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Author Topic: How big a role does the epigenome play in evolution?  (Read 56259 times)

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #150 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.
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #151 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.
 

Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #152 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.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #153 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]
« Last Edit: 18/04/2010 17:01:05 by norcalclimber »
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #154 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  :)
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #155 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
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #156 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.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #157 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)?
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #158 on: 19/04/2010 11:30:17 »
I assume you know that mules are infertile, so we'll need epigenetics to do the impossible.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #159 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. 

 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #160 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.
 

Offline rosy

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Re: How big a role does the epigenome play in evolution?
« Reply #161 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.
 

Offline rosy

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Re: How big a role does the epigenome play in evolution?
« Reply #162 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).
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #163 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.
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #164 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.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #165 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
« Last Edit: 21/04/2010 02:12:17 by echochartruse »
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #166 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.
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #167 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! 
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #168 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!
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #169 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.
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #170 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.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #171 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?










« Last Edit: 22/04/2010 02:24:23 by echochartruse »
 

Offline grizelda

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Re: How big a role does the epigenome play in evolution?
« Reply #172 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.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #173 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?
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #174 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.
 

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Re: How big a role does the epigenome play in evolution?
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