A Commentary on James A. Shapiro’s Post-Darwinian Work


Seeing Past Darwin II:
James A. Shapiro

A molecular biologist at the University of Chicago by the name of James A. Shapiro (left) recently published a masterly synthetic work which constitutes the most substantial contribution to date to post-Darwinian thinking in contemporary biology.(1)

The volume in question is entitled Evolution: A View from the 21st Century (FT Press, 2011), and it is simply stunning in every respect.

However, Shapiro's masterpiece is packed with technical detail, and for that reason it may not be as widely read as it ought to be outside of academia. That is why it is so encouraging that Professor Shapiro has decided to publicize the core insights of his work through an ongoing series of short essays---comprising some 15 pieces to date---on Huffington Post's science blog.

I say I'm "encouraged" by his decision to do this, because the importance of bringing the insights of Shapiro and others to a wider audience can scarecely be exaggerated. Much in our culture depends upon the public's being made aware that Darwinian theory as standardly interpreted is intellectually bankrupt.(2) And little that I have encountered communicates this fact so well as the work of James A. Shapiro.

I will proceed by first looking at a few of the most significant of Professor Shapiro's blog posts, and then turning to his magnum opus.

In his very first essay for Huffington Post earlier this year---"More Evidence on the Real Nature of Evolutionary DNA Change" (1/6/2012)---Shapiro opens with a shot fired directly across the bow of that antique and sharply listing battleship, Darwinism:

Conventional wisdom has it that the genetic changes underlying evolution are random accidents, each having a small chance of making incremental improvements in fitness. These ideas came about before we knew about DNA. Now that we have almost 60 years of DNA-based molecular genetics and genome sequencing behind us, a different picture has emerged.

In this brief piece, Shapiro goes on to cite new research underscoring the conserved---hence functional---nature of a large percentage of non-coding DNA regions in a variety of mammals. Next, he notes that many of these are mobile regulatory elements formerly dismissed by Darwinists as "junk." He then explains how such research further vindicates the ideas of Nobel Prize--winner Barbara McClintock on the evolutionary importance of mobile genetic elements---pathbreaking work that was long derided by the Darwinian consensus.

Finally, Shapiro stresses that all of this is only the tip of the iceberg. In the many ensuing posts he has written this past spring, he pursues each of these topics in greater depth, as well as several others. His two essays on McClintock (right)---who was a mentor and close friend of Shapiro's---are especially interesting: "Barbara McClintock, X-Rays, and Self-Aware, Self-Healing Cells" (3/8/2012), and "Barbara McClintock, Genome Self-Repair and Cell Cognition: A Revolutionary Vision for the Future of Biology" (3/9/2012).

Throughout the whole remarkable series of Huff Post essays, Shapiro stresses the importance of a key concept for understanding how both life and evolution work---"natural genetic engineering." While the technical details of this phenomenon can be forbidding, the basic idea is simple enough. In a nutshell, the phrase "natural genetic engineering" refers to cells' ability to "reprogram" their genomes as necessary---that is to say, purposefully---in order to meet changed environmental conditions.


In the two most technical posts in the series---"Purposeful, Targeted Genetic Engineering in Immune System Evolution" (2/6/2012), and its follow-up, "Your Life Depends on Immune Cells Doing the 'Impossible': Purposeful, Targeted Genetic Engineering (Part II)" (4/3/2012)---Shapiro explains for a lay audience in some detail how this process works in the particular case of the immune system:

Your life depends on purposeful, targeted changes to cellular DNA. Although conventional thinking says directed DNA changes are impossible, the truth is that you could not survive without them. Your immune system needs to engineer certain DNA sequences in just the right way to function properly. . . .

How do cells with finite DNA, and finite coding capacity, produce a virtually infinite variety of antibodies? The answer is that certain immune cells (B cells) become rapid evolution factories. They generate antibodies with effectively limitless diversity while preserving molecular structures needed to interact with other parts of the immune system.

Immune cells achieve both diversity and regularity in antibody structures. They accomplish this by a targeted yet flexible process of natural genetic engineering: they cut and splice DNA.(2/6) . . .

Three remarkable things about [two particular types of natural genetic engineering] are explicitly excluded from the prevailing philosophy of genetic change. First, they are adaptive and purposeful genome changes. Second, they are functionally targeted. Third, for [one of the types], targeting involves intercellular signals that depend on how other cells in the immune system perceive a particular infection.

If immune cells can do all the above, is there any scientific reason we would assume that other cells cannot do the same? Coupling DNA restructuring to transcription is of major significance. All cells can target transcription to functionally relevant sites in the genome. Given that the immune system is how evolution evolved rapid protein evolution, should we not look to it for clues about basic evolutionary processes?(4/3)


It is this last claim, in particular---that natural genetic engineering is significant for our understanding of evolution---that has gotten Shapiro into hot water with the reactionary guardians of Darwinian orthodoxy.

I will not enter into the details of the ensuing online debate here. It will be more fruitful to explore further what Shapiro is saying and why it is important for helping us to see past Darwin.

But for those with a particular interest in the debate itself, see the following posts: "Cell Cognition and Cell Decision-Making" (3/19/2012), Jerry Coyne Fails to Understand Yet Again (4/10/2012), What Is the Best Way to Deal with Supernaturalists in Science and Evolution (4/16), and Natural Genetic Engineering and Natural Selection: Perplexing Delusions of Certain Neo-Darwinist Advocates (4/23/2012).

In any case, the main point at issue in this debate is whether Shapiro is justified in saying that natural genetic engineering is "purposeful." And the main reason why Shapiro's work is so important is that he has the courage to state unequivocally that it is:

Recent postings have provoked numerous questions about my application of the term "cognitive" to cell regulatory processes. I base this usage on the notion that cognitive actions are knowledge-based and involve decisions appropriate to acquired information. It is common today for molecular, cell and developmental biologists to speak of cells "knowing" and "choosing" what to do under various conditions. While most scientists using these terms would insist they are just handy metaphors, I argue here that we should take these instinctive words more literally. Cell cognition may well prove itself a fruitful scientific concept.(3/19)

Shapiro's book covers much of the same ground as his series of blog posts, though of course it goes into far greater depth---perhaps too much so, for the layman. I will try here to say briefly why the book is so important. Anyone with an interest in the technical details may turn to the book itself, which has an excellent index.

Shapiro's work is important because he is both able to think clearly and willing to call a spade a spade.

As to the first point, he states in no uncertain terms that the prevalence of natural genetic engineering falsifies the standard Darwinian interpretation of natural selection, one of whose most central assumptions is the randomness of genetic changes.(3)

This is the crucial point with which Shapiro begins his book:

Innovation, not selection, is the critical issue in evolutionary change. Without variation and novelty, selection has nothing to act upon. So this book is dedicated to considering the many ways that living organisms actively change themselves. . . . Conventional evolutionary theory made the simplifying assumption that inherited novelty was the result of change or accident. . . .

The perceived need to reject supernatural inervention unfortunately led the pioneers of evolutionary theory to erect an a priori philosophical distinction between the "blind" processes of hereditary variation and all othe adaptive functions. But the capacity to change is itself adaptive. . . . . The capacity of living organisms to alter their own heredity is undeniable. Our current ideas about evolution have to incorporate this basic fact of life.(pp. 1--2)(4)

Shapiro's clearsightedness in this passage is matched only by his courage, which he demonstrates in many passages that he well knows will be bitterly distasteful to the majority of the members of the professional guild to which he belongs.

For instance, he rejects François Jacob's famous image of natural selection as a "tinkerer." Instead, Shapiro says:


. . . the term engineering seems to be more appropriate for the built-in processes of self-modification that have operated over the course of evolution.[original emphasis](p. 132)

Another example:

Despite widespread philosophical prejudices, cells are now reasonably seen to operate teleologically: their goals are survival, growth, and reproduction.(p. 137)

When a man is even willing to utter the dreaded T-word---teleology---you know he's got guts. This is even better:

If the ideas of cell cognition, decision-making, and goal-oriented function are within contemporary biological perspectives---and if the natural genetic engineering concept is subject to empirical investiation---we can legitimately ask why the idea has been so firecely resisted by manstream biologists, and evolutionists in particular. My personal opinion is that the oppostion is deeply philosophical in nature and dates back to the 19th Century disputes over evolution and also to the early 20th Century "mechanism-vitalism" debate. The notion that random, undirected processes fully characterize natural systems (as they do in theoretical thermodynamics) was uncritically accepted at those times in much of the biological community. Over time, it came to be unchallenged conventional wisdom that cogntivie, goal-orietned processes have to be relegaed to the realms of unscientific fancy and religion.(p. 138)

Or yet again:

Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth, and proliferation. They possess corresponding sensory, communcation, information-processing, and decision-making capabilities.(p. 143)

Or take this pithy statement of the obvious, that will nevertheless stick in many a Darwinist's craw:

Selection operates as a purifying but not creative force.(p. 144)


Or best---most incisive and most devastating---of all:

One of the most profound lessons from the past six decades of molecular cell biology is that all aspects of cell functioning and cellular biochemistry are subject to regulation. We have no scientific basis for postualting that genome function and DNA biochemistry are any different in this regard. In other words, we have every reason to expect that natural genetic engineering functions will also be subject to regulation and will not operate in an uncontrolled way, and abundant experimental evidence exists to support this expectation.(p. 69)

From these quotes, the reader can see that Shapiro does not mince words. He knows the vision of evolution he proposes is revolutionary---it does not "extend" the standard Darwinian account of evolution, it completely overturns it---and he is not afraid to say so.

But what does "natural genetic engineering" really amount to?

Clearly, it cannot be explained by natural selection, because it is the motor of all morphological and physiological variation, and thus is presupposed by the concept of natural selection. On Shapiro's view, natural selection is reduced to a superficial description of the evolutionary process, not an explanation of anything of much interest.

But if natural selection cannot explain natural genetic engineering, what can?

On this point, Shapiro is admittedly not as forthcoming as one might like. One can see why his opponents---Darwinists and intelligent design advocates alike---become impatient with him here. While he is quite correct to point out the philosophical prejudices of his Darwinist opponents, he nowhere comes to grips with the philosophical problem that he inherits from them---namely, how can teleology and intelligent agency be understood scientifically?

He is not entirely oblivious to this problem. But he has a tendency to wave his hand in the direction of such vague notions as "systems" and "information" at this point. For example, throughout the book he says things like:

Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-based random walk through the limitless space of possible DNA configurations.(p. 6)

This is fine as far as it goes. But the problem is that the notions of "information" and "systems engineering" are themselves in considerable need of clarification.

This difficulty stems primarily from the fact that our concept of a living thing is different from our concept of a nonliving thing in certain very fundamental respects. The difference, in a nutshell, is that our normative concepts---such as purpose, need, good/bad, right/wrong, succeed/fail, meaning, reason why, ought, and dozens more---all clearly apply to living things but not to inanimate objects. And we have no good explanation for why this is so.

However, though Shapiro nowhere comes to grips with this problem in a clear and straightforward fashion, we ought not to fault him for this failure too harshly.

The reason is that his book does not pretend to offer a complete alternative metaphysical system in competition with Darwinism. Rather, he is content to offer the evidence for the existence of natural genetic engineering, and to leave the full explanation of this astonishing phenomenon to the future progress of science.

Which is a far more humble and scientifically respectable attitude than the posture of dogmatic omniscience assumed by the Darwinists.

I have a modest proposal for Professor Shapiro.

To his opponents, the way he invokes "natural genetic engineering" will reek of "vitalism," while he himself sees it as plain, empirically substantiated fact. He could go a long way towards satisfying his opponents by making the following distinction explicit:

"Vitalism" has two very different meanings: Either it can mean that life differs from nonlife in fundamental ways---without further specification of what the difference consists in, leaving the possibility of scientific inquiry into the nature of the difference open. Or else it can mean the dogmatic assertion that science is in principle powerless to inquire into the difference, and will always remain so.

Shapiro ought to make it clear that he endorses the scientific form of vitalism---which assumes that science will eventually make headway on the problem of what makes life essentially different from nonlife---and that he resolutely rejects the anti-scientific form of the doctrine.

The mere fact that he himself does little to direct us towards a deeper understanding of the distinctiveness of life is not a sensible objection to his work.

It is not necessary to say what is right in order to show that something is clearly wrong. Therefore, Professor Shapiro cannot legitimately be be required to explain how Darwinism will eventually be replaced, in order to demonstrate that Darwinism as we have known it is radically defective and must be abandoned.

In any event, others are working on this very problem, as we shall see in future installments of this series.(5)


(1) This is the second in a continuing series of articles on post-Darwinian theory in contemporary biology. Part I identified the machine metaphor as outdated, and the notion of "intelligent agency" as lying at the heart of attempts to construct a more adequate theoretical foundation for biology. This and subsequent posts will examine just what is involved in those efforts.

(2) One small example: An important recent essay by Charles Murray ("Out of the Wilderness," New Criterion, 2012, May, 30[9], 32--40), which analyzes the reasons for the decline of the arts in our time, is seriously marred by the author's unreflective obeisance to neo-Darwinism. Murray's otherwise insightful essay suffers greatly because he doesn't realize that Darwinian thinking is at the root of many of the cultural trends he deplores, and seeing past Darwin in biology is a prerequisite to the renewal of culture along the neo-Aristotelian lines he advocates.

(3) Their gradualness is another. Shapiro also addresses this point, in Part III  of his book, where he rehearses the many lines of evidence pointing to rapid transitions and wholesale genetic reorganizations as the usual modes of significant evolutionary change.


(4) This and all subsequent quotes are from Shapiro's book, Evolution: A View from the 21st Century, cited above.

(5) James A. Shapiro was gracious enough to respond to this post here. I then replied to Professor Shapiro's response here.