Talk:Genome

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1 Request for improvement
2 Definition debate
3 book promotion
4 Genome v. Gene Pool
5 base pairs
6 Reference Book Removed
7 References
8 Human genome is Science Collaboration of the Week

[edit] Request for improvement

This page really needs to be improved. Is anyone planning on taking on the job? Right now it is very basic, disjointed, and even repetitious. Not trying to crticize what has been done, but to look forward to what still needs to be done.Evolver 13:17, 4 September 2005 (UTC)

[edit] Definition debate

Here's what the Oxford Dictionary of Biology says about genomes:

http://www.xrefer.com/entry.jsp?xrefid=461212&secid=.-&hh=1

That definition, while brief, supports my idea of genome (and that of the molecular geneticist sitting next to me), which is that plasmids don't count (b/c they aren't chromosomes and they're optional). 168...

Then again, opinions seem to differ. This is from a FAQ at the Web site of TIGR

What place do microbial plasmids have in defining the

                       genome of microbes? It seems as though the term
                       "microbial genome" refers solely to the microbial
                       chromosome. How are plasmid genes, that often
                       define key traits, included, or are they not included?

                       By definition, a genome is all the DNA contained in
                       an organism or a cell. A chromosome is the main
                       DNA structure that contains the genes required for
                       life. In microbial genomes, most often there is a
                       single circular or linear chromosome and there are
                       may be many extra-chromosomal, self-replicating,
                       linear or circular DNA known as plasmids. In
                       eukaryotic genomes, the chromosomes are within
                       the nucleus and the extra chromosomal DNA is in
                       the mitochondria as well as plastids in plants. In our
                       genome projects of organisms that contain
                       plasmids, ei. Borrelia borgdorferi, Methanococcus
                       jannaschii, and Deinococcus radiodurans, the
                       sequencing, finishing and annotation are done for
                       the entire genome, chromosome and plasmids.

http://www.tigr.org/about/faq.shtml

But to me the question, which was expressed in words that don't sound naive, proves that the traditional sense of genome is that it's the chromosomes. The definition in the answer above disagrees with the usage of "genome" in humans and other eukaryotes: "All the DNA" would include mitochondrial DNA, which is typically considered its own genome (the "mitochondrial genome") 168...

Plus there's the issue that it's really only half of the chromosomal DNA in diploid cells. I guess the article needs work. Not tonight from me though. 168...

I was under the impression that genome, when applied to an entire species, does refer to the generic sense, without encompassing any of the genetic diversity of the species, and so can be reduced to just one of the sets of chromosomes, but that genome, when applied to an individual, refers to the specific set of allelles that individual possesses, and so cannot be so reduced. Hence references to chimeras being "multiple genomes in one individual." Am I mistaken in this? Geoff 22:46 18 Jun 2003 (UTC)

I've never encountered "chimera" being used like you used it (in the uses I know, people talk about two "genes" being spliced together, which proves there's some looseness in the use of the word "gene," [strictly I guess it's "alleles" that are spliced], but that doesn't mean people are equally loose with "genome"). I suppose I can imagine I've read news stories that say things like "once doctors have your own genome sequence" (even though nine times out of ten it's "THE human genome" the stories talk about). But that imagined or remembered phrase has the words "your own" in it, which I think is because you have to overcome the natural sense of genome as something general and impersonal. Is your chimera quote an actual excerpt from a magazine article, or just your recollection of the kind of thing you've read or heard?168... 00:38 19 Jun 2003 (UTC)

I've heard "chimera" described this way in at least a few places. I was paraphrasing, not quoting exact text (otherwise I would have given a citation), but I'm fairly sure that it was phrased in roughly those terms, although you're right, I could be mistaken. I believe the first place I read of chimeras was in Science News. We seem to have different ideas of what the term refers to, so I'll give my understanding of it.

In the very early stages of embryonic development (I hesitate to quote exact stages since I'm freely recalling this, not refering to anything, but I think it's prior to blastulation) two seperately fertilized embryos may come into contact and fuse. If it's early enough, the fused embryo will continue developing normally, with the result that the chromosomal DNA in a cell in one part of the body is only as similar to the chromosomal DNA in a cell another part of the body as one would normally expect the chromosomal DNA between siblings to be. This is uncommon in humans, since usually there's only one egg present during fertilization at a time, but more common in, for example, dogs, which commonly have many eggs present simultaneously.

Thinking about it more, actually, I think the first place I heard of chimeras was in my high school AP Biology course; my teacher may have been the one to describe chimeras as multiple genomes in a single individual. I'll be the first to admit that information taught in high school science classes is not always to be trusted, but I have a great deal of respect for the knowledge and integrity of my particular biology teacher.

Anyway, I'm not sure what bearing, if any, this has to the way one should interpret the word "genome." It could be that from a scientific standpoint, the only proper usage is, as you say, in reference to the general species-wide genome, and its usage in reference to an individual's set of chromosomal DNA is only a colloquialism, but it still seems to me that there would be a gray area. What about cases of speciation in progress? Do subspecies have seperate genomes? Also, if the word can be used colloqiually, if "incorrectly," to refer to an individual's set of DNA, shouldn't we acknowledge that? Language does reflect usage, after all. Maybe we should make a few of these issues clearer in the article? Geoff 22:09 19 Jun 2003 (UTC)

O.K., I remember now this other context of chimeras. I think it's related to how they make transgenic mice--manually combining embryoes. Also I was confused before and thought you were talking about spliced genomes, not about individuals who are genetic "mosaics" (which I think is the more common way people talk about this kind of chimera-ness). Your subspecies question sounds reasonable to me, though I'm not sure it's a problem for the "genome" concept (my hunch is that subspecies would be spoken about as having different versions of the same genome, b/c they are the called the same species, and one species has one genome, I believe). I can't disagree with your philosophy of usage and how the article should accomadate it, but I'm just not sure we aren't talking about an idiosyncratic usage. e.g. If it were only your biology teacher who talks about mosaics having two genomes, I don't think it would be time yet to update the dictionary. I guess according to that usage regarding mosaics, it takes two sets of chromosomes to make a genome, and in a mosaic it takes at least four. Hmmm. I guess a reasonable person could hold that view. But besides your biology teacher, is anyone out there publishing it? 168.150.238.72 00:58 20 Jun 2003 (UTC)

Your argument sounds good to me. Unless someone else disagrees, I'm willing to let the point be settled. Geoff 22:03 21 Jun 2003 (UTC)

Not so clear on what you're saying.. but a genome does not represent two sets of chromosomes. It does in humans, and most animals, but in plants, fungi etc. a genome may have only one set of chromosomes or many. Wheat is octoploidy, seedless watermellons are triploid. -adenosine

[edit] book promotion

Somebody stuck the following on the front of the genome article.

":Genome is also a popular science book by Matt Ridley."

Looked like shameless book promotion to me, so I took it out. Would one start an article on relativity by a reference to the latest Einstein Biography? I would hope not. If somebody is still convinced of the importance of Ridley's contribution, perhaps mention of his book could be added further down.

Hate mail to: Nickthompson@earthlink.net

Fair enough, but some people may come to Wikipedia looking for information about Ridley's book, which was quite well known.70.31.67.60 19:54, 3 September 2005 (UTC)

Ridley's book should be mentioned in the human genome page, not here. Although he called it "Genome", it was specifically about humans. It is also not a primary reference work but a popular discussion. If someone wants to make a separate new page about the book to avoid confusion with this page, that's fine, but I don't think the book needs to be cited on this page.Evolver 21:03, 3 September 2005 (UTC)

Looks like a standard Wikipedia:Disambiguation link to me. If Einstein's biography is called "Relativity" and there is a Wikipedia article about it, the Relativity page should have a disambiguation link to it. Joe D (t) 00:28, 4 September 2005 (UTC)

I agree with that. Evolver 01:13, 4 September 2005 (UTC)

[edit] Genome v. Gene Pool

I have heard and read the word geneOME used as a synonym for gene pool, meaning all the possible variants of all the genes carried by all the organisms in a population, rather than referring to all the genes carried by an individual. I am pleased to see the narrower usage defended here. However, I am wondering if there is any significant body of opinion out there that the term ought to have the broader meaning. If so I would like to hear it.

nickthompson@earthlink.net

[edit] base pairs

does the genome count include base pairs from both strands or just one side? Since both would be mirror images of each other. - Omegatron 23:13, Jun 21, 2005 (UTC)

The genome count is of basepairs, pairs of course being plural. Thus, a basebair is both individual bases. However, often people will just refer to a genome size in terms of bases, but what they really mean is baispairs.--Doucher 23:34, Jun 21, 2005 (UTC)

Heh. "Pairs." Yeah, I, um, didn't notice that. - Omegatron 01:07, Jun 22, 2005 (UTC)

[edit] Reference Book Removed

I am removing (again) the book added as a reference by 70.31.67.60. Please explain why this book, as opposed to many others out there, should be added as a reference, considering that 1) the text was written well before the reference was added, 2) the addition is coming from an anonymous user, 3) the link goes to an Amazon page to help people buy the book, 4) the history of 70.31.67.60 shows that not only has the user created a page on the book, but is inserting it as a reference in other pages on Wikipedia as well (example one) (example two) Turnstep 19:30, September 3, 2005 (UTC)

1) it is the most recent and comprehensive book that covers all the (previously, and now again, unreferenced) statements made, 2) who cares who added it -- it is referenced so you can check it yourself, 3) no it doesn't now, 4) indeed, because it provides summaries -- in some cases the ONLY ones available -- of the topics discussed, but those pages also include LOTS of other references as well. 70.31.67.60 19:53, 3 September 2005 (UTC)

Incidentally, if you think B chromosomes, ancient genome duplications (now merged with polyploidy), and other topics are not worthy of inclusion in Wikipedia, may I ask why not? It so happens that I noticed these were all missing, and added brief articles plus LOTS of references, including to the book in question (since again, it contains the most detailed and up to date reviews I am aware of -- please by all means feel free to expand these articles and add more references if you are an expert). In your example one, the book is one of five references, and in example two it is three of 13 references. I also considered making links to every journal I cited, but I was not sure if it was worthwhile adding so many external links. It occurred to me that linking to Amazon was not really appropriate, so I created a summary page for the book within Wikipedia. I did not realize it was an issue to create a summary page about a book. Initially I included everything I could find about it (including the back cover copy), but was told that was too promotional and might be a copyright issue, so I removed everything except a short summary. I hope this is satisfactory now.70.31.67.60 20:13, 3 September 2005 (UTC)

There is obviously nothing wrong with creating a book page. And once made, it makes perfect sense to inject references to it where appropriate (including in new pages that are created by the same user). I don't understand what the criticism is about.Evolver 01:13, 4 September 2005 (UTC)

[edit] References

This page is sorely lacking in references and links to further published material. I have added some in the section discussed above, but we need to insert more throughout. Hopefully as this page grows, we will incorporate citations of primary sources as much as possible, as this is one area where people will definitely need to look for more detail than Wiki pages can ever provide. Note that I have included a link to the book discussed above -- I think that is appropriate since a page exists. If people make pages for the other books, I will link to them also. However, I agree that linking to Amazon is not a good move. Note: please only put references cited in the text in the "References" section. Relevant but uncited publications could be provided in a "Further reading" section if need be. Evolver 15:48, 4 September 2005 (UTC)