Epigenetics

[Loudmouth]

I keep hearing from creationists that epigenetics is a huge problem for the theory of evolution. Is there anyone who can explain this?

Just so we are clear, epigenetics is a process where gene regulation is influenced by two mechanisms: DNA methylation and histone ubiquitination.

https://en.wikipedia.org/wiki/DNA_methylation

https://en.wikipedia.org/wiki/Histone

To what extent are differences between species affected by these two mechanisms? Can a chimp give birth to a human by simply changing the pattern of DNA methylation in the chimp genome?

 

[RickG]

Are creationists experts in the field of epigenetics? I don't know squat about it.

 

[Loudmouth]

Are creationists experts in the field of epigenetics? I don't know squat about it.

They are "experts" at quote mining scientists talking about epigenetics, but I have yet to meet a creationist who really knew anything about it.

 

[sfs]

I keep hearing from creationists that epigenetics is a huge problem for the theory of evolution. Is there anyone who can explain this?

Just so we are clear, epigenetics is a process where gene regulation is influenced by two mechanisms: DNA methylation and histone ubiquitination.

https://en.wikipedia.org/wiki/DNA_methylation

https://en.wikipedia.org/wiki/Histone

To what extent are differences between species affected by these two mechanisms? Can a chimp give birth to a human by simply changing the pattern of DNA methylation in the chimp genome?

As I understand it, there's considerable fuzziness in the definition of "epigenetics" at present; Wikipedia has a decent write-up on the issue. The biggest dispute is whether to only count heritable changes or not (where "heritable" almost always means heritable across cell divisions, not across generations of the organism).

 

[Loudmouth]

As I understand it, there's considerable fuzziness in the definition of "epigenetics" at present; Wikipedia has a decent write-up on the issue. The biggest dispute is whether to only count heritable changes or not (where "heritable" almost always means heritable across cell divisions, not across generations of the organism).

If epigenetics doesn't cause change from one generation to next, then it hardly seems a problem for the theory of evolution. You would still have evolution operating through something that does span the generations, which would be DNA sequence.

 

[sfs]

If epigenetics doesn't cause change from one generation to next, then it hardly seems a problem for the theory of evolution. You would still have evolution operating through something that does span the generations, which would be DNA sequence.

Oh, sure. I'm just trying to be precise, since it seems unlikely that you'll get substantive responses here.

 

[whois]

evolution/DNA can't explain all inherited biological traits, research shows.
www.sciencedaily.com/releases/2015/04/150402161751.htm

in my opinion, the biggest unknown is if epegeneics can shut down gene expression, and if it can cause certain other genes to become fixed.

it's also my opinion that epegetics along with transposons and HGT might be responsible for some of the major evolutionary transitions that maynard smith speaks of.

 

[Loudmouth]

evolution/DNA can't explain all inherited biological traits, research shows.
www.sciencedaily.com/releases/2015/04/150402161751.htm

So what does explain those other traits? What is the mechanism? How many generations does it last?

in my opinion, the biggest unknown is if epegeneics can shut down gene expression, and if it can cause certain other genes to become fixed.

What are the mechanisms that cause genes to become fixed in a population? Isn't it natural selection?

it's also my opinion that epegetics along with transposons and HGT might be responsible for some of the major evolutionary transitions that maynard smith speaks of.

First, transposons and HGT may not be strictly Darwinian, but they are certainly evolutionary mechanisms. They both involve changes in the DNA sequence of a genome that are then passed through natural selection. They are completely separate from epigenetics.

Second, how can epigenetics produce the diversity of eukaryotes over hundreds of millions of years if the effects of epigenetic mechanisms only last 1 or 2 generations?

 

[FreeinChrist]

MOD HAT

A clean up was done of off topic posts and flaming. Please do not respond to obvious violations - just report them.

 

[whois]

So what does explain those other traits? What is the mechanism? How many generations does it last?

i have no idea what explains it, koonin introduces the term fundamental unit of evolution.
in regards to the number of generations, it might be an unknown number.
this epigenetics stuff might be setting the stage for further genetic additions down the road
in some cases it might make HGT possible.
the fact remains that it's even possible to begin with, a change in an organism without a corresponding change to DNA?

What are the mechanisms that cause genes to become fixed in a population? Isn't it natural selection?

there's reason the believe that the ABO blood group gene was acquired by HGT and was fixed immediately into DNA.

First, transposons and HGT may not be strictly Darwinian, but they are certainly evolutionary mechanisms. They both involve changes in the DNA sequence of a genome that are then passed through natural selection.

i wouldn't necessarily call transposons "fixed"

They are completely separate from epigenetics.

i don't agree with this either.
i think this is the major reason koonin and noble both are calling for darwinism to be trashed.
gould wrote a paper on spandrals, but gould didn't look close enough.
i believe epigenetics could very well be a molecular type of spandral.

Second, how can epigenetics produce the diversity of eukaryotes over hundreds of millions of years if the effects of epigenetic mechanisms only last 1 or 2 generations?

by using goulds concept of spandrals.
goulds paper dealt with structural changes in the bony part of the skeleton.
maybe epeigenetics is the molecular counterpart of this concept.

 

[Loudmouth]

i have no idea what explains it, koonin introduces the term fundamental unit of evolution.
in regards to the number of generations, it might be an unknown number.

So you don't know what causes epigenetics or how long it sticks around, but you are utterly convinced that it explains all of these evolutionary changes. Wow.

this epigenetics stuff might be setting the stage for further genetic additions down the road

What epigenetics stuff? How does it set the stage?

in some cases it might make HGT possible.

Why can't HGT be possible without epigenetics? How does epigenetics make it more possible? What are the mechanisms?

Are you just making stuff up at this point?

the fact remains that it's even possible to begin with, a change in an organism without a corresponding change to DNA?

That isn't evolution. You getting a tan in the summer is not evolution. Evolution is a change in a population of organisms over several generations.

Also, HGT is a change in DNA, so be careful not to lump it in with epigenetics.

there's reason the believe that the ABO blood group gene was acquired by HGT and was fixed immediately into DNA.

When in vertebrate evolution did this occur? How many vertebrate genes are the product of HGT compared to VGT?

i wouldn't necessarily call transposons "fixed"

Why would they have to be? When a transposon moves in the genome it changes the DNA sequence of the genome. It is a change in DNA sequence. That is not epigenetics.

Also, when a transposon produces a new insertion in a genome there is no guarantee that it will always be beneficial. It is entirely possible for a new transposon insertion to be neutral or harmful. Therefore, the production of new transposon insertions is a random mutation of DNA with respect to fitness. It is entirely Darwinian.

i think this is the major reason koonin and noble both are calling for darwinism to be trashed.

As has already been shown, what you think and what Koonin/Noble think are not always the same thing.

For example, Koonin thinks that the tree of life concept works just fine for the vast majority of eukaryotic evolution. His only argument is that since HGT is much more prevalent in the other domains of life that we should not apply the same concept to all life. You try to misrepresent this as meaning that Darwinian evolution doesn't work for anything.

i believe epigenetics could very well be a molecular type of spandral.

You seem to believe a lot of things. The tough part seems to be producing evidence for those beliefs.

 

[Loudmouth]

For those who think epigenetics is evidence of an intelligent designer, how do diseases caused by epigenetics figure into this conclusion?

"Fragile X syndrome is the most frequently inherited mental disability, particularly in males. Both sexes can be affected by this condition, but because males only have one X chromosome, one fragile X will impact them more severely. Indeed, fragile X syndrome occurs in approximately 1 in 4,000 males and 1 in 8,000 females. People with this syndrome have severe intellectual disabilities, delayed verbal development, and "autistic-like" behavior (Penagarikano et al., 2007).

Fragile X syndrome gets its name from the way the part of the X chromosome that contains the gene abnormality looks under a microscope; it usually appears as if it is hanging by a thread and easily breakable (Figure 3). The syndrome is caused by an abnormality in the FMR1 (fragile X mental retardation 1) gene. People who do not have fragile X syndrome have 6 to 50 repeats of the trinucleotide CGG in their FMR1 gene. However, individuals with over 200 repeats have a full mutation, and they usually show symptoms of the syndrome. Too many CGGs cause the CpG islands at the promoter region of the FMR1 gene to become methylated; normally, they are not. This methylation turns the gene off, stopping the FMR1 gene from producing an important protein called fragile X mental retardation protein. Loss of this specific protein causes fragile X syndrome. Although a lot of attention has been given to the CGG expansion mutation as the cause of fragile X, the epigenetic change associated with FMR1 methylation is the real syndrome culprit."
http://www.nature.com/scitable/topicpage/epigenetic-influences-and-disease-895

Did the intelligent designer design us so that we would have children who are mentally handicapped?

 

[Ada Lovelace]

We studied epigenetics relatively extensively in my biology class this past school year, and I wrote one of my papers on epigenetic cancer research with some resources provided by the Noreen Fraser Foundation at UCLA. During the spring when there was so much hullabaloo about epigenetics on here piquing my curiosity I asked my teacher about whether it it any way compromised the TOE. She said it doesn't, at all, not even a teeny tiny bit, and that Koonin's quotes had been bastardized.
In a nutshell she said creationists will seek any reason to try to undermine TOE, and to stop taking things seriously here, haha.

@RickG if you're interested there are actually interesting lectures about epigenetics on TedEx. I didn't go to this school, but this link was shared on a thread on another forum about preparing for the AP Biology exam. The videos were not created for high schoolers, though, so I don't think you'd feel talked down to or anything by them.

https://sites.google.com/a/parishepiscopal.org/savage-science/home/ap-biology/9--unit-ix-regulation

 

[The Cadet]

@whois

i think this is the major reason koonin and noble both are calling for darwinism to be trashed.

Please stop lying about what Eugene Koonin has to say about evolution.

 

[whois]

@whois


Please stop lying about what Eugene Koonin has to say about evolution.
View attachment 161351
View attachment 161350

please stop with the strawman crap.
koonin didn't say a word about evolution.
he specically said darwinism and its modern incarnations (neo darwinism AKA the modern synthesis).
any further attempts like this will be reported.
capeesh?

and yes, koonin did in fact say darwinism belogs in a museum, so get over it ok?
maybe you need to read a few of his papers published at NCBI.
also, give his book "the logic of chance" a once over.

edit:
hey, try this on for size, published by koonin at NCBI:
The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the Tree of Life as we knew it but also another central tenet of the Modern Synthesis inherited from Darwin, gradualism. In a world dominated by HGT, gene duplication, gene loss, and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.
Equally outdated is the (neo)Darwinian notion of the adaptive nature of evolution: clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection 16, 17. And, with pan-adaptationism, gone forever is the notion of evolutionary progress that undoubtedly is central to the traditional evolutionary thinking, even if this is not always made explicit.
The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution (Box 1). So, not to mince words, the Modern Synthesis is gone.
-the origin at 150.

but hey, i'm lying, right?
what a laugh.

i will take the word of NCBI over an internet nobody any day of the week.

BTW, the files i uploaded in post 7 were authored by noble and jablonka, NOT by koonin.

 

[Loudmouth]

We studied epigenetics relatively extensively in my biology class this past school year, and I wrote one of my papers on epigenetic cancer research with some resources provided by the Noreen Fraser Foundation at UCLA. During the spring when there was so much hullabaloo about epigenetics on here piquing my curiosity I asked my teacher about whether it it any way compromised the TOE. She said it doesn't, at all, not even a teeny tiny bit, and that Koonin's quotes had been bastardized.

Which Koonin quote are you talking about?

Also, is the epigenetic pattern in cancer cells transmissible to the next generation?

 

[Loudmouth]

hey, try this on for size, published by koonin at NCBI:
The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the Tree of Life as we knew it but also another central tenet of the Modern Synthesis inherited from Darwin, gradualism.

"The comparative infrequency of HGT in the eukaryote part of the biological world means, however, that in this case the conceptual implications for the TOL might not be as drastic: the evolutionary histories of many eukaryotes appear to produce tree-like patterns."--Eugene Koonin
http://www.biologydirect.com/content/6/1/32

Koonin's argument focuses mainly on bacteria.

but hey, i'm lying, right?

You are mischaracterizing what Koonin says, as he himself indicates.

 

[whois]

"The comparative infrequency of HGT in the eukaryote part of the biological world means, however, that in this case the conceptual implications for the TOL might not be as drastic: the evolutionary histories of many eukaryotes appear to produce tree-like patterns."--Eugene Koonin
http://www.biologydirect.com/content/6/1/32

Koonin's argument focuses mainly on bacteria.



You are mischaracterizing what Koonin says, as he himself indicates.

yes, and you know for a fact that i have provided 2 sources, one of which states HGT is more pervasive in the animal kingdom than previously thought, and another source which explicitly states that species trees and genes trees rarely align.
this last paper was authored by doolittle and koonin, the new biology, beyond the modern synthesis.
do i need to search for the post or are you capable of it.
the last post of mine was sourced from the origin at 150, google the title and read it for yourself.
you know, i really get tired of people saying i'm lying, misrepresenting, bastardizing, or whatever.

instead of people penning emails then trying to pass it off like it's something i posted, why doesn't anyone send koonin my posts verbatum?
what's up with that?

i have no qualms whatsoever in saying koonin said darwinism belongs in a museum, and that it needs replaced rather than merely extended.
koonin and noble both have said this.
i have stated this over and over and over, but yet i'm lying.
yeah, get a grip, both of you.
i get tired of this attempted character assassination, and i'm going to start reporting posts if it doesn't stop.

 

[Loudmouth]

yes, and you know for a fact that i have provided 2 sources, one of which states HGT is more pervasive in the animal kingdom than previously thought,

And I have asked you time and again how pervasive it is. You never reply.

If it was first thought that HGT contributed 0.01% and it turned out to contribute 0.1%, that would be 10 times more pervasive that previously thought. However, it would still be insignificant as it applies to the overall evolution of eukaryotes.

and another source which explicitly states that species trees and genes trees rarely align.

Which source? Was it referring to bacteria?

the last post of mine was sourced from the origin at 150, google the title and read it for yourself.

It isn't my job to supply your references.

you know, i really get tired of people saying i'm lying, misrepresenting, bastardizing, or whatever.

Then don't do it.

i have no qualms whatsoever in saying koonin said darwinism belongs in a museum, and that it needs replaced rather than merely extended.

Did you read his email?

 

[whois]

Which source? Was it referring to bacteria?

i have provided the source twice already and i won't provide it again, it's not my fault you do not read my material.
so, go away, very very far away.