Talk:Epigenetics/Archive 2

Archive 1

Archive 2

Archive 3

intro definition

I have to leave soon, but I notice there's some back and forth occurring on the definition. The definition of epigenetics is fuzzy and changing due to its recent and emerging nature, and I think it needs to get discussed here. Adrian Bird (one of the big names in DNA methylation research) wrote an article in the latest Nature: "Perceptions of epigenetics" Nature 447, 396-398 (24 May 2007). (I recommend, if you can get access, to read this, since its about defining the field.) After touching upon Waddington's original definition, he gives a good present definition: "Arthur Riggs and colleagues defined epigenetics as "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence". The intro material has tried to reflect this, but with a simplification in saying "heritable" without noting "mitotically and/or meiotically" -- probablematic because the common definition of "heritable" implied inheritance over the reproductive cycle of organisms, but most epigenetics in multicellular organisms is mitotically heritable, but not "meiotically" (or rather, not heritable over multiple generations).

He goes on to formulate his own definition, but I think the wikipedia article should try to use Riggs' definition, for now I think it represents the consensus definition in the field. I think maybe something like "epigenetics is the study of changes in gene function preserved through rounds of cellular division" and then something like "a small but notable subset epigenetic features are also preserved over reproductive generations of organisms". Madeleine 11:38, 29 May 2007 (UTC)

Madeleine, are there two meanings of epigenetics? I see lots of abstracts like this one ([1]) which I just now picked at random searching for "epigenetic" at PubMed. In this abstract, the word is used to mean methylation/acetylation changes to a viral gene altering viral gene expression. I have run across the term several times in a usage where it refers to reversible genetic regulation changes within the lifespan of one cell division, esp. when those are produced by an external influence like a chemical or foreign genome. Heathhunnicutt 15:24, 29 May 2007 (UTC)

Unfortunately, there's lots of definitions of epigenetics... that's why we need to discuss it.  :-/ The Waddington definition boils down to "everything in biology other than genes", the Riggs definition tries to narrow this, and the Bird definition narrows it further -- his is limited DNA and chromatin modifications, this would be consistent with your definition. That's also the stuff I'm mostly familiar with, too. But I admit that this definition excludes phenomena like prions [2] (which the Rando & Verstrepen paper refers to as epigenetic) and it seems to neglect the role of RNA in paramutation (this article [3] was included in Cell's recent feature on epigenetics) ... so... that's why I proposed using the broader definition, but I'm not heavily invested in it. The multiplicity of definitions here may deserve a section in the article.

Maybe something more like "Epigenetics usually refers to DNA and chromatin modifications which influence chromatin structure and the transcription of DNA. These modifications tend to be heritable over the course of cell division, and epigenetics can also refer to other non-DNA features which have this property. Although most epigenetic features are dynamic, a small but notable subset of epigenetic features are have some multigenerational inheritance." ? -- Madeleine 18:17, 29 May 2007 (UTC)

Since I didn't hear any response, I went ahead and redid the first paragraph along the lines of this definition. I think the rest of the lead should probably get compressed or moved into separate sections. Some issues:

• "epigenesis" paragraph -- from what I understand, this term doesn't actually get used much to refer to development. From Adrian Bird 2007 "Perceptions of epigenetics":

  "To Conrad Waddington, [epigenetics] was the study of epigenesis: that is, how genotypes give rise to phenotypes during development. [...] Waddington's term encompasses the activity of all developmental biologists who study how gene activity during development causes the phenotype to emerge, but it suffers from the disadvantage that developmental biologists themselves rarely, if ever, use this word to describe their field. In this sense, the usage is obsolete."

• next paragraph, not sure it introduces any new information. Also, the reference to transposable elements does not relate to the material it is supposed to be supporting. Transposable elements are genetic features in DNA sequence, notable in "epigenetics" because epigenetic control is used to suppress them ... this reference is not about multigenerational effects. It's about how nutrition can impact development by having an effect on the epigenetic regulation of transposable elements.
• last paragraph, list of epigenetic features, can keep for now but in the future I imagine the article organized well enough that I think they shouldn't need to be listed like this in the intro, since it doesn't really convey much information beyond a set of links...

-- Madeleine 16:54, 2 June 2007 (UTC)

I fear that this definition is getting more and more technical and gives the reader who doesn't already know almost no idea what we are talking about. It is also clear that, as people become aware of more epigenetic effects, it will be less exclusively focused on the chromatin/methylation issues. Perhaps we should start with something like "In its widest sense, epigentics is the study of changes in biological function that are not caused by changes in the genome". I'm also increasingly of the view that we should have a separate article on epigenetic inheritance because the topics of interest there are rather wider than the scope of this article. (BTW I've found the rats reference, it's Anway et al Science 308 1466-9) NBeale 05:51, 3 June 2007 (UTC)

"In its widest sense, epigentics is the study of changes in biological function that are not caused by changes in the genome" is so wide that it includes learning... Pete.Hurd 20:02, 3 June 2007 (UTC)

I was referring to "biological function" not psycological, economic or cultural functions. Learning through maternal conditioning of the antibody system, for example, can be considered an epigenetic effect (eg per Noble's The Music of Life) NBeale 20:26, 3 June 2007 (UTC)

You are making a distinction here that I don't quite understand. By "biological function" not "not psyc(h)ological" you mean to restict it to physiological changes? As a behavioural ecologist, the phrase "changes in biological function" means something completely different to me than "epigenetics". Pete.Hurd 21:50, 3 June 2007 (UTC)

I'm not familiar with the passing of antibodies from mother to fetus being called "epigenetic", could you point to a journal article that does this? This is a tough word to pin down, since a lot of people use it differently, so I need to read primary material to figure out if and how the definition needs to be broadened. Given how the word is currently used in journal articles, I think it is best to start with the more narrow definition (like the one Bird has created; epigenetics really does get used to refer to DNA/chromatin structure most of the time) and then follow with a second definition that allows for other features also called epigenetic. Maybe there is a way to reword this to make it less technical without losing specificity. Madeleine 22:46, 4 June 2007 (UTC)

Although I'm having second thoughts about this. Maybe it's better to start with the broad definition and then say it can more specifically refer to DNA/chromatin. I'll try to work up some alternate versions of the intro people can comment on? Madeleine 03:03, 5 June 2007 (UTC)

Great idea. I'll see if I can find refs for broader use (though if it isn't epigenetic, what is it?). I did however find this paper "Epigenetic programming by maternal behavior", which although not relevant to the antibodies point is fascinating and should surely be refed in the article somewhere. NBeale 06:02, 5 June 2007 (UTC)

Yeah, I ran across that in my search for maternal immune stuff (and it falls into the DNA / histone modification definition)... there should be a section on environmental effects on epigenetic features (more specifically, environment external to the organism, not the internal intercellular environment). I added one to the evolution section about diet and the agouti gene, I should replace it with this one because its actually an adaptive change, although neither of these studies are multigenerational. (Or, rather, the epigenetic features are not themselves multigenerational... the feedback loop of maternal behavior affecting behavior in pups is presumably multigenerational.) Madeleine 15:22, 5 June 2007 (UTC)

• (A) DNA/chromatin mod first, then broaden definition

Epigenetics usually refers to DNA and chromatin modifications which influence chromatin structure and the transcription of DNA. These modifications tend to be heritable over the course of cell division, and epigenetics can also refer to other non-DNA features which have this property. Within multicellular organisms, epigenetic events during development lead to the differentiation of fetal cells. Although most epigenetic features are dynamic, a small but notable subset of epigenetic features have some multigenerational inheritance. Unlike most genetic traits, in epigenetic inheritance the DNA sequence itself is not changed.

• (B) start with semi-broad definition simplified to mitotic, add transgenerational, note more specific usage

Epigenetics generally refers to features in organisms that are heritable over rounds of cell division but do not involve changes to the DNA sequence of the organism. A subset of epigenetic features have transgenerational inheritance, creating traits that are passed from parent to child without associated genomic changes. Epigenetics is often used more specifically to refer to DNA and chromatin modifications which influence chromatin structure and the transcription of DNA. Within multicellular organisms these epigenetic changes during development allow stable differences in phenotype to exist between cells containing the same genome material, aiding the differentiation of embryonic cells into different cell types.

• (C) (current version) start with original Waddington definition, much more of a developmental focus, notes DNA/chromatin as an example

“Epigenetics” is a word coined by Conrad Waddington to describe the interactions between genome and environment that give rise to differences between cells during embryonic development. Today, the word is more specifically used to refer to features of unicellular and multicellular organisms (eg. chromatin and DNA modifications) that are stable over rounds of cell division but do not involve changes in the underlying DNA sequence of the organism. These epigenetic changes play a role in the process of cellular differentiation, allowing cells to stably maintain different phenotypes despite containing the same genomic material. Epigenetic features are inherited when cells divide despite a lack of change in the DNA sequence itself and, although most of these features are considered dynamic over the course of development in multicellular organisms, some epigenetic features show transgenerational inheritance and are inherited from one generation to the next.

• (D) another definition, I just now removed from current intro because it seemed redundant.

Epigenetics includes the study of effects that are inherited from one cell generation to the next whether these occur in embryonic morphogenesis, regeneration, normal turnover of cells, tumors, cell culture, or the replication of single celled organisms. Recently, there has been increasing interest in observations of epigenetic inheritance maintained through the production of germ cells (meiosis), therefore enduring from one generation to the next in multicellular organisms.

Which is the most understandable? Which feels the most correct? Madeleine 19:49, 7 June 2007 (UTC)

All are much better than it used to be, but I like C best as it seems quite clear what it all means, even to my untrained eye (I'm not a geneticist, so I can't say which is most correct). Next best is A, IMHO. --h2g2bob (talk) 18:20, 8 June 2007 (UTC)

Thanks for taking a look! I was using C because it seemed the most understandable, good to get confirmation on that. I think I'll replace "phenotype" with something like "characteristic" or "trait". Madeleine 19:32, 8 June 2007 (UTC)

Yes, it has to be C. It benefits from a nice gentle lead-in, rather than shoving the technicalities straight down the reader's throat. Well done! Snalwibma 19:38, 8 June 2007 (UTC)

Prions

"Infectious diseases are not typically described as epigenetic, but prions are a rare case where the transition from useful protein to infectious agent is dependent only on 3-dimensional structure and not the result of a change at the genetic level. Although the capability of prion proteins to transition from non-infectious (predominantly alpha-helical) to infectious (predominantly beta sheet) can be directly attributed to its unique sequence of amino acids (and therefore its DNA) it is somewhat debatable whether it qualifies as epigenetic."

I just removed the section. Prions are not considered to be epigenetic. David D. (Talk) 16:10, 3 July 2007 (UTC)

Alright I just did a quick literature search and yeast prions are definitely considered epigenetic. This makes sense since the maternal protein is inherited by daughter cells and the switched form can be inherited. But mad cow disease proteins are not transmissable through the germline (as far as I am aware). This distinction is not really brought out here. David D. (Talk) 16:19, 3 July 2007 (UTC)

Yeah I try and make the case that prions are epigenetic only because the section that was there did not make any sense. I think its debatable whether they fall under epigenetic (certainly not in its most restrictive sense). They are transmissible through the germline in the sense that every animal inherits a gene that creates a prion protein capable of becoming infectious (it rarely transitions naturally, so carries out normal function). Whats not heritable is the transition itself (purely environmental), which I guess is where the case can be made for epigenetic. I agree it doesn't belong in this article though. -Id711 16:35, 3 July 2007 (UTC)

As an aside, a case can also be made that, as independent replicating entities (albeit ultra-obligate parasites), infectious prions don't constitute an example of epigenetic inheritance per se, since they don't "belong" to the organism that carries and transmits them. This is most obvious when one considers cross-species transmission, where the prion leaves one genetic line to infect and parasitise a completely separate one. However, one has to accept that prions represent "independent replicating entities" rather than bizarre molecular mistakes before making this leap.  ;-) --Plumbago 16:45, 3 July 2007 (UTC)

I always have a problem thinking of prions as being "independent replicating entities". Technically they do not replicate but transform their neighbours. This does not seem to fit the biological concept of replication or reproduction. David D. (Talk) 16:56, 3 July 2007 (UTC)

One just has to get imaginative about what constitutes inheritable information. Prions, instead of using a digital code of nucleotide base pairs, use (fairly well conserved) "analogue" spatial configuration. As well as being inheritable information, this spatial configuration allows prions to transmute proteins with the same (or similar) amino acid sequence into this same configuration (i.e. replicating the crucial inherited information). This all leads to a chain reaction of transmutation, with a concommitant loss of function in the "infected" organism (i.e. like other parasites). Anyway, I'm not being entirely serious, and this line of argument doesn't merit a place here (so I'll stop wasting talk space), but I just like to push the claim of prions as selfish replicators whenever I can.  :-) Cheers, --Plumbago 17:05, 3 July 2007 (UTC)

It is one of the great discussions. That, and are viruses alive! Topology as information is a cool idea, a bit reminiscent of the diamond code. David D. (Talk) 17:16, 3 July 2007 (UTC)

I've done some reading and have re-added a prion section, all new writing. While the argument for prions as epigenetic in the context of prion diseases seems a bit weak, it looks like there are fungal prions that are the basis of unusual inheritance patterns for traits discovered decades earlier. Madeleine 19:30, 3 July 2007 (UTC)

I agree with this re-add. It didn't make a lot of sense to me, but after reading your sources I got it. I rewrote some sentences in order to stress why prions are considered epigenetic. Also Sup35 is a yeast protein not fungal so I changed a few sentences to reflect that. A good summary is this review (not sure if it is open access): David A. Harris and Heather L. True. New Insights into Prion Structure and Toxicity. Neuron. Volume 50, Issue 3, 4 May 2006, Pages 353-357. [4] Anyone who cares let me know if it makes sense. -Id711 21:03, 3 July 2007 (UTC)

Actually... yeast is a fungus. I had a question on the word "prion" -- should it refer generally to a protein that has this ability, or does it refer more specifically to the catalytically infectious folded state of a given protein? Madeleine 21:13, 3 July 2007 (UTC)

Copied from my talk page: Madeleine 22:25, 3 July 2007

I think in the most restrictive definition Prion refers to only the infectious form. But common nomenclature refers to both forms as Prion proteins with only a superscript to differentiate between the two conformations (PrP^C for normal and PrP^Sc for infectious). This is a result of the fact that the protein was discovered because of its infectious nature and its normal function was unknown. -Id711 21:38, 3 July 2007 (UTC)

I've edited it again... because I prefer the more restrictive definition. These proteins have other functions in the cell, I think "prion" should only refer to the infectious conformational form of the proteins. Madeleine 23:05, 3 July 2007 (UTC)

Definition in the lead

The lead reads:

Epigenetics is a term in biology used today to refer to features such as chromatin and DNA modifications that are stable over rounds of cell division but do not involve changes in the underlying DNA sequence of the organism.

while later on the current and accepted definition is stated as

The modern usage of the word "epigenetic" is more narrow, referring to heritable traits (over rounds of cell division and sometimes transgenerationally) that do not involve changes to the underlying DNA sequence.

The term "heritable traits" is more generic and presumably includes physical constraints that may be involved in morphogenesis. The definition in the lead seems to dismiss these. Hope someone can fix what appears to be a contradiction here. Shyamal 03:47, 14 November 2007 (UTC)

You seem to be referring to traits heritable over generations but not heritable on the scale of cell division ... while one might want to consider this an "epigenetic" influence, including something on this scale would appear to include all developmental influences (eg. the teratogenic effect of retinoic acid) as "epigenetic". It's not a usage I've encountered, but I'd be open to changing my opinion if I could see an example of this usage of the word? Madeleine ✉ ✍ 05:58, 26 November 2007 (UTC)

PS - the intro does say "such as", so it accepts anything heritable over rounds of cell division. The difference is that it doesn't actually use the word "heritable", it uses the word "stable" - I think this second word is at least as accurate and less likely to be misinterpreted as necessarily implying transgenerational inheritance. Madeleine ✉ ✍ 06:01, 26 November 2007 (UTC)

Okay, sorry I was incoherent... I want to restate this in this way: As far as I know, all cases of transgenerational inheritance have epigenetic inheritance on the scale of cellular division. Thus, the transgenerational epigenetic inheritance is a subset of cellular epigenetic inheritance. It's possible that you could have some large-scale morphological scenario (no cellular level epigenetics) like "mothers with square wombs have daughters with square wombs" and "mothers with round wombs have daughters with round wombs", and it's possible that someone might describe this as "epigenetic". But until anything like this is actually observed, I think it would unnecessarily complicate the lead to include the hypothetical usage of a word for a hypothetical scenario. Madeleine ✉ ✍ 21:14, 29 November 2007 (UTC)

Fair enough, will assume that this is the official definition. If the polarity (of blastomere cells is changed for instance in space) and it subsequently affects tissue formation - that would not be an epigenetic effect since it is not heritable. Shyamal (talk) 01:14, 30 November 2007 (UTC)

On second thoughts, I googled for "gravity epigenetics" and it results in the usages that I had in mind. "craniomandibular morphology is determined by epigenetic factors including gravity, " [5] Shyamal (talk) 01:49, 30 November 2007 (UTC)

Thanks for the reference! It's really hard to know what to do here. The usage of the word by most scientists that "study epigenetics" is the one given by wikipedia - in that quote above I would have used the word "non-genetic" or "physical". From Nature's Epigenetics supplement in May 2007, the intro (Nature 447, 395 (24 May 2007)) starts with "Epigenetics is typically defined as the study of heritable changes in gene expression that are not due to changes in DNA sequence.". Then Adrian Bird's article "Perceptions of epigenetics" (referenced for the definition in the lead, Nature 447, 396-398 (24 May 2007)) goes into some depth about the history of and evolving usage of the word. I settled on a definition very close to Arthur Riggs' (I didn't want to put and/or into the lead), which is "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence". Bird himself more narrowly redefines it as "the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states", a definition which excludes structural inheritance, RNA, and prions.

What do you think? Obviously it's not an easy subject, I've tackled it before. Personally I'm reluctant to expand the definition in the lead based on the usage within an obscure journal, I'd prefer to adhere to a usage used by self-described researchers of the field.

What about adding a sentence to the "Etymology and definitions" section instead of changing the lead? I've made an edit here, maybe you can look it over? Madeleine ✉ ✍ 20:58, 30 November 2007 (UTC)

Fits my view of the term but a definitive reference is needed. There are less obscure sources that make use of similar usages.

Epigenetic effects in the developing chicken embryo subjected to in ovo or ex ovo environmental changes.

• Neuroscience and Biobehavioral Reviews 29 (2005) 1089–1105 [6]

The purpose of this review is to examine the possible mechanisms for the epigenetic effects of early social experience on the subsequent expression of social behavior. We propose that social interactions during the neonatal period organize the subsequent expression of behavior by altering sensitivity to neuropeptides and steroids. Both neuropeptides (e.g. oxytocin and arginine vasopressin) and steroids (e.g. estrogen) regulate or influence the expression of behaviors such as affiliation, aggression, sociosexual behavior, parental behavior, and responses to stress.

• [7]

how alcohol metabolism regulates DNA methylation and other epigenetic events and how these epigenetic events modify gene expression

Shyamal 07:35, 1 December 2007 (UTC)

And to complicate it there is some content here

Waddingron (1939, 1940) is credited with originating the concept of epigenetic factors which arise from interactive activities during development. Epigenetic interactions are fundamental to understanding the mechanics of development and their relationship to evolutionary change. As shown by Atchley and Hall (1991), contrasting intrinsic and heritable epigenetic effects can greatly clarify the concept of pleiotropy and the origins of genetic associations among different traits.

— The Skull by James Hanken, Brian Keith Hall

From the same source on maternal effects

Maternal effects fit atl the attributes of an epigenetic factor, i.e., they represent heritable phenomena, they extrinsically regulate the expression of a cell's DNA, they are indirect in their action. However, maternal effects are a special class of epigenetic factors, because the effect is interorganis-mal in origin, since two separate genomes are involved (maternal and progeny), and, as a result, it involves organisms from two generations. Therefore, it is important to make the distinction between "intraorganis-mal" epigenetic effects arising from interactions among the progeny's own genes, and maternal effects where another genome is involved.

Shyamal 07:38, 1 December 2007 (UTC)

Waddingtons definition is still used although the more modern usage does not take it into account. David D. (Talk) 07:54, 1 December 2007 (UTC)

What's a "definitive reference"? These weren't enough?

• Eccleston A., DeWitt N., Gunter C., Marte B & Nath D., "Introduction: Epigenetics", Nature 447, 395 (24 May 2007)
• Bird A., "Introduction: Perceptions of epigenetics", Nature 447, 396-398 (24 May 2007)
• Russo V. E. A., Martienssen R. A. & Riggs A. D., "Epigenetic Mechanisms of Gene Regulation", Cold Spring Harbor Laboratory Press, 1996

Maybe you can propose modifications to the article that you think would improve it? Madeleine ✉ ✍ 15:12, 2 December 2007 (UTC)

Sorry, no library access here. Hoping that someone with access to reviews of the term and its usage such as this one [8] E. Jablonka, M. J. Lamb (2002) The Changing Concept of Epigenetics. Annals of the New York Academy of Sciences 981 (1), 82–96. can cover the historical changes in the definition. Shyamal 01:16, 3 December 2007 (UTC)

I doubt they are discussing the definition but rather the revival of Lemarkian-like genetics. David D. (Talk) 04:09, 3 December 2007 (UTC)

OK forget that, I just read the abstract you linked too. Looks like a good cite but don't have access to complete article right now. David D. (Talk) 04:11, 3 December 2007 (UTC)

US spelling

Re the recent "Remodelling" -> "Remodeling" edits by TedPavlic, the earliest for of this article seems to be in US Spelling "socialization", so enforcing US Spelling seems to be in accordance with WP:ENGVAR. Still, equating non-US spellings with typos isn't really the best thing to put in edit summaries. Not all articles on WP are in US English. Pete.Hurd (talk) 21:15, 13 February 2008 (UTC)

Epigenetic definition too complicated

The original definition of epigenetics, I think, was too technical to be understood by someone with little/no understanding of biology. I have inserted a more simple definition, and have left the original definition in place, for the more technical reader. This is the new definition I wrote: Epigenetics is a term used to describe the idea that environmental factors can cause an organism's genes to behave (or "express themselves") differently, even though the genes themselves don't change. Is this ok with you?--Luke (talk) 00:57, 13 May 2008 (UTC)

I don't think it's appropriate to aim all encyclopedia articles at the 8th grade level. The first sentence of an article on a relatively subtle scientific topic is no place to teach "someone with little/no understanding" the fundamentals of that topic, that service is better served by links within the lead section. Pete.Hurd (talk) 03:25, 13 May 2008 (UTC)

I strongly disagree. I think that the introductory sentence (or two) of an article is the perfect place to introduce the subject being discussed and explain what it is, for people who don't already know. If they're interested then they can attempt to read further, if they aren't, then they can bale out. The first sentence of a Wikipedia article should ideally //not// be gobbledegook to non-specialists. One of the skills associated with writing a good encyclopedia article is the ability to introduce a subject without unnecessary jargon, in a way that allows the basic concept or term to be widely understood, within the conceptual vocabulary of the general reader. Biochem pages on Wikiedia are sometimes very badly written - technically correct, but lacking an intelligible non-specialist introductory summary or definition - the general rule is, that the reader shouldn't already need to be an expert in a subject to understand an intro. The reader shouldn't need to be a "rocket scientist" to understand the first sentence of an article on "rocketry".

It's easy for specialists like biochemists and mathematicians to fall into the trap of writing an opening paragraph that's incomprehensible to outsiders, even if a concept is very simple. My favourite example of "bad" encyclopaedism was the case where somebody tried to introduce the concept of a minus sign by "explaining" to readers in the first sentence that it was a "additive binary unitary operator" (!?!). That's the difference between defining and explaining. Dictionaries define. Encyclopaedias convey information.

Epigenetics is not a difficult concept to explain. All we have to do is say that while "genetics" deals with heritability via sequences encoded in DNA ("genes"), "epigenetics" is a broad term deals with heritability by other means. That gives us the basis of our first sentence. Maybe we then elaborate and give a little more background info by mentioning that the idea of non-DNA inheritance has been around for a while, but that its become a "respectable" term comparatively recently, and mention some of the recent developments. That then gives a nice overview of the subject for the introductory paragraph(s) that almost anyone should be able to understand. Then we follow up with the table of contents, and then the following sections (which can be technical or not, depending on what's reckoned to be required). But the first sentence of an article is there to explain to the general encyclopedia readership what the rest of the article is about. If they have to scroll down to a links section to find out what the gist of the article is about, then the introduction section is a failure.ErkDemon (talk) 21:54, 12 November 2008 (UTC)

I added a more simple definition in the second sentence. Is that ok with you? This way, more people can learn. I kept the original, more technical definition. --Luke (talk) 03:37, 13 May 2008 (UTC)

Hi, I'm really not sure where to put this and don't have time since I'm in the middle of studying for a genetics exam, but I noticed what seems to be a small error in this line: "Basically, certain enzymes (such as Dnmt1) "prefer" the methylated cytosine. If this enzyme comes to a "hemimethylated" portion of DNA (DNA where only one strand contains the methylcytosine, and the other side still contains cytosine) the enzyme will methylate the other half." Specifically, where it says: "the other side still contains cytosine." Shouldn't the other side be guanine as the base complemnting cytosine? That's all. Thanks for reading. —Preceding unsigned comment added by 66.165.179.131 (talk) 00:27, 2 November 2008 (UTC)

Etymology and definition

In the "Etymology and definition" section, it states: The modern usage of the word "epigenetic" is usually more narrow, referring to heritable traits (over rounds of cell division and sometimes transgenerationally) that do not involve changes to the underlying DNA sequence.

Is this definition correct? I believe that epigenetics refers to when the heritable traits change due to environmental factors. The definition above does not make sense, no? I am going to change it to: The modern usage of the word "epigenetic" is usually more narrow, referring to changes in heritable traits (over rounds of cell division and sometimes transgenerationally) that do not involve changes to the underlying DNA sequence. --Luke (talk) 03:50, 13 May 2008 (UTC)

epigenetic inheritance

I think that we should make a section for epigenetic inheritance. Anyone disagree?

—Preceding unsigned comment added by John0101ddd (talk • contribs) 03:54, 13 May 2008 (UTC)

History section

I think there should be a history section where the Epigenetics could be introduced in simple words.

The section could look something like this:

Epigenetic is a new field in biology that studies new and not yet fully understood phenomena where environment factors can cause physical characteristic changes in an organism’s offspring. The DNA information of the offspring does not change. The manifestations of some genes do, however. The main focus of the epigenetic research is to that part of the DNA which initially believed to be junk because they were not involved “directly” to decode enzymes.

This part of the DNA is believed to be responsible for epigenetic heredity. Ervinn (talk) 23:20, 25 May 2008 (UTC)

Explanation of reversion

I reverted a {{cleanup-rewrite}} dispute template today. the article is clearly written and easy to follow if one has sufficient vocabulary. The usual editors might think of writing a short article in the simple English Wikipedia to help out those who are learning the language.Trilobitealive (talk) 22:39, 29 June 2008 (UTC)

Disagree, article is difficult to read. The intro alone is problematic. Remember this is an encyclopedia, pre-requisites should be minimal. Dumpster muffin (talk) 06:15, 3 July 2008 (UTC)

I have to go with Dumpster muffin on this, the concept is much simpler to grasp than this article, which is a jargonistic stunner. It's one of the least accessible articles I've seen on Wikipedia, including higher math and quantum mechanics. --Blechnic (talk) 06:25, 3 July 2008 (UTC)

I disagree. I found the intro to be quite understandable. This page is meant to be understood by those who have an understanding of basic genetics and molecular biology. No more knowledge is needed to understand this article. —Preceding unsigned comment added by 69.181.2.134 (talk) 06:48, 3 July 2008 (UTC)

A "basic understanding of molecular biology" is too much to ask for a wiki reader. There are now at least 3 editors who think this is too technical, looking at the top of the page I see a quote starting with "This is an article for academics by academics. By writing at this level, you will lose 90% of potential readers." And, 69..... seems to have an attraction to me Dumpster muffin (talk) 02:51, 4 July 2008 (UTC)

I won't revert the {{technical}} template today before reconsidering your points but I have serious concerns over the concept that wikipedia should be written down to the level of the lowest common denominator. You suggested that 10% can easily read it so should that 10%, the ones who really need the information, have to suffer with insufficient writing? I (probably one of the dumbest and most illiterate of the people to have stumbled across this article) took my last biochemistry and genetics courses in 1977; to me the article is transparent and easily readable.

The founders of Wikipedia realized that there were readers who struggle to understand normally complex terminology and that is why they created the sister-project in Simple english. Trilobitealive (talk) 05:19, 4 July 2008 (UTC)

If you "really need" this information, you better not be coming to Wikipedia to get it. I would never get a technical background in a topic from Wikipedia. I might get a reference, but, no, Wikipedia is a general encyclopedia.

Readers with a basic background in genetics and mcb aren't coming to Wikipedia for information. I have less than a basic background in genetics and molecular biology (not my field), and I never use Wikipedia when I need technical information--that's not what it's for. And, there are tons of reliable, useful resources all over the web for professionials seeking information. --Blechnic (talk) 07:14, 4 July 2008 (UTC)

True, but Trilobitealive is correct that wikipedia's target audience doesn't top out at high-school. There are some things that really can't be simplified down to the level of someone with zero understanding of the background topic. That's fine...the intro should in that case make it clear and send the reader somewhere to learn more (ideally the more general idea or basic concepts, for which the article at hand is technical/special-case/advanced/etc). A good article needs to provide accessibility, but not at the expense of depth. Consider a single article on all of genetics...would certainly be general, could easily be accessible, would have a sentence or two about some advanced ideas. Those sentences get expanded because someone cares, and eventually it becomes too much, too deep, too long to stay in the general article, so it gets forked into its own. That article (this article) is just a component of the larger topic, doesn't need to stand completely on its own. I agree that the intro needs to make it clear in simple terms what the topic is, but it doesn't need to bring the whole article down to a level of someone who doesn't understand anything about genetics. DMacks (talk) 20:13, 4 July 2008 (UTC)

I didn't make any of these claims, "a basic backround in genetics and molecular biology" is higher than a simple college biology course, and anyone with college level biology or botany or chemistry has some understanding of genetics. Please don't argue with me what I didn't say" "the articl should be dumbed down to a level of someone who doesn't understand anything about genetics." It's pointless to argue your points with me, rather than discussing what I have said. Epigenetics can be reasonably well understood by someone with a limited background in genetics. --Blechnic (talk) 20:25, 4 July 2008 (UTC)

I completely agree that "[e]pigenetics can be reasonably well understood by someone with a limited background in genetics." I disagree that "[r]eaders with a basic background in genetics and mcb aren't coming to Wikipedia for information". Right there, you're setting an upper bound on who the target audience is, and (as I understood your comment) suggesting that anything that requires more than that background is not appropriate. WP isn't just for lay audiences...if someone cares enough to write on something that can only be understood by grad students, that's not out-of-scope for Wikipedia. OTOH, I agree that much of epigenetics is not such a topic. I agree that things that can be rewritten accessibly should be improved to be understandable by as wide an audience as possible. I disagree that the page at present is written with insufficient contentcontext for the lay reader (intro seems to assume only high-school or maybe freshman-college bio). DMacks (talk) 20:40, 4 July 2008 (UTC)

It's just weird to find Wikipedia editors claiming that their articles are sources of technical information for graduate students in that area. It's not. It's not intended to be, and it isn't. The introduction is not even good Standard English, much less this being a useful understandable article for laymen or graduate students. --Blechnic (talk) 20:49, 4 July 2008 (UTC)

...weird to find Wikipedia editors claiming that their articles are sources of technical information for graduate students in that area... Just for the record for anyone who reads this discussion, I'm not the editor who claims this to be a source of technical information for grad students. My contention is that anyone who seeks to develop a cursory understanding of basic principles in any field of knowledge needs to have access to an encyclopedia article which is not Bowderized. It doesn't matter the field. Take a random look at Taylor's theorem, Epistemology and Irish mythology. You'll see that to read each one requires some basic vocabulary. Otherwise all our written communication ends up as a Pidgin like Him big talk. Me go fella by river. Him go fella by house. Bimiby him go fella me go.Trilobitealive (talk) 23:32, 4 July 2008 (UTC)

Looking at your three examples, Epistemology currently has an excellent introductory sentence that explains the concept and its origins without using any niche technical language. That's quite an achievement. The introductory sentence on Taylor's theorem is middling-to-bad. "In calculus, Taylor's theorem gives ..." is bad wikistyle. It should be replaced by something more like "In calculus, Taylor's theorem is an [insert phrase] that gives ...". The authors also forgot to wikilink the word "theorem". The intro to the article on Irish mythology is awful. Instead of the opening sentence outlining the scope of the following article, it launches straight into discussion: "The mythology of pre-Christian Ireland did not entirely survive the conversion to Christianity ...". It ought to be rewritten more along the lines of "The mythology of pre-Christian Ireland represents the most extensive and best preserved of all the branches of Celtic mythology. Although many of the manuscripts have failed to survive, ...". The rule here is that one shouldn't say what subsequently happened to a thing before you've introduced what the thing is. This isn't about "bowdlerisation", it's about the ability of writers to follow clear and logical style rules. If a specialist can't write an "accessible" opening sentence, it doesn't mean that they aren't clever, or that they can't write for the textbook market, it just means that they're lacking the particular niche skill (or the neutral perspective) required for the intro to a good wikipedia article. In that case, they should probably concentrate on editing parts of the technical content of the article, and leave the opening sentences to someone else. Experts in a field aren't always also expert encyclopaedists, and sometimes some quite good Wiki articles have been ruined by experts who don't understand the difference between an encyclopaedia article and a textbook page.

It's wonderful that experts sometimes get involved and add more "serious" content to wikipedia, but the specialist content needs to supplement or extend the more generally-accessible material, not replace it. The needs of the casual general reader should always be given priority in the opening sentence - the specialist reader can be supported by material deeper into the article. ErkDemon (talk) 23:38, 12 November 2008 (UTC)

See WP:OTHERSTUFFEXISTS and Wikipedia:The perfect article. This article is bad. It assumes a LOT more than high school bio. Carry around that intro in your back pocket and go to a coffeehouse or park and ask randoms what they think of it. Could be eye opening. Dumpster muffin (talk) 16:26, 5 July 2008 (UTC)

What I see missing in the article is that it does not make clear that epigenetic, (that environmental factors can cause an organism's genes to behave or express themselves differently) is also coded in the DNA. In other word, what environment factors can cause genes to express themselves differently is also well determined by the DNA. The article does not explicitly state that, and I think it should. Because of that the article mystifies epigenetic. It is true that they don't exactly know how epigenetic works, but it is very likely that information is also stored somewhere in the DNA. I read it in a book. Someone more knowledgeable about the subject should add that info in, or disagree with me, otherwise I will add that. Ervinn (talk) 17:36, 5 July 2008 (UTC)

P.S. It also means that the human DNA project is not complete. It is true that, they mapped all genes that decode enzymes, but they also have to map all the existing environment factors that can change genes expressions. Ervinn (talk) 17:43, 5 July 2008 (UTC)

Can't believe everything you read in a book, Ervinn, especially not in a crackpot thing like Survival of the Sickest (book). --Crusio (talk) 17:37, 5 July 2008 (UTC)

Crusio, :How do you know which book I refered to, anyway thanks for reminding me Crusio, that you can't believe everything you read, "I did not know that before". The book, Survival of the Sickest (book) may contain bizarre ideas, but it is not a stupid book, it makes people think, which can help focus the directions of new research. Einstein’s relativity theory was once a “crackpot thing”; and it is probably still is for you. Ervinn (talk) 18:04, 5 July 2008 (UTC)

Hi Ervinn, I thought it must be that book as it is the only one that I know of that claims something like "epigenetics is coded in the DNA". Now how on Earth did you guess that I am still occasionally baffled by Einstein's relativity theory? WP:AGF. --Crusio (talk) 18:45, 5 July 2008 (UTC)

The author, or is it the editors, of this article are failing the intent of Wikipedia and are not helping its readers. Trilobitealive is clearly unaware of the opacity of his writing style, and will never be the one to change the article. Trilobitealive thinks that a clear writing style is akin to Him big talk. Me go fella by river. Him go fella by house. Bimiby him go fella me go. This reveals a lot of "attitude". Writing clearly and avoiding jargon can be difficult, especially for those immersed in detail, and can take more time to make the improvements, but is not impossible. Richard Dawkins' "The Selfish Gene" is a fine illustration of how a new perspective, even a new advance in a technical field, can be made in a book which is entirely written in clear language--in fact, more simplified than would be required in a Wiki article. An article on Epigenetics at http://www.hopkinsmedicine.org/press/2002/november/epigenetics.htm is a good example of a clear style. It does not cover the whole field, and is a few years old. But it illustrates clearly how to be clear. Hambleton (talk) 19:08, 25 July 2008 (UTC)

I look forward to reading an improved version of this article. You clearly understand the material and have seen better (in your opinion, not meant pejoratively--just nobody else has commented on it), so clearly you could help us out here. After all, Wikipedia is the encyclopedia that anyone can edit, so please help improve this part of it and everyone will thank you. DMacks (talk) 19:42, 25 July 2008 (UTC)

Today I made a series of edits for style, hoping my pitifully inadequate editing skills would be sufficient for the task. Now I'll rest, exhausted from the effort. (The Hopkinsmedicineorg article does have a nice flowing style. Perhaps it might be appropriate as a reference for a Simple English Epigenetics article.)Trilobitealive (talk) 21:50, 25 July 2008 (UTC)

Epigenie - Epigenetics News and Discussion site

Epigenie Epigenetics news site is a site devoted to interviews, commentary and news about Epigenetics. Is this a worthwhile addition to the Links section of this article? --Paulg99 (talk) 17:29, 25 October 2008 (UTC)

An excellent BBC Channel 4 program

An excellent BBC Channel 4 program on epigenic transgenerational research discoveries is found at http://video.stumbleupon.com/#p=yes9e6lz9v. John D. Croft (talk) 11:00, 12 November 2008 (UTC)

I do not agree that the BBC did a good job here. from a scientific point of view many of the proposed 'epigenetic' events may not be epigenetic at all. it rather appears as if some people wanted to heavily promote epigentic research by putting 'epigentics' into a catching but inappropriate context. it is a promotional program that obviously lacks editing by peers that have a different opinion.Musikutiv (talk) 18:11, 30 November 2008 (UTC)

epigenetics = non-genetic? (methylation)

The third sentence: "[...] instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently". What about DNA methylation? DNA methylation does not change the DNA sequence, but changes something very much associated with a gene. So I would say DNA methylation is a genetic alteration. I'd replace "non-genetic factors" with "other factors". —Preceding unsigned comment added by 130.60.228.187 (talk) 09:40, 1 April 2009 (UTC)

Lamarck

Someone should explain why epigenetics isn't an argument for Lamarckian Evolution. In particular, under 4.3 Evolution, are environmentally-induced epigenetic changes heritable? Are they one-shot hybridization-type events or can they be passed along through several generations? --Virgil H. Soule (talk) 17:13, 4 July 2009 (UTC)

Nova Science Now, episode on Epigenetics

This article is very technical. It was clearly written for a biologist. I'm really interested in the subject, so I came to wikipedia to find out more information, but the article is too difficult for me to read. It would be nice if the article were more accessible to the general public. One thing that would help is adding more links to the article, so readers can find news articles and other non-technical sources.

One such link that I would like to see in the article is the television episode on Epigenetics by Nova Science Now: http://www.pbs.org/wgbh/nova/sciencenow/3411/02.html

It's a very interesting episode that describes Epigenetics in a way that is exciting and understandable by the general public. Please consider adding this link to the article.

Thanks. —Preceding unsigned comment added by KUYTREDCFVGBHJ (talk • contribs) 15:33, 28 August 2009 (UTC)

We failed. Wikipedia articles are supposed to be understandable by the ordinary public WP:NOTPAPER. I'm going to try to edit this, after I finish the Nov. 2010 Science magazine special issue on epigenetics. --Nbauman (talk) 20:00, 7 November 2010 (UTC)

Fringe science

Is there a name for the fringe science people using this idea to promote stupid ideas, like interconection with aliens?--Stone (talk) 14:18, 15 November 2009 (UTC)

I removed the first sentence in the Etymology section. I don't know who Dr Foster is, but his name doesn't belong at the beginning of the first sentence of a major section of the article, and his opinion doesn't belong at the top of this article. The new first sentence now cites Waddington, which is appropriate, given his position in the history of this subject.

MarkinBoston (talk) 02:34, 11 February 2010 (UTC)

probably just pseudoscience. E.g. Deepak Chopra talks about consciousness affecting genes which hasn't been proven. 202.78.240.7 (talk) 22:15, 3 October 2011 (UTC)

Science Functional Genomics Resources: Epigenetics

Science Functional Genomics Resources: Epigenetics is a quite useful resource.

Ph.eyes (talk) 07:46, 17 May 2010 (UTC)

Dr. Bruce Lipton

I first heard about epigenetics from interviews and books by Bruce Lipton. I thought it very odd that he isn't mentioned here. He has excellent credentials, but his research has led him to espouse 'fringe' ideas. Is that why? J Shirk (talk) 01:07, 23 April 2011 (UTC)

SciAm resource

Epigenetics Offers New Clues to Mental Illness "Experience may contribute to mental illness in a surprising way: by causing "epigenetic" changes—ones that turn genes on or off without altering the genes themselves" Scientific American November 30, 2011 by Eric J. Nestler

97.87.29.188 (talk) 00:23, 22 November 2011 (UTC)

Excerpt ...

Studies in mice demonstrate a role for long-lasting epigenetic modifications in such disorders as addiction and depression. Epigenetic changes can also affect maternal behaviors in ways that reproduce the same behaviors in their offspring, even though the changes are not passed down through the germ line.

See Germline. 99.181.147.59 (talk) 08:10, 23 November 2011 (UTC)

Possible merge of Epigenetics-related topics

Recently, a deletion discussion was started for Epigenome. During the discussion, the merging or redirecting of that article either into either this article or Epigenomics was suggested. The closing admin opted to close the AfD as keep, because "the possibilities for merging are too diverse to be properly decided here by a simple merge close". I am bringing this here because this article has a history of recent contributions, so it is likely to be seen here by interested editors. I'd like to have an informal discussion on how people think we should move forward first. I will inform anyone who commented on the AfD. First, I will make a statement of what I think is the probem:

• Epigenome is short, and not so sweet, the only useful content is a definition, however there is source material available on the topic.
• Any expansion of that article (which I have volunteered to do, should that be the result of this discussion) may overlap too much with Epigenomics.
• Epigenomics itself overlaps significantly with this article.
• Is there a need for three articles in this topic area?

Anyone have any comments on this? Quasihuman | Talk 21:02, 5 January 2012 (UTC)

• 3 articles - did you mean Epigenetics?

• Well, what to do? If you were starting from scratch, you'd begin with Epigenetics, wouldn't you? And then what would you do if you had a completely free choice? Just make 2 redirects, or what? What needs covering, really? Chiswick Chap (talk) 23:58, 5 January 2012 (UTC)

Yes, I meant Epigenome, Epigenomics and Epigenetics. If we were starting from scratch, we would start with Epigenetics, as you said. Personally, if Epigenetics was getting a bit big, I'd make Epigenome next, and then if the study of epigenomes, epigenomics, was a significant topic in its own right, as it is with Genomics, I would then make that. I think that epigenomics is a sub-dicipline to epigenetics, as genomics is to genetics. I'm not entirely sure that Epigenomics is notable enough to stand as separate article, none of the references cited cover it. If it was my choice, I'd merge Epigenomics into this article or {{Epigenome]], however, the Epigenomics article is quite substantial, Epigenome is not. Quasihuman | Talk 15:22, 6 January 2012 (UTC)

Rat pups/licking article in the intro

I took it out. I read the article it linked to twice, and apparently psychology journals don't understand the definition of "epigenetics" - they have to be *heritable* changes, and the article never proves that. Despite having "epigenetics" in the title (must be the hot thing nowadays), it's really just an environmental/developmental response study unless they prove that it's heritable. — Preceding unsigned comment added by 129.137.240.11 (talk) 18:16, 13 February 2012 (UTC)

Epigenetics and the Environment

There is no mention in your article that Epigenetics is environmentally influenced/borne. You wrote about cell memory but what it made so? The answer there is the environmental influence. Papers (in epigenetics) nowadays talk about environmental regulation of epigenetics and the environment's role in the formation of individual's epigenetic characteristics so you better update your article to give it some sense. Here is even a 2005 article-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1314949/ — Preceding unsigned comment added by 206.165.222.157 (talk) 03:10, 30 April 2012 (UTC)

Hey, 206.165.222.157, you can fix these problems. See Editing_Wikipedia. Butwhatdoiknow (talk) 13:47, 6 May 2012 (UTC)

Must epigenetics be heritable?

Do epigenetic changes have to be heritable, or can epigenetic changes occur in somatic cells? I know there has been some controversy about this distinction, and this article seems to be inconsistent. (First of all: I'm assuming the word "heritable" has the usual definition of "able to be inherited by offspring." If there's another meaning of the word, referring to inheritance in a cell line within a single organism's lifetime, then this is a moot point.)

The lead sentence reads: "epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by...". Third paragraph: "These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations." The rest of the article seems to take the side that such changes in non-germ-line cells still fall under the term "epigenetics." Personally, I think it's silly to limit the term to heritable changes, as there is no alternative umbrella term for the same set of mechanisms. If we're taking that side, though, shouldn't we remove the word "heritable"?

On a related note: the definition "changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence" could also refer to transcriptional and translational regulation. Should that be clarified? SSSheridan (talk) 23:43, 17 March 2012 (UTC)

heritable purely refers to modifications that persist after cell division. Completely removed from heritability through progeny. Dcherub (talk) 04:09, 6 September 2012 (UTC)

The problem come about because some scientists have used epigenetics to describe things which haven't been shown to be heritable, like histone modification. It is actually a misuse of the term if we want to use the standard definition. I added a sentence on that, but it probably requires further expansion on this. Hzh (talk) 21:28, 1 November 2012 (UTC)

Edit request

Under "Molecular basis of epigenetics", we have:

. . . Most epigenetic changes only occur within the course of one individual organism's lifetime, but, if a mutation in the DNA has been caused in sperm or egg cell that results in fertilization, then some epigenetic changes are inherited from one generation to the next.

I don't understand "that results in fertilization" -- what does "that" refer to? -- Thanks -- Jo3sampl (talk) 22:43, 20 March 2012 (UTC)

And surely if DNA has bee mutated this is genetics, not epigenetics. Jon the id (talk) 14:14, 19 October 2012 (UTC)

Thank you, John and welcome to Wikipedia! —MistyMorn (talk) 14:45, 19 October 2012 (UTC)

Too technical

This article is becoming more complicated. Are you including here the Epigenetic theory which is also discussed in Wikipedia? Are you focusing only to Epigenetics? What is the real source of epigenetics- how come you are not including it here? What are you doing here is definition of terms..This is so technical without a beginning. Here are 2 recent articles that you can clearly gauge your article. http://www.medicalnewstoday.com/releases/220079.php and http://www.time.com/time/magazine/article/0,9171,1952313-1,00.html By reading these 2 articles people can understand epigenetics much better than what you are writing about it. — Preceding unsigned comment added by 206.165.222.144 (talk) 21:24, 5 May 2012 (UTC)

Hey, 206.165.222.144, you can fix these problems. See Editing_Wikipedia. Butwhatdoiknow (talk) 13:47, 6 May 2012 (UTC)

An excellent BBC Channel 4 program

An excellent BBC Channel 4 program on epigenic transgenerational research discoveries is found at http://video.stumbleupon.com/#p=yes9e6lz9v. John D. Croft (talk) 11:00, 12 November 2008 (UTC)

Epigenetics

I would say, this article needs to be integrated as a subsection of the article Epigenetics Chemberlen (talk) 21:40, 8 August 2010 (UTC)

• Integrating this article into the epigenetics subsection may be useful in creating one comprehensive article. However, the epigenetics article is written from a molecular biological perspective - whereas, this article is written from a psychological perspective. Perhaps this article could be considerably expanded, after which, readers might better assess whether this article should be a stand alone article or integrated into other articles.Owleye769 (talk) 23:19, 26 January 2012 (UTC)

Article review

This article gives a nice survey of some of the historical theorists and theories that pertain to epigentics and psychology. Perhaps the article could be enhanced by expanding the "historical" nature (biological, epigenetics, etc.) versus the nurture (environment) - in terms of the their influences on development, behaviour, cognition, perceptions, and personality. The current article touches on this theme - but, maybe concrete examples that support both the nature and nurture debate could be presented - as part of a historical perspective. In addition, recent research that suggests that both epigenetics and environment interact to affect behaviour, etc. could then be presented to show that both "historical" competing theories (nature versus nature) have merit - as is now suggested by international research. Specific examples of environment and epigentics interacting to affect the psychological and biological could be presented in a way that would make the concept of interaction between epigenetics and environment more concrete, thereby helping the reader relate to the article in a personal way. Owleye769 (talk) 23:24, 26 January 2012 (UTC)

Maybe this article could use a short paragraph on the microbiology of epigenetics that would expand on the last paragraph that starts with "Genes produce proteins.... Or conversely, maybe a link to the epigenetics website would suffice. Owleye769 (talk) 23:26, 26 January 2012 (UTC)

Epigenetic landscape

I included a link to the Wikipedia's page on Epigenetic landscape. --Jcmg1964 (talk) 18:31, 2 November 2012 (UTC)

Content from Talk:Epigenetic landscape

I added to the definition the one corresponding to the systems dynamics approach.--Jcmg1964 (talk) 21:52, 31 October 2012 (UTC)

I added a new reference to open the discussion about how the formalization of the epigenetic landscape opens the door to the understanding of the interplay between stochastic fluctuation and physical fields in biological development. I think that it would be necessary to link the page with the one corresponding to the ABC model of flower development.--Jcmg1964 (talk) 19:25, 1 November 2012 (UTC)

Heritable effects of experience?

I'm really not happy with the statement - 'Conclusive evidence supporting epigenetics show that these mechanisms can enable the effects of parents' experiences to be passed down to subsequent generations'. I feel 'experiences' is too broad a term, the statement seems to suggest that if I have a terrible experience (such as a very messy divorce) with no physical change in my environment, that somehow my future offspring (from my next wife) will be affected somehow. Is their conclusive evidence that this is indeed the case? I'm aware of the research in Scandinavia showing health problems in the offspring of parents who went through feast and famine - but this is more than a mere experience, there is a large change in the physical environment. Jon the id (talk) 14:29, 19 October 2012 (UTC)

I've been bold and removed this statement. I think the article now reads better and is less confusing to the average reader Jon the id (talk) 14:44, 19 October 2012 (UTC)

I'm not certain whether the above text was intended to address psychological experiences or not, but I'd reason that it's more than plausible for such an effect to exist: neurological functions often produce significant chemical effects.   — C M B J   09:27, 11 November 2012 (UTC)

epigenetics and shamanism

Shamanism probably evolved with the earliest form of H. sapiens some 30000 years ago (see the Cro-Magnon burials of presumed shamans in Sungir and Arene Candide). Shamanism is the only “religion” that is genetically determined and cannot be learned – unlike recent agrarian (“hypersocial”) religions like Judaism and its followers (Christianism, Islam, Protestantism, Capitalism, Marxism-Communism, Nazism, Hollywood). In fact, shamans become schizophrenic by the age of 10, but then are able to heal themselves completely by some still unknown epigenetic neurological mechanism. In this way, they become deliberate wanderers between two worlds – the empirical world of their own social group, and the “other world”. Shamans are not only extremely stable and strong beings, but they also have astonishing map-making skills (“aerial view during flight”, drawing skills, strategical hunt planning skills) and theory-of-mind skills, i.e., they perfectly know the maps of their surrounding animals (including other group members) and are able to play with them and even to “tame”, teach and heal them as “magicians” and therapeutic “psychopompoi”. Although Julian Jaynes mused about some “schizophrenia” or “bicameral mind” still extending to recent periods (until ancient Greece), there may be a big epigenetic difference between shamans, i.e., schizophrenics who have been able to heal themselves and may then even be able to play with their genes epigenetically by some astonishing mind techniques (with or without the use of hallucinogenics), and the much more common adult schizophrenics in modern (pathological) times – the latter being not able to heal themselves nor being healable by contemporary medicine. Hence, studying the paleogenetic, genetic, and epigenetic mechanisms involved with shamans (prehistoric or recent ones) may be of crucial importance not only for the understanding of the “evolution of our modern mind” per se, but also for the clinical investigation of modern schizophrenia. — Preceding unsigned comment added by 85.1.151.22 (talk) 11:04, 20 April 2013 (UTC)

That sounds fishy, could you provide more references, please? Kinaro7 (talk) 00:36, 6 August 2013 (UTC)

Eductional assignment

I am considering developing this page further as part of an educational assignment in Fall of 2013. If someone is also working on this, please send me a message and let me know soon so we don't duplicate initial efforts in page development. Ran21 (talk) 01:56, 7 October 2013 (UTC)

This article is very detailed with many informative definitions. I would suggest connecting the studies of epigenetics on twins a little more. This seems to be the least discussed section and going further than referencing a few articles can make this a stronger submission. For example, explaining research that has shown epigenetics to influence genetic traits and the variation in gene expression for monozygotic and dizygotic. Ran21 (talk) 02:07, 7 October 2013 (UTC)

Savillo's New Theory

10/14/2012-- The Impermanence of Epigenes. If Genes could or would not change and be expressed with various factors around it (biotic and abiotic) as an epigene , then the epigene could definitely change by itself too- not necessarily dependent on the gene and its internal environment but also being influenced by the external environment. Therefore to be able to survive successfully there is the polishing of the epigenes for the most capable of existence. Can Natural Selection be an epigenetic factor? From his theoretical biology website..112.205.157.113 (talk) 05:23, 14 October 2012 (UTC)rhyu -- From Savillo's web page- 10/27/2013``Epigenes: How fast (by seconds, years etc.) are the phenotypes (cellular to organismal/cellular) produced/realized by an epigene after the epigenetic interaction with the gene in question took place? A nice topic to dwell with and write about! — Preceding unsigned comment added by 112.202.16.66 (talk) 02:38, 27 October 2013 (UTC)

Medicine >> Obesity

Hey all, I was thinking that it would be beneficial if "Obesity" was included as a sub-section of "Medicine." At the very least, we could provide a link to the genetics of obesity Wikipedia article. I'm planning on working on this next week but any help or advice would be much appreciated! --Christyhulett (talk) 06:18, 17 February 2016 (UTC)

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Claim about organization needs independent source

Regarding this revert, [9], I removed this sentence because this claim needs to be supported by a reliable source independent of the organization. I did not find any independent source that even mentions this organization. CatPath (talk) 18:17, 21 May 2016 (UTC)

Agree with User:CatPath (WP:V is quite important to avoid the appearance of being WP:SPAM. But it's also off-topic here, too specific for this higher-level/general article. DMacks (talk) 18:45, 21 May 2016 (UTC)

Sample Sizes in Twin Studies

Should the problems of sample sizes in twin studies be raised in the section pertaining to twins? This seems to me to be a significant enough problem to mention, ie.see the recent discussions in the community on the Tuck Ngun 'study' on homosexuality which was skewed so by media sensationalism.Charley sf (talk) 18:51, 23 October 2016 (UTC)

Should the paragraph about an unreliable study be removed?

In the section titled 'Development' there is a long paragraph that begins "Controversial results from one study..." Because the study seems to lack rigour, lack being reproduced, and is heavily criticised, I believe it does not contribute in anyway to a reader's understanding of the topic.

The experiment conducted seems to be something that could be easily reproduced because it does not require rare skills, resources, or equipment. It is also testing for something that would have great significance and public interest. Failure publish results reproduced in an independent experiment, contribute to making the results seem unreliable. If other supporting publications can be found, then they should be included here. Otherwise I believe the paragraph should be removed.Eltimbalino (talk) 09:39, 24 May 2017 (UTC)

Additions

I have added an example of insect/animal epigenetics experiments. Thanks!

Ichooxu (talk) 01:30, 15 November 2013 (UTC)

Stem Cells

I have added a section about stem cells, specifically talking about the epigenetic differences between reprogrammed iPSCs and embryonic stem cells. I focus on DNA methylation, since recent research focuses mostly on this type of epigenetic modification in iPSCs. — Preceding unsigned comment added by 149.43.126.65 (talk) 18:19, 2 May 2014 (UTC)

Heritability of traits

In the definition section, changes in the DNA sequence are excluded. Nonetheless, I seem to remember being taught as a biology student in the 1980's that epigenetic changes in the DNA were by definition heritable changes in the DNA - NOT the normal modifications required for cell differentiation in the lifetime of an organism. Of course the idea was rightly ridiculed by my teachers. The modern notion is a very different use of the term, in fact the two definitions of the term are practically mutually exclusive. I wonder how this confusing situation has come about. It would be useful if an older geneticist who knows better the history of this term can comment and clarify in the article. Much of the misunderstanding of the term may arise from the two very different uses of the word. I cannot imagine that a neuron that differentiates to become a pyramidal cell of a certain kind in a certain part of the brain used in language will have the capacity to confer via epigenetic changes to sperm or egg DNA sequence better linguistic skills to the offspring. Nor can I imagine that any scientist using the term epigenetic today considers something like that to be a possibility. Skamnelis (talk) 14:55, 24 March 2015 (UTC)

"Historically, some phenomena not necessarily heritable have also been described as epigenetic. For example, epigenetic has been used to describe any modification of chromosomal regions, especially histone modifications, whether or not these changes are heritable or associated with a phenotype. The consensus definition now requires a trait to be heritable for it to be considered epigenetic.[4]" This source explains how epigenetic marks are transmitted from a cell to its daughter cell and that is what they call "heritable" but the text on this page seems to use "heritable" as transmission from a parent organism to its offspring which is confusing. It should be clarified for it's quite important to define epigenetics correctly. Grobert1234 13:15, 2017/05/19 —Preceding undated comment added 17:17, 19 May 2017 (UTC)

Not only "the text on this page seems to", it actually does imply transmission from a parent organism to its offspring by saying "phenotype" which is about organisms, not specialised cells. Does epigenetics in this page exclude things like embryology? Compare Epigenesis (biology). --Dominique Meeùs (talk) 13:10, 19 July 2017 (UTC)

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Controversy Section

Hi guys, the controversy section has to be rewritten as it has multiple problems as of now. (I don't know the right templates to tag it properly, so your helps would be great.) There are two sources at hand; the first one is an op-ed by Adam Rutherford at the Guardian, and the second is an article by David Gorski at sciencebasedmedicine.org. I have read both sources completely. As I've done my M.Sc. thesis research on epigenetics and have published it in a peer-reviewed journal, reading Gorski's article was both easy, light and pleasant. I actually enjoyed it a lot. All the parts where he spoke about epigenetics itself, it wasn't personal opinion, it's basically what all scientific articles agree upon (may be excepting the omition of the effects of retrotransposons at a relevant point, an extremely small detail in the huge article he wrote), and the parts he spoke about the misuse of the word epigenetics his writing is quite neutral and balanced. However unfortunately, I can't say the same thing about Rutherford's writing. His article has been written with a very personal take. It is quite far from being a scholarly or even a balanced article or take on the subject, it's rather of a passionate nature, so I don't know how reliable is it for us to use this op-ed as a reliable source.

Coming back to the point, the important problems in the controversy section are as follows:

David Gorski and geneticist Adam Rutherford advised caution against proliferation of false and pseudoscientific conclusions by new age authors, such as Deepak Chopra and Bruce Lipton.

• Nowhere in the given long source, David Gorski mentions the term new age authors, or Deepak Chopra.
• Deepak Chopra, is only mentioned by Rutherford as a new age guru. Rutherford simply states his personal opinion in a sceptic tone, on what he understands of Chopra's words.
• The sentence above, is a personal conclusion (of whoever wrote it) and uses a combination of things from both sources in an OR fashion. It's not a clear reflection of what the sources are saying. It's not neutral and balanced.
• Gorski's article covers very well the extent of the misuse of epigenetics, it includes Bruce Lipton, some websites such as mercola.com, the creationists, and if I don't recall wrongly some others. It should be properly and neutrally written and in a balanced way from that source. I already expressed my doubts to the reliabilty of an op-ed (not much different than a blog) and even if it isn't, it doesn't really add anything that Gorski doesn't cover.

I'm just before travelling now and if I'll have the time may be I'll rewrite the entire section but if anyone could tag it properly or edit it, it would be great. I'm going forward and already removing Chopra's name from there. Thanks in advance :) --Universal Life (talk) 20:43, 31 August 2017 (UTC)

True, we don't need to isolate individuals, but both Lipton and Chopra are easy targets for labeling as quacks. For the record, an "op-ed" has the added-value of editors reviewing the work before publishing it, unlike a blog. I'll rewrite the sentence and you can improve it. Thanks. --Zefr (talk) 23:00, 31 August 2017 (UTC)

Zefr & UL, that all sounds great. I'm wondering also about the scope of the term. In the first cell of a multicelled organism, what percentage of the body plan, architecture of the heart (for example), shape of the ear (for example), is actually in the DNA, as compared to residing somewhere in the first cell itself. The term epigenetics seems well suited to focus on that field of study, so perhaps it's being defined too narrowly. Bob Enyart, Denver KGOV radio host (talk) 16:06, 25 December 2017 (UTC)

Possible rewrite

I think the Definition section doesn't make that much sense structurally- with a little work it could be converted to a history section. Is that something people would be intereted in seeing? Xavier.bower (talk) 14:57, 3 May 2018 (UTC)

DNA From Some Other Planet

For generality, Wikipedia here shows the DNA of creatures from some other planet, where it has a counter-clockwise or left handed screw-thread.

Earthlings should note that their local DNA curls in the opposite direction to that shown here.

Note that DNA with an Earth-type, right-hand screw-thread, DNA can still have a large scale curl in the opposite direction. (Think of rope on a ship's deck: you can arrange it in a spiral in either direction without it affecting the right-hand thread within the actual hawser.) That is not, however, what the illustration here shows. The DNA shown here has both a left-hand screw-thread and is then shown arranging itself in a counter-clockwise spiral higher up in the picture.

We do not yet know of any other life-form using this sort of genetic coding, and I don't know whether any Yang-Mills-ish bias to our local Universe might allow such a thing, but it's an amusing speculation.

David Lloyd-Jones (talk) 15:27, 23 October 2018 (UTC)

examples please

I still do not get just what epigenetics is? Why is there no section of examples, or another way to help the reader find a concrete example of epigenetics? tahc ^chat 20:45, 1 March 2018 (UTC)

There already are multiple sections on applications. Natureium (talk) 21:12, 1 March 2018 (UTC)

Do understand epigenetics so well that you find no example needed? Since I don't even understand very well what epigenetics might be, how can I know which parts of the article you think are "on applications"? There is no section called "on applications" and I have already done a search for the word "application". This word appears only once, and in a paragraph with zero examples.

Please try to understand that any Wikipedia articles on nebulous ideas should have concrete examples to help explain them, and such examples should in the lead of the whole article-- if not in the very first paragraph.

If you think there is at least one half-way decent example, why don't you just tell me the key words in that example? tahc ^chat 22:46, 1 March 2018 (UTC)

The second paragraph of the lead gives several examples (using the word "example"), and the section called "Mechanisms" is really a list of examples. I understand your confusion -- this is a very difficult topic for anybody without a pretty deep understanding of genetics -- but there really are plenty of examples here. Looie496 (talk) 20:38, 3 May 2018 (UTC)

I have looked at it and none of the "mechanisms" are meaningful examples... because the "mechanisms" (as they are described) lack any concrete terms. The "mechanisms" are all given in abstract terms that may be clear you wrote the article or already know what epigenetics is, but since I am not that person they do not help an outsider very much.

Here is how you might word a concrete example... "As an example of epigenetics, the way DNA strands are wrapped in female cuckoos dictates which bird species is targeted by the cuckoo to raise their young." tahc ^chat 20:57, 16 October 2018 (UTC)

Sigh.

David Lloyd-Jones (talk) 15:35, 23 October 2018 (UTC)

Epigenetic transmission via extracellular vesicles

It appears that another mechanism of epigenetic transmission of paternal stress has been identified. This report on a conference contribution describes the transmission of paternal stress by means of exttracellular vesicles that are ejected from cells and fuse with the sperm. --Chris Howard (talk) 06:10, 14 November 2018 (UTC)

Lamarckism category

When I said "Lamarckism is not even mentioned in the article" (left side), I obviously meant "in the Wikipedia article" and not "in the article by Jablonka and Lamb" (right side) or "in the article on page 43 of the leftmost of the magazines that are lying on the table I am writing this on".

I know that some people make a connection between epigenetics and Lamarckism, but it is not mainstream that such a connection exists. Therefore, if the article contains the word "Lamarckism", it should not be in the shape of a category, coming from nowhere, but in a real sentence - you know, one of those thingies making up the actual article. And then it should not be "epigenetics is Lamarckism", but more on the lines of "some people make a connection between those two, but that is a minority position", plus a source. --Hob Gadling (talk) 20:19, 6 March 2019 (UTC)

Is this where we should mention “correlated regions of systemic interindividual variation” (CoRSIVs)

“correlated regions of systemic interindividual variation” (CoRSIVs) [10] - may be a neologism. - Rod57 (talk) 17:06, 14 June 2019 (UTC)

being abused by far left and far right extremist zealot idiocy

     depending on which side of the simpleton binary spectrum you're looking at-certain people are predetermined to be certain ways because of their ancestor's experiences and overall way of being.everyone was always looking at the far right to keep an eye on any fascist uprising allowing it to gradually sneak up on us from this resentful dogmatic intolerant hypocritical far left extremism with a win at all costs mentality.protected and emboldened with a beyond reproach shield of invincibility.just like any group of zealots-protect the belief system at all costs,it's more important than the people within it.and way more important than the people without it."as long as we're opposed to that,we can't be wrong".worldviews and belief systems are now passed along in a strictly predetermined genetic way,why not language and the accent you speak it with?strip away all choice as eugenics makes a 21st century comeback by the very people who rightfully railed against it a century ago.meet the new boss-same as.......................  — Preceding unsigned comment added by 67.245.249.141 (talk) 17:15, 6 July 2020 (UTC) 

Use of the word "heritable" is seriously misleading

There is a serious problem with the article, which is the repeated use of the word "heritable" to describe epigenetic phenomenon. This is SERIOUSLY misleading, because the word "heritable" usually implies stable transmission of a trait over several generations. There is no evidence that epigenetic modifications to DNA are transmitted over more than one or two generations AT MOST, and compelling reasons to believe this will not occur (DNA is re-programmed epigenetically during early embryonic development). The writers of the article are not at fault; the error is embedded in some of the source material -- but that doesn't make it any less misleading. Unfortunately I don't have the time to do the re-write. — Preceding unsigned comment added by 155.247.36.120 (talk) 16:26, 10 July 2019 (UTC)

Agreed. Such is the current hysteria on this subject, that there is a disappointing amount of ignorance leaking into actual academic sources on it as well, which is then taken enthusiastically by the pseudoscience crowd... Fig (talk) 16:43, 11 October 2019 (UTC)

Fig wright if you have time it would be good to expand the misuse of epigenetics. Steven Pinker covers this in the afterword to the second edition of The Blank Slate. Kevin Mitchell also covers this in his excellent 2019 book Innate. The misuse of epigenetics is not good news. You may wish to also take a look at the Transgenerational trauma article because it is seriously overstepping things. Sxologist (talk) 23:53, 6 November 2020 (UTC)

Regarding "heritable", if there is an accuracy problem and something can be done about that by using quality sources...something should be done. But we can only go by what the sources state and with WP:Due weight. And sources on this topic do consistently use the term "heritable." And that includes this 2018 "Epigenetics, Nuclear Organization & Gene Function: With implications of epigenetic regulation and genetic architecture for human development and health" source, from Oxford University Press, which begins with the following on its Google Books page: "Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence." Flyer22 Frozen (talk) 01:38, 7 November 2020 (UTC)