Talk:DNA/archive 2

Contents

1 Protected 2 Version T4 3 T5 4 Pynnor and Addock agree 5 Peak and 168... agree 6 Recruiting for Wikibooks Biology book(s) 7 Proposed addition 8 DNA essential? 9 T6 9.1 T6.1 first para 10 22 hours 11 T6.2 12 new process 12.1 work in progress 12.2 acceptable to me 12.3 T7.1 12.3.1 acceptable to me

Protected

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)

I'd suggest that Version Q is better due to two issues. 1) It is much more concise and easier to read, yet has almost exactly the same information content. 2) In my view, the presence of a genes is a property of certian stretches of DNA rather than, as version Z suggests, a gene is made of DNA. Either way, it is nothing more than splitting hairs. Stewart Adcock 03:53, 6 Jan 2004 (UTC) (I'll also add the disclaimer that I haven't studied biology since I was 13, i.e. I'm no expert).

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)

I think I'm probably mostly responsible for version Z, and as can probably be deduced from the page history I prefer this version over Q. In general, I favor succinctness, but not with these two choices. I don't like Q's use of the semi-colon, which I think makes for a clunky and hard-to-read sentence. Re: your point #2, "gene" has many meanings, but in what I think must be the primary molecular biological sense of the word, a gene is a piece of DNA. Hence, DNA is the material of which genes are made. Because "gene" is a culturally important word, and because many people have only a weak mastery of, and because I think to speak of genes being made of a material is cool and provocative and instructive, I like seeing this idea expressed explicitly. Q's construction, "component of chromosomes and genes", doesn't express it explicitly. Z's construction does and, although it's longer than Q's, I think it reads even better; partly for being less abstract and partly for being less dense.168... 04:10, 6 Jan 2004 (UTC)

As an editor, you have certain responsibilities. That means, if you don't like my use of the semi-colon...then you edit my semi-colon. A semi-colon is not grounds for reversion. The same goes for whether one says "made of" or "composed of". Lirath Q. Pynnor

Let us bring the topic of discussion away from what people should have done in the past and focus on what we are going to do in the present. Lir, could you make some comments about the differences between versions Q and Z? -- Cyan 04:41, 6 Jan 2004 (UTC)

---

Z is excessively long and wordy. It neglects to note that DNA is a nucleic acid. Q could better illustrate that genes are a "chunk" of DNA (although, thats probably not necessary in the first paragraph); however, I was hoping someone else would make that edit (rather than reverting). Since chromosomes are formed of genes are formed of DNA, its not necessary to explicitly refer to genes in the first paragraph; although, Q does refer to "genetic inheritance". Lirath Q. Pynnor

---

[Peak:] Firstly, I would like to say that it is indeed appropriate that these kinds of issues be discussed on the Talk page. If someone finds that his or her "improvements" to an article are not generally seen as such, then that person should be encouraged to explain their position on the Talk page rather than persistly making numerous changes on the main page, especially when it is evident that a considerable amount of work and care has already gone into an article.

[Peak:] Secondly, I would like to point out that the choice being presented above (Q vs Z) trivializes the situation a bit. Here is the preamble as it was at 19:38, 4 Jan 2004:

Version J:

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)

Who refers to it as the "molecule of heredity"? I think if a user makes edits, and you don't like them; YOU need to go to the talk page, instead of reverting. Lirath Q. Pynnor

Who?These people (http://www.google.com/search?hl=en&ie=UTF-8&oe=UTF-8&q=%22molecule+of+heredity%22&btnG=Google+Search) 168... 06:28, 6 Jan 2004 (UTC)

Oh, so if I find a list of people who refer to DNA as the "genetic code of life"; does that mean I can include it too? Lirath Q. Pynnor

Of course, so long as they are reliable people. 168... 06:35, 6 Jan 2004 (UTC)

Well there you go: [1] (http://search.yahoo.com/search?p=%22genetic+code+of+life%22&ei=UTF-8&fr=fp-tab-web-t&n=20&fl=0&x=wrt) [2] (http://search.yahoo.com/search?p=DNA+%22genetic+code+of+life%22+-fcsc+-berkeley+-newton+-icpd+-music+-cucumis+-roytaylorministries+-primeval+-casi+-worldpath+-proteomicsSURF+-ENC+-unk+-genome+-harten+-csuchico+-gregory+-trevors&ei=UTF-8&n=20&fl=0&x=wrt)

On a quick skim, I didn't see any reliable sources for your assertion. Only one I saw was academic. None used the word DNA in close connection with the phrase as you propose to do. 168... 06:45, 6 Jan 2004 (UTC)

Well, your quick skim isn't exactly appropriate. Please do not waste my time arguing with me, if you can't be bothered to act appropriately. Lirath Q. Pynnor

(Lir altered this comment on 10 Jan. Here is a link to what Lir would like to have posted (http://en2.wikipedia.org/w/wiki.phtml?title=Talk:DNA&diff=2125955&oldid=2124190).)

Just pick your favorite piece of evidence and I will be happy to take a careful look at it. I was just telling you that from skimming I don't expect that you'll be able to find even a single piece of evidence that I regard as good. But I would encourage you to try and then to show it to us.168... 15:47, 6 Jan 2004 (UTC)

---

Okay after making my comment, I went away for a while thought about other things. Later, without reference to the original passages (other than anything I could remember), I wrote what I think should be the opening passage:

S:Deoxyribonucleic acid (DNA) is the biochemical constituent of chromosomes, the biomolecules in which genes are encoded. During reproduction, parent organisms transmit copies of their DNA to their offspring and this process is the primary mechanism for biological inheritance.

This short summary introduces the fact that DNA is some kind of biomolecule, and that it is involved in inheritance. What else would you possibly want in the introductory paragraph? Hmmm, actually, it seems closer to version Z. Any waffle about "molecule of heredity" belongs in the body of the article. Just my 2 cents. Stewart Adcock 06:29, 6 Jan 2004 (UTC)

One problem with that version is that genes are not encoded by anything. Genes encode other things. Other things don't encode genes. 168... 06:33, 6 Jan 2004 (UTC)

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)

(moved subsequent niggling to my Talk page)168... 01:55, 7 Jan 2004 (UTC)

Another problem is that DNA is one of many biochemical constituents of chromosomes as they normally appear in eukaryotic cells...not "the biochemical constituent". I also think the word "biochemical" is obscure and that its chief and perhaps only legitimate usage is different from the use that you are making of it. I think it's a bit of vocabulary that isn't helpful to what this article is explaining and having it as a link makes it look important and threatens to lead people on an unnecessary excursion. Overall, I think the paragraph is more abstract and less engaging than either Z or the pre-Z version with "molecule of heredity" in it. 168... 07:16, 6 Jan 2004 (UTC)

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)

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)

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)

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)

Discussion of the composition of chromosomes belongs at chromosome, not at DNA. So the first sentence is too wordy. The rest of it is also too wordy, see my version above. Lirath Q. Pynnor

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) (Your version is the most efficient in terms of bytes that need to be downloaded ;-) )

If anything, my version is less hard to understand; most readers are turned off by the number of words, not by their so-called "complexity". "interesting" is POV, and is not a suitable reason to mention genes within the opening paragraph...of course, we could refer to genes instead of chromosomes; but, since Q refers to "genetic inheritance"; there is no need to do that. There is no need to remind that reader that "parents" produce offspring. Lirath Q. Pynnor

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

[Peak:] Lest my silence be misinterpreted, please note that I remain in agreement with 168... on every point. For those who don't see the point about the phrase "genetic code", please see the Wiki article at genetic code. Some consideration should be given to 168...'s evident expertise and superlative track record. Peak 09:57, 6 Jan 2004 (UTC)

Well, no need to build a religion or anything around me. Oh well, all right. Fasting is on Fridays. Wear no green on St Patrick's Day. Dot your i's with a little heart and you go straight to Hell. That is all.168... 15:44, 6 Jan 2004 (UTC)

---

Well, we've brought up some different versions, and discussed their perceived advantages and disadvantages. The next step is to try to come up with a consensus introductory paragraph.

Version T (for temp):

DNA is, like, this cool goo, okay?

When this version has been altered to a form that has the approval of every person on our "resolution of conflict" committee, I will place it in the article. Let the compromising begin! -- Cyan 17:58, 6 Jan 2004 (UTC)

I am OK with the current version of the article, in which "molecule of heredity" does not appear until paragraph 3. I also liked the earlier version of the intro paragraph when the phrase appeared in there too. Actually, my impression is that the current version already is a compromise. Does this version bother anyone besides Lir? If indeed lots of other people are OK with it, and now that some arguments in favor of it have been spelled out, would Lir be willing to go along with it? 168... 18:23, 6 Jan 2004 (UTC)

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)

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)

Fair enough. Stewart Adcock 00:28, 7 Jan 2004 (UTC)

Well, Lir is busy in a fuss over Socialism, so I'm just going to unprotect the page. I'll be watching to see if another edit war breaks out. Cheers, Cyan 18:15, 7 Jan 2004 (UTC)

Protected again. That didn't take long at all... -- Cyan 19:34, 7 Jan 2004 (UTC)

It brings to mind the words of Rodney: "Can't we all just get along?" Gandhi would probably have something to say about this too. Anyway, that's where I'm going for inspiration in this time of conflict.168... 20:10, 7 Jan 2004 (UTC)

Okay, so judging by that farce, Lir isn't happy with that version. I've looked at the edits by Lir and 168 and after applying a single-point genetic crossover to those versions I get this:

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)

New rule: if someone proposes a change, and 24 hours passes without comment, silence will be considered assent by me. Starting... now! -- Cyan 02:08, 8 Jan 2004 (UTC)

Addendum: a response that doesn't include a progressive counterproposal will also be considered assent. And I decide if a counterproposal is progressive. I call this style "progress by brute force". -- Cyan 02:15, 8 Jan 2004 (UTC)

The paragraph uses "primary" twice. I think the first instance should be changed to chief. Yes, I strongly prefer chemical, as Stewart anticipated, but if that turns out to be the only thing holding us back I will accept biochemical. I liked "material of which genes are made" a lot, but I could give it up as well. 168... 02:31, 8 Jan 2004 (UTC)

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

But in the event that Lir decides to just walk away in frustration, as seemed to happen before, my progressive proposal is to keep the current protected intro paragraph.168... 02:37, 8 Jan 2004 (UTC)

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

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)

---

• I propose this version as T3.
  • Deoxyribonucleic acid (DNA) is a nucleic acid, it is the primary component of chromosomes. Organisms transmit replicated DNA to offspring, facilitating reproduction and genetic inheritance.
    • • If someone knows what a gene is, they don't need a link. If they don't know, they probably don't know what a chromosome is. Genes are clearly referred to by the links to genetic inheritance and chromosome. My version is shorter, and contains links to DNA replication and nucleic acid.
        • Lirath Q. Pynnor 07:05, 8 Jan 2004 (UTC)

Version T4

For rationale, please see all the comments above :-) In particular, I agree with Lir that using the word 'genetic' obviates the need to include 'gene' in the preamble. T4 does not include 'chromosome' either -- that can be explained elsewhere.

Deoxyribonucleic acid (DNA) is the chemical that carries the genetic instructions for making all living organisms. Parents transmit copied portions of their DNA to offspring during reproduction. This transmission is the primary mechanism of biological inheritance.

Peak 07:35, 8 Jan 2004 (UTC)

T4 is just begging for that common quote, "DNA is the genetic code of life".

Fortunately, it's not so common: Google gives 4 hits. "DNA is the secret of life" has 45 hits :-) Perhaps you or someone else would like to make use of this formulation:

Each gene, a segment of DNA, encodes the instructions for building a single protein.

Peak 07:56, 8 Jan 2004 (UTC)

Each gene, a segment of DNA, encodes the instructions for building a single protein. -- I'm not sure whether you were being serious or not, but I just want to make it clear that this is very wrong! (a) Many genes encode RNA that is never translated into a protein (an obvious example being the RNA genes) and (b) Through alternative splicing most genes provide instructions for many more than 1 protein (which is why as a human, you have 200 000 different proteins but only about 30 000 different genes (of course depending upon how you define gene)). Stewart Adcock 17:43, 8 Jan 2004 (UTC)

I assume, now, that you were joking. (I'm not too smart at this time in the morning) Stewart Adcock 18:20, 8 Jan 2004 (UTC)

You haven't looked very hard. lots of hits (http://search.yahoo.com/search?p=DNA+%22genetic+code+of+life%22+-fcsc+-berkeley+-newton+-icpd+-music+-cucumis+-roytaylorministries+-primeval+-casi+-worldpath+-proteomicsSURF+-ENC+-unk+-genome+-harten+-csuchico+-gregory+-trevors&ei=UTF-8&n=20&fl=0&x=wrt)

Could you give us a specific piece of evidence to look at?

[Peak:] Lir - As has already been emphasized, the phrase "genetic code of life" is perfectly valid, and there is a fine Wiki article on the genetic code, so your query is totally irrelevant. Once the fog lifts, perhaps you will be able to tell us whether or not the confusion here is the result of confusion about the difference between the noun "code" and the verb "encode". Peak 17:59, 8 Jan 2004 (UTC)

T5

• 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)

Here are my issues with that:

• "Facilitating" does not give DNA enough credit for its role in reproduction and doesn't tell readers anything about what its role is.
• "genetic instructions" uses a lot of syllables to be a lot less explicit than "gene"
• "carrying" is abstract and conveys less than "made of" or "of which...are made"
• "transmit" sounds complicated and doesn't explain
• "nucleic acid" appears in the bold face word Deoxyribonucleic acid and so is, if not completely then at least partially redundant. Also "nucleic acid" is a name archaic in origin which doesn't convey much about what we now think of as important about DNA, and since often it doesn't even come up in discussions of DNA, I think it doesn't deserve to take up space in the intro.
• "inheritance" is ambiguous ("you mean my mom's diamond ring?") and is a weak guide for the reader. "Heredity" is better.
  • My mistake. I was reading in the edit mode and somehow didn't register the word "biological." So I don't find that ambiguous and just consider heredity a strong and folksier concept that it is worth mentioning in addition, if not instead.168... 19:09, 8 Jan 2004 (UTC)
• "replicated" is not a part of common speech and I believe will make the sentence hard for a naive reader to understand. I think DNA replication is a subject in itself and one that doesn't absolutely have to be touched on in the intro, especially since somebody who doesn't know what DNA is will know nothing at all about replication. That said, I wouldn't mind seeing a link to DNA replication worked in invisibly, for example, like this: "copied portions of their DNA"
• "biochemical" is redundant and to the extent it's not redundant it's uninteresting. If DNA is a component of the chromosomes then of course it is addressed by the science of biochemistry. At least, it wouldn't be surprising to a reader who knows that DNA is a chemical and knows that it is involved in biology. Even if they don't know that it is a chemical, I suppose being told that it is addressed by biochemistry might allow a naive but astute reader to deduce that it is a chemical. But that is assuming they know what biochemistry is. However, if they know what biochemistry is they probably know what DNA is. We want this article to be understood by people who don't know what DNA is, don't we? 168... 18:31, 8 Jan 2004 (UTC)

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)
• "replicated" is part of common speech although it does have a special, specific, meaning in this context which won't necessarily be understood -- but that's why the link is there. A good point, nonetheless.
• You already know that I disgree on the "biochemistry" point, but not enough that I'd cry if this was changed.

Stewart Adcock 18:55, 8 Jan 2004 (UTC)

How did you know I was just being obstinate?! That is impressive. Not! Although I acknowledge that it might feel like I'm just being obstinate to you.

• Re: "transmit." Darn! you're right. I don't know if it was in the "molecule of heredity" version. I guess it's just context.
• Re: common speech, perhaps I should have been more precise. What I mean is that most non-scientists would never spontaneously reach for the word "replicate" in constructing a sentence during a conversation. At least, that's what I believe, and I think that's a worthwhile standard to keep in mind in composing an introduction for a broad readership.168... 19:09, 8 Jan 2004 (UTC)

---

Much better, but I offer a slight tweak: T5.2

• Deoxyribonucleic acid (DNA) is the primary biochemical component of chromosomes. DNA is a nucleic acid carrying genetic instructions. Organisms transmit replicated DNA to offspring, thus facilitating reproduction and biological inheritance.

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

I sense a total difference of writing philosophy lurking behind the paragraph suggestions that descend from Lir's early revision and paragraphs similar to the one that's up and protected right now. This potential difference in philosophy makes me worry that the intro paragraph is only the beginning, and that I am going to be asked to sign on to a complete recasting of every paragraph from the top to the bottom of this article. I think this article as it stands now carries just the right tone, has clear and engaging explanations, and embodies more or less exactly the philosophy that I would like it to. I suppose it's no suprise and not persuasive that I should feel this way, because this article has my fingerprints all over it. Yet despite being one of the most highly viewed pages on Wikipedia (according to a list I saw somewhere on the site), it has been stable for a long time. It's very tempting to make one's mark on an article about an important subject, and lots of people know what DNA is and so could indulge their desire to give in to temptation. I think the fact that it's remained more less unchanged for a long time shows that the vast majority of a large number of people must have found this article at the very least acceptable. It's even listed as Wikipedia: Brilliant prose, for whatever that's worth. So I would like to ask Lir in particular and anybody else who would care to chime in: Can you predict what your long-range approach to this article is likely to be? What do you think of it as it stands now overall, in particular with regard to its structure and tone? Do you expect to be pretty close to being satisfied after some changes are made to the intro? Or do you think the whole article needs a lot of work?168... 23:38, 8 Jan 2004 (UTC)

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)

[comment to the effect we're being silly removed]

---

Ignoring, for the moment, the long-term fate of the article, I want to verify my understanding of the present state of affairs. 168 has brought up some issues with respect to version T5 which also apply to the tweaked T5.2. I'm assuming that these issues are not considered resolved by 168. If this is the case, I ask 168 to propose a further evolution to T5.2, one which moves towards being acceptable to all active parties. (Or if T5.2 suits you, leave a note to that effect.) -- Cyan 05:36, 9 Jan 2004 (UTC)

I don't understand. According to your recipe, shouldn't it rather be up to Lir to propose a more acceptable step forward from T4, since I found T5 unacceptable (and indeed seemingly so did Stewart)? Or shouldn't we be going back to T4, since Lir didn't actually say anything against it that was implimented in T5, and neither did anyone else. Anyway, whatever the rules, I don't feel like wracking my brain for what for me will be an unhappy compromise if this compromise is to be just the thin end of a wedge. I will not be participating in the conversion of the article we have now to something approaching the style of T5, so why participate in even the first stage of such a process? I'd like to read what Lir says in response to my question before proceeding...which is why I asked it in the first place. 168... 06:06, 9 Jan 2004 (UTC)

We can wait for Lir to respond, if you like. (In case it wasn't clear: when I say "ask", I don't mean "require". My style is autocratic, but not that autocratic ;-). -- Cyan 06:21, 9 Jan 2004 (UTC)

Also, my ability to assume good faith wanes as Lir continues to ignore my efforts to pursue a discussion to a conclusion. Lir ignored my first request for a specific piece of evidence for "DNA is the genetic code of life" for days and has not yet responded to my recent repeat of the request, which I made after it became clear that Lir did not consider the matter resolved. Are we dealing with someone who can conduct a reasonable conversation or aren't we? 168... 06:29, 9 Jan 2004 (UTC)

Pynnor and Addock agree

Mr. Addock's T5.2 is totally acceptable to me. There are two links to evidence that DNA is sometimes referred to as the "genetic code of life"; those links are found on this page, and are marked as such. I would probably edit "carrying" to "which carries"; but I doubt that is a serious issue. Lirath Q. Pynnor

Lir, you have not answered my question. I must now assume bad faith, or at least that you have different goals for discussion than I do. I will not be discussing anything further with you.168... 14:35, 9 Jan 2004 (UTC)

I have answered your question no less than three times. Lirath Q. Pynnor

Lir, could you please post links to the edits where 168's question is answered? Thanks, Cyan 23:15, 12 Jan 2004 (UTC)

Except we don't agree about my name! ;-) Stewart Adcock 08:02, 9 Jan 2004 (UTC)

Peak and 168... agree

[Peak:] T5.2 is not horrendous but it is significantly worse than what's currently at DNA. I agree with 168...'s criticisms of T5.2, but perhaps it will help highlight the problems if we go through T5.2 sentence by sentence:

1. Deoxyribonucleic acid (DNA) is the primary biochemical component of chromosomes.
   1. Is this actually true? What percentage of a chromosome is DNA anyway? Who cares?
   2. Why the fixation on chromosomes in this very first sentence? Imagine reading an encylopedia article on Water that began: "Water is a chemical found in hoses." (Or as Lir would probably want us to say: In chemistry, water is an inorganic chemical often found, in its liquid state, in garden and fire brigade hoses; when the faucet (or tap) is turned to its on state.)
   3. Minor problem: biochemical
2. DNA is a nucleic acid carrying genetic instructions.
   1. Since we've already said that DNA is "deoxyribonucleic acid" it's tiresome to have to read it again. But "carrying genetic instructions" is good :-)
3. Organisms transmit replicated DNA to offspring, thus facilitating reproduction and biological inheritance.
   1. "facilitating" !?!?!

And is there anything in all this that even hints that there is DNA in many viruses, mitochondria, etc?

Please note that T4 was an attempt to think a tiny bit outside the box. If you don't like it, I invite you to improve it or to step even further outside the box (but watch out for the cliff over there :-) Peak 08:11, 9 Jan 2004 (UTC)

---

1 -- We care.

Well, what is the percentage? Peak

So close to 100% that it might as well be 100%. Stewart Adcock 18:59, 9 Jan 2004 (UTC)

[Peak:] I am no expert, but one source says:

# isolated chromosomes (metaphase) approx. 15% DNA, 12% RNA 70% protein

The main point, however, is that the importance of DNA has nothing to do with this percentage, whatever it may be.

Yeah, yeah, sorry, I was answering a slightly different question to what you actually asked. There is indeed lots of gunk to hold the chromosomes together. Your source is almost certianly correct. Stewart Adcock

2 -- That is a personal attack, and is inappropriate.

It was not a personal attack on you (I don't even know you). It is a criticism of the havoc that the abstract entity known as Lir has wreaked on various well-written articles. Peak

Responding with a personal attack is not an appropriate way to respond to the observation that personal attacks are not acceptable.

The original remark does seem rather baiting. Stewart Adcock 18:59, 9 Jan 2004 (UTC)

[Peak:] It was partly intended to be a wake-up call to Lir - to help Lir see how Lir's interventions might appear to others, and thus avoid being nominated for a ban. Given that it was Lir's behavior that has resulted in this page being Protected for an extended period, I think the parody was fairly mild criticism.

Responding to additional comments regarding your personal attack by arguing that your actual attack would have been more accurate if it you had been more harsh...qualifies as an additional personal attack. Lirath Q. Pynnor

Henceforth, let us keep our criticisms for the proposed texts, and not for the contributors involved here. The object of this exercise is to work together, not to try to push each other's buttons. Lir, I commend you for not responding in kind to a perceived personal attack. -- Cyan 05:54, 11 Jan 2004 (UTC)

[Peak to Cyan:] Your intervention on this page (making it protected to encourage discussion to take place here rather than through constant reversions) has been most welcome, but you have already seen what happened when you tried unprotecting the page. In my opinion, this article has been held hostage to Lir for too long now (i.e., no-one has been able to make updates because the page has been protected because of Lir). Regrettably, it has become necessary to look at the larger picture, as it no longer makes sense to adhere to the goal of getting EVERYBODY to agree to every single word. That's why Lir's record has become relevant. Peak 11:31, 11 Jan 2004 (UTC)

While Lir's behavior and/or the larger picture may be legitimate topics for discussion, I continue to hold that such a discussion is out of place on this page. As for the goal of eventually getting everybody to agree on a particular form for the article, I believe that my responsibility as protecting sysop is to try to be as optimistic about that as possible, even in the face of the kind of breakdown that has occured here. -- Cyan 03:40, 12 Jan 2004 (UTC)

Peak's suggestion moved to bottom.

3 -- Linking is an important part of the wikipedia.

The official wiki guidelines wisely state:

Use the links for all words and terms that appear in your article for which it could be worthwhile to read the linked article. However, don't overdo it.

Note in particular that it says to link the words in your article, not to rewrite the article to maximize the number of words that can be cross-linked. The "See also" section is the appropriate place for all those extra cross-references. Peak

Note that a link to nucleic acid from a page about a nucleic acid is hardly "over-doing it".

I think that Lir is right here. The articles linked in that opening paragraph (v. T5 etc.) are all highly relevant. In my opinion, if I read this article I'd want those terms prominently linked. Lir was initially trying to exclude the gene link, but he apparently compromised after pressure from the rest of us. Regardless, we don't need to link/mention both "gene" and "genetic", but I think one of the two should be there.

Stewart Adcock 18:59, 9 Jan 2004 (UTC)

[Peak:] T4 allows plenty of links.

4 -- Yes, facilitating. Without DNA, reproduction would be more difficult.

You can't have it both ways: either it facilitates, or it's essential. Peak

I can have it both ways.

Actually, without DNA, it would be impossible. Stewart Adcock 18:59, 9 Jan 2004 (UTC)

[Peak:] Yes, that's the reason why "facilitating" is inappropriate (or maybe even wrong) here.

Of course, this being an NPOV site with articles on scientific research into the possibilities of alternative forms of life...it soon becomes clear that it would be inappropriate to say that DNA is required for reproduction. Lirath Q. Pynnor

5 -- Yes, in paragraph 2.

2 != 1. Peak

So? Lirath Q. Pynnor

What? I don't undertand what point Peak is trying to make here. Stewart Adcock 18:59, 9 Jan 2004 (UTC)

"2 != 1" was shorthand for "2 is not equal to 1", referring to Lir's numbering scheme. Please see above for the original point.

I'm not sure how we can proceed if one side of the dispute is trying to have the other side banned. For consensus editing to work, everybody needs to be honestly oriented towards the goal of satisfying both their own desires and those of every other party (the prerequisite being to understand other parties' desires). If you aren't prepared to try to understand each other's visions and then try find a form for the article that satisfies everbody, then this article is dead, finished, kaput. It's up to you all to decide how you want to handle this. -- Cyan 05:54, 11 Jan 2004 (UTC)

I'm not prepared or, I think, capable of understanding Lir. I am now agnostic and deeply dubious about Lir. I am happy to interact with you others, and have enjoyed doing so, but I will not involve myself in a Wiki project that is simultaneously catering to Lir.

I am a little offended, Cyan, that you considered my post about the ban deserving of censorship. I strongly disagree with your assertion that my announcement was off-topic. Proposing that Lir be banned is an aspect of my stance regarding the negotiations going on here, and I thought announcing it would communicate to others both where I'm coming from and how serious I am. I also thought that the people who had participated in discussions here would want to weigh in on the matter of whether Lir deserves banning, since you all have extensive recent experience interacting with Lir. Unless you think the chances of Lir being banned are small, then if you are against a ban, I would expect you to feel obliged to go and speak in Lir's favor at the conflicts page. Silence can be damning.168... 06:58, 11 Jan 2004 (UTC)

I would have preferred that the announcement be made on the talk pages of the people whose attentions you wanted to direct to it. I very much want discussion on this page limited quite narrowly to the article and its contents. I did not intend to offend you, and I apologize for doing so. -- Cyan 07:32, 11 Jan 2004 (UTC)

Another thing pertinent to this page is that readers should take care in interpreting the discussions that are recorded on it. Lir made at least one undated and unnoted change to a post that was part of a conversation that concluded four days earlier. I would say the change makes Lir's post look nicer for posterity, because to me it makes Lir come off as more civil and reasonable. But changes like that might make the surrounding posts that other people made at the time hard to interpret properly. In any case they devalue the page as a historical record, which I think people should keep in mind.168... 07:13, 11 Jan 2004 (UTC)

I shall tag the altered post. -- Cyan 07:32, 11 Jan 2004 (UTC)

<off-topic announcement zapped>

[Peak:] This article has already been protected for almost a week, and it seems clear that there is little chance of any progress with respect to the T5 branch. In order to minimize the period of protection, I believe you might consider taking these two steps:

1. Declare some particular version (*) of the preamble to be the stable version, and prohibit all changes to it that are not first agreed to on this Talk page; that is, anyone would have the right to revert any change made to the Preamble that were in violation of this prohibition;
2. Unprotect the page.

(*) It seems to me that at this point, the main candidates are:

a) the status quo;

b) T4, since there do not seem to have been any significant objections to T4.

c) Some other proposal you may care to present for general discussion.

--Peak 05:40, 12 Jan 2004 (UTC)

The only actual power I have is to protect and unprotect the page, and to edit it while it's protected. By custom and policy, only I or another disinterested sysop can unprotect the page. I'm loath to assert or declare that a certain version shall be the stable version, since I have no moral standing to enforce such a declaration, because by custom and policy, unprotected pages are freely editable. However, if all concerned parties will agree to abide by a choice by me as to a particular preamble, then I will do my best to find a version that pleases everyone equally, or at least displeases everyone equally. -- Cyan 20:11, 12 Jan 2004 (UTC)

I agree (strongly) with Peak's suggestion, if by the status quo he means the version currently in the article. Stewart Adcock 20:29, 12 Jan 2004 (UTC)

I believe since peak has some objection to T5, its up to him to attempt to write a T6 which improves upon T5. Certainly, that was the spirit in which I wrote T5 -- under threat that failure to do so would have some negative consequence. Lirath Q. Pynnor

Recruiting for Wikibooks Biology book(s)

Warm greetings from sister project Wikibooks where I am writing a general biology textbook all by my lonesome. My profs donated a sizable bunch of notes that make up the structure of an entire introductory biology book. However these notes are in outline form and need to be fleshed out into full text. Then, some images .. I am confident that this will become the standard college text over time but need some help to get it there. --karlwick

Proposed addition

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)

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)

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)

DNA essential?

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)

T6

[Peak:] Lir asked for T6. I would like to propose that we think a little bit outside the box again, and view the PREAMBLE as a whole. Thus Proposal T6 is that the preamble consist of the following two paragraphs. The first is based on T4 since (at least so far as I can tell) no substantial objections have been directed specifically towards it. In revising it, however, I have tried to take into account many of the concerns that have been expressed, including Lir's concern about including many wikilinks (and specifically "nucleic acid"), as well as the possibility of extra-terrestrial life. Here then in T6:

Deoxyribonucleic acid (DNA) is a nucleic acid that carries the genetic instructions for making all living organisms on Earth. Parents transmit copied portions of their DNA to offspring during reproduction. This transmission is the primary mechanism of biological inheritance.

In bacteria and other simple-cell organisms, 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 06:53, 13 Jan 2004 (UTC)

I don't think that listing any minor niggles at this point will be at all helpful, so I am going to fully support this entire preamble except for the first sentence, with which I have two issues. The "on Earth" statement is just silly.

[Peak:] It's obviously only there for Lir, but if you step back for a second, I think you'll see that it's not really all that silly. It's a bit more thought-provoking that 'known', but obviously (or at least, I hope it's obvious!) I'm OK either way. Peak 02:44, 14 Jan 2004 (UTC)

I know you submitting to Lir's desires there, but even so. If someone can prove that extraterrestial lifeforms have their genetic information stored in another way, then we can discuss this! ( ;-) ). But having said that, even on Earth, it isn't true. (Uh-oh, I hope we don't get into a debate about whether a virus is a "living organism". I'm not sure).

[Peak:] Wikipedia is, so far as I can tell, consistent in taking the view that viruses are not organisms (see organism), and I think it's appropriate, given the wikilink, to piggyback off that.

Oh. Okay, sounds fair. Stewart Adcock 17:26, 14 Jan 2004 (UTC)

As indicated above, some lifeforms (RNA viruses) don't carry their genes in DNA (although DNA is essential during their reproduction). Second, the "information" link doesn't offer anything relevent.

[Peak:] If you mean that the article on information can be improved, I wholeheartedly agree, but I've read elsewhere that we're supposed to be optimistic about such things. Since the fundamental importance of DNA is attached to the information it stores, mentioning information seems appropriate. However, I'm also OK with instruction (though instruction has even less to offer).Peak 02:44, 14 Jan 2004 (UTC)

What I actually meant was that it should be safe to assume that the reader will already knows what an instruction is, so no link is needed. Especially since the hidden link to information isn't very helpful. Stewart Adcock 17:26, 14 Jan 2004 (UTC)

I, therefore, propose an alternative first sentence:

T6.1 first para

"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)

I am ignoring Lir's request for T6. I don't see why you two aren't ignoring it too, but that's up to you. My vote remains cast for the status quo version, which seemingly was bothering nobody but Lir when we started. 168... 18:59, 13 Jan 2004 (UTC)

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)

22 hours

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)

On balance, I prefer T6/6.1 to the status quo, but I won't complain if everyone else wants that. Stewart Adcock 02:36, 15 Jan 2004 (UTC)

These versions were developed with reference to versions of Lir's and as a compromise with those versions. I consider Lir's suggestions as insincere and designed to stir up dust. My favorite version is what's up now. Since Lir has disappeared and everyone once seemed happy with it, I think that's the natural point of reference. I'd like read what people have to say in favor of T6/6.1 over that version. I do not expect to be persuaded, but in response I will offer my reasons in the hope of persuading you. But really I'd rather we just go with what's up and ban Lir if he starts making trouble again, since Lir's silence has proven that he can't be negotiated with. 168... 03:24, 15 Jan 2004 (UTC)

I will wait for others to reply before making changes. -- Cyan 03:38, 15 Jan 2004 (UTC)

[Peak:] Unfortunately, 168...'s argument is based on wishful thinking. That is, 168... is suggesting that we keep the status quo, unprotect the page, and if Lir intervenes, ban him or her (which is it???). But in this scenario, the last part probably would not happen, because the conflict resolution process was not followed. On the other hand, T6/T6.1 was formulated to address Lir's concerns, so if Lir messes it up, then the case for some kind of ban is much clearer, and we ought at least to be able to count on Cyan's support.

Also, since we've gone to the trouble of forumulating and discussing various versions, I think we should pick the best. I'm certainly willing to be told what I'm missing, but in comparing T6/6.1 with the status quo, I agree with Stewart. It seems to me that the main problems with the status quo version are:

• the bit about "chief chemical component of chromosomes".

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)

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))

168... 06:05, 15 Jan 2004 (UTC)

P.S.No.2

• While it's certainly very important that the instructions for development are encoded by DNA, I don't think we need to say this in the intro to the DNA article and that it's better to emphasize what I called the "most important thing" above. This is a matter of taste, I suppose. My reason for feeling comfortable leaving this out is that not all DNA is instructions and the gene article gives genes the credit for controlling development, which I think is a little more accurate. Also development is secondary to being (metaphorically in the language of calculus it might be called the second derivative of being). Most importantly DNA is why we have traits, although the curious will certainly wish to learn that it is how we develop them. 168... 16:38, 15 Jan 2004 (UTC)

I'm not weighing on the relative merits of the versions proposed (most of them are fine in one way or the other, Lir's proposal below is also OK), but I would suggest the following minor tweak to T7 should it (or some derivative of it) became the accepted intro:

...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)

---

T7

• Deoxyribonucleic acid (DNA) is a nucleic acid which carries the genetic "information" necessary for the biological development of all known organisms. DNA is inherited; during reproduction, it is transmitted to offspring. In bacteria and other prokaryotes, DNA is distributed throughout the cell; in eukaryotes, most of the DNA is located within the chromosomes of nuclei. Chloroplasts and mitochondria also contain DNA, as do many viruses.
  • I find it rather rude that such a big deal was made about my meeting the 24 hour deadline. I had said nothing when the 24 hour deadline for my "opposition" passed without their attempting a compromise version. My email is listed on wikipedia, my aim contact information is listed here, you all know the site is having technical difficulties.
    • The article at nucleic acid can explain that nucleic acids are biochemicals.
    • There is no need to inform the readers that offspring come from parents, not at this article. Because we can link words, we don't need to define what are really basic technical terms (such as eukaryote). There is a seperate wiki for writing in that style.
    • We also shouldn't say "simple-celled" when we are referring to prokaryotes, if you think they should be known as "simple-celled organisms" -- you need to move the relevant page first. I will oppose such a move.
    • The article on information notes more than once that biological information is really a sort of "information". True information could be defined as being something created by intelligent life.

• • • • Lirath Q. Pynnor

I don't understand the rules well enough to say if the version Lir posted above counts as "progressive," but I would like to note that he posted it 12 hours after Cyan posted the 22 hour warning. I wouldn't have to say this if Lir dated his posts. 168... 16:57, 15 Jan 2004 (UTC)

Lir, in order for T7 to be considered progressive, you need to state how you think it addresses and reconciles the concerns of the other participants. At this time, I would once again like to remind the participants to try to focus on the text of the article, not each other's past behavior. (My behavior is fair game.) -- Cyan 17:28, 15 Jan 2004 (UTC)

And I would like to remind participants that I am curious to know if I have heard all your reasons for preferring T6/6.1 over the status quo and what you think of the arguments I made against them. I will not be focusing on anybody's past behavior, but I remember it, and I refuse to not use this information in deciding how I will myself behave toward them in the future. So if anybody senses that I have interpreted anybody's behavior unfairly, I would encourage them, in the interest of fairness to everybody, to let me know and persuade me otherwise. 168... 18:08, 15 Jan 2004 (UTC)

P.S. Not that I am by any means a strict quid pro quo person, and I don't think anyone here has seen me take an "eye for an eye". I just think that in interacting with a particular person, there can come a point where one has to stop "forgiving and forgetting" in order to serve or to pursue other values besides the mere principle of "forgiving and forgetting." 168... 18:45, 15 Jan 2004 (UTC)

P.S. No.3, Re: "is a nucleic acid"

• (quoting a post of mine from earlier) "nucleic acid" appears in the bold face word Deoxyribonucleic acid and so is, if not completely then at least partially redundant. Also "nucleic acid" is a name archaic in origin which doesn't convey much about what we now think of as important about DNA....". What do we hope people to learn by linking to "nucleic acid"? I could imagine such an article that did nothing more than relate the history of the term and to say that now it refers to DNA and RNA. The exact atoms are specified in the articles on the nucleotides, so "nucleic acid" doesn't have to talk about those. The nucleic acid article at that link now describes phosphodiester linkages, which is useful, but that's not info that ranks anywhere near in importance with the other things we have to say about DNA, and if it did we could just say it instead of linking "nucleic acid." It's an academic point that DNA belongs to the category "nucleic acid."

I have emailed Lir regarding T7. -- Cyan 18:20, 15 Jan 2004 (UTC)

T6.2

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)

No snow needs shovelling here... in fact, I might go surfing later :-). I think T7 was a huge step backwards. The most important point I'd like to make is that I think we should avoid the can of worms associated with the word "information". The layperson will associate information with "knowledge", as a chemist I (inversely) associate it with "entropy", as a computer scientist I associate it with the useful content of "data". As part of the recipe for life, the term "instruction" is much better (and doesn't really need to be linked). I am not motivated to list other critisms at the moment. T6/T6.1 are still the best options, in my opinion. Stewart Adcock 20:14, 15 Jan 2004 (UTC)

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)

• T7 is almost verbatim identical to T6. T7 lacks a few things such as "plants are eukaryotes" and "parents produce offspring". It is hard for me to be any more "progressive"; since my versions are routinely derived from the version presented by detractors.
  • I find it unfair that I am constantly threatened with not "cooperating enough. Nearly every direct suggestion made directly to me, about my version, has been accepted. I find myself unable to proceed, since nobody has specifically criticized any one specific aspect of T7 -- with the exception of Adcock who stated that he preferred "instructions" over "information"; I hardly have an opinion either way. Lirath Q. Pynnor

Who is threatening you, Lir? -- Cyan 20:52, 15 Jan 2004 (UTC)

168 is. Lirath Q. Pynnor

Lir, T7 is nothing like any of the T6 versions. For a start, Peak has written clear and readable sentences. Do you really take issue with the facts that "plants are eukaryotes" and "parents produce offspring" get implied? (Neither is explicitely stated, as you suggest) If so, why don't you mind the implication that "Bacteria are prokaryotes"? Regardless, we now appear to just be going around in circles so I'm glad Cyan has just proposed a new process, below! Stewart Adcock 21:50, 15 Jan 2004 (UTC)

It is everything like T6, as Cyan notes below. (Actually, I specifically refrained from making any such comparison. -- Cyan) What is so unclear and unreadable about T7? Yes, I take issue with "plants are eukaryotes" and "parents produce offspring" -- these concepts do not need to be spelled out at this article. I do not take issue with the bacteria statement because I does not say "bacteria are prokaryotes"; it says, "bacteria and other prokaryotes", implying that some prokaryotes (but all bacteria) are being referred to -- if that is wrong, then bacteria should be removed, as the reader should either know that bacteria are prokaryotes, or the reader should click on prokaryote. Lirath Q. Pynnor

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)

Feel free to continue the old process, if you think it can yield useful results. Also, feel free to fork (or maybe fork) the new process, but be aware that the processes won't terminate until everyone has signed off on the working copy. -- Cyan 22:15, 15 Jan 2004 (UTC)

It doesn't make sense to me. We'll just edit war over it. Lirath Q. Pynnor

new process

I would like to try a new process, to see if it can work better. Here is what I propose: in the section below, entitled work in progress, is a freely editable (wikiwiki :-) working copy for everyone to collaborate on. The section underneath, entitled "acceptable to me", is a list of people who have agreed to the current working version. This means that if you make any change to the working copy, you have to remove the names of everyone else from the "acceptable to me" section. When a version exists that has everyone's support, I will place it in the article and we can move on to the second paragraph under contention(!), which was, as you may recall, the lead paragraph under the heading "Overview of molecular structure". I have primed the "work in progress" section with a goofy couple of sentences. -- Cyan 21:10, 15 Jan 2004 (UTC)

The object of this process is to move towards wiki-based editing, and away from pure argumentation. Yes, edit wars are possible, but I can imagine no better demonstration of their fruitlessness.

The idea is that the greater the number of people who accept your version, the more prestige you will have. Right now, only Lir and 168 have tried, and each of their versions' acceptability ratings is at the minimum possible: 1. -- Cyan 16:21, 16 Jan 2004 (UTC)

work in progress

Deoxyribonucleic acid (DNA) is the primary 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.

In bacteria and other simple cell organisms, DNA is distributed more or less throughout the cell. In the complex cells that make up plants, animals and in other multi-celled organisms, most of the DNA resides in the cell nucleus. The energy generating organelles known as chloroplasts and mitochondria also carry DNA, as do many viruses.

acceptable to me

168... 21:16, 15 Jan 2004 (UTC)

T7.1

• Deoxyribonucleic acid (DNA) is a nucleic acid which carries the genetic "information" and "instructions" necessary for the biological development of all known organisms. It is sometimes referred to as the "molecule of heredity" or the "genetic code of life".
• DNA is inherited and used to propagate traits; during reproduction, it is replicated and transmitted to offspring. In bacteria and other prokaryotes, DNA is distributed throughout the cell; in eukaryotes, most of the DNA is located within the chromosomes of nuclei. Chloroplasts and mitochondria also contain DNA, as do many viruses.

acceptable to me

• Lirath Q. Pynnor

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I solicit feedback on this new process from all participants on my talk page, or by email if there's something you don't feel comfortable posting publicly. -- Cyan 21:25, 15 Jan 2004 (UTC)

[Peak:] So far the new process has only taken us backwards. 168... wants to start at or very near the beginning, and Lir now wants to include the phrase that I believe everyone else has agreed long ago is unacceptable. I propose we define a new, new process, based on some procedure that is guaranteed to produce a selection in a pre-determined number of rounds. I will describe two examples of such procedures, one based on RANKINGS, and the other based on ACCEPTABILITY, but of course there are many other such procedures. Since it would take agreement beforehand to adhere to the outcome of such a process, I would ask Cyan to propose a new, new process. But let me explain what I have in mind by giving two examples:

1. RANKINGS: Each of us proposes a version. Each of us then ranks all the versions. Based on the outcome, the universe of possibilities is reduced by some procedure (e.g. based on pairwise comparisons). If the procedure fails to reduce the universe by at least one, then the judge gets to eliminate one. If the reduction is to 1, we're done. Otherwise, the authors of the remaining versions have an opportunity to make revisions; and the process continues from the top. This process is guaranteed to achieve a single result.
2. ACCEPTABILITY. Again we start with N proposals, and everyone is allowed to cast as many "ACCEPTABLE" votes as they wish. If there is a winner (a single, most acceptable choice), then we're done. If not, then reduce the size of the universe by removing proposals with the least number of acceptability votes; if all proposals get exactly the same number of acceptances, let the judge remove one candidate. And continue.

As I mentioned, there are many variants of these, and there are other possibilities. Peak 15:34, 16 Jan 2004 (UTC)

The reason the page is protected is to try to resolve the edit war. I am agreeable to any text-centered procedure that will achieve this goal. -- Cyan 16:08, 16 Jan 2004 (UTC)

I don't like that plan, and here's why

• I don't think Lir deserves to vote and will not recognize Lir's vote.

[Peak:] My impression is that Cyan wants UNANIMITY or at least agreement on a procedure. I think we need a process such that this page (or any other) is not held hostage to any one person.Peak 22:17, 16 Jan 2004 (UTC)

• We are a small and arbitrary set of voters, and we are liable to conclude something different than the entire electorate or a larger sample of voters would conclude.

Yes, Cyan, God bless his optimistic heart, has made it clear he wants unananimity. I don't believe it will be my fault if he doesn't get it, because in the meantime minimally it will be Lir and I both who are holding the page hostage. Furthermore, I will be open to honest well-reasoned and good faith dialogue with everybody after Lir goes away.168...

[Peak:] As it happens, I've given that some thought too. If N people engage in a process that results in some "wikistability", then it would take N additional people to reopen the matter. Peak 22:17, 16 Jan 2004 (UTC)

I think I don't understand the thought you have. Any one person any time can come by and edit an unprotected page. There's no required quorum.168... 22:34, 16 Jan 2004 (UTC)

• I don't see why we can't just discuss the relative merits. A small group of people letting themselves be governed by reason is liable to conclude the same thing as a large group doing the same, and the decision is likely to be reasonable.168... 16:51, 16 Jan 2004 (UTC)

[Peak:] The problem is that Wikipedia's current rules and processes make it easy for any one "subvandal" to subvert any one page, even if only through indefinite Protection. Let's be a little creative, and maybe Wikipedia as a whole can benefit from our experience. Peak 22:17, 16 Jan 2004 (UTC)

I think excluding Lir's is highly non-traditional and creative. Why aren't you willing to try that? I've brought up questions like this all over the site, and not one person has responded with words in support of Lir or any mention of the merits of his participation.168... 22:34, 16 Jan 2004 (UTC)

I find it absurd to reject 7.1 solely because it states, "some people refer to DNA as the "genetic code of life"" -- some people do. Furthermore, 7.1 contains more than that, so a rejection of it based solely on that is entirely inappropriate. Lirath Q. Pynnor

[Peak to Lir:] What do you think of first agreeing on a PROCESS that will guarantee the selection of a single alternative in a small number of steps? Peak 22:17, 16 Jan 2004 (UTC)

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