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James Shapiro responds to Biologic Institute’s Doug Axe and Ann Gauger

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(Background: Bill Dembski started it all by asking Shapiro, based on his observations, why aren’t you a design theorist? Then everyone had a say. Great stuff!)

Now, Shapiro tells Axe and Gauger:

Proteins evolve largely by shuffling and accreting functional subregions called “domains,” not through the Darwinian modifications of individual amino acids (Doolittle and Bork 1993). Domain accretion and shuffling are inherently natural genetic engineering processes (i.e. non-Darwnian) because they involve the rearrangement of extended DNA segments that encode the different domains. As my book details, we have many examples of this process mediated by mobile genetic elements in nature as well as its replication in living cells in the laboratory. Moreover, we know a great deal about the roles of mobile genetic elements as sources for completely novel domain coding sequences through the process currently known as “exoneration.”

I suggest you review this literature to see that well-documented natural processes are more than adequate to explain how protein evolution for new functionalities can occur in a purely natural and combinatorial fashion. One of the motives behind my book was to acquaint readers with these and other poorly known examples of revolutionary discoveries in molecular genetics and genomics that allow us to view evolutionary processes in a new light.

Well, they are definitely “poorly known.” Most non-ID folk are still insisting that “Darwin done it.” Over to Axe and Gauger …

By the way, James Shapiro is not to be confused with Robert “Dr. No” Shapiro (1935-2011), a skeptical origin of life chemist.

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Arthur, it sounds to me like the processes Shapiro is talking about don't appear to be random; that they are under control and/or are cued by the environment. The other problem is that all creatures have these internal capabilities, thus making individuals evolve. Darwinism says only populations evolve. vh
I'm actually convinced, from my time here, that about 50% of the disagreement between IDists and Darwinists is non-shared understanding of key terms. It's good to get some of that out of the way. 2012 has got off to a good start :) Elizabeth Liddle
Exactly the point I'm trying to make to Timaeus on the other thread Elizabeth Liddle
My observation is that in this world strange things may happen. So Darwin might well have ended up not being hardline Darwinian enough, esp. in view of the fact that the theory of evolution keeps evolving. Eugene S
Jon: Ok. But still it is random variation or NS. Or design. Let's say that today RV is more various :) gpuccio
I'm pretty sure the original Neodarwinians with their population genetics didn't have in mind HGT, whole genome doubling,chromatin formatting, epigenetics, transposons, LINES and SINES etc. They'd have regarded those "variations" in the same light as the "variation" of a dog giving birth to a parrot and a peccary. Jon Garvey
Adding to Petrushka's comment, "Darwinian" means "descent with modification, with natural selection acting on the products of naturally-occurring heritable variation". The shuffling and swapping of protein domains is one form of generating new heritable variation, and is entirely consistent with Darwinian mechanisms. Arthur Hunt
Jon: Am I missing something? What evolutionary mechanisms are on the table, except for RV+NS and design? :) gpuccio
It's likely to mean Non-Neodarwinian, taking that in the old-fashioned sense of random variation with natural selection rather than the modern sense of "whatever-evolutionary-mechanisms-are-on-the-table-just-now-except-design". Jon Garvey
Petrushka: I agree with you fully on that! Well, this is my agreement day, it seems :) gpuccio
How can something be non-Darwinian when Darwin didn't speak to it? It's just nit-picking, but I don't understand. Darwin knew nothing about the molecular basis of variation, so discoveries in molecular biology can't possibly be non-Darwinian. Darwin even considered the possibility of Lamarkian variation. More to the point, the shuffling that Shapiro refers to has to pass through the sieve of selection. Just because a segment of DNA shuffles doesn't make the change useful. Petrushka

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