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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 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 shouldhe do if 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...

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

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

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.

Some news on a research program

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

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

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 Misplaced Pages 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)

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.

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 Misplaced Pages 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 Misplaced Pages help says, "be bold" ... sorry if you need to revert something! Mike Serfas 02:22, 18 August 2006 (UTC)

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)

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 (Misplaced Pages 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)

Epidemix review

This article has been quoted and reviewed on 'Epidemix' and later featured on Wired. In the article, it is suggested that the first paragraph (an probably several other areas of the article) are too advanced for the average reader. --TheTallOne 07:53, 12 May 2007 (UTC)

I work in the epigenetics field, have an advanced degree and the first paragraph does a poor job of defining what epigenetics is. Epigenetics is defined as stable, heritable changes in gene expression that don't involve changes in the primary DNA sequence (ATCG) itself. These modifications include methylation of cytosine base and methylation, de/acetylation and/or ubiquitination of histone proteins which associate with the DNA. DNA and histones make up what is called chromatin. These modifications to the DNA or to the histones influence chromatin structure in such a way to either allow or prevent accessibility of the proteins responsible for gene expression. These changes are heritable across cell divisions (ie daughter cells have the same epigenetic pattern as the parental cells) and reproduction (epigenetic patterns are reestablished during embryogenesis based on the original epigenetic pattern of the gametes). I think the definition of epigenetics can be best understood contrasted with the more familiar "genetic" changes, such as mutation of the DNA. Most people understand what a mutation is, whether it be a point mutation, deletion, or some kind of translocation. Genetic alterations change the primary DNA sequence and unless they occur in gametes, won't be inherited by the offspring. Epigenetics involves the DNA/Chromotin. I've never heard any definition which involves protein modification by anyone in the field. I think its important not to out think ourselves and define the concept as it is generally used in the field. --Mawst95 20:42, 12 May 2007 (UTC)

Why not replace the Introduction in the article with what Mawst95 wrote above? Starting with "Epigenetics is defined as..." Psoreilly 21:50, 13 May 2007 (UTC)

Genetic determinism verses determinism in Winston lecture.

I think it is misrepresenting Winston to link to genetic determinism when the lecture really was about determinism. Winston mentioned Dawkins book/idea, The Selfish Gene but failed to advance Dawkins' views on the myth of genetic determinism which are better spelt out in The Extended Phenotype but we must assume he was aware of Dawkins' position on genetic determinism. I guess that subtle omission pales when Winston advanced a timeline of Darwinism to Eugenics and forced sterilization and then the Auschwitz concentration camp thus trying to paint some scientists and writers in colours both unethical and anti-semitic. Winston could do much to advance the public understanding of Epigenetics (which to most of joe-public the closest they have heard of is with prions in Mad Cow Disease) and this lecture isn't it. But then the public wasn't the target audience anyway. Ttiotsw 09:24, 14 May 2007 (UTC)

The whole Philosophical implications section should be removed. It seems to me to have been added solely as a stick to beat "determinism" (whatever that is) with. It adds nothing scientific or philosophical to the article, and is sourced primarily to two Winston pieces, one a lecture, the other an interview. The nod to Bateson is precisely that, a nod; while the quote of Jablonka's work is out of context, it is from a section not strictly about epigenetic mechanisms (more about (mis)perceptions of genes). Returning to Winston's remarks (or, at least, the reported versions here), they are very unclear, at times worryingly so ("some inherited genetic variations are not random"???). Furthermore, blandly stating that "calls this an argument against the 'selfish gene'" overplays the strength of the sources here. --Plumbago 16:18, 15 May 2007 (UTC)

Yup. Whatever that "philosophical implications" section is there for, it certainly does not address any philosophical implications... Snalwibma 16:22, 15 May 2007 (UTC)

Perhaps our mutual friend NBeale could answer this. I just love it when people base arguments on "determinism" as it it trivial to destroy. It is like grist between the two millstone of 3-body problem and emergent behaviour (just plucking two stones from my rockery). Ttiotsw 18:02, 15 May 2007 (UTC)

Looks like he has bigger fish to fry for now. Anyway, let's look at some of the statements in the offending section.

• genes are not the only unit of heredity

And? Is this statement disputed by anyone? I accept that it might come as a surprise to non-scientists though.

• some inherited genetic variations are not random

What exactly is meant here? Is mutation not random? Does this statement mean: a) that not all genes mutate at the same rate, or b) mutation is directional (a "guiding hand" perhaps)? This statement is too important for its ambiguity to be left as is.

• environment has a powerful effect on how genes work

High school biology triumphs again. The Extended Phenotype provides a nice intro to this.

• acquired information can pass onto the next generation i.e to say Lamarckism is not the necessarily wrong

True, but only in a limited way. Proper Lamarckian evolution is more or less precluded (c.f. The Blind Watchmaker for a nice intro), but there are well-known cases where Lamarckian-like processes occur (e.g. prions).

• evolutionary change is not necessary due always to natural selection

Again, high school biology triumphs. When I was at school I even wrote a computer program to simulate genetic drift.

• It is accepted by working geneticists that "the popular conception of a gene as a simple causal agent is not valid" and the gene cannot be seen as an autonomous unit

This is accepted by just about everyone! (Dawkins included NBeale) Everyone knows that there is a yawning gap between the genetic code and a specific phenotypic effect; a gap that's filled/obscured by all sorts of environmental factors (many of which are, of course, the product of other genes). It's certainly the case that the width of this gap is variable and not well-characterised in most cases (although in others it can be fairly straightforward, e.g. GM luciferase), but it's clearly also the case that despite "environmental effects" organisms tend to develop in the same way time and time again.

Anyway, beyond confusing things, I really can't see the purpose of this section (or, rather, I think I can ...). I'd remove it now, but I'd prefer some feedback first before doing so. --Plumbago 08:34, 16 May 2007 (UTC)

• Yes - as you say, it is a section devoted to knocking down a selection of elementary misconceptions and straw men, really just a list of obvious points which does not by any stretch of the imagination live up to the "philosphical implications" billing. The whole of what is in this section could in fact be reduced to a simple statement added to the very first sentence on the article - something like "Inheritance does not depend solely on genes". But in effect it already says that (though perhaps not quite as starkly as that!). So I reckon it can all be deleted. But I too will refain for a while from doing this. I'd like to hear what others think. Snalwibma 10:03, 16 May 2007 (UTC)

OK. No further discussion. I'll remove it. --Plumbago 21:26, 18 May 2007 (UTC)

Sorry guys - I've been v busy and only just had a chance to come to this. It could be argued that any attempts we might make to draw philosophical implications were OR, but the fact is that Robert Winston certainly suggests in his lecture that the fact of epigenetic inheritance has significant philosophical implications - he singles out Dennett and Pinker as egregious examples of people who write about genetics and seek to draw philosophical conclusions without knowing what they are talking about. And his main point is that the idea that our understanding of science and genetics is nearly complete (bizzarely pushed by Dawkins in his Times interview) is simply wrong. Furthermore the "Evolution in 4 Dimensions" book also specifically draws philosophical implications, and I think we should reflect these. It got a v good review in either Nature or Science. NBeale 21:31, 18 May 2007 (UTC)

Twas Nature 435, 565-566 (2 June 2005) by Massimo Pigliucci no less! NBeale 21:39, 18 May 2007 (UTC)

BTW the summary of Winston that was in the article was not at all the one I wrote, but someone elses which I thought rather destroyed the force of what he was saying. NBeale 22:02, 18 May 2007 (UTC)

OK. Can we drop Winston already? Epigenetics is not his primary field, and though he may discuss it in his lecture, his sources are far from the best for a technical article on it. Anyway, the material you've re-added about Winston is basically to do with Dawkins (yet again), so at best is only appropriate over there. Regarding epigenetics' "philosophical implications", you need to spell them out properly here rather than merely allude to them. And why aren't they "technical implications" anyway? To my mind, epigenetic inheritance is simply an additional mode of inheritance, with no obvious "special" significance beyond it contravening earlier models of inheritance. It has really rather limited effects (as the article already states). And as for statements like "Thus the simplistic view of evolution solely in terms of 'selfish genes' ...", well, they are referring to a straw-man and have no place here (or elsewhere). --Plumbago 06:45, 19 May 2007 (UTC)

Paternal effects

I have removed this, which was in ref tags after "maternal effects":

However Robert Winston cites a study Vaigron in North Sweden of families in the late 1800s and early 1900s which showed that the paternal (bur not maternal) grandsons of people who had been involved in famines were four times more likely to develop diabetes. Lecture at University of Dundee)

I haven't seen the original study, but in the absence of anything in this article to explain otherwise, I can see no reason why this must be caused by "paternal effect" rather than imprinting, therefore I can not verify that it is relevant. Joe D (t) 14:33, 15 May 2007 (UTC)

The ref is "But Paternal effects are not unknown: Robert Winston mentions a study by Pembry & Bygren (European Journal of Human Genetics 14 159-166) of families in North Sweden the late 1800s and early 1900s which showed that the paternal (but not maternal) grandsons of people who had been involved in famines were four times more likely to develop diabetes. Lecture at University of Dundee)" I am relying on Winston's summary, I haven't seen the original article either, but the fact that it was paternal and not maternal grandfathers that mattered strongly suggests a paternal effect. PS: looking at the discussion at Leeds University I think it's quite clear that this is a paternal effect, so I'm putting it back. NBeale 06:17, 16 May 2007 (UTC)

Did he actually say "paternal effect"? It could very easily be imprinting, and that seems a far more likely explanation to me. Joe D (t) 06:37, 16 May 2007 (UTC)

I have amended the reference so that it includes a link to the Pembrey article: PMID 16391557 - and we can go and judge for ourselves whether it deserves mention as a possible paternal effect without relying on Winston's interpretation. What I don't understand is why Winston needs to be mentioned at all. I have stopped short of cutting him out, but it would seem reasonable to do so, even if the ref stays. Snalwibma 10:39, 16 May 2007 (UTC)

I see no objection to removing the Winston ref now that we have the primary one. Originally I have got the name phonetically and Bygren became Vaigron!! NBeale 22:40, 16 May 2007 (UTC)

Excellent! I was indeed totally mystified by "Vaigron"! Snalwibma 06:12, 17 May 2007 (UTC)

Does anybody have the full text of the original article? My library isn't subscribed to the journal so I can't get it. I read the "comment" article that went with it though, and it was pretty clear that the mechanism was, at the time, unknown, but states that it's likely just to be another case of imprinting -- a slightly interesting twist to an established mechanism. I've yet to see a reference that states that this isn't the case. Joe D (t) 23:01, 16 May 2007 (UTC)

• Full text? Try this. It seems to be available without subscription. If you have problems, send me a message on my talk page and I can email you a copy. Snalwibma 08:44, 17 May 2007 (UTC)

Thanks, I guess it wasn't a subscription issue at all, just a problem with Nature's DOI redirecting thing. Anyway, this bit stood out:

Little is known about the transmitting mechanisms, except in the specific study of epigenetic states at the AxinFu allele, and the altered DNA methylation patterns at two loci in the epididymal sperm of rats with reduced spermatogenic capacity due to their paternal ancestor being exposed (in utero) to the endocrine disruptor vinclozolin.

So, it appears to be a kind of ad hoc version of imprinting, not an effect of paternal gene expression. Joe D (t) 22:28, 18 May 2007 (UTC)

Actually, the more I think about it, the more obvious the irrelevancy of this study seems. I wonder, does NBeale actually know what "maternal effect" is? Joe D (t) 22:34, 18 May 2007 (UTC)

Context section

How about something like this. "It used to be thought by working scientists, and is still popularly supposed, that biological inheritance is nothing but genes (possibly even "selfish" genes) and DNA. It is now understood that, in addition to the fundamental roles of genes and DNA, there are other mechanisms of biological inheritance. In Biology, epigenetics is the..." NBeale 21:59, 18 May 2007 (UTC)

Hmmmm. It certainly shouldn't go at the very start. This is an article about a biological subject; heading up with some statement about the historical position of epigenetics overplays things. Especially an overblown statement that appeals to popular misconceptions of a technical subject. However, I would certainly agree that the article intro is a bit technical (and long). It might be an idea to write a new semi-technical intro, and consign the existing intro to a proper "Introduction" section. Among other things, it would (to my mind) help to just point out that epigenetic inheritance deals with several distinct mechanisms by which information is passed inter-generationally outside of the genome. The part about altering genetic sequences in the opening sentence, while correct in itself, is misleading it seems to me (and omits consideration of entities like prions). Maybe, "In biology, epigenetics refers to a class of mechanisms by which heritable information outside of the genome is transferred from parent to offspring organisms." Too clunky perhaps? --Plumbago 07:09, 19 May 2007 (UTC)

I propose something along the lines of:

In Biology, epigenetics is the study of all heritable and potentially reversible changes in genome function that do not alter the nucleotide sequence within the DNA. At the molecular level, the majority of biological processes are carried out by proteins, collectively the proteome, while the structure, and thus function, of these proteins is determined by genes, collectively the genome. The proteome changes in response to the cell's environment, thus allowing it to perform various functions, and this is most obvious in multicellular organisms, where different cells perform different functions. The genome, however, is static, and epigenitic mechanisms are thus an important mechanism of "cell memory", allowing cells to differentiate and cooperate in multicellular organisms. Additionally, some epigenetic inheritance is trans-generational, and thus may be subject to evolution, including the potential for the genome to be modified in response to the environment in germ-line cells.

Because:

1. what the article is about should be established in the first sentence,
2. epigenetic inheritance is very important in development and differentiation, but only an interesting side-note in evolution.

However, I can see a potential issue with it: we're talking about the implications before really mentioning the mechanisms. The implications are indeed important though, and I imagine most laypeople (and indeed, developmental and evolutionary biologists) will be more interested in the implications than the mechanisms.

Joe D (t) 16:27, 19 May 2007 (UTC)

One problem I have with the current intro is that it rather narrows the definition of epigenetic inheritance to genome interactions. These are, to be fair, the predominant epigenetic mechanisms, but there are other processes that are examples of epigenetic inheritance that do not directly involve the genome at all. For instance, some proteins self-template such that functional forms can only be assembled in the presence of existing functional forms which are inherited from parent organisms (e.g. Cheng, M. Y., Hartl, F.-U. and Horwich, A. L., 1990, The mitochondrial chaperonin hsp60 is required for its own assembly, Nature 348, 455-458). This sort of structural inheritance is implied in the case of infectious prion agents, and more generally applies to cytoplasmic properties (e.g. Meyer, E. and Beisson, J., 2005, Epigenetics: Paramecium as a model system, Médecine/Science 21, 377-383). My point in raising this is that perhaps the first sentence should be altered to something like, "In Biology, epigenetics is the study of inheritance that occurs via mechanisms separate from traditional genetics", and then follow on with some examples. Otherwise it seems like we're missing a trick. Anyway, as this is pretty far from my own field (to say the least!), I'm likely to be out of date here. Cheers, --Plumbago 09:12, 21 May 2007 (UTC)

P.S. Centrioles have been thought of as self-templating structures that represent an example of epigenetic inheritance. However, a paper published just this past week in Science finds instead that they can be synthesised from scratch (using genetic information), suggesting that they don't represent inheritable epigenetic information after all. The full citation is: Rodrigues-Martins, A., Riparbelli, M., Callaini, G., Glover, D. M. and Bettencourt-Dias, M. (2007) Revisiting the Role of the Mother Centriole in Centriole Biogenesis, Science 316, 1046-1050 (DOI: 10.1126/science.1142950). --Plumbago 12:22, 21 May 2007 (UTC)

Hi Plumbago - thanks for the ref. But I don't think this is a correct inference. The paper (which doesn't mention epigenetics at all) says that "The mother centriole is not a bona fide template but a platform for a set of regulatory molecules that catalyzes and regulates daughter centriole assembly." but this is by no means incompatible with the idea that alterations in the mother cenrtiole will be inherited by daughter centrioles. No-one suggests that epigentic effects would operate in the absence of genes, merely that they are another, important, dimension and the popular misconception that DNA=Genes=Biological inheritance is simply wrong. NBeale 20:55, 21 May 2007 (UTC)

Regarding the centriole paper, it does specifically address the issue of self-templating. Possibly not in the abstract - I had a look at the paper too. And from my old biologist days, I'm pretty sure that centrioles were cited as an example of "structural" (= epigenetic) inheritance. They might still be - the paper is only looking at them in a model system (Drosophila). There are other structural examples too - the pattern of cilia on the surface of Paramecium as I recall.

On the other point, I think we all agree that "genes = all biological inheritance" is incorrect, but that's not to say that "genes = 99% of biological inheritance" isn't correct. As it stands, epigenetic mechanisms don't appear to provide anything near the "bandwidth" of genes. Also, the epigenetic mechanisms we do know about appear a very crude means of transferring information between generations. And on top of that, as I read things, some epigenetic mechanisms may ultimately be genetic in basis, but transferred between generations by epigenetic means (i.e. imprinting; the extended phenotype). For all these reasons, I'd argue that it's overplaying things to make the sort of strong statements in the "philosophy" section - the "genes = biological inheritance" line is a straw man, plain and simple. --Plumbago 21:41, 21 May 2007 (UTC)

Epigenetic effects and evolution

The evolution subsection of the functions/consequences section, previously entitled "Epigenetic effects and evolution" somewhat misses the major point in my opinion. The section is mostly concerned with somatic epigenetic inheritance, leading to the differentiation of cells. It goes into detail of trying to justify this within the existing model of the modern synthesis, for two paragraphs. I can justify it in one sentence: somatic epigenetic inheritance is no different from the rest of the proteome and mechanisms of expression regulation in that it is a product of the genotype. Chromatin remodelling, for example, is carried out by HATs, HDACs and remodelling complexes with the aid of transcription factors, morphogens, cell signalling, etc, and needs no more justification or special treatment than glycogen production or the TCA cycle. Where evolution is interesting is in the germ-line, and transgeneration epigenetic inheritance. Does anybody have any objection to an overhaul of that section? Bits of it may be worth incorporating into the development section? Joe D (t) 17:19, 19 May 2007 (UTC)

Possible epigenetic downregulation of reelin and GAD67 in schizophrenia and bipolar disorder

If you are interested, you might want to look at the reelin page. I'm not a specialist in genetics, let alone epigenetics, but thought that this may interest you. Best regards, CopperKettle 18:33, 19 May 2007 (UTC)

Philosophical implications

Still struggling to see what this section adds to the article. All it really says is "inheritance is more than genes", with a couple of philosopher-scientists mentioned to lend weight to this obvious restatement of the article's opening sentence. Where are the implications? Where are the comments (by others, not by a wikipedia editor!) on how epigenetics does or should change our view of the world? And what does this mean: "... and argue that empirical evidence for the importance of epigenetic inheritance systems comes from the partial failure of the gene-centred approach that gave us genomics"? How can the failure of the gene-centred approach have provided empirical evidence for anything? I assume the point is really that it has come to be realised that genes (genomics etc) aren't the be-all and end-all of inheritance - and hence it's really just yet another restatement of the simple central point of the article. I'm still for deleting the section, unless it has some proper content that matches its heading. Snalwibma 09:14, 21 May 2007 (UTC)

I'd second this. Personally, I find epigenetic inheritance fascinating, but I seriously doubt that it has significant implications for evolution, it's just too limited in its effects. I'm also a little suspicious that there's an agenda behind the scenes here. --Plumbago 09:48, 21 May 2007 (UTC)

I am struggling to see what the text in the section has to do with the section title. Philosophical? Why? How? If there are scientists or authors who use epigenetics as an argument against something Dawkins writes, it can be mentioned, but it should be mentioned that it is their opinion, not facts. And it should be mentioned how the argument goes, not simply "epigenetic inheritance is an important factor in the inadequacy...". Again, how and why? And the section title should describe the content. Mlewan 10:05, 21 May 2007 (UTC)

It's worth looking at the sources. I haven't yet read the book, though from the extract on the web and from the review in Nature it's clear that they see this as having major philosophical implications (and so does MIT Press). Winston actually cites it as a major plank of a deep philosophical critique of the whole Dawkins/Pinker/Dennet platform - we are being very kind to them to tone this down (he actually says, of Pinker and Dennet, that "the basically know nothing about genetics so it's a pity that they write about it" or words to that effect). Neil Greenberg, Professor of ecology and evolutionary biology at the Univesity of Tennesee Knoxville also suggests that "Epigenesis has significant philosophical implications". There is also an article Genes as Followers in Evolution – A Post-synthesis Synthesis? by Jablonka in Biology and Philosophy, 21, 1, Jan 2006, pp. 143-154(12) and a 1998 discussion on The case for epigenetic inheritance in evolution by J. Griesemer University of California, Department of Philosophy, Davis, CA 95616, USA in J. evol. biol. 11 (1998) 193-200. NBeale 20:17, 21 May 2007 (UTC)

I have partially re-reverted. At least the version that I have restored makes grammatical sense, unlike the one NBeale reverted to. This time I have left Winston in, though I completely fail to see how he is relevant. If there are indeed sources about the philosophical implications of epigenetics, let's have them properly represented here. Meanwhile, the "selfish gene" theory that is currently paraded in the article as "inadequate" and somehow disproved by epigenetics is a sorry caricature of what is really meant by the "selfish gene" idea, and indeed the "epigenetics" that is used as a stick to beat Dawkins/Dennet looks like no more than a feeble misunderstanding of epigenetics. Nobody - not even the antichrist called Dawkins! - believes the sort of rubbish that these additions to the article are so solemnly "disproving". Snalwibma 20:35, 21 May 2007 (UTC)

Well if Winston is talking rubbish people can make their own minds up. At least Winston asserts that epigentics is a problem for the Dawkins/Dennet/Pinker view. You of course may know better. Another book that discusses this is a book called Philosophy of Experimental Biology CUP (2004). What the Philosohical implications are is open to debate, but I think there is now conclusive evidence that there are alleged to be some in reliable sources. NBeale 20:47, 21 May 2007 (UTC)

I did not say Winston is talking rubbish. I mean that you are writing rubbish. You have also failed to demonstrate how what Winston says is relevant to the topic of the article. If he says something relevant, put it in the article - not hidden in a convoluted footnote and a link to another website, and not just on the talk page. Write a sentence or two which shows how it is relevant. Go ahead! Snalwibma 20:54, 21 May 2007 (UTC)

(a) Why you have reverted the Pauli material, which is carefully refed (and now double-refed) is beyond me.

(b) Winston cites Epigentic inheritance as a major reason why the neodarwinian synthesis needs revising and why D/D/P are wrong to be so certain and arrogant. Listen to his lecture. Argue with him if you like, but I am reporting what he says. NBeale 21:46, 21 May 2007 (UTC)

OK - apologies - removing the reference to Pauli was a bit hasty. I should have raised it here first. I will do so now: How exactly does Jorgensen's conference abstract constitute "an admirer of Pauli" discussing epigenetics as "a vindication of his repeated criticisms of neo-Darwinian positions in evolutionary biology"? I see nothing of that in the abstract. You are putting a spin on it which simply isn't there. Snalwibma 05:49, 22 May 2007 (UTC)

Well according to the conference organisers: "After more than a century of neo-Darwinian positions in evolutionary biology, often criticized by Pauli, there is now much evidence that genetic inheritance operates with both random and directed mutations. Results from the last 10 to 15 years confirm this visionary conjecture by Pauli and led to comprehensive research programs in many countries. Moreover, there are novel observations concerning epigenetic, behavior related and cultural forms of inheritance, which are insufficiently taken into account in many contemporary debates (e.g. bio-ethics)." (italics added). I suppose it never actually says that the orgainsers are admirers of Pauli, but it's pretty clear from the fact that they are organising the conference. NBeale 06:00, 22 May 2007 (UTC)

And Jorgensen? How does he fit in? Why pick on that specific abstract? How does that specific reference support the statement you make in the article on epigenetics? Seems to me like reference-buttressing and putting a spin on things. It appears to me that you are pointing to the mere existence of a reference, however irrelevant, as some sort of evidence in support of your opinion. When challenged, you say "it's double-referenced", but do not address the key issue - does the reference you cite support the inference you draw from it? I am also concerned about using conference publicity material in support of a scientific opinion. Such things are not considered summaries of established facts; they are advertising material, designed to attract attention and provoke a response. BTW, what do you understand by "directed mutations" in that conference puff? Snalwibma 06:15, 22 May 2007 (UTC)

Well my ref was to the conference announcement, and it clearly supports the claim that "Contemporary admirers of Wolfgang Pauli point to epigenetic inheritance as a vindication of his repeated criticisms". I added a ref to the abstract for good measure. Change it to "given at the conference" if you like. NBeale 08:14, 22 May 2007 (UTC)

Nicholas, it is still not clear to me how epigenetics would in any way contradict Dawkins, or even what in Dawkins' writings it is supposed to contradict. Dawkins shows how religion can be explained using materialistic mechanisms. Whether those mechanisms are DNA or epigenetics seems completely irrelevant for those of his arguments I know of. Mlewan 08:28, 22 May 2007 (UTC)

Seconded (Snalwibma). This sort of citation is a nonsense. As Snalwibma correctly points out, these abstracts are for a conference and act as advertising. And, as I'm sure most working scientists will admit to, conference abstracts tend to be overblown because a) the work has often not been done yet, and b) puffing up one's work is a good strategy for getting a valuable talk-slot. If the work is really as impressive as the ideas that it's being (mis)used to bolster here (i.e. a revolution in biology) it'd have been published in Nature or Science and cited by Tom, Dick and Harry (*). And as for the shameless name-dropping of Wolfgang Pauli, that's just simple argument from authority. I notice, by the way, you've recently edited Pauli's article too - is this going to be your strategy from now on? Find some tenuous quote critical of "selfish gene theory" (= Richard Dawkins; let's not beat about the bush), use it to attack said subject and then carefully backfill to other articles to give the impression that the argument has some validity? That's certainly what brought all of the recent attention to epigenetics (Winston now seems but a distant memory). Anyway, sorry if I'm being unconstructive here, but NBeale you don't appear to be interested in being entirely accurate here. Time and time again it seems to me (i.e. my POV) that you're scratching around to find material to support your views (which we all know about from your blog), and then using it here without properly considering its context. If it really was the case that, for instance, directed mutation (please define; as per Snalwibma) was as important as you're making out, surely it'd be all over the scientific literature, rather than confined to a few papers in odd places like consciousness journals? Crazy ideas (in the good sense) appear all over the scientific literature, but until they become established, non-crazy ideas (i.e. "I knew it was right all along") editing them into articles isn't helpful. We can always revise the picture later if they become part of the establishment (or inspire further work; see my note immediately below). Anyway, my apologies again for getting annoyed - you're quite a taskmaster NBeale! Cheers, --Plumbago 08:54, 22 May 2007 (UTC)

(*) As it happens, there is an interesting backstory to directed mutations, and it was published in Nature. Back in 1988, John Cairns (I think this is the correct "Cairns"; same institute) published a paper on mutation that suggested it may not all be non-random (Cairns, J., Overbaugh, J. and Miller, S., 1988, The origin of mutants, Nature 335, 142-145). Flash-forward to the present-day and understanding of the sort of situation described by Cairns has moved on. More subtle understandings of selection (e.g. Roth, J.R., Kugelberg, E., Reams, A.B., Kofoid, E. and Andersson, D.I., 2006, Origin of mutations under selection: The adaptive mutation controversy, Annual Review of Microbiology 60, 477-501) and new mechanisms such as enhanced random mutation (e.g. Kang, J.M., Iovine, N.M. and Blaser, M.J., 2006, A paradigm for direct stress-induced mutation in prokaryotes, FASEB Journal 20, 2476-2485) have come to the fore. --Plumbago 08:54, 22 May 2007 (UTC)

Well Evolution in Four Dimensions is already cited by 40 publications including Patrick Bateson (J. Nutr. 137:1060-1062, April 2007) Massimo Pigliucci (The Quarterly Review of Biology, volume 81 (2006), pages 377–379) and got an approving review in Nature - this is very serious and becoming increasingly mainstream, though as Pigliucci suggested it meets resistance from people whose thinking is rather hidebound. As for Pauli, there are a large number of primary refs cited in the paper. Please accept the fact that serious scientists have views you don't like, and resist the temptation to hide them. NBeale 21:36, 22 May 2007 (UTC)

PS FWIW Epigenetic inheriance is described as a "fundamental biological process" in a featured paper in Science (Ying Huang, et al. Science 312, 748 (2006)) NBeale 21:44, 22 May 2007 (UTC)

It is indeed a fundamental biological process. That's hardly a revelation. But the issue here is - how exactly does it change our perceptions of evolution? Same old question: What are the "philosophical implications"? If whatever-it-is is all "serious" stuff which is "becoming increasingly mainstream", please go ahead and write a section of the article which makes sense and clearly states what the implications are, how they relate to epigenetics, what exactly is demonstrated, by whom or by what, and how. I look forward to reading a clear exposition of the issues. Snalwibma 22:00, 22 May 2007 (UTC)

Well an essay from me would be OR but I've tried to expand the section with what J&L and P say. Hope you enjoy it. NBeale 22:44, 22 May 2007 (UTC)

There is one big improvement now to the section, and that is that it actually explains some things, like "evolution can proceed very rapidly and phenotypic modification can precede genetic changes". However, I still cannot see anything that is both useful and not mentioned in other parts of the article. There is still nothing about any "philosophical" implications in the section. The word "bold" is POV. So are "ultra-reductionist, gene-centred approach". Besides it is not clear who would be behind the ultra-reductionist approach. Did anyone step forward and say "I am an ultra-reductionist, and I am proud of it"? It is hardly worth mentioning what "admirers" of Pauli think, as that almost by definition would be POV and of little value as reference. Mlewan 09:18, 23 May 2007 (UTC)

I've edited it slightly to make it clear that "bold" and "ultra-reductionist" etc.. and P's words in Nature, not mine or ours. It really is playing a major role in the huge changes in the way people think about evolution. NBeale 18:41, 23 May 2007 (UTC)

The trouble is, I think, that the philosophical implications are all lurking beneath the surface. When an attempt is made (and thanks to NBeale for doing so) to bring it out into the open, all that actually emerges is a basic restatement of the central point of epigenetic inheritance - that inheritance and evolution are not quite as simple as the popular misconception encapsulated by phrases like "ultra-reductionist, gene-centred approach" would suggest. No biologist subscribes to that sort of ultra-reductionist nonsense, so to come over all philosophical on the subject of epigenetics and emerge with the triumphant discovery that "it's not that simple" is pointless. This leads me to wonder what the true motive of the "philosophical approach" is. There is a danger that phrases like "regulated and partially directed" will get taken out of context (i.e., completely misunderstood) and before you know where you are, creationism and intelligent design are invited to the party. I can envisage a particular kind of "philosophical" spin on epigenetics which would aim to do precisely this - to drop those sorts of phrases into the discourse in the hope that the creationist door will be opened a chink, apparently by the scientists themselves. Is something like this going on? A clever philosopher picks out some words used by a biologist and proclaims, "that has philosophical implications, you know" - either without actually understanding the biology or in a cynical attempt to twist the meaning. There isn't in fact anything there beyond some recently discovered basic biological processes, but as soon as you wave the "philosophical" flag and point to some of the technical phrases used, all it takes is a nod and a wink and all sorts of Big Important Issues and Serious Implications are hinted at. I smell rats, ulterior motives, etc. Snalwibma 13:22, 23 May 2007 (UTC)

Philosophical - per the sources

It's great that 2 editors with strong technical expertise have worked on this section. But I fear that they have not looked at the sources refed and applied their own PhD-level understanding. If a serious (atheist as it happens) Prof like Massimo Pigliucci makes statements in an article in Nature then even if someone with a PhD in Molecular Biology disagrees with the statement that is not a reason to remove it! I've tried to keep all the positive aspects of these edits, but we must let the sources speak for themselves as far as possible. The para about Pauli, Winston etc.. is not at all "name-dropping" each of these very serious thinkers has a slightly different position and our readers need the opportunity to see what they are. The changes in the philosophy and theoretical grounding of evolutionary biology that are going on at the moment are very significant in my view. NBeale 06:52, 24 May 2007 (UTC)

Misplaced Pages articles cannot turn into a list of names that agree with a particular point of view. While I have not read the book you are referencing (nor do I have the patience to sit through a lecture rather than reading a transcript of it), it is my opinion your view regarding this evolutionary significance (or, at least, your way of characterizing it) is not the scientific consensus on the matter.

The journal Cell had a special "epigenetics" issue on February 23rd this year that contained nothing but epigenetics articles and reviews. The leading essay "Epigenetics: A Landscape Takes Shape" that introduces the material does not mention evolution within it at all. One review addresses the matter of epigenetics and how it might be involved in adaptation: "Timescales of Genetic and Epigenetic Inheritance", O.J. Rando and K.J. Verstrepen, pages 655-668. In that article, they cover some ways that epigenetics could be involved in adaptation. My summary of the article is this: Epigenetics can provide a way for organisms to control the gene localization and timing of genetic variability, similar to the behavior of contingency loci (which I don't think are referred to as "epigenetic"). These are important updates to the view of evolution in that variations in phenotype may be produced in a more targeted manner -- but this is still "blind", not directed, and cases like contigency loci demonstrate that this update to our understanding is not purely due to "epigenetics". Could it be a directed process? They briefly address the possibility in the article, and again the example they give there for directed change is not an epigenetic process but a genetic one (the fimbriae genes in E Coli). In conclusion -- although it is currently mostly speculation, epigenetics could be playing these roles in adaptation and evolution, but the examples given in this article demonstrate that these effects are not uniquely epigenetic -- epigenetics is not making a revolutionary update to our understanding, because that updating is already occurring with genetic observations (and whether that updating can be characterized as some sort of revolutionary fundamental shift in our understanding is a POV issue). Madeleine 10:10, 24 May 2007 (UTC)

Appealing to the opinions of "serious Profs" and "serious thinkers" in support of a particular point of view is precisely name-dropping, in the sense that it is a mere argument from authority which does not actually engage with the scientific evidence. Snalwibma 10:58, 24 May 2007 (UTC)

PS - Personally, I would be in favor of deleting both paragraphs created by Nbeale, it seems to me that the material is little more than a collection of vague name-associated opinions rather than a set of well-defined statements explaining a general viewpoint in the field. Part of the problem here is the way name after name is being referenced -- this is not how wikipedia articles are typically written. Unless there's a single particularly notable person involved in the topic (and I see none here), I think any material here should read "some argue that... "; the names of these people involved is given by the references. Madeleine 11:16, 24 May 2007 (UTC)

Nicholas, I'm in a hurry here, but "they have not looked at the sources refed" is irrelevant. No one should have to look at the references. All relevant data should be in the article. Try expressing whatever it is you try to express without references. If you think what you wrote makes sense, then, afterwards, add the references. Mlewan 11:38, 24 May 2007 (UTC)

I concur with Snalwibma and Madeleine (especially Madeleine's point on the scientific consensus; as discussed endlessly before). Regarding Pauli, the quotes from Pauli in the cited article seem to centre on a misunderstanding with biologists more than anything else (the definition of "chance"), and the article itself notes that Pauli's objections were discounted at the time (Ernst Mayr anyone? ). His connection to epigenetics (at least from what one can judge from the article) is somewhat tenuous, with most of the cited article's points on the matter coming from later authors. It's difficult to judge from the one source, and I'm probably being uncharitable, but the cited article reads as if Pauli's followers have simply jumped onto epigenetic inheritance because it seems to fit some of Pauli's musings ("Probably ... there exist processes with a directed goal and also causal influences of the environment on inherited properties on the way over the cytoplasma"). This is hardly surprising given that he was working at a time when very little was known about molecular mechanisms in biology (the structure of DNA had only just been worked out; epigenetics was tarred as heretical Lamarckism then). Checking if he's more widely influential in the epigenetics literature would certainly help on this particular point (I can well understand him being cited this way by admirers - he's a genius!). As for the philosophical vs. evolutionary heading, surely evolutionary is better given that we're talking about evolution? This is a science topic after all, and its implications for evolution are surely the most pertinent. --Plumbago 11:53, 24 May 2007 (UTC)

To shamelessly name-drop myself.  ;-) --Plumbago 11:53, 24 May 2007 (UTC)

Deleting both paragraphs

NBeale, I realize now that you started adding material (May 18 edit) before having read the book itself, based on a book review from June 2005 (not exactly recent news) and only later reinforcing it (notably, the highest page number in the citations to the book at this point is page 10, I suspect you still haven't read it fully -- in fact, I suspect you have read very little material at all about epigenetics).

From your May 18 blog entry: Been putting in some effort on Epigenetics in WikiPedia - it's a fundamental refutation of the "Selfish Gene" nonsense. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life looks very interesting, but will I have time to read it?

It appears to me that you're trying to use this article to push a particular point of view. Notably your other references added that day were all Dawkins related — a "friendly disagreement" essay and a lecture apparently criticizing Dawkins entitled "The Science Delusion". I think perhaps you don't like the guy. Because of this, I no longer trust your additions to be knowledgeable and unbiased characterizations of the material you are referencing. It is also clear that the consensus of this page is critical of the content you are adding. I am going to delete both paragraphs. Please do not restore them; if the content is going to return to wikipedia it should be at the hand of another editor. I would appreciate it if you stopped editing the article for now and used this talk page to suggest any content you think needs to be addressed. Madeleine 17:48, 24 May 2007 (UTC)

Hi Madeline. Good luck with your graduate work. You don't yet seem to have any publications in science or philosophy. Perhaps you could explain on what basis you consider yourself qualified to ban another editor (who has) from contributing to a section on philosophical implications. You may not agree with my POV and perhaps I don't agree with yours, but we should respect each others POV and if reliable sources assert relevant facts then it is wrong to try to hide them because the challege the preconceptions of some atheists, IMHO. NBeale 21:50, 24 May 2007 (UTC)

I am not banning you, I am making a firm but reasonable request. If your material has merit, someone else can add it back in. Although I have not yet published, I am currently a graduate student in George Church's lab in the Genetics Department at Harvard Medical School and my current project is developing technology to profile epigenetic patterns. It's strange to me that you think this book (or did you mean something more like this?) is a relevant publication to this subject. Madeleine 22:21, 24 May 2007 (UTC)

I strongly support Madeleine here. NBeale has a clear and acknowledged POV-pushing agenda in relation to this article, and he further confirms this by making strange accusations about the motives of his fellow-editors (such as that they are suppressing things because "they challenge the preconceptions of some atheists" - what on earth has that got to do with it?!). Does this disqualify him from adding material to the article? I think there's a case for saying that it does. Gnusmas 22:30, 24 May 2007 (UTC)

Ah the well-known WP Policy "Atheists are entitled to block theists from editing science-related articles and to hide information they don't like." Where is that found, precisely?? It is indeed remarkable that some atheist editors work so hard to remove carefully refed material that challenges their preconceptions, but then atheist regimes are like that so perhaps groups of atheists feel entitled to act in this way as well?? The point about philosophers (esp perhaps social philosophers) is that we try to integrate understanding across different fields and although ideas about business and evolution have more in common than you might think ("survival of the fittest" comes from economics) and some of my contributions to Computer Science (again closer to this stuff than you might imagine eg this) are fairly widely cited, it's my long collaboration with John Polkinghorne that's probably my most relevant published work, during which time we have answered dozens of questions about evolution. I've also learned a fair amount from talking to and reading leading researchers in this space. But we should stick to the refed facts in the articles, not go all credentialist! NBeale 06:20, 25 May 2007 (UTC)

Hi, NBeale. What does your patent on trading systems have to do with methylation or chromatin insulators? Heathhunnicutt 07:51, 27 May 2007 (UTC)

Seems we are having a friendly disagreement :) But I actually think this debate over whether we are experiencing a paradigm shift in biology is rather interesting, and might deserve coverage... if it is carefully and neutrally written. Biology and Philosophy will soon publish Jablonka and Lamb's response to reviews, and that might spark further discussion. There is also a recent paper entitled "Reports of the death of the gene are greatly exaggerated", which I assume is arguing the opposing case. It seemed to me that the main objections to NBeale's section was the style, its bias and his conflict of interest. If only I knew some biology, I would try to re-introduce the material in a way that was more in tune with the rest of the article. Reading that journal was quite fun, and if some of you biology gurus would consider reading up on this, then it might actually be an interesting addition that adds flavour to the article. Respectfully, Merzul 23:11, 24 May 2007 (UTC)

Those look interesting, I printed these papers out and started reading them. I notice Jablonka & Lamb specifically say "We agree with Godfrey-Smith that the change that is occurring in evolutionary theory is not a Kuhnian revolution," (Kuhnian revolution = paradigm shift) ... but then proceed to say "but will argue that ... the new facts and ideas ... do have radical, revolutionary, implications for evolutionary theory" (??? Is there a difference? It sounds to me like they're playing with words here). So far I have to say I agree with Godfrey-Smith's criticism, I think the evidence so far is creating an updating of understanding, not a revolution. Also, I am suspicious of anyone who wants to characterize any of the many steps in our updating of biological understanding a "revolution". If there's a revolution here, I am personally not feeling it. I see a gradual process of updating occurring. I'd be curious to see what an evolutionary biologist thinks about whether this is a "revolution", though.

While this "updating of understanding" sounds like interesting material to add somewhere to wikipedia (and for all I know it already exists somewhere), I hesitate to say that it's appropriate to this article. It seems to me like it belongs in an evolution article. J&L's book covers "four dimensions" (of which epigenetics is one) and the genetic examples from the article I mentioned earlier ("Timescales of Genetic and Epigenetic Inheritance", O.J. Rando and K.J. Verstrepen) indicates to me that epigenetics is not the sole cause of the updating. Madeleine 02:17, 25 May 2007 (UTC)

I don't think anyone is saying it is the "sole" cause. However all the authorities I cite assert that Epigentic Inheritance is a major factor in their thinking. What I suggest we do is re-introduce this section, which as Merzul says is fascinating and I think you would agree with that - under the heading "Suggested Philosophical Implications", with a lead something like "Although most of the discussion of Epigentics and Epigenetic Inheritance is at a technical level, some scientists and philosophers suggest that it has philosophical implications..." NBeale 06:26, 25 May 2007 (UTC)

Well, I don't like this "suggested" idea. It seems to evade the responsibility to present the actual content of the debate fairly and accurately, and instead reduce it to what a few important people suggest. Perhaps this whole thing should indeed be taken up at evolution, if only for the reason that more biology people are watching that article? --Merzul 09:01, 25 May 2007 (UTC)

NBeale - your comments (e.g. "some atheist editors work so hard to remove carefully refed material that challenges their preconceptions") suggest that you perceive this as a disagreement between atheist and theist contributors, and between atheist and theist perceptions of epigenetics. I see nothing to justify this. What has god got to do with it? Which of the many people who disagree with you about this article are atheists, and how can you tell? And how does anyone's (lack of) theistic belief colour their perception of how this article should best be shaped? Gnusmas 07:21, 25 May 2007 (UTC)

I'll try to respond to this in my blog - doesn't belong here. NBeale 13:55, 25 May 2007 (UTC)

For the record, I consider myself a Christian. However, I much prefer balanced arguments against religion that bad ones in favour of it. And this section has had as little to do with religion as it has had to do with philosophy. Keep those paragraphs deleted. Thanks, Madeleine, for your excellent contributions to this article! Mlewan 16:30, 25 May 2007 (UTC)

More interesting philosophical material

I've had a quick search in the Nature site and there are some very interesting refs. I commend esp:

• Richard C. Strohman " The coming Kuhnian revolution in biology" Nature Biotechnology 15, 194 - 200 (01 Mar 1997). This provoked a number of follow-ups
• Denis Noble's review of The Pinnacle of Life by Derek Denton in Nature Medicine 1 11, p1210 Nov 1995

I'll try to read these in detail - and come up with a revised section draft - over the Bank Holiday if I have time. NBeale 13:55, 25 May 2007 (UTC)

Special section in today's Nature

There is a huge section (7 review articles) on Epigenetics in the current Nature. I'll try to read it over the next few days - I'm sure there will be lots more material for the article. NBeale 18:48, 23 May 2007 (UTC)

You may be interested in last month's Cell, which also had several epigenetics reviews. Joe D (t) 09:55, 24 May 2007 (UTC)

Please do not copy and paste journal abstracts into this article

This passage appears to be plagarized into the content of the wikipedia article. Although the journal article in question was given as a citation, I suspect this particular usage is a copyright violation. (While it would be "fair use" in the context of quotation, this was added without quotation, into the content of the article.) Link to the edit adding this material.

From Rando & Verstrepen, "Timescales of Genetic and Epigenetic Inheritance" Cell, Vol 128, 655-668, 23 February 2007 (and yes, it is fair use to give the material, unchanged, as a quote):

However, recent findings suggest that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. Interestingly, these mechanisms seem to tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin's theory, they suggest that selection and variability are less independent than once thought.

NBeale's version:

Recent research demonstrates that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. It appears that these mechanisms tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin's theory, they suggest that selection and variability are less independent than once thought.

I have removed this. I have also read the article and added some content that cites it to the Evolution section. Madeleine 03:21, 26 May 2007 (UTC)

Hi Madeleine. The whole point about Misplaced Pages is that it is meant to be a tertiary source, therefore all our edits should be carefully based on reliable sources. Especially in highly technical fields, it is very desirable to give summaries in the exact words used by the source, to avoid any possibility of misunderstanding/misrepresenting. Provided the source is properly acknowledged in the reference, as this was, it is unquestionably fair use and not plagarism at all. When I first started editing I did tend to use quote marks but was told firmly that excessive quote marks was not part of Misplaced Pages style. I will charitably assume that this was due to your inexperience and (comendable) youthful zeal, rather than a failure to assume good faith or an attempt at at personal attack. NBeale 06:02, 26 May 2007 (UTC)

I'm sorry you're taking this so personally — I strongly disagree with this editing style and I do not want anyone carelessly adding abstract material to articles. If it is going to be done, it should be introduced carefully and with context and, in my opinion, clearly be quoted material. The material you added mentions two specific examples: contingency loci and error-prone DNA replicases — these are genetic phenomena, not epigenetic. I would characterize this mistake as a misrepresentation and misunderstanding of the material added. Madeleine 06:59, 26 May 2007 (UTC)

It's important that your text describing sources is accurate and a fair summary. It's not important that text use the exact words. In fact, in order to avoid copyright violations, point of view, and consistent tone, it's frequently essential to avoid using the exact word. More importantly, is absolutely essential if you do not mark things clearly as quotations. If you are using quotations marks too much, it's because you are quoting too much and the answer is absolutely not to just remove the quotation marks and leave the text! The answer is to engage in the type of summary and synthesis that is the job of any encyclopedia writer. While you're at it, try to not patronize the other editors with references to what you feel is their youthful zeal. mako (talk•contribs) 21:24, 26 May 2007 (UTC)

Good catch, Madeleine. It was plagiarism, and completely out of context. Note also the subtle change from "recent findings suggest" in the abstract to "recent research demonstrates" in what was added to the article. This is either a gross misunderstanding or a serious distortion. GNUSMAS : TALK 10:06, 26 May 2007 (UTC)