Theory of Intelligent Design, the best explanation of Origins

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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » TESTING THE CO-OPTION OPTION


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1 TESTING THE CO-OPTION OPTION on Tue Jul 14, 2015 6:34 pm



From Stephen C. Meyers book Darwin's doubt:


But does generating novel genes and proteins require coordinated mutations? Behe and Snoke  inferred as much based upon an undisputed fact of molecular biology: many proteins rely on sets of amino acids acting in close coordination in order to perform their functions. In addition, in The Edge of Evolution, Behe argued on functional grounds that many complex biological systems would require coordinated adaptive mutations since in these systems, the absence of even one or a few gene products (proteins or traits) will cause them to lose function. Behe specifically showed that several molecular machines within cells (such as the cilium and intraflagellar transport system, and the  bacterial flagellar motor) require the coordinated interaction of multiple protein parts in order to  maintain their function. Nevertheless, in making this argument, Behe did not address an alternative idea about the pathway by which new genes and proteins might have evolved, and thus did not  establish conclusively that new genes and proteins themselves represent complex adaptations.  Some neo-Darwinists have proposed a model of protein evolution known as "co-option." In this model, a protein that performs one function is transformed, or "co-opted" to perform some other function.

This model envisions new features requiring multiple "mutations" arising in a step-by-step  way to produce some protein, call it "Protein B," from some other protein that lacked those features,  call it "Protein A." In proposing a series of single separate mutations, advocates of co-option acknowledge that the initial individual amino-acid changes, the first few steps in evolution, from Protein A, the protein lacking the multisite feature, would not allow Protein A to perform the function of Protein B. Nevertheless, they propose that these initial changes might have allowed Protein A to perform some other advantageous function, thus making it selectable and preventing protein evolution from terminating due to diminution or loss of its initial function. Eventually, as mutations continued to generate new proteins with slightly different functions, they would have generated a protein close enough in sequence and structure that just one or a very few additional changes would suffice to convert it into Protein B.  Aware of these imaginative scenarios, Douglas Axe and his colleague, molecular biologist Ann Gauger, now working together at the Biologic Institute in Seattle, decided to put them  to an ingenious experimental test. In so doing, they sought to determine whether the evolution of new  multisite features does indeed typically require multiple coordinated mutations, or instead whether such a feature could arise by co-option. Axe and Gauger scoured protein databases looking for proteins that are as similar as possible in sequence and structure, but that nevertheless perform different functions. They identified two proteins that meet those criteria.

One of these proteins (Kbl2) is needed for breaking down an amino acid  called threonine, and the other (BioF2) is needed for building a vitamin called biotin. Gauger and Axe realized that if they could transform Kbl2 into a protein performing the function of BioF2 with just one or very few coordinated amino-acid changes, then that might demonstrate  (depending upon how few) that the two proteins were close enough in sequence that a conversion in function of the kind envisioned by co-option advocates is plausible in evolutionary time. What's more, because they knew the difficulty scientists have had in showing any real change of protein function to be feasible, a positive result would suggest that they had at last discovered a functional gap that one or very few mutations could plausibly jump—as co-option envisioned.  If, however, they found that many coordinated mutational changes were needed, then that could establish—depending upon how many were needed—that the Darwinian mechanism could not accomplish the functional jump from A to B in a reasonable time. That would imply that an even greater degree of structural similarity between proteins would be needed for the co-option hypothesis to be plausible. Having carefully examined the structural similarities between members of a large  class of structurally similar enzymes, they knew that Kbl2 and BioF2 were about as close in sequence  and structure as any two known proteins that performed different functions. Thus, if it turned out that converting one protein function into the other required many coordinated mutations—more than could be expected to occur in a reasonable time—then the outcome of their experiment would have devastating implications for standard accounts of protein evolution. If proteins that perform two  different functions have to be even more similar than Kbl2 and BioF2 in order for mutational changes  to convert the function of one to the other, then for all practical purposes co-option would not work. There simply aren't many known jumps that small.

Axe and Gauger first identified those amino-acid sites that were most likely, if mutated, to cause a change from Kbl2 function to BioF2 function. They then systematically mutated those sites individually  and in groups involving various amino-acid combinations. Their results were unambiguous. They found that they could not induce, with either one or a small number of amino acids, the change in  function they sought. In fact, they found that they could not get Kbl2 to perform the function of BioF2,even if they mutated larger numbers of amino acids in concert—that is, even if they made many more  coordinated mutations than could plausibly occur by chance in all of evolutionary history.  Although their attempts to convert Kbl2 to perform the function of BioF2 failed, their experiment  did not. It allowed them to establish experimentally for the first time that the co-option hypothesis of protein evolution lacks credibility—simply too many coordinated mutations would be required to convert one protein function to another, even in the case of extremely similar proteins. That implied that generating new genes and proteins would require multiple coordinated mutations, and thus, the waiting times that Behe and Snoke had calculated do present a problem for neo-Darwinian theory.  The experimental work also enabled Axe to calculate expected waiting times for various numbers of coordinated mutations given different variables and factors. Axe developed a refined population- genetics mathematical model to calculate various waiting times. His results roughly confirmed the previous calculations of Behe and Snoke. He found, for example, that if he took into account the probable fitness cost to an organism of carrying unnecessary gene duplicates (as was necessary to give the evolution of a new gene a reasonable chance), that the probable waiting time for even three coordinated mutations exceeded the duration of life on earth.

He therefore effectively determined an upper bound of two for the number of coordinated mutations that could be expected to occur in a duplicate gene during the history of life on earth (taking into account the negative effects of carrying gene duplicates in the evolutionary process). He also calculated six coordinated mutations as an upper bound, neglecting the fitness cost of carrying gene duplicates. Nevertheless, in their experiments, he and Gauger could not induce a functional change in a single gene with more than six coordinated mutations. So, even that more generous—and, again, unrealistically generous upper bound—does little to render the co-option hypothesis credible. Indeed, Axe and Gauger's experiments showed that the smallest realistically conceivable step exceeded what was plausible given the time available to the evolutionary process. In their words, "evolutionary innovations requiring that many changes . . . would be extraordinarily rare, becoming probable only
on timescales much longer than the age of life on earth."


By showing the implausibility of the co-option model of protein evolution and the need for multiple  coordinated mutations in order to generate multisite features in proteins, Axe and Gauger confirmed that genes and proteins themselves represent complex adaptations—entities that depend upon the coordinated interaction of multiple subunits that must arise as a group to confer any functional advantage.  The need for coordinated mutations means that evolutionary biologists cannot just assume that mutations will readily generate new genes and traits, as neo-Darwinists have long presupposed. Indeed, by applying mathematical models based on the standard principles of population genetics to the questions of the origin of genes themselves, Behe and Snoke, Durrett and Schmidt (inadvertently),  Axe and Gauger, and other biologists35 have recently shown that generating the number of multiple  coordinated mutations needed to produce even one new gene or protein is unlikely to occur within a realistic waiting time. Thus, these biologists establish the implausibility of the neo-Darwinian mechanism as a means of generating new genetic information.

 There is one other aspect of this. The body of work published between 2004 and 2011 also  provides additional confirmation of Axe's research showing the rarity of genes and proteins in  sequence space. In fact, that research helps to explain why such long waiting times are necessary. If functional sequences are rare in sequence space, it stands to reason that finding them by purely random and undirected means will take a long time. Moreover, waiting times increase exponentially with each additional necessary mutation. Thus, long waiting times for the production of new functional genes and proteins is exactly what we should expect if indeed functional genes and proteins are rare, and if coordinated mutations are necessary to produce them. Thus, the various experiments and calculations performed between 2004 and 2011 indirectly confirm Axe's earlier conclusion about the rarity of functional genes and proteins and supply further evidence that the neo-Darwinian mechanism cannot generate the information necessary to build new genes, let alone a new form of animal life, in the time available to the evolutionary process.

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2 Re: TESTING THE CO-OPTION OPTION on Fri Jul 17, 2015 10:16 am


For a working biological system to be built by exaptation , the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if sub systems or parts are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

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