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Another windy day in the junkyard …

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From Jason Palmer at BBC News (19 May 2011), we learn, “Protein flaws responsible for complex life, study says.” This time mistakes produce more functional proteins:

Tiny structural errors in proteins may have been responsible for changes that sparked complex life, researchers say.A comparison of proteins across 36 modern species suggests that protein flaws called “dehydrons” may have made proteins less stable in water.

This would have made them more adhesive and more likely to end up working together, building up complex function.

Remarkably, we read,

Natural selection is a theory with no equal in terms of its power to explain how organisms and populations survive through the ages; random mutations that are helpful to an organism are maintained while harmful ones are bred out.But the study provides evidence that the “adaptive” nature of the changes it wreaks may not be the only way that complexity grew.

Natural selection is a theory with no equal – in terms of much belief and little evidence. But it can be supplemented by tiny structural errors that somehow produce co-operation.

The authors suggest then that other adaptations occur that “undo” the deleterious effects of the sticky proteins.

Convenient, that.

Fred Hoyle, wherever you are, check your mail: Your Boeing 747 is ready.

Isn’t this the sort of mess that Steve Fuller says “floored astrology”?

Comments
Oh, and our results even then would only generalise to the environment we provide. If we then sell the seeds to someone else, our feature may prove to be their bug, all over again :) The point being, of course, that in a Darwinian context, selection simply means: this allele tends to breeds more successfully in this environment.Elizabeth Liddle
June 3, 2011
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Then we'd have to record allele frequencies in the population over time, and see which alleles became more frequent and which less. Even then we may not actually be able tell the difference between an actual flaw and neutral or slightly beneficial variant that fell foul of stochastic processes and decreased in frequency (i.e. due to sheer bad luck) and vice versa. Although being good scientists, we would run parallel experiments with random samples of the original population, and determine whether a particular allele increased in frequency more often than would be expected under the null hypothesis of neutrality. But clearly very small effects (i.e. the effects of Very Slightly Beneficial Mutations) would take very great statistical power to detect. The smaller the "real" effect, the more drift effects will dominate the picture.Elizabeth Liddle
June 3, 2011
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Elizabeth Liddle, In short: a flaw is something that decreases breeding chances in the current environment. When the environment changes, what was a bug can become a feature, and what was a feature can become a bug. Naturally. Let's go back. No, the flower breeder is irrelevant unless the flower is in the flower breeder’s greenhouse. While in the breeder’s greenhouse, “flaws” are whatever will cause the breeder to discard the flowers seeds. Alright. And if we don't know whether the flower is in the breeder's greenhouse?nullasalus
June 2, 2011
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Hi there, nullasalus
Let’s think about a case like this: We have a single organism, let’s say a flower. The only thing we know for certain is that the flower was bred purposefully by a flower breeder. Given that, would it be the case that we could not therefore say whether the traits were flaws or features without getting input from the flower breeder?
A subtle question! But I'm going to give a subtle answer: No, the flower breeder is irrelevant unless the flower is in the flower breeder's greenhouse. While in the breeder's greenhouse, "flaws" are whatever will cause the breeder to discard the flowers seeds. Once the flower is in your garden, "flaws" are whatever causes you to neglect it or kill it. So if the breeder bred a pink daisy, but you had a rabbit that liked eating pink daisies, then what was a beneficial trait while the flower was being bred, has now become a flaw because it increases the probability that the flower will be eaten by the bunny. In short: a flaw is something that decreases breeding chances in the current environment. When the environment changes, what was a bug can become a feature, and what was a feature can become a bug.Elizabeth Liddle
June 2, 2011
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Natural selection is a theory with no equal – in terms of much belief and little evidence. But it can be supplemented by tiny structural errors that somehow produce co-operation.
The 'somehow' is more readily understood from the original paper than its popular summary: Non-adaptive origins of interactome complexity.paulmc
June 1, 2011
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There are complications in that story, because of drift effects, but, yes. Fair enough, that's what I expected. Let's think about a case like this: We have a single organism, let's say a flower. The only thing we know for certain is that the flower was bred purposefully by a flower breeder. Given that, would it be the case that we could not therefore say whether the traits were flaws or features without getting input from the flower breeder?nullasalus
June 1, 2011
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Yes, I would say so :) There are complications in that story, because of drift effects, but, yes.Elizabeth Liddle
June 1, 2011
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The only “flaws” from a Darwinian point of view or features that bias against successful reproduction, and even then, a flaw in one generation can become a feature in the next. Is it therefore tautological to say that flaws are never selected for, given the "Darwinian point of view"? I realize that 'a flaw can become a feature' of course, but if something is being selected for, then by the DPOV it cannot be a flaw. Yes?nullasalus
June 1, 2011
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"flaw" makes no more sense from a Darwinian perspective than an ID one. Less, probably. The only "flaws" from a Darwinian point of view or features that bias against successful reproduction, and even then, a flaw in one generation can become a feature in the next. I don't know if it's sloppy journalism or a sloppy attempt by scientists to write a "lay" press release, but it's highly misleading. Unless they are using it a highly technical sense, like a "flaw" in a regular lattice. Still, careless writing, whatever.Elizabeth Liddle
June 1, 2011
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I'm scratching my head like you.
We introduce a quantifiable structural motif, called dehydron, that is shown to be central to protein-protein interactions. A dehydron is a defectively packed backbone hydrogen bond suggesting preformed monomeric structure whose Coulomb energy is highly sensitive to binding-induced water exclusion.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303363/
In the past decade, research has demonstrated that defectively packed hydrogen bonds, or "dehydrons," play an important role in protein-ligand interactions and a host of other biochemical phenomena. These results are due in large part to the development of computational techniques to identify and analyze the hydrophobic microenvironments surrounding hydrogen bonds in protein structures. Here, we provide an introduction to the dehydron and the computational techniques that have been used to uncover its biological and biomedical significance.
http://www.ncbi.nlm.nih.gov/pubmed/20865532Mung
June 1, 2011
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Bad design? Sure, but what's the bad design here? The flaws are said to have been possibly important for causing complex life. If that was the goal, then this flaw was a feature, assuming the scenario is true.nullasalus
May 31, 2011
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What makes this a ‘flaw’?
Bad design?Mung
May 31, 2011
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"Natural selection is a theory with no equal in terms of its power to explain ..." As an "explanation," natural selection is, at best, a tautology -- those which survive, survive. Well, yes, they would, wouldn't they? On the other hand, when one tries to make of natural selection something more than a mere minor tautology, one gets one of those "explanations" which "explains" everything and its opposite.Ilion
May 31, 2011
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A simple, single question. What makes this a 'flaw'?nullasalus
May 31, 2011
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