Michael Behe posted a kind, brief comment on my previous post. As I began to write my reply, I realized his comment and my reply would interest many readers, and hence this separate post.
Here is his comment, and my reply follows.
Good day, Mike (if I may): Thank you for your kind words. I do appreciate the fact that you remain upbeat about my lab’s research, and much other work that you describe in your writings, even though I disagree with the “big picture” that you take from the evolution literature.
I find it interesting and personally enjoyable (despite some frustrations as well) that evolution remains such a “hot” topic. That’s true scientifically, with many extraordinary discoveries in recent years—from fossils like Tiktaalik and Archaeopteryx [edit: this one was discovered long ago, but it’s better understood now] to the DNA-based evidence that Denisovans and Neanderthals contributed to the genomes of many of us living today. It’s also the case that evolution remains “hot” for many non-scientists, and that’s wonderful. Whether for secular or religious reasons, we humans are deeply interested in where we came from and how we came about. In my own small way, I take pleasure in knowing that my lab’s research helps people get a glimpse of how evolution works.
I’m concerned, though, when these scientific and religious perspectives get intertwined and confused, even when they concern those big, important questions that interest all of us. I get even more concerned when I see what I regard as non-scientific ideas (such as “intelligent agents” introducing “purposeful design” by unstated and untestable means) being used to undermine the admittedly imperfect (and always subject to revision) understanding of evolution that science provides to those who want to learn. And I am most disturbed when these confusions appear to be part of a deliberate “wedge” strategy with ulterior sociopolitical motives. People will undoubtedly have diverse views about whether scientific explanations are adequate and/or satisfying ways to understand the world, but I see danger in trying to undermine scientific methodology and reasoning to advance religious beliefs and political goals.
Telliamed Revisited 
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Sir,
Very much appreciated the ideas in this article, and the concern about intertwining scientific and religious methods. … but for what it is worth: my own sympathy with Intelligent Design is actually due to its pursuit of the scientific and testable. It seems self-evident to me that intelligent agency may well be testable and detectable by scientific methods. This is entirely uncontroversial in realms of archaeology or the search for extraterrestrial intelligence (SETI). For instance, if SETI scientists started receiving radio signals that were clearly inexplicable by any natural phenomenon (e.g., signals enumerating prime numbers), no one would accuse them of being “unscientific” for postulating the work of an intelligent agent(s). Similarly, no one accuses archaeologists of being unscientific after postulating certain markings on a rock to be the result of intelligent agency rather than strictly natural phenomena.
On the other hand, I am more inclined to trust the outcome of a scientific approach if the method is willing to follow the evidence *wherever* it leads, rather than ruling out certain conclusions (e.g., intelligent agency) from consideration at the outset. If someone rules out intelligent agency as a possible conclusion from the outset of any investigation, I simply cannot be impressed when they conclude a natural cause…. they had in effect already determined that conclusion before beginning the investigation.
It seems to me that the approach that *a priori* rules certain conclusions as (if I dare use the word) “heresy” is the one that is intertwining and confusing the scientific and the religious/philosophical; while the approach that is willing to follow the evidence wherever it leads, with no conclusion a priori considered “off-limits”, is the one that has maintained true scientific integrity.
Very humbly and respectfully submitted,
Daniel
Science already has identified a set of evolutionary processes — mutation, recombination (including horizontal gene transfer in some cases), drift, and selection — that can produce, improve, and change functions, giving the appearance of “top down” design in nature. Thus, science doesn’t appear to require an additional “intelligent design” process to explain the diversity of life. But if Michael Behe, or anyone else, produces evidence for how that “top-down” design occurs — I’m talking about real evidence, not the usual hand-waving god-of-the-gaps evolution-can’t-do-that incredulity — I’ll pay it a lot of attention! But it hasn’t happened yet, and I’m not holding my breath …
Professor Lenski,
I think your describing living things as having “the appearance of ‘top down’ design in nature” is the key to the controversy. Normally, as in SETI and archaeology, we take the appearance of top down design as providing prima facie evidence for intelligent agency. Now perhaps you are correct that there are processes that are not the result of intelligent agency that can give that appearance with regard to living things. But it’s not clear to many of us that you or the rest of the scientific community have succeeded in making that case. I, along with Professor Behe, look forward to hearing what else you have to say in favor of your view.. But until then, I would appreciate a little more sympathy from you for those of us who think that the appearance of top down design is reasonable evidence for believing in top down design, instead of throwing harsh invectives at us of being unscientific.
P.S. I’m trying to post this under my name, Julian. But it might show my old pseudonym.
Julian: I have not thrown any invective, though I get impatient with repeated, unsupported assertions that evolution cannot do certain things.
Sir,
As before, I am sincerely thankful for your time in responding. Hoping not to sound contentious, but this actually well illustrates the basis of my own skepticism, if interesting to you. Specifically, I glanced at the article you previously mentioned to me that “identified a set of evolutionary processes” for digital computer programs – namely that they “self-replicate, mutate, compete and evolve”, and that in these programs, “complex functions evolved by building on simpler functions.” And I take no issue with any of these particular processes or their observed improvements. But if someone seriously suggested that these processes, alone and unguided, were sufficient, adequate explanation for any of even the simplest programs, drivers, or applications I use on my computer (so perfectly designed for certain functions), I would remain incredulous, but I would think my incredulity quite justified.
Similarly, I’m familiar with and fully endorse the processes you mention (mutation, recombination, drift, and selection), and their ability to induce certain improvements and benefits. I conducted such basic experiments with fruit flies in my undergrad days. But I’m then asked to believe that these processes, alone and unguided, are sufficient explanation for the development of, say: a fully integrated, near-instantaneous, pinpoint-accurate active sonar system, including the novel fully integrated organ; rewiring of the teeth/jaw to function as directional, active-sonar-intercept-hydrophones, all alongside the sophisticated software/neural computing and mathematical algorithms required to instantaneously compile and process the incoming data… all this in a (relatively) meager 500,000 generations or so.
So yes, I’m afraid I am “incredulous” that the processes you mention are sufficient to explain that level of sophistication. But similarly, I do not find my incredulity unjustified…. particularly as observation of long-term evolution in rapidly reproducing species (while demonstrating certain impressive improvements and adaptations ) has shown nothing approaching the leaps of sophisticated innovation, coordinated rewiring and integrated cooption, or novel structures necessary to demonstrate that these processes could cause the novel development of such sophisticated echolocation in such a (relatively) short evolutionary timespan. In other words, we haven’t observed anything approaching these kinds of leaps in sophistication over the 60,000+ generations we have observed, but I am asked to believe (on faith?) that these same processes can undoubtedly achieve far, far more intricately integrated sophistication over some 500,000 generations in a different species?
So like you, I am certainly looking for “hard evidence”…. for me, evidence that unguided evolution could, in fact, accomplish the utterly astounding feats attributed to it. But I feel I am typically given (not meaning by yourself, but in general) what come across to me like “hand-waves” in the opposite direction…. if I may be so bold to borrow your phrase, “I get impatient with repeated, unsupported assertions that evolution *can* do certain things.”
Humbly and respectfully,
Daniel
Sir,
Understood and appreciated. Thank you so much for taking the time that you have., recognize how valuable your time must be.
Respectfully,
Daniel
Daniel: Except the assertions about what evolution can do and has done are supported by comparative studies, paleontology, and experiments with biological and computational systems, etc. Not so the unnamed, unknown agent who supposedly has purposefully introduced new genetic information over the course of history.
I’m going to close comments now. I may open them again after future posts, but all this is getting very tiresome. And if I do open them, I’ll probably restrict every poster to 800 words, just like our book review in Science :>)
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Thank you for your patience in responding to people who approach science in a – how to word it politely – pre-ordained way. Fascinating how difficult concepts which need some thought are hastily dismissed – and replaced with mind-bogglingly unlikely ‘supernatural’ alternatives without explanation!