Talk:DNA/Archive 2

message: I have protected this page. Full disclosure: I have edited this page. My last edit to it was on August 18. If anyone feels this disqualifies me from being disinterested enough to mediate this page, I will unprotect it and involve myself no more.
The disagreement seems to focus on two paragraphs: the introductory paragraph and the lead paragraph under the heading "Overview of molecular structure". Let's focus on the introductory paragraph first. 
Version Q: 
:Deoxyribonucleic acid (DNA) is the basic  biochemical component of chromosomes. This nucleic acid is the primary mechanism of genetic inheritance; it is transmitted to offspring, via reproduction.
Version Z:
:Deoxyribonucleic acid (DNA) is the chief  chemical component of chromosomes and is the material of which genes are made. Parent organisms transmit copied portions of their DNA to offspring during reproduction. This transmission is the primary mechanism of biological inheritance.
What are the reasons for prefering one version over the other? Start discussing here. -- Cyan 03:28, 6 Jan 2004 (UTC)
replies: text: Admirably modest to offer that disclaimer, but based on your Web page, I'm thinking it might be more accurate to describe your expertise in biology as "patchy." Proteins intersect with biology in my book and I think they do in most other people's too. If I were in your place, I would consider that disclaimer to be skirting a little too close to inviting any person who has a vivid memory of being 13 and who has grade 11 bio under his belt to revert at will anything I might write about proteins. On the Internet, nobody knows you're being modest. 168... 16:13, 6 Jan 2004 (UTC)

text: Deoxyribonucleic acid (DNA) is the chief chemical component of chromosomes and is the material of which genes are made. It is sometimes called the "molecule of heredity," because parents transmit copied portions of their own DNA to offspring during reproduction, and because they propagate their traits by doing so. This transmission of DNA is the primary mechanism of biological inheritance.
I am not saying this is perfect, but it does introduce the idea of DNA being the "molecule of heredity", a phrase which is used later in the article. My suggestion is that we use this Talk page constructively to attempt to devise a formulation that is better than J, Q and Z. Peak 06:02, 6 Jan 2004 (UTC)

text: We will have to disagree on that point.  Since there isn't a universally agreed definition for gene, there's not much we can do about that.  I say that genes are encoded, by the nucleotide alphabet, in the chromosomes. Stewart Adcock 07:42, 6 Jan 2004 (UTC)

text: So what is the only legitimate usage of "biochemical" then?  Maybe I'm being hopeful, but perhaps a lay person could indicate whether "biochemical" is any more obscure than "chemical".  Both words could be said to be correct, but "biochemical" is far more precise.  Stewart Adcock 07:48, 6 Jan 2004 (UTC)

text: I suspect the only legitamte usage of "biochemical" is to mean "relating to biochemistry." You seem to be using it in the sense of "what biochemical is in this beaker?" Although that usage exists for "chemical," I think "biochemical" used this way is a neologism.168... 15:44, 6 Jan 2004 (UTC)

text: Okay, I possibly conceed that point although only in the sense that what I'd written obviously wasn't unambiguous.  I was using the "constituent" to mean "chemical" as saying "biochemical chemical" is just silly.  Hence in "biochemical constituent", I was using "biochemical" in the sense you describe. Stewart Adcock 20:23, 6 Jan 2004 (UTC)
replies: text: Sorry. Now that I look again I don't get the impression you were using it in the beaker-of-biochemicals sense. I read the sentence now as "constituent to do with biochemistry" and making conventional use of "biochemical." So my objection really is just that I consider the word obscure and distracting.168... 20:47, 6 Jan 2004 (UTC)

text: With respect to the first sentence, this is exactly what makes the DNA so interesting/important.  The remainder may be too wordy, but it is clear and unambigous.  Your final sentence is far more concise and provides almost exactly the same information... but at the cost that it increases the required reading age significantly. Stewart Adcock 07:42, 6 Jan 2004 (UTC)

text: I am truely baffled... :-/ Stewart Adcock 20:23, 6 Jan 2004 (UTC)

text: I am also happy with the current version in the article.  One minor nit-pick is that I think "chief" should be replaced by something like "primary".  When I read it, as it is, I get the feeling that the writer intended to imply that the DNA is in charge/in control.  You may argue that is true, but I don't think that's really what was intended.  "most significant", "most abundant", maybe.  Ignore this point if you like. Stewart Adcock 20:23, 6 Jan 2004 (UTC)
replies: text: I changed it to "chief" when I introduced a sentence using "primary" later in the same paragraph. I was trying to avoid an echo. "Primary" was my first choice, but "chief" strikes me as just fine. The sentence doesn't look at all metaphorical to me, so I think readers are unlikely to read the word in the sense you are worried about. And as you say anyway, it's not as if that other sense creates a lude or obviously incorrect image. 168... 20:38, 6 Jan 2004 (UTC)
replies: text: Fair enough. Stewart Adcock 00:28, 7 Jan 2004 (UTC)

text: Deoxyribonucleic acid (DNA) is the primary biochemical component of chromosomes and genes.  Parent organisms transmit copied portions of their DNA to offspring during reproduction. This transmission is the primary mechanism of biological inheritance.
I propose this version as T2.  I think both Lir and 168 can accept the first sentence, although 168 would prefer the term "chemical component" instead of "biochemical component".  (I'd prefer "biochemical constituent", but I won't push this issue).  This brings us to the second portion.  Lir will say that it is too wordy.  I definitely don't agree with that.  But if Lir can suggest an alternative version that contains the same information, and that isn't, "This nucleic acid is the primary mechanism of genetic inheritance; it is transmitted to offspring, via reproduction." then maybe we will have something that we can agree on?  The ball is firmly in your side of the court.  Stewart Adcock 22:38, 7 Jan 2004 (UTC)

text: I agree with this suggestion. Stewart Adcock 02:45, 8 Jan 2004 (UTC)

text: I also agree with this suggestion (other than changing chemical to biochemical ;-) ) Stewart Adcock 02:45, 8 Jan 2004 (UTC)

text: Please note that there is a simple solution to the 'chief/primary' problem: use 'main' and then 'primary'.  I agree with 168... that 'biochemical component' is completely inappropriate here. However, I don't think that any version that implies that genes have something besides DNA is acceptable. Ergo T4 below. Peak 07:35, 8 Jan 2004 (UTC)
thread_title: Protected

message: *Deoxyribonucleic acid (DNA) is the primary biochemical component of chromosomes. As DNA is a nucleic acid carrying genetic instructions, organisms transmit replicated DNA to offspring, thus facilitating reproduction and biological inheritance. 
** Lirath Q. Pynnor 07:38, 8 Jan 2004 (UTC)
replies: text: Whoo!  So we are out of compromising mode then?  I agree with a lot of what you say, but most of it is just being obstinate.  Anyway, one-by-one:
* "Facilitating" is fine by me.  It is just indicating that DNA is somehow involved, and since this is only an intro paragraph we can stick with that.
* Upon consideration, I think the use of "genetic instructions" is better than gene, especially since great portions of the chromosomes don't encode ("make up", blah blah) genes.
* Seems fine to me.  Either way.  Prefer "carrying", but this goes back to our gene definition discussion.
* Wan't transmit in your version anyway?
* Mention of "nucleic acid" is helpful, but only since it provides a convenient link to that article in a highly prominent position.
* I agree fully.
**I just changed my mind about the "inheritance" point.  It's "biological inheritance", which probably isn't any more ambiguous than any phrase using "heredity".  So I retract my "I agree fully" statement. Stewart Adcock 19:01, 8 Jan 2004 (UTC)
replies: text: Stewart Adcock 18:55, 8 Jan 2004 (UTC)

text:  Just easier to read and comprehend. Stewart Adcock 17:43, 8 Jan 2004 (UTC)

text:  Based on my vote at Wikipedia:Refreshing brilliant prose - Science, you can assume that I think the article, overall, is excellent.  (Excluding the "More on DNA replication" section, of course!) There are a couple of mistakes in it though.  "The role of the sequence" section needs an overhaul.  Stewart Adcock 01:23, 9 Jan 2004 (UTC)
thread_title: T5

message: Since the page is protected, I'll have to make a proposal here.
While the traditional Watson-Crick pairings are the most common, it is known that G and T can also form a base-pair.  This is less common than the G-C pairing, but it is within the natural capacity of DNA.  It can be important in determining DNA secondary structure when it is transcribed and may have a function in gene regulation. -- Dogface
I am guessing you are talking about "Wobble base pairs" and that the secondary structure you are talking about applies actually to the RNA transcript (where the wobble pair is G-U) and not to the DNA. Could that be right? Could you expand on or provide a reference for what you're describing? I think I recall that wobble base pairs figure in replication errors and spontaneous mutations. If that turns out to be their only relevance directly to DNA, then I'd be tempted to relegate the topic to the articles on those specific topic and/or to base pair.168... 05:49, 11 Jan 2004 (UTC)
replies: text: I'm talking about GT pairing of DNA, not GU pairing of RNA.  Contrary to the presentations given in undergrad textbooks, DNA does not statically sit around in its happy little double helix every single moment.  It is capable of a great deal of secondary structure that involves partial "unwinding" of the double helix.  These structures are usually transitory but can be important in transcriptional regulation. 68.74.58.247 00:58, 12 Jan 2004 (UTC)
replies: text: Interesting. Are you talking about secondary structure in the UTR? In the promoter? While wrapped around the nucleosome? Can you give me a keyword to search on Medline?168... 02:35, 12 Jan 2004 (UTC)
thread_title: Proposed addition

message: Stewart Adcock writes "without DNA, [reproduction] would be impossible". I query this. My understanding is that reproduction is possible using only RNA, in some micro-organisms. --(anon)
As far as I know, RNA viruses are the only replicative entities that lack DNA. But viruses don't reproduce themselves. It's cells that produce viruses, and (so far as I can recall from graduate school, and supposing nothing new and surprising has been discovered since then) infected cells always copy the infecting RNA into DNA in order to make new viruses from it.168... 22:56, 12 Jan 2004 (UTC)
thread_title:  DNA essential? 

message: "Deoxyribonucleic acid (DNA) is a nucleic acid that carries the genetic instructions for making all known organisms."
:This leaves us to debate whether an RNA virus is an organism after the page has been unprotected? Stewart Adcock 18:35, 13 Jan 2004 (UTC)
replies: text: Cyan wants the dialog to continue. Now that Cyan is paying attention, I think it would be most conducive to getting this page unprotected if you could indicate whether you think T6 and/or T6.1 is OK. Peak 02:44, 14 Jan 2004 (UTC)
thread_title: T6.1 first para 

message: Well, we're closing in on 24 hours since Peak's last edit, so I would like to make some comments.
Peak and Stewart, if you would prefer the status quo to T6.1, please say so soon. 
Lir, I'm taking silence as assent.
168, I'm taking your lack of progressive discussion about the proposed text as assent. 
-- Cyan 01:03, 15 Jan 2004 (UTC)
replies: text: Many of us don't like "chief"; some of us dislike "chemical" (what would be lost by omitting "chemical"?); and as previously discussed, the emphasis on chromosomes is unwarranted);
* the status quo version does not mention what many would agree is probably the single most important thing about DNA: its ability to store information/instructions.
Of course I'm not saying that T6 or T6.1 is perfect. Peak 05:33, 15 Jan 2004 (UTC)

text: Peak, do you really think your own thinking as you described it is any less wishful? 
*chromosomes are important to mention because they establish cellular context and they are what you see when you look at DNA through an optical microscope, as hundreds of thousands of cytologists in hospitals and universities around the world do every day, and as many students do in biology class.
*I don't recall anyone saying anything against "chemical", only that Stewart said he liked "biochemical" better. I believe you and I, Peak, agreed in considering "biochemical" not very good for the sentence, and I believe Stewart said at one stage of the negotiations that he would settle for "chemical."
*the "single most important thing about DNA" to most people is that it transmits traits from parents to offspring. "Information" and "instruction" are abstract and in themselves almost completely non-explanatory. 
*DNA is the "primary" component of chromosomes because you can have a chromosome without proteins but not without DNA, and because many things called "chromosomes" (e.g. BACs) are composed only of DNA. I guess "chief" really isn't as good as "primary" here, so I propose we go back to "primary" and substitute something else at the second instance. (this last point a postscript168... 15:52, 15 Jan 2004 (UTC)

text: ...nucleic acid which carries genetic information necessary for the development of all known organisms
this avoids implying an overly genetic deterministic view of DNA.  Most biologists have largely abandoned a simplistic notion of a DNA as a "blueprint". --Lexor 13:33, 15 Jan 2004 (UTC)
thread_title:  22 hours 

message: Wikipedia has been slow, my edits have been getting trounced, and the snow needs shovelling... So, in brief, here's a combinations of T6, T6.1 and T7, offered in the spirit of combining the best of what has been proposed:
Deoxyribonucleic acid (DNA) is a nucleic acid that carries the genetic instructions necessary for the biological development of all known organisms. Parents transmit copied portions of their DNA to offspring during reproduction. This transmission is the primary mechanism of biological inheritance. 
In bacteria and other prokaryotes, DNA is distributed more or less throughout the cell. In the complex cells that make up plants, animals and other multi-celled organisms, most of the DNA is found in the chromosomes, which are located within the cell nucleus. The energy generating organelles known as chloroplasts and mitochondria also carry DNA, as do many viruses.
Peak 19:50, 15 Jan 2004 (UTC)
replies: text: Re: not being motivated to respond to the parallel track of negotation that I have unilaterally initiated in a way that casts aspersions on one of my fellow Wikipedians, I sympathize with your frustration with the extra trouble this represents and even sympathize with your frustration with me, that I should attempt to put you through this extra trouble (note though that really I'd like you all to quit dealing with Lir and think this would save you trouble in the long run). But if I feel people aren't willing to discuss 6 or 6.1 versus the version I like, it will be hard for me to resist the temptation of reverting 6 or 6.1 if it's posted. Some things are a matter of taste and so perhaps must be decided by majority vote, but I don't think everything distinguishing my favorite from yours comes down to taste. I have the patience to justify what I want and respond to your points. If you don't have the patience to really analyze the reasons why you like yours better, which means taking the risk that you will change your mind, then I think you are not bargaining in good faith. Yes it is EXCEPTIONALLY tedious to write an article this way--perhaps foolhardy even--but what choice do we have? I'm sorry that this inconveniences you, but I really care how this article comes out. 168... 20:37, 15 Jan 2004 (UTC)

text: While T7 may or may not be like any of the T6 versions, I find it easy to see that Lir has in fact taken T6 as a model and modified it to produce T7. Apply each of the bullets listed below T7 to T6, and T7 comes out the other side. -- Cyan 23:11, 15 Jan 2004 (UTC)
thread_title: T6.2

message: 168... 21:16, 15 Jan 2004 (UTC)
thread_title:  acceptable to me