Talk:Gene

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Article Grading: The following comments were left by the quality and importance raters: (edit · refresh) This was once an FA, but has been demoted. Currently has few references, and its discussion is mostly at high-school level.

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Contents 1 Gene exactly? 2 Overhaul table of gene number and genome size? 3 kudos 4 Request for references 5 Sentence moved here from article. 6 new models of evolution and genes - call for experts out there to address an issue 7 Cistron currently redirects here ... 8 Typical numbers of genes in an organism: Differentiate for plants 9 Human genome is Science Collaboration of the Week 10 WP:FARC 11 What are Thrifty Genes? 12 Modifier gene 13 0.5 version nomination 14 Usually? 15 embryology

[edit] Gene exactly?

The article states that "in molecular biology, a gene encodes the chemical structure of a protein". Is that one and only one protein or peptide per gene? Is a gene the amino acid code between and including start codon AUG, GUG and stop codon UAG, UGA, UAA?

Thanks - Jerryseinfeld 08:16, 2 Oct 2004 (UTC)

In eukaryotes, the matter is far more complicated. There's alternative splicing, in which the RNA transcript can be modified post-transcriptionally into any of several different mRNAs. The issue of what a eukaryotic gene is is also somewhat more complicated as a result. Prokaryotes don't do splicing, as a general rule, so they're pretty much one-gene-one-protein beasties. Also, the regulatory sequences in noncoding regions around a gene are often very important to its function, so they might be included in the definition of a gene. Bryan 18:44, 2 Oct 2004 (UTC)

• "genes" were for a long time theoretical entities. Chromosomes can be observed under a light microscope, so they seem to qualify as "physical entities". Molecules (including DNA), once theoretic entities, now would seem to be indirectly observable via electron-microscopes. In the scheme of things, genes would seem to be intermediate between atoms & chromosomes. I see usage of the term genetic material within a DNA molecule, but is it too early yet to say that genes can be identified as being particular pieces or strands on DNA molecules (as a string of atoms)?--JimWae 04:25, 2005 Mar 27 (UTC)

It goes without saying that life breaks boundaries and defies its own conventions all the time. So our shorthand definitions, our abstractions, are going to be wrong sometimes. I don't think hard-and-fast definitions are that important, really, just delivering the broad strokes. That's pretty much how biology works - learn the broad strokes, and fill in lots and lots of nuance. We can work on filling in some of the nuance - e.g. the original query highlights the fact that RNA genes are ignored by the given definition. Graft 04:45, 27 Mar 2005 (UTC)

I noticed some bias on the table on genes. It shows humans having the most genes and most base pairs among all the examples given. One could conclude that we are the most "advanced" specie, or that the number of genes is a sign of intelligence maturity, name it.. I'm no specialist in this field but I recall reading that there are organisms that have a higher number of genes than humans... I think that would be a good addition to the table to dismiss the notion that humans ar at the top of the scale.... 08:46, 5 Oct 2004 (UTC)

[edit] Overhaul table of gene number and genome size?

I think the table listing the gene count of different organisms is slightly misleading, and overly simplistic. Categories such as 'Plants' or 'Flies' are too wide. I think the range of genome size and gene count in plants will be substantial. Maybe the table should only show examples from specific species and actually list the species name to avoid further confusion. E.g.

Arabidopsis thaliana (thale cress) 120 Mb ~25,000 Saccharoymces cerevisiae (yeast) 14 Mb, ~6,000 Drosophila melanogaster (fruit fly) .... etc.

I don't mind doing this if there are no objections.

Keith

Also, could someone explain what the significance of the genome size actually is? It seems surprising that rice (decoded today with about 37,500 genes, see [1]) has more genes than humans (25,000). Why is this? Are human genes longer? Are plants more complicated than humans? Are there lots of dormant genes in plants?

• I believe it is because plants are more complicated: not only do they do cell growth, cell division, cellular respiration in a manner similar to other organisms (animals, fungi), but they also do photosynthesis. They must take in raw materials -- ammonia or nitrate, phosphorus, etc, and construct all sugars, amino acids, and nucleotides from scratch. Heterotrophs can absorb pre-constructed molecules. Furthermore, they have a complex 'secondary metabolism' that varies among taxa and is involved in defense against herbivores and pathogens, and other aspects of their ecology. It's tough being a plant! Satyrium 19:12, 18 August 2006 (UTC)

[edit] kudos

A year or two ago I was active in this article and involved in various edit wars. Today is the first time I have read over it in a long, long, time -- and I want to congratulate all the people who have been working on it. While I am sure it can still be improved, I think you have really turned out a well-written, clear, comprehensive article. It restores my faith in Wikipedia, Slrubenstein 21:51, 7 Dec 2004 (UTC)

Regarding the Dawkins - I haven't read him, but characterizations of his description seem far too anthropomorphic. That is, DNA does not exist to selfishly propagate itself. DNA is a stupid molecule that, left to itself, would slowly degenerate into nucleic acids. But genes that are good at propagating themselves, even at the expense of their organism, will thrive and become prevalent. This isn't as succinct an idea as the "selfish gene" sentence, but it is more accurate. The question is, is this Dawkins' charcterization? Graft 23:00, 7 Dec 2004 (UTC)

Well, I am pretty sure you are referring to the text that was there before I made my additions. I too have problems with the anthropomorphizing, but my sense is, it is in Dawkins (and anthropologists and other social critics who object to this aspect of Dawkins' work usually use this as a jumping off point, that this kind of sociobiology is just the theory of evolution refracted through contemporary bourgeoise ideology). Note there is a problem even in your phrasing, "genes that are good at propegating themselves" because of course it is not the gene that propegates itself but the organism, which involves that gene and many more and environmental and random factors. In any event, IF you want to keep in the Dawkins paragraph, the task is to represent hs views accurately, not to represent our own views. I myself am pretty critical of him, I just wanted his view to be presented more fairly. Slrubenstein

How ironic... hard to escape the urge to attribute intent to everything, I guess. Um, but, okay, this is all I wanted to clarify: that Dawkins actually does anthropomorphize that way. Graft 21:07, 8 Dec 2004 (UTC)

It's been many years since I read The Selfish Gene, but I don't recall that Dawkins was particularly anthropomophic in his descriptions; not more than most biologists who talk about the "purpose" of some aspect of biology. I've rewritten that section to better conform to my memory. I'll try to double check a copy of the text. --Rikurzhen 22:03, Dec 8, 2004 (UTC)

The very word "selfish" anthropomorphizes. Slrubenstein | Talk 20:09, 27 Mar 2005 (UTC)

"anthropomorphizes" isn't quite accurate, since non-human animals could righly be said to be selfish. Dawkins could be charged with the pathetic fallacy, but from my reading of The Selfish Gene, the term selfish isn't meant literally, but rather just to describe--by analogy to an easy to understand term--the equilibrium outcome of gene evolution. --Rikurzhen 22:29, Mar 27, 2005 (UTC)

Isn't it awesome how time has almost no meaning on Wikipedia? 06:01, 28 Mar 2005 (UTC)

[edit] Request for references

Hi, I am working to encourage implementation of the goals of the Wikipedia:Verifiability policy. Part of that is to make sure articles cite their sources. This is particularly important for featured articles, since they are a prominent part of Wikipedia. The Fact and Reference Check Project has more information. Thank you, and please leave me a message when you have added a few references to the article. - Taxman 18:55, Apr 21, 2005 (UTC)

[edit] Sentence moved here from article.

"Some people say the "got lost in the gene pool" to say they are ugly."

This sentence was a sore thumb where I found it in this article. Feel free to add it elsewhere in the article. P.MacUidhir (t) (c) 16:19, 15 November 2005 (UTC)

Dude, it is a sore thumb even on the talk page. Slrubenstein | [[User talk:Slrubenstein|Talk]] 18:48, 15 November 2005 (UTC)

[edit] new models of evolution and genes - call for experts out there to address an issue

While the paragraph on Dawkins is important, I think by itself it carries too much weight in the article. I am not an evolutionary biologist, but I know that among evolutionary biologists there is much talk of a new model of evolution that takes into account the fact that all organisms share a great deal of genetic material, that what makes (literally) one organism different from another — just like the process that makes one organ different from another (in the same organism) — is not that they have different genes for a given trait, but rather that they have or lack genes that switch on the gene for a given trait (in other words, the cells in my hand and liver contain the same genes, but in the process of embryonic development "hand" genes switched on in some cells but not others, while "liver" genes switched on in some cells but not others. Similarly, humans have genest that play a role in the embryonic development of dogs, but that just never get switched on in humans; conversley, dogs have genes that play a role in the embryonic development of humans, but they just never get switched on in dogs). This model has significant implications for the theory of evolution, because natural selection would not be acting on the genes for given organs (e.g. gills or lungs, wings or arms) but rather the genes that function as switches. This is a different model than Dawkins. I know full well that this model is not universally embraced by evolutionary biologists, and that even among those who embrace it, there are differences in the importance they claim for our understanding of speciation. Nevertheless, I do know that these are things evolutionary biologists are discussing, and I think it should be reflected in the article. Since I do not know any of the scholarly literature on this, I am not competent to provide an accurate NPOV account of it in the article. But is there anyone out there who knows what I am referring to, knows it well enough to see where I am misinterpreting or misunderstanding it, and knows it well enough to add a section to the article that makes its significance, or potential significance, clear? Slrubenstein | [[User talk:Slrubenstein|Talk]] 19:06, 15 November 2005 (UTC)

You're getting at a subject of study at the interface of developmental and evolutionary biology sometimes called evo-devo. (You may be mixing that up a bit with the matter of inclusive fitness, which is linked closely with the gene-centered view of evolution.) Evo-devo is AFAIK at a different level than the question of whether evolution operates from a gene-centric view. But yeah, there's tons of stuff that could be added to this article. --Rikurzhen 19:33, 15 November 2005 (UTC)

Yes, evo-devo, that is what I meant to say. I am not rejecting the principle of inclusive fitness, but as an outsider it does seem to me that evo-devo has implications concerning the gene-centered view of evolution. Clearly you know far more than I do, I hope at some point you will find the time to put some of it in, to the appropriate articles. Slrubenstein | [[User talk:Slrubenstein|Talk]] 21:09, 15 November 2005 (UTC)

There very well could be a connection. I just don't know of one -- but my lack of familariity is not an indication that no one was written about it. However, inclusive fitness has implications even for single celled organisms, whereas evo devo is mostly about animals. --Rikurzhen 22:39, 15 November 2005 (UTC)

There's two things at work here: one is that the idea of "genes as the unit of selection" is obviously too simplistic, and now that molecular biology and genomics allows us to chase function down to the individual base-pair level, we don't need to restrict ourself to thinking in terms of gross elements like whole genes. The other is the fact that functional divergence in genes doesn't seem to meet up with the picture set by organismal complexity (e.g. human and C. elegans have a similar number of genes); also, divergence of form by contemporary accounts has a lot more to do with differences in gene expression (e.g. the faddish "Hox" genes) than changes in genes themselves. Thus the desire to chase evolution into regulatory regions. Since that's relatively unknown territory, it'll probably be a while before we can know whether this is a reasonable line of argument. Graft 18:13, 16 November 2005 (UTC)

[edit] Cistron currently redirects here ...

Cistron currently redirects to this article, but the current article content does not support that redirection. Is there a more appropriate article that addresses prokaryotic genes to which "cistron" could be re-targeted? User:Ceyockey (talk to me) 16:10, 15 January 2006 (UTC)

[edit] Typical numbers of genes in an organism: Differentiate for plants

The number of genes in plants vary hugely, so we should probably differentiate that part. I seem to recall that Arabidopsis thaliana and some Pinus species are at the extremes of the known distribution... - Samsara _contrib ^talk 22:18, 25 January 2006 (UTC)

Plants have several times undergone genome duplication events (and some have done so recently without changing much), so it's not unusual for them to have ridiculous chromosome numbers and correspondingly large genomes... Graft 00:26, 26 January 2006 (UTC)

I'm aware of that. Although your post is not directly countering my suggestion, I might point out that many (most?) genes have arisen by duplication. - Samsara _contrib ^talk 00:52, 26 January 2006 (UTC)

Yeah, but gene duplication is not the same as genome duplication. I'm merely suggesting that a huge number for plant genome size is probably representative. Graft 17:45, 26 January 2006 (UTC)

gene duplication is not the same as genome duplication

True, though both have the potential to lead to divergent gene function. I don't know what the wikipedia consensus is for what constitutes a plant (no time to read the article just now), but we have to be careful not to think only of angiosperms. - Samsara _contrib ^talk 20:49, 26 January 2006 (UTC)

[edit] Human genome is Science Collaboration of the Week

Just to let you know that Human genome has been voted Science Collaboration of the Week. - Samsara _contrib ^talk 10:32, 27 January 2006 (UTC)

[edit] WP:FARC

I hate to do this but I'm going to list this article on FARC - it simply does not deserve to be featured in my opinion. Why?

1. Lacks inline citations
2. the lead is too long & does not conform to WP:LEAD
3. neither "History" nor "Evolutionary concept of gene" are comprehensive.

As a courtesy, I'll give the contributors to this article some time to address these concerns before I take it to FARC. Mikker ^... 17:20, 11 February 2006 (UTC)

I've now listed the article at FARC. Mikker ^... 21:02, 12 February 2006 (UTC)

[edit] What are Thrifty Genes?

I've heard the term used a couple times, but since it's being used to advertise a dieting concept I'm not sure how verifiable it is. It does quote a journal though, is it a good journal? Here's the quote:

Journal of Applied Physiology 96:3-10, 2004

“Survival of Homo sapiens during evolution was dependant on the procurement of food…

To ensure survival during periods of famine, certain genes evolved to regulate efficient intake and utilization of fuel stores. Such genes were termed “Thrifty Genes” in 1962. Farther more, convincing evidence shows that this ancient genome has remained essentially unchanged over the past 10,000 years and certainly not changed in the past 40-100 years.

Although the absolute calorie intake of modern day humans is likely lower compared with our hunter-gatherer ancestors, it is nevertheless in positive calorie balance in the majority of the US adult population. We contend that the combination of continuous food abundance and physical inactivity eliminate the evolutionary programmed biochemical cycles emanating from feast-famine and physical activity-rest cycles, which in turn abrogated the cycling of certain metabolic processes, ultimately resulting in metabolic derangements such as obesity and type2 diabetes.”

“Manu V. Chakravarthy 1 and Frank W. Booth 2

1Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis 63110; and 2Departments of Biomedical Sciences and of Medical Pharmacology and Physiology and the Dalton Cardiovascular Institute, University of Missouri, Columbia, Missouri 65211”

Now obviously such concepts have to do with how genes are activated and deactivated. My knowledgee is limited, but it's endocrinology, hormones and steroids that control that kind of thing, right? As diet may influence those, I wonder if there may indeed be adaptory aspects. Whether or not it's proven though, is confusing. So, can anyone help in forming the beginnings of an article on this, linked to in this page and possibly others such as diabetes and fat loss? --Tyciol 09:38, 14 February 2006 (UTC)

[edit] Modifier gene

... missing. --129.11.76.216 14:30, 13 March 2006 (UTC)

... inscrutable. Graft 20:28, 13 March 2006 (UTC)

[edit] 0.5 version nomination

Failed on quality: (Not a FA, as stated) failed for same reason it was at FARC. Chuck^(척뉴넘) 01:47, 29 May 2006 (UTC)

Why? If you tell me your problems about the article, I'll work on it. I find it important to put Gene into V0.5. NCurse _work 10:33, 29 May 2006 (UTC)

[edit] Usually?

The article reads ". . .encoded in the organism's genetic material (usually DNA or RNA). . ."

usually? Is there an exception to DNA or RNA?

It depends on the organism. We know RNA-based viruses. NCurse _work 13:49, 23 August 2006 (UTC)

[edit] embryology

Does anyone happen to know any embryologists? I think Embryology really needs a lot of expert attention. would sympathtic editors consider a positive vote here? [2]Slrubenstein | Talk 16:56, 28 August 2006 (UTC)

I take a look, thanks, but maybe you should search for experts here: Wikipedia:WikiProject Expert Request Sorting or have a look at that: Category:Pages needing expert attention. NCurse _work 20:06, 28 August 2006 (UTC)

Thanks! Slrubenstein | Talk 20:43, 28 August 2006 (UTC)