Dear 168...: I gather that we have both been frustrated by Lir's no-doubt well-intentioned attempts to improve various articles related to biological topics. I was trying just now to fix the DNA article, but you reverted ("ibid.") in a way that also undid the changes I had incorporated. I agree that the changes that I'd made did not address all the problems of Lir's creation, but my plan had been to fix things incrementally (section by section). In short, I'd like to work with you on improving the article, but at present I'm not sure whether your reversion was specifically intended to "undo Lir's damage as quickly as possible" or whether you also had some reservations about the specific changes I'd made. Peak 09:12, 4 Jan 2004 (UTC)
I was intending to do the former. Sorry for squelching your additions and not having the patience to work with them. I agree it would be good to mention where DNA is found.
168... 16:47, 4 Jan 2004 (UTC)
If it's esoteric, it's only because people are sloppy. To the people whose business is molecules, namely chemists, a linear fragment of double-helical DNA is very definitely two molecules, because the strands are connected only by H bonds, which are not "chemical" or "intramolecular" bonds. Why perpetuate vagueness and sloppiness? 168... 06:13, 6 Jan 2004 (UTC)
[Peak:] Please understand that I understand and respect what you're saying. However, after having done quite a lot of checking, it is clear that your position is by no means universally held, and appears not to be shared by many biologists. Various authorities are quite explicit that, in the words of Michael W. Davidson:
Allow me to help:
Similarly, there are many references to "the double helical structure of the DNA molecule". In particular, JDW seems to write consistently in this manner.
The reason may simply be that there are effectively two definitions of "molecule" in circulation: the detailed one that emphasizes covalent bonds, and the general one that goes like this:
Perhaps biologists tend to take the viewpoint that the double helix is a macromolecule, and that every macromolecule is (hopefully) a molecule.
Physical organic chemists distinguish between a "molecules" and "molecular entities", the latter term covering both "molecules" and other complexes. This is a perfectly valid distinction for physical organic chemists to make, and perhaps it's the one you are making, but do physical organic chemists in fact insist that the DNA double helix consists of two molecules?
In summary, it seems that whereas the criteria you are using exclude the significance of the intertwining of the DNA strands in a double helix, others would say that such intertwining does have significance for the physical and chemical properties of the double helix.
In any case, regarding the introductory parts of the DNA article, one simple solution would be to describe the DNA double helix as a "macromolecule" composed of two DNA strands. Peak 05:58, 7 Jan 2004 (UTC)
I'm impressed by your diligence and research, but I'm sticking to my guns. Watson's a crank and a nut and on top of all that a biologist, not a physical scientist. Although I realize that human language isn't consistent or logical, I try to be anyway, and I don't see how one could get two molecules--as I think everyone would regard two non-interwined DNA strands--from "one molecule"--as some people seem prepared to call a piece of double-helical DNA--without breaking a single chemical bond in that "molecule." I am familiar with the shakey terrain of "macromolecule" and in particular that which goes with "protein." I have created new articles and made the rounds of existing ones spelling out the ambiguity in that word, which no biochemistry book or paper ever spelled out for me, and which I think few are conscious of. But "protein" is used equally often to refer to single molecules, such as protein subunits and to refer to multi-subunit holoenzymes and assemblies such as hemoglobin. On the other hand, although microtubles and actin are composed of subunit proteins, I think scientists never refer to one of them as "a protein", and instead call it more often "a macromolecular assembly" or something along those lines. Meanwhile an ion channel is called a protein in some contexts and a "multimer" in others. I think these usages illustrate that neither "protein" nor "macromolecule" is used consistently. Perhaps this supports your point. Nevertheless, my sense is that this looseness is confined to biology. Since not only biologists read Wikipedia, I think it's best to use a conservative definition of molecule. But anyway, I don't think that in anyone's book it would be regarded as inaccurate to call a strand of DNA a molecule, and I think that doing so as the article does now both alerts people to the possibility of confusion and helps them along in understanding what the double helix is. 168... 06:37, 7 Jan 2004 (UTC)
That was kind of rambling. Let me just say this: The word you suggest, "macromolecule" is vague and esoteric. It's probably a worthwhile word to expose people to in this context, but unlike "molecule," I think we can't expect it to do explanatory work for us. 168... 07:18, 7 Jan 2004 (UTC)
I think that's an unfair burden of proof. How about a third party endorsement in favor of calling a DNA strand a molecule and a failure after due diligence to find a strand called "half a DNA molecule"? 168... 08:21, 7 Jan 2004 (UTC)
[Peak:] Looking a little further:
Features of the Model for B-form DNA * Two strands. * Strands are wrapped plectonemically in a right handed helix (Figure 4.10c). * Phosphates are on the outside of the molecule. * Base pairs are in the inside of the molecule stacked close to each other.
Yes, that's 'molecule'! You'll have to try again :-) Peak 08:28, 7 Jan 2004 (UTC)
It's clearly standard to call a double helix a molecule. I am just trying to show that it's accurate to call it two molecules according to a standard definition of "molecule". I take it your "Looking a little further" excerpt comes from my source 3. What that shows is that the same person uses "molecule" inconsistently. S/he calls a strand the "primary structure" of DNA and a "molecule", but as you saw s/he also calls a double helix a molecule, as is the tradition. 168... 08:38, 7 Jan 2004 (UTC)
Just to interject, this is something I think I am qualified to comment upon. A DNA strand is a single molecule. A DNA double-helix is a single complex. Although this double helix is commonly refered to as a molecule, this is a mistake; it is definitely two molecules. It is very easy to cite some eminent scientist or other who refers to the double-helix as a molecule but it is still, strictly speaking, wrong! Stewart Adcock 17:53, 7 Jan 2004 (UTC)
Another interjection here from a scientist in the field of DNA structure. To be precise, a strand is a molecule. But scientists (myself included) are sloppy with language and often refer to the double helix as a molecule. But when it really matters whether it is a single molecule or not (crystallography, mass spectrometry, annealing, single molecule experiments, chemical modification, etc.), it is the strand that is recognized as a molecule. In addition, in cases of uncertainty, I suggest consulting review papers or reference texts , such as texts on nucleic acid structure and chemistry, rather than web pages or introductory biology textbooks. Cheers. Holeung 10:09, Jan 12, 2004 (UTC)
I hope you aren't dissing Streiwieser when you refer to "introductory biology text books"! (his is an organic chemistry textbook with chapters on hybrid electronic orbitals and antibonding). I think you have a point that nucleic acid research papers are one of the best places to look for usage and the authors of these papers represent one of the groups of people who are "DNA experts" and might be invited to have the last word. But DNA extends beyond one group's research interests. I think we have to make a subjective judgment call when we decide which experts to pick to give us the right language for a general readership such as WikiP is trying to reach. My preference was to ask a physical organic chemist, and I could offer reasons for it, if you are interested. I encourage you to be more open minded about the Web as a research tool. For example, if you were to read Nucleic Acids Research online, you could save yourself a trip to the library. 168... 17:21, 12 Jan 2004 (UTC)
(spun off from Talk: DNA)
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)
Can't you imagine a conversation such as this in a molecular biology lab:
These people are talking about a gene that is made up of nucleotides, some of which are radioactive. I think they are making a standard usage of the word "gene." Could you spell out the sense or meaning of "gene" in which it is reasonable to say that a gene is "encoded" by nucleotides? 168... 18:26, 7 Jan 2004 (UTC)
I would have to imagine that because I try to avoid entering molecular biology labs at all costs. ;-) Anyway, yes I agree that one might hear such a discussion. But to be strictly correct, I believe, they should say "a mutant GFP cistron", and maybe, "so when the sequence inserts into chromosome 3 it'll be hot". My preferred definition for gene goes along the lines of, "A gene is any portion of a chromosome that exists as a unit for natural selection". So rather than having nucleotides making-up genes and genes making-up chromosomes, nucleotides make chromosomes and some (not-neccesarily contiguous) chunks of the chromosomes have the property of being genes. By my definition (actually, IIRC, it's G. Williams definition according to Richard Dawkins) it is more natural to say that the genes are encoded by the particular nucleotides in the chromosome, since as soon as it is out of its original chromosomal context (i.e. it is a string of nucleotides synthesised in a lab) then its no longer a gene! (indeed, I am told that after moving those exact nucleotides to a different location in that chromosome or another chromosome then they might no longer act as a gene (or cistron).) I've also just realised something: Note that my use of encode is somewhat different from that in "this gene encodes a protein", which might be causing some confusion. Stewart Adcock 07:55, 9 Jan 2004 (UTC) (while he awaits T6 with baited breath! ;-) )
"Gene" is famous for being hard to define, but really it should be more famous for having multiple uses and meaning different things in different contexts. It's hard to say what might be the primary sense of "gene," but one I've heard again and again in mo-bio labs applies to pieces of DNA. If by "gene" we were refering to a sequence in the abstract, I believe we wouldn't talk about cloning it. People don't seem ever to say they "typed a gene" into a computer. They seem to prefer to say they typed in "the sequence of a gene." I think that when one inserts a gene into a chromosome material is being inserted. The chromosome becomes bigger and weighs more in proportion to the amount of sequence that was inserted.
168... 17:12, 9 Jan 2004 (UTC)
Well, then probably you have agreed that it is accurate to say nucleotides 'make up' genes, in the same sense that Latinos make up a percentage of the U.S. population. You didn't seem to agree that this was fair to say before. 168... 19:15, 9 Jan 2004 (UTC)
Dear 168...: I gather that we have both been frustrated by Lir's no-doubt well-intentioned attempts to improve various articles related to biological topics. I was trying just now to fix the DNA article, but you reverted ("ibid.") in a way that also undid the changes I had incorporated. I agree that the changes that I'd made did not address all the problems of Lir's creation, but my plan had been to fix things incrementally (section by section). In short, I'd like to work with you on improving the article, but at present I'm not sure whether your reversion was specifically intended to "undo Lir's damage as quickly as possible" or whether you also had some reservations about the specific changes I'd made. Peak 09:12, 4 Jan 2004 (UTC)
I was intending to do the former. Sorry for squelching your additions and not having the patience to work with them. I agree it would be good to mention where DNA is found.
168... 16:47, 4 Jan 2004 (UTC)
If it's esoteric, it's only because people are sloppy. To the people whose business is molecules, namely chemists, a linear fragment of double-helical DNA is very definitely two molecules, because the strands are connected only by H bonds, which are not "chemical" or "intramolecular" bonds. Why perpetuate vagueness and sloppiness? 168... 06:13, 6 Jan 2004 (UTC)
[Peak:] Please understand that I understand and respect what you're saying. However, after having done quite a lot of checking, it is clear that your position is by no means universally held, and appears not to be shared by many biologists. Various authorities are quite explicit that, in the words of Michael W. Davidson:
Allow me to help:
Similarly, there are many references to "the double helical structure of the DNA molecule". In particular, JDW seems to write consistently in this manner.
The reason may simply be that there are effectively two definitions of "molecule" in circulation: the detailed one that emphasizes covalent bonds, and the general one that goes like this:
Perhaps biologists tend to take the viewpoint that the double helix is a macromolecule, and that every macromolecule is (hopefully) a molecule.
Physical organic chemists distinguish between a "molecules" and "molecular entities", the latter term covering both "molecules" and other complexes. This is a perfectly valid distinction for physical organic chemists to make, and perhaps it's the one you are making, but do physical organic chemists in fact insist that the DNA double helix consists of two molecules?
In summary, it seems that whereas the criteria you are using exclude the significance of the intertwining of the DNA strands in a double helix, others would say that such intertwining does have significance for the physical and chemical properties of the double helix.
In any case, regarding the introductory parts of the DNA article, one simple solution would be to describe the DNA double helix as a "macromolecule" composed of two DNA strands. Peak 05:58, 7 Jan 2004 (UTC)
I'm impressed by your diligence and research, but I'm sticking to my guns. Watson's a crank and a nut and on top of all that a biologist, not a physical scientist. Although I realize that human language isn't consistent or logical, I try to be anyway, and I don't see how one could get two molecules--as I think everyone would regard two non-interwined DNA strands--from "one molecule"--as some people seem prepared to call a piece of double-helical DNA--without breaking a single chemical bond in that "molecule." I am familiar with the shakey terrain of "macromolecule" and in particular that which goes with "protein." I have created new articles and made the rounds of existing ones spelling out the ambiguity in that word, which no biochemistry book or paper ever spelled out for me, and which I think few are conscious of. But "protein" is used equally often to refer to single molecules, such as protein subunits and to refer to multi-subunit holoenzymes and assemblies such as hemoglobin. On the other hand, although microtubles and actin are composed of subunit proteins, I think scientists never refer to one of them as "a protein", and instead call it more often "a macromolecular assembly" or something along those lines. Meanwhile an ion channel is called a protein in some contexts and a "multimer" in others. I think these usages illustrate that neither "protein" nor "macromolecule" is used consistently. Perhaps this supports your point. Nevertheless, my sense is that this looseness is confined to biology. Since not only biologists read Wikipedia, I think it's best to use a conservative definition of molecule. But anyway, I don't think that in anyone's book it would be regarded as inaccurate to call a strand of DNA a molecule, and I think that doing so as the article does now both alerts people to the possibility of confusion and helps them along in understanding what the double helix is. 168... 06:37, 7 Jan 2004 (UTC)
That was kind of rambling. Let me just say this: The word you suggest, "macromolecule" is vague and esoteric. It's probably a worthwhile word to expose people to in this context, but unlike "molecule," I think we can't expect it to do explanatory work for us. 168... 07:18, 7 Jan 2004 (UTC)
I think that's an unfair burden of proof. How about a third party endorsement in favor of calling a DNA strand a molecule and a failure after due diligence to find a strand called "half a DNA molecule"? 168... 08:21, 7 Jan 2004 (UTC)
[Peak:] Looking a little further:
Features of the Model for B-form DNA * Two strands. * Strands are wrapped plectonemically in a right handed helix (Figure 4.10c). * Phosphates are on the outside of the molecule. * Base pairs are in the inside of the molecule stacked close to each other.
Yes, that's 'molecule'! You'll have to try again :-) Peak 08:28, 7 Jan 2004 (UTC)
It's clearly standard to call a double helix a molecule. I am just trying to show that it's accurate to call it two molecules according to a standard definition of "molecule". I take it your "Looking a little further" excerpt comes from my source 3. What that shows is that the same person uses "molecule" inconsistently. S/he calls a strand the "primary structure" of DNA and a "molecule", but as you saw s/he also calls a double helix a molecule, as is the tradition. 168... 08:38, 7 Jan 2004 (UTC)
Just to interject, this is something I think I am qualified to comment upon. A DNA strand is a single molecule. A DNA double-helix is a single complex. Although this double helix is commonly refered to as a molecule, this is a mistake; it is definitely two molecules. It is very easy to cite some eminent scientist or other who refers to the double-helix as a molecule but it is still, strictly speaking, wrong! Stewart Adcock 17:53, 7 Jan 2004 (UTC)
Another interjection here from a scientist in the field of DNA structure. To be precise, a strand is a molecule. But scientists (myself included) are sloppy with language and often refer to the double helix as a molecule. But when it really matters whether it is a single molecule or not (crystallography, mass spectrometry, annealing, single molecule experiments, chemical modification, etc.), it is the strand that is recognized as a molecule. In addition, in cases of uncertainty, I suggest consulting review papers or reference texts , such as texts on nucleic acid structure and chemistry, rather than web pages or introductory biology textbooks. Cheers. Holeung 10:09, Jan 12, 2004 (UTC)
I hope you aren't dissing Streiwieser when you refer to "introductory biology text books"! (his is an organic chemistry textbook with chapters on hybrid electronic orbitals and antibonding). I think you have a point that nucleic acid research papers are one of the best places to look for usage and the authors of these papers represent one of the groups of people who are "DNA experts" and might be invited to have the last word. But DNA extends beyond one group's research interests. I think we have to make a subjective judgment call when we decide which experts to pick to give us the right language for a general readership such as WikiP is trying to reach. My preference was to ask a physical organic chemist, and I could offer reasons for it, if you are interested. I encourage you to be more open minded about the Web as a research tool. For example, if you were to read Nucleic Acids Research online, you could save yourself a trip to the library. 168... 17:21, 12 Jan 2004 (UTC)
(spun off from Talk: DNA)
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)
Can't you imagine a conversation such as this in a molecular biology lab:
These people are talking about a gene that is made up of nucleotides, some of which are radioactive. I think they are making a standard usage of the word "gene." Could you spell out the sense or meaning of "gene" in which it is reasonable to say that a gene is "encoded" by nucleotides? 168... 18:26, 7 Jan 2004 (UTC)
I would have to imagine that because I try to avoid entering molecular biology labs at all costs. ;-) Anyway, yes I agree that one might hear such a discussion. But to be strictly correct, I believe, they should say "a mutant GFP cistron", and maybe, "so when the sequence inserts into chromosome 3 it'll be hot". My preferred definition for gene goes along the lines of, "A gene is any portion of a chromosome that exists as a unit for natural selection". So rather than having nucleotides making-up genes and genes making-up chromosomes, nucleotides make chromosomes and some (not-neccesarily contiguous) chunks of the chromosomes have the property of being genes. By my definition (actually, IIRC, it's G. Williams definition according to Richard Dawkins) it is more natural to say that the genes are encoded by the particular nucleotides in the chromosome, since as soon as it is out of its original chromosomal context (i.e. it is a string of nucleotides synthesised in a lab) then its no longer a gene! (indeed, I am told that after moving those exact nucleotides to a different location in that chromosome or another chromosome then they might no longer act as a gene (or cistron).) I've also just realised something: Note that my use of encode is somewhat different from that in "this gene encodes a protein", which might be causing some confusion. Stewart Adcock 07:55, 9 Jan 2004 (UTC) (while he awaits T6 with baited breath! ;-) )
"Gene" is famous for being hard to define, but really it should be more famous for having multiple uses and meaning different things in different contexts. It's hard to say what might be the primary sense of "gene," but one I've heard again and again in mo-bio labs applies to pieces of DNA. If by "gene" we were refering to a sequence in the abstract, I believe we wouldn't talk about cloning it. People don't seem ever to say they "typed a gene" into a computer. They seem to prefer to say they typed in "the sequence of a gene." I think that when one inserts a gene into a chromosome material is being inserted. The chromosome becomes bigger and weighs more in proportion to the amount of sequence that was inserted.
168... 17:12, 9 Jan 2004 (UTC)
Well, then probably you have agreed that it is accurate to say nucleotides 'make up' genes, in the same sense that Latinos make up a percentage of the U.S. population. You didn't seem to agree that this was fair to say before. 168... 19:15, 9 Jan 2004 (UTC)