Talk:Epigenetics

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Contents 1 Questioning 2 putting 'et' into epigenics. 3 Some news on a research program 4 Merge request 5 How Karma works..... 6 Revisions 7 Bookmarking 8 Comment on Style

[edit] Questioning

This is an example of name clash. There are two schools - one is a "nurture" school, which argues that the configuration of the carbon atom, the state of the cellular environment, the protein expression, and the womb environment, then through the adult, is all epigenetics. The only people who believe in the definition you cite here, are those who believe that genes contain all the information to express the phenotype, which is demonstrably not true (have you seen the pictures of the five different sheep cloned with Dolly?).

So, the environment-centric definition must at least be mentioned. Frankly, I didn't think the other one still existed, as I haven't heard it used by a serious biologist in that sense in a while. As I understood it, the old use of the term you cite here is now part of proteomics or genetics proper. Note the criteria for what is considered "epigenetic" in biology:

http://www.cshl.org/AnnualReport1999/rh5.html "Not all clones are created equal. As genetically identical cells (such as those in an embryo) multiply, different sets of genes are switched on and others off, giving rise to cells and tissues with distinctive properties (e.g., liver versus muscle).

Such differential gene expression is often established by alterations in the large-scale architecture, or chromatin structure, of DNA. ... Such states of chromatin are said to be epigenetic because they can be inherited in a stable manner."

This implies pretty damn strongly that anything that "can be inherited in a stable manner" is epigenetic. Your definition is the wrong way around - it tries to limit epigenetics to the expression, whereas the expression is only part of epigenetics, and considered so because of the "stable manner", not because of its relation to the physical structure of the genome or program... if gene expression depends on hormones or environmental stimuli, then those are epigenetic factors.

The open question leading to the debate implied is whether expression of the trait in the phenotype is what is important (as it is for sexual selection and ecological selection both), or whether it is the capacity for its being passed on to offspring as a latent (unexpressed or only partially expressed) gene that the field should study. That's a big difference between molecular and evolutionary biology.

Also, look at the use of the term "epigenetic" in every field outside biology:

There are dozens of conferences on epigenetic robotics, and unless you are going to argue that they believe that robots have animal-like genes, well... http://www.lucs.lu.se/epigenetic-robotics/ http://www.google.com/search?q=epigenetic+robotics

If you want to say that "epigenetics" is "the study of traits that can be inherited in a stable manner", and includes all forms of selection, natural and otherwise, and that "epigenetic expression" studies the biological influences, e.g. the chromatin structure, and that "epigenetic robotics" attempts to duplicate the behavioral and perceptual traits using non-genetic entities, I wouldn't argue with that. But proteomics is epigenetic too, by any definition I've ever heard, because the protein folding characteristics in cellular media aren't determined by genes but are stable across generations. So you're taking a position on the genetic expression versus environmental mediation by using the term in this very narrow sense.

My definition isn't "real" only if you believe in genetic determinism of the phenotype - which corporate geneticists believe in, and nobody serious does. 24

--- Various non-bullshit references showing the intersection of the ways the term is used. I don't see how there can be an "epigenetic view" of robotic outputs of biomimicry unless the word has a broader sense than molecular:

References: Sipper, M. et al (1997) "A Phylogenetic, Ontogenetic, and Epigenetic View of Bio-Inspired Hardware Systems", IEEE Transactions on Evolutionary Computation, 1(1).

Sanchez, E. and Tomassini, M. (eds) (1996) "Towards Evolvable Hardware", Springer-Verlag, Lecture Notes in Computer Science, 1062. Higuchi, T. et al (1997) "Proceedings of First International Conference on Evolvable Sys-tems: From Biology to Hardware (ICES96)", Springer-Verlag, Lecture Notes in Computer Science.

Beyond that, there are lists of biological references these people refer to: "A good exposition of current population Biology modeling is J. Maynard Smith's text Evolutionary Genetics. Richard Dawkin's Selfish Gene and Extended Phenotype are unparalleled (sic!) prose expositions of evolutionary processes. Rob Collins' papers are excellent parallel GA models of evolutionary processes (available in [ICGA91] and by FTP from ftp.cognet.ucla.edu:/pub/alife/papers/ ). As fundamental motivation, consider Fisher's comment: "No practical biologist inter-ested in (e.g.) sexual REPRODUCTION would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should[s/]he do if [s/]he wishes to understand why the sexes are, in fact, always two?"

A full and proper biological epigenetics would probably have to explain why two sexes evolved, but three never did in any species. That's not necessarily going to be coming from the chromatin, although it might...

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The word "epigenetic" has nothing to do with "epigenetics". It comes from "epigenesis". There is no name clash over "epigenetics". AxelBoldt

• There were some biologists floating around giving lectures to the contrary in 2000. It was from one of these that I learned the definition I used... maybe he was *arguing for* this broader definition and it was original to him? Hard to tell standard from novel use when the work is state of the art - as I recall this was a single biologist explaining the phenomena so that the robotics folks could follow to explain how their biomimicry worked... maybe the moleculars won a terminology fight some time back, or maybe this more behavioral biologist was being way loose with epigenetic vs. epigenetics... whatever. It appears the narrow use is universal and the other is not. Perhaps if you related proteomics to this narrower and strictly-molecular definition of epigenetics, it would be clearer... perhaps a new name has been placed on the field studying the whole environment... However, I suspect strongly that this is reductionism by the molecular boys, trying to find clues to everything in little bits of DNA, rather than looking at stuff like wombs and environment conditions... 24

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Should we mention Trofim Lysenko in this context, or is that too far-fetched? --Magnus Manske, Monday, April 15, 2002

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[edit] putting 'et' into epigenics.

http://www.pitt.edu/~sshostak/

Waddington should be credited with injecting 'et' into epigenesis, turning it into epigenetics and drawing attention to the role of genes in development.

Harvey might also be mentioned by way of coinage, but he credits Aristotle, the Philosopher, with originating the concept of organic unfolding. See Shostak, S., "Death of Life: The Legacy of Molecular Biology." London: Macmillan; 1998.

[edit] Some news on a research program

Some scientists at Cancer Research UK and Cambridge's Babraham Institute think enzymes stablize epigenetics [1]

That would be canalisation? - Samsara 16:42, 1 January 2006 (UTC)

[edit] Merge request

The articles to be merged are epigenetics and epigenetic inheritance. There is a difference between these subjects in that the former is a field of study while the latter is the phenomenon itself. Therefore for clarity I think that both pages should remain separate. There will be some information more appropraite for each page, and there may be some overlap, but Wikipedia is not paper. Bensaccount 17:40, 18 February 2006 (UTC)

On second thought, I think that a merge might make organizing this easier. Bensaccount 17:55, 18 February 2006 (UTC)

[edit] How Karma works.....

There are compelling evidences showing that events such as holocaust and 9/11 have impact on the next generations

see the discusstion at

http://jcem.endojournals.org/cgi/content/full/90/7/4115

http://www.peakoil.com/fortopic18784.html

http://www.bbc.co.uk/sn/tvradio/programmes/horizon/ghostgenes.shtml

I wish to see these references are to be cited here

I second this. I've come here from seeing the BBC Horizon programme. I hoped to learn more, more history, current state of the research. Instead I found myself a little lost.

[edit] Revisions

I apologize if I stepped on any toes with my last revisions - I've deleted a considerable amount of text that was in my view redundant within the article or which should be referred to other Wikipedia articles referenced in the text, while making some additions. Some points on which you may disagree: I removed text suggesting that mitochondrial DNA mutations are epigenetic, because I don't think that's a typical usage; I distinguish epigenesis from epigenetics as an early 18th-century theory opposed to preformationism; I accept the idea of epigenetics as "anything but DNA" even though this practical distinction is historically fairly modern. As the Wikipedia help says, "be bold" ... sorry if you need to revert something! Mike Serfas 02:22, 18 August 2006 (UTC)

[edit] Bookmarking

The is the stub article Bookmarking related to this? Bookmarking has very few links, after I fixed the ones looking for bookmark (computers). Someone who knows the difference between epigenetics and epigenetics should (heh) should throw a few links at it. -- Kendrick7 22:12, 10 October 2006 (UTC)

[edit] Comment on Style

Although my degree in Biology is over 20 years old, I should be able to understand this article. I found it to be very hard to read. —The preceding unsigned comment was added by Oswalia (talk • contribs) 16:47, 11 December 2006 (UTC).

• I concur. I have tagged this article with a request for consistency in reference formatting as I feel this is its worst failing, but the style could do with improvement in addition. StoptheDatabaseState 14:40, 13 December 2006 (UTC)

I think both of your comments are too kind. The opening section, to say nothing of the rest of the article, is completely incomprehensible for me. Someone like me, who has taken a college-level biology survey course, should be able to at least understand the opening of an article like this, if not the entire article (Wikipedia is not a biologists' Wiki). Since the topic was discussed recently in Discover magazine, it must be possible for reasonably intelligent lay people to understand this topic on some level. As it is, the article is nigh worthless since it means nothing to people who don't already understand the subject. It needs heavy revision, IMO. 205.157.110.11 04:49, 25 January 2007 (UTC)

• I agree with the above comments. It is both welcome and essential that experts in the field contribute their knowledge in what is evidently a complex topic, currently apparently in the research phase, but the opening paragraph, at least, needs to give the layman some understanding. By the time I got to the 5th word in the opening paragraph I was lost. The wikilinks help, but they go to pages with the same issue. Could the meaning be stated in a second way? Could examples be used? Scanning further down the article I saw reference to a half-liver half-intestine cell, which suggested to me that this must be about understanding how some cells develop livers and some develop into other organs etc.--Rye1967 10:07, 20 February 2007 (UTC)