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The Design Matrix: A Consilience of Clues

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A friend of mine has an overly strong commitment to things she learned when she was growing up. "Doctors say you need to drink eight glasses of water a day" is one. I ran across a story in which a leading researcher in his field told of his attempts to track down the source of that belief. He found no medical evidence for it; it just showed up one day in some magazine, and grew. He said there was no truth to it whatever. My friend's response: "I don't believe it." She wouldn't look at the source material; she already had her facts.

There's research out this week casting doubt on whether stretching before sports activities reduces injuries. I'm not going to bother telling my friend. She won't read the report, and she won't believe it. She knows we should all drink eight glasses of water a day and that stretching before exercise reduces injuries. She knows it because that's what she has always heard.

I expect similar reactions from evolutionists to Mike Gene's The Design Matrix: A Consilience of Clues. Everyone in the pro-evolution, anti-Intelligent Design crowd knows that

- ID is thinly disguised creationism
- ID is just negative science (nothing but picking points against evolution)
- ID has no positive research program
- ID makes no predictions
- ID relies on a "God of the gaps" approach to knowledge
- ID presents no testable hypotheses
- ID is dogmatically driven by people with a theological/philosophical agenda

Everybody knows these things. Mike Gene shows that none of them are true. The evolutionists, I fear, are not going to read it; they're just going to say, "I don't believe it." Like my friend, they will stick with what's always been "true" for them in the past.

The author says in the intro to the book that he remains anonymous so that his ideas can be evaluated for themselves, without prejudice concerning who is presenting them. It seems likely he's also carrying out some career protection, too. If he's working in a university biology department (and yes, he does know his science), it could obviously risky for him to "come out" as an ID supporter. (See his Design Matrix website for more.)

The way that he supports ID is refreshingly unique, however. He doesn't argue for a conclusion of Intelligent Design at all. He argues more modestly, for a suspicion of Intelligent Design. He would have a beef with dogmatists on either side of the issue. Quite helpfully he distinguishes between the strong evidence required for conviction by a court of law, and evidence required by an investigating detective. A detective arrives on the scene with nothing but questions. His first objective is to move toward reasonable suspicions. A little hint there, a vague clue there: these things can move him toward a theory of a crime; and from there he can begin to look for more definite signs. Eventually, much further down the road, proof may come. Mike Gene believes we should recognize ID is in the developing suspicion stage: there is no hard scientific proof of design, but there are hints and clues that raise a most reasonable suspicion, and which can lead to a search for more definite signs.

These hints and clues he summarizes into his "Design Matrix," four relatively independent factors to test for in nature:

- Analogy with known instances of design
- Discontinuity with observed or means by which evolution works
- Rationality apparent in the design of the natural feature
- Foresight apparent in the design of the natural feature

These are defined such that they can all lead to testable research hypotheses. We're not talking about black/white, unambiguous research results, however ("Evolution never could have done this!" or "Evolution absolutely could have done this, it's easy!"). Natural phenomena can be scored on a continuum, Mike Gene says; we're still in the detective stage, not the judge and jury stage. We're looking for suspicions of ID, so we should be open to gradations on the scales of the Design Matrix. Only one of them, by the way (Discontinuity), bears any relationship to the tired stereotype that ID is nothing but a negative science that resorts to god-of-the-gaps thinking.

Mike Gene wrote this book with a sense of humor. (Thank God for an evolution/ID-related book with a sense of humor!) The book wraps around a theme of the Rabbit and the Duck. It's a metaphor about our preconceptions, and the way they can color our perceptions. I won't try to replay it for you; I'll just quote the book's final paragraph, and leave it to you to read the book and chase down the metaphor for yourself:

"So as we begin our journey, these lessons, coupled with all the lessons in these chapters, must be kept in mind. We are not engaging in a Duck Hunt; we are going to chase the Rabbit. So, do you see that rabbit hole over your shoulder? Yeah, that one. Wanna have some fun? Well, grab your Design Matrix, and follow that Rabbit."

(There's much more Rabbit fun on the Telic Thoughts blog, where Mike Gene writes frequently.)

Some of you reading this "know" that ID is nothing but negative science, it's just god-of-the-gaps, and it's a mere religious ploy. You won't read the book; you won't accept that ID-related thinking can lead to genuine research questions; you'll just say, "I don't believe it." I strongly urge you to get your hands on a copy of this uniquely creative approach to Intelligent Design, and find out where the Rabbit leads you.

This is probably the first book on Intelligent Design, on either side, to which I've given five stars. I'm not sure it's a brilliant book, and it's certainly not a satisfying one: "Mike Gene" hardly even pretends to begin to answer the main question, whether there is good evidence for purposeful, conscious design in the biosphere. In fact, Design Matrix is best understood by analogy to C. S. Lewis' Miracles: A Preliminary Study, in which Lewis discusses the philosophy of miracles for most the book, then looks briefly at a few examples once he has explained why he thinks they're possible, in theory. There's a big chunk of philosophy here, too. (Though also enough science both to persuade me that Mike knows what he's talking about, and to illustrate basic concepts.) It is only at the end that he feeds a few critters into his "Design Matrix," for a taste test, nothing more.

The Design Matrix is a preliminary study to a full and fair-minded scientific study of the evidence for design in biology. Unlike Lewis, Mike does not so much interogate the theoretical rationality of "miracles," (or rather intelligent intervention) as prepare a methodology for finding it. He seeks to place the question of ID on a really scientific footing -- which of course makes this primarily an exercise in the philosophy of science.

This he does quite well. Mike cites a broad range of mostly primary literature. His discussion of Irreducible Complexity is open-minded and illuminating. Logically, in a step-by-step manner, he takes us down different evolutionary pathways, showing dead-ends, detours, and "go" signs. He should win fair-minded readers on both sides over with his even-handed discussion -- if (I am tempted to add) there are any.

There's lots of good stuff in the book, but two things I don't miss are hype and hysteria. Once the jihadists find this volume, they will no doubt find nits to pick (harder hunting than usual), and issue fatwas, anathamas, and excommunications. Don't buy it. Mike is competent, underspoken, careful, fair, informed, and very much worth reading. Some parts of the book are a bit technical, but he also adds a touch of whimsy from time to time. He shows what an open mind might look like, studying biological forms in the light of design. The question seems broader and more open when he is done. This book is a challenge to pat answers on both sides. Still, this is a preliminary, and it can be frustrating to talk methodology when the real question is substance. I look forward to more filling entrees in the future. But this is a thought-provoking and mouth-watering hors d'oevre.

Author, The Truth Behind the New Atheism

The ID debate is one of the most polarized and ugly fights you'll ever come across, and Mike is well aware of the difficulty he faces even being heard. He makes it clear from the beginning that he does not believe Intelligent Design is science, does not think it should be taught in the public schools, and does not deny evolution. He simply has no interest in the political side of ID. Rather, he is interested in the insights that telic thinking may bring to looking at the origin of life. He is interested in the beginnings of an investigation.

Mike deftly reframes the debate away from the traditional template, which focuses on either disproving evolution (thus establishing design) or showing evolution to be possible (thus removing the need for design). The origin of life, after all, is not a matter of absolute certainty or mathematical law, but of history. We are not ultimately interested in what could have happened, but what we think actually did happen. Thus Mike suggests we eschew dogmatic absolutes for the attitude of a private investigator. It is certainly possible that life was designed, but what sort of clues might make us think it plausible? What sort of evidence and confirmation would convince us that it is not only plausible, but probable?

It's interesting how far meekness can go in a polarized debate - be it over science, politics, philosophy, or religion. There's no shortage of bombastic apologists for both sides, railing about how only a total fool could fail to see the rightness of their position. When one person confidently boasts that the evidence for design is overwhelming and another loudly screams that it is nonexistent, most folks are inclined to avoid the whole discussion. But when Mike says the idea is interesting and invites us to take a closer look, we want to join him.

Curiouser and Curiouser

Having established a tone of curiosity, Mike considers the clues. At the most basic level of the cell, life looks like sophisticated nanotechnology. Though we once considered it little more than a sac of chemicals, it turns out that biology at this scale has a great deal in common with engineering, to the point where biology journals sound more like engineering publications than those of other physical sciences. Calling multiple-protein complexes "molecular machines" is more than mere metaphor. To get a faint glimpse of what he's talking about, take a look at the computer animated journey into the cell created by the Harvard Biovisions group. The core architecture of life has the complexity and organization of a modern city, all easily resting on the point of a pin.

The grandeur and majesty of life on this scale never ceases to amaze me. To think of it as a bunch of chemical reactions is as misleading as considering Mont St. Michel a stack of stones, the ceiling of the Sistine Chapel a series of brush strokes, or Google's search database a series of ones and zeroes. When biologists fail to develop the discipline and intuition of engineers who actually build things, I suspect they risk giving hostages to fortune. The stuff has to work, after all, and that's a pretty harsh requirement for any system - be it constructed out of molecules or metal.

Mike, of course, finds this all very suggestive. William Paley once argued that one may reasonably infer life to be designed in the same way you assume a watch on the beach is not a natural phenomenon. David Hume countered that, though life might appear to be in the same category as the watch, the similarities are superficial and the analogy weak. But, while Hume may have been right about human organs like the eye, the recently discovered and unexpected echoes of technology in the most basic unit of life are another matter entirely. Mike then turns to Darwin's theory of Evolution - which has some much more challenging observations for any design inference.

Front Loading Evolution

Darwin showed how systems which may appear designed from the outset may nevertheless have evolved over time through purely natural processes. Natural selection is a fact of life. It is what happens to any flexible self-replicating system over time or in a changing environment. Mike recognizes the power of natural selection to act as a designer-mimic, but he doesn't abandon his suspicion of design in the face of evolution. Instead, he suggests a way where Darwinian evolution might actually be employed in the service of intelligent design.

And so he offers his front-loading hypothesis. Since the basic architecture of life seems to be the most difficult thing to explain by modern origin of life theories - the characteristics of the genetic code, the modularity of proteins, and the interdependency of DNA, RNA, and molecular machines - he suggests we envision a human-like intelligence designing a single cell as a seed for life on Earth. Would it be possible to employ Darwinian evolution to unfold a carefully-packaged design?

Mike looks at the clues that make such an idea seem plausible. Every life form on earth shares a huge proportion of the same DNA. Evolution, on the genetic level, seems to operate mostly by tinkering with copies of genes. Mike goes into great technical detail to show how key templates for advanced organisms could be encoded into the core functions of the cell, ready to pop into use as soon as there is a need. It is the very blindness and short-sightedness of Natural Selection that would make it exploitable by careful foresight. According to Mike's hypothesis, if we were to obliterate all life on Earth and replace it with the same seed cell it started with, we would see it unfold in much the same way as it did billions of years ago, and eventually find creatures not all that different from the ones we have today.

Those who create computer programs, which eventually crash due to unforeseen bugs, will appreciate front-loading as a huge challenge, one which is solvable only by the most brilliant of minds. For those who believe on different grounds that there is a mind ultimately responsible for the creation of the world, the picture Mike paints evokes wonder and awe at the glory and wisdom of God. If this is the mode of creation, it also raises some fascinating philosophical and theological questions, which I may explore elsewhere.

The Matrix

The presence of a front-loaded current running through evolution poses a unique problem for detecting design. How do you distinguish between the core design and the jerry rigged solutions of natural selection? True to his modest methodology, Mike eschews black-and-white certainty for his design matrix: a subjective (but useful) scoring system to gauge our confidence in a design inference.

The matrix score is based on four parameters: analogy, discontinuity, rationality, and foresight. Analogy looks at how closely the solution matches something we ourselves have designed. Discontinuity looks at irreducible complexity, and how difficult it would be for natural selection alone to arrive at the solution by cooption. Rationality looks at the elegance and quality of the design based on its assumed purpose. Finally, foresight judges the design based on any long-term planning present. If a solution only scores high in one area, we wouldn't have conclusive evidence for design, but if it gets high marks in all four, we may conclude that intelligent design is indeed a probable explanation.

Mike ends the book with an invitation to join him on his quest. Having established his theory and methodology, the next step will be to explore the living world in more detail - and see just how well his hypothesis holds up. If he's right, this approach may turn out to be a fantastic research guide, yielding bold new insights and discoveries about the living world.

I, for one, am intrigued by the possibilities, and I hope you are as well. My recommendation is that everyone go and buy all their friends a copy of his book so that he'll have the money to publish volume II!

This is not a book about "what's wrong with evolutionary theory." Rather, author Mike Gene has presented some very intriguing ideas about how evolution works. He starts with an overview of arguments pro and con tracing the history of the sociopolitical debates. We are introduced to what it means to infer design in any phenomenon we might encounter in our explorations of nature. This goes right to the bone of contention, right up front.

Gene presents dry scientific facts as if they were clues in a fine mystery, and this makes the chapters flow like a well-crafted novel. It becomes obvious quickly that Gene knows his biology, and crafts his tale as an enthusiastic teacher would. Clues pile up one by one to lead toward further clues which lead to... open questions. I suspect we will be hearing much more about "front-loaded evolution" from the scientific community in coming months and years.

This is not a book designed to incite frenzied denouncements by either the guardians of all things Darwin or their theistic challengers. It's not a book that can definitively answer questions about whether life evolves with or without design. The way it approaches those questions, however, is a breath of much-needed fresh air in a stale 'culture war'. Gene's lively approach will have the reader eagerly chasing rabbits through an extensive warren of wonders.

I would recommend The Design Matrix to curious students, interested laity, confused biology teachers, and seasoned culture warriors. It's well written, full of fascinating details, and outlines a completely accessible approach to the great mysteries of life that is neither threatening nor stifling.

The Design Matrix: A Consilience of Clues is one of the best books I have read on the problems with Neo-Darwinism and the evidence for Intelligent Design. The author, a friend has informed me, is a professor at an Ivy league university and uses a pseudonym to avoid repercussions for questioning orthodox Neo-Darwinism. He stresses that his arguments should be accepted on their own merits, a point I agree with. He points out, correctly, that the internet can be an extremely hostile environment but, nonetheless, he learned a great deal about the now hot topic of Intelligent Design (ID) from internet discussions on his web site. There are people out there who are willing to debate this topic on a scientific level, and this book is a result of the debates Mike Gene has encountered. Dr. Gene stresses that there are people like him that are tired of the "name calling, innuendo, and political fights" and would rather debate the scientific issues. Dr. Gene stresses that he is an evolutionist and does not favor teaching ID in the schools, but does find the topic "tremendously intriguing." And knowing what has happened to others who took this position, he wisely prefers to say in the closet. Having said this, both supporters and detractors of ID will find his book excellent. Most of the text focuses on molecular biology, cell biology, evolution, and general biology. As such, it was an excellent read and I find many of the author's arguments very persuasive, often compelling. One example of many is the discussion of the optimized code on page 74-75 and the dozen or so complex proofreading systems covered on page 77-80. Highly recommended. I did noticed very few mistakes in the book, but I plan to reread it more carefully and may pick up some then.

No matter what you think about the ID debate, there is little doubt that a lot of smart people on both sides are writing books about it. Mike Gene (pseudonym) is no exception. When I first began reading his book and realized how inspired it was from blogs and internet chat I was fearful of a less than rigorous treatment. Happily this was not the case, and his goal (less ambitious than most) of at least making the case for the possibility of ID seemed more than accomplished.
The author adopts about as humble and conciliatory a tone as can be imagined in this contentious climate, and that helps keep the read pleasant. Much of the ground he goes over had been discussed before, but he does a better job than I've encountered, at least, of showing the strong, strong similarities between man-man designed machines and the way cells work. He did a lot of word searches which were very interesting to help accentuate this similarity. They are not conclusive and not meant to be, but they make the reader pause.
His design matrix idea, I guess based a bit on the explanation filter of other ID authors, didn't wow me, but it does allow the serious researcher a process to begin at least thinking of ways to have a metric for rating probability of design.
As for the writing style I would rate it as very good. It's not laugh out loud funny or anything, but it's certainly not tedious and it flows well. He does a good job of reiterating his central theme that a lot of the observations depend on the observer. And again, he is very gracious and non-inflammatory about the discussion, and takes the tack of just trying to get people (re: macro-evolutionists) to at least consider the possibility of design.
The weakest part of the book I thought was his explanation of how much evolution could actually be front-loaded by a designing force. It seemed awfully speculative, although I know he was just trying to explore possibilities, but even for that it seemed a little vague to me. Overall it's not a turning point work like "Black Box", but I'd seriously put it in the next level below that. It's definitely a book to add to your list if it is a topic that interests you.

Executive summary - Don't waste your money on this book.

Chapter 1 - The example of the Face on Mars is used to show that we can detect design without detecting or identifying a designer. Sadly, this "Face on Mars" argument is pathetic. He argues that we can detect design without any knowledge of the designer. Left unsaid in this example is the FACT that the design detected is a HUMAN FACE. We suspect design in this instance because we are familiar with HUMANS AS DESIGNERS. This unspoken assumption applies to every ID "design detection" scheme ever formulated.

Put another way, if there were a Face on Mars that resembled the face of a Martian, and Martians resembled nothing we have ever seen before, what methods would we use to detect design? What would be the clues, consilient or otherwise?

If you don't want to read further in this long review, just read this.

1) The basic premise of ID is that one can detect design without any information about the designer.

2) An auxiliary assumption for this premise is that the designer must have some or all attributes that are human-like, so that the designs seem "familiar" to us.

3) This auxiliary assumption, if assumed to be true, means that you DO need some information about the designer. Mike has admitted this in his own words; it is also glaringly obvious to the objective observer.

4) If you assume that the auxiliary assumption is false, you cannot detect design.

Ergo, by assuming it to be true, you have negated the basic premise of ID, and by assuming it to be false, you have negated the basic premise of ID. On epistemological grounds alone, the basic premise of ID is false.

The point is that design detection implicitly includes assumptions about the designer. Saying that we can detect design without considering the designer is disingenuous at best, and feeble always.

The cell is more complex than Paley and Darwin imagined; hence it might have been designed. Like all of Gene's arguments, this floats outside the realm of useful inquiry. Yes, this COULD be the case, but where is the evidence beyond this tentative conclusion?

Chapter 2 - Debates between teleologists and non-teleologists have been going on for centuries, dating back to Epicurus and Aristotle. The point of this seems to be that these arguments are not inherently religious, so as to deflect the current criticisms of ID as the stealth son of creationism. This approach ignores the reality that current criticisms ARE religious in nature (Democritus is rarely excoriated from the pulpit nowadays). It ignores the fact that the majority of current philosophers of science reject the teleological approach. Finally, it ignores the reality that the teleological arguments have not been buttressed by modern science, but rather have progressed more and more toward a situation where natural laws and natural processes CAN explain what we observe. So this chapter, while interesting and readable, is basically a straw man argument writ large. More unfortunately for the author, there are more complete treatments of this history elsewhere (e.g. Foster, Clark and York's "Critique of Intelligent Design: Materials versus Creationism from Antiquity to the Present").

Despite the pronouncements of the radical fringes (Provine vs. standard Christian creationists), evolution and design are not necessarily incompatible. This is weak wine, and again evidence-free. Yes, teleology is a possibility. Those who maintain that it is a genuine possibility, approaching the edges of being a useful approach to science, still fail to provide evidence. Hunches are not hypotheses; clues are not data.

An "Explanatory Continuum" can be used to address questions or disputes (e.g. solve murder cases). Again, so what? This sort of analysis, like the Face on Mars, includes an assumption that the causal agent was a human being. We know the agent from experience; we KNOW nothing about the designer. The EC is useless in detecting design or intentionality if we exclude the assumptions that include some knowledge about the agent, the tools available to that agent, the time-frame, and the techniques available to the agent. Why is this not mentioned? Perhaps because the implicit assumption of Christian denialists of evolution is that they are made in the designer's image. Admitting that we KNOW nothing objectively about the designer would deflate all of these arguments to the hot air that they are revealed to be.

Chapter 3 - Cells are really really really complex, and this is a "clue" that they were designed, because all the complex things we know about were designed. Another conclusion masquerading as hypothesis, without the intervening step (experimentation and testing) that defines the scientific method as it should be practiced. Metaphors of agency abound in this section (e.g. "How does the cell know...?"). This section ignores the reality that metaphors and analogies are traditional human pathways to understanding, but are often wrong. The sun does not travel around the earth, despite the analogy to Apollo's fiery chariot. Thunder is not the action of an angry deity, despite the metaphor of Thor. And physics at the molecular level is not at all similar to the physics of the machines used as metaphors here, nor are computer programs at all analogous to the central dogma (DNA makes RNA makes Protein). Analogies are not clues; they are simply analogies. Where are the data that make support a teleological conclusion? There are none, only "clues" derived from a Judeo-Christian notion of a god who made us in his own image.
Chapter 4 - A standard explication of basic molecular biology, with a few over-generalizations and lots of teleology tossed in. For instance, on p 70 we read "When I first learned about the genetic code I was totally struck by the fact that biologists behaved as if they had discovered something ordinary. In philosophy and other areas of science, people would comment on the uncanny implications of the Big Bang or quantum physics. But that life is encoded raised no one's eyebrows." Perhaps the author does not recall that multiple Nobel Prizes were awarded to the folks who discovered the genetic code, broke the genetic code, and unraveled the mechanisms by which DNA is transcribed and mRNAs are translated. I don't know what he means by "raised no one's eyebrows", but that seminal work in the 1950's and 1960's was followed breathlessly by the biological science community. One reads that his surprise lies in the fact that there is an information-storing and -processing basis for life, but that fact had to be true if the observations about heredity, both ancient and modern, were true. Why be surprised at the elucidation of the mechanisms of something that had to be true? That seems rather naïve.

Then he launches into the standard ID notion that "The fact that DNA contains encoded information in the form of a one-dimensional linear string of symbols is very suggestive positive evidence for Intelligent Design behind the fabric of life. If we set aside life for the moment, then every other example of a sequence of characters representing convention is because of Intelligent Design." Again, no experiment, just analogy. Conjecture becomes conclusion - it resembles a designed thing; thus it must be designed. This unscientific approach only serves to mask the underlying argument from incredulity. Gene at al. don't know of any information-encoding system that didn't come from someone who thinks like they do, so they conclude that this information-encoding system MUST come from someone who thinks like they do. It certainly might be true, but an analogy is not a substitute for an experiment. They also ignore the failures of the analogy. Stop codons don't encode for an amino acid; thus allowing an IDist to argue that this is a good design, because it allows proteins to end with any one of the standard 20 amino acids. But if that is a good design, how does the IDist explain the start codon, which does code for an amino acid, and thus constrains all proteins to start with the same amino acid? Is that also a "good design"? How do we recognize design if these two diametrically opposed strategies are labeled as "good design"? This is a conundrum for the IDist, because the standard rejoinder of the previous generation (creationists) was that we can't understand the mind of God, we just have to accept that God does things differently than we would. The IDist is denied this weaseling strategy because their whole premise rests on detecting design, and in order to detect it, we have to assume that it looks "well-designed" by our standards as well as those of the designer. Epic fail.

Gene then launches into another canard, this time using language directly borrowed from creationism. He quotes actual scientists who concluded that the genetic code seems to be optimal, with regard to avoiding the most lethal types of coding errors. His conclusion? "Chance alone would not be expected to produce a code that was better than any other million randomly generated codes when it comes to protecting against harmful mutations." But "chance alone" is a strawman; natural selection winnows the possibilities, and the "chance alone" strawman disintegrates. He continues with a nonsensical argument that the universality of the genetic code makes it difficult to consider natural selection as an agent here, calling this an ad hoc argument. It is, unfortunately for him, no more ad hoc than invoking a creator/designer.

The next argument from incredulity comes when he invokes the existence of "proof-reading" (aka DNA repair pathways, tRNA charging enzymes) as something that "underscores our intuitive suspicion of Intelligent Design". Never mind that this is exactly what one would expect if selection worked on traits that had to be transmitted faithfully from generation to generation; Gene still sees this with a teleological eye, yet still he has no experiments to propose, nor new observations to offer. Paleyism is clearly still with us, even if the data supporting it today are no more extensive than they were in the 19th century.

Gene relates an anecdote that, according to him, shows that ID inferences are not scientific dead ends; they can act as a "research guide". This is his "prediction" that proofreading also occurs during transcription. He predicted it from a teleological standpoint, and it turned out to be experimentally verifiable. Of course, in the spirit of ID researchers everywhere, he did not do any of the hard work; he merely hunted through the literature published by real scientists. Nevertheless, that does not stop him from exclaiming Voila! Design can predict stuff! Unfortunately he overlooks an important fact. Proofreading at multiple levels makes sense from an evolutionary standpoint as well. If design is going to supplant evolutionary theory in the scientific marketplace of ideas, not only will it have to be predictive, it will have to predict things that are the opposite of what evolutionary theory predicts, AND ID researchers will have to do some real work to generate these novel and paradigm-shifting observations. Gene attempts to address this problem, claiming that "Darwinian logic was used to explain" why transcriptional proofreading did not occur. One would like to read the papers where this "Darwinian logic" was invoked, but the only footnote for this assertion invokes an idthink.net article by Mike Gene, and idthink.net is no longer to be found on the web. And, as Jens Hegg has pointed out : "He did not infer proofreading based on the system being designed, rather that his observation was that he had never seen a system work without proofreading at every step. Coincidentally his only experience was human and thus a product of design." (http://fdocc.blogspot.com/2005/10/intelligent-design-predicted.html)

Chapter 5 - Molecular machines! Cells are full of tiny machines! It must be design, because only designers make machines! This basically summarizes the chapter. One long argument from analogy, complete with even more incredulity

Chapter 6 - Evolved things can resemble designed things, and vice versa. People can be fooled by their preconceptions. Still no evidence, still not a whiff of a testable hypothesis. I only marvel at the author's ability to get so many words from such trite aphorisms.

Chapter 7 - What if the first cells were designed, and evolution took over after that? A lovely notion, but still untestable, although the author tries to convince us otherwise. Evolutionary theory posits that mutations are random with regard to fitness. Gene says that design/teleology would posit some foresight in the mutations and thus in the variation in a population. Note again that this is pulling a rabbit out of a hat, there is no a priori reason to expect any particular behavior from a non-human super-intelligent designer. But if that ad hoc assumption is true, where does it leave us? Front-loading! The earliest cells were programmed by the designer to evolve splendidly into (what a coincidence!) the sort of cells and organisms we see today! Pure speculative baloney, begging the question, and (yet agin) not a whiff of a testable hypothesis..Gene does attempt to show that the recent demonstration of genes which are related to but not identical in lower invertebrates and humans is evidence of front-loading. Unfortunately for this prediction, not only is this observation consistent with common descent and evolution, he misleads the reader into thinking that the lower invertebrates have functional forms of genes found in humans. This is simply not true; they have proteins with related structures and different functions. Realted proteins can have different functions; this is no surprise, and is also easily accommodated within evolutionary theory. He also ignores the wealth of evidence against front-loading, e.g. the vast stretches of useless derelict chunks of DNA from ancient retroviruses. Why would a designer frontload garbage into the genome?

Chapter 8 - We can detect design without knowing anything about the designer. Unfortunately his example (pp. 194-5) does not help his case. The detection of transit lightcurve signatures for planetary objects might allow us to detect intelligences at great distances in space precisely because these would be distinguishable from those signatures left by a normal planetary transit. Deviation from natural laws would allow us to detect design, just as deviation from common descent (unrelated genes inserted into an organism's genome) allow us to detect human-designed organisms. What deviations from natural laws are found in cellular life? Exactly none, to date. So where is the evidence for design from these observations? Nonexistent, per usual. Other aspects of this chapter are equally unrewarding. Gene argues that arguments from analogy might be suspect in this arena because the original such argument, Paley's watch, was an attempt to prove the existence of God. Proving a designer is not the same, he would have us think. Sadly, this ruse fails. The designer of all of these Christian ID theorists is, unequivocally, the Christian God. Arguments from analogy, including this latest variation on Paley, are still bogus. Behe's irreducible complexity (IC) argument is invoked, although it is not clear which version of IC he argues for, since Behe has moved those goalposts quite a few times recently.

The summary for this chapter says everything you need to know about this book. From p.235 - "The suspicion of Intelligent Design can be strengthened in two ways. First, the proposed analogy between a biological feature and something known to be designed can be explored. If, for example, designed biological features known to be designed are compared with advanced versions of our own technology, we would expect that analogy between them to deepen over time. If a biological feature is designed, yet there are differences between the feature and our own products of design, we would predict that the biological feature, when properly understood, exhibits aspects of superior design." If someone would point out to me anywhere in that passage where it is possible to generate a testable hypothesis and do an experiment, I'd appreciate it. Suspicions are not hypotheses, analogies are not arguments, and conclusions are not justified without positive outcomes from testable hypotheses. Finally, this argument falls down in millions of cases where it can be demonstrated that a biological feature, e.g. the recurrent laryngeal nerve of the giraffe, is woefully designed. How do you explain that, using this paradigm?

Chapter 9 - In which our intrepid author makes more arguments from analogy, engages in wishful thinking about observations which may border on becoming candidates for suspicions, but again fails to outline a single testable design-based hypothesis which could yield results supportive of teleology and incapable of being accommodated within evolutionary theory. Move along, nothing to see here.

Chapter 10 - Finally, what we have all been waiting for, and hoping that it would make reading all those ignorant arguments worthwhile. Sadly, we are disappointed yet again. The "Design Matrix", like the Explanatory Filter before it, fails because its assumptions are faulty. The assumption is that we can detect design by analogy with human designs; the intelligently designed feature should be superior. Yet some human designs (e.g., the wheel) are far superior to anything found in nature, and other biological features (e.g. the aforementioned recurrent laryngeal nerve of the giraffe) are wretched designs that even a kindergarten-aged engineer could readily improve. We can detect human design using this matrix; it is simply useless for its alleged purpose of detecting the intelligent designs of a superintelligent telic entity.

The entire book is an argument from analogy, in which the author tries to elevate his hopeful "suspicions" to the rank of hypothesis. Suspicions are not hypotheses, analogies are not arguments, and conclusions are not justified without positive outcomes from testable hypotheses. When the ID community generates and tests a design-based hypothesis where the results are consistent with teleology and incompatible with evolutionary theory, science will pay attention. Until then, hand-waving arguments like this book, consisting of words that cannot (or at least have not) been translated into hypotheses and observations, cannot be taken seriously by scientists.

Mike Gene and I have had several frank discussions (some would say "heated") over his tendency to presume a designer with "human-like intelligence" as a starting point. I feel it is an unwarranted and unnecessary presumption on his part. Furthermore, I think it distracts from good points Mike is trying to make.

Mr. Rintoul's 1-star review is a case on point showing how distracting this side issue can be.

My take on Mike's book is that it is an earnest and realistic attempt at approaching the controversial subject of Intelligent Design.

Most other ID books attempt to knock it is out of the ballpark for a homerun only to end up striking out. The Design Matrix is a respectable standup single.

I recommend this book to anyone seriously interested in the subject of Intelligent Design, pro or con. Even ardent ID critics can benefit from reading this book because it provides insight into the more nuanced ID arguments beyond a thinly-disguised "God did it".

I give Mike 4 stars for his realistic and modest approach. This includes Mike's recognition that...

1. ID is not science, yet

2. ID is not a subject to be taught in public schools

3. ID augments current Evolutionary theory (doesn't replace it).

Is there a middle way between the design inference and natural causation? Between teleology and non-teleological evolution? Mike Gene's "The Design Matrix" gives an affirmative answer to these questions.

Take design seriously, and new scientific insights and testable hypotheses become available - so says Mike Gene. Follow the Rabbit (Gene's proxy for the teleological agent), and we shall discover things beyond the reductionism offered by the Duck (Gene's proxy for the blind watchmaker).

Regarding the structure of the cell, Gene (page 16) writes: "Amorphous vessels and balloons filled with molasses would not arouse suspicions of design. But this is not what science has discovered. Modern science teaches us that `the cell is understood to be highly organized, with specialized areas for different functions and molecular motors shuttling components around.' Hume's objection to Paley's argument certainly has not been strengthened by scientific discovery." And Gene takes the question to higher resolution, to the level of molecules, and adds: "Here we find proteins organized into large complexes that are thought of as molecular machines because they actually look and work like machines. Other proteins form tracks to connect and shuttle the molecular machines via motor proteins. The proteins in the membranes work as selective gates, pumps, and sensors. The entire intricate organization of gadgets is due in large part to the encoded information stored by the molecule of DNA."

Gene (page 22) remarks: "The debate between teleology and non-teleology is at least 2500 years old and has involved some of history's greatest thinkers. The notion that current arguments about design are nothing more than a fundamentalist reaction to the painful truth of Darwinism is a notion divorced from historical context. If history stretches back no further than one hundred years or so, it is easy to get the impression that the non-teleological perspective has been vindicated and teleology has been refuted. But if history spans 2500 years or more, consider the possibility that the non-teleological view has just recently gained the upper hand with more sophisticated versions of the same arguments from old."

Gene (page 28) notes that the blind watchmaker is compatible with teleology, for the simple reason that the watchmaker is blind: "We know from artificial selection that such evolution can be and is guided by design, where human intelligence intervenes to manipulate matings, as well as the environmental conditions of the resulting offspring. For example, the gene frequencies of the world's dog population differ from that which existed in the ancestral populations of wild dogs and those which were first domesticated. But this change in gene frequency does not mean there was no design behind the process or behind the changes in gene frequencies of the current population of dogs today."

Regarding the challenge scientists face, given the confusion of Ducks and Rabbits (i.e., between Darwin's view and teleology), Gene writes: "The investigator must have a certain level of sensitivity to detect the existence of clues, coupled with a tolerance for ambiguity.... Until the hypothesis reaches a state of high probability, the investigator must be psychologically prepared to abandon the hypothesis if the evidence mandates it." And so Gene endeavors to study the Rabbit, while not falling for its sublime beauty and while not abandoning the Duck. The two must somehow coexist.

Gene (page 45) writes about proteins, and their function: "It does not matter if biological molecules are not conscious. What matters is whether or not the biological molecules can be placed into the same class as mechanical components designed by humans." Gene gravitates to the machine metaphor that attaches to proteins, and their functions, and he does this by ignoring the issue of consciousness. Machines that hold only functionality are not conscious, otherwise a toaster would feel itself baking bread, and a computer would feel itself playing chess. Gene (page 57) runs with the machine metaphor: "Without these mechanical design functions, molecular biologists would have tremendous difficulty understanding what is happening inside the cell, planning experiments and interpreting the meaning of the results of experiments."

Gene (page 73) admits: "The fact that DNA contains encoded information in the form of a one-dimensional linear string of symbols is very suggestive positive evidence for Intelligent Design behind the fabric of life." Regarding proteins as machines (e.g., enzymes), Gene (page 90) writes: "The DNA information encodes the machines and the machines decode the DNA information. The code and the machine are partners in an elaborate dance we call life." Gene (page 100) writes: "The machine-like boundaries are imposed by a free and rational mind. Machines can thus be viewed as the physical actualization of the mind's conceptual world."

While noting that living organisms are not machines, Gene (page 102) writes: "Every feature that distinguishes a living organism from a machine fails to distinguish a molecular machine from other machines. Molecular machines do not build their own parts, do not truly `differentiate' simply as a function of time, do not undergo self-generation, and do not behave as organism; they fit in the same category as man-made machines." Nevertheless, the vital is close by given that the Duck and Rabbit are unified, and this vitality is beyond machine-like metaphors. Gene still finds a stronger analogy when nanotechnology is considered, and so the question of design goes very deep; even as the vital lurks behind the appearance of design. Gene (page 106) writes: "the consensus among the nanotechnologists is that nanotechnology can work because we already know it works inside our cells and we can learn from the cell's machines as we begin to design our own nanomachines."

Regarding the ineffable that is vital, Gene (page 122) writes: "we live in a reality where it is possible for Intelligent Design and evolution to co-exist, where evolved things can look like they were designed, and designed things could look like they evolved, it becomes clear that a design versus evolution dichotomy can be very misleading."

In treating Intelligent Design, Gene goes well beyond the machine metaphor (and my review is limited by space). The topic of front-loading comes up; an implication is given that the deck was stacked. Gene (page 147) writes: "Since evolution would proceed outward from the originally designed cells, evolution may have been endowed with various sequences and structures to increase the odds that certain future states would be found through a random search stemming outwards from this front loaded state." Gene (page 171) writes: "Cooption is clearly a mechanism that a front-loading designer would exploit." The design inference anticipated the extreme examples of cooption found in life. Darwin's theory did not predict cooption, rather cooption must be assumed to save Darwin's theory from its own demise. Gene tells us that the question returns, with deeper issues that pertain to cooption by way of a blind watchmaker.

Gene treats Behe's concept of "irreducible complexity," Gene considers the concept of discontinuity as evidence for design. And Gene distills the design inference into four categories: analogy; discontinuity; rationality; and foresight. Gene makes a strong case by keeping the Duck and the Rabbit both alive and healthy, and Gene discovers remarkable insights by leaving the question open.

How would life recognize itself without its own contrivances that only look to be designed by an outside source? Life must be able to empathize with its self, despite the heated exchanges! The heated arguments indicate the truth of what is vital and what is felt. There is only one way to design a toaster that feels itself baking bread. That we also perceive design means only that we ourselves are part of the same vitality that permeates all life; a vitality that somehow escapes our toasters of today. And so it must be that evolution finds itself when Ducks and Rabbits coexist, but what is being described is an innate vitalism.

I bought this book based on the positive reviews and it didn't disappoint me: not pro- or anti- either side of the evolution/intelligent-design debate, but willing to view all the evidence and follow it to reasoned conclusions. Mike Gene writes clearly and persuasively, citing sources of his scientific examples and evidences.

This is what science should be-- examine the detailed evidence and use our common intelligence to make hypotheses. The hypothesis of design in nature is not new: it fell out of fashion throughout the 20th century, but, with the discovery of genetics/epigenetics/cellular nanotechnology, it is becoming embarrassing for established scientists, both in research and academia, to deny the possibility of this path.

I read Sean Carroll's "Endless Forms Most Beautiful: The New Science of Evo Devo" and was appalled at his dismissal of design in nature when many of the words he used to describe his subject evoked engineering and manufacturing language.

My own opinion-- If the God of the Bible IS the designer, it makes sense that he works within the realm of science and invites us, his most masterly creation, to wonder at the intricacy of what he's accomplished. There is no intrinsic conflict between science and religion: science is invention, discovery, connection, and examination; religion answers questions of purpose and ultimate truth. Science complements religion and vice-versa.