Talk:Horizontal gene transfer/Archive 1

One editor approval

Anthony Sebastian MD has nominated this version of this article for approval. Other editors may also sign to support approval. The Biology Workgroup is overseeing this approval. Unless this notice is removed, the article will be approved on January 22, 2007.

Note to David re Anthony Sebastian's nomination for approval

David: I nominated HGT for approval, after many readings. You have five days to tidy up, respond to feedback, etc., or more days if Biology Group does not concur. --Anthony.Sebastian (Talk) 14:45, 18 January 2007 (CST)

Thats moving things along Anthony. I have updated the URL in the nomination to the latest draft in the history section, and will continue to do so with any non-major change David Tribe 15:32, 18 January 2007 (CST)

Comments by Gareth Leng, Chris Day, Larry Sanger

I think you've done a great job here DavidGareth Leng 06:14, 31 December 2006 (CST)

I understand where the Mariner name came from but is it relevant to have the verses in the abstract? The context of the verses are not made clear and it leads to confusion as currently presented. Wouldn't it be more appropriate in the transposon section? Chris Day (Talk) 16:16, 3 December 2006 (CST)

Nice article. I've done some tidying of the reference formatting. Think you should decide either to abbreviate HGT or not, at present it's mixed.Gareth Leng 09:02, 23 December 2006 (CST)

Also, looking at this for one second, I see the title phrase is made bold several times. It should be boldened only the first time --Larry Sanger 21:41, 23 December 2006 (CST)

Thanks for the feedback. I deleted the Ancient Mariner verse picke up a typo and redirected the link in the for approval template. David Tribe 00:56, 3 January 2007 (CST)

various

Everything there is good, but there are a few minor points: All gene names and organism names go in italics without quotes. You've got to explain at least in a few words what "mariner" is--this is going to get complicated when we start getting to Drosophila names, some of which are apparently Japanese puns. DavidGoodman

Fixed a few organsim name problems with italics David Tribe 04:53, 8 January 2007 (CST) In the "further reading" I think it is less confusing to have the name of the book/article first, followed by the short description. And there are more PMID links to the journal articles--they probably all have one. Are we going to get DOIs from the start, or add them later? I suppose we also have to decide whether to use journal abbreviations. I think that for a general audience we need full names in every case. Envir Microbiol or Mol Biol Evol are not the least transparent to a non biologist--not well enough to enter into a library online catalog, and I think that is the criterion. And one of the entries has a linked title. DavidGoodman

File size is demanding we make references compact or eliminate some David Tribe 07:10, 15 January 2007 (CST)

phylogeny

I suggest that introducing this in the middle of this article is a mistake. "domains" are mentioned in para 4 without definition, and an ignorant reader might think that insects are a domain. I suggest that the second half of the article be split off into "horizontal gene transfer in evolution", that we find some common standard for what domains there are, in a nondefinitive way, because it will come up frequently, The "Biology" article doesn't mention them, and maybe it should have. Perhaps we should have another main article on "Domains (Biology)" Archaea--Prokaryrota--Animalia--Plantae would be my choice for a basic set, although it evades the eukaryotic protists and the fungi. Possibly these have to be evaded in an elementary article. The legend to the tree diagram gives 3: Archaea, Bacteria, Eukaryotes. But the tree you display uses names that only make sense after a considerable knowledge of microbiology. I don't think we should use a diagram with words not explained in the article. We could of course link, but its hard to do in a diagram.

Should we have a sentence at the top: you may want to read "Genetics" and "Microbiology" first?DavidGoodman 03:22, 3 January 2007 (CST)

Did a read-through copy editGareth Leng 08:28, 3 January 2007 (CST)

I discovered a CZ article on the Three domain system and hot linked to it David Tribe 00:42, 13 January 2007 (CST)

Re comments

Reference style. We don't yet have an agreed reference style for CZ but I'd favour making these compact (for journals), not least to keep the length down, but the key is to link to PMID to get expanded details. Again with the PMID link the doi is redundant? For books it would be nice to link to a book review or some further information, and then I wonder if we can't omit publishers' details, at least if we have an ISBN number.Gareth Leng 10:59, 3 January 2007 (CST)

I very strongly feel in general that if this is not an encyclopedia for specialists full journal titles must be used every time, as well as full article titles. But the availability of PubMed may not require this, and I would like to see it discussed.

I would certainly feel that if we get into fields of biology where not all titles have a PMID, or where articles are cited from before the PMID era (now I think about 1965 but it may go back a few years further) the ones that do not need full details. How else will the beginner know where to find them? I am not sure about cases where say 1/3 of the articles do not have PMID--the use of different formats may be confusing. It is possible to say: ask a librarian, but as a librarian I know people do not usually ask, & this will be accentuated for the many users not in a library. From experience, the abbreviations whose expansion is second nature to us, will not be to them.

As for DOIs. it is standard practice in all scientific journals to absolutely require the use of dois when available, and I see no reason why we should be different.

PMIDs link to repository versions of OA papers in PMC only, not yet to those elsewhere. For ones not in PMC, a link to the best available free version should be given. (There us not yet a standard format for this yet--I personally put it in parenthesis in the RW, but here it would logically be an external link, Open access version.

I am also concerned about the fact that PubMed does not indicate whether the journal will be OA, until the user goes to the last step. Since so many of our expected users will not have access to academic libraries, I think we needto indicate these in some way.

I've mentioned all of this in one place or another in the forums, but I've put it all together here.

I am unwilling to approve any article that does not have at least consistent references. This one does not yet do it--some of the ones without PMIDs almost certainly have them. That's the minimum. We can upgrade other factors if we ever agree. (I am not happy about this, but otherwise I fear I will be an obstacle until I am over-ruled, and I'd certainly want to avoid that stark a conflict.)DavidGoodman 22:49, 4 January 2007 (CST)

There is a point in linking to the PMID even if an open access version is not availanble because PUBMED supplies fairly rich additional links and the abstract usually. David Tribe 04:59, 8 January 2007 (CST)

template

I have removed the template, not because of problems with references, but because I remain concerned by the difference in level between the first part of the article and the phylogenetic part. I mentioned this on the article talk page, I mentioned it here. I may be very much wrong & my feeling idiosyncratic, but tell me so -- and why. I see some signs of deferring to our own mutual expertise. DavidGoodman 20:24, 5 January 2007 (CST)

- Guess there are a umber of key points here that need going carefully over. I don't consider myself an author of this article by the way, think my contributions are all in copy editing. Anyway

1) Level. I think the intent is to have articles on CZ aimed at many different levels of readership; we had discussed ways of flagging more technical articles in some way without coming to a clear resolution, and I think we suspected that to a large extent the issue of level would be self correcting in that the only people likely to look up horizontal gene transfer say will already have a substantial levelof knowledge and understanding. At the same time, every article should be written as clearly as possible of course....

2)On references; I've been adding PMID links, but only when there isn't a full text link, which I felt made the PMID redundant. This makes some inconsistency, but my view was that the important thing about the references are that they are verifiable and a gateway for the reader.

I have converted to PMID wherever possible- file size is one issue Im dealing with and addressing DGs crits another David Tribe 00:19, 15 January 2007 (CST)

2)As for Journal abbreviations - I really think we have to be pragmatic, people will get references from PubMed etc or their own files and they will always be abbreviated, expanding them will be tedious and will just take up space (on screen, and for printing out, I favour compactness). If we have a link its surely not necessary. Ideally Id like to see a tool for lifting PMID references straight into CZ format.... Gareth Leng 05:17, 6 January 2007 (CST)

Probably I am the "author" and I value very much the comments. With each of these articles we learn some new general rules/ issues and develop better standardized procedures. The use of PMID is very powerful. These group criticisms continually make us achieve the higher standards that we want. I agree with Gareth's responses though . I've had a few days away from the article and that will help. Ill spend a few days more on this and try and address some of David Goodmans worries. Thanks also to Gareth for the reference work and other additions David Tribe 04:43, 8 January 2007 (CST)

After further thought and writing, Ive come round to seeing that David Goodmans suggestions are the path to follow, and Ill implement them David Tribe 21:32, 8 January 2007 (CST)

Ive gone through and edited references to a consistent format. The result is using PMID as the standard link. There is a problem with file size if URL and other details are added to the refs and use of PMID solves this. (It links through to any open access version via the PUBMED page) . I have not sought to get DOI s or used full journal names. I dont feel strongly about any referencing issue except consistency, but feel we have to be pragmatic. David Tribe 00:49, 13 January 2007 (CST)

"Mad props"

This article is crushing WP version. Grats! Just out of curiosity, how do we make wikipedia cite CZ when they copy and paste this article in to theirs? -Tom Kelly (Talk) 19:43, 13 January 2007 (CST)

For those who need a translation for 'mad props' please see http://www.urbandictionary.com/define.php?term=mad+props "you best be knowing your different vernaculars, yo" if you want to dominate in trivia. I crack myself up. -Tom Kelly (Talk) 19:45, 13 January 2007 (CST)

requested comments by another biology editor

Going through and making "storybook" language changes, trying just to make language more obvious. I know we have no style book yet, but I have changed the initital sentence because when I read text like: ABC (AB, from XYX, also known as CDF) is a trio of letters. I get confused. So I changed it. This overall looks good and I will go through carefully. Nancy Sculerati MD 09:44, 15 January 2007 (CST)

general comments

Section 6.1 is now more balanced & fits in OK, but I dont think it should be our final article on the subject, and there should be a linkL main article at (but possibly wait until its been written, because I dont think the current WP article on ToL is suitable.)

Thanks DG. On this I fully agree and think that a Root to the Tree of life article should be developed. Its interesting that the Tree of Life website declined to write comments on this topic (the Root of Life) as the field is moving so quickly. In some sense its part of Microbiology which Im moving on to, and developing a Root to the Tree of Life page (and a good asset for CZ) it will involve a substantial effort that I'm willing to do, but it will take time. David Tribe 01:33, 16 January 2007 (CST)

Evolution of cells stub created and some content and references moved to it David Tribe 20:49, 16 January 2007 (CST)

Leaving aside reference format as too complicated to do right now, I think there are too many references for an article that is not the most specific one in the subject. There's no need to give them all on this p.

This I agree with too, and already had it in mind to do the reference surgery, which will simplify things. David Tribe 01:33, 16 January 2007 (CST)

I think it would be good if some of the external links were moved up into suggested reading. Also, for suggested reading in an article not at the most technical level, more of the suggested reading should be openly available material, and the linksshouldsay so, both here and in the external refs. Details in a day or two. DavidGoodman 19:07, 15 January 2007 (CST)

These type of suggestions are what I was hoping for in drawing this to your attention thanks NS AS and DG. David Tribe 01:40, 16 January 2007 (CST)

Approval status

I can approve this article in its present form. --Anthony.Sebastian (Talk) 21:40, 15 January 2007 (CST)

Consider this

David:

Asuming you have access to Nature, check these and see if they deserve mention in your HGT article:

http://www.nature.com/nature/journal/v441/n7097/edsumm/e060629-03.html

http://www.nature.com/nature/journal/v441/n7097/full/nature04789.html

—Anthony.Sebastian (Talk) 22:00, 15 January 2007 (CST)

If not here, then in another article Anthony.thanks David Tribe 15:37, 16 January 2007 (CST)

I think all PNAS articles are freely available as well as PLOS Biology, so these are maybe priorities for retaining.Gareth Leng 04:23, 16 January 2007 (CST)

Thanks. Im also intending to give priority to more recent or contraversial issues and cut those issues covred in general older reviews. The trimming may allow us to also use key direct links. David Tribe 15:36, 16 January 2007 (CST)