I was trained as a developmental geneticist, a person who explores the role of genes in the process of development from an embryo to an adult organism. My graduate student and post-doctorate days date back into the “dark ages” of this field—the late 1960’s through the mid-1970’s. At that point all we had were glimpses of how genes influenced the process of development. Those all-too-fuzzy peeps were tantalizing to young impressionable minds, but that’s all they were—just little hints—and they were deeply enshrouded in mystery. Everything changed beginning in the late 70’s as a result of two wonderful technical revolutions which started to provide elegant answers to simple questions about genes and proteins and what actually takes place following the momentous arrival of a sperm cell at the egg’s threshold.
The first revolution was created by the advent of recombinant DNA: Amazingly genes could be manipulated in test tubes using techniques not unlike the sorts of things that we all did in high school chemistry. The second involved a technique for identifying almost all of the genes which control the early stages of the developing embryo in the fruit fly, Drosophila melanogaster. Eric Weischaus and Christiane Nusslein Volhard exposed flies to DNA-damaging chemicals and identified a slew of mutant strains that stopped embryonic development at highly specific stages. Using these mutant strains and the elegant techniques of manipulating DNA that had just become available, various investigators were able to characterize in fairly specific details the molecular processes at work in generating a fly. Not only that but the scientists quickly began to show that the rules that governed the development of a little fruit fly were similar to those which applied to vertebrates—even humans. Indeed, the “molecular toolkits” (the genes and their products) which are used to build a body were found to be remarkably similar in a wide spectrum of animals.
Stephen Meyer summarizes this quite nicely in his book. He also provides, I think, an accurate state of the impact these developments have had on biology, especially evolutionary biology. Here is what I wrote to Deborah Haarsma as I reflected on the book.
I expected the book would be largely about paleontology, but as you know that represents only the first four chapters of a twenty chapter book. What the book really is, is a continuation of Signature in the Cell. In essence, it is about the generation of the information needed for animal development. To be frank, I think it’s an amazingly effective book. I think he’s wrong, of course, and there are certain things that I think he does which are misleading… But as a whole, it is, in my opinion, somewhat of a masterpiece for accomplishing their agenda. Part of its success is that it really is a fairly accurate summary of the state of the biology. The depth of knowledge he displays in molecular genetics, developmental biology, and population genetics in addition to paleontology, animal diversity, biochemistry, and even some cell biology is very impressive.
I went on from there to summarize my reaction to Stephen’s statements about a revolution taking place in mainstream biologists’ thinking about macro-evolution:
Meyer has successfully put his finger on one of the great mysteries in evolutionary biology today. He documents the mystery well—Eric Davidson is the single most important person in the field of the molecular genetics of development dating back almost 50 years and he [Meyer] refers knowledgeably, I think, to his work.
I taught a course in General Genetics each year beginning in 1977 and extending throughout most of my career as a professor. Near the end of every year’s class, I would come to the population genetics section. It was just assumed that what we taught about microevolution—the chief focus of population genetics—held for macro-evolution1 as well. Indeed once I moved into a Christian college setting in the mid-80’s, I would sometimes tell my students that we had come to a very critical part of the course—the genetics behind the process of creation of all life forms—understanding God’s tools for carrying out God’s handiwork. They were always a little disappointed in this section, partly because the mathematics made it seem somewhat abstruse and partly because the concepts seemed so far removed from the real point of it all—the generation of new body plans and structures. So it was with no little frustration on both of our parts that this section of the course came to a close. Indeed, so anti-climactic was it that I eventually tried to find ways of rearranging the course—moving the population genetics topic to an earlier part of the course—so that we could end our semester together on a more exciting note.
I now understand that what I as a geneticist was trying to do at that time was wrong. The heart of explaining the process of macro-evolution is not a description of the quantitative details of changes in the frequency of genetic variants in response to migration, or natural and sexual selection. As important as all of that is at the species level and genus level, the really interesting questions relate to how mutational changes resulted in altered developmental processes that generated whole new body plans. How have novel structures been generated through evolutionary time? Is the evolutionary process itself evolving such that what we observe today is fundamentally different not only because the environment is different but because the cellular machinery itself has stabilized? Natural selection is a real phenomenon and an important filter, but it’s not the driving mechanism, and we are at a fascinating time as biologists from an array of sub-disciplines explore this matter using the new and powerful techniques at hand.
In the final chapters of the book, Stephen goes on to explore the best explanation of the current conundrum. Here is my reaction to that section.
I know that others know much more about his philosophy of science section, but I will say that I was very impressed with the case he made. He was careful to emphasize that science simply seeks the best explanation and doesn’t seek to prove. He has laid out each of the alternatives and has dismissed them as unlikely in a manner not unlike how it is really done in science. (True he dismisses some too quickly, but still he is very effective—given that this book is for a general audience.)
So have I softened on Intelligent Design as a scientific endeavor? I don’t think so, but I have grown to appreciate the skill and the sincerity of various individuals I have met in the ID movement over the last five years. Many of them share my faith, a faith firmly grounded not just in polite interchange, but outright love. I don’t take back my opinion on the other ID biology books that have come out over the past quarter century or so. I have long thought that Darwin on Trial, Darwin’s Black Box, Icons of Evolution, The Edge of Evolution, and Signature in the Cell were not scientifically strong and still do. And I don’t think Darwin’s Doubt makes scientifically warranted conclusions either (see part II tomorrow). Still, Stephen has identified one of the most exciting questions in all of biology. I respect his skill in becoming well-informed about a vast swath of biological material and to communicate it in such an engaging fashion. I do not think he’s right, but I do appreciate the sincerity of his lifelong perseverance in laying out the case for something to which he and others have given their careers and a large part of their lives. They think the philosophical naturalism of many leading scientists has significantly influenced their conclusions, and I certainly agree that there have been times when that is the case. However, where we don’t agree is that the whole applecart of evolutionary biology needs to be turned upside down and replaced with a new science—one grounded in the scientific demonstration of Intelligence. I see no scientific, biblical, or theological reason to expect that. Natural processes are a manifestation of God’s ongoing presence in the universe. The Intelligence in which I as a Christian believe, has been built into the system from the beginning, and it is realized through God’s ongoing activity which is manifest through the natural laws.2 Those laws are a description of that which emerges, that which is a result of, God’s ongoing presence and activity in the universe. I see no biblical, theological, or scientific reason to extend that to extra supernatural “boosts” along the way, although I also perceive no good reason to close the door on that possibility.
Soon after sending along my reflections of Darwin’s Doubt to BioLogos president Deborah Haarsma, I had the privilege of reading Robert Bishop’s essay and passed along my comments to Robert and her. Since, as a biologist, I didn’t see the book through the same lens as Robert (an expert in the history and philosophy of science) I’ve been asked to post those thoughts to accompany his. So herewith is a summary of four places where Robert and I may see things through somewhat different lenses.
1. Does Stephen Meyer exaggerate the nature of the rethinking going on in mainstream evolutionary developmental biology?
I don’t think so. Many evolutionary developmental biologists think that we are on the verge of a significant re-organization in our thinking about the mechanics of macro-evolution. The much respected developmental biologist Scott Gilbert states: “If the population genetics model of evolutionary biology isn’t revised by developmental genetics, it will be as relevant to biology as Newtonian physics is to current physics.”
That and many other similar statements that I’ve seen in the literature3 really do suggest that we are on the cusp of some major rethinking about the forces at work in macro-evolution. Those studies will focus more on how biological information is generated, changed, and used, and less on the natural selection filter. Clearly, the evolutionary process itself has been evolving through time and we are seeing that more poignantly than ever before. Although Stephen himself thinks that the tenets of evolutionary biology are essentially bankrupt, I do not think he misrepresents what others think about it. For example he states: “Biologists, Scott Gilbert, John Opitz, and Rudolf Raff have attempted to supplement classical Neo-Darwinism, which they argue, cannot adequately explain large-scale macro-evolutionary change” (emphasis, added). Biologists, he says, are seeking a supplement. Stephen himself thinks they need to start over, but he acknowledges that they do not see it as desperately as he does.
2. The timing of the perceived information problem
Stephen puts considerable effort into showing why he thinks that the well-accepted methods of generating new genes and proteins are ill-conceived. I agree with Robert Bishop that this matter is somewhat beside the point for this particular book. The book, after all, is focused on the Cambrian explosion, which occurred after much of the gene/ protein “tool box” had already been put together through a process spanning 2 billion years or so. However, I do think most of us understand why Stephen did this. He is building a story and he wants the reader to see why he and other leaders of the ID movement think the very core of evolutionary thinking (the method of generating new information) has failed. If, as he sees it, biology can’t explain how new genes were generated in the preceding two billion years, it certainly can’t explain that which results in the generation of a plethora of new body plans in a time interval that is only one to two percent of the time utilized to put the entire cellular tool box together. He has chosen to highlight the effort of Michael Behe in Edge of Evolution and Doug Axe on protein folding. This work has not drawn the applause of mainstream scientists (and for good reason), but that’s not the point. Meyer is trying to build a case for his view that the derivation of information needed to build bodies in any way other than external intelligence is seriously flawed. He’s making his case as strongly as he can and working hard on communicating that clearly to a general audience. I remain amazed at the breadth of his knowledge and communicative skill, even though as I dig into the depths of the scientific papers, I see matters much differently than he does.
3. Generation of new body plans de novo
The big mystery associated with the Cambrian explosion is the rapid generation of body plans de novo. There was never a time like it before, nor has there ever been a time like it again since. Stephen is right about that. Also, as he points out, the big question in exploring the generation of new body plans in that era is how this squares with the resistance of today’s gene regulatory networks to mutational perturbation (i.e. they seem to be almost impossible to change through genetic mutation because virtually all such alterations are lethal). We really have little idea at this point how things would have worked to generate body plans de novo back then given the sensitivity of the networks to perturbation today. As Douglas Erwin elegantly argues in his 2011 paper, there must have been something different taking place as the system was being put in place 550 million or so years ago. I think figuring that out will turn out to be one of the most fascinating pieces of puzzle-solving that molecular biology has ever done. However, unlike Stephen, not only do I think this research is not at a dead-end, I think it will turn out to be among the most exciting frontiers in biological research over the next couple of decades. The work, as most developmental biologists see it, has only just begun, and it is the kind of thing that happens at this cutting edge stage, which makes science so much fun. I’m with Ralph Stearley [pdf] on this: to study the diversity of life and the mechanisms which characterize it is to be enraptured in joy.
4. Living cells as information systems
I agree with Robert that it is quite a stretch to jump from the “failure” of materialistic explanations of the Cambrian explosion (so far) to a scientifically based conclusion that life is intelligently designed. The only case that Stephen makes—so far as I can see—is given that the cell can be considered an information system (and I agree with Stephen that it can), and given that all other known information systems require an intelligence to design them, so the cellular systems that constitute life must be intelligently designed. In building his scientific case, he examines each of the other possibilities that have emerged from biological research and declares, one-by-one, that each has failed. With that only one is left that doesn’t fail his examination—intelligent design. I hope I’m not being facetious, but the main reason that it can pass his test as I see it, is that with one exception it makes essentially no predictions. The one exception of course is that all other information systems will turn out to be designed by outside intelligence. So far that has indeed turned out to be the case; we humans have used our intelligence to design them all.
Stephen is right, that none of the other models fit the bill in a fully satisfactory manner yet, but it’s pretty early to declare one to be the winner on the basis of an analogy to human-designed information systems. But more perplexing to me is trying to fathom how this investigation can continue as a scientific project. How will proponents of Intelligent Design take their biological studies from the level of the “best explanation on the basis of analogy” to a project which makes a set of positive predictions? How will they move forward by building a positive research program rather than a negative one based upon the critique of mainstream ideas? What are the biological predictions that will emerge from within their paradigm and how will they test them? I sense the topic for another biology book coming on. If so, and as they proceed, I wish them…joy!