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Since biological inventions only benefit their possessors after they work, their origins cannot be attributed to their selective effects. One proposed solution to this conundrum is that selection perfects activities that already existed in rudimentary form before they became beneficial. An example of this idea for protein origins is the promiscuity hypothesis, which claims that minor aberrant side-reactions in enzymes can be evolutionary starting points for proficient new enzymes. Another example—the junk hypothesis—claims that proteins arising from accidental expression of non-genic DNA may likewise have slight activities that, through evolutionary optimization, lead to proficient enzymes.
Here, we tested these proposals by observing how the endpoint of simple evolutionary optimization depends on the starting point. Beginning with optimization of protein-like constructs in the Stylus computational model, we compared promiscuous and junk starting points, where design elements specific to the test function were completely absent, to a starting point that retained most elements of a good design (mutation having disrupted some). In all three cases, evolutionary optimization improved activities by a large factor. The extreme weakness of the original activities, however, meant even large improvements could be inconsequential. Indeed, the endpoint was itself a proficient design only in the case where this design was largely present from the outset.
Laboratory optimization of ampicillin-resistance proteins derived from a natural β -lactamase produced similar results. Our junk protein here was a deletion mutant that some - how confers weak resistance without the original catalytic mechanism (much of the active site having been lost). Evolutionary optimization was unable to improve that mutant. In contrast, a comparably weak mutant that retained the active site surpassed the natural β -lactamase after six rounds of selection. So, while mutation and selection can improve the proficiency of good designs through small structural adjustments, they seem unable to convert fortuitous selectable activities into good designs.
Andrew McDiarmid talks to Dr. Ann Gauger, a senior research scientist at Biologic Institute and co-author with Dr. Douglas Axe of a new paper recently published in the journal BIO-COMPLEXITY that probes the limits of evolutionary optimization. Gauger explains how she and Axe tested popular hypotheses for protein origins and discovered that while mutation and selection can improve the proficiency of good designs through small adjustments, they seem unable to convert fortuitous selectable activities into good designs.
BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal's scope.
BIO-Complexity is (or, perhaps more properly, was) an open access journal published by the Biologic Institute. The journal "aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life."
The first two articles exploit ambiguities in biochemical mechanisms in the typical "God of the gaps"-type argument, and neither provides evidence for an intelligent designer; neither even mentions a designer in the paper. Both articles have authors from the Biologic Institute's editorial board (which also includes ID leaders William Dembski and Michael Behe). The Discovery Institute lauded the journal's formation, implying that intelligent design papers were ideologically blocked from publication.
The Biologic Institute is a Creation science group dedicated to verifying intelligent design through pseudoscientific research. It is a non-profit group funded and staffed by the Discovery Institute. The concept was first developed as part of the wedge strategy which called for Douglas Axe to create an organization to do intelligent design research. In 2005 Axe created the Biologic Institute.
In 2008, the Biologic Institute published its first "research" in the open access journal PLoS ONE. The paper introduces a computational model for protein simulation call Stylus. The program creates 2d protein structures out of amino acids coded by genes and then compares these to Han Chinese characters.
Since the Han characters have a function that emerges from their structure the paper argues this is a computationally efficient analogy to real life proteins. 
The paper makes no claims in regards to evolution or intelligent design. It is merely a description and publication of protein modeling software. In a press release about the research the Biologic Institutes claims that it might eventually be able to use this simulation to show the "edge of evolution" but admits that they might wind up showing the power of evolution instead. 
In 2010, the institute started its own journal, BIO-Complexity.
This research is certainly not pseudo-science. Is the testing of evolution hypothesis, as is done here, biased? I am inclined to think it is not.
originally posted by: deliberator
As I said in my OP I expected some vociferous posts. What I am actually looking for is constructive critique of the research.
I call this experiment 'replaying life's tape'. You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past--say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original. If each replay strongly resembles life's actual pathway, then we must conclude that what really happened pretty much had to happen. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self conscious intelligence? Or of mammals? Or of life on land? Or simply of multicellular persistence for 600 million difficult years?
Notice that this sort of "let's play science" baloney isn't actually meant to convince normal, rational people.