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Talk:Gene

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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 wold 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 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 paranthetical 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 resonsibly.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 machinary, 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" refering 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 refering 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 -- ideosyncratic 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 nucleotieds 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 nucleotids; 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 chromsome, 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 refering to, and trust that s/he or Mav will make the apporpriate 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" refered 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 [1] (http://www.euchromatin.org/Crick01.htm). 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 [2] (http://gnn.tigr.org/timeline/1957_Crick.shtml) 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, prefferably 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 [3] (http://www.euchromatin.org/Crick01.htm). 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...

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

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