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Author Topic: How big a role does the epigenome play in evolution?  (Read 56252 times)

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #125 on: 16/04/2010 02:35:50 »
What about the progeny possibly receiving the environmental information from both parents, and using that combination to possibly determine it's own changes at the initial moment of conception?  So instead of the parent "deciding" the mutation, it would be the progeny itself.

Ah well em, how would the progeny receive that environmental information? As far as I know, the only thing that happens during conception is the combination of the parents' DNA.

Also, with humans at least, I understand that all of the mother's eggs were produced while the mother was still an embryo, so it's hard for me to imagine how any environmental information could be communicated from the mother. 
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #126 on: 16/04/2010 04:06:56 »
What about the progeny possibly receiving the environmental information from both parents, and using that combination to possibly determine it's own changes at the initial moment of conception?  So instead of the parent "deciding" the mutation, it would be the progeny itself.

Ah well em, how would the progeny receive that environmental information? As far as I know, the only thing that happens during conception is the combination of the parents' DNA.

Also, with humans at least, I understand that all of the mother's eggs were produced while the mother was still an embryo, so it's hard for me to imagine how any environmental information could be communicated from the mother. 

But it has been proven that environmental information is passed on, that is kinda the point behind epigenetics.  After enough generations without the factor which stimulated the epigenetic trait to begin with then the organisms revert, but it is now an established fact that information is passed epigenetically to offspring for a minimum of several generations.
 

Offline PhysBang

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Re: How big a role does the epigenome play in evolution?
« Reply #127 on: 16/04/2010 04:43:22 »
Ah well em, how would the progeny receive that environmental information? As far as I know, the only thing that happens during conception is the combination of the parents' DNA.
In many animals, there is also a significant biological component from the mother. This includes not only the machinery required for life, but also a collection of proteins that can signal developmental changes.

Grasshoppers in North America have been known to pass on radical changes brought about by the environment to their offspring.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #128 on: 16/04/2010 05:29:38 »
Grasshoppers in North America have been known to pass on radical changes brought about by the environment to their offspring.

That's interesting. Is there any evidence that their genome was altered?
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #129 on: 16/04/2010 05:52:22 »
Grasshoppers in North America have been known to pass on radical changes brought about by the environment to their offspring.

That's interesting. Is there any evidence that their genome was altered?

If it was environmental that would mean it was epigenomic, not genomic change.

If you read the article by Time magazine I posted earlier it cites several examples of epigenomic changes being passed on to offspring.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #130 on: 16/04/2010 06:11:39 »
I'm reasonably sure I passed my genes on to my offspring. I was also able to pass on other things that had little to do with my genes. (You can ask them if you don't believe me.)

Are you trying to prove something, or disprove something?

It might help if you would be good enough to describe your theory is some detail.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #131 on: 16/04/2010 06:31:52 »
I'm reasonably sure I passed my genes on to my offspring. I was also able to pass on other things that had little to do with my genes. (You can ask them if you don't believe me.)

Are you trying to prove something, or disprove something?

It might help if you would be good enough to describe your theory is some detail.

At least for this last post, I wasn't trying to prove anything or present any theory.  You seemed to be saying that epigenomic information does not get passed to offspring, that is counter to the science of epigenetics which is already proven.  I have presented the links if you are unfamiliar with that aspect of the science, but at least this part of what I have suggested on this thread is already proven science.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #132 on: 16/04/2010 08:13:05 »
that is counter to the science of epigenetics which is already proven. 

Well, no. I do not think that is quite right.

Epigenetics is all about how an organism interprets (expresses) its genes. It receives its genes from its parents. Lots of things may influence how an organism interprets its genes.

Epigenetics is real enough, but it did not eliminate genetic inheritance.
 

Offline PhysBang

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Re: How big a role does the epigenome play in evolution?
« Reply #133 on: 16/04/2010 15:34:47 »
Grasshoppers in North America have been known to pass on radical changes brought about by the environment to their offspring.

That's interesting. Is there any evidence that their genome was altered?
No, there seems to be no change to their genome at all. And generations later, when the environmental conditions change, the grasshoppers change their morphology back to the previous morphology. These are the "locust" species of grasshopers.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #134 on: 16/04/2010 17:14:13 »
that is counter to the science of epigenetics which is already proven. 

Well, no. I do not think that is quite right.

Epigenetics is all about how an organism interprets (expresses) its genes. It receives its genes from its parents. Lots of things may influence how an organism interprets its genes.

Epigenetics is real enough, but it did not eliminate genetic inheritance.

I think there is some confusion here.  I am not saying it eliminates genetic inheritance in any way.  What I am saying is that epigenetic information is in fact passed on to offspring, which has been proven.  If you feel epigenetic information is not passed to offspring, then that is counter to the proven science.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #135 on: 16/04/2010 19:24:38 »
that is counter to the science of epigenetics which is already proven. 

Well, no. I do not think that is quite right.

Epigenetics is all about how an organism interprets (expresses) its genes. It receives its genes from its parents. Lots of things may influence how an organism interprets its genes.

Epigenetics is real enough, but it did not eliminate genetic inheritance.

I think there is some confusion here.  I am not saying it eliminates genetic inheritance in any way.  What I am saying is that epigenetic information is in fact passed on to offspring, which has been proven.  If you feel epigenetic information is not passed to offspring, then that is counter to the proven science.

The epigenetic information is contained within the DNA that is passed to the offspring.

 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #136 on: 16/04/2010 19:42:00 »
I assume when you say DNA you are referring to the whole package, not just the genome itself?  But I think some people may not realize that DNA is not just the genome, actually the genome itself is merely a fraction of what makes up DNA.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #137 on: 16/04/2010 20:35:56 »

Example of epigenetic (which regulates gene expression) making permenet changes

Quote from: http://www.highlighthealth.com/research/irreversible-gene-expression-changes-from-smoking/
Recent research published in the online open journal BMC Genomics shows that smoking leads to changes in gene expression, some of which are reversible and some of which are permanent.

mutation may not be required?

Gene expression is about how genes may, or may not, affect the development of a biological entity. In other words, an entity may interpret its genes in many ways based on external factors (like smoking for example).

That does not mean that the entity has altered its genes in any way.

We all have genes. I don't think I can alter mine. Can you explain how you can alter yours?

I can't alter my genes, mutation of genes(to the best of my knowledge) can only occur at conception.

But in reading http://www.thenakedscientists.com/HTML/articles/article/the-ion-channel-through-the-keyhole/ I had a thought on how an epigenomic element could "choose" a mutation.

According to the article, cells have "ion channels" and some of those channels can select to allow only a specific ion to pass through. 

Could it be that the same mechanism, which is used to allow only a specific ion to pass through, be used to allow only a specific base to attach to another when the initial DNA strand is forming?  Couldn't this then be used by an organism to specify only one possible mutation, which had been previously determined to be necessary?
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #138 on: 16/04/2010 20:38:38 »
I assume when you say DNA you are referring to the whole package, not just the genome itself?  But I think some people may not realize that DNA is not just the genome, actually the genome itself is merely a fraction of what makes up DNA.

I don't think that's quite right. The genome contains the entire coded sequence, so all information is passed on by the genome.

Perhaps you mean that only a very small part of the sequence is used to encode protein? That is certainly true. There is a lot of coding in the genome that is not well understood.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #139 on: 16/04/2010 22:03:10 »
I assume when you say DNA you are referring to the whole package, not just the genome itself?  But I think some people may not realize that DNA is not just the genome, actually the genome itself is merely a fraction of what makes up DNA.

I don't think that's quite right. The genome contains the entire coded sequence, so all information is passed on by the genome.

Perhaps you mean that only a very small part of the sequence is used to encode protein? That is certainly true. There is a lot of coding in the genome that is not well understood.

The genome contains all the codons for the genes, but is surrounded by what was previously considered junk DNA but we have since learned is actually crucial, and we call it epigenomic markers.  This "junk" DNA represents the vast majority of what we call the DNA strand, with the specific gene codons only being a small fraction of the full strand.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #140 on: 16/04/2010 22:36:40 »
The genome contains all the codons for the genes, but is surrounded by what was previously considered junk DNA but we have since learned is actually crucial, and we call it epigenomic markers.  This "junk" DNA represents the vast majority of what we call the DNA strand, with the specific gene codons only being a small fraction of the full strand.

"In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding DNA varies greatly between species"

From http://en.wikipedia.org/wiki/Noncoding_DNA

The genome is not surrounded by noncoding DNA (junk DNA). The genome contains the entire sequence including the noncoding DNA. There is only one thing - the genome.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #141 on: 16/04/2010 22:53:32 »
The genome contains all the codons for the genes, but is surrounded by what was previously considered junk DNA but we have since learned is actually crucial, and we call it epigenomic markers.  This "junk" DNA represents the vast majority of what we call the DNA strand, with the specific gene codons only being a small fraction of the full strand.

"In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding DNA varies greatly between species"

From http://en.wikipedia.org/wiki/Noncoding_DNA

The genome is not surrounded by noncoding DNA (junk DNA). The genome contains the entire sequence including the noncoding DNA. There is only one thing - the genome.

Perhaps I was mistaken, I was under the impression that genome referred only to the specific codons which we know as genes.

But it has also been recently shown that non-coding DNA still has a "function".  I believe I posted evidence for this on the turtle/intelligent design post.

However, by definition, the epigenome is outside of the genome; and since it is certainly carried over to offspring there must be more than just the genome.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #142 on: 17/04/2010 00:24:36 »
Yes - some of the noncoding DNA in the genome does seem to have functions.

However, the only thing that is inherited is the genome. The epigenome is a mechanism that controls gene expression in response to chemical signals.

 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #143 on: 17/04/2010 00:34:16 »
Yes - some of the noncoding DNA in the genome does seem to have functions.

However, the only thing that is inherited is the genome. The epigenome is a mechanism that controls gene expression in response to chemical signals.



That is incorrect, the epigenome is inherited as well.  That is why epigenetic mutations persist even after the element which stimulated them is removed, for several generations.

See the Time magazine article which I linked before, or just google epigenetics; it has been proven that the epigenome is also inherited.
 

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Re: How big a role does the epigenome play in evolution?
« Reply #144 on: 17/04/2010 01:06:12 »
Yes - some of the noncoding DNA in the genome does seem to have functions.

However, the only thing that is inherited is the genome. The epigenome is a mechanism that controls gene expression in response to chemical signals.



That is incorrect, the epigenome is inherited as well.  That is why epigenetic mutations persist even after the element which stimulated them is removed, for several generations.

See the Time magazine article which I linked before, or just google epigenetics; it has been proven that the epigenome is also inherited.

Ooooo! I see what you mean. If I understand it correctly, there is additional information being carried with the genome so that an environmental effect that the parent experienced can be inherited without the child directly experiencing the effect.

Fascinating!
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #145 on: 17/04/2010 01:11:06 »
Yes - some of the noncoding DNA in the genome does seem to have functions.

However, the only thing that is inherited is the genome. The epigenome is a mechanism that controls gene expression in response to chemical signals.



That is incorrect, the epigenome is inherited as well.  That is why epigenetic mutations persist even after the element which stimulated them is removed, for several generations.

See the Time magazine article which I linked before, or just google epigenetics; it has been proven that the epigenome is also inherited.

Ooooo! I see what you mean. If I understand it correctly, there is additional information being carried with the genome so that an environmental effect that the parent experienced can be inherited without the child directly experiencing the effect.

Fascinating!

You got it   :)
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #146 on: 17/04/2010 22:19:19 »
As this is reminiscent of the 19th century Lamarckian hypothesis of inheritance and evolution, I can understand why some have a mind block and cant except it, should they be loyal Darwinists. Carl Jung also received much critique for his idea that the collective unconscious has acquired traits over the millennia. Also I understand the actual word “intelligence” used in science makes most cringe.

The facts: Epigenetic influences can alter our gene profile and can be inherited. We have proof epigenetics can also influence change in our nervous system and in our brain. Multigenerational epigenetics, from both maternal and paternal factors is today is clearly regarded as another aspect to evolution and adaptation. “Our lifestyle can alter our gene profile”.

The idea that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called the histone code. Epigenetic changes of this type thus have the potential to direct increased frequencies of permanent genetic mutation.

As I mentioned previously, twins with identical DNA are influenced by their epigenetics.
Both twins having identical DNA but one twin’s lifestyle, location, epigenetic influence has flicked a gene switch causing only one twin to suffer from a genetic disease such as breast cancer, schizophrenia, autism, Alzheimer's, diabetes, alcoholism, or any other.

I have looked high and low and still can’t find a gene mutation that isn’t a disease or detrimental to our survival. Even sickle cell is a fatal disease.

Which brings me back to the Australian Tasmanian Devil.

Prior the DFTD, “The majority of devils in Tasmania were immunological clones and therefore susceptible to DFTD,” I believe this is described as genetic bottle neck.

When an individual is infected with DFTD cancer cells, their immune system doesn’t see the cancer cells as foreign because the cancer cells have the same MHC markers as they do.

The DFTD is a rare cancer which is believed to have come from a genetically modified version of native tree which has been planted in a mono culture style, near where the cancer initially affected the devils. Consintrated natural oils and so forth run off from the mono culture has affected the water supply and 3 people in that particular area out of 5 world wide also suffer from a rare cancer.

The DFTD is a cancer that is contagious. Only 3 cancers known in the world are contagious.

Since DFTD was first discovered several different strains of the cancer has been found. So the disease is mutating quickly by uncontrolled cell division. Yes it is an evolving disease that has evolved many times in just a short period and it is infectious and exceptionally rare.

Since DFTD outbreak over a decade ago, the Tassie Devil’s genes have become more diverse just over 3-5 generations which supports the idea that there may be some inherent resistance associated with these genetically different devils and which may have spurred on the devil’s evolution and could be epigenetic due to this disease.
.
Another fact is that Tasmanian devils are breeding early in response to the Devil Facial Tumor Disease (DFTD), scientists from the Save the Tasmanian Devil Program have discovered.

Researchers explain that this is the first known case of infectious disease leading to increased early reproduction in a mammal.

DFTD usually kills the devil 2-3 months after contracting the disease. 2 of the diseased animals successfully weaned their young before being overwhelmed by the cancer.

Now "The devils are under intense selection for early breeding because the disease is 100 per cent fatal. Any devil that’s successful in breeding more than once is putting out more of its genes into the pool of survivors." Now they have found a colony of devils that may have some type of immunity and a breeding program has been put in place.

So this is proof that evolution can happen within short periods of time and how epigenetics has control over our genes to change or evolve. All relevant links are posted previously.

So how about including the word "epigenetic" in the spell check, Please.

In regard to whether epigenetics evolved at some stage of our existence. My personal view is: Random mutation is not random just that we do not have the knowledge yet. Life doesn’t take vast periods of time to evolve. Epigenetics has always been involved in evolution even though the environment may change.
 

Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #147 on: 17/04/2010 22:56:51 »
I have looked high and low and still can’t find a gene mutation that isn’t a disease or detrimental to our survival. Even sickle cell is a fatal disease.
It's survival to breed that is important here.  Sickle cell anaemia may shorten your life, but if you're more likely to breed then that mutation is an evolutionary advantage.

Being immune to alzheimers would be beneficial to an individual, but evolutionarily wouldn't really be relevant.  Same goes for most late adulthood-onset diseases.

Some people are less susceptable to cancers - this is because of gene mutations (what do you define as "standard" vs "mutant"?).  Some are seemingly immune to HIV - same again, there's likely to be a genetic cause, and that will be a mutation, substitution, duplication or similar.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #148 on: 18/04/2010 00:41:48 »
As this is reminiscent of the 19th century Lamarckian hypothesis of inheritance and evolution, I can understand why some have a mind block and cant except it, should they be loyal Darwinists. Carl Jung also received much critique for his idea that the collective unconscious has acquired traits over the millennia. Also I understand the actual word “intelligence” used in science makes most cringe.

The facts: Epigenetic influences can alter our gene profile and can be inherited. We have proof epigenetics can also influence change in our nervous system and in our brain. Multigenerational epigenetics, from both maternal and paternal factors is today is clearly regarded as another aspect to evolution and adaptation. “Our lifestyle can alter our gene profile”.

The idea that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called the histone code. Epigenetic changes of this type thus have the potential to direct increased frequencies of permanent genetic mutation.

As I mentioned previously, twins with identical DNA are influenced by their epigenetics.
Both twins having identical DNA but one twin’s lifestyle, location, epigenetic influence has flicked a gene switch causing only one twin to suffer from a genetic disease such as breast cancer, schizophrenia, autism, Alzheimer's, diabetes, alcoholism, or any other.

I have looked high and low and still can’t find a gene mutation that isn’t a disease or detrimental to our survival. Even sickle cell is a fatal disease.

Which brings me back to the Australian Tasmanian Devil.

Prior the DFTD, “The majority of devils in Tasmania were immunological clones and therefore susceptible to DFTD,” I believe this is described as genetic bottle neck.

When an individual is infected with DFTD cancer cells, their immune system doesn’t see the cancer cells as foreign because the cancer cells have the same MHC markers as they do.

The DFTD is a rare cancer which is believed to have come from a genetically modified version of native tree which has been planted in a mono culture style, near where the cancer initially affected the devils. Consintrated natural oils and so forth run off from the mono culture has affected the water supply and 3 people in that particular area out of 5 world wide also suffer from a rare cancer.

The DFTD is a cancer that is contagious. Only 3 cancers known in the world are contagious.

Since DFTD was first discovered several different strains of the cancer has been found. So the disease is mutating quickly by uncontrolled cell division. Yes it is an evolving disease that has evolved many times in just a short period and it is infectious and exceptionally rare.

Since DFTD outbreak over a decade ago, the Tassie Devil’s genes have become more diverse just over 3-5 generations which supports the idea that there may be some inherent resistance associated with these genetically different devils and which may have spurred on the devil’s evolution and could be epigenetic due to this disease.
.
Another fact is that Tasmanian devils are breeding early in response to the Devil Facial Tumor Disease (DFTD), scientists from the Save the Tasmanian Devil Program have discovered.

Researchers explain that this is the first known case of infectious disease leading to increased early reproduction in a mammal.

DFTD usually kills the devil 2-3 months after contracting the disease. 2 of the diseased animals successfully weaned their young before being overwhelmed by the cancer.

Now "The devils are under intense selection for early breeding because the disease is 100 per cent fatal. Any devil that’s successful in breeding more than once is putting out more of its genes into the pool of survivors." Now they have found a colony of devils that may have some type of immunity and a breeding program has been put in place.

So this is proof that evolution can happen within short periods of time and how epigenetics has control over our genes to change or evolve. All relevant links are posted previously.

So how about including the word "epigenetic" in the spell check, Please.

In regard to whether epigenetics evolved at some stage of our existence. My personal view is: Random mutation is not random just that we do not have the knowledge yet. Life doesn’t take vast periods of time to evolve. Epigenetics has always been involved in evolution even though the environment may change.


Acording to the article from Time that Norcal posted, currently, there is no evidence that epigenetics directly affects the genome. The hereditary effects appear to be temporary.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #149 on: 18/04/2010 02:46:56 »
I've been thinking about it, and I think that we can actually pretty much guarantee epigenetics played a truly massive part in creating the diversity of life we see.  My basis for saying that is this:

First let's look at what we know:

1. Epigenetic mutations are not permanent changes to the genome.

2. Epigenetic mutations can happen very quickly.

3. Epigenetic mutations will continue as long as the element which stimulated it persists(plus a few generations for good measure)

So based on this, we can expect that many life forms have been exposed to stressors which evoked an epigenetic response in the past.  As soon as any epigenetic trait begins to be expressed it is subject to natural selection.

Hypothetical: Mutation A(epigenetic) deals with Stressor B.  Stressor C is only slightly dealt with by Mutation A.  Mutation A + Mutation D(genetic) can deal with Stressor C.  At this point, Stressor B can disappear and Mutation A will still remain because it has become something more through natural selection.

Since epigenetic mutations are both specific responses to environmental conditions and much faster than genetic mutations, and subject to natural selection as anything else it is clear they probably play a huge part in the diversity of life.

I know this doesn't prove that epigenetics could "choose" mutation, but since the epigenome is subject to natural selection; then simply by mutating, life is providing or choosing a route for natural selection to work on.
 

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Re: How big a role does the epigenome play in evolution?
« Reply #149 on: 18/04/2010 02:46:56 »

 

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