I thought @vjtorley’s review was excellent. For the sake of those intimidated by its length, I’ve taken the liberty of pasting some of what I thought were the highlights, just to kick-start some more discussion.
"What bothered me most was that the book misrepresented Darwinism, and exaggerated the strength of the case against it, by appealing to a series of poor analogies. In the end, these errors provoked me to such a degree that they made me want to take up the cudgels on behalf of Darwin - something I have not done for a long, long time.
"After all, there’s no need to disprove a naturalistic account of origins; all Axe really needs to show, in order to render belief in Intelligent Design reasonable, is that the case for a Creator is stronger than the case for naturalism. One thing Axe does very well in his book is to demonstrate that there are no good naturalistic explanations for the origin of systems with a high degree of functional coherence, such as are found in all living organisms. Another thing he does very well is to describe the mind-boggling complexity found in living things, in language accessible to laypeople. He doesn’t really need to argue the case for design when he does this: it makes itself.
"If he had stuck to his strengths, Dr. Axe could have written a book that evolutionists would have found very hard to attack. Unfortunately, he aimed too high. Reading and reflecting on Axe’s book has convinced me that while the case for Intelligent Design is a very powerful one, it is far from being undeniable. From this point on, I will be playing devil’s advocate in the role of a Darwin defender, even though I am deeply skeptical of the possibility of abiogenesis and very much in sympathy with the thinking behind Axe’s Universal Design Intuition.
"The final formulation of Axe’s Universal Design Intuition, on page 254, is the most precise one: “No high-level function is ever accomplished without someone thinking up a special arrangement of things and circumstances for that very purpose and then putting those thoughts into action. The hallmark of all these special arrangements is high-level functional coherence, which we now know comes only by insight - never by coincidence” (italics mine). What Axe is saying, then, is that when a functional hierarchy contains a sufficiently large number of levels, laypeople can instantly infer that it couldn’t have originated by chance, and their inference is a mathematically justifiable one.
"Fine, but what is this critical number? We are never told. Axe might respond that the number is context-sensitive, but that doesn’t help us much. How are we supposed to tell? Another response Axe could make is that the critical number of hierarchical levels is simply whatever number yields a likelihood in 1 in 10116. But how are laypeople supposed to figure that out?
"To his credit, Axe makes a noble attempt in his book to justify the inference we all share, that certain objects could only have originated through intelligent design, and he states his case with flair and panache, using illustrations that will appeal to readers. In the end, though, his case for the Universal Design Intuition remains unsatisfyingly vague. I don’t blame Axe for this: he is, after all, a scientist, not a philosopher. But there are a couple of trained philosophers among the fifteen people who reviewed his book, and I have to say I am very surprised that they didn’t notice these gaps in Axe’s argumentation and point them out to him.
"I’d like to make a modest suggestion. In my humble opinion, Dr. Axe’s Universal Design Intuition would be much more persuasive if it were formulated as follows: “If we find a level of functional coherence in living organisms which surpasses anything which our top scientists can create, then we should conclude that the systems displaying this level of functional coherence were designed, and that the accidental invention of these systems is fantastically improbable and therefore physically impossible.” This formulation of Axe’s Universal Design Intuition borrows from the STOMPS principle which I blogged about, a few years ago:
"So far I have explained why some people are open to Intelligent Design, but what makes them believe it? I think the answer consists in what I will call the S.T.O.M.P.S. principle (short for “Smarter Than Our Most Promising Scientists”).
"I now pass to Axe’s discussion of fantastically large numbers. … What Dr. Axe ignores, in his argument for the validity of the Universal Design Intuition, is that there is an important difference between an event which is extremely improbable (but still physically possible) and one which is fantastically improbable (and therefore physically impossible). Axe fails to demonstrate that the origin of new life-forms from a hypothetical Very Simple Replicator (the first life-form on Earth) would have been fantastically improbable, because he overlooks the fact that making something useful by chance is a lot easier than creating something meaningful by chance - say, generating a patent for a new invention by boiling up some alphabet soup (to borrow an example of Axe’s). Contrary to what Axe asserts, life is not at all like alphabet soup.
"In order for an accidentally generated string of letters to convey a meaningful message, it needs to satisfy three very stringent conditions, each more difficult than the last: first, the letters need to be arranged into meaningful words; second, the sequence of words has to conform to the rules of syntax; and finally, the sequence of words has to make sense at the semantic level: in other words, it needs to express a meaningful proposition. For a string of letters generated at random to meet all of these conditions would indeed be fantastically improbable. But here’s the thing: living things don’t need to satisfy any of these conditions. Yes, it is true that all living things possess a genetic code. But it is quite impossible for this code to generate anything like nonsense words like “sdfuiop”, and additionally, there is nothing in the genome which is remotely comparable to the rules of syntax, let alone the semantics of a meaningful proposition. The sequence of amino acids in a protein needs to do just one thing: it needs to fold up into a shape that can perform a biologically useful task. And that’s it. Generating something useful by chance - especially something with enough useful functions to be called alive - is a pretty tall order, but because living things lack the extra dimensions of richness found in messages that carry a semantic meaning, they’re going to be a lot easier to generate by chance than (say) instruction manuals or cook books. Hence it may turn out that creating life by chance is extremely improbable, but not fantastically improbable. In practical terms, that means that given enough time, life just might arise.
"Axe’s argument also misconstrues the nature of the evolutionary search, by focusing on the likelihood of this or that accidental invention. However, evolution isn’t a hunt for a single target; it’s a search with a fantastically large number of targets: the set of all possible life-forms - by which I mean: all possible configurations of matter in our cosmos that would qualify as being “alive.” [By “search,” Axe means any process that could potentially find something, regardless of whether there was a goal (p. 114).
"By now, readers will have detected a recurring theme in the foregoing criticisms. The real problem with Axe’s argument, on an epistemic level, is that human beings are not good at reasoning about fantastically large numbers - especially when these numbers are unknown, and when they are required to divide one fantastically large number into another fantastically large number (e.g. when calculating the very small proportion of organisms - out of a very large number of possible life-forms - that are reachable by a blind evolutionary search over a four-billion-year period). Additionally, humans are not very good at distinguishing between extremely large numbers and fantastically large numbers. Axe’s “layperson’s case” for Intelligent Design assumes that most human beings are capable of reasoning soundly about large numbers - and as we’ve seen, they’re not: the holes in Axe’s own arguments prove that. For this reason, a skeptic might argue that the widely shared human intuition that living things such as whales, tigers and butterflies are products of design should be taken with a very large grain of salt, and that science should steer well clear of making inferences to the existence of a Designer of life.
"In brief, the three major arguments put forward by Axe are: the astronomically low odds (as calculated by Dr. Eugene Koonin) of a coupled replication-translation system emerging by chance on the primordial Earth (pp. 227-231); the vanishingly small proportion of long amino acid chains (which are essential to life on Earth) that are functional (p. 57); and the enormous difficulty of converting one protein into another, similar-looking protein which folds up just like the first one (pp. 81-86). The first two arguments relate to the physical impossibility of abiogenesis, while the third is supposed to demonstrate the inability of natural selection to produce new forms (after all, if it can’t even build a new protein from a very similar one, how much less is it capable of building a new organism from a genetically similar one?) My opinion of these arguments has dramatically changed during the past three weeks, and I have come to conclude that all of these arguments are mathematically dubious, for reasons that I shall now explain. Their conclusion may well turn out to be right, but at the present time, we have no way of knowing that.
At this point, I’d like to introduce three professors, whom I emailed regarding Axe’s mathematical arguments. All of them are biologists of various stripes, all of them are well-published professors, and all of them are Christians. I promised the first professor I would not reveal his name, and the second professor would prefer to remain anonymous, so I’ll simply refer to them as Professors A, B and C. (I’ll say more about Professor C anon.) Professor A could fairly be described as a Darwinist, while Professor B has strong doubts regarding the possibility of abiogenesis, but adheres to the neutral theory of evolution. Professor C is sympathetic to the Intelligent Design movement and has vocally criticized theories of abiogenesis. In short: if these three professors doubt the cogency of Axe’s mathematical arguments, then it’s fair to conclude that the arguments don’t work. As it turns out, none of the professors was willing to endorse any of these arguments.
Now, let’s examine Dr. Axe’s second argument, that functional proteins consisting of 150-odd amino acids (which are required by all living things) are extremely isolated in sequence space (1 in 1074 is the figure he quotes in his book).
The importance of this particular argument to the case for Intelligent Design cannot be over-emphasized. Putting it succinctly: if it fails, then we’re back at square one, in terms of building a mathematical case for ID. Dr. Stephen Meyer’s two Intelligent Design best-sellers, Signature in the Cell and Darwin’s Doubt, are built on the bedrock foundation of this argument: their whole case would collapse without it. The same goes for The Design Inference, by Dr. William Dembski and Dr. Jonathan Wells. Speaking for myself, I can’t count how many times I’ve cited Dr. Axe’s argument in my posts on Uncommon Descent, and referred readers to his paper, The Case Against a Darwinian Origin of Protein Folds, as well as his follow-up article, Correcting Four Misconceptions about my 2004 Article in JMB. Whenever I’ve had doubts about Intelligent Design, this argument has always been my shining star.
So, what did the three professors whom I contacted think of Axe’s argument? In a nutshell: not much. Professor A thought it ignored the possibility that the first life relied on much shorter proteins; Professor B queried the 1 in 1074 figure and said there was no way we could be sure about that; and Professor C said that he had no idea, when I asked him about the argument.
Professor B added that that he was very sympathetic towards arguments against the natural origins of the first cell, and that of all the arguments raised by evolution critics, this argument had the most likelihood of being correct. He concluded by saying that he did not think that Dr. Axe was necessarily wrong about the unlikelihood of abiogenesis, but that Axe seemed to be trying to calculate the probability of an unknown process, and was therefore overstating his case…
The take-home message from all this is that Dr. Axe is trying to put a full stop where science leaves a comma. We don’t really know how rare functional 150-amino-acid proteins are in sequence space, and we don’t know that they couldn’t have been derived from shorter proteins.
Reviewing the comments by Professors A, B and C, I was struck by the fact that not one of them was willing to endorse Dr. Axe’s mathematical arguments against abiogenesis and unguided evolution, even though all of them are Christians, two of them are skeptical of abiogenesis, and one of them is sympathetic towards Intelligent Design. So where does that leave me?
On a final note: I believe that when you present a scientific argument to the general public, you have a responsibility to draw notify your audience about the uncertainties attending that argument. It seems to me that Dr. Axe has not done that. Each of the three mathematical arguments for intelligent design in his book is highly questionable. For that reason, I shall refrain from citing them as arguments in support of ID, in future.
But without a doubt, Axe’s silliest argument against natural selection is that it cannot invent. He calls this the Gaping Hole in Evolutionary Theory (p. 97). I would refer Dr. Axe to a recent post by University of Chicago Professor Jerry Coyne, in which he endeavors to summarize the entire theory of evolution in a single paragraph. His concluding point is as follows:
Finally, the “designoid” features of organisms–the features that make them look so well adapted to their environments and lifestyles–are the product of natural selection: the combination of a random process, mutation, that generates genetic variation without regard to whether it’s “useful” or not, and a deterministic process, selection, that winnows the variation by retaining those mutations that are better able to make copies of themselves and eliminating the worse copiers. There are other important processes of evolutionary change, like random genetic drift, but only selection can produce the design-like features that so excite our wonder.
There you have it. Natural selection doesn’t generate “inventions” (or biological innovations), because that’s not its job: that’s the job of mutation. It may be objected that Coyne is not typical of all evolutionary biologists; however, the respected evolutionary geneticist Allen MacNeill of Cornell University, whose perspective on evolution is very different from that of Coyne, agrees with him on this point. In a 2009 blog article titled, “Can Natural Selection Produce New Information?”, MacNeill points out that natural selection has three prerequisites, one of which is Variety, generated by the “engines of variation.” He continues:
…[T]he real dispute between evolutionary biologists and “intelligent design” supporters is not over natural selection per se, but rather the properties and capabilities of the “engines of variation”. I have written extensively about these here and here.
Yes, natural selection … is conservative not creative. It produces no new genetic nor phenotypic information, which is why Darwin eventually came to prefer the term “natural preservation” rather than “natural selection”. However, it is also clear that the “engines of variation” - that is, the processes the produce phenotypic variation among the members of populations of living organisms - are both extraordinarily creative and extraordinarily fecund. The real problem in biology is therefore not producing new variation, but rather limiting the production of new variation to the point that the “engines of variation” do not cause the inevitable disintegration of living systems.