For proponents of intelligent design, James Shapiro’s constant dancing in the DMZ between Darwin and design can be frustrating. On the one hand, Shapiro is as dismissive of Darwinism as any ID proponent. On the other, he constantly gives public notice that he is not on the side of ID. And yet, methinks he protests too much.
Shapiro is a molecular biologist on faculty at the University of Chicago. When it comes to ID, Shapiro admits that it has identified some legitimate problems, such as Michael Behe’s irreducibly complex biochemical systems (in this he is light years ahead of Richard Dawkins and Kenneth Miller, who deny that any problem exists). Shapiro admits that these are unresolved in Darwinian terms.

I got to know Shapiro at Wheaton College in 1997 at a symposium devoted to Behe’s then just published Darwin’s Black Box. In place of Behe’s design hypothesis, Shapiro proposed that organisms evolve through what he called “natural genetic engineering.” Briefly, organisms are intelligent and guide their own evolution.

Shapiro’s proposal, which in 2011 he elaborated into an entire book (Evolution: A View from the 21st Century), faces a fundamental conceptual difficulty. This came to light in 2002 in an online chat. In that chat, I posed the following question:

James, we met the first time at Wheaton College at a symposium in the spring of 1997 featuring principally you and Michael Behe along with Paul Nelson and David Hull. At the time, I asked you about the origin of such “natural genetic engineering” systems. As I recall, you indicated that this was not really the problem you were addressing. Have you thought any more about this problem? Specifically, how do such systems arise that can take over their evolution? And how much complexity do they require? Are you confident that non-teleological mechanisms can account for the rise of natural genetic engineering systems, and if so why?

Shapiro’s reply was illuminating for what it failed to say:

I am not sure how to answer your question. All existing living organisms possess natural genetic engineering capabilities. So they must be pretty fundamental. Any self-organizing evolving system has to have the capacity to alter its information store. That’s what they do. Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cells.

Where do the fundamental biological structures that make natural genetic engineering possible come from in the first place? Shapiro punted on this question back then and continues to punt to this day.

Fast forward to two days ago, January 8, 2012. In the Huffington Post, Shapiro wrote an insightful article on the mechanisms involved in antibiotic resistance, rejecting the standard Darwinian picture of antibiotic resistance being conferred by the gradual accumulation of slight adaptive modifications. Appealing to lateral gene transfer as a way of bacteria quickly acquiring complex biological structures and functions, and then appealing to natural genetic engineering to adapt those structures to new circumstances of life, Shapiro offers a picture that seems utterly congenial to intelligent design.

And yet, intelligent design is anathema in the circles in which Shapiro moves, so he must utter the mandatory denunciations:

Thus, there has been a wide-ranging use and reuse of these elaborate systems in the course of bacterial evolution. Since the Intelligent Design (ID) advocates point to the bacterial flagellum as an example of an “irreducibly complex” structure that could not have evolved by Darwinian evolutionary processes (Behe 1996), they need to address how such intricate and clearly related biological inventions have come to be diversified for so many different uses. Certainly, the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure. At the same time, it is fair to recognize that the evolutionary science community is also challenged to come up with detailed explanations for the origin and diversification of a basic complex functional design.

And toward the end of the article Shapiro repeats essentially the same point:

How did the first functional envelope-spanning complex originally arise in evolution? Although we can easily reject the supernatural solution ID advocates propose in response to this question, we also have to acknowledge that we still have no clear scientific answer to it.

So Shapiro admits that the basic structures required for life are unexplained within his framework, and yet intelligent design is off the table. But why should it be off the table? In the last quote above, he interprets ID as requiring constant supernatural interventions. But ID is hardly limited in that way, a point he tacitly admits in the quote before that: “the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure.” Note the conditional.

ID does not have to invoke supernatural interventions for every modified adaptive structure. Indeed, ID does not have to invoke supernatural interventions at all. ID only requires that intelligence acted in the formation of biological systems. How that intelligence acted — the precise timing and mode of implementation — is left wide open.

Shapiro’s natural genetic engineering is a design theory — organisms are intelligent and do their own designing. But the structures they need to do their own engineering are themselves devastatingly complicated. How did these arise? Indeed, why should it be a stretch to think that these structures are themselves the product of design? But since they are presupposed by living systems (all cells do natural genetic engineering according to Shapiro), they must derive from a non-biological source.

At this point, the options become quite limited: one is thrown either to brute material processes or to a designing intelligence (which may be external to nature or immanent). Far from refuting intelligent design or minimizing its relevance to biology, Shapiro is thus actually supporting it. So, in answer to the question that is in the title of this piece, I would say “Yes, Shapiro is a design theorist.”

One final note. It’s often said that ID is poor on predictions. Here is a prediction related to Shapiro’s natural genetic engineering. According to Shapiro, natural genetic engineering within cells allows them to take existing biological structures from other organisms and adapt them to a cell’s present needs.

Such an adaptive ability, I hypothesize, represents an immense feat of engineering technology, whose precise mechanisms we will uncover as human engineers understand and build increasingly elaborate artificial adaptive systems and understand their theoretical underpinnings. Moreover, I predict that as we build such artificial systems and learn how their organismal counterparts work within cells, we’ll find that the ones in cells are far more sophisticated than any we have or ever will build.