Philosoraptor, the geneticist

Yes, it could still be a gene, it all depends on how you promote it. :p

It is still a gene because it will pass to the next generation if the organism has offspring. There is a chance for it to mutate generations down the road and express.

Hmm, I thought the answer was obvious at first, but the more I think about it, the more confused I become. Hooray for philosoraptor.Considering all of the DNA we have that is never transcribed, those aren’t called genes. So if a “gene” is never transcribed, why would it be called a gene? Then again, if it has the potential for expression, why wouldn’t it be called a gene? I guess the real question is whether we know that the “gene” actually can be expressed or not.Gah, I hate you for making me think so hard about this!

Hmm … seems to me it’s a matter of degree. On one end of the spectrum, you have undeniable genes that are expressed under specific circumstances, a little further along, genes that may not be expressed in a particular individual, but can be expressed in other members of the population (a good example being sex-related traits which might not be expressed in a male, but can be expressed in said male’s daughter), further along the spectrum, you get genes that are rarely expressed, and then stretches of DNA that were expressed genes in evolutionarily recent times, but are not expressed in modern members of a species. Would this be a gene? If it can be potentially expressed (perhaps be epigenetic modification), then I suppose I would call it a gene. However, over time, such unexpressed genes would be freed from natural selection, causing them to accumulate mutations. At some point, it would cease to be an even potentially expressed gene and would be labeled a pseudogene, and eventually, as mutations accumulate, pure junk.At which point in that spectrum does it cease to be a gene?

But the real question is did Jesus love that velociraptor?

But surely this makes the concept of discrete genes so broad as to be pointless? The entire genome, coding and noncoding, conserved and unconserved, becomes “gene” under this definition?

The gene credo—freedom of expression!Canadian version: If Bruce Cockburn falls in the rainforest do the trees laugh?

No. Definitely and simply no. If it really is never expressed then there is no evidence that it is a gene.Genes is as genes does.

“New” genes can enter the genome of an organism in a variety of ways, like horizontal transfer or duplication. The idea that non-transcribed DNA and pseudogenes are sitting around just waiting for the ‘ON’ switch to be flipped so they can begin performing a useful function – and, moreover, that selection favors the collection of non-transcribed DNA for this reason – doesn’t really make much sense. There may well be some function performed by certain “junk” regions of the genome, but it certainly isn’t held against some possible future need. Natural selection cannot maintain a trait because it might become useful in the future.Rate of evolution depends upon what you mean. The rate of molecular evolution, that is, the rate at which DNA actually accumulates mutations from generation to generation, varies between regions of the genome but remains essentially the same at a given locus for a given species, irrespective of external influences. This is the foundation of a lot of techniques in molecular phylogenetics that we now take basically for granted, like applying a molecular clock to human and chimpanzee DNA and saying, “Aha! We shared a common ancestor 6 million years ago!” The rate of molecular evolution can be influenced by selection, but that gets complicated; for simplicity’s sake, assume that rates of mutation are constant at a given locus.What changes under selection (and what you might be thinking about) is which mutations are retained or purged from the genome. The status quo for most loci is assumed to be drift; the large majority of mutations that stick are neutral and don’t have any effect on the fitness of the organism. If a mutation is synonymous (that is, it doesn’t change the protein product produced by the gene), it will usually be neutral. Most nonsynonymous mutations (which do change the protein) are deleterious, and eliminated. If they’re positive, they are more likely to spread through the population. A population in stressful circumstances might be expected to show more positive selection on nonsynonymous mutations at certain loci, and there’s experimental evidence to back this up. So that makes sense.Still, I think that a gene is something fairly discrete. A lot of the junk DNA in our genomes consists of things like tandem repeats and microsatellites and has no ability to be turned on or off in the sense of being expressed with a product, especially with a simple mutation. So I think your definition is a bit tautological; if a piece of junk DNA can be turned on, like flipping on a light switch, it’s basically a gene by definition: it has the structures that allow that to happen.

If it codes for a product, and you can induce expression, it’s still a gene. If not, nope.

I think the correct philosophy geek response to the question: “If a gene falls in the woods, does it make a noise?” is Define falls. And define noise.Thought I’d stop by to tell you your fans are still making a lot of noise. My prof teaches Boob Quake right alongside the Gettier problem in his first year epistemology classes.He’s also the type of prof that gets his students to consider Free Will and Authority by asking us if we think Homer Simpson is free :-D

It probably is a gene, but it won’t be fore long. If it is truly not expressed, then there will be no selection maintaining the sequence and it will begin to decay away into a pseudogene and then into just meaningless sequence. So the real question is: how long has the gene not been expressed?

Could be picked up by a bacteria via horizontal gene transfer, and become a gene.Could enter a plasmid and be exchanged and become a gene.Could be between a transposon and insert into a coding frame and become part of a gene.Could be coupled to a promoter as has happened many times, and become a gene.Could be picked up by a retrovirus and become a gene, like in some tumour promoting viruses.

I’ve got a better one:Define “gene.”It’s not as easy as it sounds.