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State of affairs 04/29/04

The introductory passage is unnecessarily protected. Bensaccount 23:08, 29 Apr 2004 (UTC)

List of people currently interested in this page:

  1. Bensaccount 23:11, 29 Apr 2004 (UTC)
  2. P0M 01:00, 30 Apr 2004 (UTC)
  3. Stewart Adcock 01:10, 30 Apr 2004 (UTC)
  4. Peak 04:40, 8 May 2004 (UTC)

Learner's point of view

From some who is actually reading this article to learn rather than a point of interest it's not very usefull. While there is a lot of foot work the discussion of DNA is shallow. In places quite wordy and in others completely superficial and giving no new information. Wolfmankurd 13:52, 29 May 2006 (UTC)

How? This is written in a summary style, deeper subjects are covered in subarticles. Ie. how DNA is constructed, it's structure, it's translation, etc. Elle vécut heureuse à jamais (Be eudaimonic!) 17:43, 29 May 2006 (UTC)

Free editing again...

Since it would appear that the main agonists in the prior arguments have left wikipedia (or got bored with this article) I have taken the liberty to remove the HTML comments in the article warning people to not edit the first two paragraphs. I've placed the particular versions into the article which we had an earlier vote on, but these should now be considered by all as open for editting. Stewart Adcock 22:18, 7 May 2004 (UTC) (If the edit wars start again, then I'll happily slap myself around the face)

Credit due to Franklin.

For the paragraph on credit due to Franklin, see Talk:Rosalind_Franklin.

DNA for Dummies

Given the fact that DNA and genetic manipulation in general is a hot topic these days, I propose a DNA for Dummies section in this article, explaining as much as possible of the topic in plain English, for the plain mortal. I know it sounds silly for you scientist types buzzing with controversies around this article, but us plain folk don't quite get the part with "two polynucleotide strands can associate through the hydrophobic effect" for instance, which is part of the "Overview" section in this article.

Here's what I managed to learn as a layman mildly interested in the topic, just to get you started with the level of understanding you should assume:

  • DNA is made of genes, and genes alone;
  • Genes are the organism's cookbook;
  • DNA contains genes similarly to binary sequences, in the following way: you can only pair A with T and C with G, no other "atoms" are available, and no other combination works (no need to use the improper term "atom" as I did, I was just trying to convey the Greek meaning of the word for you guys to understand what I mean);
  • The order does matter: A+T is not the same with T+A, just as C+G is not the same with G+C;
  • Stupid, since there are just four possible combinations, only one element on a conventionally chosen side of the strand is enough to describe the sequence;
  • Replication is done not by some magic digital copy machine, but rather by splitting the strand in the middle via relatively trivial chemical reactions, and drowning it in a "gene soup" (yes, I know, faulty layman terms; again, this is why I write this, just to make you see the level of understanding for non-scientist types). Since each of the "atoms" can only combine with a single type of pair, each element in each half-pair will only stick to their predetermined match. This way, each half of the strand ends up as a replica of the original, mutations notwithstanding;
  • Mutations are simply chemical imperfections in this process: the chain is trimmed, split or other elements get stuck at the end of it; all other basic mutations can be described as combinations of these accidental "operations".

I'm sure that you can describe the whole process better and a lot more accurate than I did above, even in layman's terms, and that's why I didn't write that section myself, although I believe that my general grasp of the phenomenon is reasonably accurate. I think that we're trying to build an encyclopedia "by everyone, for everyone", therefore such a section shouldn't be out of place in this article.

Thank you at least for reading all the proposal! --Gutza 02:32, 3 Oct 2004 (UTC)

Well, one fears that such a section would die the "death by a thousand cuts" that the rest of the article has...nonetheless, hoping you'll have good luck with it, but perhaps I can help you with a formulation that would be less likely to mislead by over-simplification.

  • Genes are the organism's cookbook;
  • DNA is made of genes, areas that regulate genes, and areas that either have no function, or a function we don't know;
  • DNA is organized as two complementary strands, head-to-toe, with bonds between them that can be "unzipped" like a zipper, separating the strands;
  • DNA is encoded with four interchangeable "building blocks", called "bases", which can be abbreviated A, T, C, and G; each base "pairs up" with only one other base: A+T, T+A, C+G and G+C; that is, an "A" on one strand of double-stranded DNA will "mate" properly only with a "T" on the other, complementary strand;
  • The order does matter: A+T is not the same with T+A, just as C+G is not the same with G+C;
  • However, since there are just four possible combinations, naming only one base on the conventionally chosen side of the strand is enough to describe the sequence;
  • The order of the bases along the length of the DNA is what it's all about, the sequence itself is the description for genes;
  • Replication is done not by some magical copy machine, but rather by splitting (unzipping) the double strand down the middle via relatively trivial chemical reactions, and recreating the "other half" of each new single strand by drowning each half in a "soup" made of the four bases. Since each of the "bases" can only combine with one other base, the base on the old strand dictates which base will be on the new strand. This way, each split half of the strand plus the bases it collects from the soup will ideally end up as a complete replica of the original, unless a mutation occurs;
  • Mutations are simply chemical imperfections in this process: a base is accidentally skipped, inserted, or incorrectly copied, or the chain is trimmed, or added to; all other basic mutations can be described as combinations of these accidental "operations".

I'm sure this can be improved on, or made clearer. But I'd avoid saying DNA consists only of genes in any case, because it's not true.- Nunh-huh 02:52, 3 Oct 2004 (UTC)

Thank you for the clarifications!

I would really hold on to something along the lines of my "drowning in a gene soup" in the replication part, if that is reasonably accurate, and obviously with rephrasing to convey the proper idea. I think that's a very good visual representation of the "magic" and beauty of the DNA replication process -- the fact that the process is so robust that it allows for reasonably accurate replication without very controlled conditions.

Apart from that, I think your version is extremely close to what I had in mind, thank you for the adjustments! I'll wait for revisions here for a couple of more days, and then I'll insert it in the article if nobody else beats me to it. By the way, do you think the section title "DNA for Dummies" would be out of line in this article? --Gutza 12:12, 3 Oct 2004 (UTC)

Oh, I just realized that we miss the part where we explain the double-strand structure; unfortunately my terminology is so incomplete that I can't even start to explain that part without making a fool of myself. Can you please add another bullet point between the second and the third explaining this? A nucleotide is composed of three parts: 5-phosphate groups,

Thank you again! --Gutza 12:18, 3 Oct 2004 (UTC)

There are no genes in "gene soup": genes are on the DNA. The "soup" as it were includes the four bases, but no genes. Genes are ordered sequences of bases, and a soup is by its very nature unordered. - Nunh-huh 20:35, 3 Oct 2004 (UTC)

Thank you for the structure bullet point! Regarding the gene soup, this is precisely why I think this section is needed: I was unable to make the clear-cut distinction between genes and bases until you made the point above. I reordered some of the points as to make more sense, included your explanation about the genes and explained the "soup" thing at the replication bullet point. The section "DNA for Dummies" is now complete as far as I am concerned, this is exactly the level of understanding and detail I was going for.

Please make any final corrections you feel are required, and tomorrow I'll copy it in the article. Thank you for the patience, I think the result is great - never saw such a great brief and comprehensive explanation of the topic when I was trying to understand it! :-) --Gutza 07:38, 4 Oct 2004 (UTC)

I agree -- it would be more accurate to say that DNA is a long chain of "bases" (nucleotides). I like the analogy of dunking a strand in a "nucleotide soup" of all 4 kinds of bases.. --DavidCary 02:03, 16 May 2005 (UTC)

Split off the history section

I think this came up a while ago. It was proposed at one point to split off the "The discovery of DNA and the double helix" section into its own article, so that it can be expanded. It is a facinating story, and I'm wondering if we're doing it justice bunched in with the "science" content. Any objections to moving forward with that? Any suggestions for a name of the new page before we do it? I'm partial to something simple like Discovery of DNA. It's a slight misnomer, since the interesting part is the discovery of the helical structure, but a simple title like that has its benefits. -- Netoholic @ 07:03, 2004 Oct 14 (UTC)

I think that would be a good idea; go ahead and do it. I'm not so sure about the title though. Maybe something like Discovery of DNA structure? or, History of DNA research? Stewart Adcock 16:59, 14 Oct 2004 (UTC)

Don't change comment

While I see nothing wrong with the DNA in brief section, I'm afraid I do object to the HTML comment as a matter of principle. Wikipedia is all about anyone being able to change anything they want. When we intimidate people into not making changes with scary comments, it obstructs that. Perhaps better would be a brief reminder that that section is an overview and a reference to a section of the talk page. We all want to preserve content we think is good, but content can always be made better, and if someone makes a bad change and you don't catch it, someone else probably will. Deco 03:19, 12 Nov 2004 (UTC)

Just a very, very late comment by the author of that (old-gone) notification. I wrote it out of fear of the "death by a thousand cuts", as Nunh-huh put it in a previous comment on this very page (at least it was the same page at the time of this writing, might've been archived in a different place by the time you read this.) Now that someone has removed that notification, it looks like my "warning" wasn't really called for, since the "in brief" section still stands, and still matches the original goal. Therefore I salute your pro-wiki attitude, Deco, and I'm mildly ashamed that I felt the need for that warning sign, in the Wikipedia context! :-) --Gutza 21:25, 7 May 2005 (UTC)

Other natural information encodings?

Is anyone aware of any other naturally occurring examples of information being encoded and read? Is DNA known to be uniquely suitable for this task, or is it just accidental that the role of encoding information fell to DNA? -- RussAbbott

You might find a few other methods in epigenetic inheritance. Also, there are viruses whose genomes are encoded with RNA, but that might not be different enough from DNA to count for your purposes (PNA may also have once been used as a genetic matieral when life first began, but that's just hypothetical. See also Origin of life for some other discussion and possibilities). Prions appear to pass on information about their conformations without DNA being used in the process, but I suspect this might be getting near the fuzzy boundary between information transmission and something simpler like crystal growth. Bryan 08:38, 16 Nov 2004 (UTC)
I'm really looking for other examples of naturally occurring digitally encoded information that is clearly separated from the medium in which it is encoded. RNA is too much like DNA to be a good example for me. -- RussAbbott
Coding, reading, and manufacturing is very much a life process. Bees make their wax combs according to some kind of innate pattern. It is not known whether there is a pattern for combs in the DNA, or in some intermediate structure that is itself produced on the basis of what is encoded in DNA, or whether the hexagonal form may simply the the form that tightly packed cylinders of wax would take, i.e., that the hexagonal shape is not based on an internal plan at all. It is known, however, that bees can be encouraged to make larger or smaller cells by supplying them with flat wax sheets onto which have been imprinted the shapes of the bottoms of cells. If the hexagonal forms imprinted on the wax sheets are smaller/larger, then the cells constructed on them will be smaller/larger. I doubt that there could be anything else on a molecular level -- unless somebody does something in nanotechnology like that. So the only thing you might find would be an animal that carries around a sample of something (a saw, for instance) and uses that sample as a pattern to make another copy. As far as I know, it is considered remarkable for non-humans to use slightly fabricated artifacts as tools. I can't think of any animal that uses a pattern to make something. The earliest instance of the human use of a pattern that I know about appears in the Book of Poetry (Shi Jing). One poem says, "[I] take an ax to go cut an ax handle. Can the pattern [I need] be far from hand?" Humans are part of nature, but I doubt this is really the kind of thing that you want. P0M 00:38, 17 Nov 2004 (UTC)
Using a sample is not what I'm after anyway. I'm looking for information encoded and read digitally. --RussAbbott 02:29, 17 Nov 2004 (UTC)
Uh, memory (as in human memory) is stored (human brain and also elsewhere) and read. →Raul654 02:49, Nov 17, 2004 (UTC)
Information is stored somewhere, and in some form(s), and this stored information we call memory. And it may get recalled (found) and read when it is needed. But it isn't at all clear that the storage process is done by a series of "on" and "off" states (such as are represented by 1s and 0s in binary numbers), or even 3, 4, ... or some other relatively small number of discernable states. Neurons grow and change their connections during the process of learning, but the information may be stored in some kind of an analog form. (I'm not pretending that I know how that would work any more than I am sure that I know how a binary representation of an elephant would look.) Some people think that long term memories are stored away as molecular configurations, codings analogous to DNA codings.
A related problem lies in our unclear knowledge of the nature of knowledge. Asserting that the mind creates images of things in the outside world, and that the mind knows the thing by looking at the image of the thing involves us in infinite regress or else in the idea of a little man who lives in our brain and "looks at" the images our brain creates to represent the outside things. But then the question becomes: How does the little man see and understand the images? Does he have a still smaller little man...
Understanding how single cells identify things on their own scale may be helpful to understanding knowledge and storage of knowledge. I am trusting my memory, so the following account may not be very accurate, but it may be sufficient to get an important idea across: An immune cell in the blood stream may be able to "dock" with a cowpox virus and/or with a smallpox virus. Once it has docked, the immune cell becomes functionally different than when it had a "key" in its "lock." In its new state it signals the body to make antibodies that will fight either cowpox or smallpox viruses. Note that there is not an image of the cowpox virus, but a negative image a "lock" into which the virus (or a significant part of it) will fit. A sucrose molecule will dock with (be recognized by) a sweetness detector, but so will several other molecules, some of which are useful as artificial sweetners. There doesn't seem to me to be a "digital" process going on here. One of the hallmarks of digital memory is that because, e.g., a point on a CD-ROM is either burned or not burned, one can get a very clear record of something and the record will not gradually fade away as will an old color photo. Nor will the image fuzz out to nothing as an analog image will be degraded by a process of copying and recopying. By using a technique called "cyclical redundancy checking" (CRC) it is even possible to check the digital record to see whether a point has gotten burned that was not burned when the record was originally created. So digital records tend to be less smooth. (There is no way of handling a record that really ought to be 1.5. You either write a 1 or you write a 0. It's the difference between a water-color painting and a half-tone screen image where there are colored dots scattered fairly densely over an otherwise colorless page.) But digital records can potentially be preserved forever. All you need to do is make back-up copies to double-check against and periodically copy your old and decaying CDs onto fresh new CDs, and then check them against each other point by point.
How organisms go from recognizing sugar, salt, etc. in the water they are swimming in to recognizing macro-scale entities visually (or in other ways) is very unclear to me. But some parts of the recognition process appear to have been preserved. Even whales will be identified as fish until the naive observer investigates more closely. Sheep and goats may be identified as "the same kind of animal" by the untutored observer. So on those grounds I'm doubtful about memory being a digital process. Memory has to be a record of an identification or series of identifications, or so it seems to me.
If memory and learning were digital processes, then each neural connection would either be a 1 or a 0. There would be no stronger connections and no weaker connections unless the relative strengths actually reflected the number of on and off connections involved to make a kind of aggregate connection. But I don't recall every having read of anyone asserting that neural connections are either "totally there" or "totally not there."
I take it that what you are looking for is a system of recording and reading that depends on a small number of "digits" -- u, v, w, z, for instance, that are ordered into a meaningful sequence so that, let's say, uuxuxvw would mean "hot body core" or something meaningful but simple like that. P0M 09:53, 17 Nov 2004 (UTC)
Your last paragraph captures it. The immune system and other forms of key-and-lock recognition are not the same since they are more shape-based than digital. Perhaps one needs shapes to recognize each individual digit. (That's an interesting point.) But I'm looking for an example of what we would consider naturally occurring digital recording other than DNA/RNA. --RussAbbott 23:55, 17 Nov 2004 (UTC)


The basic distinction you want to make is between forms of recording that are "digital" and forms that are analog. A vinyl phonograph recording is analog. The instantanious variations of air pressure are recorded as instantanious variations of height or width in the groove wall. If you examine the record microscopically you would not see the "stairstep" effect that one gets when one blows up a digital picture (called "aliasing"). Binary digital recordings always are a kind of square wave,i.e., there is either something on the thirteenth step of the ladder or there is not. You can't put half or a third of your weight on a ladder rung in a digital system. So you always "falsify" the data to some extent. If you want to go to a finer "grain" you swap the 100 step ladder for one with 200 rungs, and represent the 13.5 you couldn't get before with 27. In other words, you always deal integer math.
How one "reads" the digital record is probably not really relevant to your basic question. One can read a CD-ROM with a microscope if you have to. Somebody with small enough "fingers" could read it like a braille record if the intervening plastic could be removed so you could get your fingers into the pits.
The machinery needed to read DNA and to fabricate amino acids on that basis is fantastic. To have a competing system of digital recording, digital reading, and actions programmed on the aforesaid operations would be tantamount to a second form of life since such a "machine" could be augmented to fabricate instances of itself. That is one of the goals of nanotechnology that has at least been talked about. If we wanted to turn an asteroid rich in some valuable ore into neat bricks of the purified metal, one way to do it would presumably be to create nanocritters that would be able to reproduce themselves and would be able to disassemble the oxide of the metal into purified metal and "slag." But we don't know how to do that kind of thing yet. We are just beginning to operate at that size level, and many researchers are looking to world of biology for models of how to do these tasks.
One of the forerunners of an early standby of computer interfacing was the punch cards that were used by weaving mills to automatically control the production of complex woven patterns. That is at least of kind of model for the sort of digital data recording you seek. The specific material representations involved don't matter much. Whether it is an IBM punch card or a player piano roll, or a series of bottles and gaps between bottles on top of a wall somewhere, the presence vs. absence relationship can be translated into many forms. So what animal, other than man, arranges things to represent information? Humans who cannot count can keep track of the number of sheep in their flock by putting one stone into a pouch for every sheep let out of the fold in the morning and then checking to see whether, if one stone is removed from the pouch for every sheep that reenters the fold at night, there are any stones left over in the pouch. If there is a stone or two left over, that may mean that the sheep herder needs to go looking for the lost sheep. Do other animals do this kind of thing? Do other primates knot cords? Do elephants dig notches into trees to represent the number of offspring they have given birth to? The closest kind of representation like that lies in the non-linguistic parts of at least some animals. It turns out that crows have better memories than humans. If I recall correctly, if 3 men enter a blind and 2 emerge, the crows are not deceived. Even if 7 enter and 6 emerge, the crow still knows that there is a hunter down there waiting to get him/her. So if you want to fool a crow you have to exceed the buffer capacity of the crow's mind. The memory buffer in the crow's mind/brain is stuffed full at 7. Anything over that just spills over the top. Humans' buffers are generally limited to 5.
If I recall correctly, there has been some work done with the memory buffers of honeybees. I'm not sure that a chemical/mechanical/electrical basis for the storage has been identified, but it appears that bees have a relatively small number of individual memory buffers. Bees need to be able to remember things like "compass direction" (actually a measurement based on orienting to direction by observing the polarization of sunlight). Bees are known to report on the presence of nectar and to report on the presence of pollen, so it is likely that there are memory buffers (maybe just yes and no entries) for "nectar?" and "pollen?". I probably read about this stuff in an article in Scientific American ten or twenty years ago. Is that the kind of thing you want?
Any use of symbolic representations by non-humans would be considered a major find, so if there are ants keeping track of the number of ant cows they have by biting gashes in blades of grass or something like that then that fact will get intense attention when it is discovered.
A systematic way of investigating this matter would be to ask whether there are non-DNA molecular codes, whether there are digital records kept by single-celled creatures somehow, whether multi-celled creatures (rotifers, for instance) scratch marks or collect markers, etc., etc. If I had to start looking at one point I think I would ask whether birds ever collect stones to represent, e.g., the number of eggs they have laid. (Useful if you think a cowbird might have managed to sneak something into your nest.)
It would be interesting to know whether crows remember "7 predators" by writing "1111111" in their predator buffers, or whether they write "111", or, I guess they could just write "7" (in whatever language crows count in). P0M 06:54, 18 Nov 2004 (UTC)
I just remembered: Prairie dogs can identify individual predators, and they communicate such information by a kind of prairie dog language. If they can call out "three wolves" then you've got your digital representation. Then the next interesting question would be how the information is actually stored in their minds/brains... P0M 07:02, 18 Nov 2004 (UTC)

Verbless sentence

  • "Avery the medium of transfer of traits as the transforming principle; his identified DNA as the transforming principle, and not protein as previously thought."

Huh? Sentences without verbs cause of confusion for me. — Ливай | ☺ 14:33, 25 Apr 2005 (UTC)

DNA au Francais

The people at fr have an interesting approach to the organziation of the diaspora of DNA articles and pages. The page in question is at fr: DNA, mRNA, and many others I suppose. It's a big box with the research structure of DNA science organized into all the possible pages. It certainly gets an A for Wikification. It is so easy to use.--McDogm 16:13, 7 May 2005 (UTC)

Hash? What has become of this article?

It has been a while since I've looked at this article. It used to make sense to me. Now just looking at it gives me a headache. I see about 50 separate sections each consisting of 3 or 4 lines. I suppose I will have to spend hours with the history of the article to see how it has evolved (?) to its current state, but do others really think this is a desirable configuration? P0M 06:13, 8 May 2005 (UTC)

I agree with you. Gene Nygaard 10:22, 8 May 2005 (UTC)

the name "deoxyribose nucleic acid" vs. "deoxyribonucleic acid"

The article currently inconsistently sometimes uses "deoxyribose nucleic acid" and other times uses "deoxyribonucleic acid". Should the article explicitly mention why one name is preferred over the other ? --DavidCary 02:03, 16 May 2005 (UTC)

Yes, if that's the case. But is one preferred over the other? I certainly always use the full term (currently the page title), which I thought this was more common and has always been used in the intro to the page. But according to googlefight deoxyribionucleic acid is more commonly used by quite a large margin [1]. It's Wikipedia policy to use consistant spelling, so we need to pick one or the other and standardise the spelling (but still mention alternative spellings). But in the light of the googlefight result I have no idea what to go for. Is there an official body (I asume IUPAC is not relevant to biochemistry) that has set a standard? For now we could, wherever possible, use the abbreviation. Joe D (t) 02:31, 16 May 2005 (UTC)
I checked the genetics and mol bio section of Wikipedia:Library/Science#Biology and found the shorter version to be more common there, too. Joe D (t) 20:27, 23 May 2005 (UTC)
DNA is an abbreviation for Deoxyribose Nucleic Acid. Deoxyribonucleic Acid should point, but to abbreviate this would be DA, not DNA. In any case, I think the abbreviation should point to the full term, and not vice-versa. Whig 05:45, 23 May 2005 (UTC)
However you spell it, there is absolutely no dispute that DNA is its abbreviation. Tufflaw 03:32, May 24, 2005 (UTC)

Page Move

I don't really think that the page move is necessary? What are other peoples opinions?--nixie 05:51, 23 May 2005 (UTC)

  • No, and if the requestor doesn't step forward soon, I'm going to remove the listing. →Raul654 06:10, May 23, 2005 (UTC)
    • I didn't nominate it, but I think the move would conform to Wikipedia:Naming_conventions#Prefer_spelled-out_phrases_to_acronyms, what's your reasoning? --Dmcdevit 08:31, 23 May 2005 (UTC)
      • I think it should stay since joe public is going to have heard of DNA, but probably not deoxy...... There are several pages that are titled as acronyms that are in a similar situation, H.D. comes to mind, the rule is more so interpreted as use the most common name --nixie 08:54, 23 May 2005 (UTC)
        • It's more than just the common name though, IMHO. H.D. was her "official" name really, as it was how her work was attributed, similar to how the NAACP and the SAT have articles under those names because their respective organizations have officially declared those letters their official names. Whereas the ACLU and the TVA are placed at their spelled out name despite being commonly known by their acronyms. I probably could have thought of better examples, but I think these are good illustrations. Besides, it's not as if there wouldn't be a redirect. --Dmcdevit 09:28, 23 May 2005 (UTC)
        • Quoting the full text of the convention: Avoid the use of acronyms in page naming unless the term you are naming is almost exclusively known only by its acronym and is widely known and used in that form (NASA, SETI, and radar are good examples). The page should be called DNA with redirects from the full name (and that misspelling). Proto 11:18, 23 May 2005 (UTC)
          • I agree completely - the average person looking up this subject in an encyclopedia will look for DNA (I would suggest most often to find out what the acronym actually stands for). It is popularly known by its initials and should remain. Tufflaw 13:11, May 23, 2005 (UTC)
            • I think I'd prefer the article to stay at DNA. However, if the page does end up being moved, then DNA should redirect there; it should not be a disambiguation page. Also, should it be moved, the new title should be Deoxyribonucleic acid (no capitalization of "acid". — Knowledge Seeker দ 20:00, 23 May 2005 (UTC)
              • Incidentally, the article begins saying, "Deoxyribose nucleic acid (DNA) is a nucleic acid..." I've always seen it as "deoxyribonucleic acid", not "deoxyribose nucleic acid". All modern biology textbooks, medical textbooks, and journals that I can think of use the former, at least in the United States. Merriam-Webster also lists "deoxyribonucleic acid". Is there any source that uses the three-word version? Otherwise I'll change it. — Knowledge Seeker দ 20:14, 23 May 2005 (UTC)

It was requested that this article be renamed but there was no consensus for it to be moved. violet/riga (t) 09:57, 27 May 2005 (UTC)

the Other DNA

There ought to be a mention of Douglas Noel Adams on the page. 24.91.43.225 17:26, 10 Jun 2005 (UTC)

There is - the top link goes to the disambiguation page. Tufflaw 19:04, Jun 10, 2005 (UTC)

Cleanup

Ok, so this page has been listed on Wikipedia:Cleanup. Before attampting any changes I think it would be a good idea to sketch out what the article should look like here. User:Jerzy listed the page and notes: "oversized article (30K, 11 main hdgs & 19 subordinate ones) should have most main sections reduced to summaries with no subordinate hdgs but links to 'Main articles'". I agree and sugest the following sections, each with its own main article:

  • Molecular structure and mechanical properties - two subsections / two "main articles". Including information on "Direction of DNA strands".
  • DNA fingerprinting for crime and for identification of unknown people / parents etc. and also possibly in fiction.
  • Replication - this has already been done, I think the section needs to be a little longer.
  • History of DNA research.
  • What I am less sure about is The role of the sequence - should this be included in a section called, e.g. DNA and [the encoding of] genes?

Comments are very welcome! Andreww 09:37, 20 Jun 2005 (UTC)

P.S. This talk page also needs cleaning up (archiving).

I just reverted some changes to the page to make the structure agree with the project science to-do list at the top of the page. Does anybody think this list is a sensible structure for the page? Also, as nobody has complained about my proposed cleanup plan I am going to get started. Andreww 08:45, 22 Jun 2005 (UTC)

I don't really support moving content out of this article into daughter articles. The disorganised feeling is mainly due to all the ==h3== and ====h4==== headings. There should be a section on DNA applications and not where it occurs in the article now, the DNA in brief should be written as prose or deleted all together.--nixie 08:53, 22 Jun 2005 (UTC)

If you are goign to go ahead with breaking the article up the Direction of DNA strands should probably go with the mechanical properties--nixie 08:55, 22 Jun 2005 (UTC)

Hi, I feel a bit sad about that revert now that all my work is gone :-/ It was more or less my first 'effort' here in the Wikipedia and maybe I haven't understand the way of working... I thought since there is a to-do list I should follow it to arrange the structure... if not, why is that to-do list there? Who wrote it? I thought it was a group of people after a debate that took part in the past or something like this... or is it neccessary to debate about the structure again? Alzhaid 15:53, 22 Jun 2005 (UTC)

all cells have 23 chromosomes pairs?

At least that is what the opening section tells us here "every human cell contains 23 pairs of chromosomes derived from both parents, together with one copy of the mother's mitochondrial DNA.". While this is a nice simplification it ignores specialized cells (gut epithelial, for one) that undergo endoreduplication and are polyploid. I understand we need to keep the article simple but this should not be at the loss of accuracy. David D. (Talk) 17:33, 4 November 2005 (UTC)

"one copy of the mother's mitochondrial DNA" <-- this is also wrong. Many cells have more than one copy of the mitochondrial DNA. --JWSchmidt 18:19, 4 November 2005 (UTC)
Yes this is also true. Many mitochondrial genomes are inherited from the mother. These genomes can be different genotypes hence the term heteroplasmy. This is why mitochondrial myopathies have a low penetrance since the mutant genomes are present in a cell with functional genomes. The disease symptoms become more severe when the mutant genomes start to predominate. David D. (Talk) 18:43, 4 November 2005 (UTC)
JonMoulton is missing two main points: that some people just don't have 23 pairs (e.g. XXX); and that mature red blood cells lose mitochondria (see Red blood cell#Mammalian erythrocytes). I'll make changes accordingly. I'll also address the "one copy" issue. Peak 18:46, 4 November 2005 (UTC)

DNA structure discovery information posted by 80.189.241.81

This article repeats the usual error that Franklin did not authorise the handing over of photograph No51 by Wilkins to Watson . Also a key figure in the history of DNA is Ray Gosling who, as a research student but a physics graduate and former medical physicist, was involved in taking the fist photographs of both the A form (with Wilkins) and the B form (with Franklin. Yet the article in Wikipedia does not mention him. This suggests a Ph D student is unimportant but Crick was such at the time. The book by Wilkins ‘The Third Man of the Double Helix‘ clearly states that Franklin (just before she moved to Bedford College) had authorised the transfer of he No 51 photograph to Wilkins by Gosling and for it then to be used by Wilkins as he thought fit. With the history of contact between Wilkins and the Cambridge group, which was well known to Franklin, this must have included the transfer of the photograph to Watson or Crick. Gosling, who is still living and was a research student and good friend of Franklin, has not denied this. There is no doubt that Gosling handed over the No. 51 photograph to Wilkins and yet he remained a friend and Ph D student of Franklin. This is unlikely if the use of the photograph by Gosling and Wilkins was unauthorised by Franklin. Wilkins was an honourable senior scientist and there is no reason to doubt his word and yet his version of events is now hardly ever mentioned; certainly not in this Wikapedia article. The article should be up dated accordingly.

The article does not mention that Franklin was a strong opponent of the double helix theory throughout most of 1952 eg The death of the helix meeting which hshe organised an rsulted in Wilkins withdrawing from the DNA resarch for 6 months..

A detailed account of these points with bibliography is contained in the book A Quartet of Unlikely Discoveries by Sylvia AS Tait and JF Tait.

I removed the above from the article after it was added by 80.189.241.81. Some of this information can be added back to the article. --JWSchmidt 14:25, 15 December 2005 (UTC)

I have not read Wilkins book so this is a hard call. It seems to all hinge on why did Frankin not want to collaborate with Watson? And if she didn't would she want Watson to have access to her data? How do we interpret her comment to Wilkins for him to use the data "as he thought fit". Did she have in mind for him to use it for his own research only? Since we will never know what Franklin was thinking we do not want to fall into the trap of overinterpreting her second hand comments. However, it is an interesting perspective. David D. (Talk) 16:47, 15 December 2005 (UTC)

Lexor and Guzta

Two users have been carrying on a discussion within the article. The original plea to new editors not to mess with the beginning paragraphs without discussing it here seems reasonable, but any further discussion creates lots of "traffic" for people who are trying to keep an eye on the article to see that it is not being vandalized. P0M 04:53, 22 December 2005 (UTC)

Length of human DNA

Based on the estimate of 3 billion nucleotides in human DNA, with nucleotides spaced every 0.34 nm and the DNA molecule 2 nm wide, I calculated that human DNA, if strung in one line, would be exactly 1.05 meters long. This is 1.05 billion times as long as it is wide. If each nucleotide were represented by a stack of 4 US pennies (because a penny is 12.333 times as wide as it is high), and 3 billion of these "nucleotides" stacked on top of each other would be 4.65 million kilometers long, or about 2.9 million miles, enough to wrap around the Earth's equator 730 times, enough to reach to the moon 12 times, enough to wrap around the Sun once. I didn't know where to put this, but I thought it was interesting, and gives an idea of the amount of DNA a single human cell has. Twilight Realm 01:07, 4 January 2006 (UTC)

Non-helical forms

Does this subsection conform to the "no original research" rule? Can references to research articles be given (and not just a link to a pdf from "notahelix.com")?

Please sign your postings. "No original research" basically means that nobody can do his/her own research and then post it as a Wikipedia article, or include it in a Wikipedia article. It would no be any better if somebody got their own website and then quoted the website as though it were an authoritative source of information. As for websites, then, the question would be: Whose website is it? What is the publication status of the materials on the website? For instance, one of the most well known researchers dealing with human sexuality issues maintains his own website at his university and makes pdf copies of some of his published work there. Both because of that individual's credentials and because of the publication status of the articles, a link to his site would not be problematical. What is known about "notahelix"? P0M 02:37, 13 January 2006 (UTC)
If notahelix.com contained PDFs of peer-reviewed articles, that would be fine with me. When I looked a couple of days ago, it didn't seem to me as if it did. I think these paragraphs about non-helical forms give too much exposure to non-mainstream ideas, considering it is an encyclopedia. A sentence with references to peer-reviewed articles would be fine, however. 216.154.205.203 16:19, 13 January 2006 (UTC)

I would suggest this section be moved to this historical section. The SBS (side by side) structure for DNA was proposed and debated (in the scientific literature) in the 1970's and early 80's. The SBS structure is only supported currently by a very small minority of fringe scientists. Also, this section in its current form is quite unreadable. Dnasmith 07:43, 6 October 2006 (UTC)

These lead images blow

In the first two images on this page, I can't tell where's the minor groove and where's the major groove! The second image, Image:DNA-structure-and-bases.png, is definitely wrong, and the first image, Image:DNA123.png, looks wrong too, although it's harder to tell because it's shorter. I've noticed this problem in other popular publications-- that the helices are depicted as being directly oposite each other, either for aesthetic reasons or out of ignorance, I guess-- but I expect a little better out of Wikipedia.

I propose to remove both those images. One can be replaced with a still from the animation we already link to, and one can be replaced with the lead image from the German article, which seems to be public domain. Any thoughts? Melchoir 20:06, 14 January 2006 (UTC)

The German image could replace Image:DNA123.png. Image:DNA-structure-and-bases.png is probably useful as a simplified diagramatic illustration of the basics of the structure. I think the animated helix was previously on the DNA page. --JWSchmidt 23:53, 14 January 2006 (UTC)
Well, geometry aside, I don't think Image:DNA-structure-and-bases.png is even a good schematic diagram. Where's the 3' and the 5'? Which helix is ascending and which is descending? There's no suggestion that the molecule is directional at all. I do agree, however, that the images I've proposed are a poor substitute. We've got to find something else.... Melchoir 04:47, 15 January 2006 (UTC)
How about rendering twelve base pairs (e.g. PDB id 1D28) with pymol? Would that be useful and acceptable from a license view point? 128.46.94.101 23:32, 17 January 2006 (UTC)
Well, I'm no expert in this software, so PDB id 1D28 means little to me, and I don't know about the licenses. I strongly suspect that it would be okay, since the animation is from rasmol, which seems to have a similar license, and it's survived on Commons for months without complaint. That said...
(ahem)
That would be awesome! If you're so inclined, please have a crack at it! My only suggestion is to lengthen it to about 20 base pairs, to drive home the periodicity of the structure. Melchoir 01:03, 18 January 2006 (UTC)
I uploaded a new image: Image:B-DNA dodecamer (1D28).png. It shows twelve base pairs. (These are the contents of the file from the PDB. It's not possible to lengthen it to, say, 20 pairs.) Is this what you have been looking for? Clemens H 17:15, 24 January 2006 (UTC)
The problem with that image is it is hard to see the base pairs. I would suggest tilting it in the vertical plane about 10-20 degrees forward. David D. (Talk) 17:19, 24 January 2006 (UTC)
I don't know what the situation was before, but as of 2/2/06 the top image (Image:DNA_3D_Model.png)is misleading. It's a confusing angle, and supports the common belief that DNA a simple spiral, without the major and minor grooves, as Melchoir said in the first comment in this section. Twilight Realm 22:42, 2 February 2006 (UTC)

Hi all. I replaced my older, sucky lead with a sketch of how a section of DNA looks (on a very, very macro scale) along a stretch of 21 base-pairs, so the character of the helix is more visible. I plan to leave it at something like that, and follow wit a very, very detailed diagram later in the article. For the time being, that's probably better than all the other, rather misleading images we currently have. I'm currently working on the mother of all "Structure of DNA"-Graphics, which will be a combination of line drawings, 3D-models and chemistry schematics along the lines of my Image:Types of Carbon Nanotubes.png... Be patient for a while and please let me hear your suggestions regarding what you would like to have included there! Mstroeck 01:43, 4 February 2006 (UTC)

Image:DNA Overview.png is awesome. Good work, and thanks! Melchoir 09:10, 10 February 2006 (UTC)

Initial discovery

A blind spot in the current article seems to be who first isolated and described DNA. My recollection is that it was 19th century, but I can't recall whom.. Anyone? Fawcett5 23:30, 16 January 2006 (UTC)

There is no info about chymera... that's that one person can have 2 DNA signatures. Would be nice to get some info in it.

Perhaps you want the article Chimera (genetics)? Melchoir 23:02, 19 January 2006 (UTC)

Article comments

I've removed this commented-out discussion from the Overview section:

  • PLEASE, PLEASE try to refrain from transforming this section into another highly-accurate-but-impossible-to-read one! It has been assumed from the beginning that this is not necessarily a very accurate description, and that it's only meant as a generic overview.
    • Wikipedia needs to be accurate, but it can be simple and accurate. Dumbing down something too much (which I'm not saying is happening here) is also to be avoided. --Lexor|Talk
  • This is what most people need, and that's why it has been inserted at the top of the article. If you find that curious, or even absurd, think how you would feel if some article which pertains to scientific dissection in a field you don't master only contained scientific data -- that would be frustrating, wouldn't it? Thank you for understanding! --Gutza 11:47, 5 Oct 2004 (UTC)

This is what the talk page is for. Melchoir 04:10, 22 January 2006 (UTC)

I feel a bit of irritation when I see in-line comments in articles, but when I question myself about why I feel that way I cannot come up with a clear reason. I think it is probably the feeling that people are going to start a back-and-forth argument in brackets right there in the middle of the article, making the article a mess to edit. But in a case such as this one, I think that the in-line request is warranted. There has been so much controversy in the past that anything within reason that can avoid a brush fire breaking out seems like a good plan to me. Putting a warning there will tell people that shaping up this introductory material has not been easy, and disturbing the equilibrium should be avoided. It suggests to people that if they think changes are desirable they should discuss those changes here first to avoid edit wars and other forms of turbulence.
Putting such a warning on the discussion page would not do any good since it would very quickly move away from the active part of the page and then get archived. A judicious use of such comments supports cooperative efforts that may have taken lots of effort to achieve. P0M 01:18, 28 January 2006 (UTC)
I've actually used such warning comments in articles before, and if you want to make a quick comment, I won't complain. I removed what I did because it was turning into a discussion complete with signatures: as you put it, a back-and-forth argument in brackets right there in the middle of the article. Melchoir 01:37, 28 January 2006 (UTC)
I see what happened now. Strange that Lexor would start a debate there. I've reworded things somewhat, given the warning a bit more prominence, and maybe it will serve a useful purpose. If a debate flares up there, maybe we could just move the stuff added to the warning over here. P0M 02:09, 28 January 2006 (UTC)
  • I think this should be a Wikipedia policy, to try to make articles understandable to a layperson-- after all, the experts already know about it. The details can come later in the article. There are way too many articles that are impossible to interpret without significant prior knowledge, or simply use confusingly complex language. For example, look at [[2]] (the link is to the current version), with the opening sentence In mathematics, a coefficient is a constant multiplicative factor of a certain object such as a variable (for example, the coefficients of a polynomial), a basis vector, a basis function and so on. I've suggested improvement, but I've been ignored. I want to make simplicity and understandability a guideline for writing Wikipedia articles, but I don't know where to start. Any suggestions? Twilight Realm 22:55, 2 February 2006 (UTC)
An afterthought, so I don't forget (I realize this is the wrong page for this): There should also be something on the history page, like the m for a minor edit, which indicates that something was deleted. It should be automatic, so it can prevent what I see as the most dangerous form of vandalism-- someone taking out a sentence or two from the middle of the article, without messing anything up. This would most likely remain unnoticed, and that little bit of information would be lost from the article for a long time, if not permanently. Twilight Realm 23:06, 2 February 2006 (UTC)

Regarding Chimera, the article should include a link to <en.wikipedia.org/wiki/Chimera>

Reference for geometry table

Is there a reference for the numbers in "Table of comparison of the properties of different helical forms"? This would be quite useful. Clemens H 18:20, 26 January 2006 (UTC)

Double Helix

DNA is a double helix most if not all of the time, right? I'm supposed to check before changing the lead section of the article. I was going to change it to Deoxyribonucleic acid (DNA) is a nucleic acid in the form of a double helix that contains the genetic instructions specifying . . . (the bold is what I would have added). If there is a problem with this, tell me; if not, go ahead and change it (I think it could be worded better anyway). Twilight Realm 22:44, 2 February 2006 (UTC)

At normal temperatures, yes. Depending on the size of the DNA molecule, temperatures typically ranging from about 72 degrees and above (~95 degrees in PCR reactions) break apart the hydrogen bonds, allowing single stranded DNA to exist in solution. 219.89.189.91 21:24, 6 February 2006 (UTC)

So is there a reason not to include the double helix in the lead section? Twilight Realm 03:39, 7 February 2006 (UTC)

normally in the form of a double helix? Also, link to Helix — Ilyanep (Talk) 03:40, 7 February 2006 (UTC)
I think mention of DNA usually being a double stranded helix macromolecule (at normal temperatures sustainable for life) should be in the lead section somewhere. After all, It was discovered as a double stranded helix, see Watson & Cricks original nature publication (probably one of the most famous papers of all time). 219.89.189.91 09:10, 7 February 2006 (UTC)
It is, in fact, most notable for being in the double helix shape. It should definately be in there. — Ilyanep (Talk) 23:06, 7 February 2006 (UTC)

I went ahead and added it. Seriously, we are talking about obviously useful information that takes half a dozen words to be conveyed... What ever happened to be bold? Mstroeck 01:36, 8 February 2006 (UTC)

Yeah, I was actually about to do it but forgot to. I just wanted to check first, because I had been told to do so. Twilight Realm 03:25, 22 February 2006 (UTC)

Can we change "usually in the form of a double helix" to "in the shape of a double helix, at temperatures that sustain life"? This makes the sentence accurate yet still simple enough. Saying that it is usually a double helix is so uninformative as to be misleading. Among other things, it may suggest that some DNAs in nature are not in this shape. Also, a double helix is not a form but a shape. Form is a very general term, as in "form of life". -Pgan002 08:40, 3 September 2006 (UTC)

Hydrogen bonding

There needs to be more detail about the specific triple hydrogen bonds in G-C, and double (slightly weaker) hydrogen bonds in A-T pairing. There doesnt appear to be any mention of Tm values, and their simple (or more complicated) calculations for short strands of DNA

219.89.189.91 21:24, 6 February 2006 (UTC)

A- and Z-DNA not the only "other" known forms

This section in the article originally read that these were the only "two other known forms of DNA" and that they differed only "modestly". Both of these claims are inaccurate; there are many other known forms (C-DNA, D-DNA, E-DNA, etc.). Some of these (e.g. Z-DNA) do not differ modestly at all. In fact, Z-DNA is strikingly different (left-handed, zig-zag, etc. See the Z-DNA article for illustrations of what I mean).--Thorwald 19:17, 17 August 2006 (UTC)

?

y the big open space after dna pairing title? MichaelHa 03:08, 8 February 2006 (UTC)

?

whats pi stacking? MichaelHa 03:23, 8 February 2006 (UTC)

The Pi stacking is the specific aromatic interaction between adjacent nucleotides on a single strand of DNA that stabilizes the conformation that allows base pairing (mediated by hydrogen bonds) with a second strand. It's erroneous to state that the two strands are held together by hydrophobic interactions or pi stacking. I will gladly change that paragraph, doing my best to be clear and accurate unless someone tells me not to do so. --Wuicker 21:37, 21 July 2006 (UTC)

X-ray diffraction

Has there ever been an x-ray diffraction picture for this article? It would be nice to get one in the article if we have a copy. David D. (Talk) 09:18, 10 February 2006 (UTC)

Not quite what you wanted, but see Image:ADN animation.gif P0M 22:25, 11 February 2006 (UTC)
I have one that I could scan; I don't know if such an image is subject to copyright, but we could probably claim fair use to illustrate this article. Schutz 22:19, 4 March 2006 (UTC)

Supercoiling Inaccuracy

The supercoiling section in this article misses the boat. Supercoiling is the coiling of the helix around its self to preserve its topology with varying amounts of twisting. There's already a pretty good article on supercoiling, which covers just about everything except for its relevance. That is, the thermodynamically favorable removal of negative supercoils facilitates unwinding of the helix, vital for transcription and repair processes. Without the supercoiling, DNA wouldn't unwind in anything near physiological conditions. I'm not solid enough on the subject to write a good article on it as I'm worried about hitting that middle ground where the section would sound credible enough to not attract editing but still be wrong. Hopefully someone will fix it up and add in a bit on the surrounding biochemistry.

Supercoiling section needs expansion.

The section on supercoiling in this article is really lacking. There's already a pretty good article on supercoiling, which covers just about everything. I think a merger of that article into this one (or at least a link to it) would be an improvement. More information about topoisomerases and the relevance of supercoiling is probably warranted as well. I'm not solid enough on the subject to write a good article on it as I'm worried about hitting that middle ground where the section would sound credible enough to not attract editing but still be wrong.

I've made the link more prominent. I agree that the relevance of supercoiling should be explored here, but I don't think the section should be expanded too much. As in the Wikipedia:Summary style philosophy, it would be better to focus on improving the article Supercoil than to make DNA too much longer. Melchoir 09:51, 26 February 2006 (UTC)

Temperatures

There is currently no information on at what temperatures DNA becomes useless for DNA analysis, like in crime investigations etc. Knutars 23:09, 19 March 2006 (UTC)

Uh, that is covered by the fact that it is a nucleic acid. Also, even at the boiling point of water, it does not become irreversibly useless, although it can get tampered through this way. Polymerase chain reaction heats the DNA up to 95 degrees to denature it and break the hydrogen bonds, but the covalent bonds are strong enough to withstand the heat. You could be looking at a pretty massive temperature in order to try to destroy the thing through heat, combustion is the most rational cause, through an incinerator. Denaturing the DNA does not irreversibly destroy it, you can just feed it back through PCR. It has a higher chance of decomposing or degrading in an investigation, through time, not temperature. Elle vécut heureuse à jamais (Be eudaimonic!) 23:18, 19 March 2006 (UTC)

Regarding the link to Rotten.com in the references. I don't think Rotten.com should be linked to as part of any scholarly article. Imagine a child, or anyone, researching DNA to find a "Faces of Death" link at the bottom of the link to page. This should be removed as I'm sure the other links adequately cover the material. Frankly, the material there is poor quality anyway.

If this was a link, it seems to have been removed. I don't see it. P0M 03:17, 24 March 2006 (UTC)
See the article's history. Schutz 08:09, 24 March 2006 (UTC)

Person with 2 DNAs ??

Removed the following - needs sourcing:

There have been rare cases reported of a person having 2 different DNAs in parts of his body. In one case, each side of the body had a different DNA. In another case, a woman had her children taken from her because their DNAs did not match. Subsequnt testing showed that her internal organs had a DNA that matched that of her children. Tbis subject should be reviewed by a comptent authority.

Seems dubious to me. Vsmith 23:38, 25 March 2006 (UTC)

  • I agree that it seems odd, yet the paragraph is basically correct. The phenomenon in question is chimerism. There was an article in The New England Journal of Medicine: "Disputed maternity leading to identification of tetragametic chimerism" (PMID 12015394). I was not familiar with this case that the paragraph mentions, but Lydia Fairchild appears to be the woman in question. — Knowledge Seeker দ 23:59, 25 March 2006 (UTC)

Related phenomena have been noted. A year or two ago there was an article in Science News quoting research indicating that since in vitro fertilizations have become more common, it more often happens that two separately fertilized cells will clump and from that time on develop just as though the two had been the two daughter cells of one fertilized ovum. The result can be that one of those cells was fertilized by a sperm bearing a y chromosome and one was fertilized by a sperm bearing an x chromosome. One would suspect that in cases where in vitro fertilization is done rarely, if ever, would the sperm of two male donors be present. In nature, however, successive intercourse with two men over a short period of time could result in two cells clumping that happened to have been fertilized by sperm from different fathers. It shouldn't be difficult to track down citations for this kind of chimera. In the meantime the citation provided by Knowledge Seeker should be added to the paragraph and the paragraph should be restored. P0M 02:57, 26 March 2006 (UTC)

Dioxy??

I wonder if anyone noted, but it should say "dEoxyribo..." in stead of "dIoxyribo" at the very top of the article. Please could anyone change that, I was a bit scary after reading the comment at the top. --Lode 06:23, 29 March 2006 (UTC)

That one slipped in under the radar. Thanks - and don't be bothered too much by that warning, if it's obviously wrong fix it. Vsmith 12:26, 29 March 2006 (UTC)

(Animated) DNA image

From User talk:Melchoir:

Melchoir, I was wondering if you would be willing to accept a compromise. I found that animated GIF on the dutch wikipedia and thought that it was so fantastic that it should be featured on the english wikipedia. Perhaps that GIF could replace both the first and second images? The original space-filling model is not nearly half as good as the GIF, and the GIF shows just as much detail as the first image anyway. Additionally, 1MB isn't that large for an image file considering that the first image is nearly 1MB.

Lastly, there were other alterations that I made to the article that didn't need reverting. I will make those changes once again, but ask that you let me know what you think about using that excellent GIF model.

209.33.227.197 02:53, 10 April 2006 (UTC)

I agree that Image:ADN animation.gif is a fantastic image, but I still think it's too large to force users to download the whole thing just to read the article. It's 1 MB large. True, the current lead image, Image:DNA Overview.png, is nearly as large at full resolution, but the smaller version that actually displays in the article is just 166 kB. As for which one's better, that's a matter of preference; me, I actually think the current image is more appropriate for its position.
As for compromises, did you know that the animation is already linked at the bottom of the "Molecular structure" section? Perhaps you'd like to move it...? Melchoir 03:17, 10 April 2006 (UTC)
Some of us do not have ethernet connections and appreciate articles that load fairly promptly. The option to open the animation saves those of us who want a fast dip in the gene pool from frustration.P0M 01:30, 13 April 2006 (UTC)


Audio Version

I would like to request that an audio version of this article be created. I found the audio from the Evolution article to be very useful, especially with the proper pronounciation of researcher's names and with the technical and scientific terms.

DNA an acid

If DNA is an acid what is its' PH? The League of Crazy Men 11:26, 2 May 2006 (UTC)

This is an encyclopedia, and reading it would have answered your question. From the article:
"DNA is an acid because of the phosphate groups between each deoxyribose. This is the primary reason why DNA has a negative charge."
For future reference, talk pages are for discussing matters relating to the structure, direction, and content of articles. If you have a question you are simply curious about which you could not find an answer to in the encyclopedia, a good place to start is the help desk.Shaggorama 01:27, 3 May 2006 (UTC)
Actually, I think that it is sometimes all right to ask questions relating to the topic on an article's discussion page. I don't see that reading the article answers this question; certainly the selection you cite does not mention the pH of DNA. Crazy, the pH of a solution depends on the amount of the components or how you make the solution. Pure DNA will not produce any hydronium ions; for that, water is needed. You might ask what the pKa is of DNA, but that too cannot be answered; acids with more than one proton to be lost have a pKa for each proton. Only simple acids like hydrochloric acid have a single pKa value.
It is interesting that discussion has taken me off the main page and into the politics or 'death by one thousand cuts' or not to die. When I opened up the edit page the disclaimer at the top was a very good antibiotic and so reading the rules become the pass time. Historically the use of words that are not true to meaning but then become useful identifiers of meaning is how language evolves to a point when conventions crumble. But a simple question like acid in DNA will some times show up the flat earthers thinking when it evolves into stake burning. However I think it is ok for higher IQed people to be curt with less than exactly researched questioned people, it keeps the discussion grounded, real and onto it. RoddyYoung 09:34, 6 May 2006 (UTC)
Actually the Wikipedia:Reference Desk/Science is the place to ask, not the help desk. And I imagine the pH varies based on its makeup. Elle vécut heureuse à jamais (Be eudaimonic!) 17:42, 29 May 2006 (UTC)

THE NEW BIOGRAPHY OF FRANCIS CRICK BY MATT RIDLEY, PUBLISHED IN THE US ON JUNE 1ST 2006

Comments and/or criticism would be more than welcome: * Ridley, Matt; Francis Crick: Discoverer of the Genetic Code (Eminent Lives) first published in June 2006 in the USA and then to be in the U.K. September 2006, by HarperCollins Publishers; 192 pp, ISBN 006082333X

62.25.109.194mp62.25.109.194

AMUSING 'DNA' SONG PARODIES AND THE FIRST PRESS STORIES ON THE DISCOVERY OF STRUCTURE

- Both can be found on: http://www.packer34.freeserve.co.uk/selectedTATAwebsites.htm

62.25.109.194mp62.25.109.194

Duplicate sections

The Overviews and Molecular Structure sections are almost complete duplicates of each other. Can someone merge them... --Dtcdthingy 15:06, 20 June 2006 (UTC)

Intro

I appreciate notion that changes to the intro section need to be discussed on talk first, as I've come from numerous articles that represent months and months of compromise to arrive at a consensus version of the intro, only to see one shot users come in and make major changes after no discussion. What I find in this intro is that it doesn't say what DNA actually is. I was expecting for it to explain a paragraph of so of basic treatment of the topic. Is the impetus here that the intro is strong and shouldn't be changed? JPotter 04:42, 29 August 2006 (UTC)

Well something appears to have changed and the article is what I expected now. The first sentence is no longer about replciation and syntheisis. JPotter 18:52, 29 August 2006 (UTC)
I agree that the first sentence should be more clear and straightforward about the importance of DNA to reproduction of living things. -Pgan002 10:25, 3 September 2006 (UTC)

Paragraph 1

I propose the paragraph 1 to be changed from:

Deoxyribonucleic acid (DNA) is a nucleic acid — usually in the form of a double helix — that contains the genetic instructions or genocode monitoring the biological development of all cellular forms of life, and many viruses. DNA is a long polymer of nucleotides (a polynucleotide) and encodes the sequence of the amino acid residues in proteins using the genetic code, a triplet code of nucleotides. DNA is thought to date back to between approximately 3.5 to 4.6 billion years ago.

to

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of a cellular form of life or a virus. All known cellular organisms and some viruses have a DNA. DNA is a long polymer of nucleotides (a polynucleotide), and is shaped as a double helix under temperatures that sustain life. It encodes the sequence of amino acid residues in proteins. The code is the genetic code, in which each amino acid in the protein is represented by three consecutive nucleotides in the DNA (a triplet code). DNA is thought to have originated approximately 3.5 to 4.6 billion years ago.

First, the old version of the first sentence gives the impression that DNA is a thing that contains the instructions for the development of all these living things at the same time. The new formulation corrects this. Second, "monitoring" seems like the wrong word because DNA is an active part of biological development of the mentioned orgaisms. Next, the shape of DNA is less important than its function, so move it to the second sentence, which (like the shape) is about structure rather than function. Next, "usually" is so ambiguous as to be misleading. For example, it may suggest that some functioning DNA is not shaped as a double helix. It is more informative and easier to read, although it is longer, to specify that it is a double helix under the conditions that it performs its biological function. Also, a double helix is not a form but a shape. Next, split the sentence about encoding into two to make it easier to read. Next, "a triplet code of nucleotides" is confusing: explain in general terms what it is. Finally, change "DNA is thought to date back to" to "DNA is thought to have originated", and "between approximately 3.5 to 4.6" to "approximately 3.5 to 4.6". This is more grammatically correct and easier to read.

-Pgan002 10:25, 3 September 2006 (UTC)

Done: modified to a lightly different version. -Pgan002 09:15, 14 September 2006 (UTC)

Paragraph 2

In the sentence 1 of paragraph 2, I propose to change:

In complex eukaryotic cells such as"

to

In eukaryotic cells (which are relatively complex) such as

The current formulation may be misunderstood to be talking about only the more complex eukaryotic cells.

-Pgan002 10:52, 3 September 2006 (UTC)

Done! -Pgan002 06:44, 10 September 2006 (UTC)

Paragraph 3

I propose sentence 2 of paragraph 3 to be changed from:

In humans, these traits can range from hair color to disease susceptibility.

to

In humans, these traits range from hair color to disease susceptibility.

The traints not only can be, but actually are hair color and so on.

-Pgan002 10:55, 3 September 2006 (UTC)

Done! -Pgan002 06:42, 10 September 2006 (UTC)

Paragraph 4

I propose sentence 1 of paragraph 4 to be changed from:

Every person's DNA, their genome, is inherited from both parents.

to

Every person's DNA, their genome, is a combination of the DNAs of his parents.

or

Every person's DNA, their genome, is inherited from their parents; part of it is from the mother and part from the father.

The current formulation is ambiguous, and may be understood to mean that the DNA of the parents is the same.

-Pgan002

Done! -Pgan002


In sentence 2, I changed "twenty-three" to "23". By convention, numbers higher than ten should be written as numerals, especially if they are so elsewhere in the text. -Pgan002 10:56, 3 September 2006 (UTC)

Countable or uncountable noun?

Is the term deoxyribo-nucleic acid (DNA) a countable noun or an uncountable noun? Since it is a specialization of the countable noun acid, DNA should be countable. But all the uses of DNA I have seen are as uncountable. If it is countable, what is the unit -- each individual molecule is one acid? If uncountable, how can this be reconciled with the more general acid? -Pgan002 23:12, 20 September 2006 (UTC)

Specialization doesn't preserve countability. One has "a nitrate or nitrates" but just "potassium nitrate"; "an acid or acids" but just "citric acid". The counting for the general term is in the sense of multiple types, so counting the specific term by multiple units wouldn't reconcile the two anyway. (Not that reconcilation is needed.) Melchoir 03:16, 21 September 2006 (UTC)
Of course acid can also be used as uncountable ("I have some acid"), and the same is true of the other examples. But the introductory sentences of the article make it sound like DNA is one acid, like citric acid or sulphuric acid. This is confusing. As I understand, any two molecules of DNA having different sequences of bases are in fact different acids. Each of them has the structure that makes it an instance of DNA. So perhaps DNA is any acid that has the requisite properties, or in other words, DNA is a kind of acid that has those properties. I would like to make that clear, but I do not know how to weave it into the introduction. -Pgan002 02:52, 22 September 2006 (UTC)
That's... a really weird way of thinking about it. DNA is DNA. Sure, it has a few degrees of freedom, but what doesn't? Even citric acid can have different numbers of neutrons. Surely you wouldn't insist that citric acid is any acid that has the requisite properties?
An acid is defined as a compound, by which I understand any single compound, that has certain properties. DNA is not one compound. I have always been confused by the prevalent indiscriminate definition (explanation) of DNA. Before I understood this misuse of acid, I always wanted to ask book authors "You said it was an acid, but they have different structures!!??". I am sure other people are also confused. Someone else on the talk page was. Classically, citric acid is one acid, defined exactly by the structure of its molecules. All the molecules have the same structure. By neutron variation, I think you are referring to isotopes. But citric acid of any isotope is still citric acid, because it is the same compound. I would guess that DNA has much more isotopic variation because of the number of atoms that can exhibit isotopes. But the structural variation is many orders of magnitude greater in DNA. The sequences are thousands to billions of nucleotides long, and very varied. Even the article says "These allowable base components of nucleic acids can be arranged in the polymer in any order, giving the molecules a high degree of uniqueness." The pH's are different, the physical properties are different, the shapes can be helical or circular (and they code for a wide variety of organisms). How can this be one acid in the same sense as citric acid? Another way to ask this: if it were possible to rearrange some of the atoms of a citric acid molecule, would that still be citric acid? Is a DNA molecule that is one (or several) base long the same acid as a another one-base DNA molecule that has a different base? -Pgan002 22:15, 22 September 2006 (UTC)
If you want better wording for the article, that's one thing, but be careful not to do any original research... and this all sounds pretty original. Melchoir 03:30, 22 September 2006 (UTC)
Of course, I want to avoid original research on WP. Here I just want to clarify what people mean by "DNA". I am applying the definition of acid to the description of DNA in one application of modus tollens. How can this be original research?! Do experts disagree with the proposed clarification??!! -Pgan002 22:15, 22 September 2006 (UTC)
What do people mean by DNA? DNA is a substance and a medium. You can have a section of DNA, a molecule of DNA, a strand of DNA, a loop of DNA, a base pair of DNA, a solution of DNA, a crystal of DNA. Like water, steel, and paper, these are not likely to be internally homogeneous or identical between instances. And that's really okay. Human language is subtle.
I don't know what clarification you propose, but on the theme of original research, consider this: has anyone else ever uttered "DNA" and "modus tollens" in the same sentence? Melchoir 07:33, 23 September 2006 (UTC)
None of the above statements is problematic, and they may even be helpful to understand what DNA is, but none of them expresses the contested notion that DNA is an acid. Please point out the error you find in this argument: An acid is any compound that has certain properties. DNA is not a single compound. Threfore DNA is not an acid..
The purpose of the first couple of sentences is to say what people mean by DNA as concisely as possible, then the article should elaborate. We can say that DNA is a class of related nucleic acids, or a nucleic acid class of compounds. But according to the definition of acid, it is not an acid, and it is confusing to someone who does not know what DNA is to say that it is an acid.
It does not matter whether anyone has uttered the above. Whether a sentence expresses original research does not depend on whether someone has ever put that sentence together before. People construct new sentences all the time, and people even concieve of propositions (ideas) that nobody has exactly had before. But not all those sentences are original research. If I tried to publish the argument above in a paper or journal as original research, I am sure that it would be rejected. It is too trivial to be considered research. -Pgan002 00:08, 28 September 2006 (UTC)
The error is this: your idea of a strict "single compound" is not useful to biology. Look, let's just go to the sources. Here's a blast from the past: Campbell + Reece, Biology, sixth edition. The introduction to DNA contains at least four statements about what DNA is: "Genes consist of DNA, which is a polymer belonging to the class of compounds known as nucleic acids. ... There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). ... DNA is the genetic material that organisms inherit fom their parents. ... DNA is a helical, double-stranded macromolecule with bases projecting into the interior of the molecule." Or the parallel section in Mader, Inquiry into life, eighth edition: "Human genes are composed of a nucleic acid call DNA (deoxyribonucleic acid). ... Both DNA and RNA are polymers of nucleotides." This is how people speak of DNA. Melchoir 01:02, 28 September 2006 (UTC)

Defining characteristics vs facts

The opening sentences specify two properties of DNA:

  1. Its function in living organisms ("... contains the genetic instructions for the biological development of a cellular form of life or a virus. All known cellular life and some viruses have DNAs. ...that encodes the sequence of amino acid residues in proteins")
  2. Its chemical structure ("... a long polymer of nucleotides ...").

Which of these is/are a defining property, and which is/are an important fact of the world? If some cellular life (say on Mars) had its genetic instructions encoded by some other kind of structure, would that be DNA? Conversely, if a scientist artificially creates a polynucleotide of the same set of bases and similar length to some other DNA, but that does not encode the genetic instructions of any viable life form, would that be DNA? Given a sequence of bases, can I decide whether it represents a DNA molecule? -Pgan002 03:17, 22 September 2006 (UTC)

See the bolded phrase in the "Molecular structure" section. No, if it doesn't look like this, it isn't DNA. No, not all polynucleotides are DNA. Yes, scientists do work with meaningless sections of DNA for experiments. Yes, the answer is always yes: every sequence of bases can be realized by a molecule of DNA. Melchoir 08:05, 23 September 2006 (UTC)
In other words, the defining property is the chemical structure, and not the biological function. Thanks! I will think about how to modify the intorduction to make that clear. -Pgan002 04:51, 28 September 2006 (UTC)

NPOV

Comment "Watson was a Jjerk for steealing this DNA information." was removed as not NPOV. Somehow has been in there a while statsone 04:04, 13 October 2006 (UTC)

Image too big?

Under "Molecular Structure", which is under "Physical and Chemical properties", Dna_pairing_aa.gif blocks the last 3 words of the first sentence. Not particularly important, but annoying nonetheless.

In my opinion the physical and chemical properties section images are very poorly organised. Perhaps they should be arranged into a table of thumbnails, like at the bottom of ramen. In the current state, they are too small to be read clearly, as they are highly information-loaded figures, but still so big that they make the rest of the page hard to read. I shrank a couple that were taking up almost half of my viewable area; I think it needs more work though. Erk|Talk -- I like traffic lights -- 10:33, 17 November 2006 (UTC)

Chemical Nomenclature

"For reasons of chemical nomenclature, people who work with DNA refer to the asymmetric ends of ("five prime" and "three prime")."

This is not a sentence. Help? I'd fix it if I knew what the heck it meant. 68.215.226.236

Fixed it. How's that? Erk|Talk -- I like traffic lights -- 10:32, 17 November 2006 (UTC)

Can some add and find the source

I've developed this horrible habit of skimming articles, then making comments without logging in. This comment may need to be deleted because of which, but there is this quote I heard from somewhere, and I don't remember where. It is very POV, however I think it is still worthy of including in this article, if someone can find the source. It goes something like this: "DNA is not the encyclopedia; it is the table of contents." (24.99.192.9 21:39, 19 November 2006 (UTC)) User:QUINTIX

I think I heard something like that recently, and since I was already familiar with the ideas behind it I was not particularly interested in writing down the source. (Probably it it was quoted on a TV program.) Anyway, the idea is that by itself DNA does not do anything. Some other cellular mechanisms have to come in and "read" the information, and then they have to make use of it to carry out the directions that the DNA contains. The information surely is there in the DNA. There is no "text" to which the "table of contents" sends the user to get the "blueprint." So the DNA is what you need to get changed if you want to change a characteristic of an organism such as its eye color. Having zapped a large number of fruit flies, the ones in the next generation with new characteristics will turn out to have changed DNA. What you won't find is new changes in fruit flies without changes in their DNA. If the "encyclopedia" were somewhere else, then the DNA could stay the same and the index item for "eye color" could still point to page 38384 as before, but the organism would change if what was written on 38384 was changed. That kind of result isn't being reported. If it were then we'd all be hearing about it on Science Friday. Charlie Rose, and also from lots of people who would like to confound science. P0M 01:42, 22 November 2006 (UTC)

DNA is defintiely not analogous to a table of contents. More like a library where the shelves are the chromosomes and they are full of books. The books are the plans and with those plans you can make the tools as well as the house (or other structures). David D. (Talk) 23:13, 8 December 2006 (UTC)

Molecule vs. Molecules

I think this article contradicts itself a little bit. It says in "Inheritance of DNA":

"(...) most of the DNA is located in the cell nucleus, and ***each DNA molecule is usually packed into a chromosome*** (...)"

But then it says in "Molecular structure":

"(...) Although sometimes called "the molecule of heredity", DNA macromolecules as people typically think of them are not single molecules. Rather, they are pairs of molecules (...)"

Then in "Inheritance of DNA" it should read "each *pair* of DNA molecules is usually packed into a chromossome", shouldn't it? —The preceding unsigned comment was added by 200.164.220.194 (talk) 21:13, 7 December 2006 (UTC).

Good point, i reworded it, see what you think. David D. (Talk) 21:33, 7 December 2006 (UTC)
It's better now! Thanks, David! —The preceding unsigned comment was added by 200.164.220.194 (talk) 22:48, 8 December 2006 (UTC).

Downloads of Graphics

There's tons of graphics, this page takes a long time to download, even on broadband! I am on 8 mb/s broadband, and yet I was twiddling my thumb waiting for the images to load. At the moment I wouldnt have it as a Featured Article, with all the graphics. Kreb Dragonrider 01:26, 14 February 2007 (UTC)

I suspect there is some kind of problem with the animation, the article is only 77 kb in length. TimVickers 04:57, 14 February 2007 (UTC)

Just a suggestion

This article is truly magnificent. I'm not so sure how my opinion will weigh to you, but I have one suggestion. Correct me if I'm wrong but, besides in pictures, I didn't see any mention of how one side of the backbone goes in the opposite direction than the other. You know how one side goes from 5-3 and the other side goes from 3-5. I was going to edit it myself but seeing that it was restricted I have no other choice than writing it here. I just think that it is important and would make a great addition to the page. Thanks for listening --Gotninja (talk) 22:34, 7 January 2008 (UTC)

FA for DNA

I'm hoping to move this page through the peer-review and FA processes over the next month or so. There is a great deal of excellent content here, so most of my edits will be concentrating on formatting and adding references. Any help in this process will be greatly appreciated. TimVickers 23:14, 10 December 2006 (UTC)

Hi Tim, just seen your work here. It looks great. One issue is with the figure Image:Nucleosome with spacefill DNA.jpg. I wonder if it would look better with the histones as space-fill and the DNA as ribbon? At present it is hard to make out the structure even for someone who knows what they are looking at, for those unfamiliar with histones it will be very hard to interpret. David D. (Talk) 17:17, 11 December 2006 (UTC)
As an aside the title of the current figure should read ball-and-stick DNA, or similar, not spacefill DNA. David D. (Talk) 17:24, 11 December 2006 (UTC)
Is the new version an improvement? TimVickers 19:32, 11 December 2006 (UTC)
Defintiely an improvement. I added another picture I took from commons, see what you think. i think having this top view might help a bit more as well as introducing the concept of the interactions that glue the histones and DNA together. Possibly a theme that can be introduced into the text too? David D. (Talk) 21:47, 11 December 2006 (UTC)
Looks good, thank you. As you can see, I'm working my way down through the sections from the top. Much of the history section will need to be moved to a daughter article, but I haven't reached there yet. TimVickers 21:54, 11 December 2006 (UTC)

Yeay! and random suggestions

Hey Tim and David,

I'm so happy that you're tackling this article! It's already looking good. :)

A few thoughts:

  • The pictures of the nitrogenous bases and the base-pair pictures (thanks, guys! :) don't quite agree. The former don't have the connection to the sugar-phosphate backbone that is represented by the crazy wavy line in the base-pairs. Should we amend that — maybe show the sugar or even the sugar/phosphate backbone explicitly in both? Maybe that's not needed; it's probably clear enough from the context of the wonderful colored picture above them.
Yes, I suppose we could, or I could tweak the text to make it clearer what the images show.
  • Are the lines in the base-pair picture thick enough? I think I still have the ChemDraw file somewhere.
Yes, they could be a bit thicker, but that's a minor issue.
  • Should we show the methyl group in thymine explicitly, rather than as an unlabeled line? Some lay-readers might not know the conventions.
Several of the images use that convention, we'd have to change them all. Groan.
  • Personally, I'd enjoy seeing more on the biophysical/electrostatic properties of DNA, such as its extreme charge density, Manning condensation and its superficially paradoxical ability to condense (e.g., into toroidal forms) in the presence of trivalent cations. But maybe that's too technical? :(
If you can put that in non-technical language making a clear link to biology then that would be great. I wouldn't know where to start!
  • It'd be nice to reference that young fellow who did the pH titrations suggesting a two-stranded DNA back in the 1940's, the one who was killed in a train wreck?
The history section is getting smaller and will get smaller still. Maybe a daughter article?
  • I suppose that the IUPAC definitions of the backbone dihedral angles and the numerical descriptions of the inter-base geometry are also too technical, right? Drat. Probably ditto for concept of the "phosphate backbone". :(
We could put that in the mechanical properties of DNA article?
  • What about mentioning helicases, primases, etc. by name? It would give us a chance to link to that fine article, enzyme. ;) I suppose this article does have links to articles with more details, e.g., DNA replication.
This section is under development, thanks for the suggestion.
  • Perhaps include more about the connection between genes and DNA, possibly with some discussion of SNP's? Please don't laugh — OK, I'll laugh ;) — but the January 2007 issue of Marie Claire has an article about the applications of DNA technology to cosmetics — umm, "cosmeceuticals". It says something like "Thanks to the Human Genome Project and other skin-science advances,...SNPs for genes involved in the repair of DNA damage caused by chemical pollutants and UV radiation...for a mere $270, a scientific DNA analysis by dermagenetics.com will allow us to formulate the optimal skin-care cream for you..." You see how it goes. Despite its silliness, this example does suggest that we should also consider common misconceptions and how we might allay them in our science articles. It's charming to think of Craig Venter and James D. Watson as skin scientists, don't you agree? ;)
Charming! That could go in the last section, which is still entirely unedited in this new revision.

Merrily, Willow 15:53, 12 December 2006 (UTC)

Thankfully, TimVickers 19:27, 12 December 2006 (UTC)

Suggestions for the lead section

The lead section seems a little short, as I'm sure you're aware. I also noted the "Here be dragons;)" notice at the top, asking for a full discussion before we make any changes. So perhaps this can be a special section for editors to discuss changes/emphases in the lead?

Speaking for myself, I think it might be helpful for lay-readers if we discussed the qualitative function of DNA before delving into the molecular structure. I'm worried that many casual readers won't even know what a polymer is. Could we perhaps add a short paragraph after the first paragraph, something like this:

The main role of DNA in the cell is the long-term storage of information. It is often compared to a blueprint, since it contains the information to construct other components of the cell, such as proteins and RNA molecules. The DNA segments that encode for proteins and RNA are called genes. However, not all DNA belongs to a gene; some DNA serves a structural purpose or is involved in regulating the expression of genes. Unlike proteins and RNA molecules, DNA is inert and does not act on other molecules; rather, various proteins and RNA molecules act on DNA, causing it to be unwound, copied (replicated), edited, rearranged, repaired or transcribed into RNA.

What do you think? It's only a rough sketch, but such a paragraph might allow us to touch on some important themes of the article. Willow 20:00, 12 December 2006 (UTC)

I'm ignoring the dragons at the moment, go right ahead and edit. TimVickers 20:08, 12 December 2006 (UTC)
Hi Willow, you need to be careful how you define gene here. "However, not all DNA belongs to a gene; some DNA serves a structural purpose or is involved in regulating the expression of genes." I would consider sequences involved in regulating expression to be part of a gene. It sounds like you would consider a gene to be restricted to the transcribed region. This is definitely a debatable definition as well as a moving target depending on which genes are being discussed. Here is one definition i found "a DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology." David D. (Talk) 00:44, 14 December 2006 (UTC)

Hi, David, thanks very much for clarifying that for me! :) I think I'm supposed to know that (blush) but I didn't. :( If I understand correctly, open reading frame is the correct term for proteins; is it the same for RNA, too? I mainly wanted to introduce "gene" in the lead, so that we could use it to debunk common misconceptions (umm, like mine?) in the main text.

The article is looking excellent. At the risk of losing its sleekness, though, maybe we could mention a few more activities on DNA? I was thinking of recombination and viral tricks such as reverse transcriptases and integrases. Maybe a little more about the wonderful specificity of restriction enzymes; I don't recall hearing of similarly specific enzymes for RNA (I suppose there's RNase H, but that's cheating; strange omission from the RNA world, no?) or for proteases (maybe TEV? not thrombin). Perhaps mention the function of restriction enzymes in vivo, too?

I agree that the History section could be shrunk considerably. However, I wouldn't mind a verifiable statement like

Neither Watson nor Crick mentioned Franklin in their Nobel Prize lectures, despite the key role of her experimental data in developing their model.

at the end of the next-to-last paragraph. But that might provoke an edit-war, which I wouldn't wish on you for the world, especially before an FAC. It's perhaps best to stick to the science and leave such historical details for another article.

Under technological applications, I remember hearing about DNA being used in nanotechnology as a means for making regular structures reliably. I might be able to dig up a reference or two if I look hard, but I'm leaving tomorrow for the holidays and might not have the time. I probably won't have access to a computer for a few weeks, so — happy holidays! Warm and happy wishes to all, Willow 11:19, 14 December 2006 (UTC)

P.S. Would it be useful if I made a Figure of positively/negatively supercoiled DNA for the article? I've never done it, but it might be fun and instructive for me. You do have the histone picture already, though, so perhaps it's superfluous.

This is my first Wiki post, so I'm not sure if this is the right format. Anyway, I think blueprint metaphor is very misleading, although it is perhaps common. Recipe or program would be more accurate. 209.98.145.103 02:22, 11 February 2007 (UTC)

I don't think any metaphor can be completely accurate, what we gain in clarity here for people without any background in molecular biology we will inevitable lose some accuracy. "Program" for me implies a degree of control over behavior that genes don't really possess, while "recipe" implies a set of sequential directions. I was trying to convey the idea of the information required to build something, hence "blueprint" TimVickers 02:59, 11 February 2007 (UTC)

Section plan for functions of DNA

I've been struggling with this. I don't want to write a bloated overview of molecular biology and detail transcription, translation, recombination etc which are already covered elsewhere. Such an article would swell uncontrollably and lack focus. Instead, I thought it would be more effective to take a strictly DNA-based view of these processes and divide the sections thus.

  • Overview of biological functions - Tell the reader what is going to be discussed and provide links to explain the basic processes in more detail.
  • DNA/DNA interactions - Recombination, telomere structures
  • DNA/RNA interactions - RNA primer in DNA replication, siRNA control of transcription
  • DNA/protein interactions
  • DNA binding proteins - Histones, transcription factors
  • DNA modifying enzymes - Nucleases and ligases, topioisomerases, polymerases and DNA repair enzymes.

What do people think? TimVickers 16:13, 14 December 2006 (UTC)

This organization looks quite sensible to me. Great to see this article getting some help :) Gene is the science collaboration this month, but started in a very sad state and is probably less far along than your work; it would be good to make sure the various definitional issues (what is included in a 'gene', how non-coding DNA is referred to, etc.) are consistent among all of these related articles.
I also did a bit of reorganization on the computing sections, splitting bioinformatics info from DNA computing. It's common to put these two together because they both involve 'biology' and 'computing', but I think it's inviting confusion. Opabinia regalis 04:57, 17 December 2006 (UTC)

Age of DNA 4 billion years

Why has the link of June 19 2006 as to the age of DNA been omitted subsiquiently. Is not a time frame important? RoddyYoung 11:46, 10 January 2007 (UTC)

You are welcome to add some information on how DNA evolved. Of course the data are fragmentary and most of the proposed mechanisms purely hypothetical. However, I think there is some more solid stuff on the non-biotic origin of nucleobases. TimVickers 16:11, 10 January 2007 (UTC)
We both agree that non-biotic origins of matter should not be included. The time between nucleobases and DNA replecation time scale would be what percentage. Very very small. So they become one and the same in a large time scale. Look at how many nucleobases are being produced 2007 in the world due to the exsistance of DNA. Do you see my point? RoddyYoung 13:21, 6 March 2007 (UTC)

DNA image

I labeled a render I made of a DNA with Phosphate structure 3d model. Let me know if it needs tweaking and I'll make the changes. I wasn't sure if the double helix lines were too dark/strong. 3dscience 18:31, 19 January 2007 (UTC)

Nanometres vs. Ångströms

Allow me to add that just about anyone in the field of biophysics, biochemistry, bioinformatics, etc. uses Ångströms to describe distances in macromolecular structures (e.g DNA, RNA, proteins, etc). I have tried to reflect these conventions in the past. Unfortunately, people seem to think that SI units always apply to science and have reverted my changes. SI units are the rule, generally . . . however, the convention for these distances is always in Ångströms. Check any of the literature (see: PubMed); they will always be listed in Ångströms not nanometres. Please follow that convention. Thank you! --Thorwald 07:41, 23 January 2007 (UTC)

Note: the first figure uses nm and should be changed unless the text uses both Å and nm. Dr d12 22:19, 23 January 2007 (UTC)
I just changed the first figure to use Ångströms units instead of nm. The nm version is still available in wiki commons. 3dscience 19:26, 26 January 2007 (UTC)
Yes, but the interested layman can easily work out the scale of a nanometer whereas only scientifically proficient readers will have any idea what an Ångström is. I personally thought it was the distance from the earth to the sun (but maybe that's an AU). Surely the point of encyclopaedic articles is to inform the uninformed rather than to dazzle them with unfamiliar terms that are specific to a particular discipline. Far Canal 00:23, 13 February 2007 (UTC)
Firstly, there is a nice link to the Ångström article (first usage). Secondly, an encyclopaedia's first goal should always be accuracy, not making it easy for the layman to understand; the "interested layman" can always do a bit of research. Finally, there a literally thousands of examples were the professional terms are given prior usage. All units of macromolecules should stay in Ångströms, as is the convention. --Thorwald 00:37, 13 February 2007 (UTC)
Whatever Far Canal 01:07, 13 February 2007 (UTC)

This is a MoS issue; The Mos says use the appropriate unit SI unless there is a compelling reason not to, there is a compelling reason to Å. But the article should also provide the SI equivalent where Å measures are used. --Peta 00:45, 13 February 2007 (UTC)

"all known cellular life"

The second sentence, "All known cellular life and some viruses contain DNA." sounds a bit strange to me. Is it meant to imply that there is a type of acellular life that does not contain DNA? Is is simply allowing an exception for RNA viruses or is it the possibility of a future discovery of non-DNA based life? Can we build on something like this: "All forms of life on earth, with the exception of some viruses with RNA genomes, use DNA to store and propagate genetic information"? (It would replace sentence 2 and 3)Dr d12 22:19, 23 January 2007 (UTC)

Thanks, I've incorporated your suggestion. TimVickers 23:04, 23 January 2007 (UTC)

Viruses are acellular, and may not contain DNA... 193.130.128.2 15:44, 13 February 2007 (UTC)

I think viruses are not alive. ffm yes? 16:20, 13 February 2007 (UTC)
It's debatable. Personally i think they are alive despite the fact they fail many of the arbitrary criteria used to define life. David D. (Talk) 16:40, 13 February 2007 (UTC)
As far as I'm aware there is no debate. Viruses are not alive, they cannot self replicate, respire, excrete, grow, repair or move of their own volition. Viruses reproduce within living organisms by utilising the mechanics of that organism. They are odd but they don't qualify as life. As such I have a problem with "All forms of life on earth, with the exception of some viruses with RNA genomes, use DNA to store and propagate genetic information" as it suggests viruses are alive (although as I'm responding to a comment made in February this could have been hashed out already, if so sorry!!). Sorry for my first comment on here to appear negative, if it does appear so I apologise.AlanD 21:58, 13 August 2007 (UTC)
Interested to hear why you think there is no debate, in my experience there is a lot of debate among biologists? For example, a recent paper in science The 1.2-Megabase Genome Sequence of Mimivirus by Didier et. al (2004) comments that "The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms." [3] A more genral article in Scientific American says "viruses today are thought of as being in a gray area between living and nonliving" [4]. The presence of a text book definition does not exclude a debate. Biologist don't have to accept the definition and this is one debate that regularly swings back and forth with regard to the accepted wisdom, IMO of course ;) David D. (Talk) 18:46, 14 August 2007 (UTC)
I settled in the end for "Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms." Tim Vickers 22:36, 13 August 2007 (UTC)
Sounds good and conforms with the aforementioned "keep it vague" lol. Avoids many possible debates but is more than precise enough for the job. AlanD 23:14, 13 August 2007 (UTC)
Just to reiterate David, I have never come across a debate personally. I'll admit haven't been reading scietific articles for some time but I've only ever come across pseudo-scientists and those after funding or headlines who are prepared to discuss viruses as being alive. The generally accepted definition of life is not met for a virus, not just for one category but effectively for all of them. Sorry if this sounds a bit aggressive, it wasn't meant to be written that way.AlanD 22:13, 14 August 2007 (UTC)
No, you do not come across as aggressive, you have a point. For me, the definition of life is too restrictive. There is a tendancy for parasites to lose genes such that they cannot live independantly of the host. Are not viruses just the extreme of this practical evolutionary strategy? That Science paper i cite above would suggest this might well be the case. What about the paracitic plants such as broom, they do not photosynthesise, should they still be regarded as plants? This is not really a great analogy but you get the idea. David D. (Talk) 04:04, 15 August 2007 (UTC)
I get the point. I, personally, think it is the other way round; viruses aren't an extreme version of organisms loosing their ability to live autonimously but the starting point of life. I feel that in the early development of life phospholipid bilayer vesicles existed freely, as did nucleotides, proteins and so forth. I believe viruses resemble an early form of organisation that once combined with other such things eventually lead to something akin to prokaryotic cells. I feel that they are a leftover piece of evolutionary history that due to natural selection has continued and evolved (if that makes sense, I'm a little tired so I'm probably not making as much sense as I'd like).
As for paracites and symbiotes. These are tricky areas (look at lichen for example) but they are quite different from viruses. Paracites need other organisms to exist but these are often feeding strategies. In many ways the dependence of paracites on their hosts could be interpreted as their nieches rather than a loss of the functions of life. Most, if not all, paracitic organisms can be shown to have most (if not all) of the functions of life independantly if only for a limited time. This contrasts greatly with viruses that cannot perform (nor can be shown to have) any of the functions of life independant to a host organism.
When I'm teaching this to pupils I'll ask them to assess fire for the evidence of life (it could be said to grow, to reproduce (sparks acting as spores), to respire and so on) and to compare this to a virus. They conclude that fire is not alive as it only meets a few of the criterion of life (sometimes very tenuously). They are forced to conclude that, against their judgement and everything that they believe, viruses are not alive (how can it be true? They are bugs after all! They make us ill, they breed in us!)
In the end though this is biology and there is never any hard and fast definitions or categories (look at the duckbilled platapus for example) only ever the best fit for any situation. Viruses, for me, appear to be alive and contain genetic material but are far removed from living things. Prions are just bits of protein but they cause effects in a way that a layperson would consider to be akin to a virus, no one would consider a stray bit of protein to be alive. AlanD 22:04, 15 August 2007 (UTC)
I don't think there is a clear cut-off and there are going to be ambiguous cases at the boundary. For example the genome of mimivirus is about ten times larger than that of the endosymbiotic bacteria Candidatus Carsonella ruddii and twenty times larger than the genome of Nanoarchaeum equitans, but we classify the parasitic prokaryotes as living and the virus as non-living in a pretty arbitrary fashion. Tim Vickers 22:14, 15 August 2007 (UTC)

Mechanical properties of DNA

The article mechanical properties of DNA is quite long and has kind of lost purpose, any suggestions from anyone on what should be done with it? —The preceding unsigned comment was added by Zephyris (talk • contribs) 15:07, 4 February 2007 (UTC).

It needs references, but apart from that it is an excellent article on a complex topic. TimVickers 17:03, 4 February 2007 (UTC)

The "blueprint" fallacy

The introduction of this article indicates that DNA is often compared to a blueprint. This is a common misunderstanding. A blueprint is a representation of a completed whole (ie: a "plan" of the phenotype) this could not be farther from the truth. For this metaphor to work you would have to state: certain DNA sequences could be compared to a blueprint of a protein. Stating that DNA is a "blueprint is one of the greatest common misunderstandings of DNA. A much more appropriate metaphor would be: The meaningfull sequences of DNA can be compared to a receipe, ingredients that under certain conditions produce a result quite unpredictable due to the environmental conditions of development. These conditions can be compared to the barometric pressure, the oven temperature, etc, that influence the end result of your receipe (ie: the same ingredients may produce a bread that is thicker or has more air bubbles or larger air bubbles, depending on atmospheric conditions). Also we mmust account for the enormous quantity of DNA that has no meaning at all, or sequences that are used for othor uses such as regulatory sequences.

Please, Please, Please change this.

Thank you.

This "fallancy" complaint is nothing but pedantics. Raul654 01:04, 13 February 2007 (UTC)
I beg to differ. ~ UBeR 02:23, 13 February 2007 (UTC)

Copied from above - I don't think any metaphor can be completely accurate, what we gain in clarity here for people without any background in molecular biology we will inevitable lose some accuracy. "Program" for me implies a degree of control over behavior that genes don't really possess, while "recipe" implies a set of sequential directions. I was trying to convey the idea of the information required to build something, hence "blueprint" TimVickers 02:03, 13 February 2007 (UTC)

Good enough for a layperson to read off wikipedia.--Loodog 04:29, 13 February 2007 (UTC)
How about changing it to "a set of blueprints" would that make the analogy work better? David D. (Talk) 05:24, 13 February 2007 (UTC)
I think it is a reasonable analogy, after all whatever their environment E. coli never develop to look like elephants despite Trofim Lysenko's theories, so the influence of the environment on organismal development is pretty insignificant and limited mostly to details, compared to the influence of it's genome. TimVickers 22:04, 13 February 2007 (UTC)
Before anything please sit and think about the gap between phenotype and genotype. (this gap narrows drastically if DNA is a blueprint for the given life form) By environment I did not only mean "a tree" or "a plain". The proximity of one cell to another cell (its cellular environment?) during the developmental stages will influence this said cell. (ie: the chemical or physical signals of adjacent cells can determine which parts of the genome is read and copied). E.coli and elephant is one thing, but think of identical twins, the exact same genotype, but not at all the same phenotype (similar yes, but identical 3-d structure down to the very last cell, no) thus the same "ingredients", but a different result. "set of blueprints" can work fine but I think people should be aware that these are only blueprints for proteins. A blueprint implies a specific plan of an end result(phenotype). Not the case of DNA. Compare this to the "aeroplane analogy". A blueprint of an aeroplane (the body or phenotype) describes the exact location and nature of each and every component, is this the case for DNA? Can you examine someones genotype and determine exactly what this person will look like? As for the claims "clear enough for the layman", I am not sure this is a good idea, inducing "laymen" in false ideas about science by editing things into simple, often mis-representative metaphors sound like a receipe for social intellectual crisis. How average people interpret science influences our social environment drastically (ex: STEM CELL RESEARCH!) This might seem like pedantics to some, but if these people grasped the importance of language and communication it might not seem so (might I remind you of the intense emotional debates on tiny seemingly non-important issues such as the name of Israel in past centuries...etc).
I thank you for considering my complaint.
Please judge wisely. -feb 15, non-member.

OK, since this seems a reasonable compromise I have chaged this to "The genome is often compared to a set of blueprints, since it contains the instructions to construct other components of the cell, such as proteins and RNA molecules." This defines exacltly what the DNA encodes - the proteins and RNAs and makes no claims as to the eventual effects of these encoded products on the final phenotype. I hope you find this acceptable. TimVickers 00:25, 16 February 2007 (UTC)

This seems completely reasonable, and will be very understandable to the general population and is a clear representative metaphor for dna. Thanks! -feb 15 non-member

Not to be annoying and reopen this, but I also believe this is misleading in other ways. A textbook I read once explained that the "blueprint misrepresentation" also implies to the layperson that the end result (ie. phenotype) can be predictably changed in an easy fashion from modifying the DNA (as it is quite simple, in theory, to change the location of a wall, or a door, on a blueprint, for example). It goes on to explain that the recipe analogy once again is better for this, because modifying the instructions on a recipie can have extremely varried and unpredictable results, unless the "modifier" really knows what's going on, and how the modification will affect all stages of the process. It is also important to linguistically note that the qualification that has now been added to the sentence explaining the blueprint metaphor effectively makes it no longer a metaphor, for we simply need to look at definitions. The sentence couples the word "blueprint" with "instructions" ("... compared to a set of blueprints, since DNA contains the instructions needed ..."), whereas, by definition, a blueprint really has very little to do with instructions - it is a structural diagram. What does happen to be defined as a set of instructions for a particular outcome is a recipie. It is in my educated opinion that this is enough to establish my point as sound. Anyone with further comments? If anyone can remember any sources where this is mentioned, please post them, but concerning the nature of this controversy, I know it won't be given much space for debate in academic literature. Chris b shanks 06:58, 2 May 2007 (UTC)

Perhaps the problem is that "blueprint" implies that each organism has a different "genetic plan". But the "blueprint/genome" of related organisms (mammals for example) is, in very broad terms, quite similar, that is -- we share a very large number of genes. Significantly greater differences lie in the order in which genes are switched on/off - and the duration of their transcription/translation. In this sense blueprint is a poor metaphor in my view. MidgleyDJ 10:44, 2 May 2007 (UTC)
Matt Ridley illustrates this well in Nature Via Nurture: Genes, Experience, and What Makes us Human. He makes the point that David Copperfield and The Catcher in the Rye both have (more or less) the same words included in their text -- but are very different books. The difference, he asserts, is in the order of the words. Genomes can be seen in the same way. Our genome and the chimp genome have the same number of words (genes) it's the order and pattern in which they are turned on and off that's important. But perhaps this whole debate is more of an issue for Genome. As an aside it's a great book :). MidgleyDJ 10:58, 2 May 2007 (UTC)
I think the "recipe" analogy is even worse than comparing the genome to a blueprint, as this implies a list of step-by-step instructions. At the simplest level, DNA contains the information needed to construct proteins, it's information is therefore structural information needed to build things, not a list of actions. I therefore preferred calling DNA a blueprint since all it is is information. Moreover, each organism does have a very different "genetic plan" - this is the reason why people don't look like starfish. To be honest, whatever analogy we use it won't be 100% accurate, as it is an analogy. TimVickers 15:29, 2 May 2007 (UTC)

Title

Why is the title of this article 'DNA' and not 'Deoxyribonucleic acid'?

Wikipedia:Naming conventions (common names) Raul654 01:05, 13 February 2007 (UTC)
For a more detailed discussion, see Talk:DNA/Archive 6, where this exact move was proposed. GeeJo (t)⁄(c) • 03:05, 13 February 2007 (UTC)

Error found:

when Alfred Hershey and Martha Chase in the Hershey-Chase experiment showed that DNA is is the genetic material of the T2 phage.[105]


DNA is is--> double is

Fixed, thank you. Fvasconcellos 01:22, 13 February 2007 (UTC)

Semi-Protected??

Just asking, what was the reason to SP this article?? I know it is on the main page, but as per WP:NOPRO, they should only be protected under certain circumstances. Thanks!! -Hairchrm 01:34, 13 February 2007 (UTC)

It actually hasn't been today. It was semi-protected from mid-January (see the log), but the editing restrictions were removed just before it was featured on the main page. However, the template that puts the semi-protected padlock icon in the corner was only noticed and removed later. I think there must have been some sort of caching going on, as the padlock seemed to stick around for a while even after that. — blobglob talk 02:08, 13 February 2007 (UTC)
This page was getting vandalized once every couple minutes. It was becoming a revert storm, then the vandals started reverting the reverts. It was getting crazy. I guess some people really don't like DNA. (Spectrogram 02:12, 13 February 2007 (UTC))
I have restored the semi-protection. The vandalism to this page today more than warrants the step while it is on the main page. It will expire tomorrow. Johntex\talk 21:56, 13 February 2007 (UTC)

Truncated animation

Can someone please fix Image:DNA orbit animated small.gif? In Firefox, it renders only half of the final frame of the animation, and there should be a short pause between loops. —AySz88\^-^ 03:31, 13 February 2007 (UTC)

On further consideration, ideally, it should go back and forth instead of suddenly jumping back to the beginning of the loop. (Perhaps halve the number of frames to accommodate the file size?) —AySz88\^-^ 03:33, 13 February 2007 (UTC)
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