How does BSE and Scrapie have 0 DNA? --Anon
- Both BSE and Scrapie are caused by a type of rogue protein complex that biologists call prions. Prions work in a similar manner as enzymes except their catalitic action is directed at reshaping certain types of large proteins found in the host organism to be a copy of themselves -- thus reproducing without the need for DNA. Scrary stuff if you ask me. BTW, in the future, please post your comments in the Talk: page - we like to keep comments out of the main articles. --maveric149
Does anyone know when the data on this page is from? I'm learning about this in Biology class, and we were taught that humans only have 30,000 genes (and, indeed, that earlier estimates of greater numbers were wrong). I'd change it, but I know nothing compared to some of the people who visit this site. -- bdesham
30000 or 35000 makes very little differences...compared to previous suggested numbers :-)
Last time I heard (2002 public governmental research), estimates were around 35000, Réseau GenHomme sources.
If "by Gregor Mendel...explained his results in term of genes," how could the term have been invented only in 1909 as asserted in the first sentence of this entry?
168...
- You can read Mendel's work here. He doesn't use the term 'gene', but he did develop the idea of independent assortment of traits. I don't think it's fair to characterize Mendel's work as an explanation of his results in terms of genes, though you'd have to read his work more carefully than I did to be sure. Graft
Somebody commented that changes I made decreased the precision of some earlier version. I don't know which version or what you meant. Maybe I've done better with the latest changes. What got me started on this article was the allusion to precision in its first line. "Gene" really isn't precise. It's squirrelly even as molecular biologists use it. I wouldn't be surprised if philosophers of science had conferences about this.
168...
P.S. To me it's wrong to say a gene "contains information in the form of sequences of nucleotides...drawn from a universal code," if you mean "drawn" in the sense of "emerging." That's like saying the sequence of letters in "Hamlet" contains information drawn from English. The information is expressed in and understood using the rules and vocabulary of English. But Shakespeare didn't pluck "Hamlet" from English. Maybe you can improve on the tack I took, but I don't think you do with "drawn." BTW I meant the clause in question to tie to a later clause and explain how the info in a gene _specifies_ a protein.
- Well, let's take this slowly then. Your new 2nd sentence is: "It contains information in the form of a sequence of nucleotides--especially DNA sequences--which according to a universal code that is recognized with only minor variations across all forms of life, including viruses, specifies the amino-acid sequence of a protein." This is very confusing. The reader must look back and forth to discover what exactly the words "which according" refer to. Also, the use of the words "a protein" at the end make it look as if one gene=one protein, which is rarely the case. I am changing the sentence to: "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. This DNA sequence (a "gene") in turn specifies the amino-acid sequences of proteins." JDG 23:40 Jan 16, 2003 (UTC)
I guess I have to accept that it confuses if you say it does. [Deleted comments I realized were wrong on better thought] But I don't think "conforming to" is quite right for this either. It leaves things vague: "The sequence of letters in Hamlet contains information _conforming_ to the vocabulary and rules of English...which in turn specifies a sequence of events." How did the letters in Hamlet specify it? So what if they conform? I'm giving it another go.
168...
Hey 168- what was nonsensical about the prion comment? They contain no DNA or RNA yet by some definitions are "alive" JDG
The sentence implied that prions might not recognize the genetic code, but even if you want to entertain the notion that prions are a form of life (notwithstanding my unfortunate use of "including" in that sentence, no biologist I've ever met spoke of even viruses as "alive"), prions don't have ribosomes so it makes no sense to suppose one could read a gene sequence, recognize the genetic code and translate it. I meant "recognize" in the context of the way genes--defined as sequences--get used. If prions are life or if they are genes, they don't fit the sequence definition, b/c they don't replicate their sequences, they replicate their conformations. Prion disease epidemics have begun when one person's mutant prion gene, which unnaturally predisposed its protein product to assume the pathogenic conformation, infects another individual, where it melds that person's healthy-sequence prions into the pathogenic shape. PLus there's the famous frequent leaping of the species barrier. The prion leaps but the sequence doesn't.
168...
- well you sure know some persnickety biologists. Biologists I've known and read come down at least 5 to 1 on the side of including viruses under the rubric of "life", most notably Christian de Duve, 1974 Nobel winner... The fact that prions don't have ribosomes or any of the other familiar machinery of inheritance and protein production is exactly the point: if they are considered "alive" they then constitute a living entity which does not employ the code you claim is "universal". Since there is heated debate over whether they are indeed "alive", my sentence (..."with the possible exception of prions"...) was, I believe, correct. But I won't press the issue. I think though that you should get into the habit of acknowledging views held by qualified people who happen to disagree with you. JDG
I made some changes to the first paragraph, partly editorial, partly content. In terms of content, I specified that genes have two crucial functions, encoding the template for the production of proteins, and turning the production of proteins on and off. I also worked Mendel in -- I think he is too important to leave out of the first paragraph. Finally, I rewrote the last sentence. Gene's do not "generate" proteins, if "generate" means to bring into being or produce (as my American Heritage dictionary claims). Gene's "make" nothing -- proteins are "made" by a complex machinery that includes other proteins. Genes are, absolutely, an important, necessary part of this machinery. But genes can neither produce proteins, nor reproduce themselves, alone -- they require the rest of the machinary. In short, they are a crucial part of whatever it is that generates the building-blocks of life -- but they do not generate by themselves. Slrubenstein
- hey SLR, how you been?... It seems our fate is to debate. First off, could you take a little greater care before punching the Save button? Your edits almost always have what look like rush-induced errors. When someone (like me) goes in to clean it up, it's tempting to start changing this and that-- so you unnecessarily open yourself to getting rewritten... Secondly, I'd have to disagree on the "generate" issue. "Generate" is usually used to denote the prime mover of some occurrence, and here we would have to assign that role to the stretches of DNA known as genes. A power generating plant does not contain transmision lines, tranformers, end-user circuit breakers, etc., yet is correctly thought of as a "generator". In most living cells, DNA (genes) initiate and prescribe the building of proteins-- mRNA and tRNA bustle out of the nucleus to do the work, but the nuclear DNA occupies the place of generator... I agree completely that Mendel should be in the first paragraph, but the paragraph at the moment needs to cleaned up. JDG
Doing alright; you seem to be at the top of your form. Sorry about the typos -- I thought I caught them. As for "generate," I guess we are destined to disagree. Must be something in our genes. I think your analogy is misplaced -- I would not compare a gene to a power generating plant, and the other chemicals and proteins required for the manufacture of proteins to the transmission lines and transformers. I would compare the gene to one part of the power generating plant, and the proteins involved to other parts of the plant. If I were to compare anything to powerlines and transformers, I would call that the "environment" in which protein manufacture takes place -- for example, the presene of sugar lactose in the environment of coliform bacteria that triggers the production of proteins necessary to break down the lactose. In some sense that sugar is "necessary" to the production of proteins, but of course I (and I am certain you) would not consider this part of the "generating machinary" of the proteins. In other words, I grant that your metaphor has some use, but I use it in a different way than you.
I honestly do not see this as a humongous debate. I am sure many biologists see it as you do; I am sure many others see it as I do. Do you really think the sentence I wrote ("crucial to the generation" is so misleading and detrimental to the education of lay-people? I thought that phrasing (I mean, crucial is pretty serious, isn't it?) would be something all parties could agree on. Slrubenstein
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