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← Protein flaws responsible for complex life, study says

Protein flaws responsible for complex life, study says - Comments

ridelo's Avatar Comment 1 by ridelo

I don't understand why this is different from a mutation followed by selection. If the 'dehydron' produces a protein that does a better job in surviving, why can't that be selected against other proteins?

Sun, 22 May 2011 21:45:54 UTC | #629656

Steve Zara's Avatar Comment 2 by Steve Zara

Comment 1 by ridelo

I agree. I can't see any way in which this isn't normal Natural Selection.

Sun, 22 May 2011 21:54:08 UTC | #629657

God fearing Atheist's Avatar Comment 3 by God fearing Atheist

Comment 2 by Steve Zara :

I agree. I can't see any way in which this isn't normal Natural Selection.

+1

But these scientists have to flog "sticky proteins" somehow ...

... and the BBC have to flog their content to the public ... including cretins ...

Sun, 22 May 2011 22:02:01 UTC | #629658

Alan Canon's Avatar Comment 4 by Alan Canon

It's not gene-based, is it? so perhaps that's the sense in which it doesn't satisfy some people's criterion for Natural Selection. Surely Richard could weigh in, as it's right up his alley!

Sun, 22 May 2011 22:17:47 UTC | #629663

ai1888's Avatar Comment 5 by ai1888

The title is so misleading. It suggests that ALL of complexity arose by protein flaws. I am not denying that protein structure can contribute to complexity, but these "small" flaws however cannot be passed on from one generation to the next, unless these "flaws" themselves are a result of gene mutations. Otherwise, occurrence of dehydrons will be totally randon, and won't have any 'meaning'.

Sun, 22 May 2011 22:33:37 UTC | #629666

God fearing Atheist's Avatar Comment 6 by God fearing Atheist

Comment 4 by Alan Canon :

It's not gene-based, is it?

Yes it is. The "sticky proteins" are made from their RNA/DNA templates like any other protein. The "sticky regions" are thus caused by mutations in the sequence of base pairs in the RNA/DNA. Its all classic natural selection. Hence at least 3 of us are baffled by the claims. CORRECTION with ai1888, that makes 4 of us ...

Sun, 22 May 2011 22:38:05 UTC | #629672

CallumW's Avatar Comment 7 by CallumW

They may be saying that the evolution of protein complexes was selected for indirectly, by attempting to cope with the problems of genetic drift to rescue gene function that was impaired by the mutations altering single-protein solubility/stability. But that's still natural selection, just not directly from single protein -> multiprotein complex in one step. The 'motive' of the adaptation would also be to rescue gene function rather than to generate better cellular machines, however I'm unsure why that's supposed to be non-adaptive, it's just not directly due to a selection pressure causing the aspect of the change which we're most impressed by today.

I don't understand why they're trying to sell it as something else, unless it was a cynical method of getting published in Nature. Maybe they chose the wording to stabilise the article syntax but it subsequently turned out to be a bit of a PR coup for non-adaptive reasons...

Mon, 23 May 2011 00:14:47 UTC | #629684

green and dying's Avatar Comment 8 by green and dying

We've opened up the idea that the roots of complexity don't have to reside in purely adaptational arguments

Sounds like they're saying that complexity isn't necessarily an adaptation, and that there is another reason that certain populations have more complexity than others. The "defect" must be inherited for certain populations to have more than others (right?) But couldn't something else, other than the complexity-causing property of the defect, have been what was selected for and the complexity-causing part was a fluky by-product? So it's not necessarily an advantage to be complex, therefore THAT property would not be selected for.

This isn't a well-written article, anyway.

Mon, 23 May 2011 00:20:15 UTC | #629685

Jos Gibbons's Avatar Comment 9 by Jos Gibbons

Like everyone else here, my first reaction to this article (when I saw it several days ago; I was wondering when it’d make it here) was that this is simply natural selection. Sometimes, it may begin as genetic drift, with a random minority of neutral mutations becoming more common. Sometimes, “nearly neutral” mutations (ones which natural selection should mildly penalise) would spread, literally the opposite of what they should. Both of these events are of nonzero probability because population sizes are finite; indeed, the Nature article looks at the mathematical relationship between population size and these proteomic effects in some detail. And of course sometimes it’s straightforward natural selection with none of these statistical quirks.

In all three cases the environment which governs what natural selection favours and by how much it favours it is partially a matter of earlier mutations in dehydronic regions. But the BBC is wrong to characterise any of this as not part of ordinary adaptive evolution by natural selection, however interesting it is to discover a novel, presumably highly prolific subspecies of the mutations upon which natural selection can act occur.

The BBC article is at least good enough to link to the Nature article. (If you follow their link, which I've reproduced there, there's a PDF version too.) I suggest people hear read it. Unfortunately it clearly shares the fallacy of the BBC on this, especially in its title, “Non–adaptive origins of interactome complexity”. (The interactome is the set of molecular interactions in cells, so its complexity is, roughly speaking, how many chemical reactions occur therein.)

If anyone here is interested in the chemistry of how dehydrons actually work, Wikipedia has an excellent if brief account of it. Like the Nature article, it’s laden with technical terms, one thing I enjoy & wish the BBC & other journalists would be, but which presumably they never will be.

Mon, 23 May 2011 06:32:31 UTC | #629721

Steve Zara's Avatar Comment 10 by Steve Zara

But the BBC is wrong to characterise any of this as not part of ordinary adaptive evolution by natural selection

But then it's not news! It is rather irritating when something quite interesting is pitched as if it was revolutionary.

Mon, 23 May 2011 07:15:22 UTC | #629738

Schrodinger's Cat's Avatar Comment 11 by Schrodinger's Cat

I'm with #8. How do they know the 'defect' was a cause of complexity and not an effect of it ?

Mon, 23 May 2011 07:28:28 UTC | #629740

Benjamin Taylor's Avatar Comment 12 by Benjamin Taylor

I've read a few articles on this (I must confess I've not had time to read the paper yet) and I can't see how this differs from our current understanding of evolution.

It seems to be being presented as a process of evolution that is "outside natural selection".

Is this just journalistic spin to get the article more attention or am I missing something?

Perhaps Professor Dawkins or another evolutionary biologist could clarify this issue?

Mon, 23 May 2011 09:59:29 UTC | #629778

Benjamin Taylor's Avatar Comment 13 by Benjamin Taylor

Okay, I’ve read the paper now. The message seems to be that in (relatively) small population sizes, genetic drift can lead to the accumulation of neutral or slightly deleterious changes in proteins that ‘primes’ them for the ability to form protein complexes that later undergo natural selection.

This reminds me of the Lenski E. coli experiment, where a particular population of bacteria underwent earlier “potentiating” mutations that later allowed them to use the citrate in the media as a food source, which gave them a huge selective advantage.

I hope I’m not misrepresenting the science here, but the whole “evolution outside of natural selection” idea does seem to be just a bit of reporting spin by the media.

Mon, 23 May 2011 11:53:03 UTC | #629816

Bumblebat's Avatar Comment 14 by Bumblebat

If creationists had been present at the time of this 'erroneous mutation' they would have given it as an example of a 'bad mutation' leading to no further use.

Mon, 23 May 2011 13:12:02 UTC | #629842

Deako's Avatar Comment 15 by Deako

I think showing that in eukaryotes, drift has had a systematic affect on the propensity of soluble proteins to form complex interactions is pretty interesting...

Greg

Mon, 23 May 2011 19:47:05 UTC | #630013

Alan Canon's Avatar Comment 16 by Alan Canon

Comment 6 by God fearing Atheist :

Comment 4 by Alan Canon :

It's not gene-based, is it?

Yes it is. The "sticky proteins" are made from their RNA/DNA templates like any other protein. The "sticky regions" are thus caused by mutations in the sequence of base pairs in the RNA/DNA. Its all classic natural selection. Hence at least 3 of us are baffled by the claims. CORRECTION with ai1888, that makes 4 of us ...

I stand corrected: I had thought that perhaps these proteins had arisen by some other, perhaps abiogenetic, process, other than by good old ribosomal synthesis.

Tue, 24 May 2011 00:49:16 UTC | #630094

DavidMcC's Avatar Comment 17 by DavidMcC

The history of evolution shows that "sticky proteins" lead to bacterial mats and little else, until the planet stepped in, with "snowball Earth", at about 650MYa. Then multicellular species appeared, so it isn't just genetic mutations that brought us about, it must have been multiple changes in the selective conditions as well. The appearance of eukaryotes was also essential, but that did not start with a mutation either.

Wed, 25 May 2011 12:07:28 UTC | #630724

PsiWavefunction's Avatar Comment 18 by PsiWavefunction

Wow, some strong opinions on a paper few seem to understand...

For the record, the scientists involved in this paper, unlike Dawkins, are well-respected active researchers in their respective communities. They don't need to oversell their point to get published, they're long past that level. FYI.

The BBC article, as expected, isn't exactly fine journalism, but then again, biochemistry is terrifying and evolutionary biology is too seemingly simple to understand correctly – a lethal combination.

I've written a blog post hopefully answering some questions about the paper, so I won't go into much detail here, but basically the point of the paper is the following:

  • exposure of the protein backbone to water de-stabilises the protein, reducing its efficiency – this protein has a tendency to recruit others to block that exposed backbone (it's 'sticky')

  • smaller populations experience lower selection efficiency relative to drift (popgen 101), incidentally, they also have more poorly wrapped proteins with more backbone exposed (this correlation is a new thing already, AFAIK). This is explained by the reduction in the efficiency of selection

  • smaller populations also have a higher density of protein-protein interactions, even when correcting for total number of proteins.

  • at least part of the drastic increase in protein-protein interactions in organisms with a smaller effective population size can be accounted for by the recruitment of secondary (and tertiary, etc) proteins initially to cover that biochemical weak point – the exposed backbone. Eventually, these interactions can be exapted for what we now see as functional partnerships, but that is not the initial reason for their rise.

  • There's nothing in the paper about protein flaws being "responsible" for [all] complex life, like the BBC headline horribly implies, just that these particular 'flaws' can be conducive to enabling more protein-protein interactions in smaller populations. Likewise, there's nothing about [natural] selection not being involved there – in fact, Mike Lynch makes a point of describing his models as non-adaptive rather than selectively neutral – selection is omnipresent, albeit the most important and vastly more powerful category of selection is the so-called 'negative' variant, where insufficient things are culled rather than fitter organisms being favoured. Punishment is more rampant than favouritism in evolution...

    For more detail, read here: (Sticky proteins, complexity drama and selection's blind eye)

    Cheers,

    -Psi-

    Disclaimer: not a biochemist but involved with the neutral/non-adaptive evolution community

    Thu, 26 May 2011 07:55:38 UTC | #631012

    Troll's Avatar Comment 19 by Troll

    Removed by moderator

    Fri, 10 Jun 2011 20:40:01 UTC | #636952