Talk:DNA/Draft

Article Checklist for "DNA/Draft"

Workgroup category or categories	Chemistry Workgroup, Biology Workgroup [Categories OK]
Article status	External article: from another source, with little change
Underlinked article?	No
Basic cleanup done?	Yes
Checklist last edited by	Petréa Mitchell 22:06, 28 March 2007 (CDT)

To learn how to fill out this checklist, please see CZ:The Article Checklist.

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Approval Area

I placed the ToApprove template for this article and given two weeks per Biology editor Nancy Sculerati. Matt Innis (Talk) 15:38, 7 June 2007 (CDT)

Copyright violation?

This looks like just a rip of a Wikipedia article... can someone fix it? Shanya Almafeta 15:28, 11 February 2007 (CST)

We should all edit it. Before the unfork, we had all the WP articles, and as they became different we made them CZ live. I see your concern, but it is legitimate to import articles and then work on them. Nancy Sculerati MD 15:33, 11 February 2007 (CST)

Proposition:

This article is far too big.

Lets identify 1. the correct sections for a coherent comprehesive introduction to understanding the key biological roles of DNA

2. Packages that form the nuclueus of other vital biology topics.

I'm talkin' RADICAL SURGERY HERE.

Che?

David Tribe 01:33, 12 February 2007 (CST)

Here is the current content:

1 Physical and chemical properties

1.1 Base pairing

1.2 Sense and antisense

1.3 Supercoiling

1.4 Alternative double-helical structures

1.5 Quadruplex structures

2 Chemical modifications

2.1 Regulatory base modifications

2.2 DNA damage

3 Overview of biological functions

3.1 Transcription and translation

3.2 Replication

4 Genes and genomes

5 Interactions with proteins

5.1 DNA-binding proteins

5.2 DNA-modifying enzymes

5.2.1 Nucleases and ligases

5.2.2 Topoisomerases and helicases

5.2.3 Polymerases

6 Genetic recombination

7 Uses in technology

7.1 Forensics

7.2 Bioinformatics

7.3 DNA and computation

7.4 History and anthropology

8 History

I have bolded what seem to be fundamental and should be kept at some level for a primer article. Feel free to add or subrtract from this initial cut. Chris Day (Talk) 01:44, 12 February 2007 (CST)

I disagree with both of you and really like the long detailed article. You just hit cntrl+f or apple key+f and you can find whatever you want in the article. Why not make a simple version as a separate article? -Tom Kelly (Talk) 01:57, 12 February 2007 (CST)

I think what David is suggesting is a primer version, although I don't what to speak for him too much. In my opinion the two could definitely co-exhist. We can have our cake and eat it. Chris Day (Talk) 02:02, 12 February 2007 (CST)

Im not wanting to be dogmatic and don't want to throw anything out just (thinking of) putting some of it elsewhere. It might work if we concentrate on developing all the essentils first but keep it all in one place,

but my point remains that many of these sections are part of important bifgeer stories we also need to write Eg

3.1 Transcription and translation

6 Genetic recombination

7.1 Forensics

7.2 Bioinformatics

7.3 DNA and computation

7.4 History and anthropology'

all these are specialist fields each with a huge story to tell that cannot be done justly here. Why not get those jobs started>, and also do them well

Some comments TEMPORARILY transferred to Talk:Primer on DNA David Tribe 17:23, 12 February 2007 (CST)

But a few hours later RETURNED

Separate Primer rejected

Then returned after discussion with Larry: Still want the lead in developed better and a beeter layout that has a lot of thought about what content is appropriate 22:02, 12 February 2007 (CST)~

DNA essentials?

Top priority is to find a way to create an article that novices will learn a lot of important stuff easily.

Lets keep talking to discover whats the best structure that achieves this and whether for instance thats with a primer plus a big article.

In important topics like DNA a separate primer maybe a good idea. Maybe we can start a tradition of primers, maybe not. Larry might have some argument that its bad.

One way is to have a little link at the top saying DNA primer for those who need the simplest essentials. Unfortunately DNA primer by itself has a special meaning so we could call it DNA for beginners. waadya think? David Tribe 03:47, 12 February 2007 (CST)

Again I put it as a proposition., not a firm judgment and I appreciate the courteous contrary opinion. Maybe we should wait for some others to say something? David Tribe 03:56, 12 February 2007 (CST)

The following analogies are well intentioned but I judge them to be deeply misleading and factually incorrect. DNA is NOT , emphatically NOT, analogous to an operating system. Its not used like a blueprint either- there is no overall physical correspondence between DNA and cellular morphology:

"All cellular organisms contain DNA. DNA, along with other organic molecules, provides a sort of operating system for an organism. It's also compared to a blueprint, since it contains the instructions to construct other components of the cell, namely proteins and RNA molecules. " David Tribe 14:20, 12 February 2007 (CST)

Anaologies for the function of DNA are very difficult to get right across all levels. I agree the blueprint and operating systems are inaccurate and probably not that useful. With repect to hierarchy the best I have seen is a library (the nucleus) with the community as a cell; including police, builders and hospitals. Within the library the shelves were the chromosomes, the books the genes the words the code, the letters the bases. In this usages the DNA is much more than a blue print. The operating system does not work well since it represents information in action, more like the whole cell than just the DNA. Anyway, since no really good analogies are out there it might be best to stick to reality. Chris Day (Talk) 14:28, 12 February 2007 (CST)

Just had a long and fruitful telephone conversation with Rob Tito about analogies (and more importantly COFFEE heck Ive used so many languages for this essential chemical of life that Ive forgotten the english spelling for caffe'). We explored a version of analogy with operating system and Zipfiles that might work. It may well return to the text in a form thats satisfactory David Tribe 15:29, 12 February 2007 (CST)

I just looked to see what is on the web and there are quite a few anaologies out there. Here is one for an operating system where the nucleus of the cell is the kernel of the operating system and the DNA is represented by the source code. This is simlar to my idea above where the DNA represents a subset of the operating system. Chris Day (Talk) 15:38, 12 February 2007 (CST)

Here is another nice one. Chris Day (Talk) 15:50, 12 February 2007 (CST)

Matrix of biology and computer science.
Biology	Computer science
1. Digital alphabet consists of bases A, C, T, G	1. Digital alphabet consists of 0, 1
2. Codons consist of three bases	2. Computer bits form bytes
3. Genes consist of codons	3. Files consist of bytes
4. Promoters indicate gene locations	4. File-allocation table indicates file locations
5. DNA information is transcribed into hnRNA and processed into mRNA	5. Disc information is transcribed into RAM
6. mRNA information is translated into proteins	6. RAM information is translated onto a screen or paper
7. Genes may be organized into operons or groups with similar promoters	7. Files are organized into folders
8. "Old" genes are not destroyed; their promoters become nonfunctional	8. "Old" files are not destroyed; references to their location are deleted
9. Entire chromosomes are replicated	9. Entire discs can be copied
10. Genes can diversify into a family of genes through duplication	10. Files can be modified into a family of related files
11. DNA from a donor can be inserted into host chromosomes	11. Digital information can be inserted into files
12. Biological viruses disrupt genetic instructions	12. Computer viruses disrupt software instructions
13. Natural selection modifies the genetic basis of organism design	13. Natural selection procedures modify the software that specifies a machine design
14. A successful genotype in a natural population outcompetes others	14. A successful website attracts more "hits" than others

I have decided to run with Primer on DNA. DNA primer is unfortunate, and PLoS sets the example. Ill do a link in the article and start this again and Tom will rest happy. 17:00, 12 February 2007 (CST)

LOL, I wasn't loosing sleep over it. I just think we could have one article for the nonscientific (meaning for those who have no interest or training in hard science) that is the main article that comes up when you type in DNA. Then you could write another that is really complex, putting big names in it etc etc. I would have the primer come up when DNA is typed in. However I would not call it a Primer... would you? seeing how we use primers with PCR, etc... right? -Tom Kelly (Talk) 21:17, 12 February 2007 (CST)

Should we tag with Health Sciences Workgroup category?

what do you think? -Tom Kelly (Talk) 16:13, 11 March 2007 (CDT)

No harm, I guess, although it seems a little too basic to be in that category. Mutation, on the other hand, should definitely be in the health science workgroup. Chris Day (Talk) 10:08, 12 March 2007 (CDT)

Unprotecting

Doesn't seem to be a reason to have this protected. --Mike Johnson 20:04, 25 March 2007 (CDT)

Images - licensing

Most of the images in this article unfortunately aren't sourced (i.e. no links to where they came from and what license they're available under), so I've gotta delete em. --Mike Johnson 16:08, 26 March 2007 (CDT)

In accordance with the Big Cleanup guidelines, I'm removing the broken image links. Petréa Mitchell 22:00, 28 March 2007 (CDT)

Approval

This key article lacks for nothing but our attention. I am nominating it for approval with a relatively long lead time, I will spend at least 30 minutes every day until then, and I'm hoping that the DNA scientists out there will do the same- maybe in aggregate. Nancy Sculerati 14:58, 7 June 2007 (CDT)

sorry been out of the loop. Will certainly try and do some editing here too. Chris Day (talk) 15:52, 7 June 2007 (CDT)

Thank heavens! Somebody who really knows what he's doing! :-) Nancy Sculerati 16:03, 7 June 2007 (CDT)

For further informations see:

I suggest removing these directives as they are really designed for WP. In some cases, it would be preferrable to leave them and start the article that they refer to here, I think. Nancy Sculerati 09:05, 8 June 2007 (CDT)

reversion

All due respect, the last two edits are wrong, each strand gets a complimentary strand and the result is two identical double helixes. Please do not copyedit for language unless you are absolutely sure of the science. We need more new content and would love to see some new articles - especially from scratch. Nancy Sculerati 18:24, 9 June 2007 (CDT)

I am one of those novices wishing to learn more about DNA. I found this article restates what it took me years to figure out bit bit. Eventually I was surprised to find out that DNA isn't duplicated, it is the complementary that is duplicated. Kornberg explains on page 13 DNA Replication that the entire DNA process is complementary, calling this the most important feature of the duplex model. Thomas Mandel 19:12, 9 June 2007 (CDT)

The term for this concept is semi-conservative replication. Yes indeed complementarity is a key feature of both RNA and DNA. The question is : is it communicated well at CZ. The intent of my earlier revision was to display this and other things clearly. I'm not quite sure why that section was eliminated. Its not a problem to me but some further discussion of simplicity of communication is worth having. My main issue with the WP version was one couldnt see the wood for the trees.David Tribe 20:42, 10 June 2007 (CDT)

Thomas, we are trying to get this article into shape for approval. It is now nominated for approval with a long lead, because it needs expert attention. It is not the place, if you wish to help the wiki, to experiment with edits as a novice who wants to learn abut the subject. There are so many articles that are only stubs and so many subjects that are not written about here, perhaps you would help us out and work on them? If you would like to help this article, if there are sentences that don't make sense to you, as a novice, or areas that you wish were here, that yo wanted to know about but are not, if you would explain these on the talk page, we can address them and that will help make it a better article. Nancy Sculerati 19:20, 9 June 2007 (CDT)

I have authored the new article Systems Theory, don't know how I happened to read your article, notice that in systems theory the complementary plays a leading role. I wish that the complementary aspect was made explicite. Kornberg writes "The most important feature of the duplex model for DNA structure is the introduction of the concept of Complementarity. ...Complementarity has come to explain transcription and translation and thus the entire sequence of events in the expression of genetic functions."

Indeed, complementarity plays the leading role in every aspect of DNA, assuming, that is, if the concept is broadened to include complementary structures.

Thomas Mandel 20:01, 9 June 2007 (CDT)

Proposed Sentence Cut

Re: sentence: A considerable number of DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, have overlapping genes which may both occur in the same direction, on the same strand (parallel) or in opposite directions, on opposite strands (antiparallel), thus bluring the distinction made above between sense and antisense strands.

I would argue that overlap does not blur the distinction between sense and antisense, since the sense and antisense are only applicable to a particular gene - the antisense strand for one gene can be the sense strand for another gene and this distinction isn't blurred (I don't think) by the genes overlapping. Would anyone object to me scrapping "thus bluring the distinction made above between sense and antisense strands"? --Sean T. Smith 19:01, 18 May 2007 (CDT)

Reference Check

If a reference checks out, add the relevant quote, so that your checking can be verified later. If you have access to journals which require a subscription, please prioritise those marked "not checked - no access".

• 1ab, 2 not checked - no access
• 3 now fixed: ERROR - based on abstract: source gives 22-26 angstrom (2.2 - 2.6 nm) width
• 4 not checked - no access
• 5ab checked OK
  • a quote="The novel feature of the structure is the manner in which the two cheins are held together by the purine and pyrimidine beses. The planes of the bases are perpendicular to the fiber axis. They are joined together in pairs, a single base from one chain being hydrogen-bonded to a single base from the other chain"
  • b quote not applicable
• 6 not checked - no access
• 7ab ERROR
  • 7a ERROR - does not seem a suitable source: supporting information may or may not be inferred but suggest replacement with a source that provides it explicitly
  • 7b ERROR - does not provide structural information of nucleotides not explicitly state that A+G are purines while C+T are pyramidines
• 8ab not checked - no access
• 9 not checked - no access
• 10, 11 skipped
• 12 not checked - no access
• 13 ERROR - based on pubmed abstract: quote="Cro, repressor, and CAP use alpha-helices for many of the contacts between side chains and bases in the major groove" - suggest this is insufficient to make the assertion that "proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove" - suggest further scrutiny of entire text (no access).
• 14 checked ok - quote="The situation in nucleic acid systems is somewhat different: from our present model, the analysis of the different contributions seen in Table 2 shows that the components base stacking, hydrogen bonding, and van der Waals terms are the major partners; the relative contributions are 33.4% base stacking, 30.3% van der Waals, 18.2% hydrogen bonding, 12.1% hydrophobic, and 6.1% electrostatic"
• 15 skipped
• 16 skipped - too complex
• 17, 18, 19, 20 not checked - no access
• 21 checked and article corrected - quote=[N/A; see Table 1]
• 22ab checked ok
  • 22a - quote="...these short overlapping sequences may be involved in expression regulatory mechanisms"
  • 22b - quote="...approximately a third of all genes in the [microbial] genomes are overlapping..."
• 23, 24 not checked - no access
• 25 checked ok - quote="As a linear, single-stranded DNA, the parvovirus genome represents a relatively unusual structure in terms of DNA replication."
• 26 not checked - no access

Reference Check Discussion

Only a handfull of references have actually been checked, but from those that have, we can see that there are sufficient problems to prevent approving the article until all have been corrected. --Sean T. Smith 06:29, 11 June 2007 (CDT)

Overview

My gut feeling on reading this is that it is still very close to the WP article and has some way to go to be a significant improvement on what is by WP standards a very good article.

I think it is over-referenced and overtechnical for an overview article. The over-referencing is a challenge for editors to affirm that the references are accurate and appropriate choices from a vast literature, but are often used here to support uncontroversial statements that we can safely affirm on our own authority. I wouldn't trim these out myself because it's important to retain them in subarticles. (I wrote this before seeing Sean's comment above, after reading it I think even more strongly that we should radically reduce the references)

The article, despite its length, lacks an account of regulation of gene expression. It perhaps should also contain an estimate of the number of genes in the genomes of different species. On the forensic side, I think DNA fingerprinting needs some extra explanation. I think DNA computing should go straight into a separate article, it really is a very minor field at present.Gareth Leng 06:36, 11 June 2007 (CDT)

I think you have to be careful here. If we just start stripping away references, we might end up leaving in erroneous information because we didn't notice that the reference actually said something different. Take reference 3 for example. Before I checked it, two researchers in the field at Wikipedia had already gone over the article and not noticed the small error (I wouldn't have expected them to and that is exactly my point). Although there may be experts involved in this, experts aren't infallable, and without checking references, we could be leaving in false material, that due to lack of a reference (it having been already removed), is not noticed for a long time, if at all.

Stripping out references would be one way of reducing the workload, but that could come at the cost of quality of the finished article. --Sean T. Smith 09:15, 11 June 2007 (CDT)

Modify it drastically, incorporate the more recently imported version, we would have started with that, but... Make the changes that you envision. We have until the 21st. Nancy Sculerati 09:19, 11 June 2007 (CDT)

Ch-ch-ch-ch-changes

I rewrote intro, stuck two new subheadings Genes, because we should explain them before we talk about them, and Regulation of gene expression, because that idiosyncratic Englshman (or is he a Scott, yet?) insists that it has some kind of importance. (go figure). In my honored and august opinion, we should carry on and not worry about the fact that obviously, we have the daunting task of explaining the big story, and also presenting the details. I refuse to be blind-sided by the linear thinking that argues: gee, you can't talk about gene regulation unless you explain methylation in detail. You and I can, and we will, and by the end, we'll have moved things around and clarified so this might actually be a lot of fun. Shoulkd we expalin such things as methylation in detail, we will have placed the audience in a coma- instead, we have to make the mystery acute- just how could that second X chromosome get inactivated (sorry, boys, don't mean to rub it in), and make the details the denouement of the mystery- not a sedative in the intro. So- hold on to your hats, this is likely to be a bumpy ride. If ever "Be bold" applied-it's to this clunker of an article. Nancy Sculerati 10:01, 11 June 2007 (CDT)

Copyedit, please, before approving. I caught two things in the introductory section without even trying. --Larry Sanger 10:24, 11 June 2007 (CDT)

Well, Sean is very concerned with reducing workload, and Larry has carefully bolded the intro, I am taking a 2 week break. Copyedits? The article is being written, it's only been moved for approval because it is so imprtant and needed our attention. There was another article- but it's too hard to simplify adequately so that explaining the duplicate effort in articles can be followed with minimum effort and capacity. I am removing my name from approval, since I will not be on the wiki to get the article into shape. Nancy Sculerati 11:23, 11 June 2007 (CDT)

OK, it's the simple things that catch us out.

"The genetic information in a genome is held within genes. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism."

At the outset I think we need to explain what a gene is more clearly, and to explain what we mean by gene expression. I think we need to explain that the protein coding regions of genes are flanked by regulatory elements to which transcription factors bind to regulate gene expression. The point here is that perhaps most heritable information is carried in these non-coding regions adjacent to coding regions, and in practice it is differences in these regions that most commonly affect phenotype. In most species, heterogeneity in the coding regions is I think very rare. ? So, the sentence above, though often expressed in this way in textbooks, is just multiply wrong if genes are taken to be just the protein coding sequences.

In what sense a gene is really a unit of heredity I'm not clear.

I've deleted a few references and some detail to guage opinion on policy here. I think though that it's possibly more of a challenge to explain the basics clearly and accurately than to provide detail. My instinct would be to cut deep into the references but expose some of the basics (as above) to more careful thoughtGareth Leng 11:58, 11 June 2007 (CDT)

Genes and Cre lox-

I quickly drafted a genes and regulation section. Change them as much as you like.

WE NEARLY GOT INTO TROUBLE WITH A WIKI PEDIA AMATEUR EDIT ON CRE LOX

Impportantly while throwing in a link to Cre loxP recombinase, I relise there are serious factual errors in the Genetic recombination section. Homologious rec is interupted by Cre-lox and RAD521 which are not involved in homologous recombination. Im going to have to fact check in detail the whole mess but not tonite. If I rememver correctly RAD51 is involved in immune rearrangements ( my memory might be wrong) but I need to check for certain which enzymes are invoved in homologopus rec. Cre lox is definitely wrong here though. Ive commented out the problem text to simplify re-editing David Tribe 07:01, 12 June 2007 (CDT)