Dr. Kenneth Miller and the Faith of Science

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.Even today, the general public, and many scientists, are not aware of decades of research in evolutionary science, molecular biology and genome sequencing which provide alternative answers to how novel organisms have originated in the long history of life on earth. This web site is dedicated to making the results of that research available and to offering a forum to expose novel scientific thinking about the evolutionary process. The DNA record does not support the assertion that small random mutations are the main source of new and useful variations. We now know that the many different processes of variation involve well regulated cell action on DNA molecules. Genomes merge, shrink and grow, acquire new DNA components, and modify their structures by well-documented cellular and biochemical processes. Most of the scientists referenced on this web site have come to a wide range of conclusions about different aspects of evolutionary change. Many see evolution as a complex process with distinct mechanisms and stages rather than a phenomenon explainable by a small number of principles. The divergences and multiplicity of ideas, opinions and theories on this website are necessary since many fields of evolutionary biology remain relatively unexplored.

Professor Kenneth Miller has read the comments of J Cosgrove (see Mr. Cosgrove's comments, below) and has given me permission to post his response. 

What follows is from Dr. Miller:

 I will respond to the many points made in J. Cosgrove’s comments, in order :

1) Cosgrove asserts that “Darwinism” is the main reason that students enter as believers but leave Catholic Universities as atheists or agnostics. I’m unaware of any study demonstrating that, and none is cited in his comment. I would suggest that disillusionment with the institutional Church, especially in the handling of clerical sexual abuse of children, is at least as great a factor.

2) His definition of “Darwinism” as a belief system is not one I recognize as a biologist. Evolution is a well-supported scientific theory that explains the origin of species and the emergence of biological diversity. Evolutionary mechanisms as they are understood today are quite different from Darwin’s original ideas, so it is difficult to understand what Cosgrove means by Darwin-“ism.”  Unless, of course, by attaching the –ism to Darwin’s name he wishes to imply that evolution is ideological rather than scientific. He is right on point when he criticizes the tendency for some academics to construct just-so stories as to how a particular trait was “selected.” However, he seems unaware that mainstream evolutionary biology is also critical of such unsupported assertions. As an example, look at Gould and Eldredge’s classic essay, “The Spandrels of San Marcos.”

3) He cites a “Third Way” of understanding evolution that has been championed by Chicago professor James Shapiro. But Shapiro’s claims are anything but a challenge to mainstream evolutionary science.  The excerpt he quotes mentions mechanisms such as genome mergers and horizontal gene transfer as if “Darwinism” somehow ignored these processes.  In fact, as our understanding of molecular biology has grown it has provided strong support for the evolutionary process by discovering such things as transposable genetic elements, reverse transcription, RNA interference, and epigenetic modification of gene expression.  Far from being challenges to a “Darwinian” view of life, these new discoveries only expand our understanding of how evolution works by natural processes. When Dr. Shapiro asserts “small random mutations” cannot be “the main source of new and useful variations” he’s actually repeating something that has been clear ever since 1968 when Motoo Mimura proposed the neutral theory of evolution. It’s old news.

4) Cosgrove claims he read an article in the 1990s claiming that a professor in California was “forbidden from saying anything negative about Darwin.”  Really? I say negative things about Darwin in my own classes all the time, pointing out his lack of knowledge about genetics and biochemistry, and the fact that he did not appreciate the role that kin selection plays in the evolution of social behavior. No one has ever suggested I should tone down that criticism, and I suspect that no such professor was ever “forbidden” to say “anything negative” back in the 1990s either.

5) Cosgrove indicates that he was taken in by a New York City conference on ‘Intelligent Design,” and especially by the books of Michael Behe (Darwin’s Black Box and The Edge of Evolution). He claims that I have “belittled” and “distorted” Dr. Behe’s ideas. Here are the facts:

• I have never belittled Michael Behe, with whom I maintain very good personal relations. In fact, I have taken Dr. Behe seriously, and treated his ideas in the way any good scientist would hope and expect – by subjecting them to analysis and reasoned discussion. I have debated Dr. Behe, in print and in person, more than 10 times, which reflects the respect I have for him. In none of these debates was he able to point out a “distortion” of his ideas.

• Dr. Behe’s ideas were at the center of the landmark Kitzmiller v. Dover trial in 2005 on the issue of intelligent design. I testified at the start of that trial by first explaining the scientific evidence that supported evolution. Then I presented Dr. Behe’s ideas on “design” and then explained why those ideas were wrong. They were, as I explained, contradicted by scientific fact.  Dr. Behe followed my testimony two weeks later.  If I had distorted or mischaracterized his positions, he could easily have corrected me and destroyed my credibility. However, despite three days of testimony, he was able to do nothing of the sort. As the court’s final opinion pointed out, Dr. Behe’s claims for the “irreducible complexity” of biological systems were incorrect, and were directly contradicted by scientific fact.

• As an example, consider one of Behe’s central claims, namely, that the system of complex proteins that clot of the blood of vertebrates (like us) is irreducibly complex. He wrote specifically that each and every one of the blood clotting proteins had to be present for the system to work properly, and in the absence of any one of them, the system fails. We now know, as a result of whole genome sequencing, that many organisms do indeed lack several of these components, and yet have fully functional clotting systems. Furthermore, the detailed genetics of the system show, in great detail, how the clotting system evolved, something that Dr. Behe has always said would be impossible. For reference, I would recommend that Mr. Cosgrove read “The Evolution of Vertebrate Blood Clotting,” a 2013 book by Russell Doolittle, a scientific expert in the clotting system. Cosgrove regards such complex systems as the “Achilles Heel” of evolution.  As Doolittle’s research shows, such systems actually document the evolutionary process in exquisite detail.

• Finally, Cosgrove recommends Dr. Behe’s latest book, “The Edge of Evolution.” Far from ignoring Dr. Behe’s work, the scientific community reviewed that book in the world’s two leading scientific journals.  I reviewed it in the journal NATURE (June 28, 2007) and Sean B. Carroll reviewed it in the journal SCIENCE (June 8, 2007). Dr. Carroll and I pointed out the scientific errors and misconceptions in Behe’s arguments, which is why the book has won few converts to the intelligent design position.

6) It may surprise Mr. Cosgrove that I, too, am concerned with college students losing their faith. That is one of the principal reasons I have been so outspoken in support of the compatibility of evolutionary biology with religion, and with the Catholic view of science and faith in particular. To suggest that Catholicism is only valid if Darwinian evolution is wrong is a sure fire pathway to disbelief. Sadly, that is the one that Cosgrove seems to advocate.

Cosgrove asserts that “Darwinism” is the main reason that students enter as believers but leave Catholic Universities as atheists or agnostics. I’m unaware of any study demonstrating that, and none is cited in his comment. I would suggest that disillusionment with the institutional Church, especially in the handling of clerical sexual abuse of children, is at least as great a factor.

It may surprise Mr. Cosgrove that I, too, am concerned with college students losing their faith. That is one of the principal reasons I have been so outspoken in support of the compatibility of evolutionary biology with religion, and with the Catholic view of science and faith in particular.

To suggest that Catholicism is only valid if Darwinian evolution is wrong is a sure fire pathway to disbelief. Sadly, that is the one that Cosgrove seems to advocate.

Matt, I started following the evolution debate about 15 years ago. I read an article in one of the news magazines in the 1990's that some professor at one of the University of California schools was forbidden from saying anything negative about Darwin and had the option of only teaching Darwin's ideas or not teach the course. I was intrigued since I assumed for most of my life that Darwin's ideas were the basis for evolution. But I did not pay too much more attention to it. I have an undergraduate degree from a Jesuit university in math and physics and had some familiarity with biology. I had read some biology in the mid 90's because of my business (mainly about energy metabolism). My wife and I own a small business that distributes medical devices. I was curious about the censoring of the professor. Was there something wrong with Darwin's ideas. Then a few years later I saw an ad in the NY archdiocese newspaper about an intelligent design conference in New York City sponsored by a local Catholic organization. I went to it and was blown away by the presentations. It was all science. Absolutely no religion. I was hooked by the controversy. So I started to read and one of the first things I read was Michael Behe's book titled "Darwin's Black Box." I immediately saw the problem with Darwin's ideas. I then started to read books from both sides of the debate and bought a couple text books on biology to understand DNA and its role in the evolution debate. One of the things that I quickly learned is that the two sides did not debate in the same way. The Intelligent Design people would only provide scientific data and refer to biology and experiments while the Darwin side of the debate rarely used evidence that supported Darwin's ideas and would mainly use theological arguments as to why intelligent design was not right. They tried to belittle the ID people. One way they did this was to constantly refer to the ID people as creationist. I found that very strange. One of the people doing this belittling and distorting was Ken Miller. It took me a long time before it all coalesced in my thinking but I now can view the evolution debate from a framework worked out over a period of about 10 years. Darwin's ideas are mathematically, physically, chemically and biologically impossible. And Ken Miller knows it. This does not say that there might not be some other naturalistic explanation but it cannot be Darwin's ideas of mutation, recombination, differential reproduction and natural selection. And gradualism, an essential part of Darwin's thinking, is a non starter. Michael Behe is a excellent example of what I call a Catholic gentleman. He is always fair and to some extent this is one of his problems. He leans over backwards to accommodate his opponent in a debate. He is also is not a polished debater but his ideas are rock solid and backed up with evidence and reason. Miller is a polished debater and speaker but many of his ideas and criticisms of intelligent design are not logically sound. That is why I have no respect for Kenneth Miller. Many of the things you have excerpted and said by Miller, I agree with but that is far from what he has said in debates and testimony in the past. Miller defends Darwinian evolution. The link I provided to the Third Way indicates that a large group of people disagree with Darwinian processes as the source of anything major in biology. These people are not intelligent design advocates but believers in some form of naturalistic evolution. They however, recognize the deficiency of Darwinian processes. If any of them believe in design, they would not dare say it because they would be immediately ostracized from anything meaningful in their work. But none of the theories in the Third Way collection has any evidence supporting them either. Stephen Miller's book, Darwin's Doubt, reviews most of their theories. If you want to know what is the Achilles Heel for naturalistic evolution, it is the origin of proteins that work together to do something functional. It would take trillions x trillions of mutations just to get one new protein that is functional and to get a second that could work with it would take several orders of magnitude more than this. This essentially exhausts all the resources of the universe since the Big Bang just to get two proteins to work with each other let alone the thousands that are present in each cell. This is where the debate is, just how did all these proteins arise that work with each other. Darwinian processes could never begin to explain it and Kenneth Miller knows that. I recommend Michael Behe's second book, The Edge of Evolution, which discusses this issue.

The true vow of a scientist is to practice honest and open empiricism in every aspect of his scientific work.

"What kind of evolution does the Pope believe in?"

First, Darwin argued that massive changes were easily accomplished to species through selective breeding.

The two other main pillars of Darwin's argument is what is called homologies and geographic variation .

Or was it?