Originally Posted By: Orac
Originally Posted By: ImagingGeek

If you continue to read your own source you'll see it says exactly what I did - that in simpler organisms we do see inheritance of inter-generational epigenetic inheritance, but it is rare in "higher" organisms, and that such inheritance is often temporary, and is lost over multiple generations.

No it doesn't

Actually it did - I even gave you the relevant quotes.

Originally Posted By: Orac
and infact the latest publications in nature and other science journals highlights the controvesy.


Your first paper doesn't say what you think it does - its arguing that epigenetic changes may alter gene expression to allow invasive species to thrive in a different environment; i.e. epigenetics as a evolutionary strategy. It does not support the reverse - i.e. epigenetics as a mechanism of evolution.

Your second paper is about the effects of environmental contamination, and presents a hypothesis that is not widely held in the field. I'd also point out that their support for epigenetics in evolutionary responses consisted of one reference - to another hypothesis paper.

Originally Posted By: Orac
On the status quo that epigenetic changes eventually fade out there are also a number of reasonable papers


The science daily article repeated what I said verbatim - epigenetic change is rarely inherited over multiple generations and thus has a minimal evolutionary effect. The second article deals with a long-term issue of heritability (i.e. we often see a degree of inheritance of traits beyond what would be accounted for by identified genetics). All the paper does is provide a mathematical framework in which a role for epigenetics could be detected in "missing" heritability.

If you follow up on the papers citing your last paper, you'll find this study, which took the math from your paper and applied it to real-world data:

They found that unknown genetic interactions (i.e. gene regulation, protein interactions) account for the missing heritability, not epigenetic phenomena.

Originally Posted By: Orac
HOWEVER the controversy is still raging and is far from settled.

Funny, I've worked in the biomedical field for over 2 decades and never noticed the raging controversy - because there isn't one. The role of epigenetics in evolution is pretty well established; minimal effect on "higher" organisms, some effect on "lower" (I hate those terms, but I digress). While the exact degree to which epigenetic impacts the evolution of those organisms remains to be clarified, the net trend is extremely unlikely to change.

Originally Posted By: Orac
This month Nature they have 5 leading researchers and none of them can agree


The degree of conflict there is minimal; if you look closely you'll see the major difference in 'opinion' is time frame and species under consideration. Those looking at "higher" species were more muted, those looking at "lower" were more exuberant. Those considering long-term evolution were the most exuberant - which makes sense given that a) over long periods of time, rare events become "common", and b) in our deep history, we were all "lower" organisms and therefore likely more influenced by epigenetic changes.

To put the "controversy" into context, its equivalent to car-fans arguing over whether a 4-barreled carborator or multi-chanel fuel injector produces a faster car - no one is arguing over whether they work, how they work, that they work, or their imprtance in making a car go (i.e. a "real" controversy). All they are arguing over is which one makes it go faster.

Originally Posted By: Orac

To you it may be settled but to the rest of science this is far from settled.

Again, nothing in your links was contrary to what I wrote. I never said it never happened in "higher" orgnaisms - only that it was rare. And indeed, that is exactly what your articles stated. I also said it was more common in "lower" organisms - too which your papers also agreed. And lastly, I said its overall role was likely minor due to its transitory nature - to which all but your last article agreed with. And 4 of the 5 interviewees agreed in your last article - the one "hold-out" was discussion transposons in deep-time; to which he was very likely correct.

Originally Posted By: Orac
That is a load of rubbish any term in science has ambiguity because you are trying to break a very complex concept and bring it down to a word. Pick any scientific word and I will give you ambiguity on it, your example above just shows that feature in science.

No, there is no ambiguity. Epigenetics has a strict definition, as does evolution, selection, mutation, etc. as I stated, we need strict definitions to avoid confusion.

And just to highlight how well this works, consider your last article. They used "transgenerational epigenetic", rather than "epgenetics" for a reason - epigenetics covers a broad swath of processes, most of which are not inherited and thus have no evolutionary impact. They used a term which quite specifically relates to one very distinct form of epigenetics - the rare ones which may be inherited.

Our discussion of mutation is the same - mutation simply is defined as a "change in the nucleotide sequence of a genome". That is it - so any process which modifies the sequence is, by definition, a mutation. Meaning that gene conversion is a mutational mechanism.

If we want to be more specific, we use different terminology. "Gene covnersion" being one such term; other examples would be single-nucleotide polymorphisms, synonymous mutations, insertions, deletions, inversion, tri-nucleotide expansions, recombination, etc. All are mutations - they change the nucleotide sequence - but all are very different processes with very different mechanism.

Originally Posted By: Orac
I still think you are dancing around the big difference between the two that actual true mutation you can get a something that was never present in any form prior to the event. Recombination is exactly that a simple mixing of existing items.

Recombination is very much capable of creating new things. Indeed, it is far better at it than simple point-mutations. Recombination can copy genes, whciha re then free to undergo additional change without a fitness cost. Even solo - recombination is powerful - most new genes arise through recombination events - gene fusion and exon swapping can both occur during recombination, and both spontaneously create new genes with a previously non-existing sequence, structure and (potentially) function.

Moreover, you are assigning a purpose where none exists. Mutation doesn't have a purpose - it doesn't exist to create new variability or new genetic information. To the contrary, mutational mechanisms simply exist. What occurs downstream - be they adaptive or harmful, neutral or non-neutral, information-creating or information-destroying (or information-neutral), is a consequence of the mutation; rather than the function of it. A synonymous mutations, which has no effect on protein sequence, is still a mutation - despite have no biological impact what-so-ever.

I think you're over-anthropomorphising biology.


Last edited by ImagingGeek; 02/25/13 04:30 PM.