Talk:DNA/archive 11

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I dont know if people are just arguing with me for the sake of argument but there is no more procedure for posting on this page (post about any subject wherever you want in whatever section you want). Bensaccount 01:19, 20 Mar 2004 (UTC)

I think this talk page should be linked to from the "criticism of Wikipedia" page. It would only be NPOV to note that the traditional editing process becomes less and less viable as more and more users attempt to work on a page. Lirath Q. Pynnor


Contents

Should we include incorrect phrases if they are common?

moved temporarily to Talk:DNA/vote

Summary

Should we include incorrect phrases if they are common?

  1. No we should try and get rid of or correct incorrect phrases.
  2. Being common is not a reason for inclusion; this article is about DNA not about what has been commonly said about DNA. Bensaccount 21:49, 13 Mar 2004 (UTC)

Options

  1. We should introduce mention of incorrect phrases in the introduction
  2. We should introduce mention of incorrect phrases in a separate paragraph later in the article
  3. We should not introduce incorrect phrases

The "genetic code of life" and "deoxynucleic acid" and "molecule of heredity"

Allow me to clarify something for you, Bensaccount. Those of us who have been trying to make progress on this passage already know the realive merits and flaws with this phrase (refer to the archives). I, for one, would prefer if it wasn't used but it was included as a compromise to Lir. Stewart Adcock 17:18, 10 Mar 2004 (UTC)

[Peak:] It is no longer clear which of the three phrases Stewart was referring to, but please note that there was never any compromise with Lir regarding the use of "genetic code of life" as a description of (or alternative name for) DNA in the preamble. Perhaps Stewart is referring to the fact that there was at one point a proposal that included the phrase in the preamble, but it was not as an alternative name. Peak 15:13, 17 Mar 2004 (UTC)
We shouldn't lie to compromise with Lir. Bensaccount 17:51, 10 Mar 2004 (UTC)

[P0M:] At this point I'm not clear which phrase is "this phrase." When people like the writer at Hartnell make a mistake and write "deoxyribonucleic" as "deosribbonocleric" ;-) or whatever, the usual way to to deal with it, if we are required to quote the mistaken passage for some reason, is to follow the error with the Latin word "sic" in parentheses. Ordinarily there would be no reason to catalog every misspelling and beginner's mistake in an article devoted to explaining something.

[P0M:] If we are now actually talking about the "genetic code of life", then I can happily agree with both Lir and Bensaccount. The idea of a "hereditary code-script" has historical importance because it appeared in a seminal book by a physicist, Schrödinger, that got the bio-chemical researchers on the right track. So the idea has to be in the article at the appropriate point. That being said, I started objecting to several things in the introduction a very long time ago (in subjective time) and most of what I said was scrambled in the recent cataclysms. One of the things that I did not like in the introductory passage was this very phrase "genetic code of life". I object to it because it is not the most apposite way to explain what is going on. Now you are probably going to ask me why I have not provided a more apposite way and I will be frank and tell you that I have been discouraged from doing so in part because of the intrinsic difficulty of the task and in part because of the intense partisan attitude that even attempts to provide "a gentle response" have sometimes met on this talk page. P0M 18:42, 10 Mar 2004 (UTC)

Summary

  1. Deoxynucleic acid - This is a common incorrect phrase therefore it should be corrected before inclusion (see above).
  2. Molecule of heredity"hereditary code-script" - Appeared in a seminal book by a physicist, Schrödinger, that got the bio-chemical researchers on the right track. Therefore should be included in the history subsection.
  3. Genetic code of life - This is a common phrase, but phrases such as "DNA is the genetic code of life" are both incorrect (see Genetic code) and relatively uncommon (see archives for empirical evidence). Thus the preamble could in principle include the phrase, but not as a synonym or characterization of DNA.

The Two-Thirds Majority Version

A consensus-building process has taken place. A two-thirds majority agreed to the version which then became the posted version from 14 February to 6 March, as well as at various times before and since those dates:

Deoxyribonucleic acid (DNA) is a nucleic acid which carries genetic instructions for the biological development of all cellular forms of life and many viruses. DNA is sometimes referred to as the molecule of heredity as it is inherited and used to propagate traits. During reproduction, it is replicated and transmitted to offspring.
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 is found in the chromosomes, which are located in the cell nucleus. The energy generating organelles known as chloroplasts and mitochondria also carry DNA, as do many viruses.

Comments on this version

[Peak] Actually, the first sentence is partly incorrect, or at least misleading, because of the use of the word "primary". This was discussed earlier on this Talk page, and my recollection is that this was one of the main reasons for seeking consensus on an improved version. (Ultimately, this led to the "near-consensus version" that you are treating so unkindly.) Here is an extract from Talk:DNA/arhive_2#5:

isolated chromosomes (metaphase) approx. 15% DNA, 12% RNA 70% protein
... There is indeed lots of gunk to hold the chromosomes together. Your source is almost certianly correct. Stewart Adcock


Developmental biology has to do with the development of organisms. DNA is in no way limited to this. It codes for ALL the structure and functions of organisms. Bensaccount

  • is misdirected criticism as the first sentence specifically mentions viruses. User: Peak
    • That is not what I mean - follow the link to developmental biology. Bensaccount

"Molecule of heredity" is not an alternate name for DNA. It is a vague misinterperetation at best. "Molecule of heredity" should be a redirect to heredity because the typer has made a mistake (there is no such molecule). Bensaccount 22:40, 8 Mar 2004 (UTC)

    • is irrelevant as there is no claim that the phrase is an "alternate name." User: Peak
      • See updated problems with molecule of heredity above. Bensaccount


In the second paragraph DNA is dichotomized into prokaryotes and eukaryotes. If you are going to dichotomize DNA do it in the subcatagories, not the intro.Bensaccount 16:12, 9 Mar 2004 (UTC)

[Peak:] DNA is not dichotomized in the second paragraph.Peak 05:54, 16 Mar 2004 (UTC)
Yes it is. If not prok vs. euk, then in as location. Bensaccount


Discussions about this version, which were disproved, has been moved to archive 7.

The propositions as of 10/03

The original version (on the page now) was replaced by the near consensus version from above. This vesrion has been broken up into its consecutive paragraphs and they are listed with the other suggestions below.

First paragraph

The first paragraph should be a definition. (Wikipedia:Define_and_describe)


Option0A (in case some of you forgot, this is the "near-consensus" version :-))
Deoxyribonucleic acid (DNA) is a nucleic acid which carries genetic instructions for the biological development of all cellular forms of life and many viruses. DNA is sometimes referred to as the molecule of heredity as it is inherited and used to propagate traits. During reproduction, it is replicated and transmitted to offspring.

- :Lack of clarity around propagate traits (see slru)
It seems perfectly clear to me. I'm not adverse to someone suggesting an alternative wording though. Stewart Adcock
[Peak:] I agree with Stewart. Perhaps Slru would care to make a proposal?Peak 05:33, 18 Mar 2004 (UTC)
The sentence is misleading (same as heredity above). Bensaccount 22:23, 13 Mar 2004 (UTC)
- : "Biological development" is only a fraction of what DNA codes for.
[Peak:] Perhaps, but this part of the paragraph is highlighting what makes DNA especially interesting and important.
- : "Molecule of heredity" is misleading (see above)
[Peak:] I have looked "above" and do not see why you consider the phrase misleading. Slru's concern is with the "propagation of traits". The only other concern I have seen expressed is that sentences such as "DNA has been called the molecule of heredity" could be construed to imply that the double-helical form of DNA is a single molecule, which, from a certain POV, it is not. However, the sentence does not say anything about the double helix, and any confusion there may be about how to count molecules of DNA is dealt with in the body of DNA.
- : DNA replication is less than 1/3 of the role of DNA. If you include it you should include the central dogma first.
[Peak:] Mentioning "biological development" adequately covers the "central dogma" -- please try to think of "biological development" in a broad sense. However, if you still feel that the combination of "biological development" and "reproduction" is missing something important, then perhaps you could state what it is at the same level of abstraction, and thereby improve this version.Peak 05:33, 18 Mar 2004 (UTC)

Option 0S (avoid complications involving "traits" to address Slru's concerns)

Deoxyribonucleic acid (DNA) is a nucleic acid which carries the genetic instructions for the biological development of all cellular forms of life and many viruses. DNA is sometimes referred to as the molecule of heredity as it is inherited and forms the basis of the inheritance of genetically determined characteristics. During reproduction, parental DNA is replicated and transmitted to offspring.

Option 0S1 (modification of Option 0S - i.e. avoid complications involving "traits" and use biopolymer )

Deoxyribonucleic acid (DNA) is a nucleic acid biopolymer which carries the genetic instructions for the biological development of all cellular forms of life and many viruses. DNA is sometimes referred to as the molecule of heredity as it is inherited and forms the basis of the inheritance of genetically determined characteristics. During reproduction, parental DNA is replicated and transmitted to offspring.

Option 1A
Deoxyribonucleic acid (abbreviated DNA) is a macromolecule that encodes the structure and functions of a cell. This biological information is heritable, hence the common phrase molecule of heredity. DNA can also be found in viruses.

- : "Molecule of heredity" is not a clear formulation and rather mass media information (see pom)
I agree. But, at least that sentence isn't wrong. Stewart Adcock
The sentence is misleading. It should be moved to the history subsection (see above). Bensaccount 22:23, 13 Mar 2004 (UTC)
- : "Biological information" is unclear.
- : technically, it does not encode the structure and functions of a cell; it encodes the structure of proteins for enzymes that are vital to the structure and function of cells and organs. I think this is a very important and too often misunderstood/oversimplified distinction that gives people a misleading view of how inherited traits work. Slrubenstein
- : I very strongly agree. This is a vital point. It bears on the question of how cells differentiate, too. P0M 01:48, 24 Mar 2004 (UTC)
+ : I think the link macromolecule is important
Why? Stewart Adcock
It is good to associate DNA with what it is (a macromolecule). More specific would be to say its a nucleic acid. Bensaccount 00:52, 11 Mar 2004 (UTC)
Please tell me if I'm wrong, but haven't we been over this before? My prefered choice has been nucleic acid for a while. Stewart Adcock 00:59, 11 Mar 2004 (UTC) (In fact, Nucleic acid was selected in majority version of the intro. Stewart Adcock 01:39, 11 Mar 2004 (UTC))
Agreed. It's a little redundant, to the reader who already knows what is going on, but I would like to see "DNA is a form of nucleic acid that..." P0M 01:52, 24 Mar 2004 (UTC)

Option 2A

Option 3A
Deoxyribonucleic acid (abbreviated DNA) is a macromolecule that encodes the structure and functions of a cell. It is the first component in the central dogma of molecular biology (DNA → RNA → protein). DNA can also be found in other entities such as viruses.

- : the dogma is not something that is meaningfull to readers as a first sight on the topic. It should be in the body of the article itself
I agree. It belongs here no more than "molecule of heredity" does. The term "dogma" is misleading anyway. When Crick first formulated the idea back in the late 50s, he meant "dogma" as meaning "with no reasonable evidence". Luckily, most people read it as meaning "doctrine" instead. If, bensaccount, you think that it is important to introduce the central dogma in the preamble, then a third paragraph following this is probably the best place to do it.Stewart Adcock
If you don't want the central dogma in the definition I wont argue but you should not include ANY functions of DNA to be consistant. Bensaccount
- : The first sentence mentions cells but not viruses, and is therefore misleading. The first sentence should not be a half-truth.
- : What does it mean to say that something "encodes the structure and function" of something else? It sounds more like metaphysics than science. The use of the word "function" here is particularly problematic, especially in a preamble.
I Disagree function and stucture are very simple words for association and arent metaphysical. Bensaccount 18:40, 17 Mar 2004 (UTC)
technically, it does not encode the structure and functions of a cell; it encodes the structure of proteins for enzymes that are vital to the structure and function of cells and organs. I think this is a very important and too often misunderstood/oversimplified distinction that gives people a misleading view of how inherited traits work. Slrubenstein
- : The phrase "central dogma" introduces too many complexities. To someone who does not already know a lot about DNA, it conveys no specific information, and is more likely to convey vague ideas about religious dogma, or fallacious claims to absolute truth. (The primary meaning of dogma is a "doctrine or a corpus of doctrines relating to matters such as morality and faith, set forth in an authoritative manner by a church." The secondary meaning has to do with "absolute truth".) The sequence DNA->RNA->protein is important but check out the article Central dogma.


Unrelated comments moved to archive 8

Option 4A

Deoxyribonucleic acid (DNA or deoxynucleic acid) is a nucleic acid that carries genetic "instructions" which play a significant role during the biological development of all cellular forms of life, and many viruses; it is, thus, sometimes said to metaphorically be the "genetic code of life". DNA is also referred to as the "molecule of heredity" as it is inherited and used to propagate traits -- during reproduction, it is replicated and transmitted to offspring. This macromolecule encodes the structure and functions of cells; it is the first component of the central dogma of molecular biology.

- :Genetic instruction again
- :Developmental biology again
- :"genetic code of life" is a metaphor for what? (unclear, see above)
- :molecule of heredity again
- :heredity and propagation of traits involves meiosis, genetics (mendels laws etc), the expression of traits (the central dogma) and so much more. DNA is just a nucleic acid.
- :structure and function again

Option 5A (combines pros of above without cons)
Deoxyribonucleic acid (DNA) is a nucleic acid. It encodes the structure and functions of an organism. DNA can be found in all cells and many viruses.

- :structure and function again. Technically, it does not encode the structure and functions of a cell; it encodes the structure of proteins for enzymes that are vital to the structure and function of cells and organs. I think this is a very important and too often misunderstood/oversimplified distinction that gives people a misleading view of how inherited traits work. Slrubenstein
[P0M:] I agree. What seems to be lacking is an explanation of how cells differentiate. P0M 02:12, 24 Mar 2004 (UTC)

Option 6A (Slrubenstein)
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 these copied portions play a crucial role in the propogation of traits from one generation to the next.

Second paragraph

(Description?)


Option0B (This is the "near-consensus version of the second paragraph)
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 is found in the chromosomes, which are located in the cell nucleus. The energy generating organelles known as chloroplasts and mitochondria also carry DNA, as do many viruses.


- : This paragraph is an attempt to dichotomize prokaryotes and eukaryotes. It should be put into the subheadings. Bensaccount 18:01, 10 Mar 2004 (UTC)
I don't believe that this paragraph is making such an attempt. It is stating the cellular locations of the DNA which is, of course, distinct accoss these cell types. Stewart Adcock 22:40, 10 Mar 2004 (UTC)
Well then it should go into the Location subheading. Bensaccount 22:33, 13 Mar 2004 (UTC)
[Peak to Bensaccount:] As you yourself pointed out, a preamble is supposed to "define and describe". This paragraph provides a brief but comprehensive description of where DNA can be found in living things, and implicitly makes two important points: it is found everywhere except in some viruses; and it is not just in chromosomes. This paragraph complements the first one, so that together, they provide a roadmap for the remainder of the article. Peak 06:44, 20 Mar 2004 (UTC)

Personal attacks moved to archive 8


I dont think we need a second paragraph yet (see wikipedia: define and describe. Bensaccount 18:32, 18 Mar 2004 (UTC)

The proposed second paragraph belongs under the location heading. Bensaccount 18:32, 18 Mar 2004 (UTC)

[Peak:]Many people believe that the preamble should mention chromosomes. Since not all DNA is in chromosomes, and since not everything in a chromosome is DNA, some people felt that the connection between DNA and chromosomes could be left to a second paragraph within the preamble. This is not to say that there shouldn't be a section on "Location". That depends on how much we want to squeeze into the preamble. Peak 04:36, 18 Mar 2004 (UTC)

Personal attacks moved to archive 8


propogation of traits

I know people have been doing a great job, but we still need to do something about "because they propagate their traits by doing so." It is inaccurate in part because DNA doesn't exactly "do" things, and because the contribution of DNA to the propogation of traits, however significant, is not total; the propogation of traits involves other things. Slrubenstein

I am not sure, but think the first two paragraphs may be frozen. So I have reverted my own change to the first paragraph. But I hope people will discuss this issue (which I brought up about ten days ago) so we can resolve it, Slrubenstein

You won't see any discussion here unless you join me in demanding that the mediation committee do something. Lirath Q. Pynnor

I din't think I have ever demanded anything, as a contributor to Wikipidia, and this makes me uncomfortable. Are you saying that no one will discuss my ideas because they don't value my ideas? Well, I'm not sure that is true (but I don't mean to sound egotistical), but really, if no one else here thinks my point is valid, that's that. Slrubenstein

We dont need a mediation comittee. We are doing fine. Bensaccount 22:05, 17 Mar 2004 (UTC)

Bensaccount is right. You are doing fine Lir. Please make new propositions, tweak already existing one, and just generally give your opinion. Given the complexity of the issue (multiplicity of contencious points, number of options...), it is probably much wiser to take of the whole issue here, on this talk page.
Please Slru, do not feel like your ideas are no valid just because Lir ask for mediation. Anyway, a mediator does not take side, nor give more value to one option than to another.
Lir, we are currently discussing together to see who could take care of your requests, and I think we are on the way to have specifically someone to discuss with you. Meanwhile, you are all doing fine here.
And Lir, thanks with regards to Erik matter :-) FirmLittleFluffyThing 18:38, 18 Mar 2004 (UTC)


CURRENT PROPOSITIONS (POINT FORM)

These are the current propositions cut up into stand alone points. The second paragraph has not been included as of yet.

The points have been organized according to topic. Bensaccount 19:52, 19 Mar 2004 (UTC)

First paragraph

(The first paragraph is a definition (simple association).)

  • DNA is a nucleic acid.
  • DNA is a macromolecule.
  • DNA is the primary chemical component of chromosomes.
  • DNA is the material of which genes are made.
  • DNA can be found in all cellular forms of life and many viruses.
  • DNA can be found in cells and viruses.
  • DNA can be found in cells and also in other entities such as viruses.
  • DNA can be found in all cells and many viruses.
  • DNA carries genetic instructions for biological development.
  • DNA encodes the structure and functions of a cell.
  • DNA carries genetic instructions which play a significant role during biological development.
  • DNA encodes the structure and functions of an organism.
  • DNA cointains biological information which is heritable, hence the common phrase molecule of heredity.
  • DNA is sometimes referred to as the molecule of heredity as it is inherited and used to propagate traits.
  • DNA is also referred to as the molecule of heredity, as it is inherited and used to propagate traits.
  • DNA is sometimes called the "molecule of heredity," because parents transmit copied portions of their own DNA to offspring during reproduction, and because these copied portions play a crucial role in the propogation of traits from one generation to the next.
  • During reproduction, DNA is replicated and transmitted to offspring.
  • DNA is, sometimes said to metaphorically be the genetic code of life.

Article location

Moved to Talk:DNA/vote

About squares and circles...

this may be useful to the current decision...or not...and may be useful to next ones...so will be used later on as well


A square is not a circle because more people think it is a circle. A square is still a square. DO NOT ARGUE THIS POINT!. (It will make me very angry). Bensaccount 01:05, 19 Mar 2004 (UTC) (see above)

Actually, if you find that most people are telling you that your idea of a "square" is actually what they all refer to as a "circle" -- chances are, they are right and you are wrong. Lirath Q. Pynnor

Are you trying to tell me that a square is a circle? There is NO way that a square can be a circle. Welcome to reality. Bensaccount 03:22, 19 Mar 2004 (UTC)

[] ← This is a circle. (ask a four year old if you are unsure)

[P0M:] I think maybe Lir is trying to say something slightly different. If I say that a person is singing off-key, and dozens of people says that the person is singing "on key" but it's not "on key" to me because I insist on equal temperament and not a Handy Blues tuning, then who is right and who is wrong? "Circles" and "squares" are not very good examples because they are abstractions and do not even exist in the real world. (Only approximations can be ""proven"" to exist.)

[P0M:} "Deoxyribonucleic acid" and "deoxynucleic acid" are more like "aluminium" and "aluminum" than they are like are "circle" and "square." The latter are really not very good examples to use to disprove Lir's original point. I hope that not enough people use "Deoxynucleic acid" to make it as popular as "aluminium," but I think it could happen. (After all, I heard a radio announcer say, "I go hospital every day," just this afternoon. Languages change and people are lazy.) That being said, it would be better to use the term that Crick and Watson preferred and avoid the use of the "mistaken" term regardless of whether they used it intentionally at times, whether it was a lazy editor's fault that a misspelling gained currency, or whether it was a typographical error. (Leaving out four consecutive letters would be some typo.) P0M

For the nth time, I am not advocating that we use deoxynucleic acid -- I am merely advocating that since the term is used, it deserves mention in this article. Lirath Q. Pynnor

{P0M:] I think it would be useful to have an explanation someplace, but not in the first part of the article, of where this term came from. From everything people are telling me it seems to be a "mistake" -- but it is a mistake that Crick and Watson appear to have made themselves at times. That's interesting.
Whats most interesting is that its your POV that its a mistake. There are people who intentionally use deoxynucleic acid. Lirath Q. Pynnor
Actually, it's not my point of view. It is the opinion or the knowledge of the chemists that I have asked about it, and the opinion of some of the people commenting on this talk page who have competency in chemistry. I suppose that I'll have to dig out the 1953 (?) Crick and Watson article and see whether examination of that article will explain what happened. That way I'll at least have an informed opinion about it. P0M 05:33, 20 Mar 2004 (UTC)

Current state of affairs

There was a reversion by Peak, and resulting discussion, Discussion moved to archive 5.

There was another discussion about the reversion by peak and the basic premise that people should not change something that is disputed without giving an irrefuted reason first. Moved to archive 5

The business to be undertaken is to comment on the proposed intro paragraphs. After a paragraph emerges that everyone agrees upon (with no negative comments only good comments) it will be posted. Bensaccount 23:35, 16 Mar 2004 (UTC)

The section above the current proposals (10/03) is about the 2/3 majority version. This version has had comments made on it and the points that were resolved are not and should not be listed in the discussion of the current proposals. Bensaccount 22:07, 17 Mar 2004 (UTC)

Who can explain the numbering system for the current propositions? Bensaccount 22:12, 17 Mar 2004 (UTC)

Option 0 is the old-consensus version. Next have been added while discussions where going on. Likely, some are now redundants or no more appropriate. Please leave them in place to insure everyone agrees on that, but strike them to make obvious they won't be part of the final choices. This clean up will be most welcome.

The versions have been point formed. The redundant points should be removed. The unimportant points should be highlighted. The remaining points should be fit together. Bensaccount 22:41, 17 Mar 2004 (UTC)

strike what is no more necessary to take care of, rather than removing preferably. Thanks. FirmLittleFluffyThing 18:41, 18 Mar 2004 (UTC)
Ok good point Bensaccount 19:25, 19 Mar 2004 (UTC)

Ok the next thing to do is organize all the points so the same ones are together. (I am doing that today) Bensaccount 19:25, 19 Mar 2004 (UTC)

Now that the points are organized by topic, the next thing to do is to assign a number to each topic and rate them by importance. This is the tough part. If people have different orders in mind then they would have to list all the orders of importance. If a resolution cant be reached the worst that can happen is that every topic is included. This is the wikipedia way - voting is not necessary. Bensaccount 20:02, 19 Mar 2004 (UTC)

History section

In their original publication, Watson and Crick gave a special thanks to Dr. Jerry Donohue. In his book The Double Helix, Watson explains one very critical contribution that Donohue made just before the structure was solved. Watson says that their original molecular models were wrong, and could not pair. When Donohue saw them, he told Watson that the models were wrong and how to correct them. Watson took this advice and had the models remade. Once Watson had the correct models in hand, the pairing solution was obvious. There is considerable drama in the book about this event. It would be nice to record this critical step in the history of the solution with a sentence or two. There is a certain irony in the fact that Donohue's advice was drawn from his experience in Pauling's lab, which he had recently left to come to Cambridge. There is a kind of easy chemical reconfiguration called tautomerization that occurs in the nucleotide bases. The textbook configuration at the time the original models were made showed the bases as what we now accept as the rare tautomers. The original models were made from these pictures. The Pauling group had this critical insight into the predominant chemical form of the bases from their work in x-ray diffraction, but this correction was not yet widely known. When you get into the details, there is a very wiki-like flavor to this discovery. AJim 22:40, 16 Mar 2004 (UTC)

propagation of traits request moved to the section for things that should be included in the intro.


Debate about ____ (insert topic here)

So anyone have any thoughts on how to resolve this endless debate? Lirath Q. Pynnor


  • Somebody should set himself/herself up as czar and start issuing commandmants.
  • The Czar should put a "stop" on oposing positions by saying things like:
"I hope nobody wants to argue about this."
and
"DO NOT ARGUE THIS POINT!. (It will make me very angry!)
  • If the czar does not understand another contributor's point he or she should characterize the other contributor's position as "B.S." or use some alternative fragrant expression.
  • If the critique is cogent to the czar, but not easy to answer, she or he should look for something else in the posting that can be ridiculed and attack that instead of answering the real point.
  • If somebody gets the czar a good one, he or she ought to quickly archive that part of the discussion.
  • In a process of Darwinian "Homo homine lupus," the nastiest survive. To shorten the process one must find the One with the true nastiness gene.

JimJam

moved to /Vote (it may be a reference ?)

Nomination

[Peak:] In response to Lir's question above:

So anyone have any thoughts on how to resolve this endless debate?

Yes! Let's nominate someone to install a version of his or her own choosing. All the people who participate in the nomination process would agree beforehand to respect and to defend the choice of the nominee until such time as there is a vote on this talk page that indicates a preference for a different version, provided it is supported by more individuals than voted for the nominee. Peak 06:24, 19 Mar 2004 (UTC)

Here is a list of candidates. Please only vote for ONE candidate.

  • Stewart Adcock
Peak
P0M
  • This is a wiki -- not a "vote for who gets to write the article" website.
Lirath Q. Pynnor
[Peak:] Yes, this is a wiki, but that doesn't mean people cannot work together to come up with some text that is mutually agreeable to them and which they are prepared to defend. My proposal has nothing to do with "voting for who gets to write the article"; instead, it is attempting to address the issues which have driven 168 and others from Wikipedia.Peak 00:32, 20 Mar 2004 (UTC)
I agree Slrubenstein
Ditto. In three days, I suggest the various propositions are listed and voted upon. Are you all ready :-) ? ant
[Peak to Ant]: It looks like there will be many variations. How do you propose the "vote" will be conducted? Will it be based on one-person-one-vote, some kind of preferential scheme, or approval voting? How will ties be dealt with? Will the vote be advertised elsewhere? Will people be able to change their votes before the voting period ends? Will new proposals be allowed after voting has started? Peak 00:17, 20 Mar 2004 (UTC)
What if I disagree with the vote? Im pretty sure that there are enough unfriendly people here that my proposals will be voted against because of me, and not because of their quality. Will I still be bound by the vote? Is that the way things work on the wiki? How many times have I "won" a vote only to be told this isn't a democracy -- as I said before, if you want to try voting -- lets try discussing and then voting one sentence at a time. Lirath Q. Pynnor

I would happily and unilaterally compose a preamble for this article. However, I'm not convinced that action would really follow the spirit of a wiki. I suggest that we first give Ant's proposal of listing and voting on all the propositions a try. If that fails to resolve this inane debate, then I have someone in mind as a nominee for writing the preamble. Stewart Adcock 21:49, 19 Mar 2004 (UTC)

This is not the section for the current state of affairs (This section is called "nomination"). If you think that you want to discuss the current state of affairs, we are waiting. Bensaccount 20:07, 19 Mar 2004 (UTC)

I think we should try voting on what the first sentence should be, rather than trying to encompass multiple paragraphs at once. It would be easier to discuss things if we focused our discussion a little more. Lirath Q. Pynnor

This talk page

Can someone explain to me when and how people decided to organize talk pages topically? I am used to comments on the talk page being in chronological order. I find that much easier to follow; all I have to do is go to the bottom of the page to see what people are talking about most recently. Slrubenstein

[Peak:] There are many threads, and so many sections. You might consider using the Page history and diff facilities. Peak 03:40, 20 Mar 2004 (UTC)

Thanks, good idea Slrubenstein

No more need for organization? So be it. Bensaccount 01:03, 20 Mar 2004 (UTC)
Based on my experience, it is generally better to avoid attempting to reorganize other people's contributions on Talk pages. Apart from feathers getting ruffled needlessly, it makes it difficult to see "what's new". Peak 03:40, 20 Mar 2004 (UTC)

Yes, this is my experience too, Slrubenstein


Voting

moved to Talk:DNA/vote

As for the actual work to be done...

There is already a general consensus that the first sentence should be one of the following:

  1. DNA is a nucleic acid.
  2. DNA is a macromolecule.
  3. DNA is the primary chemical component of chromosomes.
  4. DNA is the material of which genes are made.

My order of preference is: 1>2>4>3 Mar 2004 (UTC) Is there any disagreement on this?Bensaccount 17:30, 20

[P0M:] I would agree only with choice 1 (with link to nucleic acid) If I had to choose among the others my sequence would be 1, 4, 2, 3. Note that what follows each of these choices could spoil the utility of any of them.

Not if every point is stand alone. Bensaccount 22:13, 20 Mar 2004 (UTC)

I think the first sentence should be, "Deoxyribonucleic acid (DNA or deoxynucleic acid) is a nucleic acid that carries genetic "instructions" which play a significant role during the biological development of all cellular forms of life, and many viruses; it is, thus, sometimes said to metaphorically be the "genetic code of life"." -- thus, in one sentence, we sum up the basic general idea of what DNA is. Lirath Q. Pynnor

This is a run on sentence. Thus the next argument is about grammer. Bensaccount 00:38, 21 Mar 2004 (UTC)

Peak has said that the near consensus version should be posted until a new version is arrived at. (He also seems very confused about the process taking place here). I agree that the near consensus version should be posted, and would like to bring to the attention of the people on this page the reason why this whole process is taking place. The reason is that people were reverting controversial edits without reaching an agreement on the talk page.

[P0M:] I disagree, but I won't SHOUT (much). The problem has always been that people have made controversial changes without reaching an agreement on the talk page. Making a change where nobody has much ego invested in the current text will frequently be accepted by everybody as an improvement. Making an insensitive change the immediate wake of a reversion war reopens the war. Reverting a controversial edit is such a situation is a tit-for-tat response, and reverting the reversion is a tat-for-tit. The way around this problem is to be sensitive in editing, to secure agreement with proposed changes before those changes are made in the article. For one thing, doing so is much kinder to the reader who comes back for a second look at an article 'e has been studying.

People who revert without giving a reason are the problem here. During my time here there has only been one such case (Peak) although I understand before I came there were reversions made by Lir and 168.

[Peak:] If whoever wrote the above paragraph is referring to my reversion of 22:38, 14 Mar 2004, please note that I most emphatically did give a full explanation in the edit Summary. It was: "Revert to last version by Maveric149 as per Anthere's directions not to change preamble without agreement on Talk page". That was the precise reason, so if this is the episode being referred to, I would appreciate a retraction of the erroneous remark. Peak 05:51, 21 Mar 2004 (UTC)
[P0M:] People who change text without giving a reason and without securing agreement to the change are a source of turbulence. To do so is within the rules in this rather uncivilized community. It would be useful to develop mechanisms for self-government within the intentional community formed by people interested in actually making improvements in this article.

I have said this with slightly different wording time and again:

If you have an argument over an edit after an edit has been made, that edit stays frozen (free from reversion) until the argument has been resolved and an unrefuted version has been decided upon.

[P0M:] Are you aware how the above two paragraphs sound to other people?

Reversion is only justified if someone makes an edit of a disputed point and does not give a reason. If a reason is given and undisputed it should not be reverted.

[P0M] I have seen cases that I regard as a user making wholesale changes not supported by legitimate reasons. Are such changes to stand while a long and fruitless process of argument over the supposed reasons for change ensues? I think not. P0M 04:08, 21 Mar 2004 (UTC)

I hope this clears things up. Bensaccount 00:38, 21 Mar 2004 (UTC)

You have seen cases where changes for "illigitimate reasons" have occurred. You revert these changes before disputing them.

The other user makes changes for what he sees as "legitimate reasons". He sees his changes reverted for no reason. He decides to do the same as you and reverts back to his version.

Now you have an edit war.

Now try it my way:

I have seen cases where changes for "illigitimate reasons" have occurred. I leave these changes and discuss them on the talk page.

The other user makes changes for what he sees as "legitimate reasons". He does the same as me and discusses the reasons for his change on the talk page.

Now you have a discussion.

Your choice. Bensaccount 05:04, 21 Mar 2004 (UTC)

[P0M:] It is interesting to see how you have personalized your response. I once reverted a page when someone deleted 33 lines of text (here and there) and replaced them with material more in line with his/her own point of view. That change occurred in the wake of a rather intense edit-and-revert war. I've reverted a few clear cases of vandalism (e.g., if somebody replaced a paragraph on careful culling of wild herds with a diatribe on people who love to club baby seals to death, I probably would rever that). But in general I prefer to hash things out on the talk page first, regardless of whether I think the present text is flat-out wrong or just not as clear as it might be. In the one case where I did cut out something that I judged to be groundless I later regretted the hastiness of my action.

[P0M:] You seem to want to privilege the half of the cycle that edits an existing text. I might visit the article on trans-uranium elements and have a go at editing something based on my study of aetherism. I have an entire book on aetherism that I could quote to support my changes. I have an idea I could keep that article in chaos for a good long time.

[P0M:] I do not recommend the approach that reverts a well-intentioned edit with a summary like, "You <bleep>. This article was perfect before you mucked it up." Suppose that a group of people have had a reasoned discussion on the difference between carrier pigeons (an ornamental variety that now can fly only rather badly) and homing pigeons (a work variety capable of making its way home over distances of hundreds of miles), and have noted that carrier pigeons may once, early in the history of the breed, have carried messages, and have included that information in their text. I, being ignorant of anything other than what it says in the encyclopedia I bought at Safeway, correct the page to get rid of all references to "homing pigeons". Do you seriously maintain that my edit should be given higher privilege than that of the original editors of that page (one of whom may be the reigning authority on pigeon breeds, for all I know)? They are supposed to try to argue me out of my ignorance while the article makes a laughingstock out of all pretensions to accuracy?

[P0M:] I grew up thinking that etiquette was a conventional system of stupid rules regarding which finger to extend while drinking tea. One of my teachers gently demonstrated what could happen should one eat from the point of one's knife. I now regard etiquette as a systematic way of avoiding unnecessary conflicts and their ensuing turbulence.

[P0M:] A change is a change. P0M 06:09, 21 Mar 2004 (UTC)

[P0M:] I note that Bensaccount's first edit materially changed the first two paragraphs, and wiped out the words that had followed them:

 < -- Please DO NOT edit the first two paragraphs, above. These paragraphs   
caused significant debate. Instead,
suggest any putative changes on the talk page. -->
                                                                          
<--THIS PART OF THE ARTICLE IS OPEN FOR EDITION-->

P0M 06:39, 21 Mar 2004 (UTC)

Duplications

WARNING: Anthere's edit of 15:40, 20 Mar 2004 inadvertently messed up page (duplications). What is to be done? Peak 07:02, 21 Mar 2004 (UTC)

Hell if I know, this page is a mess. Lirath Q. Pynnor


arggggghh. I try to see what I can do FirmLittleFluffyThing 15:33, 21 Mar 2004 (UTC)
It seems to be o.k. now. Thanks, Anthere. P0M 16:57, 21 Mar 2004 (UTC)

When I made my single edit, the section on protection clearly said that edits were allowed. Also, nobody was disputing my edit.

You noticed correctly that I personalized my argument above, POM. As the person who makes the change for "legitimate reasons", you imply that I am ignorant, arrogant, and may be using a safeway encyclopedia.

I may be ignorant, but I am not arrogant. It seems to me that I am the only one here who admits to being wrong. I have dropped more than half my points. The best I have gotten with all the points I have made is: "Please note that I am not saying that there is nothing of value in your proposal. Rather, I am just saying that the version that was hammered out by several people with all kinds of expertise is significantly better." Bensaccount 16:18, 21 Mar 2004 (UTC)

I am leaving this messy discussion (I am too ignorant to contribute). I hope you get around to discussing the actual content on this page eventually. (Voting is not a discussion). Bensaccount 16:36, 21 Mar 2004 (UTC)

I regret your departure, and hope you reconsider.

I would like to say that you and Peak are in disagreement because of my being unclear in something I said. So, it is my fault, not yours. During one week, the edition of the preambule was not authorized. Then it was open, but I just said that it would be best to discuss it before. Peak interpretated it as "no change without first agreement on the talk page" and you, as a new person, had a healthy behavior which consisted in making a change and discussing it later on the talk page. I see that my being unclear was responsible for this misunderstanding between the two of you. I regret this. This happened because whether the preambule could be edited or not was not clear to anyone.
So, now that this is set, I would appreciate that you both resume working together on the actual issue, rather than on this technical point. Peak has indicated that he wished discussion before than modification, and Bensaccount did not try to change the preambule again. So, this issue should be over now. I think you are all knowledgeable on the matter, and that it would be best to focus on the article itself. I hope you all see that. Thanks. FirmLittleFluffyThing

Summary

I'll try to make a little summary this evening, regarding the various options. Basically, we have

  • Anarchy : do nothing, everyone is welcome to boldly edit
  • Nomination : vote for one author, and this author decides the proper version
  • Vote : suggestion of a collection of options and vote on them
  • Discussion : wait for consensus to arise.

We might as well discuss the various editing style possible on this article, and perhaps what is the goal in terms of audience. FirmLittleFluffyThing 12:54, 23 Mar 2004 (UTC)

There is apparently disagreement on what the first sentence should be, so we should probably start there. Lirath Q. Pynnor

It is my opinion that the only way we will achieve anything is if the near-consensus version from a couple of weeks ago is inserted in the article -- and then we can work on iteratively improving it, one point at a time. The goal in terms of audience is the same as for every wikipedia article, namely the set of all wikipedia users. Thus the article needs to start off using general, basic, but concise, terms which may be expanded in the comprehensive article that follows... Stewart Adcock 18:35, 23 Mar 2004 (UTC)

After more than 2 years on Wikipedia, I think that all articles do not aim for the same audience. And not all are written along the same editing style. Some of the one I wrote are more clearly designed for students with a certain level of education on that specific topic, others, more on the political side, are treated news-type and my audience was clearly largely young to middle age american, while others had a very focused audience :-) I also support for many topics a first mother level article, with limited jargon, very comprehensive, leading to more in-depth specialised article. The public I aimed at is not the same between the mother article and the children ones. While I would agree that the DNA article requires to start with basic and general, to expand further in the article, I do not believe all articles aim at the same audience wikipedia wide :-) ant
[Peak:] I agree wholeheartedly with Stewart. What is the point of having another vote if the previous one is totally disregarded? Peak 00:07, 24 Mar 2004 (UTC)
First because some users are not satisfied with the outcome of the first vote. Second because we need to see what to do in terms of inforcement, now, and for the years to come :-)
[Peak:] In every vote that is not unanimous, there will almost certainly be someone who is "not satisfied", so your argument seems to favor a tyranny of the minority. If there were valid "procedural issues" with the old vote (and not even Lir complained about procedural issues), then there should be a new vote with just two candidates: the current (i.e. very old) version, and the "near-consensus" version.
This appears fair to me (we already discussed this I think). But before deciding between a new and the old consensus, I think you all need to decide on what the new version would be :-). All I say is that even if the old version was voted for, that version is far from bringing satisfaction from all. It may bring satisfaction to you Peak, but this is not general. I do not say either that full satisfaction of all has chance to occur, but right now, from private discussion, I see that the first-version is not so widely approved. FirmLittleFluffyThing
[Peak to Anthere:] You have misunderstood the point, perhaps because you have confused the terminology or the sequence of events:
  1. The current version (with the word "primary" in the first sentence) is the "old" version.
  2. The "near-consensus version" replaced the "old" version for a short period of time until you effectively froze the page using the "old" version, partly because you (mistakenly) believed that the "old" version was factually correct.
It was my understanding that you would restore the "near-consensus" version if 168... did not return. Apart from the relative merits of the two versions, there are also issues of principle. Many people have recognized this publicly, and if anyone besides yourself believes that the "old" version should still be posted, it would be helpful if they could explain their reasons on this talk page so they can be addressed. Peak 21:32, 24 Mar 2004 (UTC)

Peak, just put the version you feel like putting. I do not think I can help people who actively resist being helped, especially when some on purpose constantly undermine the attempt, and try to negate the ability of the mediator to think properly or just to understand things. My english may not be perfect, I know the topic quite well, and I know how to recognise manipulation. For the record, yes, I understand perfectly that the current version is not the one voted some time ago, and yes, I put it by mistake following in this a mistake commited by another editor before me, and yes again, I left it on purpose.
Help from others is a gift that must be accepted, otherwise it is not a gift anymore, it is force feeding. I do not feel I want to do force feeding. So, I really wish you all my best on this article, I hope you all find *alone* a solution, I hope you do not bite newcomers. Peace User:Anthere.

I do not understand your second point (about enforcement). On the contrary, your intervention against reasoned community decision-making raises a host of issues about justice and therefore about the possibility of enforcement.Peak 06:28, 24 Mar 2004 (UTC)
As for enforcement, that is simple. The issue is not so much approval by all of you. I expect you will all approve the outcome. If not, the outcome will be protected. What I fear more is that this outcome finds itself "protected" for ever, and defended against winds and storms. And I also fear that any new comer, not aware of the background, coming innocently and editing this preambule, will be treated the same way that a user recently was. Protection by a group of users is not wiki. But we also have to protect consensus. This must be adressed.
let's take satisfying step one by one :-) FirmLittleFluffyThing 18:49, 23 Mar 2004 (UTC)


I do not believe discussion alone will get us anywhere.

So, I suggest that we begin by the easiest point, so that we can clear up some of this page content (which is really messy). The first point to decide upon is the location of the article (chance is that agreement may be reached on this). There are already 2 or 3 paragraphs on the matter, so I guess enough ink has flowed under bridges on the topic.

The options and vote are at /vote.

Next points on contention will be whether Deoxynucleic acid is included or not, and where AND the propagation points of Slru.

I hope that by picking up one after the other, some perhaps with discussion only, others with vote, we'll find way for happiness.

If anyone sees another option to add to the 4 previous ones, please do. Otherwise, vote will start in 24 hours :-) FirmLittleFluffyThing 18:49, 23 Mar 2004 (UTC)

Please /vote :-)

[P0M:] I have a little information to add to the "location" issue. I went back to the 1953 Nature issue that is cited (if you use Google you will find it) as the place where "Deoxynucleic Acid" is used. The fact is, however, that the title is "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid." In the same issue, immediately following, are two related articles, "Molecular Structure of Deoxypentose Acids" (by Stokes and Wilson), and Molecular Configuration in Sodium Thymonucleate" (by Franklin and Gosling). P0M 02:31, 24 Mar 2004 (UTC) [P0M:] Hold on, there appears to be another article in the same volume of Nature. I'll have to go back to check that one too. P0M 02:59, 24 Mar 2004 (UTC)

We wait for your info Pat :-) FirmLittleFluffyThing 06:00, 24 Mar 2004 (UTC)

[P0M:] YWIMC: Nature for 30 May 1953, vol. 171, p. 964 has the second article. It is entitled "Genetical (sic) Implications of the Structure of Deoxyribonucleic Acid." It's by Watson and Crick, and 'Deoxyribonucleic Acid' is what they use throughout the article. I think somebody probably mistranscribed the title into the bibliography of a well-known book, and the error propagated from there. Note that there is a change from the previous article, but "ribo" is nto dropped. P0M 18:45, 24 Mar 2004 (UTC)

Thankyou P0M. (I was far to lazy to walk to a library myself) Stewart Adcock 21:07, 24 Mar 2004 (UTC)

[P0M:] Prodded by one who shall remain nameless, I have begun attempting to practice what is called xun4 gu3 in Chinese -- varifying a text and finding where errors crept in. I have sent out a dozen messages to academics who have website that use "deoxynucleic acid". One wrote me right back and said that it was of course incorrect. Unfortunately she said it was not a transmitted trait but a mutation that had occurred during local transcription. Is there a meme that causes people to drop their ribos?

[P0M:] I got word back from the author of a second site, saying, "You are of course correct..." and indicating that the word would be changed. P0M 14:40, 26 Mar 2004 (UTC)


PLEASE VOTE

A series of votes is taking place at Talk:DNA/vote#VOTE HERE. Peak 17:31, 30 Mar 2004 (UTC)

[P0M:] When is this vote ending? P0M 04:04, 8 Apr 2004 (UTC)

Draft Beginning

[P0M:] I've said before that I haven't been pleased with any of the contending versions of the first couple of paragraphs. Here is my attempt to say what needs to be said without condescending to readers and without using technical jargon or buzz words when not needed.

(Preamble) In 1944, the physicist Erwin Schrodinger touched off the search for DNA when he wrote that human chromosomes might contain a "hereditary code-script" woven into their chemical structure that would solve the mystery of life.
DNA (deoxyribonucleic acid) is a chain built of four kinds of bases (adenine, thymine, guanine, and cytosine arranged in any order) that are linked by intervening phosphates. A gene is a particular segment of a longer chain of DNA, such as may be found in one or another region of a chromosome. Each gene can serve as a template for the production of a complementary chain of RNA that acts in turn as a coded communication to a ribosome to synthesize a specific amino acid or to assemble amino acids into a specific protein. The proteins thus formed can, in turn, be chemically active in the body, and can also be used as the structural components of the body. The structure of the body of a living organism is an expression of the structure of the chromosomes. When asexual reproduction occurs, the entire choromosomal structure is duplicated in the new organism. When sexual reproduction occurs, each parent donates half the genetic information contained in its chromosomes.
Because of the characteristic three-dimensional shape of the base plus phosphate modules from which DNA is formed, a long series of these modules forms into a helix. In chromosomes, each helix so formed is matched with a complementary helix forming the renowned double helix. Like four bricks each of a different size that can fit exactly into a wooden box, adenine must be matched with thymine, and guanine must be matched with cytosine. Any other arrangement of pairs (such as adenine and cytosine) would not fit properly. As a result, there is a kind of automatic self-checking function built into the double helix. If a mistake occurs in the transcription (i.e., reproduction) of one helical strand, then that strand will not fit together properly with its mirror image strand. The base excision repair enzyme, MED1, operates during cell reproduction to identify mis-matched DNA bases. When a mismatch is located, MED1 first tries to repair the mismatch. If the repair attempt fails, then the cell is killed by apoptosis. One consequence of this fact is that DNA viruses mutate relatively slowly, whereas RNA viruses (which do not have the double stranded structure) can mutate very rapidly.

2 days with no comment.

Its also a nucleic acid. Lirath Q. Pynnor
{P0M:] Good point. I've put in a link. P0M 07:07, 7 Apr 2004 (UTC)
[Peak to P0M:] These paragraphs could form the basis of a new ==Introduction== or ==Overview==, but the article needs a concise and (perhaps very) short preamble. It would be easier to comment on your proposal if it was presented with a preamble. There are some technical issues as well, e.g.
  • the second paragraph says that a single strand of DNA forms into a helix, but the topic of ssDNA is largely irrelevant and certainly far too complex for an introduction. You'd have to get into the topic of Single-Stranded DNA Binding proteins.
  • what is meant by "successful"? Peak 10:25, 7 Apr 2004 (UTC)

It is sometimes referred to as the "genetic code of life" Lirath Q. Pynnor

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