An Alternative to Mutations

[Baggins]

whats your point gawron?
epigenetics is not a problem for evolution, science has known about it longer than creationists have harped over it.
like what 30-35 years now?
as i said before epigenetics is not a problem for evolution or the ToE, only people who are building a strawman argument are claiming it is

The term epigenetics was coined 66 years ago.

For most of that time it has been part of the modern evolutionary theory synthesis.

Why are creationists suddenly saying it is a problem for the modern synthesis decades after it was incorporated within it?

 

[Naraoia]

Posted by Naraoia:

"While epigenetic modifications can affect the expression of existing genes, how would they produce novel traits that aren't just about a different expression pattern?"

It has recently been demonstrated that RNA plays a role in paramutation in mice. I am trying to find a full access link to the paper.

*learns a new concept* I haven't been much into epigenetics so far (it's quite sad that basically all the epigenetics you get in second year biology is a brief mention of DNA methylation )

Paramutation seems like an intriguing topic based on the wiki about it.

(However, it still seems to be a way of changing the expression of existing genes. So I'm a bit mystified as to why you are replying to my quoted bit with these - otherwise interesting - examples )

"Why is it that the amp resistent bacteria originated from the same spots on the parent plate (which had not been exposed to amp) every time?"

I didn't read the paper you linked to but off the top of my head it could be DNA methylation. DNA methylation is called an epigenetic modification because it is not encoded in the DNA sequence itself. It is a form of cellular memory, particularly when applied to CG-rich promoter sequences, has been shown to silence gene expression in a heritable manner.

Suppose amp resistance is a result of methylation (or whatever epigenetic mechanism). Then the question is how it would have arisen in an antibiotic-free environment, and why only in a few bacteria. (And I didn't read the paper either)

 

[Gawron]

Originally Posted by ReverendDG

whats your point gawron?

"epigenetics is not a problem for evolution, science has known about it longer than creationists have harped over it."

Why is it everytime someone new comes into any thread on this website, they are immediately attacked as a creationist? Talk about dogma. Perhaps the good reverenddg shoud change his name to reverened wright.

"Epigenetic Chickeeeennnnsss!! Are comming hooooommee!! To Roost!!!"

 

[Vene]

Originally Posted by ReverendDG

whats your point gawron?

"epigenetics is not a problem for evolution, science has known about it longer than creationists have harped over it."

Why is it everytime someone new comes into any thread on this website, they are immediately attacked as a creationist? Talk about dogma. Perhaps the good reverenddg shoud change his name to reverened wright.

"Epigenetic Chickeeeennnnsss!! Are comming hooooommee!! To Roost!!!"

Oh, I don't know, because you keep saying that evolution is wrong. And the people that do such a thing tend to be creationists. Now, as far as I can tell, you like Lamarckian evolution. Just so you know, epigenetic variation is not Lamarckian.

 

[sfs]

I'm not sure about this, but wasn't the "identicalness" based on markers that had nothing to do with the phenotypic traits in question? Wait, I've downloaded the paper, let me check... (this is the Podarcis sicula on Pod Mrcaru, right?) Yes, the analysis was based on mitochondrial rDNAs. I wouldn't imagine mitochonrdial ribosomes have a lot to do with the changes the lizards underwent. So from this genetic analysis alone it's impossible to decide whether the changes were genetic or epigenetic.

That had to be the case -- the experiment Gawron thought they did isn't possible yet. You can sequence the complete genome for one of the ancestral lizards and for one of the offspring (if you have quite a lot of money to spare), but the error rates in sequencing are high enough that you would not be able to pick out the small number of real mutations that distinguish them. In the real world you would also be dealing with a genetically varied initial population, so you would have to deeply sequence each of the original lizards -- more opportunity for error, and more money.

 

[Chalnoth]

Never mind the large number of genes which we've isolated that have very particular effects.

 

[Loudmouth]

"Why is it that the amp resistent bacteria originated from the same spots on the parent plate (which had not been exposed to amp) every time?"

I didn't read the paper you linked to but off the top of my head it could be DNA methylation. DNA methylation is called an epigenetic modification because it is not encoded in the DNA sequence itself. It is a form of cellular memory, particularly when applied to CG-rich promoter sequences, has been shown to silence gene expression in a heritable manner.

Quote:

"Although many nonmethylated GATC sites have been identified in E. coli, methylation in only a subset has been shown to control the expression of linked genes."

http://iai.asm.org/cgi/content/full/69/12/7197

This doesn't explain why specific E. coli clones were pre-adapted. All of the bacteria in the experiment were raised from a single bacterium, meaning that they all share a very recent common ancestor. From that single bacterium they produced billions and spread them on an agar plate that did not contain ampicillin (or the drug of your choice) and allowed them to grow for a bit. Using a felt covered stamp they transferred the bacteria to different plates containing amp. This allows them to keep the same spatial relationships between the bacteria on the parent plate. What they found is that the bacteria were pre-adapted to resist ampicillin, but only a few of them. Not only that, but they were clonally related.

DNA methylation can not explain this. An epigenetic mechanism needs to see the challenge first and then mount a response. In this experiment the bacteria were already amp resistant before they were exposed to amp, and this amp resistance was not found in the common ancestor (otherwise, the entire plate would be amp resistant).

 

[Loudmouth]

That had to be the case -- the experiment Gawron thought they did isn't possible yet. You can sequence the complete genome for one of the ancestral lizards and for one of the offspring (if you have quite a lot of money to spare), but the error rates in sequencing are high enough that you would not be able to pick out the small number of real mutations that distinguish them. In the real world you would also be dealing with a genetically varied initial population, so you would have to deeply sequence each of the original lizards -- more opportunity for error, and more money.

Those were my exact thoughts as well. It would seem to me that the next step (if they so choose) would be to discover the genetic differences (or epigenetic differences) that have resulted in the different morphology. It might make for an interesting evo-devo paper.

 

[Loudmouth]

See guys, this is a debate.

"That is, heritable epigenetic variation creates phenotypic diversity for natural selection to act upon"

In an example I cited before, Italian wall lizards introduced into a new environment underwent a change in snout-vent length, body mass, and head dimensions. Yet when DNA ayalysis was done from tail clips taken from the displaced lizards, it was found these lizards were genetically identical to the source population still living in the pervious environment. What accounts for this phenotypic alteration without a genotypic alteration?

One of the goals of the theory of evolution is to explain why species look different. I really doubt that exposing a chimp to a human lifestyle would cause the chimp's offspring to become more and more human like. Therefore, epigenetics can not explain the divergence between humans and chimps. The only other possibility (IMHO) is the difference in DNA sequence which is, of course, due to mutation.

"I'm asking if epigenetic changes would ever be enough to cause a population to break into multiple species."

Maybe, but this would not be the only factor in the equation. Staying with the lizards above, if the two populations were to be re-intergrated, the effect of geographic isolation (allopatric spciation) over time may cause the displaced lizards (B) to refuse to mate with the source population (A) even though they could still produce viable offspring.

If the lizards made their way back to their original habitat the would return to their original morphology, assuming that the change is epigenetic. This is not a very good mechanism for speciation.

 

[Gawron]

"Oh, I don't know, because you keep saying that evolution is wrong."

No, I don't. This is a mis-representation of my various post. I have posted information and then asked questions based on that information.

"And the people that do such a thing tend to be creationists."

I have found this to be the usual knee-jerk response both here and on other forums.

"Now, as far as I can tell, you like Lamarckian evolution. Just so you know, epigenetic variation is not Lamarckian."

The association between the two is not my idea. I simply believe it is a topic worth investigation and discussion. Is this what you disagree with? And it is 'neo-lamarckism.'

Epigenetic inheritance

"Forms of 'soft' or epigenetic inheritance within organisms have been suggested as neo-Lamarckian in nature by such scientists as Eva Jablonka and Marion J. Lamb. In addition to 'hard' or genetic inheritance, involving the duplication of genetic material and its segregation during meiosis, there are other hereditary elements that pass into the germ cells also. These include things like methylation patterns in DNA and chromatin marks, both of which regulate the activity of genes. These are considered "Lamarckian" in the sense that they are responsive to environmental stimuli and can differentially effect gene expression adaptively, with phenotypic results that can persist for many generations in certain organisms. Although the reality of epigenetic inheritance is not doubted (as countless experiments have validated it) its significance to the evolutionary process is however uncertain. Most neo-Darwinians consider epigenetic inheritance mechanisms to be little more than a specialized form of phenotypic plasticity, with no potential to introduce evolutionary novelty into a species lineage."

http://www.bionity.com/lexikon/e/Lamarckism

Excerpts from recent books on the subject:

http://books.google.com/books?id=l50tdUNgZZgC&pg=PA209&lpg=PA209&dq=epigenetics+and+%22neo+lamarckism%22&source=web&ots=iq9bfUq7XD&sig=isBUIz3GfkDft-1fQARRqPxYusE&hl=en

and:

http://books.google.com/books?id=65...7v2qAiK&sig=bQqAVD-sGyLiKVDZso45nlnEE0E&hl=en

 

[Gawron]

"If the lizards made their way back to their original habitat the would return to their original morphology"

I agree, and have made this point before, that if the two populations did begin to sexually reproduce the above would be the result. However, my point was within this construct:

"One of the best definitions is that of the evolutionary biologist Ernst Mayr:

A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so."​

 

[ReverendDG]

Originally Posted by ReverendDG

whats your point gawron?

"epigenetics is not a problem for evolution, science has known about it longer than creationists have harped over it."

Why is it everytime someone new comes into any thread on this website, they are immediately attacked as a creationist? Talk about dogma. Perhaps the good reverenddg shoud change his name to reverened wright.

"Epigenetic Chickeeeennnnsss!! Are comming hooooommee!! To Roost!!!"

did i say you were a creationist? please quote me were i did.
if you agree that epigenetics is not a problem for evolution, why did you not post so?
i was asking what your point was, since i didn't see any in the post you made.
just quotes and questions that really didn't say anything about the topic

i'll just ignore your attempt at ad homs

 

[Loudmouth]

Gawron,

True or false. The differences between species of apes (including humans) can not be explained by epigenetics.

 

[FishFace]

Epigenetics cannot account for most diversity, because we don't see the necessary responsiveness. It also doesn't explain the 3:1 recessive expression ratio, and can't account for, say, ERV orthologies.

 

[Gawron]

"i'll just ignore your attempt at ad homs"

It wasn't an ad hom, it was satire. Some of you guys are so sensitive. But, if you were offended, I apologize. Sincerely.

"True or false. The differences between species of apes (including humans) can not be explained by epigenetics."

Not as a stand alone mechanism, no. The quote I posted in my comments establishes that this was not my claim.

 

[Loudmouth]

"True or false. The differences between species of apes (including humans) can not be explained by epigenetics."

Not as a stand alone mechanism, no. The quote I posted in my comments establishes that this was not my claim.

I would agree with this part:

Most neo-Darwinians consider epigenetic inheritance mechanisms to be little more than a specialized form of phenotypic plasticity, with no potential to introduce evolutionary novelty into a species lineage.
​

Epigenetics can only produce limited adaptation, and even then the environmental stimuli has to persist in order for the adaptation to persist (population wide). This is different from strict neo-Darwinism in that maladaptions can persist if the selective pressure against them is weak. If the environmental conditions change in the future these persistent maladaptions could be the basis for evolutionary change. A good example is hemoglobin S (the sickle cell allele). This allele would persist for quite a few generations even in the absence of malaria. If malaria came back the population the resistance gene would already be in the population from the start.