How big a role does the epigenome play in evolution?

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Offline norcalclimber

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I recently mentioned this when it occurred to me in another topic, but I think it is worthy of its own.

Epigenomic markers seem to allow life to have a degree of control over its own DNA(stickleback fish, and possibly whales are examples of rather large changes brought about by epigenomic markers).  From what I have read, it is still unknown exactly how large or small a part epigenetics has played in macro-evolution.  If epigenomic markers actually allow life to direct mutation to any extent whatsoever, would that qualify as "intelligent design"?

From what I have read, life showed very little evolution over the first ~3.5 billion years it was here.  Then, roughly 750 million years ago, thousands if not millions of new, complex species emerged, and continued to evolve at a breakneck pace when compared with the first ~3.5 billion years of life. 

Could this be evidence that epigenomic markers which permitted some form of directed mutation even if very minor, in other words "intelligent design" first evolved ~750 million years ago?


Edit:  I am by no means referring to creationism or any sort of creator whatsoever.  I have changed the title question to avoid confusion.  The intelligent I was originally referring to is life in general, and individual organisms more specifically.  No omnipotent creator, no "design" by some master force, just a species evolving something because it needed it.
« Last Edit: 19/05/2010 02:05:41 by norcalclimber »

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #1 on: 22/03/2010 05:31:16 »
A couple of thoughts, although I'm not an expert in the area.

1) As I understand it from doing a little bit of Googling, epigenetics is basically akin to switching genes on or off in response to the environment, so the genes would already have to be in place to begin with.  If that's the case, then an individual wouldn't be able to spontaneously mutate new genes, only change how the existing genes work.  Therefore, an explosion of new species would probably still be due to more standard Darwinian evolution, wouldn't it?  Also, no one has seen epigenetic traits be passed on for more than a few generations from what I can tell, which would be required for it to contribute to making new species (although the field is in its infancy).

2) Using the phrase "intelligent design" might turn people off of discussing this idea, since that phrase is usually associated with an anti-science religious movement rather than legitimate science.  Also, epigenetics isn't limited to "intelligent" species, is it?  I imagine plants and microbes can also turn on or off genes in response to their environment.


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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #2 on: 22/03/2010 15:25:14 »
Epigenetics is akin to switching on or off genes, but there is more to it than that.  There are literally thousands of epigenomic markers for every gene.  We really have no idea the depth to which they affect the whole issue, epigenetics makes the human genome project look like child's play.  I have looked at lots of experiments which showed beneficial mutations, but the only ones I have been able to find, all have one thing in common.  They were all simply mutations of an existing metabolic pathway.  We also see over and over again in experiments, when the environment is stressed life evolves far quicker than we previously thought it could.  It is still unknown whether whales "lost their legs" due to epigenetics, but if so, all DNA could contain far more possibilities than we previously thought.

I assume by "standard Darwinian evolution" you mean with only random mutations, no control to it at all?  The problem with only random mutations, is that the mutation rates for life seems to have changed, and that's would imply a not so random element.  Plus, we know for a fact that life has found at least a small way to influence DNA(epigenomes).  Considering the track record of life, I seriously doubt better epigenetic controls did not evolve.

Using the term "intelligent design" might turn people off, but if they read the post they will see the context.  I use the term because it describes evolution by epigenetic mutation awfully well, and challenges preconceptions.  The discovery of epigenetics challenges a lot of our preconceived notions, predominantly the belief that the only way for DNA to change is through random mutations.  We know now, that many of the large, phenotypical changes may be epigenetic at heart.  Intelligent is a subjective word too, I believe all life has some level of intelligence, including plants, microbes, etc.

I recently watched "Was Darwin Wrong?" by Naked Science, and it further confirmed a lot of what I have been learning.  Watching it, I don't remember hearing the term "random mutation" even once.  At the end, they talked about epigenetics, and how we have learned that life is actually capable of "making" changes, and can evolve much faster than we previously thought.

With this knowledge in hand, the explosion of life ~750 million years ago, with rapid mutation since, seems awfully conspicuous.

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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #3 on: 22/03/2010 21:34:27 »
I agree with JP. The term "Intelligent Design" is loaded with many less than scientific connotations. Unless you subscribe to those concepts, it would be much better to avoid the use of the term.
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #4 on: 22/03/2010 23:49:21 »
From what I have read, life showed very little evolution over the first ~3.5 billion years it was here.  Then, roughly 750 million years ago, thousands if not millions of new, complex species emerged, and continued to evolve at a breakneck pace when compared with the first ~3.5 billion years of life. 

Could this be evidence that epigenomic markers which permitted some form of directed mutation even if very minor, in other words "intelligent design" first evolved ~750 million years ago?


Maybe we have not found any evidence from pre 750 million years ago, who knows.
I remember in another forum it was agreed that DNA only carried the information and that Mother Natured controlled it.

It is unfortunate that we try to humanise the process, even by calling it "intelligent Design" we do that but either way mutations occure for a reason. Some mutations from our environment are not all good and fortunately short lasting, some are good, such as larger nostrills for humid weather, larger brows to keep the sun out etc and these seem to be handed down the generations so there must be some type of intelligence about it.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #5 on: 23/03/2010 03:43:00 »
Quote
http://discovermagazine.com/2009/mar/02-evolution-by-intelligent-design “Based on what we know, the artificial chromosome is going to be the best way to modify the genome,” says Lee Silver, a professor of molecular biology and public policy at Princeton University. “Nature doesn’t care about individual children. Instead of rolling the dice, why don’t we take the dice and put them down in the way that parents think is best for their children.” He anticipates the development of specialized artificial chromosomes—a “good health” artificial chromosome, for instance—that could routinely be inserted into human embryos. “You could create a generic version that has lots of good genes like the ones known to protect against cancer, strokes, and heart disease,” Silver says.

Our Post-Darwinian Future
Pluripotent stem cells, gene targeting, and artificial chromosomes could leapfrog over evolution and let us take control of our genome, maybe even turn ourselves into a whole new species. “There is no scientific basis for thinking that we couldn’t,” Silver says. “There’s nothing really special about the human genome. There’s nothing that says this is the end.”.................
Evolution by Intelligent Design
Bioengineers will likely control the future of humans as a species.
by Jane Bosveld published in DISCOVER MAGAZINE From the March 2009 issue; published online February 2, 2009

I'm really counting on these scientists having more intelligents than mother nature.
« Last Edit: 23/03/2010 03:44:58 by echochartruse »
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Offline LeeE

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Re: How big a role does the epigenome play in evolution?
« Reply #6 on: 23/03/2010 16:47:16 »
The concept of 'Intelligent Design' seems to have clearly evolved from 'Creationism'.
...And its claws are as big as cups, and for some reason it's got a tremendous fear of stamps! And Mrs Doyle was telling me it's got magnets on its tail, so if you're made out of metal it can attach itself to you! And instead of a mouth it's got four arses!

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #7 on: 23/03/2010 22:34:36 »
The theory of “Intelligent Design” has been labeled Creationism by some.

Ronald Numbers, Historian of Science at University of Wisconsin, a critic of intelligent design agrees that the easiest way to discredit intelligent design is to associate it with creationism without actually addressing the merits of its case.

A couple of thoughts, although I'm not an expert in the area.

2) Using the phrase "intelligent design" might turn people off of discussing this idea, since that phrase is usually associated with an anti-science religious movement rather than legitimate science.  Also, epigenetics isn't limited to "intelligent" species, is it?  I imagine plants and microbes can also turn on or off genes in response to their environment.

Intelligent Stem Cell Culture Systems (ISCCS) – Just because we call it 'intelligent' do we label it 'creationism'?

Quote
  “Frist, a doctor who graduated from Harvard Medical School, said exposing children to both evolution and intelligent design "doesn't force any particular theory on anyone. I think in a pluralistic society that is the fairest way to go about education and training people for the future."
© 2010 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

Most cells in the human body are not human. They are microbial at a ratio of 10:1. More than 1,000 bacterial species live in us. Depending on the food source, our environment, soil, atmosphere, etc. Microbes may have either beneficial roles in maintaining life or undesirable roles in causing human, animals and plant disease. These microbes that live inside us (populate our bodies) determine our physiology and our health.  Without the co existence of these microbes and their ability to alter gene expression in specific host environments we would not survive.

"alter our gene expression"... darn intelligent microbes!
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #8 on: 24/03/2010 02:29:31 »

The theory of “Intelligent Design” has been labeled Creationism by some.


As far as I am aware, there is no theory of intelligent design. If there is such a theory it would be good to have that theory submitted to a peer review, and publish the results.
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #9 on: 24/03/2010 03:23:47 »
Could this be evidence that epigenomic markers which permitted some form of directed mutation even if very minor, in other words "intelligent design" first evolved ~750 million years ago?

It appears some are afraid to discuss this subject in fear that it could become a theory.

My thoughts are that the design was in place before anything evolved/mutated/adapted/altered or changed.

I'd like to hear your ideas
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #10 on: 24/03/2010 03:37:32 »
Gosh! You must have missed my latest post. Perhaps you would like to reply.
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #11 on: 24/03/2010 05:16:31 »
I certainly do not subscribe to creationism, and I also take a very Copernican view to the Universe.  I look around me though, and I see that life seems to be capable of solving some pretty incredible problems, and very rapidly at that.  Regardless of the specific mechanism behind mutations, we can see that an incredible number of beneficial mutations have in fact occurred, and continue to occur.  We saw the "nylon bug" evolve in a few years at the most, for instance.

Can anybody give me any single, or multiple mutation which would be more beneficial than the ability to pass on environmental experiences to your offspring and "make" whichever mutation needed to happen, happen? 

Obviously any process is far from perfect, or is it?  Really, individual survival doesn't necessarily matter for a species.  The goal is to make the species live forever.  You wouldn't want a whole bunch of mutations which would render the offspring sterile.  Perhaps this is why we have so many species with males/females?  By requiring two different DNA donors, perhaps a beneficial mutation is much more likely if both sexes have received the same environmental input?

I know that "Intelligent Design" was coined by creationists, who then use pseudoscience to defend it.  Lamarckian evolution would probably be a less "loaded" term for it.  But it certainly invokes a response, and to me "life" as a whole, is by far the most intelligent thing I've ever seen.  But I don't think scientists are entirely innocent when it comes to providing incorrect information.  Many science oriented people, can get downright touchy about some subjects which they have deemed unquestionable.  The thing is, sometimes science has been wrong.  Other times, science wasn't so much wrong, as we didn't have the full picture.  The point is, if what you believe to be true is actually true, no amount of logical questioning should ever matter.  In fact, it should always be encouraged, and we should always remember that mathematically, there will always be at least one thing you believe to be true, which is in fact false.

Purely random mutation, IMO, appears to be something which many people seem to hold on to with zeal, as if somehow the whole picture of Darwinian evolution hinges on that one thing.  To me though, I have a hard time reconciling current epigenetic evidence with the idea that somehow life never managed to evolve epigenetics with the ability to "hard" code DNA.  But a parasite evolved which uses three different animals in its life cycle, including a frog which the parasite mutates into a ~15 legged freak so the frog will be eaten by the bird the parasite needs for the next stage. 

Seriously....is complexity really an issue for life? 

Undoubtedly the process of mutation is incredibly dynamic, but with 2000-5000 epigenomic markers per gene, and 22,000 genes in the human genome.... we have somewhere between 44 million and 110 million living switches to play with, in each and every human.  I have no vested interest in directed mutation being true, I simply love learning and thinking.  From what I have learned, logically, I have to think life does have some sort of control over mutation.  If anyone can explain to me how my thinking is illogical, or missing some vital piece of information, please inform me and I will be happy to change my conclusion.

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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #12 on: 24/03/2010 05:49:18 »
I certainly do not subscribe to creationism, and I also take a very Copernican view to the Universe.  I look around me though, and I see that life seems to be capable of solving some pretty incredible problems, and very rapidly at that.  Regardless of the specific mechanism behind mutations, we can see that an incredible number of beneficial mutations have in fact occurred, and continue to occur.  We saw the "nylon bug" evolve in a few years at the most, for instance.

Can anybody give me any single, or multiple mutation which would be more beneficial than the ability to pass on environmental experiences to your offspring and "make" whichever mutation needed to happen, happen? 

Obviously any process is far from perfect, or is it?  Really, individual survival doesn't necessarily matter for a species.  The goal is to make the species live forever.  You wouldn't want a whole bunch of mutations which would render the offspring sterile.  Perhaps this is why we have so many species with males/females?  By requiring two different DNA donors, perhaps a beneficial mutation is much more likely if both sexes have received the same environmental input?

I know that "Intelligent Design" was coined by creationists, who then use pseudoscience to defend it.  Lamarckian evolution would probably be a less "loaded" term for it.  But it certainly invokes a response, and to me "life" as a whole, is by far the most intelligent thing I've ever seen.  But I don't think scientists are entirely innocent when it comes to providing incorrect information.  Many science oriented people, can get downright touchy about some subjects which they have deemed unquestionable.  The thing is, sometimes science has been wrong.  Other times, science wasn't so much wrong, as we didn't have the full picture.  The point is, if what you believe to be true is actually true, no amount of logical questioning should ever matter.  In fact, it should always be encouraged, and we should always remember that mathematically, there will always be at least one thing you believe to be true, which is in fact false.

Purely random mutation, IMO, appears to be something which many people seem to hold on to with zeal, as if somehow the whole picture of Darwinian evolution hinges on that one thing.  To me though, I have a hard time reconciling current epigenetic evidence with the idea that somehow life never managed to evolve epigenetics with the ability to "hard" code DNA.  But a parasite evolved which uses three different animals in its life cycle, including a frog which the parasite mutates into a ~15 legged freak so the frog will be eaten by the bird the parasite needs for the next stage. 

Seriously....is complexity really an issue for life? 

Undoubtedly the process of mutation is incredibly dynamic, but with 2000-5000 epigenomic markers per gene, and 22,000 genes in the human genome.... we have somewhere between 44 million and 110 million living switches to play with, in each and every human.  I have no vested interest in directed mutation being true, I simply love learning and thinking.  From what I have learned, logically, I have to think life does have some sort of control over mutation.  If anyone can explain to me how my thinking is illogical, or missing some vital piece of information, please inform me and I will be happy to change my conclusion.

Good stuff. Can you lay out your theory for us?
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #13 on: 24/03/2010 20:07:45 »

Good stuff. Can you lay out your theory for us?

Theory would be an awfully strong word, hypothesis would be better.  But you pretty much have it already right there in my post.  I'm not really qualified to propose anything as advanced as a full theory.  I just hypothesize that directed mutation via epigenomic markers is probably the primary mechanism responsible for the majority of the life and diversity of life here on Earth.  I also hypothesize that this mechanism probably evolved ~750 million years ago.  But I am definitely not putting forth a new theory, I am asking whether my hypothesis is likely or unlikely based on what is currently known both about the fossil record and epigenetics.  I am also trying to find out if scientists have already come to the same conclusion as I have.

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #14 on: 25/03/2010 03:52:44 »
From the brief searching I did (via Google), scientists don't yet have enough evidence to show that epigenetics can lead to permanent traits being adopted by a species.  Until they can show that it's more than a temporary effect lasting a couple of generations, it's a bit extreme to propose that it accounts for the majority of genetic diversity.

Also, to grossly oversimplify it, the way I understood what I read was that if you evolve a gene that can be switched to "on" or "off," epigenetics is basically letting you control whether you choose on or off, but doesn't allow you to modify the gene itself.  In order for you to change the gene, a random mutation is required.  I could be wrong on that, but that's how I understood it at least.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #15 on: 25/03/2010 04:25:03 »
From the brief searching I did (via Google), scientists don't yet have enough evidence to show that epigenetics can lead to permanent traits being adopted by a species.  Until they can show that it's more than a temporary effect lasting a couple of generations, it's a bit extreme to propose that it accounts for the majority of genetic diversity.

Also, to grossly oversimplify it, the way I understood what I read was that if you evolve a gene that can be switched to "on" or "off," epigenetics is basically letting you control whether you choose on or off, but doesn't allow you to modify the gene itself.  In order for you to change the gene, a random mutation is required.  I could be wrong on that, but that's how I understood it at least.

Why do you feel it is extreme to propose epigenetic directed mutation accounts for the majority of genetic diversity?  Wouldn't natural selection affect epigenomic mutation as well?  Since we know for sure that we have barely scratched the surface on this subject, and it seems a pretty safe assumption that epigenomic markers would also be affected by natural selection; how is it extreme to think it should have developed that ability sometime in the last ~750 million years at least?  On top of all that, it would answer the only kinks left in the theory of evolution.  It would no longer be surprising for an organism to develop mutations which took 2 or 3 mutations before they were even beneficial.  We would no longer have to come up with some way for the rapidity of "random" mutations to change.  While the basics of the theory of evolution is basically proven, there are specifics which have caused us to question some parts of it.  This would answer all those specifics, and still have no intervention from some "higher power".  IMHO.

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #16 on: 25/03/2010 04:44:44 »
I think we're disagreeing on a fundamental point: what an epigenetic change actually is.  Is it just a modulation of existing genes/traits or is it the directed mutation of genes to create new traits?  From what I briefly read, the former seems to be the case.  You seem to be saying the latter.  It would be useful if a biologist/geneticist could chime in on this to correct one of us. 

Also, is there any evidence that epigenetic changes are passed down forever?  It would have to be in order to drive evolution, and the reports I read said that scientists haven't been able to observe traits being passed down for more than a few generations.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #17 on: 25/03/2010 23:30:48 »
Why do you feel it is extreme to propose epigenetic directed mutation accounts for the majority of genetic diversity?  Wouldn't natural selection affect epigenomic mutation as well?  Since we know for sure that we have barely scratched the surface on this subject, and it seems a pretty safe assumption that epigenomic markers would also be affected by natural selection; how is it extreme to think it should have developed that ability sometime in the last ~750 million years at least?  On top of all that, it would answer the only kinks left in the theory of evolution.  It would no longer be surprising for an organism to develop mutations which took 2 or 3 mutations before they were even beneficial.  We would no longer have to come up with some way for the rapidity of "random" mutations to change.  While the basics of the theory of evolution is basically proven, there are specifics which have caused us to question some parts of it.  This would answer all those specifics, and still have no intervention from some "higher power".  IMHO.

"Higher Power" what is that exactly?...nature?

Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
Darwin taught us that evolutionary changes happen over generations. Bygren and other scientists have evidence suggesting environmental conditions can somehow leave an imprint on the genetic material in eggs and sperm. We have discovered that epigenetics does not alter the genetic code but makes an imprint on genes that is passed from one generation to the next and these can be influenced by environment, lifestyle etc and I would suggest that how long this imprint on genes last would depend on how long these influencing conditions lasts.


Researchers now realize that epigenetics could also help explain why one member of a pair of identical twins can develop bipolar disorder or asthma even though the other is fine. Or why autism strikes boys four times as often as girls. Or why extreme changes in diet over a short term could lead to extreme changes in longevity. In these cases, the genes may be the same, but their patterns of expression have clearly been changed. DNA roll is to carry information.

Baby lotions containing peanut oil is thought to be partly responsible for the rise in peanut allergies. High maternal anxiety during pregnancy is associated with the child's later development of asthma, (isn’t asthma hereditary?) little kids who are kept too clean are at higher risk for eczema. Smoking in their adolescence results in their offspring being a heavier body mass. Taking cocaine can change the way you feel and the way you behave.
Now, a study published in the Jan. 8 issue of Science shows how it also alters the way the genes in your brain operate.

Quote from: http://dnaconsultants.com/_blog/DNA_Consultants_Blog/post/Halloween_Story_Shades_of_Peking_Man/
“We wonder why Western scientists are in such a huff about the conclusions of Chinese paleontologists since there is solid proof of admixture between modern humans and archaic human groups like Neandertals, Homo erectus and Homo floresiensis (the fossils of "hobbits" discovered in Indonesia in 2004). One instance among many of publications demonstrating this possibility is:  Jeffrey D Wall, "Detecting Ancient Admixture and Estimating Demongraphic Parameters in Multiple Human Populations," Molecular Biology and Evolution, vol. 26, no. 8 (August 2009), pp. 1823-27.”



Has it been proven that mixed species can produce offspring that then can reproduce?





« Last Edit: 26/03/2010 00:06:27 by echochartruse »
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Offline LeeE

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Re: How big a role does the epigenome play in evolution?
« Reply #18 on: 26/03/2010 00:20:54 »
Has it been proven that mixed species can produce offspring that then can reproduce?

This is something that can be neither proved or disproved, for no species has been, or will ever be guaranteed against change.  The 'fact' of whether it has, or hasn't already occurred means nothing in regard to what may happen in the future.
...And its claws are as big as cups, and for some reason it's got a tremendous fear of stamps! And Mrs Doyle was telling me it's got magnets on its tail, so if you're made out of metal it can attach itself to you! And instead of a mouth it's got four arses!

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #19 on: 26/03/2010 00:45:11 »
Quote from: http://dnaconsultants.com/_blog/DNA_Consultants_Blog/post/Halloween_Story_Shades_of_Peking_Man/
“We wonder why Western scientists are in such a huff about the conclusions of Chinese paleontologists since there is solid proof of admixture between modern humans and archaic human groups like Neandertals, Homo erectus and Homo floresiensis (the fossils of "hobbits" discovered in Indonesia in 2004). One instance among many of publications demonstrating this possibility is:  Jeffrey D Wall, "Detecting Ancient Admixture and Estimating Demongraphic Parameters in Multiple Human Populations," Molecular Biology and Evolution, vol. 26, no. 8 (August 2009), pp. 1823-27.”


This is something that can be neither proved or disproved, for no species has been, or will ever be guaranteed against change.  The 'fact' of whether it has, or hasn't already occurred means nothing in regard to what may happen in the future.

surely we could stick a couple of species together without partners and try to prove it! why hasn't it been proven? Especially if our past evolution depends on it.

Are Peking Man, Homo Erectus Homo sapiens etc etc all the same species just with epigenetic changes due to location, lifestyle etc?


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Re: How big a role does the epigenome play in evolution?
« Reply #20 on: 26/03/2010 07:27:13 »
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #21 on: 27/03/2010 18:49:46 »
I think we're disagreeing on a fundamental point: what an epigenetic change actually is.  Is it just a modulation of existing genes/traits or is it the directed mutation of genes to create new traits?  From what I briefly read, the former seems to be the case.  You seem to be saying the latter.  It would be useful if a biologist/geneticist could chime in on this to correct one of us. 

Also, is there any evidence that epigenetic changes are passed down forever?  It would have to be in order to drive evolution, and the reports I read said that scientists haven't been able to observe traits being passed down for more than a few generations.

By definition "epigenetic" changes are not changes to the DNA but rather markers which decide how much or whether to even express a gene at all.  What I want to know, is whether these markers can also choose a mutation at the moment of conception?  So by definition, it would become a genetic mutation at that point, and not an epigenetic mutation; but it was still brought about by epigenomic markers which is my basic point.  It seems highly unlikely to me that life managed to evolve a way to control how DNA is expressed, but couldn't evolve a way to control how DNA is changed.

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #22 on: 28/03/2010 03:09:07 »
If evidence points to organisms being able to create actual mutations in that way, then it would be a major deal.  In the articles I read, none of the scientists claimed this was the case. 

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #23 on: 28/03/2010 03:35:13 »
If evidence points to organisms being able to create actual mutations in that way, then it would be a major deal.  In the articles I read, none of the scientists claimed this was the case. 

Nobody claimed that was the case, because we barely know anything about the power of epigenomic markers.  This science is just in its infancy.  What has been proven about epigenetics is that there is more to DNA than just a sequence of bases.  We know now, that large phenotypic changes can be made without changing the DNA sequence whatsoever.

Epigenetics is a major deal.  Scientists may not be claiming right now that epigenomic markers are capable of directing mutation, but that is only because they don't have 50 years of data to back it up.  But just because you don't have 50 years of research, doesn't mean it isn't true. 

When you consider life as a whole, and its incredible abilities to adapt to almost any scenario, and the fact that a mutation which would allow an organism to have any control whatsoever over DNA would be the most beneficial possible mutation ever.  Then you look at the evidence which shows that for 3.5 billion years life barely evolved at all, then all of a sudden.... millions of new species.  Not only that, but those species continued to evolve into millions of new species at an absolute breakneck pace for the next ~750 million years.  And now we know that all of this life can actually control its DNA to at least some extent.  Seriously, are we really going to insist that it is a coincidence?  Is "random mutation" so important to Darwin's theory that the whole thing crashes down without it?  I personally don't think so, I think natural selection is the key to Darwin's theory, and epigenetic driven mutation is extremely complementary to natural selection IMO.

I highly recommend watching "Was Darwin Wrong" by Naked Science.  Pay attention to what they show is actually proven, notice the lack of "random mutation" being mentioned.  Notice how the last few minutes they talk about epigenetics and what they say about evolution and mutation.

When you put all of the information together, and think logically about everything, it seems to me that hanging on to purely random mutation as the driving force behind the diversity of life is akin to insisting the Earth is 10K years old.  This is just my opinion, and maybe after we actually know more than .0001% of what epigenomic markers are capable of we will find out my opinion is wrong.  At the same time, I have yet to see anyone come up with a good reason why I should doubt the ability of life to evolve.

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #24 on: 28/03/2010 04:22:53 »
When you put all of the information together, and think logically about everything, it seems to me that hanging on to purely random mutation as the driving force behind the diversity of life is akin to insisting the Earth is 10K years old.  This is just my opinion, and maybe after we actually know more than .0001% of what epigenomic markers are capable of we will find out my opinion is wrong.  At the same time, I have yet to see anyone come up with a good reason why I should doubt the ability of life to evolve.

That's a problem.  It's a hallmark of bad science to say "I believe this because no one has proved it wrong."  Scientific models are accepted because they have evidence to support them. Models don't get accepted simply because no one can prove them wrong. 

I agree epigenetics is intriguing, and should be studied more.  There are places in evolutionary theory that need to be refined, but there don't seem to be sufficient facts yet for scientists to say that epigenetics is the model that answers those questions.  However, if a real biologist is lurking around here who knows more details about this emerging field of study, they could say more about it. 

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #25 on: 28/03/2010 04:49:10 »
When you put all of the information together, and think logically about everything, it seems to me that hanging on to purely random mutation as the driving force behind the diversity of life is akin to insisting the Earth is 10K years old.  This is just my opinion, and maybe after we actually know more than .0001% of what epigenomic markers are capable of we will find out my opinion is wrong.  At the same time, I have yet to see anyone come up with a good reason why I should doubt the ability of life to evolve.

That's a problem.  It's a hallmark of bad science to say "I believe this because no one has proved it wrong."  Scientific models are accepted because they have evidence to support them. Models don't get accepted simply because no one can prove them wrong. 

I agree epigenetics is intriguing, and should be studied more.  There are places in evolutionary theory that need to be refined, but there don't seem to be sufficient facts yet for scientists to say that epigenetics is the model that answers those questions.  However, if a real biologist is lurking around here who knows more details about this emerging field of study, they could say more about it. 

I don't believe it because nobody has proved it wrong, I believe it because logic and mathematics dictates it has an extremely high probability of being true.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #26 on: 28/03/2010 23:15:33 »
That's a problem.  It's a hallmark of bad science to say "I believe this because no one has proved it wrong."  Scientific models are accepted because they have evidence to support them. Models don't get accepted simply because no one can prove them wrong. 

Science is forever updating, something first proven to be fact/correct since found to be partially correct or incorrect. Bad science is agreeing with something once proven to be fact when you know there is a slight chance it can be proven to be wrong.

Breast cancer was thought to be contributed to 5-10% genetic.
Now a decade later it is proven that 45% of woman with breast cancer is attributable to BRCA1 and BRCA2 mutations.


Quote from:  http://realwomenrealstories.com.au/view-stories/?story=141
This is due to the rogue gene fault BRCA1, which was discovered only a decade ago and increases a carrier’s chances of developing breast cancer anywhere up to 85%. It is like an ancient family curse.

Quote from:  http://jnci.oxfordjournals.org/cgi/content/full/91/11/943
Prevalence of BRCA1 and BRCA2 Gene Mutations in Patients With Early-Onset Breast Cancer.


My questions are:
What causes a gene to mutate in one person and be passed down the following generations?
How would this gene mutation be benefitual to our evolution?
« Last Edit: 28/03/2010 23:19:17 by echochartruse »
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #27 on: 29/03/2010 04:25:44 »
I don't believe it because nobody has proved it wrong, I believe it because logic and mathematics dictates it has an extremely high probability of being true.

I disagree with you on that.  I also think most of the science on it also disagrees with you (see below).

Science is forever updating, something first proven to be fact/correct since found to be partially correct or incorrect. Bad science is agreeing with something once proven to be fact when you know there is a slight chance it can be proven to be wrong.

Breast cancer was thought to be contributed to 5-10% genetic.
Now a decade later it is proven that 45% of woman with breast cancer is attributable to BRCA1 and BRCA2 mutations.

Did I miss something?  When was it a "proven fact" that epigenetics causes genetic mutations that are inherited by subsequent generations?  No one here has given evidence or studies supporting the idea that epigenetics leads to permanent genetic mutations.  In fact, what I've found is that scientific studies are careful to say that the epigenetic changes are not genetic mutations. 

In other words (greatly simplified):

1) New species arise as a result of genes themselves mutating.
2) There isn't evidence that epigenetics can mutate genes. 
3) Therefore, epigenetics can't explain how new species arise.

[See: http://learn.genetics.utah.edu/content/epigenetics/inheritance/, in particular

Quote
Epigenetic inheritance adds another dimension to the modern picture of evolution. The genome changes slowly, through the processes of random mutation and natural selection. It takes many generations for a genetic trait to become common in a population. The epigenome, on the other hand, can change rapidly in response to signals from the environment. And epigenetic changes can happen in many individuals at once. Through epigenetic inheritance, some of the experiences of the parents may pass to future generations. At the same time, the epigenome remains flexible as environmental conditions continue to change. Epigenetic inheritance may allow an organism to continually adjust its gene expression to fit its environment - without changing its DNA code.

(emphasis mine)]

I agree that epigenetics would be a wonderful explanation if it allowed organisms to actually mutate their own DNA, but that just doesn't seem to have any scientific support.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #28 on: 29/03/2010 17:23:43 »
I don't believe it because nobody has proved it wrong, I believe it because logic and mathematics dictates it has an extremely high probability of being true.

I disagree with you on that.  I also think most of the science on it also disagrees with you (see below).

Science is forever updating, something first proven to be fact/correct since found to be partially correct or incorrect. Bad science is agreeing with something once proven to be fact when you know there is a slight chance it can be proven to be wrong.

Breast cancer was thought to be contributed to 5-10% genetic.
Now a decade later it is proven that 45% of woman with breast cancer is attributable to BRCA1 and BRCA2 mutations.

Did I miss something?  When was it a "proven fact" that epigenetics causes genetic mutations that are inherited by subsequent generations?  No one here has given evidence or studies supporting the idea that epigenetics leads to permanent genetic mutations.  In fact, what I've found is that scientific studies are careful to say that the epigenetic changes are not genetic mutations. 

In other words (greatly simplified):

1) New species arise as a result of genes themselves mutating.
2) There isn't evidence that epigenetics can mutate genes. 
3) Therefore, epigenetics can't explain how new species arise.

[See: http://learn.genetics.utah.edu/content/epigenetics/inheritance/, in particular

Quote
Epigenetic inheritance adds another dimension to the modern picture of evolution. The genome changes slowly, through the processes of random mutation and natural selection. It takes many generations for a genetic trait to become common in a population. The epigenome, on the other hand, can change rapidly in response to signals from the environment. And epigenetic changes can happen in many individuals at once. Through epigenetic inheritance, some of the experiences of the parents may pass to future generations. At the same time, the epigenome remains flexible as environmental conditions continue to change. Epigenetic inheritance may allow an organism to continually adjust its gene expression to fit its environment - without changing its DNA code.

(emphasis mine)]

I agree that epigenetics would be a wonderful explanation if it allowed organisms to actually mutate their own DNA, but that just doesn't seem to have any scientific support.

Sorry, but you are completely wrong.  You really need to update your knowledge on the subject.  The reason people have been clear on what "epigenetic" changes are, is to make sure people know the definition, which I already told you.  The fact that it hasn't been proven whether epigenetics can cause permanent changes to DNA, I also mentioned.  A great many scientists are taking a new look at Lamarckian evolution, because logic dictates they have no choice.  Like I said, watch "Was Darwin Wrong?" by Naked Science, and you will see what I am talking about.

You seem to be saying that since it hasn't been proven yet, we should assume it's wrong.  By that logic, we should also assume Einstein's theory of relativity is wrong, along with the standard model of physics.

How would you care to explain the explosion of life which started ~750 million years ago?

Why is it, that life spent 3.5 billion years barely evolving?

What changed, which allowed thousands of new species to emerge in just a few million years after the explosion of life started?

Seriously, basically no evolution for thousands of millions of years, and then all of a sudden we get thousands of new species..... How could anybody possibly claim that something didn't change at that point?

If you choose to hang on to "random" mutation, that is your choice.... but so far I haven't seen anybody be able to provide anything more than a very poor argument as to why I should doubt the ability of life to evolve.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #29 on: 29/03/2010 21:11:46 »
JP, I apologize if I was too aggressive with that; I should not have flatly stated that you are wrong, that was disrespectful of me.

Would you please explain why you feel most of the science disagrees?

The scientists are making clear what the definition of "epigenetic" mutation is, and it is most definitely not mutation to the arrangement of bases with the DNA.  They have also made very clear that it is completely unknown whether epigenetic mutation can eventually become a permanent or encourage a permanent change.  The reason they need to be clear on this, is because if it eventually is proven to happen the implications are tremendous.  A scientist is not in a position to say something is proven if they can't 100% back it up.  But even if something has not been proven, we can use mathematics and look at probabilities.

Imagine you are playing a game..... In this game, you are given a coin, and you are told you that for every time the coin lands on heads you get another coin.  For every coin you have, you get another chance to "win" another.

So you start playing the game, and you build up quite a stash pretty quick.  A little while into the game, another player joins.  Player 2 is given a coin, and the same instructions.  But player 2 realizes that the rules only say the coin has to land on heads, and nothing about the events which led up to it.  So player 2 starts placing his coins on heads, every time.  Player 2 rapidly outpaces you, and pretty soon your stash looks like chump change compared to his.

This shows how incredibly beneficial any mutation which allowed epigenetic markers to influence actual genetic mutation would be.  And strangely enough, that is exactly what we see in the fossil record ~750 million years ago.

So yes JP, you are 100% correct that it hasn't been proven, and if you have any evidence against it please share, I really have no interest in continuing a line of thought which is counter to hard evidence.  But from what I have seen so far, including the links you provided, there isn't even a shred of evidence against epigenetically originating genetic mutation.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #30 on: 30/03/2010 00:23:18 »
I agree with norcalclimber.

Quote
http://itsnotmental.blogspot.com/2009/09/brain-health-nutrition-and-epigenetics.html
Environmental Epigenetics
by
Keri Cross, A.S., A.A.

As we identify more and more epigenetically unstable locations in the human genome, screening for epigenetically susceptible diseases at an early age will be made possible, along with more accurate disease diagnosis. This knowledge will allow for more precise and effective monitoring of an individual’s health. Because epigenetic profiles are potentially reversible, preventions and therapies, such as nutritional supplementation and/or pharmaceutical treatments can be developed to help counteract and even reverse negative epigenetic alterations.

Studies have shown that many disorders, such as obesity, cardiovascular disease, diabetes, hypertension, asthma and schizophrenia, have roots in early nutrition and environmental exposure during gestation. The potential for epigenetic change continues from conception until the time of death. A person’s lifetime not only affects their own epigenome, permanently modifying things like appetite control, metabolic balance, and disease susceptibility, but that of the epigenome for generations to come as well.

Quote
http://www.threeriversbirth.com/?p=307
Dr. Randy Jirtle, professor and researcher at Duke University.   All of our cells carry the same genes, but it’s the epigenomes that tell our developing cells what kinds of cells they will develop into - hair, fat, muscle, cancer, heart, etc.  Epigenetic codes pass on as cells divide, but they are not necessarily permanent.

So you may say that epigenetics controlls genes and can be passed down generations but it appears there is no evidence of genes mutating. Is it possible that humans haven't found any evidence of evolution prior 750 million yrs ago? is it possible that species have remained the same with slight alterations caused by Epigenetics? That the Elephant in India is the same species as the elephant in Africa with distinct alterations due to epigenetics. The species of humans in China being the same species as the humans in Norway with alterations to their genome via epigenetics? That the turtles ansestors are the same species with variations casued by epeigenetics? I think so.

Did epigenetics evolve? I think without epigenetics nothing would have survived or changed to suit the environment and our evolution would not have been possible. My personal thoughts are that the process of epigentics has always existed.
« Last Edit: 30/03/2010 00:46:17 by echochartruse »
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Re: How big a role does the epigenome play in evolution?
« Reply #31 on: 30/03/2010 02:17:00 »
So you start playing the game, and you build up quite a stash pretty quick.  A little while into the game, another player joins.  Player 2 is given a coin, and the same instructions.  But player 2 realizes that the rules only say the coin has to land on heads, and nothing about the events which led up to it.  So player 2 starts placing his coins on heads, every time.  Player 2 rapidly outpaces you, and pretty soon your stash looks like chump change compared to his.

This shows how incredibly beneficial any mutation which allowed epigenetic markers to influence actual genetic mutation would be.  And strangely enough, that is exactly what we see in the fossil record ~750 million years ago.

I agree with you on this.  Epigenetic markers are here probably because they give an advantage to the organisms carrying them.  What I'm disagreeing on is that I don't think there's evidence to support the claim that epigenetic markers are responsible for such a huge proportion of genetic diversity. 

Quote
The scientists are making clear what the definition of "epigenetic" mutation is, and it is most definitely not mutation to the arrangement of bases with the DNA.  They have also made very clear that it is completely unknown whether epigenetic mutation can eventually become a permanent or encourage a permanent change.  The reason they need to be clear on this, is because if it eventually is proven to happen the implications are tremendous.  A scientist is not in a position to say something is proven if they can't 100% back it up.  But even if something has not been proven, we can use mathematics and look at probabilities.

I agree that if epigenetics causes permanent change then it means a huge shift in how we think about evolution.  I'm disagreeing that it's obviously the most probable answer to the questions in evolutionary theory.  Evolution is extremely complex and deals with staggering numbers of organisms and lengths of time, so it's hard to say that this theory is overwhelmingly the most probable.  (If epigenetics can cause permanent changes to DNA it becomes far likelier and if it can't, then it becomes far less likely).
Quote
So yes JP, you are 100% correct that it hasn't been proven, and if you have any evidence against it please share, I really have no interest in continuing a line of thought which is counter to hard evidence.  But from what I have seen so far, including the links you provided, there isn't even a shred of evidence against epigenetically originating genetic mutation.
That's my other issue.  There's no evidence against epigenetics leading to permanent mutations but there's no evidence for it either.  Science doesn't work by accepting new theories based on no one disproving them yet.  You mentioned relativity and the standard model of particle physics previously as having as much support as (permanent) evolution by epigenetics (meaning acquired permanent mutations of genes).  This simply isn't true.  Both those theories in physics have made predictions which have been rigorously tested, and they have passed those tests. 

Again, I do agree that epigenetics is intriguing and needs more study.  It could provide a lot of answers in evolutionary theory, but I think it's missing that crucial point that allows the creation of permanent genetic mutations.  We can hypothesize about what would happen if permanent mutations occurred within epigenetics, but until there's evidence supporting it, it's all very hypothetical.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #32 on: 30/03/2010 03:04:50 »
So you start playing the game, and you build up quite a stash pretty quick.  A little while into the game, another player joins.  Player 2 is given a coin, and the same instructions.  But player 2 realizes that the rules only say the coin has to land on heads, and nothing about the events which led up to it.  So player 2 starts placing his coins on heads, every time.  Player 2 rapidly outpaces you, and pretty soon your stash looks like chump change compared to his.

This shows how incredibly beneficial any mutation which allowed epigenetic markers to influence actual genetic mutation would be.  And strangely enough, that is exactly what we see in the fossil record ~750 million years ago.

I agree with you on this.  Epigenetic markers are here probably because they give an advantage to the organisms carrying them.  What I'm disagreeing on is that I don't think there's evidence to support the claim that epigenetic markers are responsible for such a huge proportion of genetic diversity. 

Quote
The scientists are making clear what the definition of "epigenetic" mutation is, and it is most definitely not mutation to the arrangement of bases with the DNA.  They have also made very clear that it is completely unknown whether epigenetic mutation can eventually become a permanent or encourage a permanent change.  The reason they need to be clear on this, is because if it eventually is proven to happen the implications are tremendous.  A scientist is not in a position to say something is proven if they can't 100% back it up.  But even if something has not been proven, we can use mathematics and look at probabilities.

I agree that if epigenetics causes permanent change then it means a huge shift in how we think about evolution.  I'm disagreeing that it's obviously the most probable answer to the questions in evolutionary theory.  Evolution is extremely complex and deals with staggering numbers of organisms and lengths of time, so it's hard to say that this theory is overwhelmingly the most probable.  (If epigenetics can cause permanent changes to DNA it becomes far likelier and if it can't, then it becomes far less likely).
Quote
So yes JP, you are 100% correct that it hasn't been proven, and if you have any evidence against it please share, I really have no interest in continuing a line of thought which is counter to hard evidence.  But from what I have seen so far, including the links you provided, there isn't even a shred of evidence against epigenetically originating genetic mutation.
That's my other issue.  There's no evidence against epigenetics leading to permanent mutations but there's no evidence for it either.  Science doesn't work by accepting new theories based on no one disproving them yet.  You mentioned relativity and the standard model of particle physics previously as having as much support as (permanent) evolution by epigenetics (meaning acquired permanent mutations of genes).  This simply isn't true.  Both those theories in physics have made predictions which have been rigorously tested, and they have passed those tests. 

Again, I do agree that epigenetics is intriguing and needs more study.  It could provide a lot of answers in evolutionary theory, but I think it's missing that crucial point that allows the creation of permanent genetic mutations.  We can hypothesize about what would happen if permanent mutations occurred within epigenetics, but until there's evidence supporting it, it's all very hypothetical.


The evidence I have most heard touted as evidence in support of epigenetics driving genetic mutation is whales.  Whales were mammals, and evolved first on land, then moved into the ocean and "lost" their legs.  Scientists are arguing that epigenetics drove that change. 

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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #33 on: 30/03/2010 04:44:26 »

The evidence I have most heard touted as evidence in support of epigenetics driving genetic mutation is whales.  Whales were mammals, and evolved first on land, then moved into the ocean and "lost" their legs.  Scientists are arguing that epigenetics drove that change.
 

Norcalclimber, I am no expert in this field (actually, I'm not really an expert in any field  [:D]) but it would be helpful if you can provide a reference for your source. I'm sure you are aware that it is possible to find a lot of opinions on the web that are not exactly scientific, even although they claim to be. I'm not saying that is the situation here of course, but references would give JP an opportunity to respond to your claim.
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #34 on: 31/03/2010 19:03:40 »
Thanks, I will definitely do so.  There really hasn't been enough research in epigenetics to see proof of directed mutation from that source(at least that I have found), but there is tons of peer reviewed evidence in favor of some form of directed mutation.  But lacking knowledge of epigenetics, the conclusions were just that life is obviously incredibly dynamic and not fully understood.  I have been busy with my family for the past few days as well as the next, but I will put together a few sources and post them asap.  It seems to me that the Naked Scientists should already know a lot of this as well though, unless I'm misunderstanding the last 5 minutes of "Was Darwin Wrong?" by Naked Science. 

Anyway, it's going to be a few days at least before I can put it together, but I didn't want anybody to think I'm just spouting off with no legitimate science to support my claims at all.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #35 on: 01/04/2010 06:29:10 »
If this is not Epigentics please explain....

Quote from: http://www.abc.net.au/science/articles/2009/11/26/2754494.htm?topic=
Scientists create Chinese 'gene map'
A large genetic analysis of ethnic Chinese has revealed subtle genetic differences within the world's most populous nation.

Scientists hope the results will help them to identify certain gene variants may render some people more vulnerable to some diseases, so targeted preventive measures can be taken and therapies may one day be found.

The study appears in the American Journal of Human Genetic.

Led by Dr Liu Jianjun, head of the human genetics group at the Agency for Science, Technology and Research in Singapore, the researchers found that inhabitants in northern China were genetically distinguishable from those in the south, a finding that was consistent with historical migration patterns in China.
Variations

Consistent genetic differences, or variants, showed up in 0.3% of the genes between both groups, says Liu.

"From this genetic map, it tells us how people differ from each other, or how people are more closely linked to each other."

"We don't know what these variants are responsible for. Some may have clinical outcomes and influence disease development. That is why we are interested in genetic variation. That will help us understand when we do disease studies."

The huge sample of 8200 ethnic Chinese participants were drawn from 10 Chinese provinces and Singapore.

Interestingly, the scientists also found genetic variants between different Chinese dialect groups.

"Different dialect groups are definitely not identical ... language is a reflection of our evolution, that's why you see the differences," says Liu.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #36 on: 01/04/2010 06:43:23 »
My appology for long quoted posts but this is what we are speaking of here
Quote from: http://www.abc.net.au/science/articles/2007/12/11/2115575.htm
Humans evolving faster than thought
Will Dunham
Reuters
moving forward

How will humans evolve in the next 5000 years? (Source: iStockphoto)
Related Stories

    * First farmers wanted clothes not food
    * Human DNA surprisingly diverse
    * Tropics the hot spot for speedy evolution

humans evolving faster Human evolution has been moving at breakneck speed in the past several thousand years, far from plodding along as some scientists had thought, researchers say.

In fact, people today are genetically more different from people living 5000 years ago than those humans were different from the Neanderthals who vanished 30,000 years ago, according to US anthropologist Assistant Professor John Hawks of the University of Wisconsin.

The genetic changes have related to numerous different human characteristics, the researchers say in the journal Proceedings of the National Academy of Sciences.

Many of the recent genetic changes reflect differences in the human diet brought on by agriculture, as well as resistance to epidemic diseases that became mass killers following the growth of human civilisations, the researchers say.

For example, Africans have new genes providing resistance to malaria. In Europeans, there is a gene that makes them better able to digest milk as adults. In Asians, there is a gene that makes ear wax more dry.

The changes have been driven by the colossal growth in the human population, from a few million to 6.5 billion in the past 10,000 years, with people moving into new environments to which they needed to adapt, adds Professor Henry Harpending, a University of Utah anthropologist.

"The central finding is that human evolution is happening very fast, faster than any of us thought," Harpending says.

"Most of the acceleration is in the last 10,000 years, basically corresponding to population growth after agriculture is invented," Hawks says.
Gene mutations

The researchers looked for the appearance of favourable gene mutations over the past 80,000 years of human history by analysing voluminous DNA information on 270 people from different populations worldwide.

Data from this International HapMap Project, short for haplotype mapping, offered essentially a catalogue of genetic differences and similarities in people alive today.

Looking at such data, scientists can ascertain how recently a given genetic change appeared in the genome and then can plot the pace of such change into the distant past.

Beneficial genetic changes have appeared at a rate roughly 100 times higher in the past 5000 years than at any previous period of human evolution, the researchers determined.

They add that about 7% of human genes are undergoing rapid, relatively recent evolution.

Even with these changes, however, human DNA remains more than 99% identical, the researchers note.

Harpending says the genetic evidence shows that people worldwide have been getting less similar rather than more similar due to the relatively recent genetic changes.

Genes have evolved relatively quickly in Africa, Asia and Europe but almost all of the changes have been unique to their corner of the world.

This is the case, he says, because since humans dispersed from Africa to other parts of the world about 40,000 years ago, there has not been much flow of genes between the regions.
« Last Edit: 01/04/2010 06:46:41 by echochartruse »
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #37 on: 01/04/2010 07:00:37 »
echochartruse, I don't think we're in agreement on what the term epigenetics means.  What is the definition of epigenetics that you're working from?

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Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #38 on: 01/04/2010 07:51:15 »
It seems to me that the Naked Scientists should already know a lot of this as well though, unless I'm misunderstanding the last 5 minutes of "Was Darwin Wrong?" by Naked Science.
There could be some confusion between "The Naked Scientists", the British radio show and podcast, and "Naked Science", the American tv programme.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #39 on: 01/04/2010 12:22:02 »
  In answer to JP

Quote from: http://encyclopedia.kids.net.au/page/ep/Epigenetic_inheritance
A number of experimental studies seems to indicate that epigenetic inheritance plays a part in the evolution of complex organisms. For example, Tremblay et al. (ref. 3), have shown that methylation differences between maternally and paternally inherited alleles of the mouse H19 gene are preserved. There are also numerous reports of heritable epigenetic marks in plants.
That epigenetic heredity seems to exist trangenerationally in complex organisms can be explained by allowing for minor epigenetic changes not affecting totipotency[?]. This puts some constraints on the extent to which epigenetic changes can be brought upon DNA, but it allows for EISs to play direct evolutionary roles.

My definition: In my words, (definitely not scientific ) Epigenetics is the external influences such as food, weather, location, the parants lifestyle, behaviour etc that modify/mutate/guide and effect cells which can be inherited by offspring and further generations. Genes and DNA are virtually static. From what I understand DNA in all living creatures doesn't vary much between each. We only inherit a couple of mutant genes from our parents that may or may not effect our genes/DNA, they may be passed on but lie 'dormant' until epigenetics influences them to be permanently altered/evolved.

Therfore my thoughts about the "Chinese gene map" is that they are the same species, the same race, varying in location, lifestyle etc showing 'genetic varients' between groups due to epigenetics.

Please explain if I have it wrong.




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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #40 on: 01/04/2010 12:36:31 »
Ok.  Is an epigenetic change in your definition an actual mutation of the DNA?  In other words, would two people who have epigenetic differences have different DNA?

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #41 on: 01/04/2010 12:52:06 »
Ok.  Is an epigenetic change in your definition an actual mutation of the DNA?  In other words, would two people who have epigenetic differences have different DNA?

As I see it DNA is only the carrier of information. Epigentics effects cells directly. From what I've read DNA may or may not use this information to alter genes or cells.

2 identical twins have exact same DNA, but one may not be able to reproduce.
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #42 on: 01/04/2010 13:17:51 »
So what's the answer to the question.  Do you think epigenetics changes can directly cause DNA to mutate?

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #43 on: 01/04/2010 17:39:09 »
It seems to me that the Naked Scientists should already know a lot of this as well though, unless I'm misunderstanding the last 5 minutes of "Was Darwin Wrong?" by Naked Science.
There could be some confusion between "The Naked Scientists", the British radio show and podcast, and "Naked Science", the American tv programme.

My bad, that is exactly where the confusion is from.  Lol, I thought the TV program was made by "The Naked Scientists".  Thank you for letting me know it's not the same  [:)]

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #44 on: 01/04/2010 19:07:32 »
So what's the answer to the question.  Do you think epigenetics changes can directly cause DNA to mutate?
Do I think?    I think nothing is impossible.
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #45 on: 01/04/2010 19:43:51 »
So what's the answer to the question.  Do you think epigenetics changes can directly cause DNA to mutate?
Do I think?    I think nothing is impossible.

Seemed like a simple enough question. What's all the shouting about?
There ain'ta no sanity clause, and there ain'ta no centrifugal force æther.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #46 on: 01/04/2010 21:50:27 »
So what's the answer to the question.  Do you think epigenetics changes can directly cause DNA to mutate?
Do I think?    I think nothing is impossible.

Seemed like a simple enough question. What's all the shouting about?

My appology not shouting, just refering to the words
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #47 on: 02/04/2010 03:22:56 »
So what's the answer to the question.  Do you think epigenetics changes can directly cause DNA to mutate?
Do I think?    I think nothing is impossible.

Seemed like a simple enough question. What's all the shouting about?

My appology not shouting, just refering to the words

It's an important point.  The two studies you linked to above that you say demonstrate epigenetics appear to be actually comparing differences (mutations) in genes.  All the accounts I've read of epigenetics state that it cannot cause mutations in genes.  Therefore the accounts you listed above are not a direct result of epigenetics according to the definition I've seen given. 

If you have sources stating that epigenetics does cause mutations in genes, then that would change things.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #48 on: 02/04/2010 06:08:14 »
Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
It is through epigenetic marks that environmental factors like diet, stress and prenatal nutrition can make an imprint on genes that is passed from one generation to the next..........The drug uses epigenetic marks to dial down genes in blood precursor cells that have become overexpressed.

Read more: http://www.time.com/time/health/article/0,8599,1951968-2,00.html#ixzz0jukVCxAK
.........The great hope for ongoing epigenetic research is that with the flick of a biochemical switch, we could tell genes that play a role in many diseases — including cancer, schizophrenia, autism, Alzheimer's, diabetes and many others — to lie dormant. We could, at long last, have a trump card to play against Darwin..........."I can load Windows, if I want, on my Mac," says Joseph Ecker, a Salk Institute biologist and leading epigenetic scientist. "You're going to have the same chip in there, the same genome, but different software. And the outcome is a different cell type."
Read more: http://www.time.com/time/health/article/0,8599,1951968-2,00.html#ixzz0jukwTf7h
Read more: http://www.time.com/time/health/article/0,8599,1951968-2,00.html#ixzz0jukfD3jr


As I mentioned previously breast cancer has now been recorded in 4 generations of woman and breast cancer is epigenetic, same as alcoholism which is hereditry.

Epigenetics is the process.
The Tasmainian Devil's are fighting against cancers of the face. There is now evidence that these cancers are caused through epigenetics. Mono culture trees cause water run off to be toxic. These rare cancers are also recorded in humans in the same location.
Epigenetics regulates genetic expression.
www.preventionandhealing.com/.../Duh-Vinci-Code-for-Tasmanian-Devils-Cracking-the-Cancer-Code.pdf

Quote from: http://www.sinauer.com/detail.php?id=2993
When the molecular processes of epigenetics meet the ecological processes of phenotypic plasticity, the result is a revolutionary new field: ecological developmental biology, or “eco-devo.” This new science studies development in the “real world” of predators, pathogens, competitors, symbionts, toxic compounds, temperature changes, and nutritional differences. These environmental agents can result in changes to an individual’s phenotype, often implemented when signals from the environment elicit epigenetic changes in gene expression.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #49 on: 02/04/2010 06:13:09 »
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20332811
Heredity. 2010 Mar 24. [Epub ahead of print]
Epigenomic plasticity within populations: its evolutionary significance and potential.

Johnson LJ, Tricker PJ.

School of Biological Sciences, University of Reading, Reading, UK.

Epigenetics has progressed rapidly from an obscure quirk of heredity into a data-heavy 'omic' science. Our understanding of the molecular mechanisms of epigenomic regulation, and the extent of its importance in nature, are far from complete, but in spite of such drawbacks, population-level studies are extremely valuable: epigenomic regulation is involved in several processes central to evolutionary biology including phenotypic plasticity, evolvability and the mediation of intragenomic conflicts. The first studies of epigenomic variation within populations suggest high levels of phenotypically relevant variation, with the patterns of epigenetic regulation varying between individuals and genome regions as well as with environment. Epigenetic mechanisms appear to function primarily as genome defences, but result in the maintenance of plasticity together with a degree of buffering of developmental programmes; periodic breakdown of epigenetic buffering could potentially cause variation in rates of phenotypic evolution.Heredity advance online publication, 24 March 2010; doi:10.1038/hdy.2010.25.

PMID: 20332811 [PubMed - as supplied by publisher]

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