How big a role does the epigenome play in evolution?

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #100 on: 14/04/2010 06:28:43 »
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #101 on: 14/04/2010 07:18:42 »
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.
1) Sickle cell anemia. is a genetic disease. Not beneficial
2) Bacterial resistance to antibiotics, well cant see how that is beneficial?
« Last Edit: 14/04/2010 07:33:27 by echochartruse »
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #102 on: 14/04/2010 07:31:09 »
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.
1) Sickle cell anemia. is a genetic disease. Not benefitial
2) Bacterial resistance to antibiotics, well cant see how that is benefitial?
1) It's beneficial when you tend to die young from malaria and it protects against that. 
2) It sure is beneficial for the bacteria!  (Not so much for us).

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #103 on: 14/04/2010 07:46:20 »
1) It's beneficial when you tend to die young from malaria and it protects against that. 
2) It sure is beneficial for the bacteria!  (Not so much for us).
1) It's beneficial when you tend to die young from malaria and it protects against that. -One or another way its not beneficial to our servival or evolution.
2) It sure is beneficial for the bacteria!  (Not so much for us)

This makes me wonder, Could bacteria have this intelligents we are looking for?
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Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #104 on: 14/04/2010 08:48:07 »
Sickle cell anaemia certainly is beneficial to survival, but only in certain conditions.

Bacteria developing resistance to antibiotics is entirely reactionary - there's no way it could be considered to be intelligent.

(by the way, its spelled "intelligence")

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #105 on: 14/04/2010 17:41:23 »
Thanks for the links Echo and Norcal (I hope you don't mind my abbreviations.)

I don't think there is any doubt that there are a great many factors involved in the development of living organisms. Genes provide a sort of underlying fabric, but there are many other factors at play. For example, just because my genes indicate that I am predisposed to develop a certain disease, it does to mean that I ever will develop that disease. It just means that I have a higher probability of developing that disease.

Let me take a shot at stating the question we are (perhaps) trying to answer.

"Can factors that affect my life directly alter the genes that I pass on to my progeny, or are the genes that I pass on to my progeny simply determined by the genes that I inherited from my parents, plus or minus some random transcription errors?"

That's probably a bit of an oversimplification of course, because I know that I really could mess up the genes that I pass on if I was exposed to a lot of radiation for example, but the effect would still be random rather than directed.

Anyway, is that an approximation for the question?

Yes, that is an approximation for the question.

Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

Sorry, but you cannot simply state that.  Nobody knows more than a fraction of what there is to know about epigenetics, so we are very far from being able to say for sure what it can or cannot do.  You are free to not believe it is capable of it, but a flat statement that it cannot is not possible at this point in time.

Check out this article from Time magazine: http://www.time.com/time/health/article/0,8599,1951968-2,00.html

As they state, many scientists are taking a new look at Lamarckian evolution.  It's not like what we are talking about here has no credibility among legitimate scientists, this actually is a boon for the evolution argument against creationism.  All the examples that creationists try to twist, and popular evolution theory can't quite answer, are answered by this... all without "god".

I'm not sure how you can still assert that there is absolutely no evidence of epigenetically driven genetic mutation, I could understand if you had simply said that you don't feel there is enough evidence(although I disagree obviously), but to simply say there is no evidence at all?

If you are merely stating that it hasn't been proven yet, then I would have to ask how you feel about the standard model of physics?  It hasn't been proven, it has made predictions which have occurred and therefore has gained merit, but it still isn't proven.

Evolution driven by epigenomic markers certainly hasn't been proven, nor does it have as many years or predictions as the standard model has behind its belt; but it does make predictions, and those predictions have been proven.

There are other mechanisms for quick change.  There is also reason enough for me to think (based on my understanding of the subject) that epigenetic induced genetic mutation should occur faster than the observed rates, even when mutation appears to occur faster than expected.  There are proposed non-epigenetic models that do fit this date.  There is also no evidence, based on the way epigenetics works, that it can induce genetic mutations. 

The comparison to the standard model is also flawed.  The standard model predicts the probabilities of seeing certain things when you do certain experiments.  This has been very successfully tested.  As far as I know, and in your arguments here, the prediction made by epigenetics is simply "faster mutations," although it's also missing the step of how it causes those mutations.  There are other explanations for faster mutations that do include that step, so why favor epigenetics?  Have there been any simulations comparing epigenetic mutation to these other explanations that come out favoring epigenetics?

I'm really not sure why you still think there is no evidence based on the way epigenetics works that it could induce genetic mutations.  From one of the links I posted:

Quote
The movement of insertion elements can be responsive to environmental conditions. Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements. Some conjugative plasmids can recombine with their host's chromosome, and may acquire chromosomal genes that could then spread through the population and even to other species.


From the description of "insertion elements" we know they are talking about epigenomes.  Right here it says the "how" of at least one way of "inducing" mutation.

When you say you think it should be even faster than the evidence shows, it seems to me you are ignoring the big picture.  If large mutations were "allowed" to happen any faster than they do, a species would be in great danger of severely limiting the breeding population.  If too many new species emerged too quickly, they would not have a great enough population for reproduction.  Even still, with the evolution of plasmids capable of "spreading" a beneficial mutation throughout a local population allows for relatively quick evolution.

In order to "see" the difference in rates of evolution with or without epigenomes we have to look at the fossil record.  Presumably, the farther back we go in the record, the simpler life should be.  If we go back far enough, we should be able to see life which did not have epigenomes to help them.  This is why I keep raising the point about the absolutely massive increase in evolution we can see in the fossil record.  It is pretty obvious that something changed about 750 million years ago, and the discovery of epigenetics seems to me to be by far the best answer. 

Can you think of a different/better reason for such discordant rates of evolution in the fossil record?

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #106 on: 14/04/2010 23:18:42 »
Sickle cell anaemia certainly is beneficial to survival, but only in certain conditions.
What are these conditions please?
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #107 on: 15/04/2010 02:12:41 »
Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

Sorry, but you cannot simply state that.  Nobody knows more than a fraction of what there is to know about epigenetics, so we are very far from being able to say for sure what it can or cannot do.  You are free to not believe it is capable of it, but a flat statement that it cannot is not possible at this point in time.

This has basically come down to an argument rather than a debate on the science.  I say there isn't direct evidence to support your position.  You say there is enough indirect evidence to support it and not evidence against it.  Neither of us are experts in the field, nor are we likely to change our opinions, so until an expert stops by to offer an opinion, I don't think this is worth arguing further.  We're just arguing ourselves in circles here.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #108 on: 15/04/2010 02:43:21 »
... so until an expert stops by to offer an opinion, I don't think this is worth arguing further.  We're just arguing ourselves in circles here.

Quote from:  http://www.docstoc.com/docs/22610547/differential-gene-expression/
Differentiation results from different gene expression.
All cells from the same organism have the same DNA but not all genes are expressed (turned on or off)
Differential gene expression is not a result of differential loss of genetic material.
A single cell has half the genome from each parent............This is demonstrated by the fact that fully differentiated cell types are still capable, with the right environment of giving rise to an entire new animal.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #109 on: 15/04/2010 02:51:01 »
I have not had any evidence here that mutating genes is of any advantage to evolution
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #110 on: 15/04/2010 03:16:50 »

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?
« Last Edit: 15/04/2010 03:18:39 by echochartruse »
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #111 on: 15/04/2010 04:25:37 »

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?
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #112 on: 15/04/2010 04:42:06 »

Example of epigenetic (which regulates gene expression) making permanent 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?
DNA changes little over all species.
The proof is that mutation is not necessary for permanent gene expression.
'smoking leads to changes in gene expression, some of which are reversible and some of which are permanent. '
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #113 on: 15/04/2010 04:54:37 »
Smoking, drinking, poor nutrition all lead to permanent altered gene expression in fetus which can last their life time and inherited by their off spring and theirs, throughout many generations.
Possibly if this gene expression lasts for multiple generations, the gene may never be used for multiple generations, heh and if you don't use it you lose it, right!
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #114 on: 15/04/2010 06:04:53 »
heh and if you don't use it you lose it, right!

No, I think that is entirely wrong.

If you can explain how you are able to alter your genes I might change my opinion. How do you do that?
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #115 on: 15/04/2010 06:22:13 »
They say we have evolved being much taller than ancient generations but our genes have not altered.

Why do you insist that genes need to alter/mutate before we evolve?

We can change our genetic profile quickly and easily
« Last Edit: 15/04/2010 06:39:57 by echochartruse »
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #116 on: 15/04/2010 06:25:27 »

   Is Biological Evolution An Obsolete Technology - you may need to genetically engineer your genes. Is this our future?
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #117 on: 15/04/2010 07:07:31 »
They say we have evolved being much taller than ancient generations but our genes have not altered.

Why do you insist that genes need to alter/mutate before we evolve?

We can change our genetic profile quickly and easily

That is also incorrect. We have not altered our genetic profile. Our height is simply a function of external factors. Nutrition is dominant.

Do you have anything new to add?
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #118 on: 15/04/2010 07:12:54 »
Quote from:  http://www.tutorvista.com/topic/gene-chromosome-mutation
Mutation
Mutation is defined as a chemical change in the DNA structure of a gene. A difference of a single base in the DNA molecule or a single error in the reading of the code can cause a change in the amino acid sequence which leads to mutation. The chemical substances that i..

Chemical change to genes can be done by genetic engineering, gene therapy or by epigenetics to name a few.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #119 on: 15/04/2010 07:24:16 »
Quote from: http://www.cancer.gov/dictionary/?CdrID=561400

 genetic profile (jeh-NEH-tik PROH-file)

     Information about specific genes, including variations and gene expression, in an individual or in a certain type of tissue. A genetic profile may be used to help diagnose a disease or learn how the disease may progress or respond to treatment with drugs or radiation.


Epigentics alters/regulates/controls gene expression by adding and subtracting methyl tags.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #120 on: 15/04/2010 07:28:33 »
............We have not altered our genetic profile. .............

http://www.medicinenet.com/script/main/art.asp?articlekey=90341
change your lifestyle - change your genetic profile.


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Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #121 on: 15/04/2010 11:37:01 »
We have two simultaneous conversations going on here.  Norcalclimber is making some very good points about the young science of epigenetics, asking if there is any evidence that epigenetic factors can cause heritable changes in DNA.

Echochartruse - you are confusing the issue somewhat, and posting lots of replies in sequence makes it very difficult to respond.  I'll try to get through some of your points, though they may not be in sequence:

Sickle cell anaemia certainly is beneficial to survival, but only in certain conditions.
What are these conditions please?

High prevalence of malaria.  Those with sickle cell anaemia are less likely to die of malaria, and therefore more likely to survive to breeding age, therefore more likely to pass on the sickle cell genes.

Quote from:  http://www.tutorvista.com/topic/gene-chromosome-mutation
Mutation
Mutation is defined as a chemical change in the DNA structure of a gene. A difference of a single base in the DNA molecule or a single error in the reading of the code can cause a change in the amino acid sequence which leads to mutation. The chemical substances that i..

Chemical change to genes can be done by genetic engineering, gene therapy or by epigenetics to name a few.

Well, genetic engineering yes, (but not in a living organism); gene therapy no (it's about inserting extra genes so that cells make the gene products, which may fill a gap that the organism isn't filling); epigenetics - we don't know yet - largely it affects gene expression, rather than changes to genes.

............We have not altered our genetic profile. .............

http://www.medicinenet.com/script/main/art.asp?articlekey=90341
change your lifestyle - change your genetic profile.

A quote from your link:

"You can't get different genes, but how you act can change how your genes act, report Dean Ornish, MD, and colleagues at the University of California, San Francisco (UCSF)."

Changes in gene expression are not changes in DNA.  It's DNA that passes information to the next generation.  Changes in DNA are therefore essential for evolution.  Can epigenetic factors lead to heritable genetic changes?  We don't know yet, it's an interesting area of study.

They say we have evolved being much taller than ancient generations but our genes have not altered.

Why do you insist that genes need to alter/mutate before we evolve?

We can change our genetic profile quickly and easily

We say genes must have been altered for evolution because DNA is the heritable biochemical.  If every individual has identical genes, there will be no evolutionary change.

We can't change our "genetic profile" quickly and easily.  Some things cause DNA damage, but this is localised and often leads to cell death or cancers.  Children of smokers don't inherit lung cancer.


I have not had any evidence here that mutating genes is of any advantage to evolution
Well, in that case, I don't think you understand evolution.  Mutant versions of genes are the raw material for natural selection to work on.


Smoking, drinking, poor nutrition all lead to permanent altered gene expression in fetus which can last their life time and inherited by their off spring and theirs, throughout many generations.
Possibly if this gene expression lasts for multiple generations, the gene may never be used for multiple generations, heh and if you don't use it you lose it, right!
If you mean smoking, drinking etc while pregnant, then yes, this can have an impact on the foetus - but not a heritable one.  I think you've got the wrong end of the stick about genetics.


Right, here's a very stripped down explanation:

DNA contains your genes.  This is the thing that is passed down to the next generation.

DNA is transcribed by various methods into RNA/proteins...

These RNA molecules or proteins can tell the transcription factors to start/stop transcribing.

Therefore, things can change how many times a gene is transcribed, (gene expression) without altering the DNA.

So changes in gene expression are NOT changes in genes, or changes in DNA, and are therefore very unlikely to be heritable.


Sorry for the massive post...

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Offline PhysBang

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Re: How big a role does the epigenome play in evolution?
« Reply #122 on: 15/04/2010 15:56:50 »
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.
But over time, selection can work on a population to prefer those organisms that are undergoing a specific epigenetic change. This allows for mutation and variation to go on behind that epigenetic change, so to speak. If a genetic change "freezes" that epigenetic change in place, then we can see evolution that is guided by the epigenetics, in part, not simply the specific genes.

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Re: How big a role does the epigenome play in evolution?
« Reply #123 on: 15/04/2010 17:54:10 »
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.
But over time, selection can work on a population to prefer those organisms that are undergoing a specific epigenetic change. This allows for mutation and variation to go on behind that epigenetic change, so to speak. If a genetic change "freezes" that epigenetic change in place, then we can see evolution that is guided by the epigenetics, in part, not simply the specific genes.

Yes. I would agree with that. Many things influence evolution so I'm sure gene expression plays an important part.

The real question, I think, is whether or not a biological entity can direct particular changes in its own genes and pass that change on to its progeny.
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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #124 on: 15/04/2010 18:01:20 »
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.
But over time, selection can work on a population to prefer those organisms that are undergoing a specific epigenetic change. This allows for mutation and variation to go on behind that epigenetic change, so to speak. If a genetic change "freezes" that epigenetic change in place, then we can see evolution that is guided by the epigenetics, in part, not simply the specific genes.

Yes. I would agree with that. Many things influence evolution so I'm sure gene expression plays an important part.

The real question, I think, is whether or not a biological entity can direct particular changes in its own genes and pass that change on to its progeny.

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.

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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. 
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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.

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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.

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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?
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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.

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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.
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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.

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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.
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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.

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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.

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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.

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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.

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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?

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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.
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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.

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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.
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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.

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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.

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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!
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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   [:)]

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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.
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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.

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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.
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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.