Talk:Horizontal gene transfer/Archive 1

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

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)

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 faily rich addition 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.

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)