that we know, electromagnetic,gravity,weak force and strong force energy in the nucleus of the atom. These nuclear forces are made of a weak energy(bosons) and a stronger energy (quarks). These forces keep atoms together so matter can be formed. Combined ,called gluons or "glue".These energy forces can also be particles such as neutrinos,pisons,mesons etc. At very high temps it is thought that all of these energies were actually one. This idea is called the Unified theory of the Universe. It is not proven, but much evidence shows that at the time of the Big Bang all energy was in one form. At the moment of the big bang,and immediately thereafter, the universe was so dense (perhaps the size of an atom!) that all energies were bound together as one. Unified. As the matter and energy spread from the big bang the temps cooled and allowed the various forms of energy to separate and begin the process of protons,neutrons and electrons to form atoms of different types. The idea is that all solid matter,as we know it,is temporary and can be transformed one to another.

The Universe should be cooling and its rate of expansion slowing down. That is not what is happening. Instead the universe is expanding more rapidly. It is thought that the early universe was influenced by gravity as the main force. This attracted bodies to each other and slowed their expansion from one another. It is now thought that a mysterious form of energy "Dark Matter" is filling the space between galaxies and this energy is one that promotes expansion or stretching of space. It seems it is actually space that is expanding,like a enlarging balloon,and the galaxies are simply filling the enlarging space. Gravity is losing its influence.

Space can be very heavy

2009-09-10T14:33:00.000-07:00

There are areas in space that are so dense that one teaspoon of the matter in these areas weighs 1 billion tons! Thats heavy. These areas are called black holes since nothing can escape the gravity,including light. These areas are very common. They result from large stars expanding to millions of miles then suddenly collapsing into a very small collection of all the matter they are made of. The star is a balance between gravity,trying to collapse it,and the heat of the reactions,expanding it. When the reactions go from hydrogen and helium to many heavy elements such as nickel and iron, the gravity takes over and the star collapses ,and sends masses of space dust outwards. Once this occurs they begin to attract surrounding matter and gasses. These are then pulled into the hole and it gets bigger and more powerful.

There are black holes at the center of almost every galaxy. Our galaxy has a large black hole in its center. Planets and all matter move in different ways and at high speeds the closer they get to the pull. This is the way they are detected. They periodically engulf other matter and get more mass and density. It seems the the large dying stars in the billlions of past years collapsed

into these holes and they have grown and have attracted many billions of stars and planets into new galaxies. These are sometimes attracted to other galaxies and are absorbed and the galaxy is now part of a much larger galaxy. The resulting black hole is now increased.

When black holes absorb large amounts of matter and gaseous material only a certain amount can be ingested. A significant amount is actually "vomited' back into space with millions of miles of space dust spread in many directions.

It is now thought that Black Holes were important in the birth of our galaxies. As little as 200 million years after the Big Bang black holes formed. As time went on they attracted each other and became massive holes. As early as 800 million years post Big Bang these large holes would created shock waves as they absorbed other matter. These waves clumped the space dust into areas where stars could form. Galaxies were beginning.

It is possible the "Big Bang" was a large,large black hole that finally engulfed a huge meal of galaxies and vomited the materials to form our universe. These gases and matter are still expanding at great speeds. Perhaps they will slow and contract and galaxies will absorb one another until the situation for another big bang will occur.

Recent observations of the Cosmic microwaves background has shown concentric circles that are thought to represent previous black holes. These are thought to represent large black holes that were active before the "Big bang". It is thought that as matter gets very old it loses its mass,yet traveling at the speed of light and this causes time to then stands still for these massless items. This allows them to become infinitely small and form another big bang.

Our "Big Bang" may be one of many that has occurred.

The amazing chemical factories of our cells

2009-09-03T18:39:00.000-07:00

This discussion follows up on the previous discussion about mitochondria. The process whereby this amazing structure creates energy is an example of the fine tuning of evolution. The production of ATP is the end result. Food is used to create this energy. The beginning reaction is glycolysis which breaks down the 6 carbon glucose to 3. Then a citric acid reaction breaks this down to CO2. However,if this was the only reaction available the energy production would be suboptimal for cell activity. The production of ATP is limited.

The really efficient production of ATP is done in the mitochondria. This is called oxidation-phosphorylation. The cell membrane of the mitochondria is a double one and the inner is lined with special proteins that allow a proton pump to move protons (H+) into the inner part. This power house generates 150 millivolts which is a tremendous amount of energy in this small structure. This requires a oxidation-reduction reaction with free electrons. These electrons are transferred through a series of special proteins and act as a electric wire to conduct them and and H2O and a significant amount of energy is produced. This increased ATP production allows the cell its energy.

The balance between the production of NADH and NAD+ is vital to the cells health.The NAD+ is a coenzyme found in the mitochondria and in the nucleus of the cell. It is at the heart of our metabolic functions. Less NAD+ and a unhealthy cell. This is also the substrate for Sirutin enzymes. If this is low then the Sir gene cannot be activated and produce vital chemicals for the cell. Nicotinic acid,Nicotinamide and Nicotinamide Riboside are all key sources for the cells to recycle NAD+ from the reduced NADH. These niacin products are found in food (Tuna,salmon,chicken,turkey,mushrooms,peanuts,lentils and whole wheat). Whey protein is a source also. These are not made in the body and need to be ingested. NAD+ is constantly being used and needs ongoing recycling.

With adequate NAD+ and with signaling by polyphenols the Sirutin genes,in the nucleus and in the mitochondria, are able to increase or initiate the following actions.

Promote DNA to quick repairs, protect the telomeres, remove damaged DNA to avoid cancer.

Control Insulin and glucose metabolism,reduce fat deposition,remove excess fat,promote insulin secretion, lower inflammation and other actions to preserve the cell health and promote longevity.

All of this is under control of the 37 genes in the mitochondria and 1,200 genes in the cells main nucleus. 50% of these nuclear DNA comes from each parent,whereas the mitochondrial DNA comes only from the mother. If there is a mutation or other damage the important metabolic machinery breaks down and many different diseases can result. These diseases can affect almost any part of the body. Because of their location the mDNA are prone to damage ,usually from too many free radicals in the mitochondria.

When the mitochondria is damaged it tries to repair itself but if too much damage to the DNA then the signal goes to the cell nucleus and the cell switches to more glycolysis then the cell receives much less energy with even more effort. It is noted that Insulin resistance is associated with the decreased activity of the mitochondria. The mitochondria appear to be at the basis of all cell activity. It has evolved over the millions of years to be a sophisticated chemical factory.

The mitochondria are turning out to be a very important part of our aging and chronic disease.

Degeneration,Cancer,and old age

2009-09-02T13:49:00.000-07:00

These three problems are part of life. There are ideas to explain these. It is thought that the life span is written into the genes. However,there are observations that question this. Caloric restrictions in some animals increase the longevity by 30 %. A certain group of people in Japan have a small change in their mitochondria DNA (DNAm) live longer with much less disease then others. Certain mutations (gerontogenes) can act to prolong life. Increasing the expression of certain genes increase life span.

Genes certainly play a role and it has been shown that long lived people have certain gene patterns that separate them from those with shorter lives. The pattern has a 77% prediction accuracy. It seems the protection comes from genes that allow resistance to chronic diseases. These protective genes are found more often in women (85%) then men(15%). Women seem to have an ability to handle chronic diseases better then men. Some think that the presence of two X chromosomes vs. one in men may be part of this protection.

A group of Dwarfs in South America who seem to be free of cancer and diabetes have a specific genetic defect. This same defect allows a significant increase in life span. This mutation occurs on a protein receptor for Growth Hormone that is fastened to the membrane of cells. When this receptor is activated it triggers off a intracellular reaction. This receptor in the Liver increases production of a hormone called IFG-1. This is important to growth,too much and Acromegaly,can result and too little dwarfism. This is related to normal growth but when absent or in low amounts it allows cells to avoid diabetes and cancer. Serum from people with these low levels of IGF-1 protect cells from these diseases and if even moderate amounts of IGF-1 added the serum loses the protection. The defect that allows a decrease in production of IGF-1 in the liver increases insulin sensitivity and promotes a strong apoptosis to any cell that shows signs of damage. These are protective and are probably related to longer life. A special strain of mice with this defect in the receptor live 2 times longer then those without this.

Some hypertension is related to mitochondria DNA. This is passed on from the mother only. The mutation appears to limit the ability of the mitochondria to overcome free radical damage and the mitochondria do not function well. It seems this is also related to a decrease in the ability to form nitric oxide which allows dilatation of blood vessels. This lack of vessel dilatation may cause constriction and hypertension. It seems that mitochondria health is very much related to our own health. Protecting the mitochondria from the free radical damage with antioxidants may be important.

It appears that bile acids (lithocholic acid) may play an important role in aging. The lives of yeast cells were increased when the acid was added to their diets. It seems the acid activates the "housekeeping" proteins regardless of calories taken in and works to restrict the action of stress genes with low calorie diets. The result is a longer life. It stimulates the protective action of genes. It also activates the Vitamin D Receptors in bone and in the immune system offering protective actions.

It is said by experts in aging studies that longevity is related to our sex,chronological age,length of the chromosome telomeres. These factors are thought to be the cause of at least 37 % of aging. The other 63% is thought to be due to oxidative stress and glycation. The latter is due to sugars binding vital proteins. It is calculated if these could be controlled that it might be possible for a man to live 500 years and a woman 1500! It may be that the females protective genes are related to these abilities to limit the damages. If so, this would demonstrate that genes are more important then realized.

A recent discovery in mice shows that a group of cells called senescent cells that are found in aged tissues such as arthritis,plaques,cataracts secrete hormones that cause the immune system to be active and cause a low grade inflammation that causes damage. When these cells are destroyed (by a certain chemical that triggers off a gene to release a destructive protein to kill the cell)these changes of aging (cataracts,arthritis,plaques,frail muscles etc,) were stopped. Perhaps these cells are always present but the body loses the ability to regulate them and they increase and cause the aging process as we get older.

However,genes cannot be excluded. In a certain worm, with similar genes to us, a gene has been discovered related to aging. By feeding the worm a special bacteria diet it allows a signal molecule to be obtained that turns the aging gene off. This alone lengthens the life span X3.

The environment speaks to the cell thru a series of proteins related to hormones that control our cell metabolism. Leptin and Insulin are two of the most important. There are 39 of these in the worm nematode. If the environment has abundant food and the animal is well (or overly) fed the Leptin- Insulin system is active. Diabetes ll in humans is related to the mitochondria not producing energy normally. If small amounts of food, Insulin is silent. The silence actually puts the cells on "hold" waiting until things get better. During this period the cells health is kept at a optimum level. This is shown by the semi starvation diets allowing longer life. A trout species transferred from a highly nutrient environment to a scarce one will increase its life span 6 times. The caloric reduction silences Insulin and also activates certain genes (SIRT1 and TOR) that are found in almost all animals and plants. They activate large groups of proteins that stimulate important protein synthesis and cell metabolism while stopping cell breakdown. Actually the TOR is a immunosupressant that lowers the inflammatory reaction and SIRT1 is more of the maintaining of cell metabolism.

Caloric restriction induces a number of chemical changes in the cell concerned with chronic disease and aging. A protein,S6K1, involved in the bodys response to food intake is associated with control of growth and aging. Blocking this protein increases life by 20 % in mice with reduction in disease. A drug used for immune protection in transplants,Rapamycin, is able to block this protein and seems to increase life span. Another molecule,AMPK, regulates energy in the cell and is activated with lower calorie levels. A drug used in Dibetes 2 ,Metformin, activates AMPK. This seems to be the protein that increases the life span and lowers disease. Leptin production is also very much related to our health and depends on the amount of calories we consume (see discussion on Leptin). A enzyme that destroys hydrogen peroxide (a very dangerous free radical) is lost as we age, Caloric restriction causes this enzyme to be increased and allows protection from free radical damage.

A transcription factor,CBP and other associated proteins,that help control the expression of genes concerned with aging are present. This protein accounts for 80% of the variation in mammal lifespan. Low calorie stimulates production and a 30% decrease in calories increases lifespan 5o% (in worms study).Blocking this decreases the life span. Increased calories block this important protein. When these are increased it promotes a longer lifespan and less disease. Decreasing them ,the opposite. A pharmacologic agent ,histone acetyltransference that enhances histone acetylation, reproduces the effects of CBP. Another example of possible drug treatment to increase life.

We now know there are drug sensitive pathways involved in aging.

Aging occurs when the molecules that compose our cells become dysfunctional. During life all cells experience some changes and dysfunction. However,the body is able to autophage these molecules and keep the cells healthy. This repair mechanism is the key to keeping young and healthy cells. The Insulin signaling mechanism (ISM) appears to be a key to this activity. Insulin removes glucose but it is also the producer of proteins. The protein production,and carbohydrate removal,usually takes place during the day when we are well fed. The blood levels of amino acids and glucose and insulin are all elevated. This rise in these factors also suppresses the repair (autophagic) ability of the cell. The process removes the "garbage" from our cells and is very much related to chronic illness and aging. When a cell needs to be replaced or destroyed it sends out chemotactic signals. One signal is a combination of ATP/UTP which signals a macrophage cell who has a ATP/UTP receptor on its membrane. This occurs for most of the day. However,at night, when the sugar,fats and amino acids levels are decreased, the repair system is stimulated and the removal of dysfunctional products is done. This process recognizes signals in the cell of damage and enzymes are activated to destroy abnormal proteins and produce amino acids. When these breakdown amino acids exceed a certain level the autophagic process stops. A immune suppressor protein (mTOR) is activated and limits the activity. Unfortunately,during the day if amino acids and glucose reach high levels the mTOR protein is released and repair process stop in the cell.

SMRT, a protein involved with metabolic functions.appears to be increased in aging cells. All cells depend on a protein,PPARs, that balances metabolism of fats and sugars and keeps the mitochondria function at best efficiency. It reduces the amount of oxidative stress to the cell. Increasing PPARs allows better function. The SMRT actually inactivates the PPARs and allows more damaging oxidative stress to occur. This increase in our cells as we age maybe another factor in aging.

Inflammatory response is one of our main evolutionary developments to protect against outside pathogens as well as trauma. After an animal bite the body begins to clot off the area blood supply,phagocytes rush to the area and go into the tissue to engulf bacteria and to release various signals to bring more anti inflammatory cells, and Reactive Oxygen radicals are formed to kill bacteria, chemicals such as C-Reactive Protein (CRP) are released to signal for more phagocytes and damaged cell destruction. These Inflammatory markers have been associated with almost all chronic diseases. It has been shown that they may protect cancer cells from apotosis and make them resistant to treatments. It may be that we have low grade chronic infections,left over from earlier exposure,that create an inflammatory condition that stimulates antibodies and release inflammatory markers that damage our own cells and create the diseases of old age. It has been shown that people who had a high incidence of childhood disease live shorter lives then those from affluent societies where childhood diseases were much less. (Senescent cells increase ?).

Arthritis is a chronic inflammatory process. The body has macrophages that are an important part of our immune defense. When a inflammation source is found by these constant patrolling cells they will act to engulf it and limit it. This source can be any number of things including bacteria,viruses,toxins,or allergens. Sometimes the cells confuse our normal tissues with foreign ones and attack our own tissues (autoimmune disease). This may be what happens with arthritis. The macrophages then send out chemical signals (cytokines) to tell the other parts of the immune system to come and help. It appears that in arthritis the signals do not stop and are a cause of the persistent chronic pain. Recently, there has been a method used on mice that allows a chemical to be transferred into the macrophage that then stops the path of cytokine production and reduced the inflammation and pain.

Recent work shows that the Beta Amyloid found in the brains of Alzheimers patients is similar to a anti inflammatory protein LL37 produced by certain genes in the brains innate immune system. These same genes are associated with Alzheimers. The Beta Amyloid shows ability to kill many of the same microbes as LL37. It may be that the same proteins that help the brain fight disease also can destroy certain brain cells.

It has been shown that a key factor in Alzheimers disease is dysfunction of the mitochondria. There are 10 sets of genes that are shown to have low function in patients with this disease. This dysfunction occurs even before the symptoms begin. All of these are controlled by a master gene ,PGC 1 alpha,that controls many functions of the mitochondria. By enhancing the activity of this gene the symptoms can be stopped. It seems that loss of the vital mitochondria activity is at least one of the causes of this disease. There are drugs that might be able to activate the master gene and reverse this disease. By discovering the disease early (which is possible) the patient may be spared.

It appears that glucose and glutamine are both interrelated and necessary for glucose metabolism. Glutamine blocks a key gene that is a cancer suppressor gene. This gene,when expressed, allows the cell to not use glucose, and the cell dies. If blocked,the cell continues to use glucose which is the metabolic choice of cancer cells. Growth factors are usually necessary for the utilization of glucose,and cell survival. If these are removed the glucose use decreases and the cell dies. Cancer cells have a mutation in a protein,Akt, which promotes glucose use and cell survival even when the growth factors removed. This bypasses the normal cells regulating system and allows a immortal cell (cancer). If glucose is removed the action of the protein stops. A gene, PK-M , produces two protein isomers,PkM1 and PKM2. In cancer cells the M2 is found only . MK1 is found in normal cells. The MK2 promotes glucose metabolism. 3 proteins are involved in the production of the MK2 by reducing the production of MK1. These 3 proteins are found in cancer cells but not normal cells. It may be possible to block the effect of these proteins and stop the overproduction of MK2.

An extract from a fruit,bitter melon, has been shown to increase the action of AMPK which allows glucose to enter cells and lower blood sugar. It also stops division of some cancer cells and causes cancer cell death.

The homeostasis activity of the cell is dependent on a number of factors but the level of amino acids,glucose and fatty acids and the insulin signaling mechanism are key factors. This mechanism is triggered by excess amounts of these food products and by oxidative damage. If the cell has high levels of free radicals during the night the repair process is no longer in cycle and is limited.

Cancer cells are able to survive stress such as chemotherapy and low oxygen levels. They can actually autophage parts of themselves,reduce the need for food and O2 and wait out the stress. When the stress is removed they start dividing again. This is the recurrence often seen in all cancers. These mechanisms are now being studied and treatments to stop the ability of these cells to survive is being tested. Hydroxycholquine, an anti malarial drug,can block this process. There are markers on the cancer cell surface that signal for this autophagic process. There are chemicals being studied that could bind to these receptors and stop the autophagic process that protects cancer cells. NV-128 is one of these being tested. It maybe that a single pill each day,like a vitamin, would allow all tumors to be destroyed.

Certain Melenomas have a single gene defect on a gene that predisposes to this disease. If the patient is shown to have this defect a drug is given to block the defective protein produced by this gene and the cancer is killed..

A study with fruit flies ,with similar genes to humans, shows that varying the amounts of lipids,glucose,vitamins and minerals had no affect on life span. However,varying the amino acids did. Methionine was the key one and when it is reduced in a HIGH calorie diet the life span increased. Adding it to a LOW calorie diet and the lifespan decreased. This showed an effect of a certain type of food to effect lifespan rather then the total calories. It is interesting to note that this amino acid,methionine,is a receiver of free radicals and is used by the cell to protect its proteins from free radical damage. People on a diet high in animal protein have a higher incidence of cancer then those on low animal protein intake. The active form of vitamin D(dihydroxy) is bound to the cells nucleus and regulates a variety of gene functions. It helps keep cellular proliferation in control and if abnormal, promotes apotosis. A form of vitamin D,calcitrol, induces a cancer suppressor gene to be active in breast tumors. Patients with high levels of Vitamin D had a 40% reduction in colon cancer.

Mutations occur all during life. However these usually effect a small number of cells,and often have no significant functional change. These acquired mutations are passed to the daughter cells but usually make up a small number of the cells of a certain organ. Many are removed by apoptosis. There is little significance from mutations on aging. This is unlike inherited mutations that are passed on to almost the whole body cells. However,the actual gene expression or activity does vary dynamically as the body cells responds to new environments. When there is a low level of radicals, and cell damage, the cells use their maintenance system to keep this under control and the cells stay youthful. But,when the damage signals increase the signals become distorted and the various genes increase activities like sending out inflammatory distress signals and make proteins that attract immune cells and perhaps begin to breakdown important molecules. An example would be the overloading of the arterial cells with oxidized LDL cholesterol,and the genes expression increases and inflammatory proteins signal for macrophages to arrive and the attempt at undoing the damage begins.

Diabetes 2 is related to the sudden spike of sugar after eating certain foods. Recently a study of foods that change the absorption time of glucose has shown that the markers of diabetes can be lowered significantly. Rye,Barley and Oats are foods that humans digestion evolved with. Corn,wheat and soy are more recent (last 10,000 years). If a person eats a Barley bread they have an effect on digestion that lasts up to 18 hours. Even though other foods are eaten (i.e.breakfast) the indigestable starches in Barley allow fermentation by bacteria in the bowel and the markers of the disease are lowered. Less spike in sugar,less insulin surge,lower inflammatory markers and a increase in a protein ,Glucagon P, that promotes cell use of glucose. Less fatty acids are produced which are instigators of these inflammatory changes. Hot red peppers ,taken with a meal,reduce the amount of insulin spike after the meal.

White beans have an extract called phase 2,that keeps enzymes in the gut from "cutting" long chained sugars into short ones. Also ,this same extract decreases absorbtion of starch by 66% from the gut. This results in increased metabolism of the longer chains into energy rather then fat storage. One gram of this results in lower blood sugar levels.

Normally the Immune system creates an inflammatory change around a pathogen or injury or damaged cell in the body. This allows the macrophages to remove the problem. However,if there is a overreaction of the inflammatory response then the immune system is overworked,tissue that is not seriously damaged is removed etc. To avoid this the Immune T Regulatory cells release a signal to tell the macrophages to not send out inflammatory changes and therefore avoid action. However,if the system is overwhelmed with serious damage it may get confused and regulate the macrophages when they are actually needed. This would allow the cancer to escape the bodies defense system. The opposite can occur when the T cells allow unopposed action of the inflammatory response in chronic diseases like rheumatoid arthritis. Identical twins,with the same genes, will often have a different disease history. The expression of certain genes and the lack of expression in one or the other twin allows this difference. Even though they have the same genes they have different life exposures, and the genes will be expressed differently in both.

It is appearing that the inflammatory response of our immune system is at the heart of many degenerative diseases.Emphysema,which is usually caused by smoking,appears to be related to the fragmentation of the elastase that protects the air sacs. These fragments create a "foreign body" that sends out signals and causes the immune system to send macrophages to destroy these. By producing antibodies against these fragments this can be prevented. It is thought that incomplete digestion of animal protein products allows the immune system to form antibodies to protect against these "invaders'. However,since these proteins are similar to ours, the same antibodies may recognize normal cells as foreign. This could be the cause of some auto immune chronic diseases.

The mitochondria are the important structures to keep in good repair. Damage to them produces a cycle that promotes less and less repair and more oxidative damage. Premature aging in mice is shown to be related to the point mutations in the mDNA where the proteins produced are unstable and breakdown and the cell ages.

The result of this seems to involve the valuable power factories of the mitochondria. Billions of years ago the mitochondria were single cell free living bacteria. They were processed by phagocytosis into a early complex cell and incorporated into their cell machinery. A similar process led to these mitochondria becoming chloroplasts in the leaves of plants. Some cells have hundreds and others ten thousand. They replace themselves at various times (CNS sometimes every 30 days). The total mitochondria in our bodies make up 10% of our weight.

It is important to note that the DNA of the mitochondria is separate from the cells DNA. The mitochondria DNAm resides in the mitochondria not in the cell nucleus and is more susceptable to free radical damage. The DNAm is passed down from the mother,intact,no recombination, as with regular cell DNA. The DNAm has a higher rate of mutations. It is now thought that as many as 1 in 6000 births may have significant disease due to abnormal DNAm.

Mitochondria use Oxidative phosphorylation to create energy (ATP) In doing this some oxygen is produced with an electron imbalance (free radical). This is very reactive and is in the mitochondria itself and will quickly react with an adjacent molecule. The two vulnerable areas in this structure are the DNAm and the membrane that controls the passage of chemicals in and out. If these free radicals damage the DNAm enough the Oxidative process is slowed or even stopped. The energy production is down or is switched to another method . This alternate method (glycolysis) does not produce free radicals . The loss of the free radicals causes the cell to miss its signal to repair the damaged mitochondria.

The cell that the mitochondria service has a "janitor" group that will recognize signals to intervene and breakdown certain components who are worn out or malfunctioning. These are enzymes (lysosomes) and the weakened cell membrane of the mitochondria is their signal to act (apoptosis). The lysosomes are small containers of enzymes that breakdown all the damage chemicals,mitochondria etc. in the cell. It then removes the breakdown products. As we age the cell accumulate lots of damage due to free radical and glycation changes. If these damaged products are too much the lysosome increases in size,loses its ability to function and can even burst open releasing these damaged chemicals into the cell. The dividing cells are able to dilute this damage and the remaining functioning lysosomes will keep the damage under control.

Catabolic insufficiency is the inability of our body to breakdown certain substances that develop over time. Oxidized cholesterol and Carotenoid Lipofuscin (In Macular degeneration) are examples. Certain bacteria,fungus and plants have enzymes to do this. It may be possible to develop these for the removal of these damaging substances.

However,in non dividing cells like the heart,neurons,stem cells,this damage accumulates with no dilution. The cell now has a hodge podge of junk chemicals called Lipofuscin (LIP). The lipofuscin is so damaged the lipososome enzymes cannot work,the junk increases and the lysosome function decreases. Damaged mitochondria,normally removed,are now allowed to remain in their damaged condition. These are passed on in cell divisions with a new generation having damaged mitochondria.

In atherosclerosis the LDL cholesterol has been exposed to Free radicals and glycation, is damaged and sticks to the vascular walls. This creates an inflammatory signal and the macrophages rush to engulf this and allow its lysosomes to break it down to harmless products. With ongoing signals (high cholesterol,nicotine,diabetes etc.) the macrophage becomes overloaded and its lysosome system fails,it fills with the junk chemicals,the macrophages die,more come,other inflammatory cells,blood cells and the macrophages break open with release of these damaged products. Plaque forms,debris breaks off and stroke,heart attack etc. follow. The same type process appears to occur in the neurodegenerative diseases of Alzheimers and Parkinsons.

The membrane is leaking and free radicals are spilled out. If the DNAm is so damaged it is not working and no free radicals are produced (due to glycolysis) the damaged DNAm is not noticed. The scavenger cells are not signaled, or perhaps, the cleanup system is also damaged and ignores the signal. This allows this structure to divide and pass on the non functioning DNAm to the next generation. A damaged structure rather then a new well functioning mitochondria. These will also not produce free radicals and will continue to produce deficient structures. Many of the offspring from diabetic 2 mothers have damaged DNAm with loss of 60% of their metabolic action.

The damaged mitochondria use a non oxidative method to make energy. This method can create a large amount of a molecule that can damage the cell itself. This is prevented by the membrane stripping electrons from this (NADH) and going back to a non harmful NAD+ state and adding a number of free electrons and these usually react with O2 to form H2O.. However, the problem is to do this in the damaged mitochondria the electrons are released from the Mitochondria into the cell cytoplasm. Here,these free electrons are attracted to the many oxygen molecules forming free radicals rather the H2O. These can damage various proteins including RNA and DNA.

This free radical increase does send a signal to the cells DNA and many genes respond with activity to try and get the cell back to normal. This may be where gene expression that have been silent are activated and a general inflammatory condition results. Many diseases of aging are associated with a generalized inflammatory condition. The most recent research shows Alzhiemers disease is probably due to this type of damage . The results of the TOR gene may be due to its immune function to stop inflammation. Gene IKKe is associated with these same inflammatory conditions in the body. It limits the production of a protein in the mitochondria(UPI1) that will burn off extra fat cells as heat rather then storage. This, and other inflammatory genes, may be activated in a cell with too many free radicals and cause fat to form in the cell, and this appears to farther the inflammatory process.

The tumor suppressor gene P53 is inactivated or under expressed in almost all cancers. This gene is a switch gene which sends a signal to a damaged cell to correct itself or it will also cause cell death. This is a important process to regulate the health of our cells. Damage to the DNA and over division are stimuli to activate the gene. If the gene is over active it can cause premature aging due to cell overactive apoptosis. Mice given a "boost" to their P53 gene function have a significant decrease in tumors compared to normal,same genetic strain,mice. By regulating the amount of the switch the mice do not age prematurely. Vitamin D appears to be

able to activate a cancer suppressor gene ,CST5,that causes a reduction in colon cancer. Also,this same vitamin in its active form,calcitrol,induces a tumor suppressor gene in breast cancer.

70% of longevity is non genetic. Diet,exercise,social interaction all contribute.However,after age 60 genes begin to play a bigger role. The older cell has had more damage. A gene variant called FOXO3A is found often in people older then 90,and very often in those over 100. When two copies are found they have 3 X the chance to make it to 100. This gene promotes the repair process in the cell.They also have very little chronic disease. It controls the Insulin pathway for metabolism,and how the body processes food. It releases proteins that protect against free radicals. They also promote the programmed death (apoptois) which is thought to rid of damaged cells and protect against cancer. These protections are from the things that damage to the mitochondria makes happen.

It is now thought that 90% of cancers are due to environmental cause. Smoking and diet ,toxins in our environment all interact with our cells to form cancer conditions. It is thought that only 10% of cancers are directly related to genetics.

Age related disease seems to be related to the biological age not the chronological age of the cell. This biological age is related to the free radical production. Some birds have a long lifespan,and this appears due to them having very low free radical leak in their mitochondria. Also,many birds have a increased number of mitochondria per cell. Catalase is a antioxidant enzyme that occurs in the body. When this is added to the mitochondria of mice the DNA mutations are reduced, chronic disease is reduced and the mice live 20% longer. Adding this same antioxidant to the nucleus DNA of the main cell reduces mutations but does not affect the life span.

There are some cells (skin,lung,white blood cells,) that can use glycolysis as an energy source rather then mitochondria. Stem cells also have little dependence on mitochondria. These cells are often associated with cancer where cells like neurons ,dependent on mitochondria,do not. However,these cells are suceptable to degenerative diseases. The CNS astrocytes are often the site of brain cancer and are able to use glycolysis. Cells dependent on mitochondria get old and sick and have a program to die. Those cells that can switch to glycolysis are immune from programmed cell death and are subject to the stimulus of the inflammatory conditions and proliferate and suffer mutations and are farther free of the constraints of a normal cell.

It has been noted that in diseases related to mitochondria dysfunction that there are low levels of Glutathione . This is one of the best antioxidants in the body. By replacing this antioxidant it may protect and restore the mitochondria functions.

A recent discovery shows that a drug , Dichloroacetate (DCA) that has been used to activate an enzyme in the mitochondria, is very useful in cancer treatment. Many inherited diseases are due to mitochondria dysfunction and DCA has been shown to be useful. Cancer cells bypass the OXPHOS system of the mitochondria and use glycolysis which is more efficient in low O2 environments.. This is less efficient but does not produce free radicals so the cell is free of any control (aptosis). Also,the glycolysis produces lactic acid which destroys the collagen matrix holding cells together and allow spread of the tumor cells to other areas (metastases). Blocking key enzymes in the glycolysis cycle kills cancer cells.

It has been thought that the mitochondria in cancer cells were "knocked out"but the DCA actually "reawakens" the mitochondria in these cells. It maybe as the tumor grows there is less and less O2 and the mitochondria shutdown and glycolysis begins. Usually the mitochondria supply 90% of the cells energy and this is reversed with the mitochondria shutdown. When the mitochondria are active (with DCA) the tumor cells wither and die.

Tumor cells are stimulated by hypoxia. They shift to glycolysis,controlled by a protein PKM2, and many new proteins are created under these hypoxic conditions. A protein,MCT1 promotes the use of a waste product from glycolysis ,lactate, to feed the tumor cells. Lysyl Oxidase or LOX is produced by hypoxic tumor cells and promotes spread of the tumor. It appears that if the tumor cell is not hypoxic it decreases in size and has less chance to spread. The hypoxic state appears to allow many new molecules to be produced which promote the cancer. The oxidative metabolic state appears to block this.

It has been shown that a group of genes are located at the ends of the chromosomes. These are called telomeres and are created by a enzyme,telomerase. These genes are vital to a cells growth and life. As chromosomes divide they would leave off their ends at each replication. Soon,they would have no genes left to replicate. The ends would fray,recombine and cause lots of mistakes. The nonactive telomeres prevent this. Bacteria use a circular configuration of their chromosomes to prevent this. Most cells divide 50 to 70 times and then the telomeres are too short and the telomerase enzyme is turned off. The cell can't divide and the process of aptosis is begun by the cell to get rid of the damaged DNA. Cancer cells are thought to need 300-400 divisions to survive and spread. They are able to promote a constant telemerase enzyme production in order to do this. They bypass the bodies defense system. Certain cells (gut,stem cells,WBC's) maintain active telomerase due to their need of rapid and many turnovers. Cancer cells reactivate the telomerase enzyme. This allows them to escape the signal a short telomere chromosome would give and therefore avoid the controls of normal cells. People with increased levels of alpha 3 omega acids had a slower loss of telomeres then those with low levels.

When cells chromosomes have too short telomeres and no replacement they degenerate and die. The aging process is related to the telomeres. People with short telomeres live less long then those with longer telomeres. The length of telomeres appears to be influenced by inheritance but environment may also effect them. Also,the enzyme telomerase may add benefits besides the telomere length. Vitamin D is an inhibitor of inflammatory response and increases the telomerase levels in Rats. However,the telomeres are not significantly increased. The rats with higher telomerase levels did live longer then a control group. People exposed to stress have a accelerated shortening of their telomeres. Patients given yoga,meditation and low fat diets increase their telomerase levels. Recent studies show well trained athletes have longer telomeres and higher telomerase levels then a control group.

We now know that oxidation reactions, glycation , inflammation and telomere-telomerase are related to our cells health and life span. The normal byproducts of living,free Radicals and glycation appear to be at the basis of aging and disease. By learning to control these processes we may increase our life span considerably. There appear ways in which specific drugs can increase our life span. There may be "drugs" in our diet that will help control the free radicals and sugar increases that appear to be part of the problem. Our diet itself may prove to be an important component of cell health. A "epigenetic" diet is one that promotes methylation and perhaps gene expression. Animal protein ingestion is associated with a higher level of cancer and other diseases then when proteins are obtained from plants. Many chemicals in plants allow protection from the damage of free radicals.

Consciousness,feelings ,and the Brain.

2009-08-31T13:42:00.000-07:00

Is a state of consciousness separate from the Brain itself? Is it separate from the "outside' world we live in? Are feelings handled differently then other mental tasks? Do these areas of animal actions belong to a idea called the mind? If so,did the mind evolve along with the rest of the animal ? Do we have free will to choose? These are all religious and philosophic questions debated for centuries.

Language ,memory,speech,and even the ability to think has been programmed into computers and robots. If consciousness is the ability to perceive something,realize how it will affect you and then have an action because of this, then robots can also have consciousness. Both Invertebrates and Vertebrates have consciousness.

This consciousness is due to stimuli coming from outside sources,perceived by our senses, and sent to various areas of our brain. Our senses are far from perfect and they vary from one individual to another. Right from the start there are differences in perception. None of our perceptions are actually totally "Real". They are bits of light or sound or smell that is processed through imperfect sense organs with limits on their ability to see,hear,or smell many things around us. We are handicapped by these imperfections.

The signals leave the senses, and then are passed,as electrical impulses, (at 240 mph) along the nerves to specific areas of the brain. Again, some handicap exists as the nerves need time to polarize and are not able to receive any signal until this happens. There are "blind" spots. Once the signals reach their area then the neurons must process these and connect with many others to interpret what the signals are saying. In order for the brain to have a total perception the neurons need to connect with many areas of the brain that allow the visual,auditory,and smell all be included. This means many millions of neurons,thru many nerves interconnecting instantly. These connections are reenforced by use and neurons that fire together will wire together. These collections that occur are called "maps" and give us our ability to have "consciousness". It is the knowledge of objects in the outside world and how they might affect us. Often this leads to an action. Its a tiger! run,run! That girl will hurt my feelings,stay away.

The brain operates often by itself without a conscious awareness by ourselves. It is shown that there is not a conscious "self" who decides things and then causes an act. There is a time of up to 10 seconds in advance that the brain decides to act before the person is remotely aware of the act. The brain makes these decisions at a unconscious level due to the sensory organs reacting to physical stimuli, and the person only later "feels' they made a conscious decision.

What happens "out there" is actually occurring in our own minds. What we see and experience of the outer world is actually the workings of our brain-mind. The energy fields (photons,air wave changes,) are physical events that are then changed into electrical and chemical events that our brain then perceives. Different animals see and hear the physical events surrounding them entirely different depending on their anatomical and physiological states. Some can see more colors,others only gray shades,some can hear high frequencies ,others very few frequencies etc. The reality that we perceive is actually our own consciousness. This is determined by the various physical events occurring and by our own sensory equipment.

Genes are the basis for our anatomical and physiological Brain. The size and configuration are found in our genes. However, the "fine tuning" of the brain is done by our use of this anatomy. If a antigen of one type is used to stimulate the immune system it will soon create millions of antibodies but the rest of the system will wither and not develop. If certain neurons in the brain are not stimulated they die. 20-50% of Neurons are lost in the first month of life! At the same time,those other neurons develop trillions of pathways and synapses. The ability for this development is called neuroplasticity and is most found in young animals but is available our whole life. Even all of the 30,000 genes (probably a lot less for actual brain development)cannot account for the trillions of pathways.

Feelings are bodily sensations that are constantly being monitored by the brain. Temperature, hunger,thirst,pain,sexual desire are all feelings that all animals possess. These are more internal signals (compared to outside stimulus for consciousness). Most of these feeling centers are in the older brain (midbrain,brain stem) not the neocortex. Again,the nerves from various areas of the body,as well as certain chemicals (hormones) are the way that these systems let the brain know their status at all times. Under constant stress the hormone cortisol acts on these centers. Again, to get a complete picture of the feeling the neurons interconnect by the millions and "fire and wire" together. These neurons have the same handicaps of transmission as with consciousness but are less dependent on outside stimuli and use the internal sensory nerves. Feelings often create an action-eat,drink,mate,withdraw your hand from the hot fire (compared to a conscious signal that sees a fire and tells you to stay away.)

Evolution has allowed us feelings and a consciousness that has indeed evolved along with our brain. Our intellect problem solving,thinking and memory all use similar anatomical and chemical structures as do our perception of feelings and consciousness awareness.

Oxytocin,a hormone,is an important mediator of some of our social interactions. It has been shown to be key in our reading of others faces,sympathy for others,recognizing stress in others and trust of others. It may be a key for the mothering instinct and the ability of a father to be a responsible care provider. It also functions as a neurotransmitter,like serotonin and DOPA, and its actions are genetically influenced. It has one protein it effects (unlike other neurotransmitters which effect 5 or more). However,the protein differs among different individuals and a "A" oxytocin causes a different effect then a "G" type. The "A" type has less empathy for others,is less able to see emotions in others, and responds more to stress then the "G" type. Again,we are limited in our perception of outside stimulus by our own brain.

Because of our neuroplasticity it may be we can reinforce certain behaviors over others by the frequency that we do these things. We are dependent on our limited sensory organs to recognize outside physical forces and on our brain to organize these into our idea of "consciousness". Our genetic makeup is also a key factor and we are not all the same.

"Hot" versus "Cold" Blood.

2009-08-30T14:56:00.000-07:00

Hot bloodied animals and cold bloodied animals have been selected over the millions of years. There are many advantages and disadvantages to each. Hot blood (a higher metabolic rate) means a shorter life,lots of time gathering food and eating,depressed population,decreased size and number of offspring. The advantages seem to be stamina and sustained activity. This allows longer pursuits,and the ability to avoid predators. More success in mating and ability to raise their young with a higher survival rate.

At the basis of hot blood is an increased metabolic rate. This ability is due to a group of master genes that allow increased mitochondria to develop in the internal organs for increased metabolism. Also,the organs are larger. Both of these are under the control of "Master Genes" which allow these changes.

It appears that different species developed this ability. Birds (derived directly from Dinosaurs) have this ability and also have very efficient lungs as well as a 4 chambered heart, All of these are important to increase the metabolic rate. The 4 chamber heart is controlled by a gene (TBX5) that is present during the formation of the left ventricle and allows septation. This gene is absent in three chamber heart formation.

After the Permian age,260 million years ago, almost all of life was extinguished by the activity of volcanoes,loss of much O2 and increased CO2. During the age that followed a carnivore-herbivore creature the cyndont, developed and appears to be a "hot" bloodied creature. It is thought this was our ancestor.

For better or for worse Nature selected us to be hot bloodied animals.

The eyes have it

2009-08-29T21:37:00.000-07:00

Deep in the ocean are thermal vents with many varied and interesting species. These areas appear to be the chemical factory for beginning the evolutionary process. One of the species is a shrimp that has two flat areas on its back. These are retinas and use a pigment, rhodopsin, to register light. It seems that when a thermal vent is active a faint green light from the chemicals and heat is given off. The shrimp use their light sensitive retinas to spot this and move in that direction. Certain algae also have light sensitive areas in their leaves. This allows them to turn towards the light. The pigment in these is also rhodopsin. The pigment is actually found in the chloroplast membrane. This structure was a free floating bacteria at one time. It was engulfed by other cells and formed into the chloroplasts of all plants and algae.

The retina in our eye depends on rhodopsin and this is the same protein type as from these primitive relatives 600 t0 1000 million years ago. Our actual eye (as well as many other models of eyes) developed during the cambrian period 500 million years ago. The organization was due to numerous changes but the basic building materials were available to be acted on. This pigment is found in many vertebrates and invertebrates . Transfer of a mouse gene to a fly will allow eyes to develop in the fly at unusual places. The gene to build an eye uses the same materials in many species. The material and the DNA to direct the construction appears to be from a single ancestor. The Algae were probably this ancestor.

Color vision is found in many species. It is due to the structure of proteins called opsins.Our opsins are found in a specific area of the retina called cones.There are 3 different opsins which allow detection of green,blue and red colors. The shark and some birds have 4 opsins and can see 4 colors. The opsins are bound to a vitamin A derivative and is called Retinal. It changes in shape when a photon hits it and this starts a signal to the brain. Different species have different opsins which allow detection of different wavelengths of light and therefore different colors. Insects see UV light and birds see red light.

The "master Gene" is Pax6 and is found in almost all vertebrates. It is behind the formation of the eye and a large part of the brain. The marine ragworm and other species have the same

pigment .

The early eye was probably just a photoreceptor (thermal vent shrimp) but when the retina became curved and recessed it needed a lens. The lens is structured by various materials in different species. Some actually use a special crystal of limestone that focus the light. The high concentrations of Calcium are acted upon by proteins that crystalize the Ca into a transparent lens. Any acidic protein can do this and they are commonly found.

Our eye,and many other species, have a protein lens made of a protein called crystallin. This protein is commonly found and is present in the liver,lungs,guts and other organs it is a catalyst. Almost all proteins are transparent and by changing their concentration they can "bend' light. These proteins were recruited by the DNA committee to make a lens. The sea Squirt has the DNA to make a lens from these proteins and this "lens" can be found in their brains. There was an easy transfer from the brain to the eye and it happened at least 11 times in different species.

Once O2 was in the atmosphere and the Cambrian age with the sudden explosion of many different species began the eye was a valuable addition. The materials for the eyes were available from the past and the DNA to assemble these structures developed. Although there are many differences in the large number of eyes developed they appear to have a common ancestor from over a Billion years ago.

Why choose sex?

2009-08-28T13:07:00.000-07:00

Cells have evolved sexual methods to transfer their genes. This appears to be due to the advantage of bringing about the best combinations of genes,eliminating the worst, and allowing the passing on of helpful changes (mutations)

At the basis of this is the ability to recombine the genes on the chromosomes and pass on these new innovations.

Meiosis is a variant of cell reproduction. Meiosis is used by the sperm and egg cells to allow 4 single chromosomes to be mixed and placed into their cells. Not only do the "sex' cells get only one chromosome they get one that is a random mixing of the individual genes. This is done by a process of recombination. Individual genes are randomly replaced on different parts of the chromosomes. Like shuffling cards.

It is thought that this method has allowed the best results. Other ways of reproducing is with simple division (like bacteria) and cloning. All of these methods can be found in our world. it appears for the complicated cells that we are made of sexual methods offer the best way to accomplish the goals.

Food from light-photosynthesis

2009-08-27T14:45:00.000-07:00

Perhaps the most important event in our evolution was the creation of chlorophyll and its ability to use light from the sun to make food and release Oxygen. The basic structure of chlorophyll is a porphyrin which is very like our blood component heme. Porphyrins are found in many light sensitive enzyme systems and have been isolated from astroids from outer space.

Every plant and algae has a small factory in its leaves called chloroplasts. These bacteria shaped structures are the source of this amazing reaction. Basically a light photon from the sun activates electrons in the H2O molecule and they go to a higher level of energy. As they begin to fall back to their lower energy level there is excess energy released to be used by the cell. A second light photon again lifts the electrons to a higher energy level and even more energy is released as they go back towards their normal level. This energy is converted into a high energy molecule and this allows atmospheric CO2 to form a sugar-the basic food of all life. The most abundant protein in our planet ,RuBisCo enzyme, helps this reaction.Along the way the oxygen is free and appears as O2 in our air. This reaction allowed the many paths of evolution to begin.

The very early bacteria in the thermal vents had a different source of electrons and used iron and hydrogen sulfide. They would strip electrons, use the energy to react with CO2 and also form sugars. They probably used manganese rather then light as their beginning energy source. Manganese was very abundant in the waters Billions of years ago and is a prolific electron donor.

Cynobacteria developed this chlorophyll system and had another "accident' in which a metal cluster was incorporated into the cell and was adjacent to the chlorophyll. This cluster of manganese,oxygen and calcium is similar to other metal clusters found in the thermal vents. This addition of the metal cluster allowed the bacteria to now get its electron by splitting the water molecule. Also,releasing free O2.

The Cynobacteria,with this important factory, was probably ingested by a host and not digested. The ability to form this chlorophyll-metal cluster metabolism was now part of the new host cell. The chloroplasts actually look like bacteria in the leaves of plants. It is not unusual to find DNA from bacteria that has been incorporated into new hosts this way. An example is the mechanism to digest cellulose by cows which came from bacteria.

Soon,all species of plants had the food factory as well as algae. All of the DNA of these chloroplasts from all the many different species is the same. A common ancestor.

The sea slug is shown to posses the genes to actually make chlorophyl. This was probably a gene transfer some time in the past. However,the slugs must eat algae to complete the metabolic process from photons of light. The algae supply the chloroplasts and these along with the slugs own chlorophyl allow them to use photosynthesis to make food and live. These are the only multicellular animals known to be able to make food from light.

This process of photosynthesis allowed the tremendous explosion of varied life on earth.

Our Ancient Origins

2009-08-26T18:56:00.000-07:00

4.5 Billion years ago there was a violent convulsion of a gigantic dust cloud covering billions of miles of space. This tossed the dust particle billions of miles in all directions. Many dust particles were mixed and when they began to cool and gravity attracted them to each other thge sun and planets and the outer positioned comets formed.

It is thought that biologically important chemicals were included in these dust particles and due to the structure of the comets life was begun in these seeming cold pieces of rock. Comets have liquid water(warmed by the presence of active radioisotopes) and carbon,hydrogen,nitrogen and vast amounts of clay. The water incubated the chemicals and the clay acted as a catalyst to began the formation of organic compounds. Ancient molecules called cyclic nucleotides can merge together in warm water to form longer chained polymers like DNA and RNA. In a acidic warm environment RNA can replicate to a length of over 100 units and at this length begin to fold into 3D shapes. They actually form double strands and join at the ends to form a circle (the configuration of bacterial DNA).

Life is basically a series of chemical events. The most important is the respiration or energy production of each living cell. Many Billions of years ago the interior of the earth was a molten mass of space debris. The energy was leaked thru the mantle and crust and met billions of tons of water. The water was saturated with CO2. The gases from the earths interior contained H2 (most common element in space),probably brought onto the earth by the star dust and collisions. These formations are seen today under many thousands of feet of ocean. Large columns of debris are seen that appear to be cities that have many forms of life, including bacteria and other more advanced forms.

The most basic form of respiration is the meeting of CO2 and Hydrogen,with the stripping of a Oxygen and excess energy produced. This is the way all cells live. The reverse of this allows cells to produce more complex molecules such as fats,and proteins and carbohydrates. These reactions are found in the thermal bacteria living in these undersea "cities".

The first forms of life appear to be in these early undersea "cities". located in these microscopic rock cells that received nutrients from the earths crust below, and the influx of the ocean waters above. Trapped in these small areas they had all the tools to experiment with forming organic molecules. Many already formed molecules had arrived with the astroids and space gases that formed the earth. Various amino acids (adenine) as wells a 8 atom sugar,glycoaldehyde,have been identified in the interstellar gases of our milky way. These allow the formation of complex molecules such as ribosomes,RNA and DNA. These,plus many minerals were available in the early thermal vents.

It is believed that a very complex experiment in this undersea environment lead to the organic molecules that are the basis for life. Once they were formed,nature and all the forces she has ,was able to begin the selection of the most favorable.

The most complex cellular structure ,of all living things,is the DNA-RNA-Protein relationship. In these same underwater mineral cells the amino acids that are at the basis of all of these processes are found in large numbers. They actually "pile" up at the pores like silt in a river and are available for many reactions. The heat in these cells cause currents and other conditions perfect for formation of RNA like structures. The RNA chains were able to gather other amino acids and form proteins. The ancient bacteria in these cells have all of these mechanisms including a very important enzyme to allow production of DNA-reverse transcriptase. This is the same enzyme found in retroviruses that allow them to invade a cell,use their RNA to copy DNA since they have no DNA themselves.

Fossils records show cynobacteria lived 3.8 Billion years ago. These primitive bacteria used CO2 and produced O2. They were probably the producers of the O2 that eventually rose to 21% from 1% in our atmosphere. This set the stage for the majority of life forms that evolved.

It appears that our most ancient relatives lived deep in the ocean and in small mineral cells that were fed with heat and chemicals from the molten mantle of the earth.

Cosmicism and survival-A new way to see our life?

2009-08-24T11:04:00.000-07:00

In the beginning, a collection of all the matter and energies in our known Universe was in a small area the size of your thumb. About 15 Billion years ago, this tiny density expanded with the Big Bang and the energy and matter scattered in all directions into the vacuum of the Universe. These things moved at speeds of hundreds of thousands of miles per second. The reason this happened is a mystery.

Particles of cosmic dust formed and areas of tremendous energy gathered . Large stars were formed with tremendous stored energy. These were millions of miles in size and lasted for short (2 billion years) time. They collapsed when cooled and shrank to a fraction of their original size. They became dense gravity fields and formed "black holes'. Collections of space gases were attracted to them and rotated around them to form galaxies. The particles grew larger and infant planets were born. Gravity interacted and astroid particles collected and crashed into these areas. These energy regions formed with masses to make stars with high temperatures and radiation of waves and particles moving at high speed like an inflating balloon thru the cosmos.

Around 5 Billion years ago, the sun as we know it, formed and began to attract large areas of cosmic dust. Our Planetary system began and the planet named earth experienced many millions of collisions as more matter crashed and brought the dust, chemicals and water needed for the forces of nature to act upon. Billions of tons of water over millions of years turned to steam due to extreme heat finally returning as rain. It was bombarded with water containing asteroids and the total earths surface was water. Red in color due to the unoxidized iron.

Most of the planet was covered with water. There was no Oxygen, only CO2, sulfides and methanes. Deep in the oceans simple life forms from the cosmos came; needing no oxygen, they survived on methane and sulfur. There was no life on the surface of the infant earth.

About 3 Billion years ago, the earth developed a magnetic shield from the inner deep collection of molten iron. This allowed protection from the suns deadly radiation. A stable orbit formed to utilize all the good energies of the sun. The moon was created when a large portion of the earths surface tore away. Stabilization to the spin of earth resulted and seasons could come and go in a timely fashion without mayhem. These accidents were important for earth to perform natures experiments.

At first there was no oxygen and the life forms exisited on CO2 and other gases. Simple bacteria evolved and was able to resist the suns radiation and live on the surface of the sea. This bacteria had the ability to photosynthesize and use H2O to make and O2. For millions of years these were the earths only inhabitants until O2 began to accumulate and complex organisms developed.

Life forms changed often due to asteroid collisions, temperature changes, droughts, volcano eruptions, the breaking away of continents and many other unforseen actions of the great forces of nature.

There were many powerful creatures that evolved and then died out. Natures forces did not hesitate but continued to randomly act on the matter of the earth.

Cosmicism is based on the relationship of all matter, living or inert, coming from the same source and depending on the same energy forces. These creative forces called "Nature". there are no plans or expectations. The forces do adhere to certain physical rules that regulate their behavior and are constantly interacting in a progression of accidents. There is no plan or expected outcome.

All matter is related and affected by the forces. The Nature has no expectations or favorites. Creations are accidental surprises with equal value. The dinosaurs existed for over 100 million years and were the dominant creatures on the earth. Suddenly, an asteroid hit the earth,changed the atmosphere and all of these creatures died. Life began all over again.

Cosmicism believes the Soul is an entity without material reality. It is the emotional or moral part of man. We believe the soul is a product of evolution and varies with each individual. Morality is often determined when the sperm and egg meet and various genes are set in action to form the brain. The Brain is our connection to reality and the brain is controlled by chemicals causing our reactions which are controlled by genes which nature has developed over millions of years with one result, to allow us to live and reproduce. The brain is driven to accomplish these two things through our senses and physical being.

However, the neurons in the brain are "plastic" and can be formed to perceive the environment from different points of view. If one believes fellow humans are kind and good then this can be the reaction that the consciousness will create. Unfortunately,if one has always seen humans as dangerous and evil then this will be the consciousness developed. The positive point is we do have some control to use the tools evolution has given us to have a more loving and peaceful world. It takes conscious effort to harness our consciousness!

While man plays with religion, philosophy, art etc., the basic animal spirit of survival and reproduction are the products of evolution. The emotion of fear is a driving force. Man has evolved to react toward a tiger in the woods, a bear, a strange person, climate change. These all create fear and resulting caution. The biggest fear is death. The development of religion and many philosophies is to mitigate this fear. In Cosmicism, we accept that we are natural spirits evolved for our own need to survive and reproduce. We recognize that man is like most successful creatures and capable of tremendous violence towards others. Spirituality is the attempt to rise above our selfish genes. Religion often is the shield we hide behind to allow the killing and exploitation of others. Ignorance breeds destruction.

To join our group you must recognize your evolutionary nature. Once this is done you can begin to lose your fear of death, respect all of the spaceship earth and find your humble position on this journey.

Let us pray-

We accept that we are a humble and insignificant part of the spaceship earth. We are no more or no less important then our fellow travelers.

We are grateful for the long series of forces that have allowed us to evolve and realize life. We respect all forms of life; the oceans, forests, valleys and the many other things that help sustain us.

We wish to help our fellow travelers accept a responsible position in this life and try not to control all things around them. To recognize they are handicapped by the physical need to protect and give help to themselves at the expense of others.

We recognize the need many have to find solace in religion or spiritual beliefs. We hope they will not become slaves to these ideas and miss the real truth.

We realize we have only been here for a few thousand of the Billions of years in our past. Many powerful species have come and gone and we are no exception.

We accept that we are evolved life forms but are susceptable to disease, violence and our own stupidity.

Let us overcome our animal nature and cooperate as a human species to sustain our lives and those of future generations.

Amen

Oh Hum,time for a nap.

2009-05-31T13:17:00.000-07:00

The Dwarf sleepy probably had a number of genetic problems beside being a Dwarf. People with Narcolepsy(falling to sleep at various times all day) have a particular version of an immune gene that is classified as HLA(Human leukocyte antigen). These proteins are very key in protecting us from disease. If they go wrong they are able to attack our own bodies cells and create havoc. (Autoimmune Diseases).

Certain neurons in the brain produce a protein called Hypercretin. This is the "time to wake up" protein and keeps us awake. If you have an altered autoimmune system these neurons are attacked and the "wake up' protein is lacking.

Narcolepsy is probably a genetic change that allows the immune system to cause these damages.

However, people with this altered gene only have a 1.5 Times chance of Narcolepsy so there are other factors involved.

Again,rather then label these folks as lazy we must recognize this as a disease.

On the other side of the sleep coin is the genetic predisposition that people with short sleep periods have. Sleep variation is related to genetic factors and a certain gene,DEC2, is found in those with short (6 hours) sleep periods. It is not found in those with a 8-10 hour sleep period. The people with the short period do not seem to be sleep deprived and have normal activities. Inserting this gene into mice altered the normal sleep period to a short one.

The Flexible Brain

2009-05-18T17:06:00.000-07:00

For many years the brain was thought to be fixed with discrete areas that were totally separate,fixed and unchangable. Research now shows the brain to be very flexible and plastic. It can reorganize itself and is in ongoing communication with the various areas. These communications can be altered.

Original work sowed that the amputation of a finger or toe or even a whole extremity allowed the sensory space that the original structure had to be replaced with other sensory sensations. In this case, the facial skin area filled in the sensory function of the absent extremity. In human amputees who have the sensation of a limb that has been removed (phantom limb) they often have pain and cramping feelings even though the limb is gone. Sensations in these absent areas can be triggered by touching the face area. Whenever the facial muscles move it also causes sensation in the phantom limb. Often these are painful and appear to be "locked in " sensory sensations from the original limb. By using mirrors and tricking the brain to think the remaining limb is the absent one the brain is fooled into thinking the limb can move and is OK. This removes the previous painful sensations.

There are a set of neurons in the frontal lobes that will fire when one reaches to grab a cup or other object. Also, when one observes another person doing this motion the neurons respond. An "empathy" reaction. These are called "mirror neurons" due to them acting with the action of others. An Autistic person has a normal firing of the neurons when they reach out but no action when observing others. They lack the "mirror" action. It may be that they are at a loss to register the outside world and are locked into their own individual actions. Research is looking into a way of causing these neurons to fire and register others actions. Our brain notices mechanical movements (cars,trucks,water) and biological (another persons actions). Autistic people have a very low ability to observe biological motion and a normal mechanical. They do not look at others eyes but focus on the mouth and chin area.

Schizophrenic victims often hear voices. It is known that when we have a thought it registers in the brain but we know we are "talking to ourselves" and do not hear this as an outside voice. The vocal cords move unconsciously as we have our inner dialogues but there is a mechanism in the brain to allow us to distingush inner from outer voices. It may be this sensory control is absent in Schizophrenics.

Stress causes many physical symptoms but also can change the behavior of the brain. With stress the brain areas related to making goal orientated decisions is decreased and that area that causes habits or repetitive decisions is increased. This is shown when depressed or compulsive people make the same decisions over and over even though they are the wrong decisions. They appear unable to make new decisions. However,after the stress is removed, the areas of the brain go back to a normal pattern. This shows the ongoing adaptive plasticity of the brain.

Exposing non childbearing animals to newborns and their taking part in the care of these infants shows new neurons and "wiring" in the subventricuar area of the brain. This new neuron production is also seen in new mothers. The behavior of child caring appears to be the stimulus for these new neurons similar to those formed in a new born mother.

The plasticity of the brain has opened the door to helping many victims of stroke and amputations. It appears that many more abnormalities can be traced to changes in the plasticity of the brain

Molecular Origami and Rusty Gates

2009-05-01T10:41:00.000-07:00

Epigenes modify the actions of genes and genes produce very specific proteins to allow our body functions. If anything happens to change the protein template the action of the protein is changed or cancelled. This can cause devastating effects.

Cystic fibrosis has a defective gene on the 7th chromosome. When this was discovered a healthy gene was substituted and had good lab results. However,with human trials the gene was immunologically blocked and was of no use. It was decided to look at the defective protein that enables the proper use of chloride in the body which is the main defect of CF.

In doing this it was discovered that most mutations can be classified into categories. One is the mutation that produces a "Rusty Gate" protein that is unable to pass into a cell to act. Another category prevents the protein from reaching the membrane of the cell. Another is the "no nonsense" mutation which stops production of the protein after a small fragment.

The modifications are like folding paper with the origami technique,if the fold is wrong the protein does not work.

Chemicals are being developed,and tested,that do fold the protein properly and allow the mutation defects to be reversed. These mutation types are responsible for potentially thousands of abnormalities in our bodies.

The actual use of these will probably be a combination of mutation corrections because most genes have more then one category of defects.

Lets only have good memories

2009-04-07T13:59:00.000-07:00

Researchers have discovered a chemical that appears to be responsible for recalling our learned memories. There are numerous learned memories including bad ones like addiction or Post Stress reactions. By blocking this important chemical the memory bank of brain cells is unable to recall the memory and it is lost.

These memory cells appear located in areas of the hippocampus and amygdala. When a memory is recalled it is like a "speed dial" effect,once the memory is recognized thousands of other cells immediately join in and contribute to the complete memory. There are over 117 different chemicals thought to be involved with this process of memory but one in particular appears to be primary .

The "speed dial" is related to the ability of many separate neurons to oscillate simultaneously, at the same frequency and amplitude over different parts of the brain. This coherence or "phase locking" starts at one set of neurons,and when it reaches a threshold level many other areas join in. Each area may represent a different part of the same memory and a smell may trigger a visual and auditory region to contribute that part of the memory.

PKMzeta,a kinase, is responsible for the spreading of the message to activate all of the cells involved in a memory recollection. It allows the signal to recall to be spread quickly. If a special chemical,ZIP, is injected directly into the memory area the PKMZ is blocked and the message is halted. Memory of a bad taste,electric shock etc. is lost and the animal starts from the beginning learning experience.

The possibility of erasing addictive behavior or post trauma memories could be a great aid. By enhancing this same substance increasing memory ability may be possible, perhaps helping Alzheimer patients. The danger may be that other positive learned behaviors will be erased along with the bad ones.

It may be that various individuals with "super memories" already have increased amounts of this chemical and vice versa. Perhaps it is the amount of this chemical in the brain that allows one person to avoid Post trauma stress and another to be severely affected. It maybe that this chemical is changed by the type of genome one inherits.

It appears that a traumatic event can cause the surge of stress chemicals (cortisol) and this strongly imprints the memory. If a person has less cortisol receptors,which may be due to a gene mutation ,or due to a epigenetic change from the environment (abuse as a child) the memory is reenforced by the continued presence of cortisol long after the event stops. This may be why certain people have PTSD and others do not. When a person recalls this memory,which may be very vivid , due to its reenforcement, the anxious stressed emotion and physical reaction is also maintained due to the release of the stress chemicals. They actually think they are reliving the event.

Many ethical question are again going to be raised with these discoveries.

Obesity and soft food

2009-02-28T17:04:00.000-08:00

In experiments it has been shown that softer food uses less energy to digest then less soft food. Animals fed soft,food had a 30% weight gain then those with the same ,but firmer,food.

Processed foods are softer and this is what people prefer. The taste buds are directly connected to the amygdala with nerves that convey the message about the softness of food. This is what is preferred and what people choose.

It may be that the softness of processed foods is a big cause of the obesity problem.

The evolution of man may have been very dependent on the ability to cook food. Cooking allows the breakdown of proteins and starches to molecules more readily available to digestion. The heat physically softens food to allow better digestion and less energy to digest. Cooking allows more food to be digested in the stomach and small intestine where it is better processed. Raw food is much less absorbed.

Is the Brain another sex organ?

2009-02-05T14:56:00.000-08:00

There is ample evidence to show the male and female brain differs. Both Brains weigh about 3 lbs. and consume 20% of our calories. The male brain is about 15% larger then the female.

Size does not seem to matter. What matters is the genetic codes that allowed the brain to develop the necessary "smart centers" to function. The female brain has 9X the white matter and the male 6X the grey matter. The female smart parts are mainly in the frontal lobes but the males' is widely distributed. A crows brain is 12 X smaller then a chimps but both have the same mental abilities. It is the quality of the brains organization,not the size. The Quality is genetically programmed.

However it is not just the genes but other environmental factors that play a role. In Mice about 14% of the genes that regulate brain behavior and function behave differently in male and female. This is probably due to the estrogen-testosterone mix they are exposed to during development.

The sexes do share one common pathway,the signal to start puberty. This is also started in the brain,not the gonads.A gene,KISS1(a good name)sends a protein message to the hypothalmus that tells it to produce special proteins that then go to the gonads and begin puberty. This occurs over a variable time in males and females. Sex does begin in the brain.

It appears that nature has evolved two separate brains-male and female. The functions are very different as all of us are aware. Both allow intelligence and adaptation but via different paths.

Money management is in the brain

2009-01-09T09:48:00.000-08:00

When we make money the brain releases increased DOPA and gives us a high like cocaine and other drugs. It may even be addicting. As with most functions of the brain it occurs without our control. When we lose money the opposite occurs. Cortisol and other stress chemicals are released and we fell great fear and anguish. These are all evolutionary developed processes. These are our "animal spirits' that have significant control of our monetary actions.

When a deal is "too good to be true" but offers great reward, our chemicals push us to get involved, even though our neocortex says "no". This is why "bubbles", subprime mortages etc. happen to so called intelligent,informed people. The brain is on a "high" and this overrides the logic. Also, people often don't relate to history more then 10 years ago and that is why we see recurrent financial "bubbles" and downturns. (Over 50 in last 50 years).

Once the good times begin to slip the brain reacts with overwhelming fear and panic often begins. Again, logic is overruled by this and our actions are at a very primitive level due to the fear in our brain.

These biochemical controls illustrate the need for steady regulations and transparency to control our inability to react in a rational manner to all these temptations. Once a chance to make money is presented the brain will go to any lengths of rationalization to join in the frenzy. Rationalization and other mechanisms will join in the flooding of the brain with DOPA and other feel good chemicals and it is analogous to using cocaine.

No matter what is said the human animal needs regulations to stay in control.

Evolution does not stop at the Neck

2008-12-22T14:55:00.000-08:00

This idea of evolution is widely held that our anatomy evolved, but our behavior is shaped by cultural influences. The evidence is the opposite-there is little room for changing behavior by social means. This is an important fact since most societies spend their resources on trying to change behavior by schools,churches and other social indoctrinations.

A "Darwanian" concept of behavior defines most of actions are determined by two evolutionary actions, survival and reproduction. Reproduction being the strongest. Alot of human behavior is showing off in ways that attract the opposite sex. A corollary of this is the need to intimidate members of the same sex (competition). In our modern society high status (money) individuals are much more likely to get the desirable mates.

Most crime is committed by young males upon each other. Those at the lower rungs of the social ladder have more stress,less health,less respect and less chance of a desirable mate. These problems will cause them to try and change their position however they can. This will involve violence,murder,crime and terrorism. No matter how many society influences are used this violent behavior will occur due to the lack of status and reproductive chance. This is shown in the middle east with thousands of young males without jobs,status and no chance of marriage. The Islamic fundamentalist offer a feeling of respect,special purpose and tries to curtail the sexual desires for reproduction .

An important consideration for younger adult males is that the maturation of the brain is often not complete until 21 years or later.The prefrontal area is associated with the ability to feel empathy towards others. Also,the ability to experience guilt for our actions. These areas are often not developed in these young males, and makes violence towards others easier to perform.

By creating jobs,respect and the ability to marry and have families is the most direct way to combat crime and terrorism. Our Billions of dollars would have been better spent and our mission better accomplished had we worked on enabling these things to occur.

How you smell may determine your mate

2008-12-21T14:29:00.000-08:00

We all have a series of genes that are related to our immune system function. This group is called the Major Histocompatibility Complex (MHC). It is important that the choice of a mate includes someone whose MHC is different then yours. This assures a hybrid and stronger immune system in the offspring. This immune function is a strong determiner of breeding. Fortunately, evolution has equipped mammals with the ability to detect certain chemicals whose concentrations vary and allow us to recognize someone with a different MHC. This detection is by a different scent that the person has.

Women will choose an object that has a different scent then their own. This will be an attraction that would make them more likely to choose that partner for breeding. They will reject one with a similar smell as their own. However, women will choose a perfume that is similar to their own smell. They are advertising their personal smell.

It is probably best to let women pick their own perfume.

Some Viruses are our friend

2008-12-18T13:29:00.000-08:00

The new area of Gene treatment depends on inserting therapeutic genes into tumors that will overcome and correct the errors caused by the cells cancer producing genes. This allows the new genes to actually kill the cancers by these corrections. Since these genes are selectively inserted only into cancer cells there are few, if any, side effects.

These replacement genes are called transgenes and are selected for their ability to correct the cause of the disease. One common gene is the P53 which normally functions to suppress abnormal cell growth or division. This function is often lost in cancer cells.It allows the encoding of a special protein in the cell that will stop the cell growth.

The genes of interest (transgenes) are placed into a adenovirus capable of invading a cell. The viruses own genes are removed to avoid carrying a potential disease into the cell with the transgenes. Also, it is important that the normal immune response to the virus is stopped. This will prevent the bodies' immune system from destroying the virus before it invades the cancer cells.

Some of these are in actual clinical trials at this time. When a brain tumor has been removed this therapy may prove important. There are mant small "invisible" areas of tumor left. Once the main tumor removed the healthy brain tissue is injected with the adenovirus containing a transgene. The patient is given an antiviral drug called Ganciclovir,which reacts with the transgenes protein and kills the cell. The normal brain tissue does not divide and the drug only acts on dividing cells (cancer cells).

Inherited Emphysema has is a defect in the gene that produces Alpha 1 trypsin and the elastin lining of the air sacs is destroyed. By using a viral vector a gene is injected that gives 70% of the macrophages that line the air sacs the ability to produce elastin. This corrects a lot of the problem.

There is concern that these virus vectors may introduce other serious diseases but these fears are being corrected and gene therapy will be an important treatment.

The Economic meltdown , the election, and our minds

2008-10-28T15:22:00.000-07:00

Perceptions,and decision making are at the heart of human error. Decision making involves two parts,gathering evidence and committing to a choice. The evidence gathering is often faulty due to the misinformation given by candidates and the underlying prejudices we all have . We "pick and choose" the evidence accordingly.There is a "tipping" point when the mind will commit to a choice. Some do this quicker then others. The "undecideds" in elections will postpone a decision until the election day. Others will commit to a candidate immediately. People with damage to the ventromedial cortex of the prefrontal area will take a very long time to make a decision. However, the decision has often been made but is not realized by the person. By asking a series of oblique questions pollsters can predict what a "undecided" voter will do.
In previous posts it has been shown that the mind has strong prejudices and will often use information that will only reenforce their previous ideas. Anti abortion,anti gay marriage etc. are examples.
Our brain evolved when things were much simpler and we struggle with the many complexities of todays world. To simplify this we often only see data that we can relate to and will ignore more difficult or less comfortable data. We refer to recent events rather then events that occurred at a longer time. We give ourselves credit for a skillful solution to a problem rather then realize it was dumb luck. We surround ourselves with others who agree with us. We reject conflicting opinions. Then,there is the group dynamics or "group think'. If we are members of a group we have a strong need to fit in,and that means agreeing with the majority of thinking.
All of these "weak links' allow us to be imperfect guardians of our best interests. Greenspan was shocked that the system failed. He should realize the system is only as good as the minds involved and evolution has not yet developed the brain to overcome all of the above problems. Even a computer program could fail since the same weaknesses would be put into the human created software.

Eat your way out of addiction?

2008-10-17T16:20:00.000-07:00

People are programmed for addiction. Activities such as sex and eating are highly rewarding. However, these reward pathways can be blocked by drugs ,alcohol,and behaviors such as gambling. These pathways depend on the neurotransmitters (serotonin,dopamine,and GABA). Addictions mimic their function so the body quits making them. Also,they may have decreased receptors or production of "feel good" transmitters. Now, the person needs the outside source for these rewards and therefore becomes an addict.

Many addicts appear to have decreased production of DOPA and decreased receptors. They pass through life with a "Gray Cloud" and miss alot of the everyday joys. It is the addictive substance that gives them a euphoria.

As with many functions it is known that much of our mental function is related to the expression or non expression of genes. These are controlled by environmental changes including stress ,drugs and nutrition. (See section on addiction and gene expression). Addictive drugs are able to change the epigenetic histones that activate or deactivate our genes. The memory is related to events and the outcome of the event. With addiction these memories are in overdrive and take over the process and results in compulsive behavior. The type of histones changed differ in acute use of addictive versus chronic use. After chronic use the memories remain long after the drug is not available.

A recent. study, shows that by including foods in the diet that have high levels of the missing neurotransmitters this will boost the levels available and reduce the need for addictive behavior. GABA precursors are found in certain nuts and seeds. By giving high levels of these to addicts there was a significant decrease in the addictions. This was especially true for gambling an 80% decrease compared to 28% in the control group.

Tryptophan,found in brown rice,meats,nuts ,fish and milk is a precursor for serotonin. Reducing the diet in these foods causes depressive symptoms. Adding these induces a more optimistic behavior. Omega 3 acids (fish oil) helps the physical characteristics of nerve cells and how they conduct impulses. The brain is 80% fat (dry weight) and a lot of this is EPA and DHA alpha omega acids. A lack of DHA (replaced by Omega 3)has resulted in learning difficulties and hostility. it may be that this would help in treating many segments of our society.

A long term study of depression in Iceland has shown diet may be a very important aspect of depression. There is a very low incidence of depression in Iceland,whereas the same genetic stock who migrated to Canada have a high incidence. The Iceland natives have 3 times the level of alpha 3 omega acids as do the Canadian icelanders. The high consumption of fish, as well as the local"green" consisting of a moss-grass, is very high in these same acids.

The epigenes that control a lot of our gene behavior appear to be modified by diet. It seems methyl producing foods (methionine,choline,folic acid,B12 and B6) are related to adding methyl groups to these epigene proteins and changing gene expression.

Drug companies have not done any studies since you can't patent food. However, a study is being done with addicted prisoners and further information may show that we can indeed eat our way out of addiction.

Your lying Brain

2008-06-28T17:57:00.000-07:00

Our brain takes in "facts" and stores them for a short time in the Hippocampus area. Weeks later it transfers this information to the cortex for long term storage. However,each time we recall the fact, it is rewritten and reprocessed by the brain. In doing this the original contex in which the fact was noted is often lost. Eg.you may know Sacramento is a capital city but you don't remember in what context you learned this.

This allows "source amnesia" which can cause you to forget whether a statement was true or false. Even if the original fact was learned with a disclaimer that it was not true this can be lost during the processing of the fact. Often people will remember the fact later but not the details that went with it. "I read this someplace". As the process from hippocampus to cortex takes place over time the fact gets more disconnected and a false fact may be thought of as true. This is especially true when your mindset already believes a certain idea of events and will try to fit the new fact into this preconceived set of ideas.(See earlier study on MRI and our set ideas).

The more the lie is used as a truth the more embedded it becomes. People who already had a strong opinion eg.pro capital punishment, will use "facts" to fit into their belief,ignoring many disclaimers that were also given about the fact.

The political strategists have learned that repeating false information will eventually become a true fact to many voters.

Dynamic Genes

2008-05-07T09:51:00.000-07:00

DNA (In genes) can actually disappear, appear in new locations or entirely new genes appear from one generation to the next.

This "Horizontal Gene Transfer" is the rapid passing ,or disappearing, of a gene in the same generation. This transfer often occurs from an entirely different organism (often a bacteria). Once the gene is transferred to the new organism it is able to function since almost all living creatures have a similar gene decoding mechanism.

A good example of horizontal gene transfer is the acquiring of antibiotic resistance by bacterial colonies. The antibiotic resistant gene is transferred "sideways' in the same generation. This can cause rapid changes vs. generational transfer.

This sideways, or horizontal change, occurs easily in bacteria where genes are well exposed in the cell itself. It can occur less rapidly in animals whose genes are protected inside a cell nucleus structure. Our DNA is coiled in the nucleus of the cell and is 2 meters long (about 3 feet) . The nucleus itself is 1/100th of a millimeter across! there are 23,000 genes and 580,000 letters of code on one chromosome.The active genes are coiled in this ball but are in a looser arrangement then the more inactive ones. This allows more easy access to these active genes then those coiled in the very dense part of the "ball" of DNA. However, the horizontal transfer can still occur. An example is the ability of the cells in a cows stomach to digest cellulose. These genes were transferred from a bacteria found in the stomach. The ability of the mammalian placenta to attach to the blood supply of the mother was passed on to mamals by a virus DNA.

When a new gene is acquired the organism can now form an entirely new protein with
potential new function. In a mutation a present protein is altered but no new one created.

It is now thought that the horizontal transfer of genes is at the basis of the original development of our living genome. Vertical transfer of genes,is at the basis of the Darwinian idea of evolution. However, there had to be a lot of things occurring to the genome before the vertical transfer took over for complex living organisms. One thing that the vertical concept does not explain is the tremendous ability of our genome to be unaffected by errors or mutations. It takes a number of mutations to change the production of a protein. This ability is not explained by vertical transfer,but does fit with horizontal transfer. This allowed "life' to acquire a unified genetic machinery that allowed sharing of innovations more easily. Through various stages the complexity of some life forms became so complex that it took a vertical type of gene transfer to allow the preservation of complex functions.

Vertical transfer mechanisms do explain Darwinian evolution ideas for the more later aspects of evolution but horizontal transfer is necessary for the early,initial formation of genetic materials.

Bacterial biomass is the greatest in the world and it is still using horizontal gene transfer as its main process.

The genome is a lot more dynamic then previously thought.

Drugs and Psychotherapy

2008-04-29T17:07:00.000-07:00

Freud psycotherapy ideas have been overshadowed by the many discoveries of psychopharmacology in the treatment of mental illness. Every week there appears to be a new drug for various mental problems. The use of imaging is able to show where and how these drugs work in the brain.
However, the use of imaging is also showing that therapy(now called cognitive behavior therapy) is also helpful,at least in certain disorders.Brain imaging is showing definite changes in th brain with the use of this treatment. This therapy emphasizes how our thoughts relate to how we feel. Even if external stressful situations remain unchanged we can remove the negative influence by how we think about them. Therapy helps to change the way one thinks of life situations so they do not cause depression or other abnormal responses.
This type of treatment has been especially useful in obsessive-compulsive disorder (OCD).Untreated ,the patient has anxiety laden thoughts that result in repetitive behavior, trying to relieve the anxiety. Hyperactivity of the neurons are seen in certain areas of these patients. This is especially seen in the caudate nucleus. PET imaging has shown that both Prozac medication and Therapy treatment can quiet these hyperactive areas.
There are many psychiatric illnesses where medications are a must. There may be other specific illnesses where therapy alone,or in conjunction with meds may be the treatment of choice. Imaging is allowing us to have an objective measurement of these choices.

Evolutions' affect on bipartisian politics

2008-02-15T15:28:00.000-08:00

Recent studies on over 8000 pairs of twins has shown some pessimistic information on the future of different political parties working together. Genes play a big role in our emotional responses to society. These emotional respones are the building blocks for our ideology.

Using carefully selected questions designed to show the ideology of the person and comparing identical(100%gene match) and fraternal (50%)it is shown that there is a strong inherited factor. Assuming a common family environment for the twin pairs it was shown that the genes accounted for 53% of the ideological differences between the conservative and progressive groups. However, the difference in Republican vs. Democrat political party affiliation had only a 14% genetic cause.

Liberal bias appears to be related, at least partially, to genetics. A dopamine receptor gene is found more often in so called liberals then in conservatives. This gene is associated with a greater degree of novelty seeking (curiosity). This may account for the seeking of new ideas and ways of acting. However the actually liberal trait of being open to new ideas was found mainly in those who had a strong peer group association. This opened them to new ideas and discussions. Those same "liberals" with the same gene change that were loners were not so interested in new ideas but other more narrowed interests such as food or music. Again,there are genetic changes but the environment is a determining factor.

Another study has shown that people who are for more police,more defense,fearful of terrorists and generally see other people as possible threats are more associated with a conservative political philosophy. They respond with definite physiological changes to certain images and noises then another group that appears to be "liberals". The Liberals have a much different physiological response to these images and noises. Liberals see threats from technical things such as guns or corporate products and are more accepting of people. The protection of individual privacy more important then the idea of security. Liberals see social inequalities as injustice where conservatives see them as justified and necessary for stability. Conservatives more fearful of death and insecurity. Conservatives desire simplicity in solutions and clarity. Fearful of uncertainty. Liberals tolerate complexity and ambiguity.

It has been shown Conservatives react more strongly to threatening images. When confronted with a eye gaze test(following the direction of others gaze) Conservatives had little reaction (did not register or react to the gaze of others). Liberals were very consistent in following other gazes.

Social attitudes tend to stabilize in the early 20's and it is at this time people who were raised in a conservative family environment suddenly switch to a more progressive one (or vice versa). The idealogies are genetically predisposed and are often very polarized (homosexual marriage,abortion,school prayer etc.) and these do not change regardless of facts or discussions.

A study using MRI (see earlier blog)also showed that conservative or progressive people only responded to information that agreed with their ideology and did not respond to any information against these ideas. The more arguments against a held position created more defense from both groups. Very few positions changed regardless of information given.

It also appears that "like marries like" so the gene pools may become even more concentrated as time goes on.

The lack of bipartisan cooperation may be due to the misunderstanding of how the different groups perceive the importance of different policies. It is like one group sees apples and another lemons. There is a definite difference in the way the two groups see the world.

The chances of a fair and open bipartisian political approach to problems is very limited.

Antiaging

2008-01-06T21:42:00.000-08:00

This desire to not grow old is as old as recorded history. We now have the knowledge to begin unlocking some of the mystery of aging. Mitochondria are the places in the cells where the metabolism of glucose is done. This needs large amounts of oxygen. some of this oxygen escapes capture by carbon to form CO2 and is free to roam the cell and is very active and combines with vital proteins and even DNA which can change their functions. This "Oxidation"reaction is thought to be a significant cause of cell damage and relates to cancer and other changes.

If these free radicals of Oxygen can be stopped from combining then perhaps cancer and aging can be stopped. Some genes actually stop abnormal division (cancer) and free radicals have been shown to damage these genes so pathological division takes place. There are now many so called "antioxidants" that are supposed to stop these actions. Two molecules that have been shown to help are acetylcarnitine and alpha lipoic acid. Also, large doses of some vitamins such as the C an B groups. This has been shown in Mice but not proven in humans.

Another antiaging method has been shown in many species is eating less. It appears that starvation like stimulus releases a protein from genes called sirtuins. Adding extra copies of this gene and life is prolonged. Sirtuins appear to control the amount of a regulatory molecule called nicotinamide adenine diphosphate which in turn controls the release of energy in the mitochondria.

Resveratrol (found in red wine) activates sirtuins. Sirtris pharmaceuticals has a concentrated form of resveratrol that is in clinical trails and has been shown to markedly reduce blood sugar levels in type 2 diabetics.

It may be possible that one or more of these discoveries will actually allow some slowing of the aging process.

Fossils in our Genes

2007-12-21T17:56:00.000-08:00

Our chromosomes are littered with fragments of viruses genes passed on millions of years ago. These genes become part of our DNA . 8% of our genome is made of this. Since most of these fragments appear to have no purpose they are referred as "Junk DNA".

A virus is a few strands of genetic material covered with a protein shell.A parasite unable to reproduce or function on its on. When it infects a cell it transfers its genes into the DNA and begins taking over cell functions and turns out thousands of copies of itself. There is only one type of virus,retrovirus, that can insinuate its genetic material into our germ cells where it can paste its genes into the DNA of the host and it becomes part of them cells DNA forever.

These retroviruses have a large role in what we are today. An example is the formation of a placenta in mammals that allow live births. Very early mammals were egglayers and the placenta was an important change. The embryo was able to actually stick to the maternal womb and the placenta allows nourishment to pass and stops foreign objects such as bacteria from entering the embryo. Retroviruses have been seen in some layers of the placenta and a protein,syncytin,which causes cells to fuse together within the placenta is the same action that retroviruses use to attach to cells.

Over the many millions of years different retroviruses have added to our genome and perhaps aided our evolutionary survival.

An example of a retrovirus is the HIV (Aids) virus. There is a small number of people who have two genes that allow them to build a defective receptor that stops the HIV virus from attaching and entering their cells. They are not suceptable to AIDs. If HIV continues to kill millions of people in Africa these special anti-AIDs genes may select only these people. It is possible this type of situation has occurred many times over our evolutionary history and the "Junk DNA" is our fossil record.

Retroviruses may well be the unseen creator that contributed to our evolution.

Synthetic DNA

2007-12-17T16:48:00.000-08:00

Using a process of high speed DNA synthesis, long strands of DNA can be produced in the lab. The basic chemicals are rearranged into a strand of looping DNA that has been specifically "programmed" to achieve certain results. Evolution in a test tube. This programming is unlike the DNA reacting ,by chance, with the environment.

These are software programs designed for very specific reasons. To make new medicines,biofuels,chemicals, and eventually perhaps new and better parts of the body. The software DNA is created and then transferred into a living cell (bacterium) and its new functions will begin to create the result desired.

There are already smaller synthetic strands that are producing biofuels,new improved chemicals and modifed plants. The next generation will be long and complicated strands of DNA specifically programmed ,much like computer software is for certain computer functions. The first of these is expected in 2008.

The first full genetic sequence of a grape variety,Pinot Noir,was recently published. Hundreds of genes that encode enzymes to produce flavor and aroma have been identified. This opens the way to rewrite the genetic software to produce specific flavors,colors etc. Also, adding certain genes from grapes resistant to fungus and other disease will allow these wines to be grown in wider areas.

Engineers note spider webs have amazing strength and can stretch 40% of their length. Different parts of the web have different properties. These serve the spiders well, but what if they could be used for other purposes? The sequences of DNA that allow these silk strands to be produced have been isolated. By shuffling the order of these genes and recruiting bacteria to turn them into proteins over two dozen novel forms of this amazing silk has been produced.

A one cell goat embryo is inserted with a human DNA that makes a anti clotting material. The human DNA was linked to the goat DNA that makes proteins in the goats milk. The embryo put into a womb and a genetically modified goat is born. The milk from this goat could make 90,000 doses of the antithrombin drug each year! The drug only appears in the milk. The modifed goat now can mate and the genes is passed on so more "drug donor" goats are available.

Recently the horse genome has shown that a fast horse has a mutation in a single gene,myostatin, that allows it to be very fast over a short distance. This gene will allow breeders to choose those parents that possess this gene to increase their chances of having a winning horse racer. Actually a variation of the gene allele will allow a fast horse at short distance,a horse with longer endurance etc. It maybe that by inserting these genes into the DNA of breeding horses a new group of "super racing" horses will be developed.

This raises a whole area of ethical considerations. Also, the possible error factor with a DNA that could get into the environment and cause harm. Harmful biological agents could be made. Those that think evolution was Gods way of creating the universe will now have to consider that man can also play at being God.

The Synthetic DNAs' are here and we will be living (or dying) with them.

Linkage disequilibrium

2007-12-14T17:49:00.000-08:00

This long mouth full of words describes a way that scientists use to spot recent mutations. Mutations are linked to bits of DNA that were present when the mutation occurred. These have not had time to break up into smaller fragments and can be seen. Over many years the swapping reaches an equilibrium but more recent mutations have not had time to break down and thus can be identified. The more recent mutations are those within the past 80,000 years.

Genes are linked together in pairs and each pair member comes from the father and the mother. When the sperm and egg meet, there is a swapping of genes and bits of DNA to create a new mixture in the offspring. The swapped bits contain the same type of gene pairs but may contain a different version of the original gene and thus have a new biological effect. This effect may enhance or diminish the chances for survival. A lot of this will depend on the environment that the gene will have to respond to.

About 1800 protein coding genes have been identified and about 7% of this total show signs of having been subject to recent natural selection. This change is thought to have been increased over the past 80,000 years.

It is thought this is due to 2 major causes. The human population has increased very rapidly ,and so a much larger gene pool to act on. And second, the various environments that humans have migrated to are very different then the original area in Africa.

Protection from new diseases (eg.Malaria)are favorable mutations and allow certain groups to evolve. Also, the ability to handle new dietary changes in various regions is important.

Gene linkage is allowing us to see the Darwinian idea of environment acting on our DNA.

Why Salmon die and we can't always remember

2007-12-12T16:42:00.000-08:00

Cortisol. This important chemical is the culprit. The body has two opposing forces, the Sympathetic and Parasympathetic. One speeds us up and the other tries to slow us down. Fear, causing stress, or any thing else that causes us to stress will trigger off reactions that have great consequences for us.

Once a stress is perceived the brain tells the adrenal gland to release a whole hosts of chemicals. Many affect the heart,blood vessels and the immune system to allow a very high level of alertness. Cortisol rushes to the brain where it affects the Limbic area,especially the hippocampus. This area of the brain has groups of cells responsible for our learning as well as short and long term memories. Unfortunately,too much exposure and the hippocampus cells will die. This appears to be due to shunting of valuable glucose to other areas of the body. The cells normally will send a signal to shut down the cortisol supply and the parasympathetic system will try to restore order.

Studies have shown that at least 1/3 of older people have constant increased levels of cortisol. This is probably due to long term stressful situations and the fact that due to these high levels they have lost up to 25% of their hippocamal cells and have less ability to stop the cortisol production. The hippocampus was up to 14% smaller in these groups. The memory tests in these people were abnormal and indicated a loss of various types of memory.In younger adults ,given cortisol before certain memory tests, decreased their ability to recall information learned earlier.

A chemical,HBeta-HSD1, promotes the increase in cortisol in the brain. When this is blocked significant improvement in memory occurs ,sometimes within 10 days. clinical trails are underway to evaluate this treatment.

Depressed people have high levels of cortisol especially when put in positions of stress. The same people have a loss of cells in the hippocampus and the hippocampus becomes smaller. This increases with the length of time of depression. Interesting, Electric Convulsive treatment helps many severe depressed patients and the number of new cells in the hippocampus is increased with these treatments.

The good news is that we are all producing thousands of new Hippocampal cells each day (Neurogenesis).( This may not be true for depressed patients.) They seem to lose cells over time. Even more are produced when people are actively learning new memories and associative memory paths. Non memory tasks do not effect the rate of cell increase. London taxi drivers,famous for the ability to know each and every London street have enlarged Hippocampus areas.

Women and men handle stress very differently and this may explain why women live longer.Women "tend and befriend" when stressed. Men get aggressive or flee to a quiet place. Also,oxytocin, an important chemical that tends to relax and calm is enhanced by estrogen and decreased by testosterone.

People with high stress also have increased atherosclerosis,high blood pressure,stroke, weak immune systems and other disorders.

It is now recognized that aerobic exercise can indeed help the brain function. The exercise seems to decrease the loss of nerve cells in the brain and decreases the loss of gray matter seen often with aging. Walking at least 6 miles per week decreases the loss of brain substance. Aerobic exercise creates a chemical (noggin) that promotes development of brain stem cells to neurons. It seems a combination of exercise and challenging new cognitive exercises is important in allowing our brains to overcome degeneration.

What about the poor Salmon? They die due to Cortisol overload and their whole body is a wreck due to the uncontrolled levels. Remove the adrenal glands and they live another year or two.

Nature and Race affect on Intelligence

2007-12-10T14:04:00.000-08:00

For many years an argument of "nature versus nurture" and its affect on our intelligence has been a standard for academic folks.

With the availability of brain imaging we have gotten closer to an answer. The work from UCLA shows that a higher intelligence ability is related to a thickening of the cortex of the brain. This is especially true in the frontal region. Also, the trajectory or rate of these changes is different in a higher IQ child. It also appears that the cortical "thinning" process that normally occurs in adolesence is greater. These changes show greater dynamic changes and these are related to a higher IQ.

No definite gene or group of genes has been identified to determine how intelligent you are. However there is some indirect evidence of certain genes affecting IQ. It has been suggested that Gaucher form of a gene might be connected with the high intelligence often seen in the Ashkenazi jews. Recently a similar gaucher type gene has been found in Asian groups. It is under question if this gene is related to a higher interlligence.Long chained fatty acids found in breast milk can cause certain genes to increase IQ. There are two gene variants ,G and C, that have enzyme production that can affect the metabolism of these long fatty acids. Those carrying at least one C gene had a consistent increase in IQ when breast fed vs. those formula fed. Those with a homozygous GG (a pair) had no increase when breast fed.

This shows the probable action of the environment on genes that contribute to intelligence.

Testing identical twins shows that they have the same anatomical changes in their language and reading skills area whereas only 60% of their siblings have these changes.Also,the parents of these twins show similar changes.In a study from Europe 9500 twins were studied and 78 genetic markers were tested for. This also showed the markers the same in the twin pairs but only 50% present in the other siblings.

The above certainly indicates that nature via our genes allows us an ability to be smarter (or less smart) then others. How much? The argument can still continue as to what percentage nature contributes and what our nurture adds.

Another consideration in our ability to be "smart" is our emotional state. It is thought that the ability to learn,achieve,and be successful is in large part due to our emotional actions. It is thought that this area is also strongly related to our genes. It has been shown there is a definite inheritance of how we react to stress.

Brain size is not related to intelligence (men versus women) and a tribe in Equador with very small heads have a range of normal intelligence.

Studies of children with German mothers and Black fathers and others with white fathers showed no significant differences in IQ scores. It is thought that the Germanness of the mother was the deciding factor.However, a black child in a white family will average a 13 point advantage in the IQ score versus a black child in a black family. This is probably related to the different environments the various children are exposed to.

In all of this it is important to question the validity of IQ tests. These are pencil and paper tests and when these tests were adjusted to allow the variations in lifes experience and socioeconomic factors included then the test scores change.When Black and white children were given tests that included the words,concepts etc. they were all familar with the IQ tests were almost even. Many tests are weighted towards white children since they reflect more of what they have been exposed to.

A surprise finding has been then discovery that when Chinese-American scores were reviewed and more recent tests were used (vs. the previous 1950s')the scores were lower for the Chinese then the Americans! However, it was discovered that due to hard work and efforts the Chinese with a lower IQ did as well in real life as their counterparts. A Chinese-American with an IQ of 90 does as well as an American with an IQ of 97.

Over the past 20 years in the USA the average black childs IQ has risen about 7 points ,probably due to better schools, and perhaps family values. There is probably no significant difference in one race being smarter then another. Recently,it has been shown that the earlier a child is taken into an adoption (regardless of race), or even a Foster home the higher the IQ (up to 10 points difference) relative to those that remain in an orphanage. The earlier they are removed the more IQ difference. However, both of these groups are below those raised from birth in a biological family. This reflects the advantage of a good nurturing environment on IQ.

Another series of studies has shown that being attractive to others is an evolutionary advantage. This "beauty" quality tells others that you are healthy, and probably smart and would be a good partner. The criteria of beauty is symmetry in the face and other body parts. This appears to be true of many species besides humans. It has been shown that attractive people do score higher on general intelligence tests (called "g") then less attractive people. Graduates of college do better (financially) then the less attractive. Politicians who are attractive are most often chosen by voters. The appearance of beauty is an unfakeable signal as a marker for good genes.

The brain is like a muscle,it needs practice and effort to improve. IQ measures not just the quality of a persons mind but also the quality of the environment that person is exposed to.

It is probably true that genetics can give us an advantage in intelligence depending on the luck of our getting the right genes. However, the actual use of this at any level of IQ is also related to our environment and emotional ability and desire to learn.

Reprogramming the cell

2007-12-03T17:48:00.000-08:00

There are different ways to "reprogram" a cell. One is to take the nucleus from body cells and put it in an unfertilized egg cell (Cloning) . Now you have a way to create a new but identical clone to the donor of the nucleus. This is called somatic cell nuclear transfer. The mystery is how a oocyte cell can take an adult cell nucleus and reprogram the DNA to become a multipurpose stem cell that can develop into all the many types of cells needed for a new organism.

A second way is to take a body cell and order it to turn into a stem cell using a set of molecular instructions. A stem cell has the potential to become any type cell in the body. The trick is to persuade such cells to forget what they are but recall what they came from. All specialized cells were at one time a stem cell and had the potential to become any cell type when mature.

What determines what a stem cell will become is the way its genes are expressed. All the cells in a persons body have the same genes but differ in the activity chosen. This activity of the genes is determined by transcription factors which are the products of genes. Extra copies of four genes were discovered that would allow this to occur. The same sets work in humans. This allows the organ cell to become an embryonic stem cell. The new cells were able to become heart,brain or any other type. These are called induced pluripotent cells. It is also possible to actually turn one cell type (fibroblast) into another (neurons).

The latest method is to take synthetic RNA molecules (avoids attack by immune system)that will reprogram the cell much faster and the RNA will then breakdown so the new cells are identical to the original. By inserting a synthetic RNA that codes for a key gene in muscle into a fibroblast you can produce a new muscle cell.

When the reprogrammed cells (now stem) were allow to grow and reproduce they formed three layers ,just like an embryo. Each layer is responsible for different types of tissue production.

Recently it has been discovered that three molecules added to a stem cell allows it to stay undifferentiated . This allows the cell to be able to go in any tissue direction. Certain genes that have been mutated can be added to the stem cell and the results in the mature cell (bone,heart,liver etc.) can be evaluated. This will be an important research tool.

The problem was the use of a virus to do this procedure. This created the risk of disease in the future. The RNA method has avoided this problem.

Silence of the genes

2007-11-30T21:38:00.000-08:00

All live birth animals receive two sets of genes,one from mom and one from dad. This is important since if one gene fails to act the other can carry on the function. Unfortunately, our everyday lives allow mutations to occur and one (and sometimes both) genes may be altered.

It is thought that part of the longevity in women and men is the fact that women have two X chromosomes and therefore a mutation on a gene in this region less drastic then if only one gene available.

If we have two sets our chances of maintaining the function of the gene is high. If we only had one then it could be lost. It is now known that at least 200 genes passed on may only have one active member of the pair. It seems a large number of genes may be "silent" and allow us to be suceptable to many diseases if the one active gene is damaged. Many of these silent genes are found in the region of chromosomes related to obesity,cancer,diabetes etc. The genes are "imprinted" by molecular signals and may silence the activity of the gene. Even paired genes can be imprinted by environmental factors.(See genes have expression).

Some women have the BRCA1 mutated gene.This gene inactivates another gene,PTEN, whose job is to produce a protein that stops the growth of cancer cells. Without this the woman has a high chance of developing aggressive breast cancer at an early age. If there were a normal (nonmutated) BRCA1 then the PTEN gene would not be supressed.

We know that many environmental factors effect the action of genes such as certain diets or even early parenting as well as radiation,toxins etc. (see the blogs on epigenes). These single genes are likely to be more easily effected by these environmental factors. If a cancer supressing gene is silenced and its partner is altered then cancer may be more frequent.

It is known that mice can be protected from cancer by manipulating certain genes that produce a protein ,Par 4,that destroys cancer cells exclusively. By manipulating the genes a high level of par 4 can be produced. If the genes for this protein are silenced then the mouse is very suceptable to cancer .

Our actions are often deeper then we think

2007-08-02T19:00:00.000-07:00

Over the many years evolution has been adding layers of our brain allowing our ability to think and reason. However, the more primitive early developed areas are still present and active. These areas allow for quick almost reflex reaction to our environment and are protective. The so called "Reptilian" brain is an example and is deep beneath the cortex. This area of the brain will make many decisions and instigate actions without any communication to our conscious brain.

The area of the brain called the Ventral Palladium is one of the key sites of these activities. This area is very active and acts independently and offers and initiates behavior as to what to do next in almost all situations. Some of these actions are modified by our cortex area but often the action will commence directly from the VP area alone. It appears we often have a "bottom up" decision path. Since these are unconscious to us we cannot modify them and they have a life of their own.

Many experiments have shown these various unconscious actions by individuals that they were unaware of and the VP showed increased activity. The early brain was developed to respond quickly to perceived stimuli in the environment and it was much later that the layers of the neobrain developed that allows our ability to reason and evaluate an action.

Designer drugs

2007-06-20T08:33:00.000-07:00

It is a source of frustration for both doctor and depressed patients when various drugs cause no change in the patients illness. Multiple trying of various classes of drugs is expensive and can cause side effects.

It has now been discovered that the many possible varitions in the actual functions of neurotransmitters in the brain can be altered by genetic differences. These transmitters are the key to allow certain antideprssent drugs to be effective. There is a big diference in treatment choice of drugs if one has low serotonin or if norepinephrine or dopamine is low. All defects have one thing in common, they all show signs of depression in the patient.

The differences in patients can be determined by genetic defects in the gene that determines the production of a protein for brain derived neurotrophic factor,which is esssential for the health of brain neurons. Patients with this defect will not respond to sertonin type drugs which require this protein to function.

Also, drugs are metabolized by certain genetically controlled enzymes and if these genes are deficient in their function the drugs can increase to a high level and cause serious side effects.

Ion channels are proteins that allow the flow of electricly charged salt particles (ions) across the pores in the nerve cell membrane. The opening and closing of these channels allow the cell to fire off bursts of electrical activity. A built in voltmeter (sensor)opens the channel when the nerve is ready to fire. A part of the volt sensor is called the "paddle'(shape). This can be blocked from functioning by certain toxins (tarantula,sea aneome)and stop the nerve cells activity. Ion channels are involved in malfunction in epilipsy,parkinsons,chronic pain and other diseases.By evaluating these sensors new drugs may become available to reverse the malfunction that may be part of the disease process.

It is hoped that soon blood tests can show which patient should take which drug and how much. Individualized for that patients genetic map.

The programs of our DNA are very complex

2007-06-16T17:45:00.000-07:00

The original idea of all DNA changes, and therefore phenotype or organ changes,was thought to be due to mutations. These were radioactive,chemical,toxic and other out side influences. Thes changes do happen but are probably not nearly as important as the programming of epigenes and microRNA.

Previous blogs discuss the histone proteins lying next to the genes and how they are important software to tell genes when and what to do. The importance is the transmision of information that does not change the gene itself. However,the genes actions are changed.

RNA has been thought to only be a messenger to the genes. The genetic instructions are passed on to the RNA molecule which then goes to the protein "factory" of the cell and allows the proper protein to be made that will cause an affect. We now know that the RNA is much more then this. Many thousands of different RNA's are produced and they are made up of less then 25 sequenced nucleotides. These microRNA (MiRNA) are single strands of short length and are encoded by genes transcribed from DNA but not translated into protein (non coding RNA).They also can regulate genes actions or expression. It is thought that MiRNA may regulate the protein encoding behavior of over 1/3 of our genes. These "fine tune" the genes expression .

It was a surprise to many that we complex humans have almost the same number of genes as do worms and flies. Now we think the big difference is the amount and diversity of the MiRNA. A single MiRNA may regulate the activity of hundreds of genes. The genes involved in a chimpanzee brain and a human are almost the same. However, there is an 8% difference in the MiRNA between the two. This shows that evolution is very dependent on changes in the genes to encode MiRNA as well as those for encoding proteins. An example might be that a gene for a color and this color could be expressed as a light brown or a dark brown or even a tan color. The MiRNA would fine tune this so that the color would be a consistent one among all the animals possessing this MiRNA.

Moss,lichen,plants all have MiRNA materials.These developed as life became more complex and varied. MiRNA may have developed as a defense against viruses since they are able to attack the virus genetic material in the cell and deactivate it. These MiRNA are called interference (MiRNAi)since they can stop the function of various genes without affecting the gene itself. They are able to attack a messenger RNA and strip it down so it cannot function and therefore stops the gene expression. An example was an overeating strain of mice given a MiRNAi that chokes off an insulin receptor gene in the animal so that the calories were not stored as fat but were excreted and the weight decreased and the life span increased by 20%. A soybean causes allergies by a certain protein produced and a MiRNAi that blocks the production of this protein allows a allergy free bean.

If a gene in mice that regulates a specific MiRNA that regulates the immune system by allowing cytokines to be made is removed. Then these chemicals that normally pass to the various complicated cells of the immune system and allow them to communicate is lost. Without this ability the mice has a weak immune system and can't develop immunity to infections. Over 150 genes appear to be involved and are regulated by this one MiRNA.

It appears that these MiRNA and MiRNAi genes are passed on to the next generation by "hitching a ride" on a sex chromosome gene.

Again, the software or operating system that controls the genes is becoming more complex as we learn more of the amazing living cell.

Exercise your heart,Exercise your Brain.

2007-06-01T10:17:00.000-07:00

It is widely understood that to have better cardiovascular health you need to exercise, to be a musician you must practice and all acquired skills can be achieved by persistent practice. This involves the Brain coordinating with the other body parts and includes changes in the various organ systems (muscles,bones) as well as opening new or enhancing older neurocircuits ("wiring").

Mental traits are habits of thinking and feelings that are manifest in our everyday activities. The normal,untrained mind , has short bursts of activities but is constantly dealing with lots of impulses or "noise". Although we do focus, it is usually for short times, and rarely on only one thing. We are all used to the more intellectual training of the brain with learning to read,math,and other academic subjects. We understand these and other skills require practice and training of the mind just as runners require conditioning of other organ systems.

It is a known fact that neuroplasticity can occur throughout our lives. This is true at birth and at older ages. The action must be a focused and ongoing learning of new skills to allow this to occur.

For many years the Buddhist monks have recognized that other ,more subtle,areas of the brain can be trained and therefore the mind changed. The practice of meditation is not a tool to just relax from stress but is a rigorous ongoing discipline in which the mind observes itself. A part of this , shamatha,is to quiet the constant noise of the mind (Trillions of cells) and replace this with stable attention to one thing. This gives clarity to focus on one object or thing with the full attention of the mind. Compassionate meditation is focused on love for all beings and total compassion for all living things. This is the type of meditation that the subjects in this study performed.

Many monks have spent thousands of hours and many years in this practice. They have been studied with MRI,PET,and EEG. The results are fascinating.

Neuroscientis want to discover whether emotional states such as joy,compassion,happiness and love for others can be influenced in an individual by brain changing practice.

One of the first discoveries was that we all have various levels of normal activity in our pre-frontal cortex (PFC) and this is assymetrical with more activity on the Left or Right side. It has been found that when one has more activity on the Left PFC the person is overall more optimistic,joyful,compassionate and overall "happy". The opposite for the Right side activity. In fact, a shift to the Right is a clue to upcoming depression. Studies of thousands of people has resulted in the conclusion that we all have a baseline of happiness,some greater then others. Although this level can change(Marriage,financial gain,death of a loved one) the result is that the overall level will go back to the baseline of the individual after a short time. The activity of the PFC is constant in adults but varies over short times in children with the most activity shifting from Right to Left. This fits with the proven concept that the brain is a "plastic" organ,especially in childhood. This may be related to the volatile moods we see in children and teens.

It should be remembered that these "normal" studies were actually a "baseline" of the emotional activity. Analogous would be studying only "couch potatoes" to establish the baseline of pulse,BP and other markers of cardiac function. No trained brains were studied.

Although the PFC is a thinking area of the brain it has strong neural connections to the Amygdala which is the "emotion" area of the brain. The PFC is suceptable to outside influences and certain stimuli will affect its activity. It is also shown that these can also affect the amygdala due to the many neural connections. The idea is that by training the thinking brain we could also affect the emotional brain.

Studies of the meditation trained monks revealed that they have a very strong Left PFC activity and as they meditate this activity is stronger then any normal measured.During meditation the activity on the Left went "off the chart". Also, the production of gamma wave energy was very high vs. normals. This wave is asociated with positive "aha" or "I now get it all" feelings. Although this wave was highest during meditation it remained very strong when they were not meditating. There was a linear relationship between the hours spent in meditation practice and the level of gamma activity. It appears that the positive emotions during the meditation can be carried over to the everyday. This would be consistent with a "consciousness change' that the Buddhists have claimed can occur.

Even beginners in compassionate meditation ,who were studied, began to show some changes in their gamma activity after a few weeks of practice. Again, training the brain is able to change the emotional mind.

It appears that the normal aging process allows some of the results as one would get with many hours of meditation. As we normally age, we appear to have more joy in our lives. The prefrontal areas become more active for positive rather then negative thoughts. The amygalada does not react to negative emotions like a younger person but will react more to positive emotions. It may be that the brain has learned that time is short and letting go of the negative is a positive.

It was also shown that the assymetry of activity in the PFC is associated with social perceptions of prejudice,discrimination against others and acceptance of violence against those we perceive as different from us. Perhaps the path to world peace is through training our brains so we can change our minds to actually love and have compassion for all others.