Talk:Gene

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Intro

I cut a bunch of stuff out of the intro and pasted it else where. I think that what i did makes sense, but those of you more familiar with the article may want to put it elsewhere. Please don't put it in the intro, the intro is already a little long (necessarily so). when i loaded this page this morning i couldn't see the table of contents on my 1080p screen because there was so much intro... The intro should really just contain a brief description of the matter at hand. The chemistry stuff about the hydrogen bonding of androsine and such has no place in the intro, neither did the history.

Definition of a Gene

There is a good discussion of the difficulties of defining Gene in Nature 441, 398-401 (25 May 2006). It suggests a valid working definition of a Gene as "A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions." The old-style view currently suggested in this article is far too simplistic. NBeale 21:54, 22 May 2007 (UTC)

At some point in time, I added that very definition to the top of this page. This definition was finalised by Richard Durbin after a meeting of the Gene Ontology group. It was the tightest definition that people could come up which still covered everything that is known about all the different types of gene (from the molecular biology point of view). I guess some people will still want a less scientific definition, but I think it should go back into the page. Nod 00:23, 23 May 2007 (UTC)

The new version produced was ungrammatical and contained fragments of incomplete sentences. I reverted back to a version that was a bit clearer. TimVickers 21:29, 26 May 2007 (UTC)

I have real problems with the idea of "unit of inheritence." Does it just mean "inherited?" Junk DNA is also inherited. Or does it mean that it corresponds to an inherited phenotype or trait? If so, this is a vast oversimplification. The rest of the definition make sense to me although I think a lot of non-scientists won't get it. Tim's edit preserves the wording "unit of inheritence" and I think we need to discuss this. I know this is not going to appeal to people, but I would define gene as, "a subset of DNA that cells transcribe into RNAs and then translate into proteins (or if you prefer popypeptides)."Slrubenstein | Talk 14:04, 27 May 2007 (UTC)

We can't ignore genes that produce an RNA product, such as rRNA and snoRNA genes. This is why I defined a gene as producing a "functional RNA product" - protein biosynthesis is one common function but it isn't nearly the only function. There is a real disconnect between geneticist's views of genes which are as "units of inheritance" and molecular biologists's views of genes as segments of DNA. I think it is important to include both, since genes are important due to their genetic effects, but their basic nature is segments of nucleic acid. TimVickers 16:24, 27 May 2007 (UTC)

Okay, I am not questioning that genes produce an RNA product - but what exactly does "unit of inheritance" mean? How is it different from saying "genes are inherited?" Slrubenstein | Talk 11:34, 28 May 2007 (UTC)

Geneticists see genes as discrete factors associated with discrete traits. This defines genes from the perspective of the phenotype. In this context, "Unit of inheritance" means this is the smallest unit through which the process of inheritance operates. I think the lead needs to cover both the molecular biology and genetics views of genes. TimVickers 15:36, 28 May 2007 (UTC)

I agree with you that the lead needs to cover both views. I question though whether this is an adequate representation of the geneticist's view. I think most geneticists would agree that many genes do not map on in a one-to-one way with specific phenotypic traits. Some do, many do not (at least in human beings and amoebas), we need to be clear about this. Slrubenstein | Talk 15:40, 28 May 2007 (UTC)

You're probably right. What wording would you suggest to cover the genetics in the lead? TimVickers 15:42, 28 May 2007 (UTC)

I'll have to think about it .. maybe both of us can think about it. I am tempted just to add the word "some" or"many" before "genes ... and leave it to the body to explain. The thing is, in many organisms most genes do not express themselves phenotypically ... but virtually all phenotypic traits are at least to some degree expressions of genes (the thing is, they may express other things too like random environmental interactions within the cell). I think one of the most important things for me is to include an account of polymorphism in the article too. Your thoughts? Slrubenstein | Talk 15:55, 28 May 2007 (UTC)

Seems to me that geneticists and molecular biologists use different concepts of gene. So it is not possible to develop a definition that is acceptable to both. You need two different words for two different concepts. M Navarro.

The term "gene" should cover its original and current concepts because it is so commonly recognized. That is, it should be inheritable, expressible and silenceable for its function. Simultaneously it should instructs one or more phenotypic traits which can be either explicit or cryptic, and it can be even null. In this sense, the working definition that it is mere a locatable DNA segment is far too simplified. The essence of a gene is the inheritable information with the instruction for traits. So far, however, the only media which can carry or represent this information is sequence of nucleotides, although the status of nucleotides and cytoplasmic environment may influence its behavior. It resembles to the concept of object-oriented programming, where the information is defined as a class to be instantiated as objects bearing properties and methods to express behavior or traits. A trait may be explicit or hidden depending on the status and environment, and it can be even just a place holder whose content is vacant. It can be copied and modified. Here the media itself which carry the class definition is of no importance. —Preceding unsigned comment added by Tosendo (talk • contribs) 01:53, 21 September 2010 (UTC)

I am a layman in the field of genetics, but I would like a better understanding of what a gene "looks like". I have the impression that genes can be identified as such by recognizable sequences terminating the gene. The material above makes no such statement, but implies that it must generate a protein, at least in the typical case. Using that definition, how is that determined? To summarize perhaps, I would like to see a section or independent article on how chromosome sequences are interpreted, and how genes are identified. I am asking about genes in the simplest, or old-fashioned sense, and not about switches and so forth. JFistere (talk) 09:20, 22 September 2010 (UTC)

In analogy, a genome is a cookbook and a gene is the instruction for how to cook a dish. The question is, which should be called a gene, the instruction or the page itself.tosendo (talk) 11:32, 30 September 2010 (UTC)

This is close to an oft-used Richard Dawkins analogy, though it is used when dissuading people from referring to a genome as a blueprint as this implies simplistic 1:1 mapping which is obviously not the case; thus it is referred to as a recipe. It adds uneccessary extra confusion here though, genes cannot be considered as units derived from the 'top-down' viewpoint. A complex phenotypic trait would be mapped to nearly every gene through different levels of interaction, this is not helpful in building a definition. Instead of thinking in terms of genomes and organisms, in terms of clarity a gene should be defined through the eyes of the Gene-centered view of evolution Jebus989^✰ 13:53, 30 September 2010 (UTC)

Citing 'Genome' from Wikipedia: In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA. It clearly states that genomes are information and genes are parts of the genomes. Is this definition wrong or genes are information? tosendo (talk) 08:07, 25 November 2010 (UTC)

Does the definition of gene include regulatory regions?

At the bottom of the article it says "all regulatory elements of DNA are therefore classified as gene-associated regions". Does that make them regions that are merely associated with a gene or regions that are part of a gene? Thanks. Cirbryn (talk) 19:34, 16 January 2008 (UTC)

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)

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)

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)

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)

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)

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)

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)

I also reached this article looking for Cistron only to find that the word is not even defined here. Should we just go ahead and start a new article? Or maybe a section within this article? --Antonio.sierra 14:28, 6 November 2007 (UTC)

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)

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)

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)

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)

Modifier gene

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

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

Not a real phenomenon, only a mathematical tool. Samsara (talk • contribs) 18:41, 5 December 2006 (UTC)

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)

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)

NASA seems to have some opinion. tosendo (talk) 08:06, 9 December 2010 (UTC)

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:Articles needing expert attention. NCurse _work 20:06, 28 August 2006 (UTC)

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

Organization of this article

The way the content in this article is organized makes my brain ache. I propose this structure, or something like it (roughly following Watson et al. Molecular Biology of the Gene, but moving expression above maintenance/DNA repair):

• Classical genetics and Mendelian inheritance (BRIEF; this already has its own article - a paragraph or two)
• The physical gene: DNA and RNA

• Promoters, repressors, and enhancers
• Introns and exons
• Differences between eukaryotic and prokaryotic genes, including operons

• Gene expression

• The genetic code, Transcription, Translation (Brief, covered elsewhere)
• Gene regulation
• Functional RNA

• Genes and inheritance

• Relationship to classical heredity

• Evolution of genes

• Mutation and repair
• Exon shuffing
• Pseudogenes

• Genes in genomes (Brief, covered elsewhere)
• Human genetic disorders (Brief, covered elsewhere)

Thoughts? I wonder about leaving the 'genome' section so far down, but this organization has the advantage of presenting the familiar classical context and thereafter following a small-to-large progression from focus on a single gene to focus on the whole genome. I also thought about giving 'mutation' its own top-level section before 'gene expression'. Opabinia regalis 06:07, 5 December 2006 (UTC)

It is a mess now I agree. It needs reworking so much I wouldn't want to discourage anyone with dispute, but I don't see anything wrong with your plan :) I like mutation being in replication, or at least after it if there is too much mutation material. - cohesion 07:01, 5 December 2006 (UTC)

Great idea. What about mess DNA? NCurse _work 18:36, 5 December 2006 (UTC)

Sorry, do you mean 'junk DNA'? Maybe there should also be a 'genomic organization' section that covers 'junk'/noncoding DNA, telomeres, etc, or is that too far outside the scope of this article? Opabinia regalis 03:11, 10 December 2006 (UTC)

We need to focus this article more on the subject of genes. Tried to edit the above list to reflect this. TimVickers 21:15, 9 January 2007 (UTC)

Largely agree, though I think there ought to be at least some explanation of the connection between classical and molecular inheritance, which necessitates some dicussion of the cell cycle. Other than that I'm happy to defer to your judgment on the matter, since you have much better intuition about writing articles for general audiences that are still complete and precise. I've been hoping someone would wander into this article since I nominated it for SCOTM, but unfortunately nothing much has changed yet. Opabinia regalis 02:33, 10 January 2007 (UTC)

Effluvia

After a recent rewrite (which surely needs editing for completeness and accessibility), I removed these two sections from the article, which I considered rather poorly written. I'm dumping them here for easier reference than in the history, because some of this material - the subjects, if not this exact text - should make it back into the article eventually. Opabinia regalis 06:06, 10 December 2006 (UTC)

---

Many steps lie between the gene and its effect

For various reasons, the relationship between DNA strand and a phenotype trait is not direct. The same DNA strand in two different individuals may result in different traits because of the effect of other DNA strands or the environment.

• The DNA strand is expressed into a trait only if it is transcribed to RNA. Because the transcription starts from a specific base-pair sequence (a promoter) and stops at another (a terminator), our DNA strand needs to be correctly placed between the two. If not, it is considered as junk DNA, and is not expressed.

• cells regulate the activity of genes in part by increasing or decreasing their rate of transcription. Over the short term, this regulation occurs through the binding or unbinding of proteins, known as transcription factors, to specific non-coding DNA sequences called regulatory elements. Therefore, to be expressed, our DNA strand needs to be properly regulated by other DNA strands.

• The DNA strand may also be silenced through DNA methylation or by chemical changes to the protein components of chromosomes (see histone). This is a permanent form of regulation of the transcription.

• The RNA is often edited before its translation into a protein. Eukaryotic cells splice the transcripts of a gene, by keeping the exons and removing the introns. Therefore, the DNA strand needs to be in an exon to be expressed. Because of the complexity of the splicing process, one transcribed RNA may be spliced in alternate ways to produce not one but a variety of proteins (alternative splicing) from one pre-mRNA. Prokaryotes produce a similar effect by shifting reading frames during translation.

• The translation of RNA into a protein also starts with a specific start and stop sequence.

• Once produced, the protein interacts with the many other proteins in the cell, according to the cell metabolism. This interaction finally produces the trait.

---

Modern concepts of the gene

When trying to understand the concept of a gene, keep in mind that it is not static. It has evolved considerably from a scarcely explained "unit of inheritance" without a physical basis (see history section) to a usually DNA-based unit that can exert its effects on the organism through RNA or protein products. It was also previously believed that one gene makes one protein. This concept has been overthrown by the discovery of alternative splicing.

And the definition of gene is still changing. The first cases of RNA-based inheritance have been discovered in mammals. In plants, cases of traits reappearing after several generation of absence have lead researchers to hypothesise RNA-directed overwriting of genomic DNA. Evidence is also accumulating that the control regions of a gene do not necessarily have to be close to the coding sequence on the linear molecule or even on the same chromosome. Spilianakis and colleagues discovered that the promoter region of the IFN-γ gene on chromosome 10 and the regulatory regions of the T(H)2 cytokine locus on chromosome 11 come into close proximity in the nucleus maybe to co-regulate.

The concept that genes are clearly limited is also being eroded. There is evidence for fused proteins stemming from two adjacent genes that can produce two separate protein products. While it is not clear whether these fusion proteins are functional, the phenomena is more frequent than previously thought. Even more ground-breaking than the discovery of fused genes is the observation that some proteins can be composed of exons from far away regions and even different chromosomes.

Referencing elementary material

Much of the content in this article will be uncontroversial, basic, standard textbook material, and Wikipedia:Scientific citation guidelines is seemingly in limbo. Not that it shouldn't also cover current research, but for accessibility and brevity, it should stick mostly to the well-established facts. This is something I always find annoying and difficult to do well - does anyone have ideas on how to provide 'sufficient' inline citations for masses of basic material without breaking up the text with repeated footnotes to the same source? Opabinia regalis 07:07, 10 December 2006 (UTC)

My suggestion here is that gene or genetics attempt to do the same as we have done for evolution and has been done for special relativity and general relativity. That is, an Introduction to Genetics article be created in Wikipedia to allow easier access to the material. I would be glad to help. I propose to use the Simple Wikipedia article as a basis, and then we can edit it to be more suitable, just as was done in the case of Introduction to evolution. --20:14, 12 December 2006 (UTC)

Lead section comments

As an outsider, I thought I would offer a comment or two on your lead section and my impressions:

A gene is the unit of heredity in every living organism.

• a bit difficult for me to understand. What is a "unit" of heredity? I am not sure about the first sentence.

Genes are encoded nucleic acid molecules known as DNA or RNA, and direct the physical development and behavior of the organism.

• the average person will have heard of DNA, but probably not RNA. The average person will not know what a nucleic acid is, and should not be required to look too much up in the first paragraph! Even if there is a wikilink, it is best to make it self contained for the reader. Also using the word encode is not very good for the general audience.

Most genes encode proteins, which are biological macromolecules comprising linear chains of amino acids that affect most of the chemical reactions carried out by the cell.

• The average person has heard the word protein, but does not know what it is aside from something we eat. Some will not know the word linear. People will know molecule maybe, but not macromolecule. Amino acid again is unfamiliar. A cell might be known as a small part of a plant or animal, but even chemical reactions might be poorly understood.

Some genes do not encode proteins, but produce non-coding RNA molecules that play key roles in protein biosynthesis and gene regulation.

• Getting too dense. Encode? How do they encode proteins? What is noncoding? What is protein biosynthesis? Gene regulation? You are requiring the reader to look too much up. They will give up.

Molecules that result from gene expression, whether RNA or protein, are collectively known as gene products.

• Gene expression ? what is that? A guy named Gene who smiles?

Most genes contain non-coding regions, that do not code for the gene products, but often regulate gene expression.

• round and round the mulberry bush

A critical non-coding region is the promoter, a short DNA sequence that is required for initiation of gene expression.

• the promoter? Like a circus barker?

The genes of eukaryotic organisms often contain non-coding regions called introns which are removed from the messenger RNA in a process known as splicing.

• blah blah blah. Just sounds like noise to the average person.

The regions that actually encode the gene product, which can be much smaller than the introns, are known as exons.

• The exon. Like the Exon Valdise? The text in the figure also is too dense. I think that text should stand on its own and tell a story without much need to follow links.

The total complement of genes in an organism or cell is known as its genome.

• Maybe understandable. But maybe not. Complement is a big word and might be misunderstood.

The genome size of an organism is loosely dependent on its complexity; prokaryotes such as bacteria and archaea have generally smaller genomes, both in number of base pairs and number of genes, than even single-celled eukaryotes.

• Compound sentences are never good. And the words are too big.

However, the largest known genome belongs to the single-celled amoeba Amoeba duria, with over 6 billion base pairs. The estimated number of genes in the human genome has been repeatedly revised downward since the completion of the Human Genome Project; current estimates place the human genome at just under 3 billion base pairs and about 20,000-25,000 genes.

• People do not know what a base pair is or what this means.

The gene density of a genome is a measure of the number of genes per million base pairs (called a megabase, Mb); prokaryotic genomes have much higher gene densities than eukaryotes due to the absence of introns in prokaryotic genomes.

• compound sentence. Bi words.

The gene density of the human genome is roughly 12-15 genes/Mb.

• meaningless. Certainly for the introduction.

So take a look at these comments, and maybe consider some rewriting.--Filll 13:26, 13 December 2006 (UTC)

Sorry Filll, I totally missed this post. The lead hasn't changed much (except for a paragraph on human genome stuff) from its former lame state; I was going to get back to it after the text was in better shape. Thanks for the comments; I'll rewrite this sometime after the holidays. Opabinia regalis 04:41, 23 December 2006 (UTC)

Good for you, Filll! And I'm saying because I’m a geneticist by training (a PhD in the field).

You’re touching on one of the most significant issues I’ve seen as I’ve looked through Wikipedia over the past. It’s the tendency of “experts” – however they define “expert” for themselves – to write jargon and in unexplained technicalities when they compose or edit a Wiki article. I’ll put it as an aphorism.

WRITING FOR WIKIPEDIA DOES NOT MEAN SUMMARIZING YOUR COLLEGE COURSE IN A TOPIC.

You are not trying to pass a final exam or a doctoral qualifyuing exam nor trying to impress your professors or fellow greaduate students. YOU ARE WRITING FOR THE GENERAL PUBLIC.

Filll asks what a “unit” of heredity is, and I’ll ask what “heredity” is. The opening sentence: “A gene is a unit of heredity.”

Reader: You mean like I inherit my blue eyes from Mom and Dad?

“Expert”: Yes.

Reader: Like I inherit money from my parents?

“Expert:” No, not at all. It refers to BIOLOGICAL inheritance.

Reader: So I inherited one blue eye from Mom and the other from Dad?

“Expert”: No, you inherited eye color through the genes, through the germ plasm.

Reader: Germs? Like having blue eyes is like being infected by a disease?

"Expert": You're too stupid for words. I'm going to ignore you.

So we have another aphorism. WRITING FOR WI8KIPEDIA MEANS BEING CLEAR, PATIENT, AND UNDERSTANDING WHERE PEOPLE CAN BE CONFUSED.

But now that I have read a good many discussion pages, I don’t think these aphorisms will be any help. Too many Wikipedia articles sound like term papers written by bright juniors in college who have an amateur “Wiki-lawyer” leaning over their shoulder and reciting incomprehensible abbreviations, like “No, can’t say that! That’s POV COI OR!!!!”

Reader: “What’s a povkoor?”

One result is Wiki GOULASH, a mixture of this, that, and the other with a sometimes overpowering dose of incomprehensible Wiki-lawyerese.

Oh well…

Timothy Perper 14:52, 4 September 2007 (UTC)

old table

Replacing the table with a cited version, which is slightly out of date but from a solid source (Molecular Biology of the Gene). Reproducing the old table here for reference. Opabinia regalis 03:08, 21 December 2006 (UTC)

Gene content and genome size of various organisms

organism	genes	base pairs
Plant	<50,000	<1011
Human, mouse or rat	25,000	3×109
Fugu fish	40,000	4x108
Fruit Fly	13,767	1.3×108
Worm	19,000	9.7×107
Fungus	6,000	1.3×107
Bacterium	500–6,000	5×105–107
Mycoplasma genitalium	500	580,000
DNA virus	10–900	5,000–800,000
RNA virus	1–25	1,000–23,000
Viroid	0–1	~500

Trichomonas vaginalis

26k genes for a protozoa. Quite impressive... [3]. Someone else can add it Nil Einne 16:55, 12 January 2007 (UTC)

Lead Problem

"Here's the first line of the Wikipedia entry for 'gene':

gene is the unit of heredity, with each gene determining one inherited feature of an organism.'

is completely wrong. 'One gene, one character' is a false idea of the relationship of genes to inheritance, since many genes contribute to the appearance of a single feature, and one gene will play a role in many different features."

Oh, dear... Adam Cuerden ^talk 19:58, 16 January 2007 (UTC)

The offending sentence is mine. The problem is that a gene is an extremely difficult thing to define, even using technical terms. Do they include promoters? Regulatory elements? What about rRNA genes, or siRNA genes? I've tried again with a transcript-based definition. TimVickers 20:17, 16 January 2007 (UTC)

Each gene encodes for one or more proteins, or other regulatory elements? Have to remember alternate splicing of introns, though that's a truncation event, in effect, it still counts as multiple proteins. Adam Cuerden ^talk 20:39, 16 January 2007 (UTC)

With rRNA, snoRNA and siRNA we can't define genes in terms of proteins any more. I think one gene - one transcript is usually true, although alternate start sites cause problems with that generalization. TimVickers 21:33, 16 January 2007 (UTC)

Not really. I do remember several proteins that have various truncated forms, caused by alternate splicings. It's common enough that we need to mention it. Anyway, a lot of the introns have regulatory functions. Adam Cuerden ^talk 21:51, 16 January 2007 (UTC)

Multiple splice forms all come from post-transcriptional processing of a single transcript. It's not true that one gene = one mRNA, but in general one gene = one transcript. TimVickers 22:05, 16 January 2007 (UTC)

Point, that. Probably implied already, though. Oh, and you know that Dawkins uses a completely different definition of gene again in The Selfish Gene? Just to make it awkward? Basically, anything that tends to be inherited together, no matter how many transcripts. Adam Cuerden ^talk 22:15, 16 January 2007 (UTC)

lacking recent changes / discoveries regarding definition of gene

I felt that this article as of May 07 lacks some recent changes in the understanding of the concept of gene. I know these discoveries make a clear definition even more elusive - long gone are they days of one gene, one protein. But since we want to accurate this info has a place here. Ok, it's not basic, i.e. not the right stuff for the lead section, but the wikipedia should not exclude detailed and in-depth info. Instead it should just go to the end of the page, so people interested in just a quick definition of the concept are not served details before essentials. Feel free to improve the section "concept of the gene still changing". Best, Jasu 14:18, 12 May 2007 (UTC)

Cistron

The entry "Cistron" has been redirected to this page, but a text search reveals no further mention of citron on this page. —Preceding unsigned comment added by Jopparoad (talk • contribs) 15:42, 22 September 2007 (UTC)

I've defined it in the lead. Tim Vickers 17:30, 6 November 2007 (UTC)

Gene count

Why is the number of human genes 20,500 in the article, when that number ignores the 4,000+ RNA genes? Unfortunatly the gene number for other organisms are given from a book, so I can't see if they too are protein-coding genes only. Narayanese (talk) 07:01, 13 February 2008 (UTC)

Extinct genes being brought back to life

It's interesting to know that this is being done now. Is is possible to request a little bit of information about this be added to the article? Or maybe a link to an article specifically about this added to this article? Reference: http://www.smh.com.au/news/science/extinct-tiger-gene-brought-back-to-life/2008/05/20/1211182749725.html 134.148.5.119 (talk) 03:44, 20 May 2008 (UTC)

Request to edit, and add this Spinal Cord gene map

I do not know where to add this, might be mistaken, not familiar with this technical subject. So please add edit this in the proper section and articles:Allen backed the the Seattle Allen Institute for Brain Science (July 16, 2008) launched $ 41 million online "Allen Spinal Cord Atlas" mouse gene map. Allan Jones, chief scientific officer, said:

"The Allen Spinal Cord Atlas offers profound potential for researchers to unlock the mysteries of the spinal cord and how it is altered during disease or injury." The spinal cord atlas is set up like the Allen Institute's earlier atlas of the mouse brain.[4] The Map could reveal new treatments for human neurological disorders. The map points researchers toward places where genes are active[5]msnbc.msn.com, Gene map charts spinal cord mysteriessciencenews.org/view, MapQuest for the mouse spinal cord--Florentino floro (talk) 09:29, 20 July 2008 (UTC)

Nextbio

www.nextbio.com is a searchengine of genes, and as I see Genecards and Entrez is there. I believe that nextbio is a more complete version of these. May I instert the link? Aminoacid91 (talk) 23:17, 11 August 2008 (UTC)

Is it a good idea to have a glossary?

Is it necessary to have a glossary in any wikipedia entry? I mean, as it is displayed now in this entry. The glossary itself might be OK. I would say that the hyperlinked terms are enough. If one wants to know about a term one just follow the link and that's it. I would like to hear other opinions. I do not know whether this is the place to discuss this. My proposal would be to remove the table and to add a link to the genetics glossary page in some prominent place. Miguel Andrade (talk) 07:36, 23 September 2008 (UTC)

Basic Mendelian Math

In the 2nd paragraph one currently reads: "For example, if one parent has blue eyes and the other has brown eyes, there is a 3/4 chance that the child will have brown eyes". If you assume the recessive trait is blue eyes, than there is a 1/2 chance the child will have blue eyes if the brown eye parent is heterozygote, and 100% chance to have brown eyes if the brown eyes parent is homozygote... Can someone fix or clarify that, please. Thanks in advance... - Signed: unlogged: Pezão —Preceding unsigned comment added by 189.107.164.43 (talk) 21:22, 16 December 2008 (UTC)

This paragraph is wrong, actually. If the recessive trait is blue eyes (b), and the frequency of the recessive allele is, say, q in the population, then the brown eyed (B) parent is BB with probability (1-q)/(1+q); and Bb with 2q/(1+q). (The frequency of BB homozygotes will be (1-q)*(1-q); of Bb heterozygotes, 2*(1-q)*q - all of these will be brown-eyed. So, the odds of a brown-eyed individual being BB are (1-q)/(1-q+2q), and of being Bb are 2q/(1-q+2q)) If the brown-eyed parent is BB, all the kids will be brown-eyed. If the brown-eyed parent is Bb, 50% will be, which makes the total probability of the child being brown-eyed 1/(1+q). Graft | talk 22:01, 16 December 2008 (UTC)

traits

I have a big problem with this line in the opening paragraph: "In general terms, a gene is a segment of nucleic acid that, taken as a whole, specifies a trait."

I know that this definition applies to those genes that were the center of the research that led to the founding of modern genetics. I also know that these are the genes most non-scientists care most about. But it is a vast oversimplification.

The introduction itself suggests something far more complicated, and I think this sentence just does not serve the article as a whole. Many genes do not do much at all. Moreover, some traits are not specified by genes alone, they are specified (if we are being specific) by genes in relation to environmental conditions (which can include enzymes produced by other genes ... or even brownian motion).

How about, "A gene is a sequence of nucleic acids that potentially plays a critical role in the production of enzymes. These enzymes are necessary for the functioning and maintenance of cells, and for embryonic development. Some genes have been linked to specific, inherited traits."

Or something like that - I invite others to play around with the wording. My objective is to be more accurate, and not to mislead people into thinking that all inherited traits are explained solely by genes, or that all genes express themselves in specific inherited traits. Many readers, sadly, read just the introduction ... and many of those will leave with this wrong impression. Slrubenstein | Talk 17:56, 18 January 2009 (UTC)

Only a minority of genes encode enzymes. Narayanese (talk) 20:01, 31 January 2009 (UTC)

Composition of the genome section

This section relies heavily or solely on computer gene predictions, which isn't a good thing. It also lacks modern sources, I see several sources from 2004, which is barely after the sequencing of the human genome. The section probably needs to be rewritten from the ground up with better sources. Narayanese (talk) 20:17, 31 January 2009 (UTC)

I've rewritten the thing, should add something on bacteria to it. Narayanese (talk) 23:43, 5 February 2009 (UTC) yeahhhh;) —Preceding unsigned comment added by 76.87.52.213 (talk) 00:50, 6 May 2009 (UTC)

Gene vs. Allele

I am interested in the differences between the definition of an allele and a gene. This article makes the statement "In common usage, the term gene often refers to what is known more accurately as an allele". I made an edit that attempted to clarify, however the edit was reverted with the comment "Seems perfectly clear to me. If I say I have the gene for blue eyes, I really mean the allele for blue eyes". Wiki clearly thinks your statement is incorrect because the terms gene and allele are two separate articles and thus mean different things. If they were the same, then one term would redirect to the other. Because these are separate articles, they are clearly not the same, and cannot be used as such in your revert example. Either the articles need to be merged or this statement needs to be removed and edited for clarity. Why do we allow the statement? // Mark Renier (talk) 09:35, 7 August 2009 (UTC)

• You have a gene for eye color, but alleles for the particular colors. People mistakenly (and very often) say "gene" when they mean "allele". An example would be "obesity gene". As can be seen in the Google News search for the term, it is touch and go whether the science journalists will say "gene" (incorrect) or "gene variant" (correct). In everyday usage, even biology professors will say "gene" where they mean "allele", confusing the heck out of their students. Since Wikipedia aims to make the subject accessible to our readers, this sentence needs to be in the article. Abductive (reasoning) 09:54, 7 August 2009 (UTC)

I would argue "gene" is the correct term as all organisms possess genes as units of inheritance of their genomes. There may or maynot be alleles or mutant versions of a gene, and multiple proteins can be translated by alternate splicing of a single gene. Further historically allele refers just to the protein coding mutated portion of a specific gene to form alleles, whereas the modern version of gene is regulatory elements as well. GetAgrippa (talk) 16:25, 28 December 2009 (UTC)

I moved this post. Ooops! Multitasking and posted on wrong subject. It was suppose to go to Evolution article. Jeez.Regards GetAgrippa (talk) 16:42, 28 December 2009 (UTC)

I think Mark Renier's error is about Wikipedia and not genetics. An encyclopedia can have two aticles on the same without a redirect for a variety of reasons. If we nee to clarify the relationship between gene and allele (in either or both articles) that is another matter ... Slrubenstein | Talk 18:25, 7 February 2010 (UTC)

Not Knowing the Definition of Gene for the Gene Wiki Page Is Lame

Clearly most of the discussion about this page is because a clear and pervasive definition does not exist. I just watched Nova and they used "gene" as being limited to protein coding DNA sequences. This leaves the highly technical term "switch" for activating sequences. [cynicism intended]

Why not just use this sensible definition? "that which is atomic, heritable, and consequential"

Just because a lay person doesn't understand "heritable" is no reason to confuse ourselves. (The other thousand lines of the page can explain what the definition actually means.) And this definition doesn't require a change every time someone makes a new discovery.

And if the thing defined above isn't a "gene" then what is it???? —Preceding unsigned comment added by 98.202.98.13 (talk) 10:32, 7 February 2010 (UTC)

I'd say that definition differs remarkably from how the word is used in genomics, and that your definition equates to 'functional nucleotide' (not a word), as anything longer (including 100kb stories like Sox2ot) that is subject to recombination/insertion/deletion/translocation won't be atomic. Narayanese (talk) 15:43, 7 February 2010 (UTC)

This is me again, Mike Layton: "that which is atomic, heritable, and consequential."

A) I didn't think wiki was a place for incestuous and specialized researchers to change the English language into whatever jargon they prefer at the moment. B) My definition certainly doesn't equate to any embellishment of "nucleotide." I make no claim that all genes [my definition] are nucleotides. I doubt they are--don't we already have proof that they are not?

This is exactly the point. We need a word for the thing I'm defining. If it isn't "gene," what is it?

By the way, I do acknowledge that my definition does match up somewhat with some of what is on the page, much of which is credentialed, unlike myself. It is just that I think my definition is simpler and clearer. (Also, not circular like "a gene is a union of genomic sequences.") 63.237.195.226 (talk) 23:23, 12 February 2010 (UTC)

Gene Ontology

Can anybody make this into a usable part of the article? I think it fits better in Gene Ontology and have copied to talk:Gene Ontology.

Gene name	GO accession	GO type	GO term	GO evidence code	PO accession	PO term
LOC_Os05g03480	GO:0005739	Cellular component	mitochondrion	IEA
LOC_Os05g03480	GO:0003824	Molecular function	catalytic activity	IEA
LOC_Os04g52210					PO:0007134	Vegetative growth
LOC_Os04g52210					PO:0007133	Leaf production
LOC_Os04g52210					PO:0009012	Plant growth and development stages
LOC_Os04g52210	GO:0016102	Biological process	Diterpenoid biosynthesis

--Ettrig (talk) 13:46, 13 April 2010 (UTC) \ My God fix that text with the press stuff. First, you don't need childish anecdotes in an article like tis, 2nd, the press is RIGHT. If all people have the gene, then the supposed person does too !! —Preceding unsigned comment added by 165.201.140.155 (talk) 18:48, 20 September 2010 (UTC)

Lede

I corrected the lede in several places, which is pretty scary as I'm not even a geneticist or a biologist. There may be many other mistakes I've missed. Andrewjlockley (talk) 00:34, 24 September 2010 (UTC)