Talk:Gene/Archive 2

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Archive 1

Archive 2

Archive 3

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I agree about "generate" being not quite right for genes. Also, it's not true that genes "initiate." It's totally a chicken-and-egg type situation. Genes encode proteins, but it falls to proteins to turn on genes and replicate genes. The stuff of life includes lipids and cellulose and other things fundamental to cells which aren't directly encoded in DNA but are made by proteins.

With respect to attributing to genes' "two crucial functions," that's just another way of advocating the loose definition that includes regulatory elements, which gets discussed lower down. If we're starting with the narrow sense of gene as it is used in molecular biology and genomics--which I think is a good idea and what I thought we were doing--then this broad view doesn't belong up there. Including prions in the initial definition blows it wide open. With respect to what biologists think about prions, viruses and life, I think what we're looking for in a definition is popular usage--and in the approach to the definition that's been taken up to now, popular usage among the common gene worker. I haven't read your guy, but Nobel prize winners go off the handle all the time from their soap boxes and in particular as they enter their "philosophical years." It seems to happen to all of them. Francis Crick of the double helix has gone into neuroscience theory late in life most people in that field think his theories are nutty. What I know about what biologists think about viruses is from undergrad and grad courses in biochemistry and molecular biology and I suppose from the odd water-cooler conversation. It's not the widest sample, but what's yours? Finally, for the sentence with prions in it as it was written, the issue was not whether they are alive but whether they read sequences that employ a code that some people regard as different than the genetic code, which these people say they recognize. Nobody talks this way, and to do so makes something simple seem totally vague.

168....

I had nothing to do with the inclusion of viruses in the first paragraph, and although I generally agree with you (168) I leave it to you and others to decide what to do. It was, however, I who included the role of genes in switching on and off protein-production. Although I agree with 168 in principle about the function of the first paragraph, the previous version focused on the genetic code as a template for the production of proteins. This is not a general, inclusive definition, it is a definition of one of the two or three main functions of genes. I thought it was important to add the stuff on on/off in order to make it clear that genes are not just "blueprints" (a very common metaphor). If you or anyone else can come up with a more general and inclusive definigion of gene for the first paragraph, please do so, Slrubenstein

About "generate"-- it really doesn't deserve the effort we've already put into it. I was just trying to make the point that Johannsen in 1909 did a fair job in coming up with a good term. You are holding him to a nuanced argument in the coining of a word that could not have been anything but a general descriptor at that time. Even now it would be hard to come up with a more fitting one word term... I still think you're missing the point about prions. If they're life, they do not use the genetic code in replication. That alone, independent of whatever sequences they do use, is enough to single them out as a possible exception to a rule we had thought to be universal. But I have no wish to pursue it because the study of prions is still so full of uncertainty that references to them in articles like this tend to create this kind of stalled squabbling... My face-to-face sample is roughly the same as yours, but quite a bit longer ago I think. You're just plain wrong about who talks what way. There's no doubt the majority of biologists would say viruses are in some real sense alive. The single greatest prerequisite for this designation is that the entity be self-replicating, a condition plainly met by viruses. JDG

Are viruses really self-replicating? I thought they depended on a host for replication (i.e. something other than them"selves") I really thought this -- and the Wikipedia article seems to confirm this -- so if I am wrong I really want to know. Also (consider this a ps.) I did not think that my qualification concerning the role of genes in generating proteins was in any way disparaging of Johannsen's work. Slrubenstein

As usual we are crashing into semantics. Yes, viruses are obligates and cannot reproduce without a host. On the other hand, the host does not itself induce this replication and the end result is a lot of new viruses, a very lifelike result. There are examples of nonliving entities (crystals, etc.) that seem to grow in number due to a kind of assortative action on the other inert materials around them, but the interior of a living cell is not inert and viruses actively hijack living processes. Viruses contain nucleic acid and these acids initiate their replication, another feature of "life"... I'm not saying the issue is decided. I'm just saying a large number of fully credentialed people come down on this side of the question. I don't think that's subject to debate.JDG

Sorry, JDG. I was not being argumentative, and am not "debating" anything; I was asking a sincere and serious question. OK, a large number of credentialed people take one position. Are the majority? Vast majority? If they are the vast majority, I have no objection but since this vast majority mean "self replicating" in the specific sense you invoke, I think the article should make that clear (a brief parenthetical would suffice). If they are a slim majority or a large number but still a minority, there should be a sentence presenting the other view. I am not arguing with you, I am simply describing what I believe would make the article clearer and more complete. This is not semantics -- your own reply suggests that there is useful information hee that should be included in the article. [User:Slrubenstein|Slrubenstein]]

There's too much wholesale blowing away of other people's work happening here. This is supposed to be collaborative, not competitive. I think it should reverted to a couple days ago and then copyedited responsibly.JDG

I have not followed all the changes closely enough to know whether I agree or disagree with JDG. I do, however, believe the first paragraph is poorly written (although informative). I deleted two senctences which I believe should be reincorporated into the article, but not in the first paragraph, and in a different form.

Genes do this with a more or less universal vocabulary called the genetic code, which the translation machinery present in all cell-based life reads and interprets (with minor variations) the same.

The above sentence has useful content but is too detailed for the first paragraph. The first paragraph should introduce the article as a whole. Discussion of the genetic code, the translation machinery, and any debates (if there are any) about universality, should be in the body of the article. Also, I am not sure the above sentence is grammatical.

This accords with both the operational and traditional meanings of "gene," which Wilhelm Johannsen coined in 1909, based on the ideas of Gregor Mendel.

For one thing, the sentence (this accords) seems argumentative and has no place in an encyclopedia article. The first paragraph perhaps should mention that the word was coined by Johannsen and refers to something postulated by Mendel -- but in a nonargumentative way. In other words, the subject of the sentence should be "gene" or "Johannsen" or "Mendel," not "this" reffering to some claim made by the article. Also, this sentence introduces two terms that are left undefined or explained: an "operational" definition and a "traditional" definition. Don't put this in without explaining what these two definitions are, who proposed and uses them, and why there are these two kinds of definitions. I suspect all this information might belong in the body of the article, but not in the introduction. Slrubenstein

Actually, I just reviewed the recent changes and now do agree with JDG. I have reverted back to the version edited by user:Marj Tiefert which is clear and well-written. This removes a series of changes made by an anonymous user that seemed to add argument but no content. JDG, what do you think? Slrubenstein

I reverted back to Marj Tiefert's last editing. This encompasses some editing I did as well (for example, mentioning Mendel in the first paragraph) -- to my knowledge, there was no change of content. What are your objections to this version? I believe it is much clearer and the prose is smoother. (the only edit of mine JDG took any issue with was my qualifying the word "generate;" as best I could tell, JDG didn't completely agree with me but considered the distinction semantic.)Slrubenstein

I think the suggestion was actually to revert to something older, which is what I just did.

I can't understand how "accords" could be perceived as argumentative, and there's other stuff I would take up if I had the patience, but I don't. I will say universality goes hand in hand with the definition of gene as a sequence that encodes a protein. To anyone new to the topic, I suspect it would make the idea more accessible.

168...

do what you want, but the current version is poorly written. Specifics: the relationship between "gene," "DNA" and "sequences of nucleic acids" is not clear in the first paragraph. Also, there is a passive voice problem (recognized by whom?) "Some elaboration can be necessary" is needlessly clunky (plus, it should be "may," not "can"). Regardless of what JTD wrote, Marj's version is simply better written. Slrubenstein

I haven't looked at what Marj did, but in her summary she called it copy editing, not rewriting, as you've done--introducing errors into the science in the process. I suggest you avoid declaring wording "good" or "bad." It's neither specific nor polite. Likewise with knocking it without offering an alternative--e.g. for the alleged "clunky" phrase, which you didn't argue was unnecessary. Incidentally, the connection between nucleotides and amino acids is the genetic code, which you think doesn't deserve mentioning in this context.

"Gene is a term coined by Wilhelm Johannsen in 1909) to refer to a unit of heredity (first suggested by Gregor Mendel). IS ORIGIN MORE IMPORTANT THAN DEFINITION? I DON'T THINK SO, ALSO I THINK THEY'RE BETTER SEPARATED, GIVEN HOW MUCH THERE IS TO SAY ABOUT BOTH. ALSO WHY SLOW FLOW WITH PARENTHETIC REMARKS?

Personally, I think this is a good way to introduce information about a technical term. I don't have any principled objection to moving this stuff later, except it seemed to me that putting it any place later would end up interrupting the flow of the article. In the last version it just seemed out of place.

It contains information in the form a universal code NO IT DOESN'T, IT EXPRESSES THE INFORMATION IN CODE. THE WORDING THERE SUGGESTS ALL GENES HAVE THE SAME SEQUENCE

Sorry, I guess I just do not see that much of a difference between expressing meaning "in code" and expressing meaning "in the form of code." I do prefer the latter phrasing when the point does not concern some generic code but rather a specific code about to be named or described.

found with only minor variations across all forms of life, including viruses WHICH AREN'T CONVENTIONALLY A FORM OF LIFE SO WE SHOULD MAKE THIS SENTENCE ABOUT "CELL-BASED LIFE" OR THE LIKE,

fair enough -- in this particular instance you are criticizing a phrase that was in the earlier version, and which I myself did not write or change.

organized HUH? ORGANIZED? HOW? into sequence of nucleotides that constitute "MAKE UP" WOULD BE LESS AMBIGUOUS) DNA. WRONG AND MISLEADING. HIV HAS GENES BUT NO DNA--IT'S AN RNA VIRUS, LIKE MANY OTHERS. ALSO THE TRANSCRIPT OF A GENE MAY BE REGARDED AS A GENE, AS CAN LETTERS ON A PAGE. THE TEXT SUGGESTS A GENE IS A PIECE OF DNA, EVEN THOUGH THE TEXT SAYS OTHERWISE FARTHER DOWN.

I am sorry if this is misleading or wrong, and you should of course correct it. I was simply trying to construct a clear sentence out of one that frankly I found very difficult to follow:

It contains information in the form of a sequence of nucleotides--especially DNA sequences--conforming to a universal code that is recognized with only minor variations across all forms of life, including viruses. (note: this was the phrase you question above) This DNA sequence (a "gene") ...

I hope given the preceding phrase you can at least see why I thought you meant that DNA sequences = genes.

"These sequences in turn specify the amino acid sequences of proteins. The identification HUH? AS IN, AT A CRIME SCENE? WHO'S IDENTIFYING? WHAT MEAN "IDENTIFICATION" of a gene is not determined solely by the specific "SPECIFIC" REDUNDANT/UNCLEAR sequence of nucleotides.

I grant that the above sentence may not be the best sentence in the world. But I insist that it is better than the one it replaces, namely, "Even with this narrow definition of the word, some elaboration can be necessary to guarantee against confusion within the intricacies of biology."

"On the one hand, two nucleotide sequences may differ, and yet they may be regarded as simply variants of one gene -- for example, as alleles (different genes in the population that occupy the same chromosomal locus WHAT'S A LOCUS? and therefore compete or combine HUH? WHY SHOULD THEY DO THAT? for similar traits ALL CONTENT BEST SAVED FOR A SEPARATE ENTRY FOR "ALLELE" OR FOR FARTHER DOWN IN THIS ONE), or mutant forms of that gene.

Here I cannot answer your questions. I did not write the above, it was in the original article, but towards the bottom. Given the organization of the article, such as it is, I thought this kind of information belonged earlier, so I moved it up. I do recall biologists using the word "locus" when reffering to alleles, so I didn't question the choice of words. But, as I say, I did not write this. Slrubenstein

168...

This page needs more work. I've rewrote the intro/summary so that non-specialists can understand what a gene is, divided the article into sections and reorganized the material. --mav

Excellent work, Mav -- it certainly is much clearer, and I think even more informative. I do have two comments, though, that perhaps you or others could respond to. First, I do not see why "use" was changed to "consult." "Use" seems to be the most general term; something can be used in all sorts of ways; "consult" is a particular way of using something, but it seems anthropomorphic. My second comment follows from this -- obviously, the article now relies heavily on anthropomorphizing metaphors (not just consult, but book, etc). I am not arguing against this, but I do observe that most people (maybe lay people) think of science and poetry as rather far apart. Metaphors gain in evocative power what they loose in precision. Perhaps the metaphors in the article are metaphors that scientists themselves rely on. I am not arguing to change it, if that is the case. BUT, if scientists have non-metaphorical language to describe the structure and functioning of genes, then that language should be included. And if scientists do rely on metaphors, I think we need to include a brief explanation of why they rely on this or these particular metaphors. Slrubenstein

Hm. I wasn't responsible for the use -> consult change and will have to look into this. But metaphors are often employed by scientists and science writers when trying to explain science to lay persons and students. The metaphors used were taught to me during my intro series to biology. I think they are appropriate for the intro/summary since this section is designed to give a broad overview of the article. We could, of course, better explain why these metaphors are appropriate in the "use of the term" section. We should also mention just how and where these metaphors break down. --mav 19:37 Jan 21, 2003 (UTC)

I made the "use to construct" --> "consult in constructing" change to guard against readers inferring that the "use" cells are making of DNA in constructing proteins is like the way masons use bricks. That sense of "use" conflicts with the notion, which the introduction everywhere else seems to be advancing, that a gene is a piece of a chromosome or a piece of DNA. A cell does use chromosomal DNA to construct _as a tool_, but it uses it as a tool to construct RNA, not proteins or other molecules. And because the sentence doesn't give the readers any cues to suggest the use might be as a tool, and because I think the natural inference is that the use is as a building material, I judged the sentence much better off with the "consult" construction, which does away with that ambiguity.

168...

okay, I see -- but consult is vague (when I see the word used in this -- to me, at least -- idiosyncratic way, I try to think of other ways I use the word "consult". I might consult an encyclopedia for all sorts of information; are you saying that genes contain all sorts of information and when cells consult genes, it is specifically for information on how to make proteins, but other things consult DNA for other information? A business might hire a consultant, who will give relatively disinterested advice that the business may or may not take; are you saying organisms consult genes but may turn to other things for additional advice? It seems to me that the word "consult" doesn't clearly describe the functional relationship between a gene and its environment/organism) How about "use as a template" (if this is indeed the use). My point is, one word simply may not suffice. Also, your reply includes more detail that, if not appropriate in the first paragraph, out to go in somewhere.... Slrubenstein

As I was hoping to communicate in my remark above, "use as a template" only applies to constructing RNA and not to proteins when you define genes as DNA/chromosomes. I didn't write the sentence, I'm just trying to make the best of it. I think you guys created some real problems with this rewrite, which changed a lot more than organization and style. 168...

I wonder whether this sentence

Genes, along with environmental factors as well as random molecular and cellular movements, play a crucial role in the production of organisms (as well as in the reproduction of genes themselves).

which currently stands along after the first paragraph, might be better following the first sentence. What do people think.

I wonder what the "random molecular and cellular movements" are. I can't imagine. The sentence makes sense without it, so I wonder why it's there. Meanwhile "play a crucial role in the production of organisms" is unnecessarily vague. I don't think it offers any information to a naive reader. 168...

Also, although I know that genes do provide information and it is as a form of encoded information that most lay-people think of them, I still wonder whether this is the best way to characterize genes. Do genes play not active role in the production of proteins? I honestly do not know, and if the answer is "yes" I assume it would have to do with molecular chemistry.

If you want to define genes as DNA,

Personally, I do not; I define them as sequences of nucleotides that provide a template for, and regulate, the production of polypeptides Slrubenstein

then they don't make protein. That's why it's silly to define genes as DNA, because the way molecular biologists talk about genes, they're all about proteins. And really not only pieces of chromosomes but also viral RNA and sequences in the abstract can be genes (how does a gene on a chromosome become a gene on a cDNA? does it disappear in the mRNA and reappear after retrotranscription?). It makes a whole lot of sense to say that genes are information, abstract as that idea is. 168...

Finally, I object to this sentence:

There are two slightly different "alphabets" that are used to store and transfer this information: DNA and RNA.

The alphabet -- if I follow the metaphor -- is the four bases, CGTA (in DNA, with the U for T substitution in RNA). DNA and RNA are more like long sections, no tthe alphabet itself. When I think of "alphabet" I think of the smallest unit. But DNA consists of many genes, which consist of many nucleotides; DNA is much bigger than the alphabet, it is somethig constructed out of the alphabet. I do understand the intended poiint, that DNA and RNA use slightly different alphabets. But even here I am nost sure if this is the best way to express it. If we want to use a linguistic metaphor, U and T are allophones; it can be one alphabet that is pronounced slightly differently... Slrubenstein

I have no trouble with the sentence, leaving aside placement. DNA and RNA differ in the last letter of their alphabets: ACGT vs ACGU . The metaphor seems nicely apt to me. 168...

I made some more changes to the first two sections, hopefully purely editorial. I do have one question about codon, and it gets to content, so I will not change the text until I have clarification from Mav and 168. It is my understanding that codons are specifically triplets of messenger RNA. The current section is clear on the function but neglects this fact. Am I wrong, or should this fact go in the article?

Codons are codons when they're DNA too. You're making a distinction that I've never heard anyone make (in many discussions about gene sequences in a laboratory) and I think you've just imagined. 168...

Given how obnoxious and childish you are being, I must really have offended you before and for that I apologize. Obviously I did not imagine it, the information comes from an undergraduate textbook. But it is equally obvious that I did not accept unquestioningly this characterization of codons, because I did not put it in the article and I specifically asked you and Mav for your views. Slrubenstein

Actually, I was totally sincere about codons, although I was snide to you a couple times before--with cause. In my conversations in lab, we talked about codons in plasmid DNA--perhaps because plasmid DNA typically is cDNA retrotranscribed from mRNA. 168...

I would rename the section "Codons" as "The Structure of Genes," and here is how I would rewrite it:

The basic unit of the genetic code is a triplet of bases, or code, [I'd nix "or code"--here it's liable to be taken as scientific terminology, plus I find it vague and unhelpful 168..] called a codon. In eukaryotic cells, some sequences of codons represent specific amino acids and are called exons. Other sequences are transcribed into RNA but then eliminated and do not translate into amino acids; these are called introns. There are three codons (ATT, ATC, or ACT in DNA; UAA, UAG, or UGA in mRNA) that signal the point at which transcription stops; these are called terminating triplets.

"are called" is passive construction: Someone remarked earlier that this was a poor way to write. Also the 'graph above is liable to mislead by transitioning from "some sequences of codons" to "other sequences." Introns don't have codons--unless perhaps you define introns as pieces of chromosome, as is being done here. (I don't know how this nomenclatural issue is handled, but I wouldn't be surprised if the "intron" spliced out of one transcript were called an "exon" with regard to an alternative splice). You might mention splice sequences and definitely you should link out to splicing or intron/exon, which have their own articles already. 168...

This is based on a couple of textbooks I have consulted but differens significantly from the text in the article. I do not want to replace the current passage in the article until Mav and 168 respond. Slrubenstein

Good rewrite. The "alphabets" wording was a crutch and I'm glad you spent some time fixing the paragraph so that it didn't need it. I've made some changes for the sake of accuracy. Please do paste in the text. However, the heading "Structure of genes" really requires a good deal more than the above. But if we are going in that direction we might as well map it out now. --mav

In case you're curious about why life has "decided" to use thymine in DNA and uracil in RNA, thus making our lives more complicated, I added a paragraph over at genetic code discussing it. It's a purely practical reason; cytosine converts into uracil by a simple deamination reaction, so keeping uracil out of DNA makes correcting that particular mutation much easier on the cell. Not really relevant to the gene article, but I thought it might make the "alphabet" issue a little clearer. Bryan

Wow - 168. Very nice edit! I would even call it Brilliant prose. --mav

I got rid of the section "codons" and renamed it types of nucleotide sequences -- given Mav's comments this is perhaps more accurate than "structure of the Gene." I did incorporate some of 168's points, as well as material from the earlier version, into my version. I am unsure of the article links 168 was reffering to, and trust that s/he or Mav will make the appropriate changes.

As for "random molecular and cellular movements," I did not write that; I was merely raising the issue of placement. I suspect it refers to Brownian motion, among other things. But 168's edit is unacceptable because it leaves the impression that specified factors (viz. genes and environment) "determine" phenotype. This is either incomplete, or there is a problem with the use of the word "determine," because random factors do influence the development of the phenotype. I added "random variation in growth and division of cells." Slrubenstein

Hello. I made another major revision to this article. My purposes were three-fold:

'Improve the structure and writing of the passage. I did this mostly by rewriting what I felt was awful prose. Sorry.
Remove discussion of biological concepts irrelevant to genes. For example, most of the discussion of codons is unnecessary, and so I deleted it. Additionally, things like Junk DNA might have their own articles, and in any event such discussion has little or no bearing on a reader's understanding of genes, as opposed to DNA or chromosomes.
Addition and reorganization of discussion. I added in text where things weren't adequately discussed, and moved sentences around where appropriate. For example, I added a discussion of dominant/recessive genes which was largely missing, but important, to an understanding of genes. Perhaps this is more appropriate in allele, but for now it fits in well here.

Apologies for generally destroying the established structure of this article. Graft

Graft, I have no major objection to your changes. But I do object to your deleting the information on codons. According to the dogma, chromosomes are made up of DNA which is made up of genes which are made up of codons which are made up of nucleotides; I think a clear description of "gene" would locate it in this molecular-chemical hierarchy. Moreover, the different types of codons help describe the different ways genes interact with other elements of the cell. I believe a minimal discussion, with links, is important. Even if you disagree with me, surely putting information back in (and really, we are talking about tree or four sentences) can't do much damage. But I would rather you put that material back in, as (for the moment) you have the clearest idea of the structure you envision. Slrubenstein

Hello SLR; I think codons are only really appropriate to discuss in the context of mRNA. A codon is basically an abstraction in DNA, especially in organisms with introns where a "codon" may be interrupted by a stretch of several hundred nucleotides. One does not need to know what a codon is except to understand how RNA is translated into protein. While this is interesting to understand, it is not wholly relevant to genes.

For reference, observe this paragraph from the old version, which is mostly a discussion of translation:

The basic unit of the genetic code is a codon, a triplet of bases (the "code" reffered to above). In eukaryotic cells, some sequences of nucleotides represent specific amino acids and are called exons. Other sequences are transcribed into RNA but then eliminated and do not translate into amino acids; these are called introns. Terminating triplets are three codons (ATT, ATC, or ACT in DNA; UAA, UAG, or UGA in mRNA)that signal to tRNA the points at which translation of the gene transcript starts or stops. Ribosomes translate the start codon as methionine and translate the subsequent codons up to the stop signal. The sequence between "stop" and "start" (called an "open reading frame") typically encodes a protein of about 300 to 1000 amino acids long.

While it may not do any substantive damage to put this back into the article, I think it disrupts the flow of the discussion of genes to insert this aside about the mechanism of translation. A full discussion should go in genetic code, but not, I feel, in gene. Graft

Fair enough -- I looked at genetic code and do agree it would work there (and I didn't see this content there), although I am not sure where. Since you have a better grasp of these issues, would you be willing to paste it into that article (if you see a reasonable place for it)? Slrubenstein

I for one think that Graft's modifications flow more smoothly and make the article more informative than the previous one. Kudos. Rgamble

I agree. The revised article is vastly more readable and seems to cover the essential information well. There is some useful information missing now (as SLR has pointed out) but the overall ability of the entry to inform the reader is increased because it is more accessible, and (with SLR) I am inclined to trust Graft to add whatever is needed back into the appropriate places (this entry or others as he judges best). When the cook is doing a great job, the wise man stays out of the kitchen and tries not to joggle his elbow. Well done, Graft. Tannin 21:16 Jan 22, 2003 (UTC)

Re: the recent reversion of some of 168's edits, here is why I think my version is better:

I include mention of the central dogma (which Crick called the Central Dogma of Molecular Biology, incidentally, and I will correct redirects for this in a second) because it describes the idea that genes are encoded in DNA; so, while 168's version makes more explicit what the Central Dogma actually says, my version emphasizes aspects of the Central Dogma that are important to genes.
In the second paragraph I wanted to be careful to explain how nucleotides are linked, so that they would get a better understanding of how it might encode information. 168's version is much tighter (I tend to be a bit verbose, it is true), but I think mine does a better job of conveying the idea of how information is stored.
I wanted to avoid a computer analogy, because it's only useful to computer scientists/hackers. This is a small fraction of the people who use the internet. Also words like 'catalytic' are jargon and should be avoided where possible.
I liked the last paragraph a lot more than my version. I removed the discussion of variants of genes/alleles, because that gets discussed lower down in the text.

Graft

I say in response,

Why does anybody need to know that the "Central Dogma of Molecular Biology" is called the ""Central Dogma of Molecular Biology" (which I don't believe it is, by the way: I believe it's the central dogma of _Genetics_)? Why do they need to know who first articulated and dubbed it? Why do they have to think it's so complicated an idea as to require "formulation" instead of mere uttering? Why do they need to know this was done by Crick? Why that he is famous? Why do they need to be mislead to believe that it is a dogma or indeed that _anybody_ regards the principle as anything more than a rule of thumb or manner of speaking? With respect to what you say the alleged dogma says, I don't think "specific biological function" is accurate to what it says and I believe the statement is too vague to be helpful. Finally, to call a gene a piece of DNA is to be stricter than any molecular biologist. If the initial articulation of the dogma did this (which I doubt), I'm sure the way it's quoted now doesn't.

168...

It's called the "Central Dogma of Molecular Biology" by Crick. See . They don't need to know who first articulated and dubbed it any more than they need to know what a gene is. However, Crick is arguably one of the most important people involved in modern biology, so I think passing mention is not wholly undeserved. I wouldn't be opposed to taking it out if you think it's distracting. It may not seem complicated now, but it definitely was "formulated" by Crick at the time (1958) (hindsight is 20/20, remember). You're right, specific biological function is not very accurate...

Crick does not talk about genes at all, he talks very non-specifically about DNA, RNA, and Protein. And actually, now that I think about it, the idea that DNA is the genetic material didn't originate with Crick, so maybe this discussion is wholly inappropriate. I'll have to hunt around for who first proposed that specific DNA elements encoded genes. And, yes, this is not 100% accurate, as there are exceptions to everything in biology, but it is basically true. Graft

I'm suspicious of that Web site you offer as evidence that people say "dogma of molecular biology." For one thing, it doesn't cite the original paper or quote from it, and only uses the dogma title as a header, unattributed. You can find "central dogma of molecular genetics" and others elsewhere on the Web. Mostly I think people just call it the central dogma (i.e. of what goes without saying). Maybe it doesn't have a universal name. Anyway, I consider a more credible looking site regarding what the dogma is, and it isn't what the wiki gene article is now saying it is. 168...

I offered this as evidence because it's a piece written by Crick himself, which I think should establish that (a) he calls it the Central Dogma of Molecular Biology and (b) that since he coined the term, we should take what he calls it as authoritative. Regardless, I wasn't attempting to state the full Central Dogma, I was only attempting to state the part about genes being DNA elements encoding proteins, which it appears Crick says in his original Central Dogma statement. Graft

Graft, thanks again for the good work you are doing here. I have a couple of specific comments on your above points, and then a general comment. First, I agree with you about the importance of mentioning the Central Dogma not only because of its content, which is meaningful to physical anthropologists and biologists, but because it provides historical specificity (although like 168 I do not think it is necessary to say he is famous; just provide the link). Second, I agree with you about the computer metaphor; a basic account of what a gene is should rely on metaphors as little as possible, and rely on those metaphors most common in the scientific literature.

My general comment elaborates on these two specific issues. Although I do agree with you that the computer metaphor is distracting to most people, I do think that the general issue of what metaphors non-scientists use is nevertheless important, especially in an article on "gene." This is because "gene" is not just a concept used by scientists in their work (or the thing to which the word refers); a "gene" is an idea of profound importance in modern culture, an idea with serious economic and political consequences. Given debates reported on in national news-magazines over both the causes of human behavior and our ability to manipulate nature, I think it is very important to have a second section for this article, a section that provides a sociological analysis of the discourse on genes. Such an analysis ideally would also account for the sociological reasons for the development of the "central dogma" and a consideration of any arguments against it. It would look at the array of metaphors used, both by scientists ("code") and non-scientists, as reflections of our culture.

I recognize that it may be too early to begin work on this section. But people will consult this article not only to help study for their biology mid-terms or research papers; they will consult it hoping to sort out popular debates about what genes "do," and it will not be enough to explain clearly (as you and others are doing) what scientists agree genes do (or do not do); they will need to know why different people talk about genes in different ways.

This is an excellent point, and I agree the article should include discussion of social issues surrounding genes. However, I think sociological reasons for discussion of the "central dogma" would be a bit broad and would probably have to range into philosophy of science, etc. I think it will take some careful thinking to restrict this discussion to an appropriate area that won't overlap heavily with existing articles like, say, nature vs. nurture or the like.

Thanks! And I agree, although I was thinking more sociology of science rather than philosophy of science -- but you've done enough for now! We can discuss the parameters of such a discussion at another time (maybe after I have had some time to research it too) Slrubenstein

This is my main reason why I think historical specificity (however abbreviated) is crucial right now, and also why I think that metaphors should be limited until the choice of metaphors itself can be analyzed. Slrubenstein

I am not sure what you mean by historical specificity... can you clarify? Graft

In this instance, the specific inclusion of the reference to the Central Dogma formulated or promoted by Crick -- this has the (laudible, in my opinion) function of making it clear that this conception of gene and way of talking about it was formulated at a particular time by a particular person. For now, that may be all the information we need. But later, we can ask -- why at this time? Was it solely because of purely technical advances? Or did institutional forces make such a conception especially appealing? I do not know the answers to these questions, I am only suggesting that one could look at Crick's influence the same way Bruno Latour analyzed Pasteur's influence. An article that makes clear when that the discourse developed at a particular time at least makes it possible to ask these kinds of questions. Slrubenstein

Re: The computer metaphor, in the sentence in question I regarded myself to be fleshing out a metaphor I didn't like myself but which was already there in an obscure way. The sentence asked readers to consider a gene as a "program or a function." To the extent these words suggest anything to a reader, it's because they are thinking of computers or (less likely I think) because they know math jargon ("function"). To the extent their minds go to the predominant means of the words they're minds will be muddled. Meanwhile, I can't see how one can object to the software metaphor and not object to the sentence in 'graph preceding which likens to "the manner in which a piece of magnetic tape or a compact disk encodes a sequence of binary digits." Meanwhile, I think the dogma has to be right or it's a disservice, and I think the article has to be careful not to suggest it's more than a rule of thumb (as in, what about retroviruses?). I find this "guiding current thought" assertion highly misleading. 168..

You're right about the magnetic tape analogy. In light of the controversy, perhaps we should eschew analogies altogether.

As to the Central Dogma, it is not a rule of thumb, and it has been modified since its original formulation to include retroviruses (in fact, the link I gave you above is to a paper by Crick discussing this very discovery), and even, with some controversy, prions. And yes, pretty much all of modern biology is built off the Central Dogma. If you are in a biology lab I suggest asking some of your labmates about it - they are almost surely familiar with it. Graft

Would you say the theory of heliocentrism "guides current understanding" of the solar system or of astronomy? I'd worry about giving people the wrong idea. 168... Also, if the modified dogma says genetic information flows in one direction only, from DNA to RNA, "except in retroviruses," how is that different from a rule of thumb?

Mostly a reply to SLR.

"Gene" is not just a concept used by scientists in their work ... a "gene" is an idea of profound importance in modern culture, an idea with serious economic and political consequences. On the whole, I think I agree. But is it possible to make the case that "gene" is simply a term that has been slipped into these debates and has not particularly affected the course that they would have taken anyway? I'm not sure.

To clarify my thinking, I'd like to see these "economic and political consequences" fleshed out, preferably with examples. (Here? Or elsewhere?) Obviously, I think right away of the sort of discourse produced by Herbert Spencer & Co. (did he actually use the term "gene?" - probably not, I think he would have died before the term became common), and I think of the pop sociobiology of the '70s - The Naked Ape and such. After that, though, I get a bit vague. I have the feeling that there is a good deal more to pull in and make sense of, but struggle to get anything to gell into a line of approach to it. Can you flesh this thought out for us, give some examples?

Turning to the specifics of the first expression and spread of the central dogma now, so far as I am aware, there is no particular social context to be elucidated here. Oh, the usual things apply: scientific research programs and their philosophical justifications, a newly fashionable interest in the physics of biology which followed on from the post-war improvement in all sorts of equipment but especially that which had relevance to radar technology, and (more importantly) the new understandings of chemistry that quantum physics allowed, and some rather .. er .. interesting ethics when it came to the race to discover and and publish the structure of DNA. But these predictable things aside, I can't think of any particular social loading to the dogma, or the terms. (If you are aware of anything, spell it out - I'm not saying there wasn't any, just none that I am aware of.)

I do think that an account of the events leading up to the realisation that DNA (not protein) was the key chemical, and then to the discovery of the structure should be included. There is a rudimentary history para already, but it should be fleshed out properly. This is probably a task best suited to a historian rather than a biologist (though, of course, Mav and/or Graft and/or 168 should look it over to check on accuracy in technical matters).

In summary, I have two conflicting responses to your thoughts, SLR. (a) That you are, in a sense, looking for a ghost that isn't there. And (b) that there is a very good case for looking more carefully at the non-biological use of "gene" and "genetics" and related concepts. This would be a much more difficult task than the straightforward historty-of-science section I suggested a moment ago, and would most likely go better in a different entry. I would find it a difficult thing to write - a rather vast and vague subject that would take a good deal of reading to get a handle on. It seems to me that you are the best equipped of us to take it on.

As a very brief starting point, are you familiar with Raymond Williams' Keywords? "Gene" doesn't rate a mention, but "genetic" does, and it's interesting reading. If you don't have it handy, let me know and I'll summarise. Over the next couple of days, I'll make the time to do a two or three para addition on the scientific history of "gene" - i.e., start with ... er ... Darwin & Wallace, I guess, and go via Mendel, Bohr and Pauling to Crick and Watson (plus several others on the way). Tannin 13:26 Jan 23, 2003 (UTC)

Tannin, thanks for your thoughtful response. On the one hand, I agree that the "ghost" may not be there -- one cannot be sure until one has looked. I do not know offhand of any of the sort of studies I am thinking of (e.g. like Latour's), but even if there have been no good sociological analyses of what was going on at Cambridge and elsewhere in the 1950s in biology and chemistry, it does not mean that the material is not there for some good study -- I know, this is not the job of an encyclopedia (to sponsor original scholarly research), I am being a little whistful. But I do believe that the word and concept "gene" is important in broader discourses. I read the Williams piece which is suggestive, but as you know highly abbreviated. I also wholeheartedly agree with you about Desmond Morris, but I am also thinking more specifically of Marshall Sahlins' and Richard Lewentin's critique of sociobiology, which relates the way people talk about "selfish" genes to the importance of self-interest in capitalist ideology. I also know there has been some good critical scholarship on the ideological implications of the human genome project (I have a book edited by Kevles and Hood which looks interesting and relevant, but I have not yet read it); I am also thinking of Donna Harraway's work (but just in general, I can't think of anything specific off hand) -- alas, although I know some of this literature it is not really my field and I do not know if I have time right now to read these books with an eye towards this article. BUT, I would like to encourage others who are more familiar with this body of critical scholarship to consider whether it has a place in this article. And to return to my original point, whether or not, or until, that happens, I think it is still a good thing that the article provide at least minimal historical information (Crick's name, maybe even the dates of the conception of the dogma), which might provide others more knowledgable of the history an opportunity to jump in, Slrubenstein

Why does anybody need to know that the "Central Dogma of Molecular Biology" is called the ""Central Dogma of Molecular Biology" (which I don't believe it is, by the way: I believe it's the central dogma of _Genetics_)? Why do they need to know who first articulated and dubbed it? Why do they have to think it's so complicated an idea as to require "formulation" instead of mere uttering? Why do they need to know this was done by Crick? Why that he is famous? Why do they need to be mislead to believe that it is a dogma or indeed that _anybody_ regards the principle as anything more than a rule of thumb or manner of speaking? With respect to what you say the alleged dogma says, I don't think "specific biological function" is accurate to what it says and I believe the statement is too vague to be helpful. Finally, to call a gene a piece of DNA is to be stricter than any molecular biologist. If the initial articulation of the dogma did this (which I doubt), I'm sure the way it's quoted now doesn't. 168...

It's called the "Central Dogma of Molecular Biology" by Crick. See . They don't need to know who first articulated and dubbed it any more than they need to know what a gene is. However, Crick is arguably one of the most important people involved in modern biology, so I think passing mention is not wholly undeserved. I wouldn't be opposed to taking it out if you think it's distracting. It may not seem complicated now, but it definitely was "formulated" by Crick at the time (1958) (hindsight is 20/20, remember). You're right, specific biological function is not very accurate...

Crick does not talk about genes at all, he talks very non-specifically about DNA, RNA, and Protein. And actually, now that I think about it, the idea that DNA is the genetic material didn't originate with Crick, so maybe this discussion is wholly inappropriate. I'll have to hunt around for who first proposed that specific DNA elements encoded genes. And, yes, this is not 100% accurate, as there are exceptions to everything in biology, but it is basically true. Graft

I'd like to point out that dictionaries separate definition from etymology. Not everyone wants to know--on first read through of a myserious new idea--matters of history and origin. Those particular matters that facilitate understanding of the idea are nice to sprinkle in, but otherwise, why not take advantage of the hyperlink, which allows the especially curious and those familiar with the idea to jump out and follow their curiosity. Scholars have more patience than the average reader. 168...

On another note, it seems that 168 has been deleting huge quantities of text from this talk page without any explanation. 168, please stop doing this; it verges on vandalism. The convention at Wikipedia is to archive previous talk when the page gets too long. But you are deleting notonly older discussion, you are even deleting comments made today. Do not do this. This page is not your personal property and whether you agree or disagree with others, or find what they write interesting and relevant or dull and trivial, does not matter. Slrubenstein

On my computer/browser, the talk gene section won't allow me to enter text without making some deletion--so I inferred the section is full. Is this not what other people are experiencing? Rather than picking and choosing and risking that comments get lost in the shuffle, I thought it would be more neutral to delete everything not to do with my talk comment. I'm not sure what else I can do. Maybe if I delete my Web cache? No one else experiences the talk page being "full"? 168

168 -- this has never happened to me. I think you should report it to a sysop. Please do NOT delete content. It is likely that the page is getting too long for your server. Let someone archive the older material first. I am truly sorry for this inconvenience to you but please do not delete. Slrubenstein

I like the new approach to "central dogma," namely, having the link in quotation marks. Slrubenstein

Aha! When I use Explorer instead of Netscape I can add text to the full talk document. Sorry for the vandalism. 168...

I am glad that we were able to resolve the problem quickly. I created an archive so people can see old talk easily; with time we can add to that archive or create a second archive. In the meantime, please go over this page and make sure that, in restoring the talk, I did not accidentally delete any of your contributions today. Thanks, Slrubenstein

Graft, I appreciate you trying to incorporate/work with the changes I suggested related to dogma, but your new version still does at least some of what I objected to before. It equates Crick's simple, sum-uppable-in-a-sentence 1957 idea about the directionality of genetic information with "Modern biological theory" (as if everybody embraces it as a dogma, and as if it's complicated, and as if "theory" in modern biology were more than a hodgepodge of ideas); and I believe it mistates both the idea and its strict implications by defining a gene as a DNA sequence. Why do you want to define a gene this way? Do you think RNA viruses don't carry around genes? Do you bite your lip and feel ashamed when you use "gene" to describe what these viruses carry around? I can see that it makes things easy and captures an essence of "gene" to define it as you do, but I see it as telling your readers an unnecessary lie. You've got a good point in wanting to get this essence up high--that genetic info flows from the chromomes to proteins--but working with your text, I think I kept that essense without bending the truth. You haven't succeeded in justifying your insistence to me, and I assume not to others. So I guess I will count to ten and revert, as seems to be the way things work around here. 168..

I can accept your complaints as they stand, but I don't think your text is "good", the way it stands. Rather than define "gene" in a more appropriate way, you seem to prefer to eradicate any sort of definition of "gene" and replace it with what then seems an entirely misplaced discussion of the Central Dogma. I certainly appreciate that we can say that viruses contain RNA genes; however, I would much rather give the reader the oversimplified picture I present, and then correct it later on. This is the way biology is taught in schools, and this makes sense as a method of explaining a complex concept, rather than simply ignoring it.

So, if you do NOT like my simplification of gene=DNA, then please replace it with something cogent that DOES explain how genes relate to nucleic acids. What you insist on reverting to (which, incidentally, includes a lot of other changes that don't have anything to do with this debate) lacks sufficient explanation of this (gene/nucleic acid) relationship.

At any rate, I am tired of this edit war and am giving up. Do what you like with the article. I don't have the patience to attempt to satisfy your demands by guessing at what you are trying to write. Write it yourself. Graft

Graft- please don't give up. You brought the article to its best version, although I happen to agree with 168 about the Central Dogma bit. Retroviruses break the dogma and with the high visibilty of the AIDS retrovirus I think an unqualified emphasis on the Central dogma will serve to confuse. Qualifying it will also serve to confuse, so it's probably best to leave it out... But I do hope you take a breather and come back to this. 168-- can we get some sort of pledge from you that if you feel any of Graft's work needs changing that you discuss it here first? You're obviously knowledgeable in the field, but I'm afraid your phrasing is often not ideal for a general interest encyclopedia. I have to disagree with mav, above-- the article at that point was far short of "brilliant prose". If we can merge your detailed knowledge with Graft's style, we'll have a winner. JDG

I agree -- wholeheartedly -- with everything JDG just wrote. Slrubenstein

Instead of all this appeal to and elevation of the dogma, something like "According a narrow view/as most narrow defined" would allow you to begin with DNA and the chromosome/protein relationship as you like. Anyway, I'm with you about patience. I can't imagine where my stamina is coming from. 168...

Look, I'm sorry to be the cause of grief for Graft. I've had my own trials of patience here too--seeing my scientifically accurate text corrupted or steamrolled and my organization scrambled without an explanation besides "text was poorly written so I...." Then I get blamed for the structure and flow of text I've posted when all I've done is remove the vaguenesses, redundancies and scientific errors in someone elses scheme, while otherwise leaving things as they laid. The blame belongs to what was there before. Pick a few sentences of Graf's and compare my edits of the same ones side by side and tell me which better suits a general interest encyclopedia. Anyway, I've discussed and read the discussions: I don't recall anybody ever saying "may I" before editing and I haven't noticed any formal votes on anything--especially not with regard to matters of style. When I see other people behaving that way, that's when I'll join in. 168...

Returning to the text after a hiatus, I'm seeing the merit again of the "what a 'gene'is is complicated" approach. Take the seemingly unobjectionable first sentence: "A gene is the fundamental unit of heredity, the factor whereby one or more traits is passed from parent to offspring." It implies that if a parent passes a trait to its offspring then it's by genes. But the article right now is nearly entirely from a molecular genetic perspective, according to which only coding sequences strictly are genes, and regulatory elements--which may transmit just many traits as genes--are not. So first of all, you would want to modify the claim of the first sentence with "According to classical genetics..." But even that wouldn't make the assertion strictly true. I don't think even a classical geneticist would say that it's through genes that parents pass _behavioral_ traits to offspring (a hair-flicking gesture, for example). And then a physical trait such as a permanent limp a parent could transmit with the whack of a club on an offspring's ankle. Is that a gene? 168...

168, I se from the above that you are not a lamarckian. If so, why do you object to "organically coded" traits? Obviously you understand that not all traits are transmitted by genes, learned and acquired traits are not transmitted by genes. The article needs to specify: What kind of traits are transmitted by genes? And yes, genes contain carbon, and yes, they are coded. Slrubenstein

I take your point. I proposed "physiologically based traits" Better, no? 168... 23:23 Feb 13, 2003 (UTC)

Well, I really would like to know why you object to "organically encoded," although if you suggested something better I'd be happy to go with it. But I do not understand why you prefer "physiologically based." Perhaps in your field "physiology" has a more precise and technical definition, but I think most readers of Wikipedia think physiology refers to the functioning of organs and organisms -- in which case it is doubly inappropriate here as the main (granted, not only) function of genes is code, and they are comprised of bases along a sugar-phosphate whachimicalit (sorry, it is late) and is at a much smaller scale than "organism" and I think even a smaller scale than "organ." Slrubenstein

"Organically encoded" is, as I read it, meaningless unless a reader knows already that we're going to get round to talking about DNA and the genetic code. If this definition is not just an exercise but is to explain things to the naive, I think those words are a mistake. Not to mention, they turn a sentence that was supposed to articulate a universal sense of gene into something less than universal. Now if by those words you mean traits that reflect underlying molecular and cellular characteristics, I'm with you. FOr me, "physiological" communicated that. If you don't like it, what else could we use? Not "biological" I think because biology includes animal culture. How about "consitutive"? It might be best to just leave it at "traits". 168... 23:56 Feb 13, 2003 (UTC)

Sorry, I am not entirely following you -- okay, I understand that organically encoded is too specific. But what is wrong with "biological?" What do you mean about animal culture? Animals have genes too, and a general description of genes should be applicable to animals also, after all, animal breeders (and horticulturalists) understood a lot of this implicitly or vaguely long before applying it to humans. Slrubenstein

I guess I meant "biology" includes behavior, and behavior can be taught and not transmitted by a substance.168...

Well, gosh, isn't this my point about physiology? In any case, biological entities may behave, but I think almost everyone in the world thinks of biology in material terms. Usually when English speakers want to refer to learned behaviors they say they are talking about something psychological or sociological or cultural or political or economic -- reserving "biological" for those things that are organic. "Constitutive" is certainly a more inclusive term than "biological" as many learned traits are "constitutive" of my personailty. I think of "biological" behaviors as things like digestion, respiration, etc which are all encoded genetically. Slrubenstein

I agree "biological" is fairly safe, so I won't be a stickler. 168... 00:58 Feb 14, 2003 (UTC)

Even cells have "physiology," BTW. At least, I'm sure that's what cell physiologists think. "Contitutive" means "always on" or "inherent" in cell biological contexts. "Biology" certainly includes behavior to the ecologists.

You know, I'm not sure I shouldn't be a stickler here: I think you make a valuable contribution when you say you understand a word differently, as a non-scientist, than the scientist who wrote it meant it; because I don't think these articles should be or are meant to be for experts. But you're on shakey ground I think advocating what an expert would regard as misuse of a word. Not that you'd always be wrong to do so. If a word has a common sense that differs from its technical sense, and if a text is obviously for non-experts, then I think the experts should defer to common usage--excepting things egregious and avoidable.

BTW, a flip side of the problem with "biological" (i.e. besides that it's liable not to express the point you want to biologists) is that it is redundant; in that traits of living things are by necessity biological.

But I'm grousing more than stickling 168... 19:10 Feb 14, 2003 (UTC)

I appreciate your thoughtfulness. I agree 100% that the article should not "misuse" words. But I do insist that articles not rely on technical jargon, or words with very specific technical meanings (unless the purpose of the article is to explain the technical meaning of the word -- for example, of course this article should explain the technical meaning of the word "gene," but it should do so as much as possible in non-technical language).

I Do disagree with you when you say "the traits of living things are necessarily biological." I know that anthropologists and many sociologists and psychologists would disagree (and they too are scientists); I believe even some biologists would disagree. And I bet that those biologists who do agree are either defining "biological" or "trait" in some specific way that diverges from common usage, or are taking a deliberate political stance. Slrubenstein

Lions don't exist in Africa and don't outnumber cheetahs there (i.e. if they do) just because of the habitat and the anatomy and physiology of lions. They exist in no small degree because they hunt and because of the way they hunt. That's behavior. That's biology. I can't see what's political about saying so. It's just how many people understand the word. 168... 20:29 Feb 14, 2003 (UTC)

I agree with you that this is biological. I never said that traits are "never" biological. Do you remember what you wrote? You wrote: "traits of living things are by necessity biological;" by using traits without any modifier the implication is all traits. Some people are Catholic, some are Lutheran -- is this "biological?" I repeat -- if you say yes, you are using "biological" in either a very specialized sense, or ideosyncratically, neitehr of which are appropriate for an encyclopedia article (or at least, not this article). As for "It's just how many people understand the word," I am not sure I follow you -- isn't this exactly what determines the meaning of a word? Slrubenstein

O.K., maybe I lost my way a bit. But I expressed my original objection in terms of "animal culture"--whether apes are Catholics or Lutherans. Goodall and many others believe some non-human animals have culture. Manifestations of such culture could be called "traits," and I believe they are liable also to be called "biological" (if only because one doesn't immediately know in studying primates [or even lions perhaps] what behaviors might be cultural). But these traits aren't transmitted by genes. 168... 20:49 Feb 14, 2003 (UTC)

But then by that reasoning I guess "traits" is as problematic as "biological traits." I'll resume nonstickling. 168... 21:03 Feb 14, 2003 (UTC)

Re: "It's just how many people understand the word," I mean it in the sense that you too seem to understand the word that way, as when you write "I agree with you that this is biological." My point was that people did not "choose" to understand the word this way for political reasons, as I took you to be suggesting. 168... 21:07 Feb 14, 2003 (UTC)

okay, I see now -- sorry for the confusion and thanks for clearing it up. Slrubenstein

Deleted

Additionally many proteins (such as Haemoglobin) are made up of multiple subunits which are encoded for by sequences at different loci. Thus the gene for Haemoglobin would be two disjunct stretches of sequences, one coding for Haem and another for the Globin subunit.

I don't think this is a counter-example to the "one gene, one protein" hypothesis (and perhaps the article has to deal with enough complex issues already). I would think of each subunit as being a separate protein, which combine to form a complex. (So, this would violate a "one gene, one complex" hypothesis.) There's some reason to argue that Haemoglobin could easily be one protein, but it isn't, and you can get carried away here; e.g., two enzymes next to each other in a metabolic pathway could also in theory be one combined protein.

Zashaw 23:23, 25 Mar 2004 (UTC)

Good! That section is just plain wrong! First, Haem is not a protein... there is no such thing as Haem. There is the "Heme group", which is a molecule synthesized by proteins, not a protein itself. . There are four polypeptide chains in a hemoglobin, but they are all globins (two alpha and two beta). Finally, while I've heard of hemoglobin being called one protein, I have never heard of the alpha and beta globin ORFs being considered one gene. AdamRetchless 01:15, 26 Mar 2004 (UTC)

While we're at it, does that 'overlapping sequence' refer to alternative splicing, or to HIV-style supergenius-type "double-meaning" sequence, where one sequence produces viable proteins in two frames (or maybe two complementary strands are both coding, I forget which - either way, super-genius)? The former is fairly common while the latter is incredibly rare, and you could probably dispute "one gene, one sequence" if there's individual promoters, no matter that the sequence overlaps. If we meant alternative splicing we should say that, I don't think the latter is any more meaningful than a PopUp Video factoid. Graft 16:47, 26 Mar 2004 (UTC)

I tried to clarify that paragraph. I think "overlapping sequence" refers to the "supergenius" idea. A good number of bacteria have open reading frames that overlap by one or two nucleotides. It isn't as extreme as what is found in viruses, but the same sort of idea. I tried to distinguish between mechanisms found in eukaryotes and those found in bacteria. I may have been too narrow in saying where a particular mechanism is found. I guess we should note that viruses often have very dense genomes with a lot of overlap. I've seen it in bacteriaphage, but I'm not familiar with eukaroyotic viruses... but if you (Graft) say that HIV does this, I guess it is common to both eukaryote and bacteria viruses. I know almost nothing about archea. Do they splice mRNA? Do they have overlapping genes? AdamRetchless 23:01, 26 Mar 2004 (UTC)

Intro

I cut a bunch of stuff out of the intro and pasted it else where. I think that what i did makes sense, but those of you more familiar with the article may want to put it elsewhere. Please don't put it in the intro, the intro is already a little long (necessarily so). when i loaded this page this morning i couldn't see the table of contents on my 1080p screen because there was so much intro... The intro should really just contain a brief description of the matter at hand. The chemistry stuff about the hydrogen bonding of androsine and such has no place in the intro, neither did the history. —Preceding unsigned comment added by 108.13.250.253 (talk) 19:46, 7 January 2011 (UTC)

I think the intro could be shortened without loss of information by removing these two sentences: "Referring to having a gene for a trait is no longer the scientifically accepted usage. In most cases, all people would have a gene for the trait in question, but certain people will have a specific allele of that gene, which results in the trait variant." The former sentence isn't very helpful without specifying what is accepted usage by scientists. The latter is downright confusing and also inaccurate based on the Wikipedia article on alleles. Scottveirs (talk) 06:24, 10 October 2011 (UTC)

The first paragraph of the intro is rather confusing. It talk about allele as it was interchangeable with definition of gene. Also, there is no such thing as 'polypetide' Karolno (talk) 11:53, 12 December 2012 (UTC)

Ignore my last comment, article was vandalised. Karolno (talk) 12:15, 12 December 2012 (UTC)

Definition of a Gene

There is a good discussion of the difficulties of defining Gene in Nature 441, 398-401 (25 May 2006). It suggests a valid working definition of a Gene as "A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions." The old-style view currently suggested in this article is far too simplistic. NBeale 21:54, 22 May 2007 (UTC)

At some point in time, I added that very definition to the top of this page. This definition was finalised by Richard Durbin after a meeting of the Gene Ontology group. It was the tightest definition that people could come up which still covered everything that is known about all the different types of gene (from the molecular biology point of view). I guess some people will still want a less scientific definition, but I think it should go back into the page. Nod 00:23, 23 May 2007 (UTC)

The new version produced was ungrammatical and contained fragments of incomplete sentences. I reverted back to a version that was a bit clearer. TimVickers 21:29, 26 May 2007 (UTC)

I have real problems with the idea of "unit of inheritence." Does it just mean "inherited?" Junk DNA is also inherited. Or does it mean that it corresponds to an inherited phenotype or trait? If so, this is a vast oversimplification. The rest of the definition make sense to me although I think a lot of non-scientists won't get it. Tim's edit preserves the wording "unit of inheritence" and I think we need to discuss this. I know this is not going to appeal to people, but I would define gene as, "a subset of DNA that cells transcribe into RNAs and then translate into proteins (or if you prefer popypeptides)."Slrubenstein | Talk 14:04, 27 May 2007 (UTC)

We can't ignore genes that produce an RNA product, such as rRNA and snoRNA genes. This is why I defined a gene as producing a "functional RNA product" - protein biosynthesis is one common function but it isn't nearly the only function. There is a real disconnect between geneticist's views of genes which are as "units of inheritance" and molecular biologists's views of genes as segments of DNA. I think it is important to include both, since genes are important due to their genetic effects, but their basic nature is segments of nucleic acid. TimVickers 16:24, 27 May 2007 (UTC)

Okay, I am not questioning that genes produce an RNA product - but what exactly does "unit of inheritance" mean? How is it different from saying "genes are inherited?" Slrubenstein | Talk 11:34, 28 May 2007 (UTC)

Geneticists see genes as discrete factors associated with discrete traits. This defines genes from the perspective of the phenotype. In this context, "Unit of inheritance" means this is the smallest unit through which the process of inheritance operates. I think the lead needs to cover both the molecular biology and genetics views of genes. TimVickers 15:36, 28 May 2007 (UTC)

I agree with you that the lead needs to cover both views. I question though whether this is an adequate representation of the geneticist's view. I think most geneticists would agree that many genes do not map on in a one-to-one way with specific phenotypic traits. Some do, many do not (at least in human beings and amoebas), we need to be clear about this. Slrubenstein | Talk 15:40, 28 May 2007 (UTC)

You're probably right. What wording would you suggest to cover the genetics in the lead? TimVickers 15:42, 28 May 2007 (UTC)

I'll have to think about it .. maybe both of us can think about it. I am tempted just to add the word "some" or"many" before "genes ... and leave it to the body to explain. The thing is, in many organisms most genes do not express themselves phenotypically ... but virtually all phenotypic traits are at least to some degree expressions of genes (the thing is, they may express other things too like random environmental interactions within the cell). I think one of the most important things for me is to include an account of polymorphism in the article too. Your thoughts? Slrubenstein | Talk 15:55, 28 May 2007 (UTC)

Seems to me that geneticists and molecular biologists use different concepts of gene. So it is not possible to develop a definition that is acceptable to both. You need two different words for two different concepts. M Navarro.

The term "gene" should cover its original and current concepts because it is so commonly recognized. That is, it should be inheritable, expressible and silenceable for its function. Simultaneously it should instructs one or more phenotypic traits which can be either explicit or cryptic, and it can be even null. In this sense, the working definition that it is mere a locatable DNA segment is far too simplified. The essence of a gene is the inheritable information with the instruction for traits. So far, however, the only media which can carry or represent this information is sequence of nucleotides, although the status of nucleotides and cytoplasmic environment may influence its behavior. It resembles to the concept of object-oriented programming, where the information is defined as a class to be instantiated as objects bearing properties and methods to express behavior or traits. A trait may be explicit or hidden depending on the status and environment, and it can be even just a place holder whose content is vacant. It can be copied and modified. Here the media itself which carry the class definition is of no importance. —Preceding unsigned comment added by Tosendo (talk • contribs) 01:53, 21 September 2010 (UTC)

I am a layman in the field of genetics, but I would like a better understanding of what a gene "looks like". I have the impression that genes can be identified as such by recognizable sequences terminating the gene. The material above makes no such statement, but implies that it must generate a protein, at least in the typical case. Using that definition, how is that determined? To summarize perhaps, I would like to see a section or independent article on how chromosome sequences are interpreted, and how genes are identified. I am asking about genes in the simplest, or old-fashioned sense, and not about switches and so forth. JFistere (talk) 09:20, 22 September 2010 (UTC)

In analogy, a genome is a cookbook and a gene is the instruction for how to cook a dish. The question is, which should be called a gene, the instruction or the page itself.tosendo (talk) 11:32, 30 September 2010 (UTC)

This is close to an oft-used Richard Dawkins analogy, though it is used when dissuading people from referring to a genome as a blueprint as this implies simplistic 1:1 mapping which is obviously not the case; thus it is referred to as a recipe. It adds uneccessary extra confusion here though, genes cannot be considered as units derived from the 'top-down' viewpoint. A complex phenotypic trait would be mapped to nearly every gene through different levels of interaction, this is not helpful in building a definition. Instead of thinking in terms of genomes and organisms, in terms of clarity a gene should be defined through the eyes of the Gene-centered view of evolution Jebus989^✰ 13:53, 30 September 2010 (UTC)

Citing 'Genome' from Wikipedia: In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA. It clearly states that genomes are information and genes are parts of the genomes. Is this definition wrong or genes are information? tosendo (talk) 08:07, 25 November 2010 (UTC)

A unit of heredity?!?

I think "a unit of genetic data" is a better definition. 68.173.113.106 (talk) 00:19, 8 February 2012 (UTC)

Does the definition of gene include regulatory regions?

At the bottom of the article it says "all regulatory elements of DNA are therefore classified as gene-associated regions". Does that make them regions that are merely associated with a gene or regions that are part of a gene? Thanks. Cirbryn (talk) 19:34, 16 January 2008 (UTC)

Gene exactly?

The article states that "in molecular biology, a gene encodes the chemical structure of a protein". Is that one and only one protein or peptide per gene? Is a gene the amino acid code between and including start codon AUG, GUG and stop codon UAG, UGA, UAA?

Thanks - Jerryseinfeld 08:16, 2 Oct 2004 (UTC)

In eukaryotes, the matter is far more complicated. There's alternative splicing, in which the RNA transcript can be modified post-transcriptionally into any of several different mRNAs. The issue of what a eukaryotic gene is is also somewhat more complicated as a result. Prokaryotes don't do splicing, as a general rule, so they're pretty much one-gene-one-protein beasties. Also, the regulatory sequences in noncoding regions around a gene are often very important to its function, so they might be included in the definition of a gene. Bryan 18:44, 2 Oct 2004 (UTC)

"genes" were for a long time theoretical entities. Chromosomes can be observed under a light microscope, so they seem to qualify as "physical entities". Molecules (including DNA), once theoretic entities, now would seem to be indirectly observable via electron-microscopes. In the scheme of things, genes would seem to be intermediate between atoms & chromosomes. I see usage of the term genetic material within a DNA molecule, but is it too early yet to say that genes can be identified as being particular pieces or strands on DNA molecules (as a string of atoms)?--JimWae 04:25, 2005 Mar 27 (UTC)

It goes without saying that life breaks boundaries and defies its own conventions all the time. So our shorthand definitions, our abstractions, are going to be wrong sometimes. I don't think hard-and-fast definitions are that important, really, just delivering the broad strokes. That's pretty much how biology works - learn the broad strokes, and fill in lots and lots of nuance. We can work on filling in some of the nuance - e.g. the original query highlights the fact that RNA genes are ignored by the given definition. Graft 04:45, 27 Mar 2005 (UTC)

I noticed some bias on the table on genes. It shows humans having the most genes and most base pairs among all the examples given. One could conclude that we are the most "advanced" specie, or that the number of genes is a sign of intelligence maturity, name it.. I'm no specialist in this field but I recall reading that there are organisms that have a higher number of genes than humans... I think that would be a good addition to the table to dismiss the notion that humans ar at the top of the scale.... 08:46, 5 Oct 2004 (UTC)

Overhaul table of gene number and genome size?

I think the table listing the gene count of different organisms is slightly misleading, and overly simplistic. Categories such as 'Plants' or 'Flies' are too wide. I think the range of genome size and gene count in plants will be substantial. Maybe the table should only show examples from specific species and actually list the species name to avoid further confusion. E.g.

Arabidopsis thaliana (thale cress) 120 Mb ~25,000 Saccharoymces cerevisiae (yeast) 14 Mb, ~6,000 Drosophila melanogaster (fruit fly) .... etc.

I don't mind doing this if there are no objections.

Keith

Also, could someone explain what the significance of the genome size actually is? It seems surprising that rice (decoded today with about 37,500 genes, see ) has more genes than humans (25,000). Why is this? Are human genes longer? Are plants more complicated than humans? Are there lots of dormant genes in plants?

I believe it is because plants are more complicated: not only do they do cell growth, cell division, cellular respiration in a manner similar to other organisms (animals, fungi), but they also do photosynthesis. They must take in raw materials -- ammonia or nitrate, phosphorus, etc, and construct all sugars, amino acids, and nucleotides from scratch. Heterotrophs can absorb pre-constructed molecules. Furthermore, they have a complex 'secondary metabolism' that varies among taxa and is involved in defense against herbivores and pathogens, and other aspects of their ecology. It's tough being a plant! Satyrium 19:12, 18 August 2006 (UTC)

kudos

A year or two ago I was active in this article and involved in various edit wars. Today is the first time I have read over it in a long, long, time -- and I want to congratulate all the people who have been working on it. While I am sure it can still be improved, I think you have really turned out a well-written, clear, comprehensive article. It restores my faith in Wikipedia, Slrubenstein 21:51, 7 Dec 2004 (UTC)

Regarding the Dawkins - I haven't read him, but characterizations of his description seem far too anthropomorphic. That is, DNA does not exist to selfishly propagate itself. DNA is a stupid molecule that, left to itself, would slowly degenerate into nucleic acids. But genes that are good at propagating themselves, even at the expense of their organism, will thrive and become prevalent. This isn't as succinct an idea as the "selfish gene" sentence, but it is more accurate. The question is, is this Dawkins' charcterization? Graft 23:00, 7 Dec 2004 (UTC)

Well, I am pretty sure you are referring to the text that was there before I made my additions. I too have problems with the anthropomorphizing, but my sense is, it is in Dawkins (and anthropologists and other social critics who object to this aspect of Dawkins' work usually use this as a jumping off point, that this kind of sociobiology is just the theory of evolution refracted through contemporary bourgeoise ideology). Note there is a problem even in your phrasing, "genes that are good at propegating themselves" because of course it is not the gene that propegates itself but the organism, which involves that gene and many more and environmental and random factors. In any event, IF you want to keep in the Dawkins paragraph, the task is to represent hs views accurately, not to represent our own views. I myself am pretty critical of him, I just wanted his view to be presented more fairly. Slrubenstein

How ironic... hard to escape the urge to attribute intent to everything, I guess. Um, but, okay, this is all I wanted to clarify: that Dawkins actually does anthropomorphize that way. Graft 21:07, 8 Dec 2004 (UTC)

It's been many years since I read The Selfish Gene, but I don't recall that Dawkins was particularly anthropomophic in his descriptions; not more than most biologists who talk about the "purpose" of some aspect of biology. I've rewritten that section to better conform to my memory. I'll try to double check a copy of the text. --Rikurzhen 22:03, Dec 8, 2004 (UTC)

You are spot on, Rikurzen.

The very word "selfish" anthropomorphizes. Slrubenstein | Talk 20:09, 27 Mar 2005 (UTC)

"anthropomorphizes" isn't quite accurate, since non-human animals could righly be said to be selfish. Dawkins could be charged with the pathetic fallacy, but from my reading of The Selfish Gene, the term selfish isn't meant literally, but rather just to describe--by analogy to an easy to understand term--the equilibrium outcome of gene evolution. --Rikurzhen 22:29, Mar 27, 2005 (UTC)

Spot on again, Rikurzen. Discussions with folk like S, usually don't go anywhere, though.

Isn't it awesome how time has almost no meaning on Wikipedia? 06:01, 28 Mar 2005 (UTC)

Request for references

Hi, I am working to encourage implementation of the goals of the Wikipedia:Verifiability policy. Part of that is to make sure articles cite their sources. This is particularly important for featured articles, since they are a prominent part of Wikipedia. The Fact and Reference Check Project has more information. Thank you, and please leave me a message when you have added a few references to the article. - Taxman 18:55, Apr 21, 2005 (UTC)

Sentence moved here from article.

"Some people say the "got lost in the gene pool" to say they are ugly."

This sentence was a sore thumb where I found it in this article. Feel free to add it elsewhere in the article. P.MacUidhir (t) (c) 16:19, 15 November 2005 (UTC)

Dude, it is a sore thumb even on the talk page. Slrubenstein | [[User talk:Slrubenstein|Talk]] 18:48, 15 November 2005 (UTC)

new models of evolution and genes - call for experts out there to address an issue

While the paragraph on Dawkins is important, I think by itself it carries too much weight in the article. I am not an evolutionary biologist, but I know that among evolutionary biologists there is much talk of a new model of evolution that takes into account the fact that all organisms share a great deal of genetic material, that what makes (literally) one organism different from another — just like the process that makes one organ different from another (in the same organism) — is not that they have different genes for a given trait, but rather that they have or lack genes that switch on the gene for a given trait (in other words, the cells in my hand and liver contain the same genes, but in the process of embryonic development "hand" genes switched on in some cells but not others, while "liver" genes switched on in some cells but not others. Similarly, humans have genest that play a role in the embryonic development of dogs, but that just never get switched on in humans; conversley, dogs have genes that play a role in the embryonic development of humans, but they just never get switched on in dogs). This model has significant implications for the theory of evolution, because natural selection would not be acting on the genes for given organs (e.g. gills or lungs, wings or arms) but rather the genes that function as switches. This is a different model than Dawkins. I know full well that this model is not universally embraced by evolutionary biologists, and that even among those who embrace it, there are differences in the importance they claim for our understanding of speciation. Nevertheless, I do know that these are things evolutionary biologists are discussing, and I think it should be reflected in the article. Since I do not know any of the scholarly literature on this, I am not competent to provide an accurate NPOV account of it in the article. But is there anyone out there who knows what I am referring to, knows it well enough to see where I am misinterpreting or misunderstanding it, and knows it well enough to add a section to the article that makes its significance, or potential significance, clear? Slrubenstein | [[User talk:Slrubenstein|Talk]] 19:06, 15 November 2005 (UTC)

(Sigh) I am an evolutionary biologist, and I wish people like you should just kindly learn something about the subject before you start sharing your wisdom with others. — Preceding unsigned comment added by 88.110.112.147 (talk) 18:07, 28 September 2011 (UTC)

You're getting at a subject of study at the interface of developmental and evolutionary biology sometimes called evo-devo. (You may be mixing that up a bit with the matter of inclusive fitness, which is linked closely with the gene-centered view of evolution.) Evo-devo is AFAIK at a different level than the question of whether evolution operates from a gene-centric view. But yeah, there's tons of stuff that could be added to this article. --Rikurzhen 19:33, 15 November 2005 (UTC)

Yes, evo-devo, that is what I meant to say. I am not rejecting the principle of inclusive fitness, but as an outsider it does seem to me that evo-devo has implications concerning the gene-centered view of evolution. Clearly you know far more than I do, I hope at some point you will find the time to put some of it in, to the appropriate articles. Slrubenstein | [[User talk:Slrubenstein|Talk]] 21:09, 15 November 2005 (UTC)

There very well could be a connection. I just don't know of one -- but my lack of familariity is not an indication that no one was written about it. However, inclusive fitness has implications even for single celled organisms, whereas evo devo is mostly about animals. --Rikurzhen 22:39, 15 November 2005 (UTC)

There's two things at work here: one is that the idea of "genes as the unit of selection" is obviously too simplistic, and now that molecular biology and genomics allows us to chase function down to the individual base-pair level, we don't need to restrict ourself to thinking in terms of gross elements like whole genes. The other is the fact that functional divergence in genes doesn't seem to meet up with the picture set by organismal complexity (e.g. human and C. elegans have a similar number of genes); also, divergence of form by contemporary accounts has a lot more to do with differences in gene expression (e.g. the faddish "Hox" genes) than changes in genes themselves. Thus the desire to chase evolution into regulatory regions. Since that's relatively unknown territory, it'll probably be a while before we can know whether this is a reasonable line of argument. Graft 18:13, 16 November 2005 (UTC)

Cistron currently redirects here ...

Cistron currently redirects to this article, but the current article content does not support that redirection. Is there a more appropriate article that addresses prokaryotic genes to which "cistron" could be re-targeted? User:Ceyockey (talk to me) 16:10, 15 January 2006 (UTC)

I also reached this article looking for Cistron only to find that the word is not even defined here. Should we just go ahead and start a new article? Or maybe a section within this article? --Antonio.sierra 14:28, 6 November 2007 (UTC)

Typical numbers of genes in an organism: Differentiate for plants

The number of genes in plants vary hugely, so we should probably differentiate that part. I seem to recall that Arabidopsis thaliana and some Pinus species are at the extremes of the known distribution... - Samsara _contrib ^talk 22:18, 25 January 2006 (UTC)

Plants have several times undergone genome duplication events (and some have done so recently without changing much), so it's not unusual for them to have ridiculous chromosome numbers and correspondingly large genomes... Graft 00:26, 26 January 2006 (UTC)

I'm aware of that. Although your post is not directly countering my suggestion, I might point out that many (most?) genes have arisen by duplication. - Samsara _contrib ^talk 00:52, 26 January 2006 (UTC)

Yeah, but gene duplication is not the same as genome duplication. I'm merely suggesting that a huge number for plant genome size is probably representative. Graft 17:45, 26 January 2006 (UTC)

gene duplication is not the same as genome duplication

True, though both have the potential to lead to divergent gene function. I don't know what the wikipedia consensus is for what constitutes a plant (no time to read the article just now), but we have to be careful not to think only of angiosperms. - Samsara _contrib ^talk 20:49, 26 January 2006 (UTC)

Human genome is Science Collaboration of the Week

Just to let you know that Human genome has been voted Science Collaboration of the Week. - Samsara _contrib ^talk 10:32, 27 January 2006 (UTC)

WP:FARC

I hate to do this but I'm going to list this article on FARC - it simply does not deserve to be featured in my opinion. Why?

Lacks inline citations
the lead is too long & does not conform to WP:LEAD
neither "History" nor "Evolutionary concept of gene" are comprehensive.

As a courtesy, I'll give the contributors to this article some time to address these concerns before I take it to FARC. Mikker ^... 17:20, 11 February 2006 (UTC)

I've now listed the article at FARC. Mikker ^... 21:02, 12 February 2006 (UTC)

What are Thrifty Genes?

I've heard the term used a couple times, but since it's being used to advertise a dieting concept I'm not sure how verifiable it is. It does quote a journal though, is it a good journal? Here's the quote:

Journal of Applied Physiology 96:3-10, 2004

“Survival of Homo sapiens during evolution was dependant on the procurement of food…

To ensure survival during periods of famine, certain genes evolved to regulate efficient intake and utilization of fuel stores. Such genes were termed “Thrifty Genes” in 1962. Farther more, convincing evidence shows that this ancient genome has remained essentially unchanged over the past 10,000 years and certainly not changed in the past 40-100 years.

Although the absolute calorie intake of modern day humans is likely lower compared with our hunter-gatherer ancestors, it is nevertheless in positive calorie balance in the majority of the US adult population. We contend that the combination of continuous food abundance and physical inactivity eliminate the evolutionary programmed biochemical cycles emanating from feast-famine and physical activity-rest cycles, which in turn abrogated the cycling of certain metabolic processes, ultimately resulting in metabolic derangements such as obesity and type2 diabetes.”

“Manu V. Chakravarthy 1 and Frank W. Booth 2

1Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis 63110; and 2Departments of Biomedical Sciences and of Medical Pharmacology and Physiology and the Dalton Cardiovascular Institute, University of Missouri, Columbia, Missouri 65211”

Now obviously such concepts have to do with how genes are activated and deactivated. My knowledgee is limited, but it's endocrinology, hormones and steroids that control that kind of thing, right? As diet may influence those, I wonder if there may indeed be adaptory aspects. Whether or not it's proven though, is confusing. So, can anyone help in forming the beginnings of an article on this, linked to in this page and possibly others such as diabetes and fat loss? --Tyciol 09:38, 14 February 2006 (UTC)

Modifier gene

... missing. --129.11.76.216 14:30, 13 March 2006 (UTC)

... inscrutable. Graft 20:28, 13 March 2006 (UTC)

Not a real phenomenon, only a mathematical tool. Samsara (talk • contribs) 18:41, 5 December 2006 (UTC)

0.5 version nomination

Failed on quality: (Not a FA, as stated) failed for same reason it was at FARC. Ch u ck^(척뉴넘) 01:47, 29 May 2006 (UTC)

Why? If you tell me your problems about the article, I'll work on it. I find it important to put Gene into V0.5. NCurse_work 10:33, 29 May 2006 (UTC)

Usually?

The article reads ". . .encoded in the organism's genetic material (usually DNA or RNA). . ."

usually? Is there an exception to DNA or RNA?

It depends on the organism. We know RNA-based viruses. NCurse

_work 13:49, 23 August 2006 (UTC)

NASA seems to have some opinion. tosendo (talk) 08:06, 9 December 2010 (UTC)

embryology

Does anyone happen to know any embryologists? I think Embryology really needs a lot of expert attention. would sympathtic editors consider a positive vote here? Slrubenstein | Talk 16:56, 28 August 2006 (UTC)

I take a look, thanks, but maybe you should search for experts here: Wikipedia:WikiProject Expert Request Sorting or have a look at that: Category:Articles needing expert attention. NCurse

_work 20:06, 28 August 2006 (UTC)

Thanks! Slrubenstein | Talk 20:43, 28 August 2006 (UTC)

Organization of this article

The way the content in this article is organized makes my brain ache. I propose this structure, or something like it (roughly following Watson et al. Molecular Biology of the Gene, but moving expression above maintenance/DNA repair):

Classical genetics and Mendelian inheritance (BRIEF; this already has its own article - a paragraph or two)
The physical gene: DNA and RNA

Promoters, repressors, and enhancers
Introns and exons
Differences between eukaryotic and prokaryotic genes, including operons

Gene expression

The genetic code, Transcription, Translation (Brief, covered elsewhere)
Gene regulation
Functional RNA

Genes and inheritance

Relationship to classical heredity

Evolution of genes

Mutation and repair
Exon shuffing
Pseudogenes

Genes in genomes (Brief, covered elsewhere)
Human genetic disorders (Brief, covered elsewhere)

Thoughts? I wonder about leaving the 'genome' section so far down, but this organization has the advantage of presenting the familiar classical context and thereafter following a small-to-large progression from focus on a single gene to focus on the whole genome. I also thought about giving 'mutation' its own top-level section before 'gene expression'. Opabinia regalis 06:07, 5 December 2006 (UTC)

It is a mess now I agree. It needs reworking so much I wouldn't want to discourage anyone with dispute, but I don't see anything wrong with your plan :) I like mutation being in replication, or at least after it if there is too much mutation material. - cohesion 07:01, 5 December 2006 (UTC)

Great idea. What about mess DNA? NCurs e _work 18:36, 5 December 2006 (UTC)

Sorry, do you mean 'junk DNA'? Maybe there should also be a 'genomic organization' section that covers 'junk'/noncoding DNA, telomeres, etc, or is that too far outside the scope of this article? Opabinia regalis 03:11, 10 December 2006 (UTC)

We need to focus this article more on the subject of genes. Tried to edit the above list to reflect this. TimVickers 21:15, 9 January 2007 (UTC)

Largely agree, though I think there ought to be at least some explanation of the connection between classical and molecular inheritance, which necessitates some dicussion of the cell cycle. Other than that I'm happy to defer to your judgment on the matter, since you have much better intuition about writing articles for general audiences that are still complete and precise. I've been hoping someone would wander into this article since I nominated it for SCOTM, but unfortunately nothing much has changed yet. Opabinia regalis 02:33, 10 January 2007 (UTC)

Effluvia

After a recent rewrite (which surely needs editing for completeness and accessibility), I removed these two sections from the article, which I considered rather poorly written. I'm dumping them here for easier reference than in the history, because some of this material - the subjects, if not this exact text - should make it back into the article eventually. Opabinia regalis 06:06, 10 December 2006 (UTC)

Many steps lie between the gene and its effect

For various reasons, the relationship between DNA strand and a phenotype trait is not direct. The same DNA strand in two different individuals may result in different traits because of the effect of other DNA strands or the environment.

The DNA strand is expressed into a trait only if it is transcribed to RNA. Because the transcription starts from a specific base-pair sequence (a promoter) and stops at another (a terminator), our DNA strand needs to be correctly placed between the two. If not, it is considered as junk DNA, and is not expressed.

cells regulate the activity of genes in part by increasing or decreasing their rate of transcription. Over the short term, this regulation occurs through the binding or unbinding of proteins, known as transcription factors, to specific non-coding DNA sequences called regulatory elements. Therefore, to be expressed, our DNA strand needs to be properly regulated by other DNA strands.

The DNA strand may also be silenced through DNA methylation or by chemical changes to the protein components of chromosomes (see histone). This is a permanent form of regulation of the transcription.

The RNA is often edited before its translation into a protein. Eukaryotic cells splice the transcripts of a gene, by keeping the exons and removing the introns. Therefore, the DNA strand needs to be in an exon to be expressed. Because of the complexity of the splicing process, one transcribed RNA may be spliced in alternate ways to produce not one but a variety of proteins (alternative splicing) from one pre-mRNA. Prokaryotes produce a similar effect by shifting reading frames during translation.

The translation of RNA into a protein also starts with a specific start and stop sequence.

Once produced, the protein interacts with the many other proteins in the cell, according to the cell metabolism. This interaction finally produces the trait.

Modern concepts of the gene

When trying to understand the concept of a gene, keep in mind that it is not static. It has evolved considerably from a scarcely explained "unit of inheritance" without a physical basis (see history section) to a usually DNA-based unit that can exert its effects on the organism through RNA or protein products. It was also previously believed that one gene makes one protein. This concept has been overthrown by the discovery of alternative splicing.

And the definition of gene is still changing. The first cases of RNA-based inheritance have been discovered in mammals.^[1] In plants, cases of traits reappearing after several generation of absence have lead researchers to hypothesise RNA-directed overwriting of genomic DNA.^[2] Evidence is also accumulating that the control regions of a gene do not necessarily have to be close to the coding sequence on the linear molecule or even on the same chromosome. Spilianakis and colleagues discovered that the promoter region of the IFN-γ gene on chromosome 10 and the regulatory regions of the T(H)2 cytokine locus on chromosome 11 come into close proximity in the nucleus maybe to co-regulate.^[3]

The concept that genes are clearly limited is also being eroded. There is evidence for fused proteins stemming from two adjacent genes that can produce two separate protein products. While it is not clear whether these fusion proteins are functional, the phenomena is more frequent than previously thought.^[4] Even more ground-breaking than the discovery of fused genes is the observation that some proteins can be composed of exons from far away regions and even different chromosomes.^[5]

[1]
[2]
Lolle & colleagues (2005) Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. PMID 15785770
[3]
Spilianakis & colleagues (2005) Interchromosomal associations between alternatively expressed loci. PMID 15880101
[4]
Parra & colleagues (2006) Tandem chimerism as a means to increase protein complexity in the human genome. PMID 16344564
[5]
Kapranov & colleagues (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. PMID 15998911

Referencing elementary material

Lead section comments

As an outsider, I thought I would offer a comment or two on your lead section and my impressions:

A gene is the unit of heredity in every living organism.

a bit difficult for me to understand. What is a "unit" of heredity? I am not sure about the first sentence.

Genes are encoded nucleic acid molecules known as DNA or RNA, and direct the physical development and behavior of the organism.

the average person will have heard of DNA, but probably not RNA. The average person will not know what a nucleic acid is, and should not be required to look too much up in the first paragraph! Even if there is a wikilink, it is best to make it self contained for the reader. Also using the word encode is not very good for the general audience.

Most genes encode proteins, which are biological macromolecules comprising linear chains of amino acids that affect most of the chemical reactions carried out by the cell.

The average person has heard the word protein, but does not know what it is aside from something we eat. Some will not know the word linear. People will know molecule maybe, but not macromolecule. Amino acid again is unfamiliar. A cell might be known as a small part of a plant or animal, but even chemical reactions might be poorly understood.

Some genes do not encode proteins, but produce non-coding RNA molecules that play key roles in protein biosynthesis and gene regulation.

Getting too dense. Encode? How do they encode proteins? What is noncoding? What is protein biosynthesis? Gene regulation? You are requiring the reader to look too much up. They will give up.

Molecules that result from gene expression, whether RNA or protein, are collectively known as gene products.

Gene expression ? what is that? A guy named Gene who smiles?

Most genes contain non-coding regions, that do not code for the gene products, but often regulate gene expression.

round and round the mulberry bush

A critical non-coding region is the promoter, a short DNA sequence that is required for initiation of gene expression.

the promoter? Like a circus barker?

The genes of eukaryotic organisms often contain non-coding regions called introns which are removed from the messenger RNA in a process known as splicing.

blah blah blah. Just sounds like noise to the average person.

The regions that actually encode the gene product, which can be much smaller than the introns, are known as exons.

The exon. Like the Exon Valdise? The text in the figure also is too dense. I think that text should stand on its own and tell a story without much need to follow links.

The total complement of genes in an organism or cell is known as its genome.

Maybe understandable. But maybe not. Complement is a big word and might be misunderstood.

The genome size of an organism is loosely dependent on its complexity; prokaryotes such as bacteria and archaea have generally smaller genomes, both in number of base pairs and number of genes, than even single-celled eukaryotes.

Compound sentences are never good. And the words are too big.

However, the largest known genome belongs to the single-celled amoeba Amoeba duria, with over 6 billion base pairs.^[1] The estimated number of genes in the human genome has been repeatedly revised downward since the completion of the Human Genome Project; current estimates place the human genome at just under 3 billion base pairs and about 20,000-25,000 genes.^[2]

People do not know what a base pair is or what this means.

The gene density of a genome is a measure of the number of genes per million base pairs (called a megabase, Mb); prokaryotic genomes have much higher gene densities than eukaryotes due to the absence of introns in prokaryotic genomes.

compound sentence. Bi words.

The gene density of the human genome is roughly 12-15 genes/Mb.^[3]

meaningless. Certainly for the introduction.

So take a look at these comments, and maybe consider some rewriting.--Filll 13:26, 13 December 2006 (UTC)

Sorry Filll, I totally missed this post. The lead hasn't changed much (except for a paragraph on human genome stuff) from its former lame state; I was going to get back to it after the text was in better shape. Thanks for the comments; I'll rewrite this sometime after the holidays. Opabinia regalis 04:41, 23 December 2006 (UTC)

Good for you, Filll! And I'm saying because I’m a geneticist by training (a PhD in the field).

You’re touching on one of the most significant issues I’ve seen as I’ve looked through Wikipedia over the past. It’s the tendency of “experts” – however they define “expert” for themselves – to write jargon and in unexplained technicalities when they compose or edit a Wiki article. I’ll put it as an aphorism.

WRITING FOR WIKIPEDIA DOES NOT MEAN SUMMARIZING YOUR COLLEGE COURSE IN A TOPIC.

You are not trying to pass a final exam or a doctoral qualifyuing exam nor trying to impress your professors or fellow greaduate students. YOU ARE WRITING FOR THE GENERAL PUBLIC.

Filll asks what a “unit” of heredity is, and I’ll ask what “heredity” is. The opening sentence: “A gene is a unit of heredity.”

Reader: You mean like I inherit my blue eyes from Mom and Dad?

“Expert”: Yes.

Reader: Like I inherit money from my parents?

“Expert:” No, not at all. It refers to BIOLOGICAL inheritance.

Reader: So I inherited one blue eye from Mom and the other from Dad?

“Expert”: No, you inherited eye color through the genes, through the germ plasm.

Reader: Germs? Like having blue eyes is like being infected by a disease?

"Expert": You're too stupid for words. I'm going to ignore you.

So we have another aphorism. WRITING FOR WI8KIPEDIA MEANS BEING CLEAR, PATIENT, AND UNDERSTANDING WHERE PEOPLE CAN BE CONFUSED.

But now that I have read a good many discussion pages, I don’t think these aphorisms will be any help. Too many Wikipedia articles sound like term papers written by bright juniors in college who have an amateur “Wiki-lawyer” leaning over their shoulder and reciting incomprehensible abbreviations, like “No, can’t say that! That’s POV COI OR!!!!”

Reader: “What’s a povkoor?”

One result is Wiki GOULASH, a mixture of this, that, and the other with a sometimes overpowering dose of incomprehensible Wiki-lawyerese.

Oh well…

Timothy Perper 14:52, 4 September 2007 (UTC)

old table

Gene content and genome size of various organisms
organism	genes	base pairs
Plant	<50,000	<10¹¹
Human, mouse or rat	25,000	3×10⁹
Fugu fish	40,000	4x10⁸
Fruit Fly	13,767	1.3×10⁸
Worm	19,000	9.7×10⁷
Fungus	6,000	1.3×10⁷
Bacterium	500–6,000	5×10⁵–10⁷
Mycoplasma genitalium	500	580,000
DNA virus	10–900	5,000–800,000
RNA virus	1–25	1,000–23,000
Viroid	0–1	~500

Trichomonas vaginalis

Lead Problem

"Here's the first line of the Wikipedia entry for 'gene':

gene is the unit of heredity, with each gene determining one inherited feature of an organism.'

is completely wrong. 'One gene, one character' is a false idea of the relationship of genes to inheritance, since many genes contribute to the appearance of a single feature, and one gene will play a role in many different features."

Oh, dear... Adam Cuerden ^talk 19:58, 16 January 2007 (UTC)

The offending sentence is mine. The problem is that a gene is an extremely difficult thing to define, even using technical terms. Do they include promoters? Regulatory elements? What about rRNA genes, or siRNA genes? I've tried again with a transcript-based definition. TimVickers 20:17, 16 January 2007 (UTC)

Each gene encodes for one or more proteins, or other regulatory elements? Have to remember alternate splicing of introns, though that's a truncation event, in effect, it still counts as multiple proteins. Adam Cuerden ^talk 20:39, 16 January 2007 (UTC)

With rRNA, snoRNA and siRNA we can't define genes in terms of proteins any more. I think one gene - one transcript is usually true, although alternate start sites cause problems with that generalization. TimVickers 21:33, 16 January 2007 (UTC)

Not really. I do remember several proteins that have various truncated forms, caused by alternate splicings. It's common enough that we need to mention it. Anyway, a lot of the introns have regulatory functions. Adam Cuerden ^talk 21:51, 16 January 2007 (UTC)

Multiple splice forms all come from post-transcriptional processing of a single transcript. It's not true that one gene = one mRNA, but in general one gene = one transcript. TimVickers 22:05, 16 January 2007 (UTC)

Point, that. Probably implied already, though. Oh, and you know that Dawkins uses a completely different definition of gene again in The Selfish Gene? Just to make it awkward? Basically, anything that tends to be inherited together, no matter how many transcripts. Adam Cuerden ^talk 22:15, 16 January 2007 (UTC)

lacking recent changes / discoveries regarding definition of gene

Cistron

Gene count

Extinct genes being brought back to life

Request to edit, and add this Spinal Cord gene map

Nextbio

Is it a good idea to have a glossary?

Basic Mendelian Math

traits

Composition of the genome section

Gene vs. Allele

I am interested in the differences between the definition of an allele and a gene. This article makes the statement "In common usage, the term gene often refers to what is known more accurately as an allele". I made an edit that attempted to clarify, however the edit was reverted with the comment "Seems perfectly clear to me. If I say I have the gene for blue eyes, I really mean the allele for blue eyes". Wiki clearly thinks your statement is incorrect because the terms gene and allele are two separate articles and thus mean different things. If they were the same, then one term would redirect to the other. Because these are separate articles, they are clearly not the same, and cannot be used as such in your revert example. Either the articles need to be merged or this statement needs to be removed and edited for clarity. Why do we allow the statement? // Mark Renier (talk) 09:35, 7 August 2009 (UTC)

You have a gene for eye color, but alleles for the particular colors. People mistakenly (and very often) say "gene" when they mean "allele". An example would be "obesity gene". As can be seen in the Google News search for the term, it is touch and go whether the science journalists will say "gene" (incorrect) or "gene variant" (correct). In everyday usage, even biology professors will say "gene" where they mean "allele", confusing the heck out of their students. Since Wikipedia aims to make the subject accessible to our readers, this sentence needs to be in the article. Abductive (reasoning) 09:54, 7 August 2009 (UTC)

I would argue "gene" is the correct term as all organisms possess genes as units of inheritance of their genomes. There may or maynot be alleles or mutant versions of a gene, and multiple proteins can be translated by alternate splicing of a single gene. Further historically allele refers just to the protein coding mutated portion of a specific gene to form alleles, whereas the modern version of gene is regulatory elements as well. GetAgrippa (talk) 16:25, 28 December 2009 (UTC)

I moved this post. Ooops! Multitasking and posted on wrong subject. It was suppose to go to Evolution article. Jeez.Regards GetAgrippa (talk) 16:42, 28 December 2009 (UTC)

I think Mark Renier's error is about Wikipedia and not genetics. An encyclopedia can have two aticles on the same without a redirect for a variety of reasons. If we nee to clarify the relationship between gene and allele (in either or both articles) that is another matter ... Slrubenstein | Talk 18:25, 7 February 2010 (UTC)

Not Knowing the Definition of Gene for the Gene Wiki Page Is Lame

Clearly most of the discussion about this page is because a clear and pervasive definition does not exist. I just watched Nova and they used "gene" as being limited to protein coding DNA sequences. This leaves the highly technical term "switch" for activating sequences. [cynicism intended]

Why not just use this sensible definition? "that which is atomic, heritable, and consequential"

Just because a lay person doesn't understand "heritable" is no reason to confuse ourselves. (The other thousand lines of the page can explain what the definition actually means.) And this definition doesn't require a change every time someone makes a new discovery.

And if the thing defined above isn't a "gene" then what is it???? —Preceding unsigned comment added by 98.202.98.13 (talk) 10:32, 7 February 2010 (UTC)

I'd say that definition differs remarkably from how the word is used in genomics, and that your definition equates to 'functional nucleotide' (not a word), as anything longer (including 100kb stories like Sox2ot) that is subject to recombination/insertion/deletion/translocation won't be atomic. Narayanese (talk) 15:43, 7 February 2010 (UTC)

This is me again, Mike Layton: "that which is atomic, heritable, and consequential."

A) I didn't think wiki was a place for incestuous and specialized researchers to change the English language into whatever jargon they prefer at the moment. B) My definition certainly doesn't equate to any embellishment of "nucleotide." I make no claim that all genes [my definition] are nucleotides. I doubt they are--don't we already have proof that they are not?

This is exactly the point. We need a word for the thing I'm defining. If it isn't "gene," what is it?

By the way, I do acknowledge that my definition does match up somewhat with some of what is on the page, much of which is credentialed, unlike myself. It is just that I think my definition is simpler and clearer. (Also, not circular like "a gene is a union of genomic sequences.") 63.237.195.226 (talk) 23:23, 12 February 2010 (UTC)

Gene name	GO accession	GO type	GO term	GO evidence code	PO accession	PO term
LOC_Os05g03480	GO:0005739	Cellular component	mitochondrion	IEA
LOC_Os05g03480	GO:0003824	Molecular function	catalytic activity	IEA
LOC_Os04g52210					PO:0007134	Vegetative growth
LOC_Os04g52210					PO:0007133	Leaf production
LOC_Os04g52210					PO:0009012	Plant growth and development stages
LOC_Os04g52210	GO:0016102	Biological process	Diterpenoid biosynthesis

A unit of heredity?!?

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