Over the years there have been many books that purport to “radically revise” or “supplant” Darwinian evolutionary biology; they come with predictable regularity. Usually they are of three kinds: something is wrong with natural selection, something is wrong with inheritance, or something is wrong with phylogeny. This book, by geneticist James A. Shapiro, exemplifies all three.
It is, I must admit, chock full of information not usually found in books about evolution. Part I has way more than I can assess regarding cell signalling, cell death and cellular reproductive strategies. Part II discusses the genetic system of eukaryotes, mostly, and introduces the core notion of the book – “natural genetic engineering”. Part III considers the evolutionary import of molecular genetics and genome sequencing, including some of the usual “post-evolutionary” suspects such as endosymbiosis, lateral transfer, and structural genomics. Part IV is where the “new conceptual basis for evolution” is presented. It is deeply disappointing.
He introduces the notion of natural genetic engineering thus:
A major assertion of many traditional thinkers about evolution and mutation is that living cells cannot make specific, adaptive use of their natural genetic engineering capacities. They make this assertion to protect their view of evolution as the product of random, undirected genome changes. But their position is philosophical, not scientific, nor is it based on empirical observations. This section demonstrates that in a large number of well-documented cases, natural genetic engineering capabilities have been utilized as part of the normal organism life cycle. In many of these cases, utilization involves the integration of different natural genetic engineering processes into a highly targeted and well-regulated series of changes with a clear adaptive benefit. The operation of a tightly regulated sequence of natural genetic engineering events in the adaptive immune system is probably the most elaborate example we have of purposeful genome manipulations. 
Immediately the contrast is suspect: “traditional thinkers”. Moreover, the framing – “living cells cannot make specific, adaptive use of their natural genetic engineering capacities” – sets up a strawman. I do not know of anyone in the field who asserts that living cells cannot employ any mechanisms of which they are capable. More on this below.
I shall presume that the science is correct, and the choice of apparent counterexamples to the ruling paradigm (which seems to be far more fluid than many of these books expect. Lateral transfer, endosymbiosis and jumping genes are many “post-Darwinian” ideas that have been easily inserted into the consensus) is illuminating. What is the illumination thus gained?
It is basically this:
Although they may go through many trial-and-error steps, human engineers do not work blindly. They are trying to accomplish defined functional goals. Can such function-oriented capacities be attributed to cells? Is this not the kind of teleological thinking that scientists have been taught to avoid at all costs? The answer to both questions is yes. [123f]
Shapiro is returing to the older style of teleology that might have satisfied an Aristotelian (such as the wonderful D’Arcy Thompson or Agnes Arber in the 1920s). The worry is that he does it in a rather hamfisted and unnecessary manner. Where they engaged with the best philosophical arguments of the day (and let there be no mistake, this is a philosophical claim being made, not a scientific one), Shapiro seems to think he can get away with statements like the one just quoted without any engagement at all.
Engineers do not accomplish defined functional goals. Instead they employ the results of prior experience on the presumption that what worked in the past will work now (and that includes the choice of goals themselves). No engineer has some cognitive “noetic ray” that allows them to see into the future; they are using the tested results of the past. When they make assumptions that fail to hold in the present case, the result is the Tacoma Narrows Bridge. Here engineers used prior art, especially with respect to stress analyses, to build an fantastic suspension bridge. They simply did not do resonance analyses, and this particular spot had winds that set thebridge resonating exactly at the frequency that tore it apart, spectacularly. Now engineers do resonance analyses.
Shapiro’s book is not, despite its subtitle, evolution for the 21st century. It is instead evolution for the 16th century, before Francis Bacon had written:
For the inquisition of Final Causes is barren, and like a virgin consecrated to God produces nothing. [The Advancement of Learning. iii. 5]
Bacon’s dictum long precedes Darwin, but the attempt to find a natural process which delivers design is treated as some kind of novel dscovery, when in fact it is simply unsupportable in the domains Shapiro appeals to. I must tell a personal story: at a workshop on microbial biology and philosophy at Exeter a few years back, I gave a talk on microbial species. Shapiro gave a talk on how bacterial colonies and biofilms were like (in fact, were) intelligent problem solving systems. Now I can accept the metaphor, if properly hedged, but really they exhibit only the sort of post hoc intelligence that all populations do, of responding to their environment in ways that either succeed to maintain the population, or fail to (in which case they remove themselves from the subject of investigation).
But Shapiro wanted to call this just intelligence. No metaphor, no analogy, the real thing. It struck me as over-reaching and so I asked “Why add intelligence to this? What is lost if we simply describe the dynamics of populational and community adaptation?” I was abruptly shut down. This is the core of the problem. What does it add to our understanding to call this “engineering” or “intelligence”?
At best I can only think this is a case of a scientist who wants to extend what Dennett once called the “white picket fence” around human specialness to the natural world. If so, it is either a case of clubfooted Aristotelianism or a kind of panpsychism, or both. Either way, this is no more a matter of a new approach than a return to animism might be.
Shapiro has been employed by more than a few intelligent design (ID) theorists on the strength of a paper he published in 1997. It is unclear whether he supports ID, from this book, despite a somewhat disparaging reference at the start of Part IV [p115]. I think he should be seen as a traditional Aristotelian rather than a modern ID theorist (which would have made him one of the few actual ID theorists in existence!), but then he fails to deal with how functional or teleological explanations explain if they are not the result of a trial and error – that is to say, natural selection – process. Since Bacon we have known that causes should not come after their effects. He does not deal with this problem, a staple of teleological discussions since then. Simply asserting something like Kant’s “purposiveness” (Zweckmässigkeit] as an explanation of living systems is not enough.
I cannot recommend this book.
Shapiro, James A. Evolution: A View from the 21st Century. FT Press Science, ISBN: 0-13-278093-3, $34.99 Publisher’s site
Late note: I messed up and confused him with Robert Shapiro. Now corrected.
Later change: fixed link to Shapiro’s site and corrected his profession. Thanks to Maureen O’Malley for spotting this.