This is a brief reply to some points raised by Keith Robison and Tim Ikeda in a series of posts. I appreciate their taking the time to read my book and comment on it, and I'll try to answer what I think are their main points. I should add that I don't intend to get involved in an extended discussion, and in any event an author can't follow his book around re-explaining it; the book has to speak for itself. Nonetheless, since Robison and Ikeda are trained in the relevant areas of science, and since they make interesting points, I'll reply here.
In "Behe's Black Box. 0: On the Frontiers of Ignorance" Robison states:
Suppose you challenge me to show that a standard mousetrap is not irreducibly complex. You hand me all of the parts listed above. I am to set up a functional mousetrap which at least mostly resembles the standard one, except I hand you back one piece. Can it be done? Yep. The wooden base can be discarded. Where do you put a mousetrap? On the floor.
That's an interesting reply, but you've just substituted another wooden base for the one you were given. The trap still can't function without a base. Furthermore, you were essentially given a disassembled mousetrap, which you then assembled. All of the parts were preadapted to each other by an intelligent agent. The point that has to be addressed is, how do you start with no pieces (at least none specifically designed to be part of a mousetrap), and proceed to a functioning, irreducibly complex trap.
In "Behe's Black Box. 1: Pseudogenes" Robison quotes me and then replies:
"In his article Miller has not told us how any of these functions might have arisen in a Darwinian step-by-step process, nor has he pointed to articles in the scientific literature where we can find the information. He can't do that, because the information is nowhere to be found."
The fact of the matter is, the answer can be found in almost any genetics textbook. There are two major mechanisms for producing such duplications in biology, and both have been demonstrated experimentally.
Behe is apparently completely ignorant of the enormous amount of literature on tandem duplication, in which one copy of a gene spawns multiple copies. A common mechanism is unequal crossing over, due to the recombinational machinery misaligning two chromosomes.....
The second mechanism is reverse transcription + integration. In this case, the mRNA for a gene is reverse transcribed into a DNA segment, which then integrates into the genome.....
I think you misunderstood me. I did not mean (and I did not say) that there is a separate mechanism for generating pseudogenes. I simply meant that the normal process of DNA replication or recombination, which sometimes generates pseudogenes, is very complex, and has not been explained in a Darwinian fashion either by Kenneth Miller or anyone else. (For example, Kornberg & Baker's 1992 edition of "DNA Replication" has virtually nothing on how any of the steps of replication could evolve in a Darwinian fashion.) The point in my book was that the pseudogene argument is essentially "God wouldn't have done it that way, so Darwinian evolution must be true." Pseudogenes may be reasonable evidence for common descent, but the assertion that they show that life was produced by Darwinian mutation/natural selection has to be judged separately.
In the same post Robison states:
That Behe is ignorant of these basic molecular genetic and biochemical facts is a depressing commentary on the level of research that went into his book.
In this group of posts I am repeatedly said to be "ignorant." That may be true, but I think there is reason to give me the benefit of the doubt. I have a Ph. D. in biochemistry from the University of Pennsylvania (received an award from Sigma Xi for "Best Thesis), postdoc'd for four years at the National Institutes of Health (as a Jane Coffin Childs Fund postdoctoral fellow), have been an academic biochemist for 14 years, have gained tenure at a reasonably rigorous university, have published a fair amount in the biochemical literature, and have continuously had my research funded by national agencies (including a five-year Research Career Development Award from the National Institutes of Health) and currently have research funds.
Well, perhaps I am a real biochemist, but am simply "ignorant" of work on the evolution of irreducibly complex biochemical systems? Perhaps. But I am not unaware that evolution is a controversial subject, and certainly tried to cover all bases when researching and writing my book. I have no death wish. I do, after all, have to live with my departmental colleagues, a number of whom are Darwinists. So I searched the literature as thoroughly as I could for relevant information and tried to be as rigorous as possible. Perhaps there are step-by-step, Darwinian explanations in the literature for the complex systems I describe in my book, but if there are I haven't seen them, nor has anyone brought them to my attention.
My book has now been reviewed quite widely, including reviews by academic biochemists. Several of them were quite hostile to my idea of design, but all agreed that the systems I described are enormously complex and currently unexplained. The hostile reviewers were confident that the systems would eventually be explained by Darwinism in the future. I do not share their confidence. Neither did James Shapiro, a biochemist at the University of Chicago who reviewed Darwin's Black Box for National Review a few weeks ago. He, too, thinks Darwinism has failed for these systems, but hopes that they will be explained by some other non-intelligent mechanism.
In "Behe's Black Box. 2: Cascades" Robison gives an argument that cascades can develop gradually. I encourage him to develop the argument rigorously and submit it to a refereed journal for publication. If he does so, he will be the first.
In "Behe's Black Box. 3: The Krebs Cycle" Robison says:
Here is a complex biochemical system, clearly an excellent hook on which to hang his thesis. Right? However, closer inspection of the literature reveals problems with such a "Krebs cycle is irreducibly complex" hypothesis.
Unfortunately, the assertion that the TCA cycle is irreducibly complex is Robison's, not mine. In my book (p. 150-151) I clearly state that an A-->B-->C-->D metabolic pathway may have developed in a Darwinian fashion (although this has not been demonstrated rigorously.) I pointedly do not argue about things like the TCA cycle. I do, however, raise questions about the biosynthesis of purines because the end product, AMP, is needed for life and intermediates in the AMP pathway have not been demonstrated to occur in origin of life experiments.
If I say a mousetrap is irreducibly complex, and someone replies that a hammer is not irreducibly complex, how has that answered my point? If I write about problems with purine biosynthesis, it is no answer to say that other pathways might have developed gradually. Parts of life may have required intentional design, other parts maybe not. To answer that question you have to deal with the hardest examples, not the easier ones.
In "Behe's Black Box. 4: Antibodies" Robison writes:
Antibodies bind to other molecules. Suppose you have a poison. The poison acts by binding to a molecule in the human body, using a very specific mechanism. Particular atoms on the poison must interact with particular atoms on the target molecule. If the antibody binds to, and covers those atoms on the poison, then the poison will not function.
Sure, that's true. Not only antibodies, but any protein might bind serendipitously to some molecule. "Binding" is not irreducibly complex. But the point made in the book stands. Antibodies do not kill off invading organisms, so they are no help in explaining the systems that do kill them.
In "Re: Behe's Black Box. 1: Pseudogenes" Tim Ikeda writes:
The fact is, it is tremendously unlikely that a lecturing professor of biochemistry, such as Behe, could be (or could remain) ignorant that recombination occurs and can ultimately lead to pseudogenes. I think it's even more improbable that a biochemist wouldn't think about these examples before deciding what to write (or choosing to leave out).
Nobody is ignoring the difficulty of understanding evolution at a biochemical level. In this Behe is presenting nothing that we biochemists didn't already know. But how can one examine the steps involved in molecular evolution when few features of cell biochemistry fossilize? The best one can do is to try to understand and compare the operations of the systems in living organisms. That work is just beginning now.
Well, I have to disagree. I think nearly everybody is ignoring the difficulty of understanding biochemical evolution. Certainly that seems to be the case when you examine biochemistry textbooks and the biochemical literature. Furthermore, in my personal experience many biochemists are astonished when I tell then about the lack of rigorous studies on biochemical evolution. I also disagree that "that work is just beginning now." I see no sign of a serious effort to explain specific, complex systems within a Darwinian framework.
Personally, I find Behe's dismissal of the fossil record (see his book) to be a terribly weak and again, diversionary sleight of hand.
I don't know what you mean. I didn't intend to "dismiss" the fossil record--how could I "dismiss" it? In fact I mention it mostly to say that it can't tell us whether or not biochemical systems evolved by a Darwinian mechanism. My book concentrates entirely on Darwin's mechanism, and simply takes for granted common descent.
Again, thanks to Keith Robison and Tim Ikeda for comments on my book. I hope this reply clarifies my thinking somewhat. Writing this post, however, has taken a hunk of time that I really won't have to give in the future. Hopefully people who read the book will be able to understand what I meant, and even if they disagree with me, perhaps it will serve to get them thinking about a stagnant area of science.
Copyright © 1997 Michael Behe. All rights reserved. International copyright secured.