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“Compelling” experimental evidence for neutral evolution offered

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In “Evolution of increased complexity in a molecular machine”(Nature 481, 360–364 (19 January 2012) doi:10.1038/nature10724), Gregory C. Finnigan, Victor Hanson-Smith, Tom H. Stevens & Joseph W. Thornton offer, according to W. Ford Doolittle, “the most compelling experimental evidence to date”:

Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

From W. Ford Doolittle (1/19/12 issue):

… A general theory, sometimes called constructive neutral evolution, to explain how neutral processes might drive a system towards complexity is more than a decade old. But the study by Thornton and colleagues may provide the most compelling experimental evidence to date. Of course, one can never prove that some subtle, unidentified selective advantage was not involved in the evolution of the V-ATPase protein ring, but neutrality would seem the most justifiable default hypothesis. Thus, a neutral theory of molecular evolution, normally invoked for nucleotide substitutions, may also apply to certain higher-order structures such as multi-subunit protein rings. How general such neutral mutational drives to complexity might be is one of evolutionary theory’s deeper unanswered questions.


From the abstract: We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. From an information perspective, overall, we have a "loss" of complexity. From a functional perspective, we have a more-or-less neutral event. When the EPA said that the material used for the O-rings on the fuel tank for the Space Shuttle was harmful, a substitution had to be made. This led, of course, directly to the shuttle disaster. But let's say that the material that replaced the first O-ring material was made out of three chemicals instead of two: Does this represent an "increase" in function? I don't think so. Supposedly, it should have worked just like the first version. Now, whatever added functionality that is claimed has occurred through basically chemical means. I don't find this very impressive. In fact, it reminds me exactly of the claims made about the vpu protein found in HIV, and the changes made to the proton pump that it codes for. My hunch is that we're likely dealing with "natural genetic engineering" on the part of the cell, and not "neutral drift". And as we already know, the question we would want James Shapiro to answer is: Where did these "engineering" functions come from? Did they arise through random processes? I know Shapiro would demur, but from a strictly information perspective, again, we're looking at a "loss" of information, not any kind of gain whatsoever. PaV
Chas D: Please look at this paper: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0008378 Out of 3464 prtein domains considered here, almost half appeared after LUCA, and up to relatively recent times. So, the emergence of new protein domains is an issue that is equally relevant to OOL and to later evolution. gpuccio
Where would you place that origin - before or after LUCA? If before, it is a 'dark age' that lacks a single comparative example to permit this kind of analysis. So yes, paralog modification is likely to be 'more comfortable for darwinists', if only for complete lack of anything to guide research on the path from protein synthesis through to post-LUCA divergence. The inability of darwinism to throw strong light on actual pre-LUCA evolution is hardly a body blow - does it have to explain everything before it can explain anything? Chas D
Joe: That's exactly the point. Darwinists continue to stick to analyzing possible evolution within protein families (a good work, anyway), but strictly avoid mentioning that the emergence of those families remains completely unexplained by their theory. So, people who have no detailed understanding of the issue really think that there is a lot of research about the origin of proteins. That's simply not true. There is no explanation of the basic origin of protein domains, in darwinian terms, exactly as there is no explanation of OOL. With the serious fact that the origin of proten domains is not limited to OOL. Now, I am not saying that neo darwinism can really explain evolution within protein families. That kind of "medium complexity" transitions, involving usually a few AAs, are exactly a field that at present is more objectively controversial: may be some of that, or all, or nothing, could be explained by the neodarwinian paradigm. May be. But I am not sure. But it is obvious that that field is more comfortable for darwinists, so it is natural that they prefer to stay there. But the biggest problems, like OOL, the origin of protein domains, and the origin of complex regulatory networks, remain. gpuccio
"Commendable research, exaggerated implications":
We are relieved to know that darwinists have been puzzled by something nontrivial — a rare admission. But we think the new analysis does not justify Thornton's broad conclusion. First, the slightly more complicated fungal protein pump does no more than the simpler version did, so no new function was gained. More importantly, the conclusion ignores something obvious. Paralogs that vary slightly from the original are ubiquitous and easy to explain, but the first version, the "original," remains unexplained. While paralogs relate to each other, the whole family usually lies well-isolated (>100 mutations removed?) in nucleotide sequence space. If it were not so, identifying and naming gene families would be much more difficult. In brief, the divergence of paralogs does nothing to explain the existence of a paralog family. And the divergence of these specific proteins does not in any way account for the creation of the proton pump of which they are parts.
Beautiful work indeed... Joe
Giants? What "giants"? Oh the New York Giants- yeah they have a chance of getting to the SB... Joe
This is some sort of break-through?
Stand on the shoulders of giants much, Joe? Peter Griffin
There's already a thread on this, isn't there? But worth another. It's beautiful work. Elizabeth Liddle
So the increased "complexity" doesn't pertain to functionality, nor an increase in total number of subunits (6) in the configuration, just to the number of slightly different proteins in the configuration? This is some sort of break-through? In more exciting news I just got a new snow-blower with a briggs & stratton 208cc 4 cylinder, 6 speed auto-drive, 2 reverse speeds serated auger and it has a head-light in case I want to blow some snow at night. And guess what? It's snowin'... Joe

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