Talk:DNA/Archive 13

Template:Wikiproject MCB Template:V0.5 Template:Maintained Featured on Template:April 25 selected anniversaries (may be in HTML comment)

Archives

• archive 1
• archive 2 <= If you want to know why this page was intially protected, read this.
• archive 3
• archive 4 <= If you want to know why this page is still protected, read this.
• archive 5 <= More about protection unprotection and co. If you want to know about the unprotection of early march
• archive 6 <= About DNA as a disambiguation page
• archive 7 <= Last discussions on the article itself.
• archive 8 <= Personal attacks not relevant to the issue at stake
• archive 9 <= Earlier proposals for intro and discussion
• archive 10 <= Discussion about how to manage the conflict
• Archive 11
• Archive 12

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)

• I had no problems with the graphics even while on a so-so wireless connection. Johntex\^talk 05:34, 14 February 2007 (UTC)

FA for DNA

Hi there. 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)

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)

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)

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)

Thalidomide a mutagen?

In DNA Damage thalidomide is listed as a mutagen. Not to my knowledge it isn't! Does anyone have a source for this statement or shall I remove it? Fantastic article, by the way! Ewen 06:55, 13 February 2007 (UTC)

Additional ref added. TimVickers 14:43, 13 February 2007 (UTC)

If you mean [1], there is nothing noted about thalidomide as a mutagen. The thalidomide article states that it is not a mutagen and references [2]. So, we have two articles with conflicting statements. --Gadget850 ( Ed) 23:25, 13 February 2007 (UTC)

Thalidomide by my reading is tetragenic - which means it interferes with normal embryo development; it does not necessarily mean that it is a DNA mutagen.--Peta 23:30, 13 February 2007 (UTC)

However these guy showed it intercolates with DNA (T. D. Stephens, C. J. Bunde and B. J. Fillmore, Biochem. Pharmacol., 2000, 59, 1489. PMID 10799645)--Peta 23:36, 13 February 2007 (UTC)

Reword to make clear that thalidomide is mentioned as an intercalator, but not necessarily a mutagen. TimVickers 00:00, 14 February 2007 (UTC)

I'd cut it from the section all together, it's just one of several examples.--Peta 00:04, 14 February 2007 (UTC)

I put it in as it is a drug many people have heard of, while most people are unlikely to have come across the other examples in the newspapers. This drug does intercalate with DNA, what is the problem? TimVickers 04:55, 14 February 2007 (UTC)

The audio version

I have a problem with the audio vesion of this article seems to imply that viruses are alive. and it does this in the very paragraph! the written article does a better job. —The preceding unsigned comment was added by Adenosine (talk • contribs) 09:37, 13 February 2007 (UTC).

• The spoken article was narrated word-for-word from a previous written article. This is stated in the Spoken Article box. From there, you will be able to access the old version of the written article in the state it was in when narrated. If you would like to replace the audio with a newer version, please feel free! All you need is a microphone, clear pronunciation, and 5-6 hours of spare time ;-) 82.45.61.117 15:11, 13 February 2007 (UTC)
• Virues are considered to be alive by many biologists. It all depends how you define alive so it's quite subjective. David D. (Talk) 16:42, 13 February 2007 (UTC)

jehovah's witness link?

the last external link is to a jehovah's witness website, which starts off sounding scientific, and then begins to explain how the Creator made the genetic code.. is that appropriate? 131.111.8.99 18:39, 13 February 2007 (UTC)

Spam addition, I've removed it. TimVickers 18:46, 13 February 2007 (UTC)

All living things DO NOT contain DNA.

Namely, retroviruses only contain RNA, which they use to produce DNA inside the host cell. --132.69.234.73 18:59, 13 February 2007 (UTC)

Viruses are typically not considered to be alive. Raul654 19:02, 13 February 2007 (UTC)

Actually, sometimes they are. · AndonicO ^{Talk · Sign Here} 19:04, 13 February 2007 (UTC)

This possible exception is noted and discussed in the first paragraph, just keep reading. TimVickers 19:04, 13 February 2007 (UTC)

Sorry. As you can see, I didn't do my homework. --132.69.234.73 19:29, 13 February 2007 (UTC)

Not a problem, it is a grey area, as you can see from the discussion above. :) TimVickers 19:42, 13 February 2007 (UTC)

Article has been defaced

In the Physical and Chemical Properties section, there is some egregious text: "The common knowledge is that gays love dna and cause dna to swirl." It probably doesn't add anything to the article, and can be removed.  :) 72.164.10.151 19:43, 13 February 2007 (UTC)

I can find no such text in the current version, try clearing your cache. TimVickers 19:51, 13 February 2007 (UTC)

Random Suggestion

In the introduction DNA is said to never act directly on molecules (unlike enzymes). Unfortunately this is not always true. It is believed that DNA may act on molecules in some situations (e.g. siDNA, although in that case it is DNA acting on DNA). Perhaps this section could be edited to read "in most cases..." or "coding DNA..." 69.255.38.193 19:54, 13 February 2007 (UTC)Byron Smith

Possibly you mean siRNA, which is not DNA. There are several examples of RNA acting on molecules. David D. (Talk) 19:58, 13 February 2007 (UTC)

Sense and antisense

The second sentence of this section is incorrect. The sense strand is not the one copied by RNA polymerase (template strand). I edited the section in Sense (molecular biology). Maybe you can look there and see how you want to change this. Telliott 21:30, 13 February 2007 (UTC)

Thank you, good catch. TimVickers 22:13, 13 February 2007 (UTC)

It says "overlapping genes increase the amount of information that can be encoded within the small viral genome". But does the amount of information actually increase, or is it just the usefullness of the gene? 131.111.8.102 00:17, 14 February 2007 (UTC)

More compact storage of information, therefore more information per unit size. TimVickers 04:49, 14 February 2007 (UTC)

fair enough; upon reading some of the information article, i see what you mean.. the data is the same but the information is different. 131.111.8.102 10:33, 14 February 2007 (UTC)

Brief congratulations

Well, the stuff of life made the Main Page :) (my, that sounded cheesy) Congrats to Tim who made the push for FA and all the editors who valiantly fought vandalism to this article today, and, in spite of and due to 260 edits, here we have in my humble opinion a rare instance of an FA which came out of its Maindate even better. Fvasconcellos 00:26, 14 February 2007 (UTC)

The AGE OF DNA

reproduction, a process in biological DNA that dates back 3.5 - 4.6 billion years.

I have removed this as it is inaccurate, early life may not have used DNA as it's genome, RNA is a possibility but we have no evidence. Similarly, we have no evidence when sexual reproduction evolved. Most of the history of life on earth is bacterial and archaeal, and these organisms reproduce asexually. TimVickers 17:07, 14 February 2007 (UTC)

I have added some material on the evolutionary history of DNA to the "Overview of biological functions" introduction. TimVickers 17:54, 14 February 2007 (UTC)