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Thread: Do proteins evolve?

  1. #1 Do proteins evolve? 
    SHF
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    Hi,

    Do proteins evolve?

    At a glance I thought no, but then there are prions etc (but do they actually evolve?). My rudimentary understanding tells me there is some debate to the level at which natural selection takes place (gene/individual/group etc), although for some reason I think the gene-centred view / selfish-gene is somewhat of a consensus (???) (perhaps I've been reading too much Dawkins, or just not enough of others). Anyway, my question is - does it make sense on any level to talk about protein evolution (in and of themselves rather than secondary evolution (if there is such a term) to primary genetic evolution).

    I had a brief google of the question and couldn’t find an answer though did find things such as the link below where a researcher describes themselves as “I'm a computational evolutionary biologist, specifically interested in protein evolution.” (Protein Evolution and Other Musings)

    I can see that protein profiles vary over time (natural selection, adapation, yada yada) but is this just a manifestation of the genetic level evolving? Why does this researcher say they are “interested in protein evolution” (are they just being a little loose with terminology?)

    Thanks
    Sean


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  3. #2  
    Forum Professor Zwirko's Avatar
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    In the same way that you can study the evolution of the immune system, the eye, or a lineage of organisms, you can also study how specific proteins have evolved. For example, in the blog you linked to the author is discussing the evolution of a translation inition factor.


    The term "protein evolution" isn't referring to another type of evolution, rather it's referring to the object of study. Molecular phenotypes, if you like.


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    Forum Professor Zwolver's Avatar
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    As you probably know, proteins themselves can not evolve, as the protein itself can not duplicate itself. But due to selection/elimination from all weaker forms of the protein on a whole, you can say that they actually do evolve, whenever they have even a slightly positive effect on the "host". This is shown most clear in bacteria, where they evolve proteins that can withstand high temperatures, that need the lowest amount of energy or aminoacids to function, or that are simply the fastest.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    SHF
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    Thanks for replying.
    I see what you (Zwirko) mean, however, if they were to be very specific should they say 'the evolution of genes that code for a translation initiation factor'
    So if I understand correctly - there is no such thing as 'protein evolution' in a strict sense, but it can be used as a rhetorical device, implicitly meaning 'the evolution of genes and the subsequent manifestation of altered protein / molecular phenotypes'. (i.e. the term 'evolution' should strictly be reserved for genotypes but is often employed in relation to phenotypes; so we all know what you mean when you refer to the evolution of the eye but you technically mean the evolution of the genes that influence/control the development of the eye)
    Although I do read that prions evolve, so perhaps proteins themselves can evolve? (as well as prions I suppose we could bring up ancient/early/primitive replicators, butwere these along the lines of nucleic acids rather than being proteinaceous?).
    Perhaps, given that you (Zwolver) said "proteins themselves cannot evolve, as the protein itself cannot duplicate itself" that stands for most proteins....except the minority that can replicate themselves (of course you may question whether prions are technically 'replicating'(?))

    Could I just ask also where you understand the scientific community position to be on the level at which natural selection occurs? Is there a lot of debate or is there a consensus? (Not that a consensus makes something true, just interested to know where the debate is if you happened to know)
    (too many questions! sorry)
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    Forum Professor Zwolver's Avatar
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    Prions can not duplicate themselves, they can only change certain proteins as to themselves (some viral-like interaction there). Usually this accounts very common proteins.

    Could I just ask also where you understand the scientific community position to be on the level at which natural selection occurs? Is there a lot of debate or is there a consensus?
    Not sure where your getting at, though my idea is that most scientists agree that proteins are not evolving, the DNA that encodes them is. But the driving force behind this selection wether the DNA has what it takes to survive and expand, depends on the functionality of the protein it encodes.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Universal Mind John Galt's Avatar
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    Quote Originally Posted by SHF View Post
    Could I just ask also where you understand the scientific community position to be on the level at which natural selection occurs?
    The notion of selection at species level and higher appears to have been largely discarded. While Dawkins' selfish gene has gained a lot of traction it was never wholly accepted (Mayr thought it was rubbish). My impression is, based on eclectic reading and not upon direct involvement with researchers, is that the consensus lies soemwhat with selection of the genotype, but not the individual gene, with a few holding out for higher level selection. That's where I put my money (hgher Level), but my money is not in a liquid currency.
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  8. #7  
    SHF
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    "Not sure where your getting at" (Zwolver)


    I was try to ask about the 'unit of selection' (in the theory of evolution by natural selection).

    Whether there was any agreement (gene-centred explanations; kin-selection; group-selection, perhaps selection is multi-level)


    (e.g. Dawkins distinguishes replicators (genes) from vehicles (individuals and groups) and says that the unit of selection
    is the gene (though of course he goes on to say that defining a gene is harder than one may think) rather than at any other level
    (everything else being an extended phenotype and thus not a unit of selection). (I was just wondering if that was the accepted view regarding
    the unit of selection or not)


    John Galt - you mention favouring higher levels, I would be interested to read works you think make a strong case for this,
    so any recommened reading there would be welcome






    Just to check, when you (Zwolver) use the term 'duplicate' you mean 'replicate' ? (i.e. to build up a copy of yourself from basic building blocks)
    Whereas a prion alters the form of another pre-existing protein to mimic that of the prion itself.
    I suppose part of my confusion is mixed messages (see article below)


    (BBC News - 'Lifeless' prion proteins are 'capable of evolution')




    Here, Weissmann says "Now we know that the abnormal prions replicate, and create variants, perhaps at a low level initially..."
    (but then this 'replicate' would still be different to the replicate I defined above)
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    Universal Mind John Galt's Avatar
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    Quote Originally Posted by SHF View Post
    John Galt - you mention favouring higher levels, I would be interested to read works you think make a strong case for this,
    so any recommened reading there would be welcome
    I want to emphasise that, as far as I have read, the notion of higher level selection seems to be in disfavour in most quarters. My attraction for group selection is based on a gut feel borne of eclectic reading practices and a slightly rebellious nature. I can't immediately think of anything that makes a strong case. If I could I would arguing for it much more strongly rather than just indicating a personal leaning.

    I know that is not a very helpful answer, but I don't want to give unequivocal support to a notion that is, apparently, not widely accepted. That would be misleading and put me in the same boat as the cranks on the forum who argue for an expanding Earth and push gravity.
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  10. #9  
    SHF
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    ok.

    Thanks to all for the clarification. It has be helpful.
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    Forum Professor Zwolver's Avatar
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    Hmm, in your point of view, it's simply terminology then. In that case, if the prion improves its self, by creating a nonidentical copy of itself, that is better then the original prion in recruiting other proteins to become like him. Then yes, in that case actually the proteins can evolve.

    Now i feel stuck on thinking there is no evolution without DNA/RNA. Ow well. But as a protein on itself is very simple, (compared to a whole) i can't see much for it to evolve into. Maybe if our proteins change, it has to "adapt" with us (loose term). Not sure if this level of adaptation is called evolution. But it is debatable indeed.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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  12. #11  
    SHF
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    I don’t think it was semantics; absolutely I wanted to be clear on terms used but my central aim was to clarify what I thought which was that genes evolve and phenotypes (which includes proteins) do not. And that while one often hears/reads about evolution of many things, that in strict biological terms it should only be used in reference to genes. I just wanted to establish that my thinking on the matter was correct. (noting of course that there is a minority who would argue for a unit of selection other than the gene). And with regards to prions being an exception, it would seem that they do propagate but the nature of this is qualitatively different from DNA/RNA replication (though I do not have clarity of thought on this at present).
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    1st rule of biology: there are no rules. Exceptions abound.




    Natural selection (one aspect of evolution) only requires there to be replicating entities that exhibit variation and that compete for resources, with resultant differential rates of survival. Genes are not a requirement for natural selection to occur. Prions are just a weird exception and are doing something that other proteins are incapable of doing. Another example would be to consider a metabolism-first origin of life. In this hypothesis there must have been natural selection occurring on simple chemical pathways.
    Last edited by Zwirko; September 15th, 2012 at 05:08 AM.
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    SHF
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    That all makes sense. I thought I would just google ‘laws of biology’ – found a nice little paper (Laws of biology: why so few?)

    Which says “…therefore useful to think of biological regularities as broad generalizations than stiff relationships among interacting components. Here we would like to discuss why absolute generalizations are rare in biology…”

    And “…Richard Feynman prefers to view Laws as rhythms or pattern in nature apparent only to the eye of the observer…”

    And of course that laws of chemisty / physics / thermodynamics etc are laws of biology in a sense also as the biological realm is based on these

    It’s interesting to think why there are ‘firm’ laws in e.g. thermodynamics but not biology (perhaps simply the scope of biology is much greater so fundamental patterns are less evident or relevant as concepts) (although the paper does mention Mendelian inheritance as being a pretty good law, though with some exceptions)
    Last edited by SHF; September 14th, 2012 at 07:28 AM. Reason: typo
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