Talk:DNA/Draft

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)