To Jerry @68:
Thanks for the words of welcome. I need to be relatively brief now, especially on Behe's work, but I'm happy to discuss biology and evolution with anyone anytime, and I welcome questions, the more specific the better. I hope you and the others here will be patient with me: I work full time in the lab, run a blog of my own, and juggle several additional writing projects among my time with my wife and four kids. When/if there's a question you really want me to address, make it clear.
First, re banning on this site, I've heard from too many decent people on this topic to believe that the policy here is a good one. And the claim that people are banned due to "ad hominems" is laughable, as anyone who reads this blog knows all too well. I've been warmly welcomed, and that's all that matters in this conversation, but please don't ask me to defend your venue. It is what it is, and I happen to think it's a mess -- let's leave it at that.
"I think design is the question, and you think it's the answer." Here, basically, is what I mean. In your first paragraph, you note that you and others here "do not believe there is any naturalistic mechanism that can explain macro evolution or the origin of life," and so you "opt for design events as the only answer." Design, for you, is the answer, and the question was how did these biological systems come about? In between, we find your conclusion that the phenomena in question cannot be explained naturalistically.
I start with the same question: how did these biological systems come about? At the same time, I notice design, "purposeful arrangement of parts," even "prodigies of nature." As I already mentioned in my first post here, I'm quite happy discussing design, and completely reject the suggestion that design has no place in science. Baloney! Design is what we're trying to understand. Design is the question. Here is this biosphere, filled with mind-blowing nanomachines and indescribably intricate processes. Do we need a mathematically-inclined philosopher to coax the specter of "design" out of modern probabilistic theories? Do we need an underinformed biochemist to locate "design" through analysis of mutation rates in Plasmodium falciparum? Good heavens, no. It's right there; it's everywhere. Detecting design, for me, is almost effortless, natural, automatic. (Consider the vocabulary of cell biology, which we can further discuss later.) And so I identify "design" as the very thing I'm trying to understand. My question becomes how did all of this design come about?
I think, then, that we can identify at least two crucial ways in which our thinking diverges. First, design for you is the stuff you use to fill explanatory gaps -- it's the answer. For me, it's the thing we seek to understand -- it's the question. Second, you are convinced that "naturalistic" explanation of natural history is not possible. I'm not at all convinced of this, and in fact I expect God's world to be largely amenable to natural explanation. In other words, I expect that naturalistic mechanisms can account for biological evolution, just as I expect that they can account for embryonic development and for, say, autism. Did that answer your question?
And what about Behe's The Edge of Evolution? Writing carefully about his errors is not easy; evolutionary genetics is challenging under the best of conditions, and laypersons are understandably poorly-equipped to grasp the necessary details. I have been planning a series on my blog, and this conversation might get that project moved up on the to-do list. I've explained some of the most dramatic errors on my blog, and I'll add three further comments here.
1. In TEoE and elsewhere, Behe presents a highly simplified vision of adaptation and microevolution, in which only beneficial mutations are maintained in populations. He gives the impression that a population would only harbor a given mutation or polymorphism if that change had been specifically favored by selection. This is a substantial mischaracterization of evolutionary genetics, overlooking some very important aspects of eukaryotic genetics. There are several mechanisms, well-known to geneticists but almost universally neglected in popular discussions of evolution and inheritance, that can lead to the maintenance of a non-adaptive or "non-beneficial" allele in a population, especially in a sexually-reproducing diploid population (like, say, Plasmodium falciparum). Moreover, during evolutionary and/or environmental change, the beneficial-ness of a particular allele can change completely. Beware of simple evolutionary stories in which adaptation can only proceed in happy little steps from good to better to best. Genetics is more complicated (and interesting) than that.
2. The book's central argument is based fundamentally on population genetics, but ignores the work of the world's most prominent and accomplished geneticists. Allen Orr, for example, is precisely the kind of expert whose work should be the focus of Behe's analysis, but Behe's references to Orr's work are minimal. He leaves untouched the entire field of evolutionary genetics, merely cherry-picking two of Orr's papers. The point is this: a serious consideration of evolutionary genetics -- never mind a complete rewriting of the entire field -- should show marks of serious engagement with existing ideas. TEoE doesn't even try to do this. And most tellingly, Behe hasn't been able to get population geneticists to endorse his book, or to follow up on his assertions. Did he even ask Allen Orr to read the manuscript before going to press? Has he asked Allen Orr to critically review the book, the way any real scientist would seek critical feedback before (or after) advancing a big new idea?
3. If Behe's claims in TEoE are correct, he will soon be the most celebrated biologist since Watson and Crick, and perhaps of all time, for he will have shown conclusively that essentially everything in the biosphere has arisen through mechanisms unknown to science. It is impossible to exaggerate the magnitude of the impact of such discoveries, and I assure you that if I thought there was anything there at all, I would hasten to follow up on Behe's skeletal introduction, devising bioinformatic analyses to bolster his hypothesis and working hard to establish myself as a part of this historic sea change in science. I would achieve scientific "immortality" for myself, worldwide acclaim for Calvin College, and maybe enough of a raise to retire my student loan debt while paying for Christian school education for my kids. Guys, if Allen Orr or Michael Lynch or Sean Carroll or Francis Collins or Craig Venter thought there was anything even remotely plausible about Behe's analysis, they would marshal resources of every kind to pursue the question, and some of them would gather investors and start an institute, bearing the name of some benefactor eager to have his/her name associated with the most momentous discovery of the 20th century and with the Nobel Laureate who made it happen.
Wake up, people. There's nothing there.
