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A Good Man Under a Bad Emperor: James Shapiro's "Natural Genetic Engineering"

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You can see why James Shapiro gets under the skin of many Darwinists. In his writing and research, the University of Chicago molecular biologist steadfastly retains the premise that valid explanations of how living systems come to be in evolutionary terms must be limited to the "natural." What does that word mean?

Coincidentally, and writing about other matters, Ronald Bailey at Reason magazine reflected the other day:

The Oxford Dictionary defines nature as "the phenomena of the physical world collectively, including plants, animals, the landscape, and other features and products of the earth, as opposed to humans or human creations." In his Metaphysics, ancient Greek philosopher Aristotle observed, "Of things that come to be, some come to be by nature, some by art." Regarding those objects produced by "art," which Aristotle called "makings," he asserted, "All makings proceed either from art or from a faculty or from thought." In contrast, according to Aristotle, natural entities have internal spontaneous sources of movement, whereas artificial objects are created by activity outside themselves.
Shapiro holds, if I understand him correctly, that there can be no concession to theorists of ID who find that the operations of the cell, for example, reflect artifice -- deliberate choices by an intelligent agent. And that should make Shapiro a safe interlocutor for his colleagues who adhere to orthodox evolutionary ideas.

It should except that, as he demonstrates in his current Huffington Post column, everything else Shapiro says on his theme of "Natural Genetic Engineering" (NGE) seems to cry out for an explanation involving some kind of deliberate art or calculation. The brief article bears careful study. It's a keeper: a highly compressed précis of what Shapiro means by NGE.

Cells have the amazing ability to edit DNA in response to stresses. They posses a complex "toolbox" of operations that results in DNA's being engineered to suit needs as they arise, suggesting in turn a certain natural intelligence -- what else would you call it? -- at work in the development of life:

NGE encompasses a set of empirically demonstrated cell functions for generating novel DNA structures. These functions operate repeatedly during normal organism life cycles and also in generating evolutionary novelties, as abundantly documented in the genome sequence record.
Shapiro compares NGE operations to, among other arts, "carpentry, architecture or computer programming." The distinction with ID seems to be that all the art going on is on the part of the natural entity, the cell, not that of an artificer who devised the processes at work in NGE. But even "natural" art implies intelligence, and if the cell is intelligent, then...but no one thinks that, do they? See here (emphasis added):
While NGE can help in understanding the molecular details of rapid and widespread genome change, it does not tell us what makes genomic novelties come out to be useful. How natural genetic engineering leads to major new inventions of adaptive use remains a central problem in evolution science.
That's an understatement. More:
To address this problem experimentally, we need to do more ambitious laboratory evolution research looking for complex coordinated changes in the genome.

If we are able to observe cells coordinating NGE functions to make useful complex inventions in real time, major questions arise. How do they perceive what may be useful? We need to find out whether there are feedbacks between sensory inputs and genome changes. Is there any connection between the biological challenge and the NGE output? Cells can adjust other activities to meet the goals of survival, growth and reproduction. Can they do the same with DNA changes? We need to figure out how to do experiments on this.

More:
If experiments show that cells can make distinct appropriate NGE responses to different adaptive challenges, we need to figure out how they do so. This almost certainly would prove to be more than a strictly mechanical process. How do cells carry out their computations to make useful goal-oriented responses? A successful answer to that question will certainly involve cybernetics. If such investigations take evolution science into areas that are more than strictly material, so be it. As long as we stay within the realm of natural processes, there are no boundaries on what science can address.
Shapiro is tantalizingly cryptic. He insists on limiting ourselves to "the realm of natural processes," but these may exceed the limits of the "strictly material." This enigmatic quality prompted William Dembski to ask last year, following exchanges here between Shapiro and Biologic Institute and Discovery Institute researchers, " Is James Shapiro a Darwinist After All?"

There is indeed something frustrating, yet also moving and admirable, about Dr. Shapiro's conservatism and restraint. Unlike some atheists and, let's be candid, some theists, he refuses to think he's got everything all figured out. On the contrary, he emphasizes how much we don't understand about NGE.

Even so, and despite being contradicted by a presupposed naturalism, his implications are in a certain way more powerful in pointing to design than some writing that unabashedly argues for ID in nature. It's his very resistance to going there and inferring design that adds the dash of special eloquence.

If you don't mind my switching contexts rather abruptly, last night I was reading about the life of the Roman historian Tacitus (56-117 AD), who wrote at a time of persecution and what amounted to thought-control by the emperor Domitian. Critics of imperial corruption stood to be executed, their books and tracts burned. Tacitus was an opponent of the principate himself, but he rejected the strategy of openly opposing the emperor.

Instead, he let the implications of his writing speak for him. For example, in his brief book Agricola, he writes in praise of his father-in-law, Agricola, who governed Roman Britain. He hardly mentions the emperor, but the contrast of virtue with corruption is intended to carry the message. In a sense, the book is about Domitian.

Tacitus wasn't looking to get himself killed, and evidently judged the good he could do by employing a conservative approach as outweighing what he could do by coming out and denouncing the government. His watchwords were restraint, modesty, and prudence. The classicist J.B. Rives says in summary that he embodied "a particular solution to the challenge of being a good man under a bad emperor."

Without doubting his sincerity for a moment in sticking firmly with a commitment to naturalism, this all reminds me somewhat of James Shapiro.

Image: Bust of Domitian/Wikipedia.