Review of Mike Gene, The Design Matrix: A Consilience of Clues (Arbor Vitae Press, 2007).

Last updated on: April 14, 2008 at 9:43 am by James F. McGrath

Review of Mike Gene, The Design Matrix: A Consilience of Clues (Arbor Vitae Press, 2007). 2008-04-14T09:43:00-04:00 James F. McGrath

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I hope that no one who knows my views and reads my blog with regularity will experience heart failure, or even more mild ill effects, when they realize what this post is. It is an essentially positive review of a book (The Design Matrix: A Consilience of Clues) whose author Mike Gene considers himself a proponent of Intelligent Design. This is not to suggest that I find all of the author’s points and arguments persuasive or satisfying. But what Mike Gene (a pseudonym – see pp.xiii-xiv) offers that other design proponents do not is an understanding of “intelligent design” that (1) does not try to deny the overwhelmingly strong evidence in favor of evolution and common ancestry, (2) does not claim to offer proof of design, (3) does not view design as an alternative explanation or viewpoint to evolution, (4) does not attempt to undermine or deal dishonestly with scientific arguments in order to win the less well informed to support ID, (5) invites people to listen carefully to the views and arguments of those who disagree with him, (6) doesn’t think ID should be taught in public schools, (7) doesn’t think ID is science (p.xi), (8) doesn’t think evolution and belief in God are incompatible, and (9) likes cute bunnies. What’s not to like?

I frequently encourage those who judge Christianity on the basis of fundamentalists to listen carefully for the other voices being drowned out by the noisemakers at the extremes. Gene seems to be doing something similar for ID. In the current debate, is there a place for those who wish to explore something that might legitimately be identified as “intelligent design” but do not understand by it the pseudoscience that some proponents of a form of ID are advocating? I will not, at this point, get into the question of whether it would be better for Mike Gene to abandon the term “intelligent design” and call his distinctive viewpoint something else. I get asked that about my Christian faith all the time. At any rate, whatever else may be said about the book, Gene’s honesty impresses me, and as I present the main points in the book, I think you will agree with my assessment, even if you remain unpersuaded by his conclusions. He explicitly aims to identify middle ground, something to which I too am highly sympathetic.

The Design Matrix begins with the example of the “face on Mars”. Design is something that one may initially perceive or suspect, but which may, on closer analysis or higher resolution may vanish, as in the case of “the face” (pp.7-8, 12). Paley’s argument about the eye and about living organisms in general now competes with Darwin’s natural explanation for the appearance of design. On closer inspection, the appearance of the eye having been designed by a mind vanished, as the possible steps for a natural evolution, and the cobbled-together look of the blind watchmaker’s handiwork, became apparent. What happens when one looks at life more closely, at the molecular level? Does the appearance of design become greater or less? The question cannot be settled only by looking at the way parts fit together, and the “matrix” referred to in the title will be offered later as a spectrum and a set of questions that may allow some assessment of the plausibility or likelihood of design in a given case.

Before getting there, however, Gene sets the stage remarkably well by showing that in fact the current debates over design are a manifestation of an ongoing disagreement over the nature of life, stretching back to ancient Greece. Then too there were those who explained the order in the universe as a result of ultimately random interactions, and those who attributed these features in some way to mind or design or reason (pp. 19-22). Quotations from Socrates, Lucretius, and Cicero sound remarkably like the points of view in the current debate. Indeed, the same point as is usually made about “monkeys and Shakespeare” was made by Cicero using letters scattered at random and the Annals of Ennius (pp.21-22). It is unfortunate that the debate is not more frequently introduced by way of this historical precedent and framework, not least because it might make clearer that the question of design is a philosophical one rather than a scientific one. As Gene points out, the notion of “intelligent design” need not by definition indicate anything about evolution (p.22). For instance, life might be “designed to evolve”. Likewise there is a sense in which the dogs and flowers we have produced through selective breeding may be considered “designed” as well as “evolved”. Teleology and evolution may in theory be different levels of description, rather than alternatives.

In claiming that Darwin never strictly speaking refuted Paley, but simply offered an alternative explanation, Gene is quite candid about why Darwin’s theory has gained the predominance it has: “The success of Darwin’s theory has nothing to do with proving design is impossible. The success stems from the manner in which Darwin’s theory has been successfully used to guide research and generates insights into biology” (p.26). Gene contrasts this deductive reasoning with an alternative Darwin might have tried, namely an attempt to prove design impossible. After showing the difficulty of making such a case to everyone’s satisfaction, Gene introduces the idea of inductive gradualism (pp.29-34). This is an explanatory continuum running from “X could not possibly evolve” to “It is certain that X evolved” with the three intermediate stages of X’s evolution being possible, plausible or probable (p.31). This attempt to define degrees of certainty and probability, rather than two alternative categories of certainty, seems more in keeping with the role of deduction and accumulating evidence in the sciences themselves. Although there are those on both sides of certain current debates that would like to declare an absolute victory, and do so immediately, recognition of degrees of evidence, of certainty or uncertainty, and a process of deduction involved in reaching a conclusion, all represent positive contributions to the discussion of intelligent design and of evolution. What matters, ultimately, is not what could have happened (since presumably there is nothing intrinsically impossible about life having either been created artificially or having evolved somewhere in our universe), but what did happen in the case of life on our planet (p.26).

Part 2 of the book turns attention to “the clues”, and notes early on the resemblance between the biological realm and that of human engineering. “The body echoes the design principles of our own technology” (p.40). The question I always find myself asking when I hear this point made is whether the resemblance does not indeed run in the other direction. How can we say that biological organisms resemble human technology, that molecular machines in living cells resemble the macro-machines we make, or that the genetic code resembles Morse code? In fact, it is DNA that has produced the makers and the users of Morse code, cellular machines that have ultimately created the metal machinery of our invention, and beings with eyes who have developed various sorts of artificial optical instruments.

Be that as it may, Gene suggests that when we refer to “molecular machines” (such as, but not limited to, the infamous bacterial flagellum), it is not simply a metaphor, in the way that talk of “hydrophobic” molecules is (p.44). A comparison of key words used in human engineering and in descriptions of molecular biology suggests that the language of “design”, at the very least, is indispensible (see the tables on p.48 and p.58). Chapter 4 then focuses attention on the genetic code and the ways it follows principles of coding and communication (including error-correction mechanisms) found in human artificial codes. The origin of the genetic code is, for Gene, the crux of the matter. DNA has clearly driven evolution across vast stretches of time on this planet, and Gene’s interest is not in any way to combat this understanding of the history of life. It is the question of origins, specifically the origin of the genetic code, that Gene is concerned with, and is convinced appears designed. At this stage, he is merely seeking to show that it is plausible to attribute the origin of the genetic code to design (p.60). Before proceeding, let us note what many opponents of evolution fail to understand: the origin of the genetic code and of life is not a question addressed by evolutionary theory. Darwin’s theory as developed and refined by scientists and discoveries since his time accounts for the development of life once it exists, not life’s origins. Indeed, it is for this reason that Gene’s book is not about Intelligent Design as an alternative to evolution, but Intelligent Design as an explanation for life’s origins. Many proponents of design hedge their bets in order to cling to supporters whose views are closer to young-earth creationism; still others are anti-evolutionists seeking to use design as a strategy. Since Gene is not in either of these categories, his views do not deserve to be lumped together with those of these aforementioned others. How to distinguish them in discussing “Intelligent Design” is not an insignificant issue. Perhaps the others should be called “cdesign proponentsists” and Gene should be allowed to keep “Intelligent Design”. The cdesign proponentsists, however, are unlikely to cede the term “Intelligent Design”, and so I’d recommend Gene using some other terminology – and will make a suggestion or two once we’ve considered his argument in all its aspects.

The question of life’s origins and the origin of the “Universal Optimal Code” that drives it and makes it possible cannot be answered by the study of biological evolution. It is a question of chemistry, regardless whether it originated through natural processes or was artificially contrived. In relation to the subject of the code, as in the case of molecular machines, I find the same objection coming to mind. Optimized codes that we regularly encounter are the products of minds. In making an analogy between the genetic code and the codes humans produce, isn’t Gene once again reversing the order of the analogy? The genetic code is the basis of life, and life is the basis of mind, and mind gives rise to communication and code-making. Our contrived codes resemble the basic stuff of which we are made. This is interesting, certainly, but how significant is it as evidence that life might be highly advanced nanotechnology (p.43)?

If Intelligent Design is a philosophical rather than a scientific hypothesis, then there are philosophical issues that cannot be avoided. While it may be a fair point to state that we can recognize design without being able to precisely identify or describe the designer, there is a sense in which appeal to design is an unsatisfying solution to the question of life’s origin. If life was designed by a mind, it must further be observed that the minds that we know of are based in precisely the genetic code for which design is being claimed. If one appeals to something as an explanation that depends on the thing being explained, then we end up reasoning in a circle, or in an infinite regress. Alternatively, we end up putting the cart before the horse, as it were. Since mind arises from life that is based in the genetic code, to claim that the genetic code is a product of mind seems akin to claiming that protons are a product of chemistry.

None of the aforementioned points is definitive. After all, sooner or later we get back to something that simply exists. Perhaps it will turn out that life, mind, design somehow does give rise to the same, in infinite regress or ending in some cause with these same features that simply is. There is nothing that is inappropriate, unprecedented or foolish about such notions – indeed, they have a long and respected history in philosophy, and in the context of that field of human thought and inquiry continue to be discussed and debated seriously. Furthermore, considered philosophically, it becomes clear that both teleological and non-teleological views of life ultimately are connected with teleological and non-teleological views of the nature of the universe and of existence itself. If it turns out that the genetic code at the basis of life can be demonstrated to arise through natural processes, this will simply push the design hypothesis back a step further for many, to a designer who “fine tunes” the laws of physics in order to produce a universe ideally suited for life to come into existence and flourish. In that case, talk of “God” is less controversial, since physicists and cosmologists are already aware that there are questions that arise from their field of investigation that lead to unanswerable mysteries. In a sense, then, if Gene is right to suggest that the genetic code indicates design, then we have in it a direct pointer to a deep mystery about our existence. If, on the other hand, a natural explanation for the rise of the genetic code can be offered, then this will simply make it an indirect pointer to the same mystery. Ultimately, the scientific data leads us beyond science to philosophical and metaphysical questions and speculations. But whereas in cosmology we are dealing with a field that leads into potentially unanswerable questions, in the case of the chemistry and code of life, it is by no means implausible that science may indeed offer a natural explanation of the processes involved. This is a fundamental difference between these fields, and presumably the reason why talk of “God” or “fine tuning” in cosmology upsets fewer specialists in that field than does the use of similar language in connection with biology.

Gene, it must be emphasized, does not favor science ceasing to investigate and seek explanations for phenomena. If we do not investigate fully the possible routes by which the genetic code could have appeared via natural processes, we may jump to the wrong conclusion, as thinkers have at times done in the past in relation to larger-scale biological structures. Yet even the long-term failure of science to explain how life arose could never prove that explanation in such terms is impossible. It may be that at some point we may feel that we have explored every conceivable scientific scenario. Even so, it may be that some natural process as yet unknown may have been involved, or that our life was designed by beings who exist because of natural processes on their planet which are not mirrored on ours. The scientific explanation of life’s origins in natural terms, or the failure to discover such an explanation, can change only what seems to us most probable. But as is emphasized by many theologians who are opponents of the majority understanding of “Intelligent Design”, the question of teleology is not about whether natural processes were involved that can be scientifically explicated. Design may be present as well as, rather than instead of, a scientific explanation.

Returning to Gene’s argument, his focus on molecular machines may resemble Michael Behe’s, but there are important differences. Gene’s design inference takes seriously the fact that previous design arguments were fooled by “designoid” organs. He states, however, that “Every feature that distinguishes a living organism from a machine fails to distinguish a molecular machine from other machines” (p.102). Yet this is difficult terrain to argue about, since unlike large-scale machines with which Paley and others made analogies, molecular machines can only be made from molecules, which are the same whether they arise naturally (if indeed they can) or are constructed artificially.

In part 3, Gene focuses much attention on the idea of “front-loaded evolution” (see e.g. pp.147-148), and it may be that this (rather than “intelligent design”) might be an appropriate label for his viewpoint, to distinguish it from others who have been criticized for fallacies that Gene does not appear to be guilty of. Using the analogy of the classic ‘duck-rabbit’ image, he suggests that the same data may be open to interpretation in two ways. Once again, Gene is not exploring an alternative to evolution, but the possibility that the original genetic code may have been designed in such a way as to make the appearance of certain outcomes later on more likely. In making this suggestion, Gene takes into account the recent work in evo-devo (evolutionary developmental biology) which shows how the same tool kit is reused throughout evolutionary history, with the same genes that exist in very simple organs being put to remarkable and impressive new uses in later evolutionary history.

One problem with this suggestion is that it seems both too risky and unnecessary. Genetic mutation seems to explore so many possibilities that it seems that even without front-loading, one might get equally complex organisms out of the mix. Moreover, it seems that the same case could be made from either sort of evidence – the ability of complexity to arise even though the first genetic sequence didn’t prepare for it could impress one as superb design, just as could the presence of genetic sequences in the earliest genome that would be put to important uses later on (see p.172). Heads I win, tails you lose. I also wondered whether a designer might not take delight in watching life explore its manifold possibilities, rather than stacking the deck in favor of a specific sort of outcome. Indeed, one other name for Gene’s point of view could be “stacked deckism” (or perhaps the less colorful “evolutionary design” or “molecular design”). That Gene’s view is different from that of other design proponents is made clear when he writes “Design can now come in two forms – the direct intervention comparable to human engineers in action and the indirect expression of such design through the medium of evolution” (p.179).

As we enter the fourth and final section of the book, Gene’s honesty continues to be impressive. He offers an honest assessment of evidence, nowhere more impressively than in assessing Behe’s claims about irreducible complexity. His discussion of the possible evolutionary explanations for such allegedly irreducibly complex phenomena appears to be fair, balanced, and accurate (pp.214-231). Although in the end he feels that the analogy of design retains its force, and that some of the proposed evolutionary accounts of the evolution of complex molecular machines through cooption of existing parts seem rather ad hoc, at no point does he try to pretend evidence is not there or cannot be interpreted in the way mainstream scientists suggest. His point continues to be that the analogy of design retains its force and, when added to the evolutionary scenario at the point of genetic origins, makes for a more plausible scenario.

It all boils down to the degree of certainty one feels one can have, based on the evidence, about design as an aspect of the explanation needed to account for existing phenomena. Gene’s focus is primarily on describing some of the phenomena that are relevant to the discussion, and to coming up with criteria whereby one can assess the evidence in relation to the question of design, in a way that facilitates conversation about the topic. His final chapter is about research and discussion questions, focusing in particular on analogy, discontinuity, rationality and foresight as characteristics of design. While one’s evaluation of the degree of analogy between human design and cellular molecular machines may differ, as this is not something objective (p.272), simply identifying the key points for discussion and proposing a scale for ranking are positive suggestions the book offers. He tests this “design matrix” on various artifacts and items, then applies it to the genetic code. Interestingly, he places the cut-off between the truly ambiguous and the apparently designed at the +2 marker, and on his own estimation the genetic code falls at +3, which is not that far over the border (pp.283-284). Here I found myself pondering what seems to be a characteristic of our universe more generally: its fine balance between order and chaos, which leads human beings to look at the same phenomena and see design or chance, contrivance or accident. If the proposed “design matrix” helps those with differing perceptions to have more fruitful conversations, that alone would justify the book’s publication and its value. This is all the more true because Gene himself acknowledges the limitations of what he offers: “It is important to again stress that the Design Matrix is not an objective, physical measurement that detects design. The Matrix is a scoring system and, as such, is ultimately subjective…Nevertheless, the Matrix focuses our thinking processes and helps clarify why people would and would not infer design in any particular instance” (p.286).

Other design proponents have (rightly) been accused of claiming scientists are ignorant about things that they understand or are working on understanding. Gene, to his credit, focuses his attention on things that are genuinely mysterious, on questions that are truly unanswered (p.288). Whether they are answerable in other terms is an open question, and one that must be fully explored. But Gene is not twisting evidence to make it seem to support a conclusion drawn in advance. For this he is to be applauded, and deserves to be taken seriously, even if in the end one draws a different conclusion than he does. For, unlike other design proponents, Gene invites you and encourages you to weigh the evidence for yourself and draw your own conclusion.

Gene has a site named for the book, as well as a blog. Unlike Uncommon Descent, different opinions seem welcome there. I encourage you to pay a visit and engage in conversation.

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