Nov 16 2010

Philosoraptor, the geneticist

Discussed in one of my classes yesterday:
The corollary was “If a gene falls in the woods, does it make a noise?” This is what happens when you give grad students too much coffee.

Genetics geeks – feel free to discuss.


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  1. 1
    Jarrad Hall

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

  2. 2
    Three Ninjas

    I’m sending this to my friend Gene.

  3. 3

    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.

  4. 4

    I think so. If a tree falls in the woods and no one hears it’s still a tree.

  5. 5

    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!

  6. 6

    If it is truly never expressed, the question is why is it conserved?

  7. 7

    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?

  8. 8

    I don’t see why it wouldn’t. Granted, it’s been a long time since BIO 101, but I was under the impression “genes” were part of the DNA, whether they are expressed or not.

  9. 9
    Jeffrey A. Myers

    But the real question is did Jesus love that velociraptor?

  10. 10

    If it’s never expressed, it’ll accumulate enough mutations to become a has-gene… :)

  11. 11
    Dave Wright

    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?

  12. 12
    Dave Wright

    It kinda depends what you mean by “part of” the DNA. It’d be very weird to describe, for example, the words you write as “part of” the letters that make them up.The issue is firstly how you define “gene”. If we’re going to try and distinguish genes from pseudogenes (which have the DNA structures of genes like promoters and enhancers, but never produce a product in the way that we understand it – we’ll leave aside whether some pseudogenes have function of their own, but in the canonical picture they’re effectively broken and useless, and therefore “not a gene”), the only direct criteria we have for observing whether something is really a gene or not really a gene is to look and see what it makes. Hence, if it doesn’t make a measurable product, how do you know it’s a gene at all?

  13. 13

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

  14. 14

    Unexpressed DNA seems to be “cheap” for an organism to carry around, and too valuable to get rid of. Any organism who purges all unused DNA is going to have to build such genes from scratch to evolve to changing circumstances. While an organism which keeps around unexpressed DNA can see a mutation turn the gene on, which, while probably harmful, is occasionally useful enough to be helpful.Evolution does not only concern adaptation of an organism to it’s environment, but to how fast an organism changes (that is, the rate of evolution). It probably even optimizes to when an organism is more likely to try to change — I’m not sure if the experimental evidence is there, but I expect to see more mutations to be seen under stressful circumstances.So any bit of junk DNA that can be “turned on” by a favorable mutation is still a gene, in my entirely unscientific opinion. While a bit of junk DNA that is too damaged to do anything, even if “turned on” is not a gene.Just my $.02

  15. 15

    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.

  16. 16

    Back in 1980 Kollar and Fisher figured out a way to express one of the genes for producing dental enamel in chickens. They used some mouse tissue as a promoter. That meant they had to do the implant in an immune system free area behind the chicken’s eyeballs. The experiment worked, and the dental proteins were created. The gene might not be ordinarily expressed, but it was still there. [KOLLAR, E.J., TOOTH INDUCTION IN CHICK EPITHELIUM - EXPRESSION OF QUIESCENT GENES FOR ENAMEL SYNTHESIS, SCIENCE 207: 993 (1980)] Even funnier were the letters regarding this, filed under “Fossil Genes: Scarce as Hen’s Teeth?”Yes, they are still genes, and that goes for the sequences which may never have been expressed, but could be.

  17. 17
    Gregory Colby

    “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.

  18. 18

    But does it make a sound?

  19. 19

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

  20. 20

    With slight reference to the post you made immediately after this one, on “how to cure a feminist” (…Ohhh dear!), I would like to suggest this variant on that common philosophical question……If a man speaks in a forest, and no-one hears him……Is he still wrong?

  21. 21

    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

  22. 22

    “This is what happens when you give grad students too much coffee.”Interesting. I had not thought it would be possible to give a graduate student too much coffee.And as long as the laws of physics allow for the possibility that a ‘gene’ could be expressed then, no matter how implausible that expression might be, it is still a ‘gene’.

  23. 23

    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?

  24. 24
    Jarrad Hall

    There are pseudogenes. Regions that could potentially code, but aren’t expressed. We can’t stick to hard rules. Some dormant pseudo genes do eventually duplicate and come under the control of a promoter, and are later expressed. Especially true of pseudo genes acquired by retroviridae.

  25. 25
    Jarrad Hall

    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.

  26. 26

    I had a pair of psuedojeans once – once through the dryer and they fell apart

  27. 27

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

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