Naked Science Forum

Life Sciences => Plant Sciences, Zoology & Evolution => Topic started by: norcalclimber on 22/03/2010 04:24:37

Title: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 22/03/2010 04:24:37
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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.

Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: LeeE on 23/03/2010 16:47:16
The concept of 'Intelligent Design' seems to have clearly evolved from 'Creationism'.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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!
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 24/03/2010 03:37:32
Gosh! You must have missed my latest post. Perhaps you would like to reply.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?





Title: Re: How big a role does the epigenome play in evolution?
Post by: LeeE 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?


Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 26/03/2010 07:27:13
Hi!

Please refer to this thread.

http://www.thenakedscientists.com/forum/index.php?topic=29147.msg305045#msg305045

Thanks!

Geezer (Mod)
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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. 
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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. 
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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. 
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.




Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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  [:)]
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.

Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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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Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 02/04/2010 06:17:29
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20216571
Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil.

Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones ME.

School of Biological Sciences, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

Infectious disease has been shown to be a major cause of population declines in wild animals. However, there remains little empirical evidence on the genetic consequences of disease-mediated population declines, or how such perturbations might affect demographic processes such as dispersal. Devil facial tumour disease (DFTD) has resulted in the rapid decline of the Tasmanian devil, Sarcophilus harrisii, and threatens to cause extinction. Using 10 microsatellite DNA markers, we compared genetic diversity and structure before and after DFTD outbreaks in three Tasmanian devil populations to assess the genetic consequences of disease-induced population decline. We also used both genetic and demographic data to investigate dispersal patterns in Tasmanian devils along the east coast of Tasmania. We observed a significant increase in inbreeding (F(IS) pre/post-disease -0.030/0.012, P<0.05; relatedness pre/post-disease 0.011/0.038, P=0.06) in devil populations after just 2-3 generations of disease arrival, but no detectable change in genetic diversity. Furthermore, although there was no subdivision apparent among pre-disease populations (theta=0.005, 95% confidence interval (CI) -0.003 to 0.017), we found significant genetic differentiation among populations post-disease (theta=0.020, 0.010-0.027), apparently driven by a combination of selection and altered dispersal patterns of females in disease-affected populations. We also show that dispersal is male-biased in devils and that dispersal distances follow a typical leptokurtic distribution. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales. Ongoing management of Tasmanian devils must now attempt to maintain genetic variability in this species through actions designed to reverse the detrimental effects of inbreeding and subdivision in disease-affected populations.Heredity advance online publication, 10 March 2010; doi:10.1038/hdy.2010.17.

PMID: 20216571 [PubMed - as supplied by publisher]

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Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 02/04/2010 06:26:02
If epigenomic markers actually allow life to direct mutation to any extent whatsoever, would that qualify as "intelligent design"?

If any process (epigentics)is involved rather than 'random change', you would think there is some 'intelligents'about it?

I think so.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 02/04/2010 16:45:53
echochartruse, I think the main point is still this:
Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
"You're going to have the same chip in there, the same genome, but different software. And the outcome is a different cell type."

Maybe I'm missing something obvious, but I can't find a point in any of those sources that says that epigenetics are causing genetic mutations.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 02/04/2010 19:17:56
echochartruse, I think the main point is still this:
Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
"You're going to have the same chip in there, the same genome, but different software. And the outcome is a different cell type."


Maybe I'm missing something obvious, but I can't find a point in any of those sources that says that epigenetics are causing genetic mutations.

To be honest, I can't find anything in them about epigenetics causing genetic mutations.  I still haven't had a chance to put together a decent post with a lot of sources(hopefully later today), but I haven't seen anywhere that said epigenetics for sure caused genetic mutation.  My support comes from the evidence that some form of directed mutation exists, and I think logically epigenetics is the likely culprit.  Here is a quick example of the types of things I will post later today:

http://www.pnas.org/content/88/13/5882.full.pdf

Abstract: A previous study has demonstrated that
adaptive missense mutations occur in the tip operon of Escherichia
coli. In this study it is shown that, under conditions of
intense selection, a strain carrying missense mutations in both
trpA and trpB reverts to Trp+ 108 times more frequently than
would be expected if the two mutations were the result of
independent events. Comparison of the single mutation rates
with the double mutation rate and information obtained by
sequencing DNA from double revertants show that neither our
classical understanding of spontaneous mutation processes nor
extant models for adaptive mutations can account for all of the
observations. Despite a current lack of mechanistic understanding,
it is clear that adaptive mutations can permit advantageous
phenotypes that require multiple mutations to arise
and that they appear enormously more frequently than would
be expected.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 02/04/2010 23:08:03
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20216571
Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil.

Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones ME.

School of Biological Sciences, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

............. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales.........

PMID: 20216571 [PubMed - as supplied by publisher]

LinkOut - more resources


They must be wrong then
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 02/04/2010 23:59:57
I'm not sure that this really supports directed mutation by epigenetic causation.  I can see how it is talking about evolution, but what it is saying doesn't really seem surprising, nor different from what has been previously thought.  If I am misunderstanding, please explain.
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20216571
Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil.

Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones ME.

School of Biological Sciences, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

............. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales.........

PMID: 20216571 [PubMed - as supplied by publisher]

LinkOut - more resources


They must be wrong then
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 03/04/2010 05:27:30
In my words...... Tassie Devil's genetics, prior to the toxins in their water, were all the same throughout their species. After the toxins from the mono culture effected their water, their genetics changed over 2-3 generations to cope with the toxins and to survive and reproduce.

So if you go to the zoo where these animals are kept away from the toxins, you will find their genes are different from the ones in the wild.

The toxins are not leaving their water system any time in the near future, so if they continue to breed their genes will be passed down throughout many generations. While the captive Tassie Devils reproduce without the altered genes.

1.Cancer is an epigentic disease characterised by the break down of DNA.
2.Prior to the environmental change all the Tassie Devils genes were the same.
3. No change in Tassie Devil's genes in zoos or that have never come in contact with the toxic environment.
4. It took 2-3 generations for the environment to effect change in their genes.
5. If the captured, zoo's Tassie devils were released and returned to their native environment they would not survive. Their environment has directly effected their evolution.
6. As I believe, if the ones in the zoos continue to reproduce together without bringing in the new genes from their wild counterparts then 2 distinct species of Tassie Devils may occur over time. One group unable to live/reproduce/survive in it's natural habitat.
Survival of the fittest!

Anyway this example was for JP, to show that epigentics does change genes.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 03/04/2010 06:28:54
Tassie Devil's genetics, prior to the toxins in their water, were all the same throughout their species. After the toxins from the mono culture effected their water, their genetics changed over 2-3 generations to cope with the toxins and to survive and reproduce.

That is truly remarkable. If I understand what you are saying;

a) All Tasmanian Devils had identical genes.

b) The Tasmanian Devils that were subjected to toxins in their water showed significant changes in their genes in two to three generations.

Did I get that right?
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 03/04/2010 07:19:25
Here is a few more examples which I feel indicate epigenetics causing mutation:

http://www.gate.net/~rwms/EvoMutations.html

In the section about exotic 5 carbon sugars we see a possible example of an overall mutation which may have started off with an epigenetic mutation, then had a genetic mutation, then had an epigenetic mutation (the author doesn't attribute epigenetics, merely states what effects occurred)
Quote

"Some five carbon sugars are very rare in nature, so very few organisms have the ability to use these exotic compounds in their metabolism. Robert Mortlock determined that the bacteria Klebsiella aerogenes was not immediately able to metabolize D-arabinose and xylitol by growing strains in media containing those compounds and noting the strains that were able to grow only after a lag time. This indicated that the original strain did not have the ability to process the compounds, but was able to evolve such a capability. Mortlock then went on to see how this capability was evolved.

In the case of D-arabinose, Mortlock showed that the arabinose could be utilized if it could be converted to D-ribulose by an enzyme (an isomerase). Unfortunately, K. aerogenes has no such isomerase for the conversion of D-arabinose. However, the isomerase for L-fucose has a low activity for D-arabinose.   But, the bad news is that the L-fucose isomerase is normally produced only when the cell is exposed to fucose. Nonetheless, in a few individuals, mutations occurred that allowed the fucose isomerase to be produced at all times - not just when L-fucose is present. This is normally a bad thing and would be selected against because it wastes the cells resources by constantly producing an unneeded enzyme. In this situation though, the mutation is a very good thing, and allows the cell to survive because it can now metabolize arabinose (albeit rather poorly). Although production of the fucose isomerase has been deregulated, the structure of the isomerase itself has not been changed. The next mutation was a change to the isomerase to make it more effective in the conversion of arabitol to ribulose. Finally (although I can't tell from Bell's description if this was actually done in the experiments), the culture could be selected to regain control of the expression of the isomerase - so that it is produced only when arabitol is present. "

It seems to me that perhaps the initial mutation which caused the isomerase for fucose to be produced without fucose present may have been epigenetic.  The next mutation seems to have been a genetic mutation which made the isomerase more efficient.  The final mutation seems to have been epigenetic again, to only produce the new isomerase when arabinose is present.

I am going off a limited understanding of the experiments involved, but it seems as if the bacteria was able to accomplish these mutations very quickly.

In another section of that page, we see this example of beneficial mutation(emphasis mine):

Quote
5.) Evidence of genetic divergence and beneficial mutations in bacteria after 10,000 generations
 

    Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R. E., Blot, M. (1999). Genomic evolution during a 10,000-generation
    experiment with bacteria. Proc. Natl. Acad. Sci. U. S. A. 96: 3807-3812

    Edited by John R. Roth, University of Utah, Salt Lake City, UT, and approved February 3, 1999 (received for review July 21, 1998)

    Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

The fact that each individual cell had its own genetic fingerprint, yet the pivotal mutations were shared by all descendants seems significant.

More from the same page:

Quote
4.) Adaptation to a Low Phosphate Chemostat Environment by a Clonal Line of Yeast
 

    P.E. Hansche and J.C. Francis set up chemosats to allow evolution of a single clonal line of beer yeast in a phosphate limited (due to high pH) environment. (A chemostat is a device that allows the propagation of microorganisms in an extremely constant environment.) The yeast clones grew slowly for about the first 180 generations when there was an abrupt increase in population density. This was later shown to be due to  better assimilation of the phosphate, presumably due to an improvement in the permease molecule. (Permease is an enzyme that controls what is allowed to come into the cell through the yeast's cell membrane.) After about 400 generations, a second improvement in cell growth rates occurred because of a mutation to the yeast's phosphatase (an enzyme that improves the cells ability to use phosphate). The phosphatase became more active overall, and its optimal pH (the pH where it is most active) was raised.  Finally, a third mutant appeared after 800 generations that caused the yeast cells to clump. This raised the population density in the chemostat because individual cells were no longer being washed out of chemostat (which is one of the methods that the chemostat uses to maintain very uniform conditions) as quickly as they had prior to the mutation. (This is just speculation on my part, but I wonder if it wasn't under some similar conditions that multi-cellularity became favored over unicellularity - perhaps on a sea bed or river bottom.)

    This experiment was repeated, and the same mutations occurred, but in different orders. Also, in one replication, the processing of phosphate was improved by a duplication of the gene that produces phosphatase. This is experimental evidence of an extremely important mechanism in evolutionary history! It is also a particularly elegant experiment because not only was all of this adaptation shown to occur in clonal lines (descended from a single individual), but the authors also determined the exact mutations that caused the improved adaptations by sequencing the genes and proteins involved.

    Francis, J.E., & Hansche, P.E. (1972) Directed evolution of metabolic pathways in microbial populations. I. Modification of the acid phosphatase pH optimum in Saccharaomyces cervisiae. Genetics, 70: 59-73.

    Francis, J.E., & Hansche, P.E. (1973) Directed evolution of metabolic pathways in microbial populations. II. A repeatable adaptation in Saccharaomyces cervisiae. Genetics, 74:259-265.

    Hansche, P.E. (1975) Gene duplication as a mechanism of genetic adaptation in Saccharaomyces cervisiae. Genetics, 79: 661-674.



These seem to be describing abrupt mutations which occur to a lot of the population at once, not gradual changes.  Also, the same mutations occurred when the experiment was repeated.  It seems so ordered, and quick, which to me implies some sort of direction.  I personally do not believe in a "higher power" so that is why I lean strongly towards something like epigenetics.


Here is an example where 2 separate mutations were required in order to metabolize salicin, and not only did they happen, but the initial mutation was not beneficial and only occurred in populations grown on mediums containing salicin:

Quote
http://www.ncbi.nlm.nih.gov/pubmed/2852143?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=1&log$=relatedarticles&logdbfrom=pubmed
Adaptive evolution that requires multiple spontaneous mutations. I. Mutations involving an insertion sequence.

Hall BG.

Molecular and Cell Biology, University of Connecticut, Storrs 06268.

Escherichia coli K12 strain chi 342LD requires two mutations in the bgl (beta-glucosidase) operon, bglR0----bglR+ and excision of IS103 from within bglF, in order to utilize salicin. In growing cells the two mutations occur at rates of 4 x 10(-8) per cell division and less than 2 x 10(-12) per cell division, respectively. In 2-3-week-old colonies on MacConkey salicin plates the double mutants occur at frequencies of 10(-8) per cell, yet the rate of an unselected mutation, resistance to valine, is unaffected. The two mutations occur sequentially. Colonies that are 8-12 days old contain from 1% to about 10% IS103 excision mutants, from which the Sal+ secondary bglR0----bglR+ mutants arise. It is shown that the excision mutants are not advantageous within colonies; thus, they must result from a burst of independent excisions late in the life of the colony. Excision of IS103 occurs only on medium containing salicin, despite the fact that the excision itself confers no detectable selective advantage and serves only to create the potential for a secondary selectively advantageous mutation.


Really I could go on and on, the evidence supporting some form of directed mutation is everywhere.  Yes, each individual event can have a possible different explanation, but it seems to happen over and over.  If we as scientists are constantly searching for a new way to explain why something observed isn't impossible, maybe we need to go back to the fundamentals and look at why we thought something was impossible to begin with.
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV on 03/04/2010 10:24:03
In my words...... Tassie Devil's genetics, prior to the toxins in their water, were all the same throughout their species. After the toxins from the mono culture effected their water, their genetics changed over 2-3 generations to cope with the toxins and to survive and reproduce.
In that case, I think you've got entirely the wrong end of the stick with that paper.

Quote
So if you go to the zoo where these animals are kept away from the toxins, you will find their genes are different from the ones in the wild.

The toxins are not leaving their water system any time in the near future, so if they continue to breed their genes will be passed down throughout many generations. While the captive Tassie Devils reproduce without the altered genes.

That's not what the paper says.

Quote
1.Cancer is an epigentic disease characterised by the break down of DNA.

No it's not.  And in particular, DTFD is a contagious cancer - tumour cells from one individual can cause tumours in another.

Cancer is a disease that can be caused by DNA damage - not the other way around.

Quote
2.Prior to the environmental change all the Tassie Devils genes were the same.
No they weren't - that would make them clones.

Quote
3. No change in Tassie Devil's genes in zoos or that have never come in contact with the toxic environment.
Well, it's not a toxin in the environment - if DTFD isn't introduced, why would you expect any change?
Quote
4. It took 2-3 generations for the environment to effect change in their genes.
The abstract says:
"We observed a significant increase in inbreeding in devil populations after just 2-3 generations of disease arrival, but no detectable change in genetic diversity."

Quote
5. If the captured, zoo's Tassie devils were released and returned to their native environment they would not survive. Their environment has directly effected their evolution.
The paper doesn't say anything about this.  It may be true that captive animals don't do well in the wild, but that may be nothing to do with their genes.
Quote
6. As I believe, if the ones in the zoos continue to reproduce together without bringing in the new genes from their wild counterparts then 2 distinct species of Tassie Devils may occur over time. One group unable to live/reproduce/survive in it's natural habitat.
Survival of the fittest!
Spot on.  This is why captive breeding programmes often swap males (or sperm) to try to keep variation high.


My analysis of the paper (based only on the abstract) is that DFTD leads to population and distribution changes, that can lead to genetic changes over a few generations.  This doesn't necessarily mean mutations, it means variability - different proportions of different alleles etc.
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV on 03/04/2010 10:29:57
If epigenomic markers actually allow life to direct mutation to any extent whatsoever, would that qualify as "intelligent design"?

If any process (epigentics)is involved rather than 'random change', you would think there is some 'intelligents'about it?

I think so.

I don't think so.

Intelligence requires consciousness and forethought.  Epigenetic changes do not.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 03/04/2010 10:33:19
Here is a few more examples which I feel indicate epigenetics causing mutation. . .

Cool.  Thanks for the links.  I'll take a look over them when I have a chance.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 06/04/2010 06:15:01
I just came across this, and I'm not sure if I am understanding or interpreting it correctly:

http://www.ncbi.nlm.nih.gov/pubmed/10690404?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=3&log$=relatedreviews&logdbfrom=pubmed

Quote
A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. 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. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.

The first part of the underlined section seems to be referring to epigenomic markers.  "Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements." seems to be saying epigenomic markers are responsible for the mechanism which allows an organism to make a large mutation?

"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."  This seems to be saying that certain plasmids may be able to "carry" beneficial mutations throughout a population?  If this occurs, mustn't it have evolved at some point?  The only reason I can think of as to why a mutation like that would be beneficial is because it allows beneficial mutations to be transmitted without direct mating.  If that is true, it seems to be just another element which is starting to show us just how advanced life is, and how much it seems to recognize(consciously or not) the need to evolve into a fitter organism is paramount to survival of future generations.

To be honest, I'm not precisely sure what transient hypermutators are specifically, but I'm guessing from the name that they are theoretical cellular "machines" capable of increasing the rate of mutation under adverse conditions.  I'm also guessing that the reason they are theorizing the mutators might exist is because we consistently see in experiment after experiment that beneficial mutations tend to happen very rapidly when they are really needed, but almost not at all when the organism is not under stress.  Even if the mutations afterward were indeed random, doesn't this still represent the ability of an organism to control mutation, and evolution to some extent?

If I have misunderstood anything I apologize, it is surely not my wish to put forth a misinterpretation of science.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 06/04/2010 23:52:00

1.Cancer is an epigentic disease characterised by the break down of DNA.

No it's not.  And in particular, DTFD is a contagious cancer - tumour cells from one individual can cause tumours in another.

Cancer is a disease that can be caused by DNA damage - not the other way around.


Quote
http://webcache.googleusercontent.com/search?q=cache:-deFKSjLe1sJ:assets0.pubget.com/pdf/17458893.pdf+Cancer+is+an+epigentic+disease+characterised+by+the+break+down+of+DNA.&cd=49&hl=en&ct=clnk&gl=au

Epigenetic alterations, such as modifications in DNA methylation patterns and post-translational modifications of histone tails, behave extremely
different from genetic modifications,

see also
www.epidna.com/showabstract.php?pmid=15881895

www.epidna.com/showabstract.php?pmid=16210093

www.ncbi.nlm.nih.gov/pubmed/19069364

www.docstoc.com/docs/20476934/02-Cancer-Epigenetics-Group/

http://atlasgeneticsoncology.org/.../GenetInstabilityCancerID20056.html

informahealthcare.com/doi/full/10.1517/17530059.1.1.17?select23...

www.pebc.cat/grupodetalle.php?idg=7

http://ajp.amjpathol.org/cgi/content/full/164/6/1883

Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 07/04/2010 06:13:41
I must admit to being totally confused (Yea, yeah. Save the cheap shots till later.)

Are we, or are are we not, debating about the existence of an intelligent designer? (which is usually what is strongly implied by the term "intelligent design".)

or;

are we debating the complexity of the process of evolution and how factors other than random mutation can play an important role in the process?

If it's the former, fine, then we are debating about the existence of an intelligent designer.
If it's the latter, does anyone mind if we change the title of this topic, because it is very confusing?
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 07/04/2010 18:31:32
My intent when I started the topic was to debate the evidence and logic in support of organisms choosing mutation, rather than merely random chance mutations resulting in the diversity of life we have.  I posted it the way I did, because if life has a way to influence and choose mutation then life would in a sense be "intelligently designed" but not by some god figure, rather by the organisms themselves.

A lot of people seem to be stuck on me using "intelligent design" in the title, I suppose I can see how with as many replies as there are it could be awfully confusing as to whether I am talking about a higher power or not.  I am most definitely not talking about "god", so if the title is just too confusing for people it should probably be changed.  Actually, it could even probably be merged with "Is evolution really down to random mutation?", since that is a very similar topic I posted before I had learned a little more on the subject.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 07/04/2010 19:17:26
Thanks for the clarification. That should do the trick. It's probably best not to change the topic title, as that might lead to even more confusion.  [:D]
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 07/04/2010 23:29:12
Just a few interesting links for those who are not bias.

Quote from: http://www.abc.net.au/catalyst/stories/s1486827.htm
Intelligent Design or ID, is being put forward as a serious scientific theory. It's even found it's way into some high schools.


Quote from: http://internationalstem.com/
Intenational Institute of Stem Cell Research and Regenerative Medician
Introduction:  California is currently becoming the main international hub of stem cell research.   Our staff is fully committed to creating this international center for stem Cell Research and clinical applications.  Dr. Schafer has been a twenty year pioneer in adipose tissue harvesting and fat transfer.  He is currently involved in the harvesting and preservation of “Intelligent” Stem cells which are naturally occurring in our bodies and not from fetuses or evoke religious taboos.   These Adult stem cells are extremely valuable and have great potential for future therapies.  It is important to note that these cells do not induce any type of immune reaction in the body.  Our Institute is at the forefront of this emerging technology.  Many of the pharmacological protocols as well as cosmetic proceedures  of  the twentieth century are being replaced by the utilization of stem cells for a cosmetic procedure.  This Institute provides world leading innovations in fat grafting with stem cells and regenerative medicine.  Dr. Schafer provides the vision and scientific guidance to advance the Institute to it’s potential of scientific excellence.

Quote from: http://en.wikipedia.org/wiki/Microbial_intelligence
Microbial intelligence (popularly known as bacterial intelligence) is the intelligence  shown by microorganisms. The concept encompasses complex adaptive behaviour shown by single cells, and altruistic and/or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.

Quote from: http://www.world-science.net/exclusives/exclusives-nfrm/050418_bact.htm
Yet the humble microbes may have a rudimentary form of intelligence, some researchers have found.

Quote from: http://www.astrobio.net/interview/2111/bacterial-intelligence
If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that's because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They'll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can't tell. You can't tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

So yes I think life itself is intelligent and there is a degree of design about it which we have not yet been able to understand
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 07/04/2010 23:52:06
Intelligent Design, otherwise known as ID, has nothing to do with science. It is creationism wrapped up in pseudoscience and mumbo-jumbo. The fact that George W. Bush fell for it should tell you something, both about ID and GWB.

ID was invented in an attempt to require schools in the USA to teach creationism by pretending that it is some sort of science.

Perhaps we will have to change the title of this topic after all.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 08/04/2010 03:07:00
It is unfortunate for all that "intelligent design" can not be looked at scientifically. That we are all in a bias pot of random selection fighting for survival.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 08/04/2010 04:26:45
It is unfortunate for all that "intelligent design" can not be looked at scientifically. That we are all in a bias pot of random selection fighting for survival.

ID would be looked at scientifically if its proponents presented some scientific evidence. However, proponents of ID are not interested in conducting real science. They are only interested in pursuing their political agenda by deceiving gullible individuals into believing that ID is science.

Personally, I have no problem with religions, but I have a very big problem with religions that masquerade as science in an attempt to trick people.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 08/04/2010 05:19:23
It is unfortunate that Science can't prove that ID is totally and specifically scientific.
I am not a religous person, yet feel that our earth's evolution and everything in it  has not been entirely random.

Quote from: http://www.livescience.com/strangenews/050923_ID_science.html
Darwin himself admitted that if an example of irreducible complexity were ever found, his theory of natural selection would crumble.
 
"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down," Darwin wrote.

"complex specified information," or CSI for short.

An example of CSI from nature is DNA, the molecule found in all cells that contains the genetic instructions for life. DNA is made up of four repeating chemical bases arranged into complimentary pairs. The bases can be thought of as "letters" in a four-letter alphabet and can be strung together to form genes, which can be thought of as the "words" that tell the cell what proteins to make.

The human genome is made up of some 3 billion DNA base pairs and contains about 25,000 genes. DNA is obviously complex. The fact that humans always give birth to humans and not chimpanzees or naked mole rats shows that DNA is also specific.

When science takes the god out of 'intelligent design' that will be the day science can go forward. Until then we will continue going in circles trying to prove the theory of evolution by natural selection.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 08/04/2010 05:51:42
It is unfortunate that Science can't prove that ID is totally and specifically scientific.

You don't seem to understand. It's not up to "Science" (whatever that is) to prove that ID is scientific. It's up to ID to prove that it has some legitimate scientific foundation.

Thus far, ID  has done nothing but try to appeal to non-science and religious fundamentalism. (Apparently, in that regard, it has been quite successful.)

We may "wish upon a star" all we want, but, unfortunately, that does not make science.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 10/04/2010 16:59:27
It is unfortunate that Science can't prove that ID is totally and specifically scientific.

You don't seem to understand. It's not up to "Science" (whatever that is) to prove that ID is scientific. It's up to ID to prove that it has some legitimate scientific foundation.

Thus far, ID  has done nothing but try to appeal to non-science and religious fundamentalism. (Apparently, in that regard, it has been quite successful.)

We may "wish upon a star" all we want, but, unfortunately, that does not make science.

Ok, but like I said, this topic has nothing to do with creationist intelligent design.

What do you think about the evidence that I posted regarding directed mutation via epigenetics?
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 12/04/2010 05:10:45
Here is a few more examples which I feel indicate epigenetics causing mutation:

http://www.gate.net/~rwms/EvoMutations.html

. . .

Sorry it took me so long, but after reading through all of those sources and watching the last 5 minutes of the Naked Science video, I still have to disagree that there's evidence for epigenetic changes causing genetic mutation.  Those experiments all show that you can "rapidly" develop a lot of genetic diversity, but they don't attribute that to epigenetics.  I still haven't seen any direct evidence of epigenetic change causing genetic mutation. There's also the difference in time scales of "rapidly."  The sources you cite seem to be talking about time scales that are long compared to the life cycle of an individual, 10,000 generations in one study and mutation probability of ~10-8 per cell division in the other.  Epigenetics seems to be a much faster process, allowing single organisms to change (so changes on the scale of 1 generation).  If epigenetics induced mutation, then I would expect it to happen orders of magnitude faster than any of those studies show. 

Again, it's not that I think epigenetics isn't interesting and promising.  It's just that there doesn't seem to be enough evidence to link it to actual genetic mutations.  If that link is made, then it certainly would change things.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 13/04/2010 04:38:30
Epigenetic regulation may be an important mechanism of both preserving and modifying genomic structure.

Quote from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691666/

Both genetic and epigenetic changes contribute to development of human cancer.
... While there has been considerable progress in understanding the impact of genetic and epigenetic mechanisms in tumourigenesis, there has been little consideration of the importance of the interplay between these two processes.

A transposon-induced epigenetic change leads to sex determination in melon
Quote from: http://www.nature.com/nature/journal/v461/n7267/full/nature08498.html
Sex determination in plants leads to the development of unisexual flowers from an originally bisexual floral meristem1, 2. This mechanism results in the enhancement of outcrossing and promotes genetic variability, the consequences of which are advantageous to the evolution of a species3.

The behavior of a person's genes doesn't just depend on the genes' DNA sequence--it's also affected by so-called epigenetic factors.

http://www.nature.com/scitable/topicpage/Epigenetic-Influences-and-Disease-895
http://www.nature.com/scitable/topicpage/Gene-Expression-Regulates-Cell-Differentiation-931

Quote
........In addition, gene expression changes can lead to changes in an entire organism.

......DNA and its associated histone  proteins (together known as chromatin) can be chemically modified by a cell's own machinery.

....Together, these lines of evidence have led to an emerging hypothesis that cell-cell signaling and epigenetic changes converge to guide cell differentiation  decisions both during development  and beyond.

I would say that epigentics doesn't need to modify DNA to cause these changes and definitely has an influence in evolution.


Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 13/04/2010 04:48:08
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.........
"Different dialect groups are definitely not identical ... language is a reflection of our evolution, that's why you see the differences," says Liu.

This is an example of genetic and epigentics working together to create subtle genetic differences
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 13/04/2010 07:14:31

I would say that epigentics doesn't need to modify DNA to cause these changes and definitely has an influence in evolution.


You don't say! (Well, I suppose you did.)

Er, but how exactly do parents pass on their inherited characteristics by means other than the transmission of their DNA?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 13/04/2010 19:05:38
"Selective Pressure"

Quote from:  http://blogs.monografias.com/sistema-limbico-neurociencias/2010/03/02/culture-and-evolution-genetic-epigenetics-exaptations-spandrels-and-jumping-genes%E2%80%A6/
The best evidence available to Dr. Boyd and Dr. Richerson for culture being a selective force was the lactose tolerance found in many northern Europeans. Most people switch off the gene that digests the lactose in milk shortly after they are weaned, but in northern Europeans — the descendants of an ancient cattle-rearing culture that emerged in the region some 6,000 years ago — the gene is kept switched on in adulthood.

Lactose tolerance is now well recognized as a case in which a cultural practice — drinking raw milk — has caused an evolutionary change in the human genome. Presumably the extra nutrition was of such great advantage that adults able to digest milk left more surviving offspring, and the genetic change swept through the population.

This instance of gene-culture interaction turns out to be far from unique. In the last few years, biologists have been able to scan the whole human genome for the signatures of genes undergoing selection. Such a signature is formed when one version of a gene becomes more common than other versions because its owners are leaving more surviving offspring. From the evidence of the scans, up to 10 percent of the genome — some 2,000 genes — shows signs of being under selective pressure.

DNA carries information. Epigenetics is the conductor/regulator/, the switch that turns genes on and off.
The information in all living things is very much the same throughout species as I have been told by TNS and is what evolution is based on as far as I can understand.

This information carried by a species can be unchanged but regulated, switched on or off.
If this information regulator had a permanent effect there would not be evolution only permanent change.
(if the sea creature left the ocean to walk on land, the information required to be able to return to water and survive would have been lost)

DNA in identical twins have exact same DNA but may have very different immunity issues.


Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 13/04/2010 19:09:36
I just came across this, and I'm not sure if I am understanding or interpreting it correctly:

http://www.ncbi.nlm.nih.gov/pubmed/10690404?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=3&log$=relatedreviews&logdbfrom=pubmed

Quote
A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. 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. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.

The first part of the underlined section seems to be referring to epigenomic markers.  "Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements." seems to be saying epigenomic markers are responsible for the mechanism which allows an organism to make a large mutation?

"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."  This seems to be saying that certain plasmids may be able to "carry" beneficial mutations throughout a population?  If this occurs, mustn't it have evolved at some point?  The only reason I can think of as to why a mutation like that would be beneficial is because it allows beneficial mutations to be transmitted without direct mating.  If that is true, it seems to be just another element which is starting to show us just how advanced life is, and how much it seems to recognize(consciously or not) the need to evolve into a fitter organism is paramount to survival of future generations.

To be honest, I'm not precisely sure what transient hypermutators are specifically, but I'm guessing from the name that they are theoretical cellular "machines" capable of increasing the rate of mutation under adverse conditions.  I'm also guessing that the reason they are theorizing the mutators might exist is because we consistently see in experiment after experiment that beneficial mutations tend to happen very rapidly when they are really needed, but almost not at all when the organism is not under stress.  Even if the mutations afterward were indeed random, doesn't this still represent the ability of an organism to control mutation, and evolution to some extent?

If I have misunderstood anything I apologize, it is surely not my wish to put forth a misinterpretation of science.

I know the other links I posted don't specifically attribute results to epigenetics, but doesn't this one specifically state that it is epigenomic markers which "allow" large genomic changes to happen?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 13/04/2010 19:21:46
L=E3

Life=epigenetics, ecology, and evolution (L=E3)
quote from Greengard, who won the 2000 Nobel Prize in Physiology or Medicine for research into how neurons communicate.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 13/04/2010 19:35:30
Er, but how exactly do parents pass on their inherited characteristics by means other than the transmission of their DNA?

Please read this you may have a better understanding.
Quote from: http://pn.psychiatryonline.org/content/45/5/12.1.full
In other words, epigenetics is the place where nature and nurture converge. The genes we are born with can determine some but not all of who we are and who we become.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 13/04/2010 20:47:06
Here is a few more examples which I feel indicate epigenetics causing mutation:

http://www.gate.net/~rwms/EvoMutations.html

. . .

Sorry it took me so long, but after reading through all of those sources and watching the last 5 minutes of the Naked Science video, I still have to disagree that there's evidence for epigenetic changes causing genetic mutation.  Those experiments all show that you can "rapidly" develop a lot of genetic diversity, but they don't attribute that to epigenetics.  I still haven't seen any direct evidence of epigenetic change causing genetic mutation. There's also the difference in time scales of "rapidly."  The sources you cite seem to be talking about time scales that are long compared to the life cycle of an individual, 10,000 generations in one study and mutation probability of ~10-8 per cell division in the other.  Epigenetics seems to be a much faster process, allowing single organisms to change (so changes on the scale of 1 generation).  If epigenetics induced mutation, then I would expect it to happen orders of magnitude faster than any of those studies show. 

Again, it's not that I think epigenetics isn't interesting and promising.  It's just that there doesn't seem to be enough evidence to link it to actual genetic mutations.  If that link is made, then it certainly would change things.

The last 5 minutes of the Naked Science video "Was Darwin Wrong?" specifically states that it appears evolution can happen for faster than previously thought using epigenetic means.  The narrator actually states that new evidence shows life may be able to(and I quote) "make" evolution happen.  It also states that the answer to how whales "lost their legs" may have been initiated due to epigenetics and the expression of the PITX1 gene(I think that was the one at least).  So I'm not really sure how you could say their was no evidence for epigenetic induced mutation in the evidence I provided.

The link I posted regarding mutation of the Trp genes in e. coli bacteria states that beneficial mutations were observed at a rate which was orders of magnitude higher than what could be expected via random mutation alone.  This is exactly what is predicted if genetic evolution via epigenetically induced methods is a reality.

I didn't see how the Tasmanian devil bit applied in what echo posted, but since that post echo has posted several links which seem to me to provide legitimate evidence of epigenetically driven evolution.

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.

Evolution by purely random mutation predicts a steady rate of evolution over a large time scale.  When we look at the fossil record we see this to be false, as very little evolution at all seems to have happened over the first few billion years; then a massive explosion of life seems to have occurred and continued since.  We also see repeatedly in experiments that very few beneficial mutations seem to happen when the environment isn't stressed; yet when an environment is stressed and there is even the slightest chance at all for an organism to survive, all of a sudden the necessary mutation occurs in relatively short periods of time.

The fact that our fossil record, and the last 100 years of experiments continue to have results which are predicted by epigenetic induced genetic mutation and not predicted by purely random mutation gives a great deal of weight to the theory, whether it has been "proven" yet or not. 

When you talk about the different time scales in the experiments, it is important to consider how advanced the organism in question is.  It stands to reason that if epigenetically controlled genetic mutation first evolved ~750 million years ago, then even that control should have been evolving since.  Wouldn't this result in more advanced forms of life having more advanced forms of epigenetic control?  So when we look at experiments using "simple" bacteria, their control should be "simple" as well?  Shouldn't we expect epigenetic mutations and epigenetically controlled mutations to actually take fewer generations in more complicated/advanced forms of life?

Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 13/04/2010 22:14:05
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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 00:00:24
"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?"

"Transcription errors?"

Is this what is described as Random Mutation?

My personal view is that there is some type of Intelligents behind the mutations which are not errors at any length.

Quote from: http://www.abc.net.au/science/articles/2007/12/11/2115575.htm
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.

prior to the TDFT “The majority of devils in Tasmania were immunological clones and therefore susceptible to DFTD,” Geneticist and devil researcher Dr Kathy Belov http://www.tassiedevil.com.au/research.html#different

although there was no subdivision apparent among pre-disease populations (theta=0.005, 95% confidence interval (CI) -0.003 to 0.017), we found significant genetic differentiation among populations post-disease (theta=0.020, 0.010-0.027),

Prior to the cancer appearing, the Devil’s genetic diversity was so low, it was thought that in 10 years we could lose the species.

Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
Yes we can influence our children’s genes and our children’s children and theirs so they become alcoholics, diabetic, have cancer, schizophrenia, autism, Alzheimer's and many others. All depending on how we live our lives today.

Why Your DNA Isn't Your Destiny
By John Cloud
http://www.time.com/time/health/article/0,8599,1951968-2,00.html#ixzz0jukwTf7h

I know this is exactly what I submitted in this forum previously, hope this is easier to understand.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 14/04/2010 00:42:57
"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?"

"Transcription errors?"

Is this what is described as Random Mutation?

I believe that is correct. The genetic duplication process is not perfect, so in the process of copying DNA, some errors creep in. There are also external factors like, for example, radiation.

Anyway, perhaps you could answer my question. I don't think it was terribly complicated.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 14/04/2010 01:13:25

My personal view is that there is some type of Intelligents behind the mutations which are not errors at any length.


Of course you are entitled to hold a personal view, but if you can't prove that mutations are driven by some intelligence, then it's just your personal view. On the other hand, there is plenty of evidence that mutations are simply caused by transcription errors.

Perhaps you should start by proving that the DNA transcription process is infallible and base your argument on that.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 01:14:02
I believe that is correct. The genetic duplication process is not perfect, so in the process of copying DNA, some errors creep in. There are also external factors like, for example, radiation.

Anyway, perhaps you could answer my question. I don't think it was terribly complicated.

Firstly isn't radiation an environmental/epigentic issue?

If evolution only required a copy of hereditary DNA, wouldn't we be clones?

Quote from:  Geezer on 13/04/2010 22:14:05
"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?"

Sorry I thought you might read the links and decide for yourself.

here is another example:
Alcohol during pregnancy chemically alters fetal DNA
www.newscientist.com/.../dn18390-alcohol-during-pregnancy-chemically-alters-fetal-dna.html -

We are aware today that what we allow our children to do, will effect future generations for example...smoking at early increases the size of their children at birth, sitting in front of the computer for extended long periods, malnutrition, over eating, gambling, where we live, religion, etc, etc does have an ever lasting effect on generations to come, even though it has been established that these inherited traits may jump generations.

Some genetic diseases are carried through the male generation, some female and others both.

I was once told I am more like my gradparent than my direct parent, yet I could be visually mistaken for my cousin.

Maybe, the errors you speak of are just the genes being switch off or on by epigentics regulators?
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 02:22:06
Firstly isn't radiation an environmental/epigentic issue?
You're consistently misunderstanding what epigenetic changes are throughout this thread.  There is some debate as to the subtle points of epigenetics, but it's basically defined as changes to DNA expression that occur without changes to the underlying DNA itself.

Therefore radiation is environmental, and not epigenetic.


Quote
here is another example:
Alcohol during pregnancy chemically alters fetal DNA
www.newscientist.com/.../dn18390-alcohol-during-pregnancy-chemically-alters-fetal-dna.html -
Alcohol is environmental.

All the links you've been posting have been missing the point, since you're confusing epigenetics with non-epigenetic methods that induce changes in DNA.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 02:40:47
I just came across this, and I'm not sure if I am understanding or interpreting it correctly:

http://www.ncbi.nlm.nih.gov/pubmed/10690404?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=3&log$=relatedreviews&logdbfrom=pubmed

Quote
A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. 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. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.

The first part of the underlined section seems to be referring to epigenomic markers.  "Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements." seems to be saying epigenomic markers are responsible for the mechanism which allows an organism to make a large mutation?

"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."  This seems to be saying that certain plasmids may be able to "carry" beneficial mutations throughout a population?  If this occurs, mustn't it have evolved at some point?  The only reason I can think of as to why a mutation like that would be beneficial is because it allows beneficial mutations to be transmitted without direct mating.  If that is true, it seems to be just another element which is starting to show us just how advanced life is, and how much it seems to recognize(consciously or not) the need to evolve into a fitter organism is paramount to survival of future generations.

To be honest, I'm not precisely sure what transient hypermutators are specifically, but I'm guessing from the name that they are theoretical cellular "machines" capable of increasing the rate of mutation under adverse conditions. 
They aren't.  Transient hypermutators are cells that mutate quickly when put under selective pressure.  The big question about them is why they happen and why they seem to favor beneficial mutations.  The cited paper on it is here: http://www.genetics.org/cgi/reprint/126/1/5?ijkey=052e053149bad47e2eaa9e5103b0b085358501d3 and gives some explanations (none of them epigenetic).
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 03:04:14
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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 03:16:07

Therefore radiation is environmental, and not epigenetic.


Alcohol is environmental.

All the links you've been posting have been missing the point, since you're confusing epigenetics with non-epigenetic methods that induce changes in DNA.

Quote
author = http://www.newscientist.com/article/dn18390-alcohol-during-pregnancy-chemically-alters-fetal-dna.html

Alcohol during pregnancy chemically alters fetal DNA
This suggests that if women drink too much in pregnancy, epigenetic changes may cause some of the permanent symptoms seen in fetal alcohol syndrome in their children.

Quote
1993 Academic Press -  Delayed Heritable Damage and Epigenetics in Radiation-Induced Neoplastic Transformation of Human Hybrid Cells, by Marc S. Mendonca, Ronald J. Antoniono and J. Leslie Redpath © 1993 Radiation Research Society.
We have reported previously that under identical experimental conditions both the establishment of plateau phase and the onset of the expression of lethal mutations also occur after Day 9. We therefore propose that radiation-induced neoplastic transformation of HeLa × skin fibroblast hybrid cells is a consequence of the delayed expression of heritable damage under epigenetic control with a resultant loss of tumor-suppressor function.

Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 03:27:38
There is also no evidence, based on the way epigenetics works, that it can induce genetic mutations. 

In regard to the links and posts I contributed for this forum about the Tassie Devil....
The genetically modified mono culture planted in the devil's region has caused the tumors.
prior to the TDFT “The majority of devils in Tasmania were immunological clones and therefore susceptible to DFTD,” Geneticist and devil researcher Dr Kathy Belov http://www.tassiedevil.com.au/research.html#different
In 3-5 generations Devil's have genetic diversity changed.

All I can say is that epigenetics controls change and mutations in genes, would you except that?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 03:52:59
WHAT IS EPIGENETICS?
The development and maintenance of an organism is orchestrated by a set of chemical reactions that switch parts of the genome off and on at strategic times and locations. Epigenetics is the study of these reactions and the factors that influence them.

EPIGENETICS & THE ENVIRONMENT
The genome dynamically responds to the environment. Stress, diet, behavior, toxins and other factors activate chemical switches that regulate gene expression.
http://learn.genetics.utah.edu/content/epigenetics/

I believe I'm on the right track, Could JP explain my mistake please. Confussed.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 04:17:51
Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 05:27:41
Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

So we have established that epigenetics changes the cell's gene expression.
We know they do this by adding and removing mythal tags.(turning on and off genes)and this epigeneome acts as a cellular memory.(tags and records onto DNA)This continues through life and is inherited.

It doesn't have to lead to mutation to make vast alterations or variations in our DNA. But could over time.[quote A large genetic analysis of ethnic Chinese has revealed subtle genetic differences within the world's most populous nation.]

Epigenetics may well be the initiating stage for gene mutation since it controls whether or not the gene is active. over generations of the gene being turned on/off

Remembering that not a single gene mutation has ever benefited life, in my opinion mutation is neither beneficial or necessary for the survival of the fittest.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 05:40:52
is skin cancer which is a mutation of the melonomas epigenetic or not and why please so I can understand.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 05:43:00
It doesn't have to lead to mutation to make vast alterations or variations in our DNA. But could over time.[quote A large genetic analysis of ethnic Chinese has revealed subtle genetic differences within the world's most populous nation.]
Yes, it does.  Altering DNA itself is a mutation.  Altering the expression of DNA is epigenetics.  Those are the points you're confusing.

Quote
Epigenetics may well be the initiating stage for gene mutation since it controls whether or not the gene is active. over generations of the gene being turned on/off
It certainly may well be, but that makes it a hypothesis to be tested and so far there hasn't been evidence of that.  

Quote
Remembering that not a single gene mutation has ever benefited life, in my opinion mutation is neither beneficial or necessary for the survival of the fittest.
If I'm reading this correctly, your opinion is counter to mainstream science and evidence.  See Geezer's comment above: http://www.thenakedscientists.com/forum/index.php?topic=30685.msg306631#msg306631
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 05:48:07
is skin cancer which is a mutation of the melonomas epigenetic or not and why please so I can understand.

It could come from a variety of sources, none of which are epigenetic.  Off the top of my head (and from a limited understanding of the cellular processes involved), it is often caused by UV radiation damaging the DNA.  This damaged DNA can then cause the cell to go haywire, causing a cancer.  It could also be caused by transcription errors which occur when a cell copies its DNA.  These errors change the DNA which could then cause a cell to go haywire.

Epigenetic changes occur when a cell wants to turn off the action of a part of the DNA.  It doesn't destroy its DNA, but just says that it should stop following instructions from that part of the DNA.  The DNA itself is still intact and will be copied properly.  Future cells will have the same DNA as their parent (unless one of the other processes for DNA damage occurs).  The cells shouldn't go haywire since there's no error in the DNA that would make them do so.

At the very least, what I'm saying throughout is that there is no evidence that epigenetic processes can damage or change DNA in the same way as radiation or transcription errors.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 14/04/2010 05:56:30
If I'm reading this correctly, your opinion is counter to mainstream science and evidence.  See Geezer's comment above: http://www.thenakedscientists.com/forum/index.php?topic=30685.msg306631#msg306631

Please explain one mutation that is benefitual to life. I can't find one.
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP on 14/04/2010 06:28:43
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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).
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV 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")
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: JP 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 15/04/2010 02:51:01
I have not had any evidence here that mutating genes is of any advantage to evolution
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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. '
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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!
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.


Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV 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...
Title: Re: How big a role does the epigenome play in evolution?
Post by: PhysBang 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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. 
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: PhysBang 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: PhysBang 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.

Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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?
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.

Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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!
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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   [:)]
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber 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.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 18/04/2010 04:32:42
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.

That would seem to be true. Another way to look at it is that some environmental effect has an opportunity to influence multiple generations of evolution even though the effect itself was temporary or fluctuating.
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 18/04/2010 09:29:58
If you look at the situation where genetic changes have been enforced, e.g. dogs, you have an artificial species, though with a wolf genome. If people disappeared tomorrow, dogs would be wolf food 'on the hoof' and would likely disappear in a few generations. The alternative would be for the environment to alter itself to accommodate them, unlikely unless we hunted the wolves to extinction first. Even then, the dogs would evolve back into wolves, indistinguishable, as the environment is still king. The rules of evolution were set billions of years ago, and no amount of wish fulfillment will change them.
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV on 18/04/2010 09:31:54
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.

This all sounds very logical and sensible - but things that are subject to natural selection appear to make "choices" only after the fact - they're not choices, they're reactions, so we're back to the status quo, only with some epigenetic factors also being selected for/against.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 18/04/2010 16:32:07
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.

This all sounds very logical and sensible - but things that are subject to natural selection appear to make "choices" only after the fact - they're not choices, they're reactions, so we're back to the status quo, only with some epigenetic factors also being selected for/against.

I certainly agree that any evolution which occurs would be reactions to stressors, and I think our contemporary view of evolution is largely correct.  I think the key though is the speed at which diversity can happen using epigenetics.  Epigenetics allows an organism to make a large phenotypic changes extremely quickly, then discard them if they are no longer needed.

Natural selection can't work on a hand when there is no hand.  So by the epigenome providing large phenotypic changes which are in exactly the area for which there is the potential for a highly beneficial mutation; large diversity and evolution of new species can happen extremely quickly.  Plus, the epigenetic response seems to be shared by the entire local population so we don't have a problem with not enough population for survival and spreading of the new mutation.  If plasmids are capable of transmitting mutations throughout a local population, then we have even less of a problem having enough population sharing the trait in order for it to be passed on.  If transient hyper mutators can adjust the rate of mutation to a specific portion of the genetic code, then even if the mutation itself is "random", the gene which is being mutated is still being "chosen" of a sort.

Obviously life does not have perfect control over mutation, but since "random" is defined by having no boundaries, how many controls/influences need to be in place for a mutation to no longer be considered truly "random"?


If you look at the situation where genetic changes have been enforced, e.g. dogs, you have an artificial species, though with a wolf genome. If people disappeared tomorrow, dogs would be wolf food 'on the hoof' and would likely disappear in a few generations. The alternative would be for the environment to alter itself to accommodate them, unlikely unless we hunted the wolves to extinction first. Even then, the dogs would evolve back into wolves, indistinguishable, as the environment is still king. The rules of evolution were set billions of years ago, and no amount of wish fulfillment will change them.

I agree the "rules" of evolution were set long ago, but what are the "rules"?  We used to think that the genome contained everything, now we know it is the epigenome which controls the genome.  We understand much more than we did 100 years ago about biology, but there is a vast amount we still do not understand.

I also do not see why dogs would evolve back into wolves.  I do not see why evolution needs to, or would go backwards(other than minor epigenetic changes which are intended to possibly be temporary).  Why would it be beneficial for say dachshunds to evolve back into a wolf?  The food source of dachshunds(rats and burrowing creatures) is not the same as wolves, and wolves are not capable of burrowing the way dachshunds are.  I can see why dogs would begin to evolve away from the strict boundaries humans have placed on them, but I do not think they would evolve backwards.

[edited to include response to grizelda, so I didn't have multiple consecutive posts]
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 18/04/2010 18:17:55
What is the epigenetic transmission method from parents to children? I got the impression that it might only be possible for the male to pass on epigenetic information that was the result of some external influence. The female (mammal at least) cannot, because the female does not produce eggs after birth, so, in a sense, the epigenetic information from the mother is "locked in" from a very early stage.

Or did I get that wrong?

There are interesting analogies betwen these mechanisms and control systems (systems with feedback). Natural selection is a very heavily damped control mechanism (it has a lot of negative feedback.) Epegenetic modification has a very fast response with a slow decay (it's like a sawtooth). Together, they would seem to steer evolution through interaction, but understanding what the overall response actually is probably going to take an awful lot of work  [:)]
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 18/04/2010 18:28:42
What is the epigenetic transmission method from parents to children? I got the impression that it might only be possible for the male to pass on epigenetic information that was the result of some external influence. The female (mammal at least) cannot, because the female does not produce eggs after birth, so, in a sense, the epigenetic information from the mother is "locked in" from a very early stage.

Or did I get that wrong?

There are interesting analogies betwen these mechanisms and control systems (systems with feedback). Natural selection is a very heavily damped control mechanism (it has a lot of negative feedback.) Epegenetic modification has a very fast response with a slow decay (it's like a sawtooth). Together, they would seem to steer evolution through interaction, but understanding what the overall response actually is probably going to take an awful lot of work  [:)]

That's a very interesting point which I hadn't really thought about, I suppose it would have to be the male which passes on the epigenetic responses(in mammals at least).  Could this be why females often(not always) stay and protect the young, while males go out into the environment?

I agree, it will certainly be a lot of work to learn the actual responses and mechanisms.  But I find it absolutely thrilling, and I am very excited to see what is learned in my lifetime.  The medicinal potential from learning how DNA is controlled would seem to be incredible, aside from the pleasure of having a better understanding of life [;D]
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 19/04/2010 02:48:52
The rules of evolution probably themselves evolved. There would have been competing systems such as immortal lifeforms (until something fell on their head) but evolution obviously won out, probably fine-tuning itself in the process to the perfect system it is today.
  Wolves did not evolve forward to become dogs. When mankind's experiments in epigenetics end nature will regain her normal course, and it won't include dogs. If dachshunds could exist outside of their artificial environment, the woods would be full of them.
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 19/04/2010 10:38:06
The rules of evolution probably themselves evolved. There would have been competing systems such as immortal lifeforms (until something fell on their head) but evolution obviously won out, probably fine-tuning itself in the process to the perfect system it is today.
  Wolves did not evolve forward to become dogs. When mankind's experiments in epigenetics end nature will regain her normal course, and it won't include dogs. If dachshunds could exist outside of their artificial environment, the woods would be full of them.

Yes, but would mules turn into horses (or donkeys)?
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 19/04/2010 11:30:17
I assume you know that mules are infertile, so we'll need epigenetics to do the impossible.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 19/04/2010 15:42:19
The rules of evolution probably themselves evolved. There would have been competing systems such as immortal lifeforms (until something fell on their head) but evolution obviously won out, probably fine-tuning itself in the process to the perfect system it is today.
  Wolves did not evolve forward to become dogs. When mankind's experiments in epigenetics end nature will regain her normal course, and it won't include dogs. If dachshunds could exist outside of their artificial environment, the woods would be full of them.

Wolves did not evolve forward to become dogs, humans bred them forward.  But it is not just changes to epigenetics that produces dogs from wolves, so I don't see dogs changing back into wolves.  Regardless of the reason, dogs are where they are now, and wolves are backwards to them even if wolves can survive in nature better than some dogs.  There would probably be a blending of breeds of dogs, but dogs simply aren't the same genetically as wolves and therefore dogs can't just revert back to wolves.  Wild dogs have existed in nature for quite some time now, and they look very different from wolves.

Evolution is a great system, but I doubt it started out with immortals and competed.  The mechanisms used by life on earth to evolve probably have evolved, but "evolution" did not evolve, the life on Earth did.  I have no doubt the "rules" of evolution evolved, but it seems to me to be somewhat of a moot point since we have no idea what those rules are.  We used to think we did, but we were horribly mistaken. 

Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 20/04/2010 08:27:46
Wolves got to where they are by successive adaptations which the evolutionary process selected for. So they got a stronger bite, warmer fur, better eyesight etc. This implies that they evolved from ancestors with weaker bites, etc. Probably they have an ancestor that was a talented burrower, but they adapted away from that. The genes for that are still in their genome and can be expressed by careful breeding, so you can get all mixtures of dogs. None of their ancestors could fly, so you can't breed a flying dog. If epigenetics worked, you should be able to do that by throwing dogs out of airplanes until they got the picture. Sorry, that would be a cruel thing to do, lawyers maybe, but not dogs.
Title: Re: How big a role does the epigenome play in evolution?
Post by: rosy on 20/04/2010 11:08:02
Quote
The genes for that are still in their genome and can be expressed by careful breeding
No, some of the genes will still be there.
Some won't.
All genes are subject to "mis-copying". If that's a mis-copying of an expressed gene, it'll have a phenotypic effect (so maybe someone who has a mis-copied gene for melanin production would lack pigmentation and be an albino). But genes which aren't expressed can be mis-copied without any effect on the individual, but "breeding back" to the original gene then becomes impossible.
Title: Re: How big a role does the epigenome play in evolution?
Post by: rosy on 20/04/2010 11:09:17
Quote
None of their ancestors could fly, so you can't breed a flying dog
Equally, in principle you could, given enough years to do it in (and possibly some nice radioactive source to up the mutation rate of the gametes).
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 20/04/2010 19:42:56
If epigenetics worked, you should be able to do that by throwing dogs out of airplanes until they got the picture. Sorry, that would be a cruel thing to do, lawyers maybe, but not dogs.

Lol, nice idea with the lawyers, but you may be misunderstanding epigenetics and how it affects evolution... nobody is saying it's some magical force which instantly gives an organism the ability to be whatever it wants.  It is not a matter of "if" epigenetics works anymore, it is a matter of "how" it works and to what extent.
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 21/04/2010 00:59:17
It's just that there are so many unexpressed genes from countless generations previous that any new trait is almost certainly a re-expression of an old gene rather than the creation of a new one. Most species have different lineages so any genetic damage would be canceled out as they interbreed. It's just the law of averages. If they become too inbred they are usually headed for extinction. Epigenetics won't save them.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 21/04/2010 02:08:57
It's just that there are so many unexpressed genes from countless generations previous that any new trait is almost certainly a re-expression of an old gene rather than the creation of a new one. Most species have different lineages so any genetic damage would be canceled out as they interbreed. It's just the law of averages. If they become too inbred they are usually headed for extinction. Epigenetics won't save them.

I think this is contrary to what is at this point in time happening to the Tassie Devil.
prior to the devil's facial tumors their genetic pool was limited. Scientists say within 10 years the entire species could have been wiped out due to their limited gene pool, stating that they were almost clones of each other.
After the cancer they adapted and breed at a younger age, (I find that amazing) able to pass on some of the immunity to their offspring before they die. Now there is a breeding program in place that takes the non infected devils from captivity to breed with the more diverse genetic pool (since the cancer) in the wild. I beleive this is an example of epigentics and evolution
Title: Re: How big a role does the epigenome play in evolution?
Post by: Geezer on 21/04/2010 03:28:28
It's just that there are so many unexpressed genes from countless generations previous that any new trait is almost certainly a re-expression of an old gene rather than the creation of a new one. Most species have different lineages so any genetic damage would be canceled out as they interbreed. It's just the law of averages. If they become too inbred they are usually headed for extinction. Epigenetics won't save them.

That would seem unlikely. I have not calculated what the number would be, but the possible number of permutations of a genome that's as long as the human genome must be an incredibly large number. I'm sure there are lots of opportunities for the creation of new genes.
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 21/04/2010 10:45:24


I think this is contrary to what is at this point in time happening to the Tassie Devil.
prior to the devil's facial tumors their genetic pool was limited. Scientists say within 10 years the entire species could have been wiped out due to their limited gene pool, stating that they were almost clones of each other.
After the cancer they adapted and breed at a younger age, (I find that amazing) able to pass on some of the immunity to their offspring before they die. Now there is a breeding program in place that takes the non infected devils from captivity to breed with the more diverse genetic pool (since the cancer) in the wild. I beleive this is an example of epigentics and evolution
Having progeny is the most important task the devils have so they are getting it done before they die. They are adapting their behavior to their environment (being wiped out) but it is a last ditch effort. No genetic changes are taking place, of course. Their lack of genetic diversity is probably fatal. I hope the efforts made by the government can help them but they are in a fix.
 I was thinking that wolves might have allowed themselves to become subject to humans in order to archive their genes to better survive their being hunted to extinction (yeah we do that). Once the humans have wiped themselves out one way or another, the dogs can breed back into wolves and regain their throne atop the food chain. Top dog indeed! 
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 21/04/2010 11:10:06
That would seem unlikely. I have not calculated what the number would be, but the possible number of permutations of a genome that's as long as the human genome must be an incredibly large number. I'm sure there are lots of opportunities for the creation of new genes.
There are lots of ways to arrange the cards in a deck, but most arrangements are losers. I think evolution has found all the winning arrangements for the game we play (our environment). If the environment changes, new arrangements can become valuable, but most changes would be covered by genes from the past. Don't throw out your old steam engine!
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 21/04/2010 20:25:14
That would seem unlikely. I have not calculated what the number would be, but the possible number of permutations of a genome that's as long as the human genome must be an incredibly large number. I'm sure there are lots of opportunities for the creation of new genes.
There are lots of ways to arrange the cards in a deck, but most arrangements are losers. I think evolution has found all the winning arrangements for the game we play (our environment). If the environment changes, new arrangements can become valuable, but most changes would be covered by genes from the past. Don't throw out your old steam engine!

I would certainly agree that old arrangements may become beneficial again, but the thing is our environment is not just weather/topography;  The environment which matters to life and evolution includes other living things within the physical environment.  The competition between different species ensures continuous evolution, a series of reactions which lead to additional reactions which leads to even more reactions, and so on.  This means that we probably haven't seen all the possible combination's of environment, and in fact our environment should always be new.  This doesn't mean old answers won't work for new tricks, but it does mean that sometimes the old answer needs to be tweaked a little, which is where evolution comes in.
Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 21/04/2010 21:29:50
I agree, but the existing species are in tune with the existing environment which flows from the laws of nature. New adaptations cannot shoulder their way in just because they are, say, more politically correct. The environment must have a place for them to fit in without changing the laws of nature to accept them.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 21/04/2010 23:57:41
I agree, but the existing species are in tune with the existing environment which flows from the laws of nature. New adaptations cannot shoulder their way in just because they are, say, more politically correct. The environment must have a place for them to fit in without changing the laws of nature to accept them.
Mother Nature, Father Time.

Due to the changing laws of nature whether human influenced or not, including the time factor, the ever adapting multitude of species struggle to survive and appears to always have.

Life depends on adaptation to our environment. Some species are lost, some adapt.
Over vast periods of time some genes may evolve never to return to their previous state.
It is fact that humans genome is very much the same across the planet, as is all life. Unlike the hugh variation we had way back in the beginning of records. It is interesting to know that because of our environment and all that it includes we are able to still establish from our gene variations the area, group of people we belong to. Such as in China where tests were done to find variations between people from one region to another and also between people of each dialect of Chinese. I would imagine that this is evident across the globe. So epigentics controls our gene variation.
Human intervention in our environment does play a large roll. Everything in our environment is effective. Our own lifestyle today is reactive in our future generations.
Gene mutation causes cancer or disease which in turn may or may not assist our adaptation.
Some cancers and diseases are epigenetic and some are genetic. It has been found that genetic disease may be attributed to epigenetic factors, and can now be treated epigenetically.
Man identifies or labels a new species when that species no longer can survive by reproduction within its group. Birds are birds, possums are possums, depending on environmental factors these animals genes vary and over vast periods of time have become labeled different species.

It makes me think if Tassie Devils are now breeding at a much earlier age, never recorded before, due to the fatal cancers that kill them within 3-5 months, to pass onto their young the variation in their genes for establishing immunity, would humans or other species, due to epigenetic factors, once their genes vary, be able to breed with another species for survival? should their survival depend on it. Or was the variations in early man just the same species with epigenetic variations?










Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 22/04/2010 09:54:55
Due to the changing laws of nature whether human influenced or not, including the time factor, the ever adapting multitude of species struggle to survive and appears to always have.
I was hoping I could change 2+2 to equal 17 for a second so I could make a quick killing on the stock market but I realized that by the end of the second the universe would have exploded.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 24/04/2010 17:24:45
Due to the changing laws of nature whether human influenced or not, including the time factor, the ever adapting multitude of species struggle to survive and appears to always have.
I was hoping I could change 2+2 to equal 17 for a second so I could make a quick killing on the stock market but I realized that by the end of the second the universe would have exploded.

I think echochartruse might have a point... if we have genetic diseases, why not epigenetic ones?

Maybe not the changing laws of nature, but the environment is always changing ever adapting.  I admit I wasn't quite understanding what echochartruse was meaning with the Tassie Devil bit, but I might be starting to and maybe there is something there.  There is certainly huge potential with the epigenome, perhaps far more control than even I suspected.

If the epigenome tells a cell what type of cell to be, isn't it plausible that cancer may actually be epigenetic?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 24/04/2010 22:00:10

Maybe not the changing laws of nature, but the environment is always changing ever adapting. 

yes better said thank you.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 25/04/2010 00:08:27

If the epigenome tells a cell what type of cell to be, isn't it plausible that cancer may actually be epigenetic?

sites in support:


http://www.news-medical.net/news/2004/12/20/6892.aspx
Rett Syndrome, the first identified epigenetic disease - linked to specific defects in the three-dimensional folding of chromatin. 20. December 2004

http://www.nature.com/nature/journal/v429/n6990/full/nature02625.html

http://cancerres.aacrjournals.org/cgi/reprint/62/22/6784.pdf

http://www.cmaj.ca/cgi/content/full/174/3/341


Quote from: http://www3.interscience.wiley.com/journal/88512946/abstract?CRETRY=1&SRETRY=0
Cancer is an epigenetic disease at the same level that it can be considered a genetic disease. In fact, epigenetic changes, particularly DNA methylation, are susceptible to change and are excellent candidates to explain how certain environmental factors may increase the risk of cancer. The delicate organization of methylation and chromatin states that regulates the normal cellular homeostasis of gene expression patterns becomes unrecognizable in the cancer cell. The genome of the transformed cell undergoes simultaneously a global genomic hypomethylation and a dense hypermethylation of the CpG islands associated with gene regulatory regions. These dramatic changes may lead to chromosomal instability, activation of endogenous parasitic sequences, loss of imprinting, illegitimate expression, aneuploidy, and mutations, and may contribute to the transcriptional silencing of tumour suppressor genes.

I seem to be flogging the devils... but I believe this tumor associated with the run off from the mono culture of genetically modif
ied native trees (modified so they are fire retardant, I believe)has silenced the devil's tumor suppressor genes. the devils are unable to identify the cancer gene, as its DNA is similar to the devils, (which has been refered to at another posted link).

The fact that no chemical could be associated with this cancer has delayed the progress to over come it. The genetically modified mono culture trees natural oils running into the water system is proving to be the culprit.
Quote from: http://www.abc.net.au/austory/content/2007/s2820402.htm
DR MARCUS SCAMMELL, MARINE ECOLOGIST: The Tasmanian Government’s conclusion was that it was naturally occurring toxins and therefore it’s okay....DR MARCUS SCAMMELL, MARINE ECOLOGIST: Everything that we knew could cause toxicity we had eliminated.....DR CHRIS HICKEY, ECO-TOXICOLOGIST, NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH, NZ: It told us we were looking for something different, something unusual. I think they really may have stumbled on something quite new.


Quote from: http://www.abc.net.au/austory/content/2007/s2827187.htm
Because what disease in wildlife populations tends to be is a harbinger of instability, of a breakdown in normal cycles of a population reaching a stable balance with other animals interacting with their ecology. And perturbations, whether they are human induced, or the fact that we’ve actually through our agency allowed for the introduction of new pathogens. This is the brave new world that we face in the 21st century.
    please read this link.

Quote from: http://www.454.com/about-454/news/index.asp?display=detail&id=139
    In order to identify the tissue of origin of the tumors, the team used the Genome Sequencer FLX System to sequence both diseased and healthy transcriptomes-- the complete set of genes that are “turned on” in a specific cell. The researchers then compared gene expression results between the two tissues and found that the tumors’ genetic signature best matched that of Schwann cells found in the peripheral nerve. The underlying mechanism for how these nervous system cells spawned cancer cells is still unknown.....Murchison et al. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. (2009).


Quote from: http://www.abc.net.au/austory/content/2007/s2827178.htm
DR MARCUS SCAMMELL, MARINE ECOLOGIS............St Marys is surrounded by natural forest. And we’ve found no evidence of toxicity in the St Marys catchment. However in the St Helens catchment directly below this monoculture of plantation trees, we had permanently present toxin.


DR ALISON BLEANEY, GP & LOCAL COUNCILLOR (at South Georges River): This is the head waters of the South George which feeds into the George River, and here we are surrounded by plantations. This used to be natural bush and farming land and now we are completely surrounded by plantations here - the Eucalyptus Niters. This is the source of our drinking water for St Helens, let alone all the animals that drink from it, and this is one of the areas where we’ve discovered that the water in fact is toxic. This should be the most pristine water. This is the very head waters of the South George. Where is this toxin coming from?

(Excerpt of Dr Alison driving to visit patient)
DR ALISON BLEANEY, GP & LOCAL COUNCILLOR: I’m off to go and see a patient who’s got a very... a very rare cancer - Waldenstrom’s Anaemia. She’s one of only approximately 18 in Australia, and we just happen to have two in St Helens. And in the last perhaps six years or so we’ve actually seen quite few people with really quite rare autoimmune diseases of their brain for instance. We’ve had a case of Wegener’s Granulomatosis; it’s actually quite a rare disease.
So now looking back on this over the last ten years, I realize that I see many things now that as a GP... that many GPs would never see one of these cases in their working lifetime. Clearly in a population of less than 3,000 to have these rare diseases - to have this chronic ill health - there must be something on the go to explain this.

therfore I believe the Tassie devil's rare cancer is epigenetic

Title: Re: How big a role does the epigenome play in evolution?
Post by: grizelda on 26/04/2010 21:48:34
Possibly the trees have introduced a new toxin into the environment which is causing cancer in the human population and wildlife. The lineages of the populations that are susceptible to this will die off and those lineages whose genetic structure can cope will survive. The Tasmanian Devils have no immunity because some event in the past reduced their numbers to a few mating pair and all devils extant are descended from them. This lineage lacks the genetic protection or it has been damaged.
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 27/04/2010 00:12:29
Possibly the trees have introduced a new toxin into the environment which is causing cancer in the human population and wildlife. The lineages of the populations that are susceptible to this will die off and those lineages whose genetic structure can cope will survive. The Tasmanian Devils have no immunity because some event in the past reduced their numbers to a few mating pair and all devils extant are descended from them. This lineage lacks the genetic protection or it has been damaged.

Yes the trees are apparently a native species and the run off is natural oils but in extremely large doses due to monoculture style of planting. It has been said the trees are genetically modified with a fire retardant. whether that has anything to contribute to the problem, needs to be established.

Because the toxins occur naturally in the trees nothing has been done about it.

This disease kills quickly and the devils seem to be responding by breeding at a much earlier age.
Yes their genetic pool was very limited as you mentioned.
But 10 years after the disease we are finding the gene variation in the devils are more varied.
Hoping to breed them with the captive devils and release them into the wild with the plan they will better breed and pass on immunity.

the cancer may have caused the devils to evolve or adapt or help them adapt over time.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 17/05/2010 20:35:10
One aspect of the epigenome which I find extremely interesting is that both advantageous and deleterious traits seem to be passed on by the actions or experiences of an organism; i.e. In the Time article I cited a bit back, the descendants of those who had experienced times of extreme abundance in food were actually less fit than descendants of those who had to struggle.

I guess what I am curious about with this is:  In the past(and present) an omnipotent creator watching over us constantly has been used to encourage morality and balance in life; I personally do not believe in said creator, but could the epigenome replace that?  If all our actions and choices will be passed on to future generations, am I potentially dooming my children and grandchildren by my actions?
Title: Re: How big a role does the epigenome play in evolution?
Post by: echochartruse on 18/05/2010 01:34:15
One aspect of the epigenome which I find extremely interesting is that both advantageous and deleterious traits seem to be passed on by the actions or experiences of an organism; i.e. In the Time article I cited a bit back, the descendants of those who had experienced times of extreme abundance in food were actually less fit than descendants of those who had to struggle.

I guess what I am curious about with this is:  In the past(and present) an omnipotent creator watching over us constantly has been used to encourage morality and balance in life; I personally do not believe in said creator, but could the epigenome replace that?  If all our actions and choices will be passed on to future generations, am I potentially dooming my children and grandchildren by my actions?

The amazing thing about our genome influenced by our actions today which influence following generations is that there is 'choice' definitely not 'random'. The fight for survival is calculated.

For example, even though the devils did not have a choice in getting the cancer, there genome has chosen to allow them to mature earlier so they may breed earlier to a benefit of their survival in hope that generations will cope/acquire immunity to fight the cancer.

It doesn't entirely depend on you passing on the diseased gene but also what the next generation does with it. As someone said earlier here, just because a family has long generation of say breast cancer/ alcoholism, diabetes, whatever doesn't mean every person there after gets the genetic disease
There is choice which some see as Random.

Maybe the 'creator' is not a man but a protein or something entirely new/undiscovered within the proteins that control and process changes in our genome.

Tibetan highlanders began to genetically adapt to prevent polycythemia, should their children live at lower altitude then their genetic adaptations would alter to suit the conditions over just a few generations.

Whatever the source is for the process's initiation for our genome to cope, it is not random but logical and calculative.

It will be very exciting when we find what actually determines which genes are expressed.
http://www.sciencedaily.com/releases/2009/10/091009104646.htm
http://www.sciencedaily.com/releases/2007/12/071214094106.htm

Definitely intelligent process.
Title: Re: How big a role does the epigenome play in evolution?
Post by: BenV on 18/05/2010 08:03:10
Once more, echo, you are seeing intent and intelligence where there is none.

Things do seem to change in a directed way, but this does not mean there is intent there. You and Norcalclimber are making very different points.
Title: Re: How big a role does the epigenome play in evolution?
Post by: imatfaal on 18/05/2010 15:28:39

http://www.sciencedaily.com/releases/2009/10/091009104646.htm

http://www.sciencedaily.com/releases/2007/12/071214094106.htm

Definitely intelligent process.


The article behind the news story in the first link deals with various proteins and cellular factors that interract with DNA to determine transcription and elongation.  it deals with the actual three dimensional structure of the RNA polymerase II - transciption factor complex and how this binds to certain codes within the DNA.  it is neither evidence nor claims to be of an intelligence behind transcription.

The second article deals with phosphorylation of rna-polmerase II (specifically the repeat of 7 peptides in the tail) and how this affects trasncription - and whilst phosphorylation is a potential path of epigenetics the article does not deal with this explicitly.  it does not touch on any intelligence or guidance behing transcription.


These articles in no way promote your argument.
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 18/05/2010 19:47:14

The amazing thing about our genome influenced by our actions today which influence following generations is that there is 'choice' definitely not 'random'. The fight for survival is calculated.

I agree that there are some changes in the epigenome which could be called "chosen" by us, because we all choose how we will live our life.  But I do not agree that everything in survival or evolution is "chosen".  In fact I feel it is pretty well proven that everything is definitely not chosen because deleterious mutations do in fact happen.

It doesn't entirely depend on you passing on the diseased gene but also what the next generation does with it. As someone said earlier here, just because a family has long generation of say breast cancer/ alcoholism, diabetes, whatever doesn't mean every person there after gets the genetic disease
There is choice which some see as Random.

I have to completely disagree, I don't think anybody chooses to get breast cancer.  You are correct that the next generation has influence as well, but I do think it is random whether you get breast cancer or not.



Maybe the 'creator' is not a man but a protein or something entirely new/undiscovered within the proteins that control and process changes in our genome.

I see no evidence anywhere of any "creator" of any type or sort whatsoever.  When I started this thread I was warned that my use of "intelligent design" could be confusing, and I see now they were completely correct.

Let me be clear;  When I referred to the possibility of intelligent design, I was referring to the possibility that experiences can be passed down to offspring via the epigenome and that maybe those changes which were specific responses to environmental shifts allow life to evolve at a much faster rate than by purely random mutations.  I feel the fossil record implies this probably developed around 750 million years ago, but while there wasn't much evolution prior to that, it would be incorrect to say there was none.  I believe that most likely all of the mutations which drove evolution prior to ~750 million years ago were essentially random.

Tibetan highlanders began to genetically adapt to prevent polycythemia, should their children live at lower altitude then their genetic adaptations would alter to suit the conditions over just a few generations.

Whatever the source is for the process's initiation for our genome to cope, it is not random but logical and calculative.

I only partly agree with this.  Yes, I do think there is a non-random element to evolution.  Yes, due to mathematics I believe this non-random element is responsible for the vast majority of the diversity of life we can observe. 

I do not believe that nothing is random though.  In fact, I think that by looking at our Universe we can see that "random" is extremely important.

It will be very exciting when we find what actually determines which genes are expressed.
http://www.sciencedaily.com/releases/2009/10/091009104646.htm
http://www.sciencedaily.com/releases/2007/12/071214094106.htm

Definitely intelligent process.

Yes, it will be very exciting to find out more about the epigenome.

No, the process is not intelligent, it is life itself, the specific individual be it fruit fly or human that I find intelligent.  The process cares for nothing, it is nothing but a process. 

But life on the other hand....absolutely brilliant!!
Title: Re: How big a role does the epigenome play in evolution?
Post by: norcalclimber on 19/05/2010 02:01:05
In order to avoid confusion with creationism, which is the origin of the "intelligent design" phrase, I am changing the title question of this thread.
Title: How big a role does the epigenome play in evolution?
Post by: echochartruse on 21/05/2010 19:53:13
Evolution through natural selection.
What comes first the change in the genome or change in the environment?
"Random mutation that natural selection can act upon"?
Or could it be due to the environment that one life form’s genome changes which effects another life form? all due to epigenetics.
Say for example a disease such as cancer caused by contaminated environment has found its way into a host species and has developed strategies to regulate cell expression to allow itself to be undetected allowing itself to be transmitted throughout a specific species of animal while this disease constantly evolves, assisted by the very low genetic diversity of that animal species. Then almost instantaneous adaptation/selection" for younger animals across the species to reproduce happens. Is this truly 'random mutation' or esential mutation for that species to exist?
Therefore over time if nature took its course the population would probably bounce back. Genetic drift is said to be random. In this case the random factor would be which individual/individuls were capable of passing on the immunity. If none did then the species is lost forever. Immunity is esential for this species to exist
Natural Selection, a specific trait increases in the population because it is better adapted to the changed environment.
With Genetic Drift, a specific trait increases in the population simply because a random event caused there to be slightly more of one and less of another leading to the more populous being more likely to breed.

Epigenics is the cause, natural selection is the effect.

Is the ability for the species genes to adapt allowing them to breed earlier random or essential?
In this case the events are random not the mutation which is essential for life itself.

I recently saw a documentary stating that without Jupiter earth would not exist. Therfore I believe epigenetics is most important for evolution and most probably the major cause for evolution/adaptaion, not because a random gene mutation happened that nature had to act upon  to compensate to allow life to exist.