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Searching for Motivated Belief: Understanding John Polkinghorne, Part 2

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March 14, 2013 Tags: Divine Action & Purpose, Science & Worldviews
Searching for Motivated Belief: Understanding John Polkinghorne, Part 2
Matthias Grünewald, The Small Crucifixion (c. 1511/1520), National Gallery of Art

Today's entry was written by Ted Davis. You can read more about what we believe here.

In my last post, I presented John Polkinghorne’s attitude to scientific and religious knowledge and explained his approach to natural theology. Today, we briefly examine his theology of nature and his attitude toward the Resurrection.

Understanding John Polkinghorne: Theology of Nature

John Polkinghorne’s interest in natural theology is important, but what really sets him apart from most others is that he combines it with an equally strong interest in theology of nature, which is not the same thing. Where natural theology involves, “metaquestions about the pattern and structure of the physical world,” theology of nature involves, “metaquestions about how its historical process is to be understood.” Rather than “looking to the physical world for hints of God’s existence,” we look “to God’s existence as an aid for understanding why things have developed in the physical world in the manner that they have.” (Belief in God in an Age of Science, p. 13)

On this front, Polkinghorne advances a strongly Christocentric theology of creation, stressing Jürgen Moltmann’s notion of The Crucified God . In the context of Polkinghorne’s theology of nature, the point is that the Creator is the crucified and resurrected second person of the Trinity. Since I devoted a column to this before, I won’t say more here, except to alert readers to the singular importance this particular idea has for him—especially when facing the problem of suffering. “The insight of the Crucified God lies at the very heart of my own Christian belief, indeed of the possibility of such belief in the face of the way the world is.” (Belief in God in an Age of Science, p. 44)

Situating John Polkinghorne: The Resurrection of Jesus

Many Christians today see science as posing dangerous threats to their faith, challenging their understanding of the Bible and undermining core tenets such as the bodily Resurrection of Jesus, the historical basis on which the Christian faith stands or falls. “Evolution” is often identified as the problem, but the real danger is unbridled naturalism. A commitment to naturalistic methods, known as “methodological naturalism,” (MN) has been an integral part of science and medicine since the ancient Greeks. Those methods have been highly successful at producing a coherent, often very convincing picture of nature and the history of nature.

Advocates of Intelligent Design and some other Christians reject MN, but many Christians who work in the sciences and related fields (such as engineering, medicine, or the history and philosophy science) support MN as a properly grounded and properly limited way of understanding reality. In their view, a robust Christian faith is consistent with a commitment to MN, provided that the limits of scientific inquiry are not simply equated with the limits of rationally grounded belief. Polkinghorne fits squarely in this category.

To understand more clearly where Polkinghorne lies on the larger landscape of science and religion, let’s consider his approach to the Resurrection. Many contemporary thinkers, including some theologians and clergy, believe that “science” has somehow made it impossible to believe in the Resurrection, the deity of Jesus, and even belief in the transcendent God of the Bible.

A prime example is John Shelby Spong, a retired Episcopalian bishop whose books have sold more than one million copies. Spong sees the bodily Resurrection as a figment of the disciples’ imaginations, a vestige of a theism that now we must throw away like a threadbare suit of clothes. For Spong, Christians today need to go “beyond theism” throwing out the baby of divine transcendence—the fundamental truth of monotheism—along with the bath water of the credulity and mythology of the pre-modern authors of the Bible and the ecumenical creeds. Spong’s message is that “Christianity must change or die,” and all in the name of “science.”

As Spong likes to say, his work is very controversial, and not just among rank-and-file Christians. Scholars have also railed against him. “I have been attacked in books from the religious right by such people as Alistair MacGrath [whose surname is actually spelled McGrath], N.T. Wright, and Luke Timothy Johnson,” he complains (Why Christianity Must Change or Die, p. xvi).

I understand (with much sadness) that we live in a highly polarized age. Nevertheless, it’s difficult for me to grant much credibility to an author who identifies McGrath, Wright, and Johnson as representatives of the “religious right.” Indeed, if anyone here is distorting the news it is Spong, not they. As the (late) great Catholic biblical scholar Raymond Brown once observed, “I do not think that a single NT [New Testament] author would recognize Spong’s Jesus as the figure being proclaimed or written about.” (Birth of the Messiah, note 321 on p. 704)

Matthias Grünewald, The Resurrection (a wing of the
Isenheim Altarpiece, ca. 1515), Unterlinden Museum,
Colmar, France

Polkinghorne certainly understands science far more than Spong does, and his conclusions about the implications of science for Christian beliefs are markedly different. With respect to the Resurrection, he is basically on the same page with his friend Wright, whose profound book, The Resurrection of the Son of God, he cites with appreciation. Belief in the Resurrection is well supported by the evidence, and the Resurrection, itself, is “the pivot on which the claim of a unique and transcendent significance for Jesus must turn.” Considering authors like Spong (although he does not explicitly name him), he adds, “it would be a serious apologetic mistake if Christian theology thought that operating in the context of science should somehow discourage it from laying proper emphasis on the essential centrality of Christ’s Resurrection, however counterintuitive that belief may seem in the light of mundane expectation.” (Theology in the Context of Science, pp. 135-6)


Looking Ahead

This is the Easter season, and I’ll return in a couple of weeks to begin examining Polkinghorne’s approach to the Resurrection more fully, using excerpts from the chapter on “Motivated Belief” from his recent book, Theology in the Context of Science.


Raymond E. Brown, Birth of the Messiah: A Commentary on the Infancy Narratives in the Gospels of Matthew and Luke. (1992).

John Polkinghorne, Belief in God in an Age of Science (1998).

John Polkinghorne, Theology in the Context of Science (2009). My review for First Things online is here.

John Shelby Spong, Why Christianity Must Change or Die (1998).


Ted Davis is Fellow of the History of Science for the BioLogos Foundation and Professor of the History of Science at Messiah College. At Messiah, Davis teaches courses on historical and contemporary aspects of Christianity and science and directs the Central Pennsylvania Forum for Religion and Science.

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GJDS - #77862

March 26th 2013

I will try again (Reply to Ted)

I am finding it difficult at times to determine how far I should tolerate comments that clearly degrade the Bible and the Faith. I understand that tolerance is required, especially for atheists who seem to have a ‘mission’ regarding these matters, but it is clearly stated that this site accepts Christianity and that we share our views in this context. Without making a lengthy comment, I found it offensive even to my elderly years to read some of the comments (as I mentioned, god talking in the head, zombies in the gospels, and so on). I regard this as very harsh language, unnecessary for the discussion, and my response(s) I suspect reflected this. Hopefully this type of thing will not occur too often, and if it does I trust you will act and ‘put a lid’ on it quickly.

In this context, I have found your column informative, as also many resposes - I am beginning to appreciate the tradition that goes back to Boyle and Newton and hopefully I may develop a better appreciation of American Evangelical/protestant outlook.  

Ted Davis - #77864

March 26th 2013

I appreciate your gracious response, GJDS. I’ve elaborated on my approach to moderation in a comment that is now at the end of the previous page, so please be sure not to miss it.

Ted Davis - #77863

March 26th 2013

In a comment a few minutes ago (#77861) I mentioned a challenge I would make to Lou, in response to something he said to Eddie in a lengthy exchange above (77804). I’m putting my challenge here rather than there, so it doesn’t get lost in the details of that conversation. Here is what Lou said:

“[David] Berlinski is currently a senior fellow of the Discovery Institute (the main pushers of ID, and famous for the dishonesty of many of their arguments).  I just now listened to Berlinski on Youtube speaking about homologies. He is a pretentious fraud. Almost everything he said was meant to obfuscate the issue and hide the extraordinary tools we now have (molecular, genetic, and fossil evidence) for studying and verifying homologies, and hide the evidence produced by those tools (evidence that is very well presented here on the Biologos site, by the way). I listened to parts of a few other videos of his regarding evolution. He is simply lying with a straight face. This is not a man who will have something deep to say about the nature of truth or how we should search for it.  I appreciate the recommendation (and I try to take everyone’s recommendations seriously) but this guy is as intellectually dishonest as any I have seen. Worse than Behe by quite a lot.”

There is much here that bothers me, Lou, relative to what I said about differences of opinion descending to character assassination. If you think that Berlinski and The Discovery Institute are profoundly mistaken, that’s one thing: you tell people why you think so, and that’s that. If you think that someone is pretentious” and engages in “obfuscation,” that’s also fair game. You seem to go quite a bit further than this, however, when you say that Berlinski “is simply lying with a straight face.” Simply to say that borders on character assassination. I say “borders on” because you then say he is “as intellectually dishonest as any I have seen,” and that is not necessarily character assassination: it depends on what one means by this. I would say myself, for example, that Dan Brown’s claim (at the start of his novel, The DaVinci Code) about the factual status of certain historical information in his novel is “as intellectually dishonest” as anything I have seen. Please clarify your claim that Berlinski “is simply lying with a straight face.” Do you mean that he is being intellectually dishonest, by playing fast and loose with the facts (my view of Dan Brown), such that readers must read him with great caution, that is one thing. If you mean that he is deliberately affirming things that he knows to be false, in an effort to deceive by hiding the truth, that is another thing. I won’t enable character assassination.

Then you say that Berlinski is “Worse than Behe by quite a lot.” This is damning by faint praise. Not exactly character assassination, but by invoking Behe’s name in this highly negative context you can be seen as implying that Behe is also being intellectually dishonest. Having known Behe for a long time myself, I have never seen any evidence that he is either personally or intellectually dishonest. Do you want readers to infer that you think he is? If so, why? If not, why drop his name into the same paragraph with Berlinski?

Lou Jost - #77867

March 26th 2013

Hi Ted, I will try to avoid such statements in the future, but in Berlinski’s case, the only options I can see are 1) intent to mislead or 2) extraordinary ignorance about a subject he often writes and speaks about. If you have a moment, check out the first 48 seconds of this video of his:


He says evolution makes no testable predictions, but excellent refutations of that are available right here in the Biologos archives. The hypothesis of common descent lets us make detailed and precise predictions about the genomes of related species; we can also make biogeographical predictions, biochemical predictions, and many others, to test the idea of common descent. An example which has recieved much publicity is the fossil Tiktaalik, found in the exact layer of rock predicted by the hypyothesis of common descent. Could he really be unaware of these things?

Watch the evolution section of this video, from 7:20-12:50:


Even the conservative Christian host of the show is dumbfounded by Berlinski’s characterization of evolutionary theory. Berlinski makes absurd statements about the theory, ignoring all the molecular and biogeographic evidence for common descent, among other things. He seems to be doing this purely for dramatic effect.

It would be surprising if he were unaware of the evidence for evolution; he works at an institute where evolution is the main subject. Even if he never discussed these issues with colleagues, he has participated in public debates with biologists, such as this one


where well-known biologists Eugenie C. Scott and Michael Ruse, among others, spoke in favor of evolution. They would have mentioned the kind of evidence that Berlinski now pretends does not exist.

As I said, Behe is in a different category, and I meant my statement as a mild compliment to him (Eddie and I had discussed his work in earlier comments). Like you, I get the sense that Behe honestly believes he is doing good science, and in fact I agree he is pursuing a good question. I think his answers are mistaken for technical reasons.


Eddie - #77877

March 26th 2013


Some factual corrections:

Michael Ruse is a philosopher with an interest in the philosophy of biology, not a biologist.  All of his university degrees are in philosophy, not biology.

Eugenie Scott has not been doing scientific research for many years—possibly a couple of decades - because she has been running the NCSE, which is an advocacy group, not a research institute.  When she was a scientist, she was an anthropologist, not a biologist.

I am sure that Berlinski would recognize that there are “predictions” on the hypothesis of common descent—that transitional fossils would be of a certain age and likely found in certain places.  Such predictions are trivial, unless one is an evolution denier.

But the neo-Darwinian mechanism which supposedly explains the evolutionary process, Berlinski finds to be lacking in predictive power, compared with the models proposed in, say, modern physics.  Neo-Darwinian theory can explain, retrospectively and speculatively, why some creatures learned to fly; but what does it say about those in exactly the same environment that didn’t learn to fly?  Could it have predicted how many flying species would develop, or even that any flying species would develop at all?  Again, the sloth is a very inefficent creature, with almost no talents or natural defenses; why hasn’t natural selection weeded it out of existence?  Again, I have seen neo-Darwinian explanations of both altruism and selfishness.  What good is a prediction of two opposite results?

In physics, chemistry, and engineering, scientists can very often say in advance what should happen, and can test the prediction.  In evolutionary biology, who can say that an insectivore was likely to evolve into a bat, or into a primate, or that a primate was likely to evolve into man, or that flowering plants were likely to come into existence exactly when they did?  Most of the explanations are retrospective, like the analysis of historical events, and more than one analysis is always possible.  Thus, Shapiro’s causal explanation differs from Margulis’s, which differs from Coyne’s, which differs from Dawkins’s, which differs from Prothero’s, which differs from Gould’s, etc.  If we put those thinkers back on the planet when the only mammals were small shrewlike creatures, what do you think their track record would be a predicting where evolution would go next?  Would any of them even come close?

If I asked a dozen organic chemists what would be the likely properties of a new compound made by breaking certain double bonds and substituting certain groups at those locations, there would be, in most cases, a near-consensus on what to expect.  There is no equivalent to this in evolutionary theory.  This is what Berlinski is talking about—the relative immaturity of evolutionary theory, in both predictive power and explanatory power, in comparison with the experimental sciences.  If he sometimes overstates that—he is given to rhetorical flourish—you have to look past the rhetoric to see his main point, which strikes me as sound.

Lou Jost - #77878

March 26th 2013

Eddie, I stand corrected on the degrees that Ruse and Scott held. But as you know, they speak and write often on the evidence for evolution and common descent, including genetic evidence. Berlinski knows this evidence exists. Did you see the YouTube videos I linked to? His statements in the segments I mentioned are not just mild exaggerations. Please listen to them. 7:41 is a good place to start in the second video.  (I hope you do not agree with his claim in the video that all academics are akin to a “criminal class” and will believe anything, and once they believe something, they engage in a conspiracy to maintain it.)

I and every other biologist agree completely with you (and GJDS) that evolution is not predictable in the same way that quantum mechanics or chemistry is. Certainly the world is far too complicated for us to be able to predict exact evolutionary trajectories. That does not mean the theory is without evidence or explanatory power. The idea of common descent has immense explanatory power. And evolutionary biology is able to make solid, widely-agreed-upon predictions. We even can make some general predictions about when to expect altruism and when to expect selfishness.

Not everything he says is without merit. Some biologists are indeed too quick to make grand claims, and to commit philosophical blunders, and to engage in circular reasoning. We are, after all, human and fallible. But the evidence for common descent is sound (as you know), and his rhetorical flourishes to the contrary seem like deliberate attempts to mislead.

Eddie - #77886

March 27th 2013


Yes, I have listened to that entire debate on YouTube before.  I would recommend you to the part where Eugenie Scott, NCSE champion of Darwinian theory, refuses to give even a ballpark figure regarding the number of morphological changes that would be needed for the artiodactyl to cetacean transformation.  And when Ken Miller takes up the point—in the first segment I hit when I clicked on your link, he changes Berlinski’s question from morphological changes to genetic changes, and we never hear his estimate for the morphological changes.  

As Berlinski makes clear to Miller, his position is not against common descent.  He’s agnostic on the question.  Still, there is no doubt that Berlinski enjoys playing the devil’s advocate.  He is trying to show that even common descent—which Behe and Sternberg and many other ID supporters accept—has some difficulties, if one really wants to get sticky about details.  He is probing to find out how deeply Miller and others have really worked out their arguments.  And if they haven’t even considered the question how many morphological changes are probably needed for the land-sea transition, it is likely that they haven’t studied that transition in any great detail, and are accepting on faith (i.e., on the assurance of the experts in evolutionary biology, since neither Miller nor Scott is in the field of evolutionary biology) that it even happened.

But suppose you got Berlinski inebriated in a pub one night, and suppose you induced him to admit that he believed that common descent is real.  He would still make exactly the same kind of Socratic-skeptical argument against, not “evolution” in the sense of common descent, but the alleged neo-Darwinian mechanism.  His point is that evolutionary science contains a good deal of speculation, guesswork, etc., and that even if common descent is granted, the mechanisms are far from clear; and as long as they are far from clear, no one can say, on the authority of “science,” that the process took place wholly naturally, without guidance of any kind.  Yet the authority of “science” has been invoked for nearly a century now—go back and read Bertrand Russell’s famous oration A Free Man’s Worship —to tell us that we originated in a purely natural process that had no aim or purpose, and are therefore a cosmic accident.  This theme can be found throughout science fiction literature, and the popular science literature I read as a child and teenager was steeped in this view.  Berlinski questions the linkage of this world-view with solid science.

The broader philosophical issue, in the final analysis, is not whether or not common descent is real, but what it means; and there is no doubt at all what Dennett, Hitchens, Coyne, Shermer, Myers, the bloggers at Panda’s Thumb, the bloggers at the Skeptical Zone, Eugenie Scott, Barbara Forrest, etc., think it means.  The transition from science to a reductionist, materialist scientism is the most natural thing in the world for these people.  Berlinski’s book, The Devil’s Delusion, is good at puncturing this know-it-all scientism.  And it should be more trustworthy for you than similar books by Christians such as Giberson, Hutchinson, etc., because Berlinski describes himself as a secular Jew who cannot pray.  He can’t be accused of doubting scientism, or Darwinian mechanisms, or common descent, based on any religious commitments.  (Note that one of his critics in The Deniable Darwin accused him of being a Christian creationist—to which he gave a delightfully witty reply.)

Lou Jost - #77887

March 27th 2013

Thanks for the elaborate reply. I have to ask whether you looked at the other videos I linked to, especially the second one. He is not making an honest critique. It is designed to mislead. The evidence for common descent is not like a mathematical proof, nor is it the kind of evidence common in physics. Nobody ever said it was. But the evidence is powerful and detailed. He sneeringly pretends there is none.  

I agree that Miller shifted the goalposts on that question, but the question itself (how many morphological changes would be needed for the transition to cetaceans) is laughably mal-formed coming from a mathematician/philosopher/raconteur. Many morphological characters are continuous variables, and it makes no sense to ask how many steps are needed to get from one form to another. A natural way to fix Berlinski’s senseless question is to translate it into the discrete space of genes. That, at least, is an answerable question in principle.

As you probably know, I do think the reductionist worldview is correct. It is not something I regard as proven (and most of the people you mention above would say the same); rather, the evidence points that way. The world looks just like it should if the reductionist view were right. Berlinski’s complaint that we don’t have absolute proof of evolution, or of materialism, is just not relevant or interesting. We don’t have absolute proof of anything outside of math and our own existence.

It seems pretty clear to me what evolution means, absent any good evidence of design. We really are the products of natural forces and an integral part of the web of life. I think many theists feel this view is so horrible that they prefer to depart from the evidence and stick to the belief that gods (Allah, Jesus, Ganesh, or whoever) are running the show behind the scenes. But I don’t see  that life is worse without gods. Sure, it is comforting to imagine an afterlife, or a caring god watching out for us. I used to believe in those things. Now that I recognize these beliefs as illusions, this life is actually far more interesting than it used to be.

How would your own position stand up to Berlinski-like criticism?

Eddie - #77902

March 27th 2013


No one who cannot first list the morphological differences between a cetacean and an artiodactyl—this is basic anatomy—has any business writing about whale evolution at all.  And the next question, after listing all the differences, is to ask:  Do we know in anything like thorough detail which genes are responsible for which features in each creature? [answer: no, we don’t have anywhere near such an exhaustive knowledge of genes and traits, especially since the old “one gene, one trait” model has been shown to be far too simplistic]; and do we know that no extra-genomic factors are involved in generating features? [answer:  no, we don’t know that, and increasingly it looks as if extra-genomic factors play important roles—roles which incidentally never seem to get mentioned on BioLogos].  Until we know such things, how can we say with certainty what it would take to make a whale, and how long it would take?

But Scott couldn’t care less about any of that.  She is too busy playing culture politics to actually read any current evolutionary theory.  She just takes it on faith that neo-Darwinian population genetics explains everything, and then goes around bullying school boards and threatening them with lawsuits if they allow teachers to mention scientists who don’t agree with her.  Berlinski is trying to show that she is bluffing, relying on hearsay and the authority of other scientists—that she can’t, standing on a stage, make any detailed argument in evolutionary theory herself.  And he’s right.  She can’t.  Nor can Miller. 

On your next point, I don’t think the evidence points toward a reductionist view.  Rather, I think that the evidence is routinely interpreted through the lenses of a reductionist view.  The philosophical position (albeit implicit more often than not) controls the interpretation of the data.  The fact that many very competent scientists (including Kepler, Newton, Clerk Maxwell, Damadian, etc.) have not been and are not reductionists show that it is not merely a question of evidence.  There are intangibles operating, personal attitudes.  And scientists, by their training—which I know a good deal about, at least in the sense that I know what they are not trained to think about—are ill-equipped to spot their own tacit metaphysical and epistemological presuppositions, the ones which operate without their knowing it.  That’s why philosophers are needed in these debates, to bring out into the open the presuppositions that people on all sides are making.    

I find Berlinski no threat to my position at all.  My own position is not much different from Berlinski’s.  I have a religious attachment that he doesn’t, but I claim no “objective” epistemological status for that attachment.  I deny that any religious tradition can be “proved” by means that would satisfy a typical historian or scientist.  What I like about Berlinski is that he shows that the world view of Dawkins etc. is every bit as unprovable as the world view of Christianity or other religions.  

That’s all I have time for now.  Talk to you in a few weeks.

Lou Jost - #77909

March 28th 2013

Your position: “I deny that any religious tradition can be “proved” by means that would satisfy a typical historian or scientist.”

I appreciate the honesty of that. In fact, the continuous splintering of religious traditions and the fact that a person’s religion is almost entirely predictable by the accidents of his place of birth and the religion of his parents, suggests that the evidence for any given tradition is very weak indeed, and rarely enough to convince a member of another tradition. In fact, the evolution of religious diversity over recorded history looks remarkably like genetic drift, with a given religion playing the role of a neutral allele (an allele that doesn’t do anything).

Contrast that fragmentation and chaos with the way science has progressed. Within 50 years of Darwin’s theory, nearly every person who worked with biological data was convinced of the basic truth of his theory. People from every culture and every background, as long as they were familiar with the biological evidence, were almost always convinced by it.

The theory of evolution, in its basic outline (common descent, with natural selection and random drift as the mechanism for adaptation) is not logically proven, granted; no scientist would say otherwise, because no empirical law can be logically proven. But that does not mean your theistic beliefs are on the same footing as the belief in evolution. The evidence for the basic processes of evolution is quantitative, makes strong predictions, and is convincing at the standard required by historians, courts of law, and empirical science. There is no symmetry between the epistemiological status of a well-supported scientific theory and a belief in a particular god. 

I’ll add that your claim of extra-genomic action in evolution cannot be disproven if that action is sufficiently weak and sufficently rare. A case could perhaps be made for it, if someone could show that current mechanisms were insufficient, or if positive evidence were produced. At present, though, there is no good evidence for it. If someone finds such evidence, and if it resisted conventional explanation, then scientists would eventually take it seriously. As we have discussed earlier, Behe’s and Sternberg’s evidential claims have serious flaws. I think you would surely agree that science should not invoke such mechanisms unless there is good evidence for them.

Jon Garvey - #77914

March 28th 2013

Just passing through on this thread - but it’s worth mentioning that 50 years after Darwin (and on from then until the 1930s) biologists were very far from convinced of his theory - quite the reverse had happened: see here.

Around the turn of the century, in particular, there seems to have been a resurgence of agnosticism even about evolution genberally - at least in my 120 volume Cambridge Zoology from that period “evolution” occurs only once in the indexes.

Darwin was in fact saved by Gregor Mendel and the reserach project of the Augustinian Friars!

Jon Garvey - #77915

March 28th 2013

Erratum - even the Cambridge Zoology isn’t that big - read 10 volumes!

Eddie - #77921

March 28th 2013

Jon, Lou:

Jon is quite right about the history.  “Evolution” was broadly accepted after Darwin, but Darwin’s particular account of evolution, heavily weighted toward natural selection, was not uniformly accepted, and was criticized by many scientists.  It was the combination of Darwin with Mendel, and the mathematical work of Fisher, etc., which allowed the Darwinian view to conquer.  And eventually the work of Fisher etc. was solidified in the “Modern Synthesis” of the 1930s and 1940s.  It is the Modern Synthesis, with appropriate expansions—working out the genetic code in the 1950s and early 1960s, etc.—which dominated evolutionary theory for the rest of the 20th century.

But now major elements of that synthesis are coming under scrutiny from the theoretically advanced, even though the old guard—Dawkins on the atheist side, and Ken Miller and most of the TEs on the Christian side—still believes that the math of population genetics with a suitable emphasis on natural selection is all you need.  But Dawkins, Miller, Scott, etc. are very probably going to be left behind as theory advances.  All one has to do is read Shapiro’s new book Evolution to how theoretically crude, and empirically out of date, are the accounts of evolution offered both by Dawkins and here on BioLogos.  

Lou Jost - #77932

March 28th 2013

I am unsure why religious people in particular are so excited by Shapiro’s book. It mostly discusses new sources of genetic variation. These only serve to make  naturalistic evolution even easier than we had previously thought. More variation means faster evolution. And as far as I can recall, Shapiro’s book does not really offer any other explanation for adaptation, apart from natural selection. Eddie, perhaps you can explain here if you think otherwise. Neither Dawkins nor the BioLogos people have any problem with accepting  new sources of variation, rearrangement, etc, and these still follow the equations of population genetics.

One thing that does shake things up a bit is methylation and epigenetics generally. This capability is itself under genetic control, though.

Lou Jost - #77952

March 29th 2013

Maybe the reason you think Shapiro is a game-changer is the hints of teleology in his work?

Eddie - #77971

March 29th 2013


The person who called Shapiro’s book a “game-changer” was no less than Carl Woese, discoverer of the Archaea!  

If by teleology you mean a sort of updated Lamarckian teleology, a “local teleology” which allows organisms to alter themselves—literally reorganize their genomes, in response to challenges—then yes; two-way causality between organism and genome was denied from the start within the classical Modern Synthesis, and that is what is daring in Shapiro’s view.  But teleology regarding the evolutionary process as a whole—I don’t think Shapiro has expressed any view on that idea.  He shies away from grand speculations.  However, if you want to look at someone with such a view, read Michael Denton, Nature’s Destiny.  

Lou Jost - #78184

April 4th 2013

Oops, didn’t see this until today.

You wrote “two-way causality between organism and genome was denied from the start within the classical Modern Synthesis”

Depending on what you mean exactly, I don’t think that is true. The modern synthesis has long incorporated the ability of organisms to influence their genes. For example, we have known for decades that mutation rates are under the organism’s control; some genes are allowed to have high mutation rates per base, and others are made to have very low mutation rates. It is quite possible that these mutation rates, or the rates at which chromosomes are rearranged, or the rate at which DNA segments are inserted or deleted,  might vary depending on the stress an organism experiences. The immune system story told recently here at BioLogos is also well known. These sorts of things   are very interesting and exciting, but they do not upset the Modern Synthesis at all. It is all grist for the mill of natural selection and drift.

You may be thinking of Shapiro’s claim that natural genetic engineering refutes Crick’s “Central Dogma”. Most molecular biologists think he is misinterpreting Crick’s principle because proteins are not regenerating DNA sequences. It seems clear that many of Shapiro’s alleged examples (eg many items in his Table I-1) do show he misinterpretats the principle. But there may be some genuine cases in that table as well. I’ll have to reread Shapiro and his critics before I can say more about this. Molecular biologist Laurence Moran at his blog Sandwalk has been particularly harsh on Shapiro and others over claims to have overthrown the Central Dogma. But there is also a growing feeling that the Central Dogma isn’t really so central anyway (implying that there is growing evidence that it is not always true).

Eddie - #78187

April 4th 2013


The “Modern Synthesis” originally referred to the harmonization of Mendelian genetics with Darwinian selection arrived at during the period roughly 1937 to 1947.  Its main leaders were Mayr, Dobzhansky, Gaylord Simpson, and Julian Huxley.  Huxley even wrote a book with the words “Modern Synthesis” in its title.  “The Modern Synthesis” is also known as “neo-Darwinism”—an inaccurate title because “neo-Darwinism” had already been used for the views of Weissmann etc. in the late 19th century.  Still, that older neo-Darwinism has largely been forgotten, and the term “neo-Darwinism” is largely the same in meaning as “Modern Synthesis of the 1930s and 1940s”.

Neo-Darwinism (Modern Synthesis) was at least a clear hypothesis.  Variation, plus random mutations for the bigger changes, plus natural selection, did everything.  Gradualism was mandatory.  Large leaps were heresy (“hopeful monsters”).  “Drift” wasn’t talked about back in those days.  Evolution basically had to proceed by the clumsiest of blind searches, hoping that the odd lucky combination would be useful.  It is this version of neo-Darwinism/Modern Synthesis that ID people have steadily—and rightly—criticized.

You might think that DNA in 1953 and the triplet codons in the early 1960s would have changed things.  No, they did not.  For the notion was still one of crude blind search, only now it was a blind search through protein space rather than for “traits” such as longer necks or sharper claws or incipient wings.   And the model was so questionable that in 1966 a major conference was held at the Wistar Institute where professors of physics and engineering from prestigious places like MIT and Los Alamos—non-religious people with mathematical training ranking up with yours—called the biologists to task, criticizing, not “evolution” but specifically “the neo-Darwinian model of evolution.”  They thought the math sucked.  You should read the proceedings sometime. They are quite interesting, including the bristling defensiveness of the Darwinians, e.g., Waddington and Mayr.  



Eddie - #78189

April 4th 2013

(continuing from 78187):

You are using “modern synthesis” to mean something much less narrow, much more inclusive.  For you, it means not “neo-Darwinism” but “the whole hodgepodge of suggested evolutionary mechanisms floating around in the literature these days.”  A little bit of random mutation, a little bit of horizontal gene transfer, a little bit of drift, a little bit of endosymbiosis, a little bit of self-organization, a little bit of natural selection—basically a little bit of anything, as long as it’s not design.  But in fact such a hodgepodge is much sloppier, much less testable, as theory, than the classical neo-Darwinism was.

But the real problem with the hodgepodge  is that evolutionary biologists simply don’t agree on which of these mechanisms are major and which are minor.  Some think that selection is greatly overemphasized; some think that it is underemphasized; many think that drift is overemphasized, many that it’s underemphasized; many think that horizontal gene transfer is a major cause of evolution; many think it’s a minor factor; many think that endosymbiosis is central to evolution; many think it’s an exceptional event, etc.  The evo-devo people think that developmental considerations are much more important than has generally been allowed.  There is dispute over just how “random” mutations are, in terms of their spread across the genome, etc.  There is disagreement over the rate of mutations, the rate of evolutionary change, the reliability of molecular clocks, etc.  There is disagreement over the very fundamental question of whether macroevolution is just microevolution writ large, or whether there are some special mechanisms—beyond variation and mutations and drift—involved in major structural changes.  The idea that there is one common “modern” view of how evolution works, that all evolutionary biologists agree on, is just false.

In fact, when they are talking only to each other, and not to Christians or the press, the disagreements are often quite sharp, and major; but when IDers or creationists are listening in, evolutionary biologists put on a fake show of unity, because they don’t want to give comfort to the creationists.  (There is an interesting documentation of this in an email exchange between evolutionists in the Altenberg 16 book, and I’ve heard Eugenie Scott admit as much.)  Much of the vaunted unity of evolutionary theory is a political construct.  

I don’t think that this sharp disagreement is a bad thing.  It means that evolutionary theory is in ferment, in a period of rapid change.  As it should be, because biology itself is in a period of rapid change.  

Do you have any evidence that Moran is competent to criticize Shapiro?  (Other than that you agree with Moran?)  Sandwalk is not a refereed publication; it’s Moran’s personal blog.  I’m told by a biology Ph.D. who monitors these things that Moran has not published any peer-reviewed articles in ten years.  Do you know if that’s true?  (I looked on his web site, where presumably he would present a fully loaded c.v., and the only things he listed from the past 10 years were popular articles on ID etc. and raw research data self-published on his university web site.  Not a name of an evolutionary biology journal in sight.  Meanwhile, in that time, Shapiro has many books and articles.)

And by the way, where did you get “most molecular biologists”?  Have you surveyed all the molecular biologists in the world, and asked them specifically about Shapiro?  Don’t fake statistics, please.  If you don’t know for sure it’s “most,” say “many,” or even (since I bet you haven’t read more than a dozen reviews of Shapiro by molecular biologists) simply “some”.

Lou Jost - #78207

April 5th 2013

“But the real problem with the hodgepodge  is that evolutionary biologists simply don’t agree on which of these mechanisms are major and which are minor. ” As you yourself note later in your comment, this is not a problem but a sign of health. With you, biologists are damned if they claim to be sure of something, and also damned if they are uncertain of something.

You claim we paint a false picture of unity in front of the public, but at the level that the public cares about, there is little or no disagreement among biologists that evolution happens, and that it happens by undirected natural selection and drift acting on blind (in the sense I explained) variation. We still have much to learn about the details, as you said. We also now have enormous amounts of new information (complete genomes of many species, and even some genomes from fossils), so we are actually now able to answer some of those questions. It is a very exciting time.

Regarding Moran, here you go again about credentials rather than quality of argument. Moran did write a textbook on biochemistry that has gone through five editions, so he may know something about the field. He can point to places in textbook editions of ten, twenty years ago where he talked about some of the things Shapiro claims are new revolutionary insights. Moran’s explanation of Crick’s Central Dogma seems correct, and is backed up by  reading Crick and others, and supported by most of his commenters (which include at least one well known geneticist). Checking that concept against what Shapiro says in his book, it does look like Shapiro is misunderstanding the point. Most of his examples allegedly refutung the Central Dogma do not do so. One or two of his examples might, however.

Regarding my statement about “most” molecular biologists, I don’t have a census, it is just my subjective assessment based on reading, correspondence and conversations with other scientists. I could be wrong there.

I have to go; will respond tonight toyour following comments.

Eddie - #78212

April 5th 2013


So Moran wrote a textbook on biochemistry.  That makes him an expert on evolutionary mechanisms?  How so?  Further, your own side doesn’t allow the connection.  Many times they’ve said the Behe may be a competent biochemist, but he’s out of his depth when it comes to evolutionary theory.  They say he has published only popular books, not peer-reviewed articles in the field.  Well, if that’s the standard, it’s fair for me to ask where Moran’s peer-reviewed articles on evolutionary theory are.  

Remember, I did not take the offensive here; I did not start out by saying that Moran was incompetent in evolutionary theory.  But you implied that he was competent when you cited his blog comments as an adequate refutation of someone (Shapiro) whose entire biological work for the past 20 years has been in evolutionary theory.  So I’m asking you how you know Moran is competent to criticize Shapiro in a field where Shapiro appears to have outpublished Moran by large percentage.  

Frankly, I’m offended that virtually this whole culture-war combat is taking place on popular sites on the internet, and not in scientific journals and at scientific conferences.  If Shapiro’s ideas are quack ideas, as in “Chariots of the Gods,” a full-time, highly-paid researcher like Moran shouldn’t be replying to him at all; and if they are serious biological ideas, but wrong, then they need to be refuted in proper academic venues.  What Moran does is refute them on his private blog, most of whose readers are laymen not qualified to weigh and balance Moran against Shapiro.  And most of them won’t have read Shapiro at all.  But they’ll take Larry’s side because they are against anyone who’s against the standard account of evolution.  This is what’s wrong with these battles—(1) ad hoc arguments made sloppily on web sites as profs take an intellectual holiday from disciplined argument, and (2) professors trying to cultivate followings of groupies on their web sites.  This isn’t how serious science or scholarship should be conducted.

On Crick, I’ve seen many statements of his view that match Shapiro’s, so I deny that Shapiro has misunderstood the point.  Or, if Crick himself later became slightly more nuanced, his earlier, more simplistic conception has been repeated many times by champions of Darwinism, so Shapiro has a right to rebut that view, even if Crick no longer holds it.

Finally, you wrote:

“there is little or no disagreement among biologists ... that it happens by undirected natural selection and drift acting on blind (in the sense I explained) variation.”

Margulis strongly disagreed.  I’ve seen her state that disagreement in more than one place.  And she made a major contribution to evolutionary biology regarding the mitochondrion, so she’s no idiot.  Stuart Newman characterized the views of many of the spokespersons for evolution (and context indicates he had in mind Miller, Scott, etc.) as “old-fashioned” regarding evolutionary mechanisms.  And when Shapiro writes about the self-engineering of genomes, he’s not talking about just one more itty-bitty mechanism to be added to the others; he means that the self-engineering business is a major part of evolution and that traditional mechanisms play a much lesser role than they are said to play.  

I sense we are not going to agree.  Shapiro claims to be challenging the status quo.  You are trying to make out that his work is not really a challenge but just a minor modification.  He doesn’t see it that way.  If you simply said his views were wrong, that evolution doesn’t occur the way he thinks it does, but in the more conventional ways, I could endure that, but you seem to be saying that he doesn’t comprehend the significance of his own work.  I find it unlikely that he would hold a chair in Molecular Biology at one of the world’s greatest universities and not know what his own thesis is.  And when I see the hundreds of references in his book to the current and past evolutionary literature, I find it hard to believe that he doesn’t know what other evolutionary theorists are saying.


Lou Jost - #78215

April 5th 2013

I wish you would stick to substance, but I’ll have to correct some mistakes of yours about qualifications.

You wrote “So Moran wrote a textbook on biochemistry.  That makes him an expert on evolutionary mechanisms?” I In fact Shapiro is also in the Dept of Biochemistry and Molecular Genetics, not in the Dept of Ecology and Evolution. I told you Moran discussed many of Shapiro’s exaamples ten or more years ago in past editions of his textbook; Moran and Shapiro are in the same branch of biology.

You make up a bunch of silly reasons to dismiss Moran’s point about Shapiro misinterpreting Crick’s Central Dogma, and then when you finally stop discussing qualifications and get to the actual point of disagreement, you finally admit that Moran was actually right (but you still defend Shapiro): “On Crick, I’ve seen many statements of his view that match Shapiro’s, so I deny that Shapiro has misunderstood the point.  Or, if Crick himself later became slightly more nuanced, his earlier, more simplistic conception has been repeated many times by champions of Darwinism, so Shapiro has a right to rebut that view, even if Crick no longer holds it.” In other words, because others misunderstood Crick, Shapiro can too. And it is fine if Shapiro ignores Crick’s clarifications (made long before the publication of Shapiro’s book).

It is ironic that you fault Moran for responding to Shapiro on the internet instead of in the scientific literature. Shapiro’s articles lately have been appearing in the online Huffington Post rather than in scientific journals. He has not written many articles recently for peer-reviewed scientific journals.

You  seem to think that scientists never exaggerate the importance of their own work. In fact exaggeration is common.

Lastly this: “You are trying to make out that his work is not really a challenge but just a minor modification.  He doesn’t see it that way”  His book is an exhilerating compedium of exotic sources of genetic variation, some of which depend strongly on environmental triggers. It is also clear from his book that exciting times lay ahead. However, the book’s consequences for evolutionary theory are not as revolutionary as you think.  I’ll respond to your 78194 below later, continuing that theme.


Eddie - #78238

April 6th 2013


I agree that Shapiro is blogging now, too, and I don’t approve of it, any more than I approve of Moran, Shallit, Myers, Coyne etc. doing so.  So let’s say they’re all guilty of that, and leave that aside.  Now, over the past 15 years, how many books and a peer-reviewed articles pertaining primarily to evolutionary mechanisms have been published by Moran, and how many by Shapiro?  I don’t know the answer to this; I know only that Shapiro has published several articles in the trade journals, and at least one serious theoretical book (called by the great Carl Woese a “game-changer”), and that I can’t find a single clear example of such publications on Moran’s c.v. on his site.

I’m not concerned with what department Moran or Shapiro is in.  I’m concerned with what peer-reviewed research on evolutionary mechanisms they have published.  Generally speaking, in all branches of academia, one is regarded as an expert in a field, not because of what department one’s office can be found in, and not because one thinks one knows a lot about the field, but because others have certified one’s expertise, by publishing his articles and books and awarding him research grants etc. in the field in question.  Now it’s obvious to me that Moran is very interested in evolution, and thinks he knows a lot about evolution, because he blogs about it all the time, argues about it all the time, antagonizes people about it all the time (calling them IDiots, etc.), and talks in the tone of Moses bringing the Law down from the mountain, as if when Moran speaks about evolutionary theory, the world had better listen.

I find all of this odd if he has not published anything in the field in 10 or 15 years.  And I don’t know how to exhaustively search the scientific literature.  You might.  So if you care to do a count of Moran vs. Shapiro—peer-reviewed articles and theoretical books about evolutionary mechanisms (not about molecular biology in general, or genetics in general, etc.) —and come up with some numbers, I’ll be grateful to you for your effort.

I don’t know whether the long-term consequence of Shapiro’s book will be revolutionary or not.  I do know what he says his thesis is, and I do know what he identifies in his thesis as differing from the views of many other evolutionary biologists.  And I do know that of the ideas he lays most stress upon in his book, not one of them has ever been discussed on this site, which purports to unite modern evolutionary thought with Christian faith.  And while the genomic and fossil data discussed here may be recent, the theoretical perspective of the columnists reminds me of Mayr, Ayala, etc. ca. 1975.  That’s preposterous, given the mission of this site.  It would be like trying to prove that Christianity fits with modern physics because it fits with Newton.  Evolutionary theory has been getting more and more complex and diverse in recent years.  You need a scorecard to follow what’s happening.  And you can’t find such a scorecard here.

melanogaster - #78263

April 7th 2013

“I find all of this odd if he has not published anything in the field in 10 or 15 years.”

But you’re afraid to look. And it’s irrelevant, as you’d have to do the same thing in thousands of other cases for your comparison to have any meaning., which it still wouldn’t.

“And I don’t know how to exhaustively search the scientific literature.”


How can you not figure it out on your own? I’m a biologist, and I have no problems exhaustively searching the philosophical literature.

You claim to be an academic, Eddie. You have no excuse.

“So if you care to do a count of Moran vs. Shapiro—peer-reviewed articles and theoretical books about evolutionary mechanisms (not about molecular biology in general, or genetics in general, etc.) —and come up with some numbers, I’ll be grateful to you for your effort.”

It’s irrelevant, Eddie. This is not Moran vs. Shapiro, it’s Shapiro vs. almost everyone in the field of evolutionary biology. Shapiro has quit doing science and has been peddling what is nothing more than a relabelling since 1999. It hasn’t gone anywhere. It hasn’t prompted Shapiro to test his own hypothesis empirically. It hasn’t inspired anyone else to, either.

How about you? It looks like your academic career in philosophy is dead in the water, particularly given your poor search skills. Why don’t you apply to grad school so that you could work with Behe or Shapiro?

Eddie - #78264

April 7th 2013


For someone who claims such great search skills, it’s odd that you seem unaware of Shapiro’s many publication since 1999.  At least, your sweeping dismissal does not make show any acquaintance with the contents of any of his publications since that date.  

As for your disdainful remark about “relabelling,” don’t you find it the slightest bit interesting that Carl Woese, discoverer of the Archaea, called Shapiro’s book not “relabelling” but “a game-changer”?  Do you think you have better judgment in these matters than Woese?

I assume, in the absence of evidence to the contrary, that you have no special qualifications to talk about evolutionary theory at the level at which Shapiro operates.  But you are free to present such evidence, e.g., a list of your publications, or the title of your doctoral dissertation on evolutionary theory.  Or you could show your competence by example, by going over Shapiro’s arguments in detail, and showing why they are invalid.  

Have you ever noticed that you speak in cliches?  For a long time it was “This isn’t a high school debate.”  Then it was “Why are you violating the Nth commandment?”  Lately it has been “X [fill in Behe, Meyer, Shapiro, etc., according to polemical need] has quit doing science.”  Whatever your academic training is in, it certainly wasn’t one that included instruction in fresh, engaging modes of argument.  

melanogaster - #78296

April 8th 2013

“For someone who claims such great search skills, it’s odd that you seem unaware of Shapiro’s many publication since 1999.”

I think I described them accurately. If you disagree, simply point out whether there’s anything empirical in them at all and what differentiates each one from the others and from his book. You won’t.

“At least, your sweeping dismissal does not make show any acquaintance with the contents of any of his publications since that date.”

The ball’s in your court.

“As for your disdainful remark about “relabelling,” don’t you find it the slightest bit interesting that Carl Woese, discoverer of the Archaea, called Shapiro’s book not “relabelling” but “a game-changer”?”

It’s about as interesting as Nobel Laureate Linus Pauling’s ideas about vitamin C. Or NAS member Peter Duesberg’s ideas about HIV and AIDS. Let me know when Shapiro inspires himself or you to do something empirical. He’s a better indicator than anyone else.

“Do you think you have better judgment in these matters than Woese?”

Definitely, as Woese is dead.

I have better judgment in these matters than any dead person. But science is only about hearsay in your fevered mind. Have Shapiro’s repetitive papers and books inspired anyone to test his hypothesis? Does he even have a testable hypothesis?

Isn’t observing the actual game a better indication than what someone says about the game, Eddie? If you think this demolishes neo-Darwinian theory, why did Sidney Altman say, “Shapiro has written a stimulating, innovative manuscript that surely Darwin would have liked”?

And if it’s a game changer, why doesn’t it change your mind—or anyone else’s—about getting in the game?

Eddie - #78302

April 8th 2013


If you want to know whether Shapiro has a testable hypothesis, you have to read his book.   You haven’t read Shapiro’s book.  I have.  Once you’ve read it, and realized that most of what you are saying about his work is entirely untrue, come back to me your apology for bluffing and mischaracterizing.  And send an apology to Shapiro for mischaracterizing him in public.

Your excuse for your dismissal of the judgment of Woese is just pathetic.  You have such a massive ego, apparently, that you think you know more than world-class biologists of undisputed accomplishments.  I wonder what achievements of your own could justify such a high self-estimation?  Care to share them with us?

Eddie - #78194

April 5th 2013

(follow-up to 78189):

You say “all grist for the mill of selection and drift”—but in fact neither selection nor drift has ever created any biological novelty.  Drift is about the shuffling around of existing genes, their proportions in the population, not originating new genes; and natural selection creates nothing; it merely vetoes existing possibilities.  The real creative part in evolution has to come from somewhere else.  For the neo-Darwinians, it was “random mutation”—a testable hypothesis, in principle, but one which even evolutionary biologists seem to be moving away from (for good reason, because, as ID people have pointed out, it’s an incredibly poor way of searching).  So now we are looking at evo-devo, self-organization, endosymbiosis, horizontal gene transfer, self-engineering of the genome—things that have the potential to generate striking change faster.  These have to be the real engines of evolution, for modern materialists.

You mentioned BioLogos discussions, as if to suggest that they acknowledged up-to-date evolutionary conceptions.  Applegate has not, to my knowledge, argued that stresses on the immune system cause organisms to literally reengineer their own genomes.  And Dennis, in scores of columns, has never discussed any mechanisms of evolution other than gene-focused ones—basically neo-Darwinism and drift.  Evo-devo isn’t discussed here, nor is self-organization as an evolutionary mechanism (Applegate’s little videos about self-organizing magnetized pieces don’t demonstrate self-organization as a cause of evolution), nor is the genetic self-engineering of organisms discussed here.   I learned about the latter from Shapiro, not from anyone on BioLogos.  And I didn’t even hear the name of Shapiro on BioLogos; I heard about him on an ID site.  I also first heard about self-organizational theory on an ID website.  

This is not a place where cutting-edge theories of evolutionary mechanism are debated and discussed.  It’s a place where a simplified understanding of evolution is offered to conservative fundamentalists by more liberal TEs, in hopes of getting them to join the evolution side.  Frankly, I don’t see why you are so enamored with BioLogos, Lou.  You can get much more technically advanced and up-to-date discussions of evolutionary theory elsewhere, and you reject the fundamental Christian premises of the site.  So why do you find this place so fascinating?  I can’t imagine that your opinion of theistic evolution is any different from that of Coyne, Dawkins, etc.  For you, it must be a hopeless halfway house between clear-headed atheism and muddle-headed revealed religion.  What’s the allure for you?  

Eddie - #77968

March 29th 2013


See my other reply on Shapiro.  My interest in his work has nothing to do with religion.  What catches my attention is that he attacks—by name—Darwinian and neo-Darwinian accounts of evolution.  And he is not the only one.  Lynn Margulis has also criticized Darwinian theory.

ID proponents have argued that ID should not be mandatory in the schools—check out all the official statements of Discovery for at least the past 8 years if you don’t believe me—but that criticisms of Darwinian mechanisms which can be found in peer-reviewed scientific literature should be completely legal to teach in the schools.  That means that Margulis, Shapiro, Newman, etc. should be legal in the schools.  But in every case where school boards or state authorities have adopted policies—even those which specifically forbid teaching ID—that enable school teachers to introduce material criticial of neo-Darwinism, Eugenie Scott and her NCSE have been there with protests and poised to start legal action if the proposed policies are passed.  

Scott’s position is anti-science, because she wants high school biology students taught the neo-Darwinian consensus and she wants the internal debate among evolutionary biologists to be kept behind closed doors, out of the public eye.  She wants students to learn the reasons for the “consensus” but not to learn about those who dissent from the consensus—even when they are religious unbelievers such as Margulis, Shapiro, and Newman.  She wants science taught as received doctrine.  This is Darwinian dogmatism.  And it’s bad science pedagogy.  Bad not only because it falsifies the nature of science as a self-critical enterprise, but bad because it fails to take advantage of the stimulus that controversy arouses in student’s minds.

Students who see that science is a living enterprise, where it is possible to disagree with the majority and still be considered competent, are going to be motivated to scientific careers.  Students who think of science as “stuff the experts have settled, that you just gotta accept” will not want to go into science, because they will see no hope that their ideas, if different, will ever be allowed an audience.  So they will gravitate to English or History or some subject where constructive criticism of established views is valued.

Shapiro’s book makes clear that he believes that organisms have a significant capacity to re-engineer their own genomes—and that is not in line with the “one-way” scheme of thinking of traditional evolutionary theory (the genome changes due to basically random processes, and then the changes just happen to be useful, so selection adopts them).  If Shapiro is right, evolutionary theory will have to undergo not just minor, tinkering modification, but significant modification.  And he’s not the only one who thinks so.  Many of the Altenberg group are saying similar things.  Your last paragraph provides examples of the sort of things that the new breed of evolutionary theorists are talking about.

The presentation of evolutionary theory on BioLogos is very old-school, basically that of about 1975, except in its inclusion of more recent genomic and fossil data (interpreted within the framework of older thinking).  There has never been a discussion of recent evolutionary theory on this website.  That is why the claim of BioLogos to reconcile Christian theology with current evolutionary science is not credible.  

Eddie - #77919

March 28th 2013


I think you’ve misunderstood what I meant by extra-genomic action.  I think you think I was talking about supernatural interventions.  I wasn’t.  I was talking about natural causes beyond genomic changes.  It is now becoming increasingly evident that even in normal inheritance (let alone any evolutionary process) the “genes” are not the sole determinants of the outcomes.  The field of “epigenetics” is becoming more and more important.  The problem with Venama’s account of evolution—and I’ve read virtually every column he’s written here, and all his interactions with critics—is that it is extraordinarily gene-focused, almost to the exclusion of all else.  That is, Dennis defends the form of evolutionary theory known as “the Modern Synthesis” which was worked out, in basic terms, by Mayr, Dobzhansky, Gaylord Simpson and Julian Huxley around 1937-1947 (see Mayr’s account of the history), albeit Dennis supplements the account with what is now known about genome sequencing.  But it’s precisely that form of evolutionary theory which many advanced evolutionary biologists (i.e., people who are, unlike Venema, specialists in the field) are now criticizing—e.g., Stuart Newman and others from the Altenberg group, Shapiro, etc.  

Again and again I have to say that I am not criticizing “evolution”—nor does ID, in principle, reject “evolution.”  I doubt the capacity of the mechanisms you affirm—normal variation, random mutation, selection, and drift—to produce the changes you think they can produce.  Even on a purely naturalistic basis, I think that Dennis’s account of evolution is at best very much oversimplified.

If I thought that Dennis was oversimplifying purely as a concession to the low level of biological knowledge of the fundamentalists he is criticizing, I could let it go.  But in four years on this site Dennis has never once addressed the serious critique of his population-genetics neo-Darwinian model that is going on in the technical discussions of evolutionary biology.  Nor did his fellow-geneticist Darrel Falk ever do so, when he was posting on this site.  Nor has Ard Louis, Kathryn Applegate, etc.  It is as if the BioLogos biologists operate within the science they learned as undergrads, and live completely cut off from evolutionary theory debates as they exist today.  I find this utterly unsatisfactory.  If Christian theology is to be reconciled with evolutionary theory, it must be reconciled with the most advanced and incisive evolutionary theory, not the evolutionary theory of 1945 or 1960 or 1972 or 1990.

Lou Jost - #77933

March 28th 2013

Eddie, I am still trying to understand what your extra-genomic influences are, and why they have theological importance to you.

I also don’t see why you put so much emphasis on distinguishing the sources of variation known to Fisher et al versus the newly discovered sources of variation. These new discoveries leave the central tenets of evolution unaffected.

Eddie - #77966

March 29th 2013


You seem to have trouble retaining what I am saying.  I have repeatedly differentiated between “evolution”—meaning a process by which some living forms change into others—and the mechanisms of evolution, whatever they might be.  I have made no criticism of “evolution” as such.  I have said that I don’t believe it could have happened if the only mechanisms were variation, random mutation, drift, and natural selection.  I think that other things have to be involved, and not just in a small way, but in a big way.  I don’t insist that those other things, whatever they are, have to be supernatural intervention—though they could be.  

I’m surprised you wouldn’t know what I mean by extra-genomic sources of evolution.  Are you unaware that biological development in the embryo is not entirely dependent on genomic information, but depends on contextual information from its surroundings, e.g., the casing in which the embryo is enclosed?  If that is the case for basic developmental processes, why could something analogous not be operating in evolution?

I did not say that the idea of extra-genomic causes of evolution had “theological importance” to me.  Again you are reading creationism into my posts, even though I’ve told you not to.  I’m talking pure science here.  I’m saying that pure, hard-nosed empirical science, without any reference to God or religion, seems to be indicating that our understanding, not just of evolution, but of organisms generally, has been overly “gene-focused” and that this focus leads to a lack of comprehension of how things work.

I don’t know if you have a copy of Shapiro’s book, but if you do, have a look at the section where he offers an extended caution on the use of the term “gene” in biology—its limitations and perils.  The standard evolutionary account—the one I learned in popular science books—the Mayr-Dobzhansky etc. account, and the one that is championed here on BioLogos by Falk and Venema—is extraordinarily gene-focused.  Shapiro is saying that this is a great oversimplification that is materially misleading.

I’m not qualified to say that Shapiro is right and Venema is wrong.  I do know, however, that Shapiro has more qualifications as an evolutionary biologist—both in terms of his formal position at the University of Chicago and in terms of his publications of peer-reviewed articles, and his new book (which Karl Woese, a world-class theorist, calls a “game-changer”), than either you or Venema.  So I think I am quite reasonable in taking Shapiro’s criticisms of neo-Darwinism seriously, and if you choose to dismiss Shapiro’s views as wrong or unimportant, I’m under no obligation to regard your judgment on Shapiro’s book as authoritative.


Eddie - #77922

March 28th 2013


I’ve never insisted on any parallel between “reasons for believing in evolution” and “reasons for believing in a particular religious tradition.”  Mathematics, biology, physics, history, theology, etc.—each of these subjects has its own criteria of relevance and standards of criticism.  I don’t think they should be mixed.

The problem with your scientism is that it applies one model of “correct thinking” to all fields, and thus tends to iron out the complexities of reality.  You are a prisoner of what Theodore Roszak called “single vision.”  You remind me of Charles Darwin, toting up scientifically the pros and cons of getting married versus remaining single.  Or of Ben Franklin, trying to overcome his sins and human flaws through a purely external “method” of self-improvement.  (An early Dale Carnegie!)  You think you see reality more clearly that religious people do, but the clarity you achieve, you achieve at the cost of truncating or crudely oversimplifying whole realms of existence.  What you call the “evidence” you have in fact forced in a Procrustean manner into the only picture of the world that your single vision allows.

I know this because your intellectual methods are exactly the ones I held for the first part of my life.  And I know that I became a much more sane, balanced and wise person when I gave up my scientism.  (Not science, but scientism.)  And it was giving up my scientism that led to my serious consideration of the possibility of the truth of religion, not, as you might suspect,  prior religious commitments that turned me against scientism.  Such prior religious training as I had was far too weak to resist the seductions of scientism and secular humanism.  It was only when I discovered that, even in their own terms, scientism and secular humanism are failures, that I considered the possibility of religious alternatives.

Lou Jost - #77910

March 28th 2013

“No one who cannot first list the morphological differences between a cetacean and an artiodactyl—this is basic anatomy—has any business writing about whale evolution at all. “

I guess you didn’t understand my claim that this question is senseless. Take one example: the last terrestrial common ancestor of whales was small (say 2 meters just to have a number). A modern whale is big (say 20 m). How many steps does it take to go from small to big? That is not a well-formed question, because this is a continuous variable; there are infinity many answers depending on how you define “step”. See Zeno’s Paradox for one consequence of the failure to understand continuity. That is why it was quite sensible for Miller, in that debate, to transform this mathematically incoherent question into a truly answerable question about how many gene differences there are (or better, how many base pair differences there are).

Eddie - #77917

March 28th 2013


I agree with you that the discussion had to get down to gene differences.  That is where Berlinski was headed.  But he was deliberately blocked from getting there.

Please note that size is hardly the main issue.  There are cetaceans (porpoises, etc.) with masses less than that of large artiodactyls (moose, etc.)  The differences are qualitative.  The difference between a hoof and a flipper is not the difference between small and big.  Nor are the differences between nursing one’s young under salt water (marine lactation) and nursing on land.  Nor is turning a pair of nostrils housed in a nose into a single blowhole on the top of the head.  Etc.

What Berlinski wanted Miller and Scott to do is: (1) provide a number such changes that would be necessary (and he didn’t ask for an exact figure, just a “ballpark figure”  —order of magnitude (tens, hundreds, thousands, tens of thousands); (2) say what would need to happen at the molecular/genetic level for each of those changes to happen.  But he was forestalled from getting to the second question because they refused to answer the first question.  And I don’t need to be a biologist to know that one needs to know what the morphological differences are before one can explain the molecular/genetic changes that would be necessary make them come about.

But of course Scott and Miller were trying to block a damaging line of questioning.  Suppose they had answered (thought neither one has the anatomical knowledge specific to whales and artiodactyls to answer it, one being a cell biologist and the other an retired anthropologist), and said:  “There would be 1,229 morphological changes necessary.”  Then Berlinski would have asked them what genetic changes would have been needed to facilitate each of those morphological changes.  And of course, neither one being either an evolutionary biologist or even a geneticist, they wouldn’t have been able to account on the genetic/molecular level for even one of the changes.  So they would hardly be in a position to calculate, based on mutation rates, reproduction rates, etc. whether or not 9 million years was enough time for Darwinian processes to make all the changes necessary for the job.  

And Scott and Miller aren’t unique in this.  99.99% of the people on the face of this planet who accept without qualm that Darwinian processes can manage such changes have never even tried to work out in detail a major transition such as that, getting right down to nitty-gritty, specifying a possible molecular-genetic pathway, how many changes it would require, how islands of fitness would be found along the way, etc.  It’s simply accepted on faith that Darwinian processes can do it.  The only people who even try to work out the details are full-time evolutionary biologists, and not one of them has yet produced a book on whale evolution specifying even a plausible (I don’t require the actual) molecular/genetic pathway from a deerlike animal to a whale.  Yet the public is asked to believe that neo-Darwinian theory is “solid science” and “as certain as the fact of gravity or the existence of atoms” etc.  It is this sort of bluff that Berlinski is trying to expose.

As I’ve said before, I have nothing against evolution per se.  I have no problem believing that it happened, or that God could have used an evolutionary process to create new types of creature.   But I think the neo-Darwinian narrative—the one that you and Venema are trying to sell—is implausible as an explanation for evolution.  And I’m not the only one.  Evolutionary biologists—non-religious evolutionary biologists—including some who are much better known in the field than either yourself or Venema—have questioned the capacity of such mechanisms.  Margulis was one; Shapiro is another.  Newman is another.  

I will not believe the mechanism is adequate, no matter how many equations of population genetics you throw at me, until you provide me with a plausible pathway.  In a long post a few weeks ago I indicated the sort of book that would be necessary to convince me:  molecular/genetic change x (specified) leads to phenotypical expression y (specified) which gives selective advantage z (specified); repeat several hundred times until all the morphological and other systemic changes have been accounted for.  

If you deem my request unreasonable, fine.  I don’t think it’s unreasonable.  I ask for an analogous set of steps for stellar evolution from astrophysicists—how do you get to helium, how do you get to carbon, etc.—and they deliver.  It’s not my fault if the evolutionary biologists can’t deliver.  And I’m glad that people like Berlinski are informing the public that they can’t deliver, or at least, have not yet come anywhere near delivering.  

Lou Jost - #77926

March 28th 2013

My turn to be disappointed. You say “Please note that size is hardly the main issue”. Of course it isn’t, but many of the morphological changes involve sizes of things, or changes in other continuous variables. You know very well that it is meaningless to ask how many steps it took to change the length of an organ or bone from x to y. There is no way Miller or anyone else could have answered that question. And there is no way that an honest mathematician would have asked the question in the first place.

The changes you mention, like the nostrils-to-blowhole transition, are also nearly continuous. The fossil record provides nice snapshots of the transition process, as you know.

I won’t comment on your guesses (presented as fact) about what Berlinski and Miller were thinking during that debate.

You demand a molecule-by-molecule story of the whale transition. That is unreasonable and you know it. How could we ever do that with certainty? Complete information would be nice but is not necessarily needed to draw reliable conclusions.

I am unsure about your position on whale evolution now. I understand that you accept that the whale transition did take place, and that today’s whales are connected by common descent to earlier terrestrial mammals. As far as I understand, you think that this transition happened too fast to be the result of random variation plus natural selection (plus drift), and so you invoke outside interference (gods). But your basis for this seems to be just plain unevidenced incredulity based on your theological preference. The visible steps in the fossil record are beautifully displayed, each fairly small, not tremendously different in scale from the wolf-to-greyhound-or-Chihuahua transition that we discussed earlier, and do not seem to show any miraculous jumps.

If someone wanted to show that the transition was unreasonably fast, they could estimate selection coefficients, population sizes, and other things, and show that the selection coefficients would have to be unreasonably large, or that the required qualitative mutations and genome rearrangements could never arise in a reasonable amount of time (along the lines of Behe’s arguments for malaria). As we discussed earlier, Sternberg’s attempt at this (at least in the form that he described it in his video) failed because it ignored natural selection. Let’s see what his upcoming book says…

Meanwhile you might rethink your incredulity by considering the cabbage, brussel sprout, brocolli, kale, kohlrabi, and cauliflower, all derived from a single species of mustard since humans began cultivating crops. These exhibit not just quantitative but qualitative differences. They arose in the blink of an eye, geologically speaking. Variability plus selection (natural or artificial) can quite clearly work wonders even in this short a time. Do you think gods (or Satan, if you don’t like brussel sprouts) were involved in the evolution of these crops? I think you agree that invocation of miracles or magic should not be ruled out a priori, but should not be used lightly either, especially if your main reason for invoking them is to preserve a certain theological concept that is itself highly subjective.

Lou Jost - #77930

March 28th 2013

Eddie, when I wrote this I did not see your #77919 above (this comment thread is getting pretty convoluted…). In light of that post, I should not have said that you think there were supernatural interventions in the course of whale evolution. I’ll write more after I check out the rest of the new posts above this one., and my apologies to you for missing that post of yours.

Eddie - #77969

March 29th 2013


I’m not going to defend Berlinski’s alleged dishonesty any longer.  If you think he is not an honest mathematician, or an honest biologist, or whatever, you should write to him personally and challenge him.  I believe he is an honest man who is trying to prick the smug confidence of the likes of Scott and Miller.  If you think otherwise, fine; I won’t discuss his motivations further.

Your examples of brussels sprouts, dogs, etc. involve the controlling activity of human agents.

On whale blowholes, etc., you confuse a fossil sequence with molecular/genetic mechanisms.  The fossil sequence, in itself, tells us nothing about the genetic/molecular causes of the transitions that the fossil sequence records.  Your statement that the transition is continuous is thus arbitrary and undocumented.  If you think you have proof that it is continuous at the molecular/genetic level, trot out your proof.  Show me a “continuous” series of mutations, from artiodactyl to whale, that could have done it.  Then collect your Nobel Prize, because no one else has offered to specify a possible sequence of mutations or even provide a ballpark figure of how many were needed.  Even real evolutionary biologists such as Coyne and Orr and Carroll don’t know the answer to such questions, so it’s hardly likely that shallow popularizers like Miller and Scott would.  

My demand for an evolutionary pathway from artiodactyl to whale is not unreasonable.  It would be unreasonable to demand the actual pathway, which is unique and irrecoverable, but a hypothetical pathway—one that could have done it—any evolutionary biologist—at least whose specialty is mammalian evolution—should be able to supply.  They should be able to build a whale from an artiodactyl before my eyes, step by step, the way a good mechanic could turn one kind of machine into another, by substituting and rearranging parts.

But the mechanic can of course do that only because he knows what all the parts can do, and knows how many parts and which parts have to be in the final product, and how many parts and which parts were in the starting product.  He has full understanding of the relevant causality.  The evolutionary biologist doesn’t have anywhere near the mechanic’s understanding of the causality involved.  There are vast amounts we don’t know.  The rise of epigenetics, among other things, is showing us how crude the older model of causation was.

I’m not blaming evolutionary biologists for not knowing all the answers.  What I’m blaming them for is their constant claim that they have proved things they haven’t proved.  And they haven’t proved that variation, random mutations, drift, and natural selection, even in combination, are enough to turn an artiodactyl into a whale in 9 million years.  And I will not believe that those mechanisms could do the job without a hypothetical pathway.  If you think I’m being unreasonable, that’s fine.  That’s my price for belief in your mechanism.  If you won’t offer my price, it’s no sale.

And just to be clear:  if you showed me the bones of Jesus tomorrow, or if you offered me irrefutable documentary proof that every world religion originated with a cabal of priests and leaders who sought to manipulate the masses—I would have exactly the same position I do now regarding your proposed mechanisms of evolution.  Even if I knew for certain that there was no God, I would not believe that the sort of mechanisms you and Venema have proposed could do the job.

But if Shapiro is right—if organisms can re-engineer their own genomes in response to environmental challenges—then it’s a whole new ball game.  Then we are into a sort of updated “Lamarckian” type of evolution, not Darwinian evolution.  And obviously such a form of evolution could work much faster, as it would not have to rely only upon blind searches.  But if that’s the way evolution works, then the patron saints of BioLogos biologists—Mayr and Dobzhansky—were seriously wrong.  It will be interesting to watch evolutionary biology over the next 20 years.  

Lou Jost - #78141

April 3rd 2013

Your reasons for thinking that known mechanisms are insuffient are not at all clear to me. You discard the counter-evidence far too frivolously.

We have seen very rapid evolution before our very eyes in pets and crops, as I mentioned above. These involved major morphological changes, on a par with the changes we see between steps in the fossil record of many lineages. The distinction between natural and artificial selection (which you just toss out as irrelevant) is mostly one of degree. Artificial selection is much stronger. But your argument above seems to focus primarily on the sources of variation; you think they are insufficient. Yet the sources of variation (acting over a very short time) in crops and pets were clearly sufficient to provide the raw material for very dramatic changes using artificial selection. So we don’t need anything more than these kinds of changes to get evolution of dramatic new forms by natural selection. It will just take longer than by artificial selection.

We could now look at the genomes of the crops and pets and compare them to wild ancestors, and we could actually learn in great detail what changes were required. Were they mostly point mutations? Gene transpositions and duplications? These are all well-known mechanisms of neo-Darwinian evolution. I think Dennis will analyze the dog genome in his next post, and you and I will get to learn what the mechanisms of change actually have been.

Eddie - #78146

April 3rd 2013


“Your reasons for thinking that known mechanisms are insuffient are not at all clear to me.”

Precisely if they are sufficient, Dennis Venema and Eugenie Scott and Ken Miller have no excuse whatever not to set forth a hypothetical evolutionary path from the artiodactyl to the whale, using exactly those mechanisms.  You may have noticed than none of them has done so.  And that Coyne, Myers, etc. have not done so—either for the whale or for any other major macroevolutionary transition.

What they have set forth are trivial changes, e.g., a pathway from a green-eyed cockatoo to a blue-eyed one.  And I and Behe and everybody else agrees that Darwinian mechanisms are up to that job.  What we don’t grant, and what you and Dennis seem to uncritically assume, is that macroevolution is simply microevolution scaled up—an assumption which even the atheistic evolutionary biologist Donald Prothero has said is not agreed upon by all evolutionary biologists and should not be accepted on grounds of a priori reasoning.

That’s why I’m demanding a hypothetical pathway, and will not relent in my demand.  Endless arguments from equations and general theory will not budge me.  I want you and Dennis to build the whale from the artiodactyl, as you would turn a Meccano set-truck into a Meccano-set steamship, step by step, in front of my eyes.  If your mechanisms are adequate, you will be able to do it.  If they aren’t, you won’t.  It’s a straightforward challenge.

Lou Jost - #78165

April 4th 2013

As you know, we are very far from knowing what all the genes (and cell components) do, especially the genes of extinct animals.  However, parsimony-based phylogenetic trees do provide step-by-step lists of gene transitions that would be sufficiennt to take us from a common ancestor to a set of current species (the actual path taken would probably have been slightly longer). Analyzing karyotypes gives us additional information about chromosome rearrangements that happened along the way. We can provide a pretty good set of steps for the changes that link man to his nearest common ancestor with the chimp.

Eddie - #78168

April 4th 2013

“As you know, we are very far from knowing what all the genes (and cell components) do, especially the genes of extinct animals.”

Exactly!  Which is why evolutionary theorists should keep their claims modest.  Something along the lines of:  “On general grounds, it seems that whales must have evolved from land mammals, and we have about half a dozen reasonably complete fossils which seem to show a possible line of progression on the morphological side, but given our meager knowledge of the relationship between genetic and epigenetic causes, and given that we don’t have a single shred of DNA from any of the fossil forms, the molecular pathways and associated mechanisms seem murky and require much further research.”

If evolutionary biologists wrote in that fashion—and even more so, if those who write loudly about evolution in the public sphere (science journalists, bloggers, apologists for materialism, etc.) wrote in that fashion—there would be much less “push-back” of an extreme kind from religious and other quarters.  However, many modern scientists and their publicists—Dawkins, Coyne, Myers, Moran, Dennett, Rosenhouse, Shallit, Miller, Harris, Shermer, Scott, Hunt, Mooney, etc.—seem unable to resist the temptation to become media stars, going on lecture tours, participating in popular stage/filmed debates, using university facilities to run opinionated blogs and gather disciples from the vulgar, etc.  If the Darwinian side would stop vulgarizing science by adulterating it with shallow materialist-ideological philosophy, and stop making grandstanding overclaims about what is empirically known, I expect the activities of the fundamentalists and other reactionaries would scale down accordingly.

I would be interested in a reference for the “pretty good set of steps” between the common ancestor and man and chimp.  Not a long string of journal article titles that deal with tiny pieces, but an overview article or book that puts together a whole series of steps, in the Meccano-set way that I have suggested.

Lou Jost - #78170

April 4th 2013

I should add that surely there are unknown mechanisms for heritable variation. The point I make above is not that there are no such mechanisms, but that the known mechanisms seem sufficient. If there are other mechanisms, most would be welcomed into the stable and would not shake up evolutionary theory. An exception would be truly teleological mechanisms: mechanisms that “knew” which variation would be successful (without this being due to past “experience”).  These would really revolutionize evolution. (Shapiro hints that there are such mechanisms.)

Eddie - #78176

April 4th 2013

You’ve nailed down exactly where we disagree:  I don’t accept that what you call “known mechanisms of evolution” are sufficient to accomplish macroevolutionary change in the timeframes given by the fossil record.  In fact, I don’t believe there are any “known mechanisms” of macroevolution at all.  I think there are “known mechanisms” of microevolution, plus an undemonstrated assumption that macroevolution is just microevolution extended over time.  

This assumption—that microevolution just slides naturally into macroevolution—is beloved of geneticists (Darrel Falk and Dennis Venema are geneticists, as were Falk’s spiritual mentors Ayala and Dobzhansky), who tend to see evolution as caused by the straightforward alteration of genomes (subsequently filtered by selection), but has been questioned by some paleontologists (e.g., Prothero) and some molecular biologists (e.g., Shapiro) and others (e.g., some of the Altenberg group, who bring in expertise from fields like physics, self-organization theory, etc.).

I don’t claim to have the biological knowledge to settle such a vast question, but my hunch is that the standard, gene-focused account (including variation, random mutation, and drift, as well as natural selection) is inadequate.  I think the “other mechanisms” of evolution (leaving aside any notion of supernatural intervention) will involve higher levels of organization than the genome, and I think that in retrospect, 50 years from now, the gene-focused evolutionary theory of the 20th century will seem a gross oversimplification of a larger organismal process.  But this is all hunch, for which I claim no proof, authority, etc.

melanogaster - #78262

April 7th 2013

“On whale blowholes, etc., you confuse a fossil sequence with molecular/genetic mechanisms.”

Lou did no such thing. He was quite clear and you didn’t like what he pointed out to you, that the fossil record shows that blowhole position—the phenotype—is a continuous variable. Real scientists are looking for the genetic changes now. Why don’t Behe and you join them?

“The fossil sequence, in itself, tells us nothing about the genetic/molecular causes of the transitions that the fossil sequence records.”

This is crazy. It tells us where to look for the causes, Eddie, when coupled with other fields. You have this weird notion that biologists build walls between fields, when in fact we are building bridges, even outside biology.

But we don’t even need fossils to point us. We can simply do comparative developmental biology to find one of the most important differences:


Here is part of what you are demanding, but I predict you’ll do whatever it takes to avoid discussing it. You might note (but you won’t) that gathering the evidence for just one change represents a major publication, which is another reason why your demand is crazy.

“Your statement that the transition is continuous is thus arbitrary and undocumented.”

It’s documented by the fossil evidence that you fear because you don’t have faith that it will support your wishful thinking.

“My demand for an evolutionary pathway from artiodactyl to whale is not unreasonable.”

It’s silly and you know it.

“It would be unreasonable to demand the actual pathway, which is unique and irrecoverable, but a hypothetical pathway—one that could have done it—any evolutionary biologist—at least whose specialty is mammalian evolution—should be able to supply.”

Your incessant labeling of people has no basis in reality, Eddie. This is a matter that involves multiple fields.

“They should be able to build a whale from an artiodactyl before my eyes, step by step, the way a good mechanic could turn one kind of machine into another, by substituting and rearranging parts.”

No, development doesn’t work like that at all.

You are actually trotting out a prediction of an ID hypothesis, and it’s simply not true. There’s no need to substitute a single part to evolve whales. Read this again—NOT ONE. There’s no need to evolve even one of Behe’s precious binding sites, but immunology tells us that they can be evolved in just two weeks anyway.

Get it, Eddie? Your view of how animals are “built” has zero evidentiary support.

“But the mechanic can of course do that only because he knows what all the parts can do, and knows how many parts and which parts have to be in the final product, and how many parts and which parts were in the starting product.”

How many different “parts” are there between you and a mouse, Eddie? Here’s a chance for you to empirically test a scientific prediction of your hypothesis about how development works. I predict that you’ll run away, hurling insults in your wake.

“He has full understanding of the relevant causality. The evolutionary biologist doesn’t have anywhere near the mechanic’s understanding of the causality involved. There are vast amounts we don’t know.”

True. But Dennis, Lou, and I know vastly more than you do, Eddie. You’re afraid to even look.

Eddie - #78267

April 7th 2013

Fruitfly wrote:

“the fossil record shows that blowhole position—the phenotype—is a continuous variable.”

That’s pompously stated, to give an air of more mathematical exactitude than the few good transitional fossils warrant.

(By the way, since you are expressing such a strong opinion on this matter, tell me—without looking it up:  within one order of magnitude (units, tens, hundreds, etc.), how many good transitional whale fossils have been found?  And tell me the rough positions of the blowhole on them.  And provide your purported correlation of the “movement” of the blowhole with the date of the fossils, if you think they approximate an evolutionary sequence.  If you haven’t examined the fossils yourself, or at least clear photos of them, and if you don’t know even roughly how many there are—one can’t generalize without a certain sample size—you have no business speaking in the assertive, magisterial tone you are employing.)

But back to the pompousness of your usage of “continuous variable.”  The fossil record, presuming that it shows what some have claimed, shows simply that the blowhole position varies from point A through to point B.  Big deal. Now tell me why it varies.  Tell me what genes and what developmental processes etc. determine its location, its size, whether it has two openings or one, etc.  Then we can discuss whether the causes of the change are “continuous.”  

Your last paragraph is puerile.  “I know more than you do, nyah, nyah!”  Takes me back to childhood arguments in the schoolyard.  But on that subject, I certainly acknowledge that Dennis and Lou know quite a bit more than I do about the details of a number of areas within biology.  They’ve proved it by doing two things that you have never done:  (1) Dennis has offered lengthy, coherent, helpful exposition, in a very polite tone, rather than brief sarcastic jabs and biting rhetorical questions; (b) Lou has linked us to his peer-reviewed publications, demonstrating that he is in fact a research scientist rather than a pseudonymous commenter who may well be faking his knowledge level.  In any case, you’ve said your field is medical genetics, not evolutionary theory.  But just let me know the titles of all those peer-reviewed papers in evolutionary theory, and I’ll check them out, and if they seem good, I’ll concede that you have a second area of expertise.

melanogaster - #78280

April 8th 2013

I asked,
“How many different “parts” are there between you and a mouse, Eddie? Here’s a chance for you to empirically test a scientific prediction of your hypothesis about how development works. I predict that you’ll run away, hurling insults in your wake.

The predictable Eddie did precisely that:
“That’s pompously stated, to give an air of more mathematical exactitude than the few good transitional fossils warrant.”

That’s hilariously hypocritical coming from someone who pompously understates the distance between cetaceans and other artiodactyls by more than an order of magnitude.

“By the way, since you are expressing such a strong opinion on this matter, tell me—without looking it up: within one order of magnitude (units, tens, hundreds, etc.), how many good transitional whale fossils have been found?”


“And tell me the rough positions of the blowhole on them.”

Words would not be useful, but that’s why you keep going back to them.


Not a speck of discontinuity, Eddie.

“…one can’t generalize without a certain sample size—you have no business speaking in the assertive, magisterial tone you are employing.)”

And your hero Behe generalised about the ability of mutation to supply sufficient variation for evolution based on what sample size, Eddie?

Oh, and be sure not to include the one for which he was wrong by a factor of infinity.

“But back to the pompousness of your usage of “continuous variable.” The fossil record, presuming that it shows what some have claimed, shows simply that the blowhole position varies from point A through to point B. Big deal.”

Developmentally, it’s not. It’s just a matter of changing relative growth rates. No new proteins, no new binding sites. Moreover, the embryonic record shows that it is unequivocally continuous. Do you know why? Have you ever looked at a time series of cetacean embryos?

“Now tell me why it varies. Tell me what genes and what developmental processes etc. determine its location, its size, whether it has two openings or one, etc.”

To begin, search Google Images for “holoprosencephaly.” Then read some papers about the genetic causes. You won’t. Your excuse that you don’t know how to search the literature is laughable. Go to the biology or biomedical library. The librarians are there to help you with such things.

“Your last paragraph is puerile. “I know more than you do, nyah, nyah!” Takes me back to childhood arguments in the schoolyard.”

Not at all. The point is that you are afraid to know more. You have no faith in your claims.

“But on that subject, I certainly acknowledge that Dennis and Lou know quite a bit more than I do about the details of a number of areas within biology.”

They don’t know “a bit” more, they know a whole lot more and you know it.

“They’ve proved it by doing two things that you have never done: (1) Dennis has offered lengthy, coherent, helpful exposition, in a very polite tone, rather than brief sarcastic jabs and biting rhetorical questions;”

But Dennis hasn’t convinced you to change your position or even to look at the evidence. I cited a major part of what you requested and you ran away.

“(b) Lou has linked us to his peer-reviewed publications, demonstrating that he is in fact a research scientist rather than a pseudonymous commenter who may well be faking his knowledge level.”

If you believe that, I’m perfectly willing to cover your bet that I am faking, but only for very, very high stakes. You won’t do it because you have no faith in what you claim.

“In any case, you’ve said your field is medical genetics, not evolutionary theory.”

I’m in several more fields than that, but the plasticity of fields within biology, like the plasticity of development, seems to be beyond your comprehension.

“But just let me know the titles of all those peer-reviewed papers in evolutionary theory, and I’ll check them out, and if they seem good, I’ll concede that you have a second area of expertise.”

Eddie, you concede nothing of significance and since my ego is nothing like yours, it would mean nothing to me. Cash does. You just keep providing massive evidence of your desperate fear of learning anything real about the miracle of life. Besides, I’m still waiting for you to point me to just one of your alleged “proper scientific debates.” When will that happen?

So the PNAS paper provides part of what you seek. Why are you more interested in character attacks than evidence?

Eddie - #78303

April 8th 2013


If you think I care enough about the identity of a bluffing and ill-mannered blogger to risk any money, you’ve got another think coming.  I never gamble on anything, no matter how great the odds in my favor.  In any case, you’re the one who loses if you don’t reveal your identity.  The level of knowledge of evolutionary theory you have displayed on this site is consistent with the hypothesis of:  “B.S. in biology, reads the biology articles in Scientific American every month, and follows lots of internet debates on evolution, but is not a specialist in evolutionary biology and has never published a peer-reviewed paper in the field.”  That’s the hypothesis I’m going with.  If I’m wrong, I’m wrong.  But of course if I am wrong, you have the power to prove it at zero cost to yourself, while greatly amplifying your prestige here.  Therefore, your refusal to prove it is prima facie evidence that I’m right.  

In addition to a weak knowledge of the history of evolutionary theory and its terminology (as was demonstrated when you made a historically false claim of the role of random mutation in neo-Darwinism), you also display a weakness in reading comprehension.  “A bit” does not mean the same as “quite a bit.”

You want to know when a “proper scientific debate” will happen?  Fine, I’ll tell you.  Reveal your identity, and challenge Mike Behe to a public debate on the claims in one of his books.  Offer him a neutral forum—not Panda’s Thumb etc.  Make sure the moderators chosen have scientific qualifications, aren’t involved in the culture wars, and are non-committal regarding ID.  Both of you will agree in advance not to discuss alleged religious motivations, but to stick with the scientific evidence for various evolutionary mechanisms.  I think Behe will accept such an invitation.  So that’s when the debate will happen.  And you can make it happen.  But you won’t.


melanogaster - #78286

April 8th 2013

“The difference between a hoof and a flipper is not the difference between small and big.”

The difference is not hard to understand if you’re willing to look at the anatomy and developmental biology evidence, Eddie. A hoof is an enlarged toe with a hypertrophic toenail. A flipper is five fused toes. The differences result from continuously variable growth rates of components built out of the same things. No new parts, no new binding sites.

Do you not realize that Embryonic Eddie had flippers and that plenty of human beings are born with flippers every day? That it’s merely a consequence of stopping apoptosis in the tissue between the digits?

beaglelady - #78301

April 8th 2013

Exactly! Same with dogs. And that’s why it’s been easy for breeders to select for webbed feet in dogs bred to be strong swimmers, e.g.  Chesapeake Bay Retriever,  Irish Water Spaniel, Labrador Retriever.  (Even some breeds that don’t work in water have webbed feet.)

melanogaster - #78366

April 10th 2013

It must be sad to live in a state of being afraid of the most basic evidence.

Eddie - #78380

April 10th 2013

It must be even sadder to be unable to reveal one’s name (since revealing it would expose all the prevarications and bluffs of the past three years).

melanogaster - #78385

April 10th 2013

Of course you’ve got more than one thing to be sad about. I never meant to imply that your being sad about the one would in any way preclude being sad about the other.

Eddie - #77918

March 28th 2013

By the way, as a student of Greek philosophy (sometimes in Greek!), I’m well aware of Zeno’s paradox.  (I also studied calculus, by the way.)  Zeno’s argument cannot be crudely applied to the messy, complex world of biological change, where very serious qualitative differences are involved, not merely quantitative differences.  Not Zeno, but Aristotle, should be your guide where biology is concerned.

Lou Jost - #77923

March 28th 2013

Heck Eddie, I was pointing out the meaninglessness of Berlinski’s question about how many steps it takes to change a continuous variable from x to y. Zeno’s paradox is an example of the problems that arise when we ask that kind of meaningless question about a continuous variable.

Eddie - #77972

March 29th 2013


You’re the one who arbitrarily, and without proof, asserted that we were dealing with continuous variables.  I deny that this is the case.  At least, for a very large number of the changes that would be necessary.  So your critique of Berlinski is based on an assertion you have nowhere proved.  And can’t begin to prove, without showing me a diagram of the organisms in question, and a diagram of the genomes, and saying:  “It has been proved experimentally that these genes control organ X, these genes control bone growth Y, so if we make this base substitution here, we can generate structure Z, etc., etc.”  And you don’t have the detailed knowledge to do that.  Nor does Scott.  Nor does Miller.  Their argument was based on hearsay—on what they think evolutionary biology has proved.  They don’t have a clue how an artiodactyl could have become a whale, and given that they don’t, it is intellectually and academically irresponsible for them to stand up on a podium and imply that they do.

Berlinski was right to show the world that the emperor (in this case, the brains behind the NCSE, Miller and Scott) had no clothes.  I won’t back down on this one, Lou.  Call me wrong if you like, but give it up.

Lou Jost - #78143

April 3rd 2013

Yes, you are wrong about Berlinski.

Eddie - #78145

April 3rd 2013


You get the last word in the conversation.  Berlinski will get the last word in the history of science of 50 years from now, when biologists will openly laugh at the crudity and inadequacy of the neo-Darwinian theory espoused by Miller and Scott.

Ted Davis - #77884

March 27th 2013

Thank you for the specific answer, Lou, clarifying your claim about Berlinski. I won’t go further with that myself, since my knowledge of the specific scientific issues is shallow. Others here might wish to get into this, but I’ll pass on it.

And, thank you also for distancing Behe from your assessment of Berlinski.

melanogaster - #78259

April 6th 2013


You wrote to Lou, “Having known Behe for a long time myself, I have never seen any evidence that he is either personally or intellectually dishonest.”

I have, and I’ll document one such case below.

In EoE (page 139), Behe wrote about HIV, “…No new gizmos or basic machinery. There have been no reports of new viral protein-protein interactions developing in an infected cell due to mutations in HIV proteins.21”

This is objectively false, as Behe finally admitted. He was off by a factor of infinity—his grudging admission of a single binding site was off by a factor of two as well.

It’s also gibberish, as mutations don’t occur in proteins.

Ted, let’s hypothesise that this was an honest mistake and that Behe actually looked for reports of new interactions. Kindly note that this hypothesis makes a clear prediction about what we’ll find in Behe’s note #21, while the hypothesis that he fabricated the claim and intended to deceive his readers makes a very different prediction. Do you agree?

“Do you want readers to infer that you think he is?”

I want readers—and everyone else—to infer from the evidence and by testing hypotheses, not from hearsay. Wouldn’t you?

GJDS - #77868

March 26th 2013

Tiktaalik’s head and body are flat with eyes on the top of its skull, more like a crocodile than most fish. Its shoulders are not connected to its skull, giving it a functional neck, a feature which fish lack. And it has ribs like some of the earliest tetrapods which were used to support the body and aid in living and breathing on land. These features in Tiktaalik show that many of the body features we associate with the earliest tetrapods actually evolved in fish first.

I can see why these features would be interesting, but how does this confirm or deny a theory that seeks to prove all creatures originated from some hypothetical ancentor? We can look at present day creatures that also show similar traits – it seems to me a long jump between seeing features of past creatures and present day ones, which shows they may have performed similar functions, to some proof of a general hypothesis.

This example and other examples I tried to discuss (without success on this site), illustrates the difference between placing data within a preferred framework, and obtaining testable data that can be examined from various angles, or subjected to a general treatment. I have read various papers that attempt to prove common descent – a recent one received publicity on the BBC web site, and I have referred to another paper a number of times on this site. These were examples of constructing a software package that fitted data to a scheme that went back to provide steps in a regression to a common point (hierarchy may be an acceptable term). In all of these cases I could not find any instance where the authors either (a) devised a software package that sought a general fit of data to provide a range of hierarchies, without inbuilt constraints, or (b) used the software to test half a dozen, also unbiased arrangements, including an absence of common origin (common descent).

I have referred to meta-analysis where workers attempted to show correlations using large data bases, between central tenets of evolution (e.g. natural selection) and their data. These papers reported weka correlations – even though they sought to obtain selectively such a correlation, and not a general treatment (which is the legitimate practice if one is seeking to show a law). And I am avoiding sections in these papers that bluntly state that only a portion of the data could fit (in an authoritative way) with the given scheme. This is where the claims of proof can and should be challenged.

Lou Jost - #77870

March 26th 2013

With Tiktaalik, I was address Berlinski’s claim that evolution/common descent offered no predictions. In this case, biologists predicted the exact age/strata of rock where a “transitional” fossil should be, and they went there, and they found it. This does not prove common descent, but it does count as a prediction made from the hypothesis of common descent.

I regard the genetic predictions as much stronger than the Tiktaalik case. Those are very nice. See


and the other parts of that Biologos series.

The evidence for common ancestry of apes and humans is especially strong, and predictions based on the idea of common descent are numerous.

The point is that Berlinski is wrong to say that evolution/common descent makes no testable predictions.

GJDS - #77871

March 26th 2013

It seems the only discussion here is a dispute with Lou - the bulk of my comments is based on publications that also rely on genetic data and fossils. Read these and then make your comment - I have stated bluntly that I am not interested is disputing anything with you.

As a general comment (and not a response to anyone, including Lou) I refer to original research papers and reviews, and not Blog sites and subjective assessments by anyone advocating a position. I also add that I read these as an interested party and do not offer a review of the work, or comment on quality issues on such work.

Lou Jost - #77872

March 26th 2013

I and perhaps others would have liked to comment on the articles you mentiones, but you didn’t provide citations.

Dennis Venema’s explanatory posts here in Biologos don’t have any axe to grind; they are straightforward reports of evidence. You can draw your own conclusions from them.

GJDS - #77873

March 26th 2013

You can look back through posts I have made and there you will find complete citations and fairly large sections directly pasted from these sources. Interested parties have had the opportunity to comment and I do not see the relevance of your statement. These three may enable you to begin:

 C Malaterre, Biology and Philosophy (May 2010),  page 10; “… the tree of life would not have a single root that would start below the level of the ancestral organisms and below the level of protoliving systems, but a system of several intertwined roots…: some of them might correspond to systems that might have been good replicators but with a poor metabolism; others to systems with a good metabolic activity yet little success in generating variants; and so forth. One might imagine ways for systems to partly evolve along one or several of the functional dimensions that correspond to their lifeness signature.” Any reasonable reading of this paper show that the roots of this tree of life is based on endless speculation, with next to no ‘data’ that would support any clear scientific, coherent theory. This is there for anyone to read and come to their conclusions.

 M. A. Ferguson-Smith, Vladimir Trifonov, “Mammalian karyotype evolution”, Nature, 2007, 8, p 950. You will see Figures which show a lineage of various species, some of which are placed in an odd position…. the authors state, (page 952) “The total number of rearranged blocks per haploid autosomal set, as revealed by cytogenetics, provides in many cases a measure of relationship between species. When compared with humans, most eutherians have 30 to 40 separate blocks of homology with the human genome. Some species are exceptional, such as dogs and gibbons, and have about twice as many conserved block. The mouse is unique in having well over 200 blocks. There have been many more illegitimate recombinations in these species during their evolution, but the reasons for these differences in rate are as yet unknown.” Again this paper can be read by anyone and I see many statements that point to uncertainty, ambiguity, and often a preference for a particular interpretation.

Maureen A. OLeary et al, Science, 2013. 

Lou Jost - #77876

March 26th 2013

You are probably right about what the first paper shows—we don’t know much about the root(s) of the tree, billions of years ago. That is widely recognized. It does not invalidate the very strong evidence for common descent of recent groups.

I’ll have to study the second paper but the evidence from pseudogenes, explained in Dennis’ post, and its match with the fossil record and morphology, is very hard to explain away.

GJDS - #77888

March 27th 2013

A couple of quotes from an evolutionist may bring sobriety to this subject (A Wagner, “The Role of Randomness in Darwinian Evolution,” Philosophy of Science, Vol. 79, No. 1 (January 2012), pp. 95-119 

“In hypothesis testing, one asks whether a series of events could have occurred by chance alone, meaning that they are consistent with a prior expectation or, in statistical language, with a null hypothesis. If not, the null hypothesis is rejected.”..... we may discover an appropriate null hypothesis, a statistical model of changing DNA….. The chances of finding such a general null hypothesis, however, may be slim,...”

“Because the vast majority of new phenotypes in the neighborhood of a well-adapted genotype G are worse than the phenotype of G itself, this ability to explore many new phenotypes can be very important to find superior phenotypes. Put more starkly, if genotype

networks did not exist, then phenotypic improvement through natural selection might be impossible, because it might be prohibitive to find rare superior phenotypes in a vast genotype space without destroying present, well-adapted phenotypes.”

“Thus, metabolic genotype space is a vast, hyperastronomical space comprising more than 25,000 metabolic genotypes, each one corresponding to a metabolism with a different set of enzymecatalyzed reactions” 

“If we want to understand effects of mutations that go beyond any one genotype and its phenotype, it must be an expectation about the organization of phenotypes in genotype space.”

Wagner shows the cosmological numbers that are required when dealing with the subject, and states, “Challenges to Darwinian thinking have focused on such complex phenotypes. Whether mutations affect such complex phenotypes randomly is ill understood.”

His thesis is that non-random mutations are unlikely to fit in with Darwinian thinking, and natural selection itself is inadequate. His answer is as yet unknown ‘mechanism’ (my words) involving both non-random ... and natural selection .. may be the answer (talk of mental gymnastic!), i.e.

..... “Both natural selection and the non-random organization of complex phenotypes in genotype space are essential for organic evolution. Together they can help us understand how immensely complex phenotypes can arise through multiple cumulative adaptations.”

GJDS - #77889

March 27th 2013

as space somehow emerged between   ‘if genotype    and network’ .... this should be read as an unbroken sentence.

Lou Jost - #77890

March 27th 2013

It is important to distinguish the claim of common descent from claims about the mechanisms of evolution. Common descent can be established even if we don’t know all the details of the mechanisms by which species change over time. The evidence that man and chimps have a recent common ancestor is very clear, to the point where no serious scientist doubts it.

Lou Jost - #77891

March 27th 2013

Oops, given human nature, I am sure there are a few real scientists who doubt it….Of course, science is not done by poll, and even if the majority believe in common descent, that doesn’t mean you should. But it certainly does suggest you should look carefully at the evidence.

GJDS - #77892

March 27th 2013

The lament of the ‘kiss my curls’ disciples of Darwin - “look, every scientist believes it”, and those who do not, are (naturally selected) not scientists!

GJDS - #77893

March 27th 2013

Ooops, given human nature…. I have quoted and sited papers that are sumbmerged and drowning in evidence, and these (devout evolutionists) scientist have serious doubts - what can we say about human nature, the Darwinists and their zeal!!?? (Ted this is not shouting, although I understand now not everyone sees the funny side as I may at times).

Lou Jost - #77894

March 27th 2013

GJDS, no, that’s fine, I knew I’d be called out on that the moment I pressed “enter”.....

But please note that the paper excerpts you gave in #77888 are not directed at the idea of common descent, as far as I can see. It seems to be a discussion about the nature of the mechanisms of adaptation.

Lou Jost - #77895

March 27th 2013

A paper that would cast doubt on common descent of man and chimp, or mammals generally, would have to deal point-by-point with the kind of evidence Dennis summarizes in the BioLogos archives.

GJDS - #77898

March 27th 2013

This does not make any sense - these papers deal directly with the topic and are original research papers in well respected journals dealing with evolution and its subtopics. Are you unable to understand the content and need this Dennis chap to do your thinking for you? I understood you claimed to have an open mind and was only focussed on evidence (and Oh yes, all of those other intellectually dishonest and inept people you rage about - what can I say?)

Lou Jost - #77900

March 27th 2013

Does the article in your 77888 claim that it has evidence against common descent?

GJDS - #77896

March 27th 2013

Two of the three papers I sites previously deal with the subject - the Science articles uses what I am told is perhaps the largest data bank (Morphobank) in existence. If you are a serious scientist, why don’t you address the method used to generte a hierarchy using computer models that can ONLY arrive at a single starting point for their so called evidence based conclusions. Even Darwinists must understand the problem with such an approach - and yes, when they do this (on the basis that a common origin MUST be found), they find a significant part of the ‘evidence’ (in fact measurements they have made) falls ouside of this skewed scheme - talk of unreal science, what!!!

Lou Jost - #77901

March 27th 2013

Again, I don’t think these papers make any criticism of the kind of evidence for common descent discussed in Dennis’ articles in Biologos. But I have yet to read them all, so maybe I am wrong.

I don’t let Dennis think for me, but I do let him explain stuff for me, since a) you seem to discount anything an atheist says, while you might listen to Dennis since he is a Christian, and b) Dennis’s explanations are really well written, better than I could do.

GJDS - #77907

March 28th 2013

I have sited papers that are writen by what appear to be well credentialed evolutionists who have not (and need not) declare their beliefs or outlooks. I have not, at any stage, focussed on anything that has become a focus of dispute or doctrinal outlook (e.g. common descent), but have instead looked at papers that deal with the thinking equated with Darwinian ideas, and I am not in the least interested in criticising anyones data (I think this is what you refer to as evidence). The Science paper is all about a common ancenstor and how this idea has been examined and methods used. You may put another ‘dimension’ to this work, and you have the opportunity to do this. Dennis also has the opportunity to do so - surely this enough for any reasonable person.

Thus, Lou, I do not think that we have any mis-understanding. I see you (and a couple of others , whatever their theological/atheistic position) who have decided to get stuck into my posts and try and stir an argument - I am not interested in such an exchange. If you dissagree with my comments, of find fault with my reading of these papers, than provide a response. If this is not what you wish to do, I cannot understand why you get involved with my posts on this site. By all means, put your opinion here and others can decide to accept it, reject it, or ignore it.

I am at a loss on how I can explain my position with greater clarrity.

Lou Jost - #77916

March 28th 2013

We were discussing the evidence for common descent. In #77868 you seemed to be participating in that discussion: “how does this confirm or deny a theory that seeks to prove all creatures originated from some hypothetical ancentor?”

So I directed you to strong evidence of common descent in Dennis Venema’s and others’  BioLogos posts. You did not look at those or discuss them. That’s fine, you may be pressed for time or have other interests. But the articles you then cited don’t have much to do with the kind of evidence for common descent discussed by Dennis’ post. In your last post you seem to acknowledge that: “I have not, at any stage, focussed on anything that has become a focus of dispute or doctrinal outlook (e.g. common descent), but have instead looked at papers that deal with the thinking equated with Darwinian ideas”.

Your extracts of articles show that science is always questioning itself, and searching for truth. Those articles nowhere call into question the common descent of animals, including humans, from a common ancestor.

I do not make claims about the very early tree, which is poorly known. We should still hedge, as Darwin himself did, about whether there were one or several ancestors at the very base of the tree. We now know about horizontal gene transfer, especially common in bacteria, which can obscure the very concept of single lines of descent. However, in mammals, lines of descent are well-defined, and the evidence is clear that humans and monkeys have a recent common ancestor. Show us articles in reputable journals disputing that, or tell us why the BioLogos posts about this are wrong. Then we would have something to discuss.

GJDS - #77920

March 28th 2013

It seems that the only thing you can do is change the topic - I remind you that you asked for papers and information about things I had posted (to get to my position I would guess). I provided you with three and told you to look for other ones in previous posts. You ignored the material I presented, did not bother looking at previous posts, and now, in your head, you have convinved yourself that we are involved in another of these pointless ‘shouting matches’. If you cannot understand what I had said, say so or simply do not respond. Again I restate - I am not interested in getting into a sordid exchange about who said what, I you are so so wrong about my post acknowledging your nonsense - just how do you twist my remarks in this way? Just look through the methodology usd to obtain a heirachy that purports to a common origin - you may have a purswasive argument to put forward - give up on your current juvenile approach.

Lou Jost - #77929

March 28th 2013

I have actually been trying to get you to focus on the specific issue we were discussing, common descent. I don’t understand the point of the journal excerpts you cite. You seem to think the articles in question throw into doubt some aspect of evolutionary theory. This is not the case.

Take the “Nature” article you cite in #77873 (actually not in Nature but in Nature Reviews- Genetics). The abstract says “Here we discuss how these rearrangements come about, and show how their analysis can determine the evolutionary relationships of all mammals and their descent from a common ancestor.” It is a beautiful article showing how new genetic tools help reveal the patterns of common descent in mammals. Karyotype characteristics, the subject of the article, are relatively independent of genotypes (which evolve more slowly). If mammals did not arise through common descent, there would be no reason to expect that the phylogenies based on karyotypes would be similar to the phylogenies based on gene sequences.  The authors note that although the method has its limitations, “The resolution is sufficient to enable the construction of pedigrees that show the relationships between species, families and orders, and the lines of descent from common ancestors as postulated in The Origin of Species more than 150 years ago. The study of karyotype evolution complements and extends other evolutionary studies that are based on the fossil record, morphological features and molecular sequence data.”

Far from demolishing evolutionary arguments, you are providing extremely strong new evidence supporting the conclusion of common descent with modification, the core of Darwinian theory. Thanks!

PNG - #77931

March 28th 2013

Just a note. The paper Lou discusses above is not freely available, but there is a more recent review on the same subject with one of the same authors (Trifonov) that is freely available. This review gives a short account of the history of karyotype studies and the limitations of the various methods.

Genomic diversity and karyotype evolution of mammals http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204295/

GJDS - #77934

March 28th 2013

Again I restate - I have purposfully chosen papers that are writen by those who support evolution - it should not come as a surprise to you that they do so. I asked for your comment on the methodololgy that I have tried to understand from various publications - in that they have NOT searched for alternate ‘fits’ to their data. Perhaps the beauty you see in this is that it does not show that evolution is suddenly dimolished - if so enjoy it. I do not do my research this way - I always search for alternate reaction pathways and THEN report what the limitations and variations in data fit mean. If you chaps do not, that is your choice. PLease please do not start with the assumption that I am interested in doing away with any theory, including Darwin’s. I have stated I do not use it, and am more interested in understanding why theists are so enthusiastic in incorporating this with theology, I have said this too many times and i now find these discussions tiresome.

Lou Jost - #77950

March 29th 2013

It is admirable that you are willing to investigate the viewpoint of evolutionists by studying these kinds of articles. This article reviews a method for reconstructing phylogenies based on how blocks of genes are arranged on chromosomes.The phylogeny produced by this technique can be compared with phylogenies produced by looking at changes in the gene sequences of particular genes, or by phylogenies based on the fossil record. All three of these methods give very similar phylogenies. With these phylogenies in hand, we can make detailed testable predictions about the genomes of particular organisms. For example, if there was a certain kind of rare mutation in an ancestor, we should see this mutation inherited by all the supposed descendants, but it should not be present in the species that are placed on other branches of the tree. This is one of the things discussed in Dennis’ posts; he shows that this prediction is confirmed over and over again.

These are some of the reasons why virtually all biologists accept the idea of common descent. So when you wonder “why theists are so enthusiastic in incorporating this with theology”, the answer is simple. A theology that insists on special creation of all species at one instant contradicts the fossil record and the clear evidence of common descent with modification. This applies to human origins as well. Theology should not mock reality, as I’ve said earlier. And unless someone believes in a trickster god like Loki or some of the North American Indian gods, he or she would  presumably believe that god is not  trying to fool us. Hence the need to incorporate common descent into theology.




You have said you are “more interested in understanding why theists are so enthusiastic in incorporating this with theology”. The reason is that we now know

Lou Jost - #77951

March 29th 2013

Oops, that hanging tail end fragment should not be there.

GJDS - #77953

March 29th 2013

Theology does not mock reality – you are still stuck in a world where the ‘latest’ philosophical/scientific outlook of the Greco-Roman world, with the simpler views of Israel, were taken by scholars particularly during Medieval times, and somehow became accepted as theological truths/special creation. Ted Davis series have thrown some light on this and you would be well served if you read them and understood what went on. 

I have stated that I regard the matter as faith and reason – science in general falls within the category of reason. I have spent sufficient time and energy on this to satisfy myself that faith and science are not in conflict. If you have arrived at another conclusion, that is just that, your conclusion. The bio-sciences have had a chequered history and I do not consider them to have advanced to the point that I should take their major pronouncements seriously. You may be satisfied with things like a common origin of various species, but from what I read from time to time, the overall theoretical framework of Darwin’s thinking leaves a great deal to be desired. I guess you may say I am convinced that a semantic approach, with the many limitations that I find in it, does not meet my criteria for serious science that falls within my faith/reason outlook. I do not need others to think for me, and as I have repeatedly stated, I decide on the work that I read and consider is of sufficient quality – my time and energy is not limitless and there are other matters that are far more important to me. Thus, as I have stated, I hope the people working on the bio-sciences progress to a far better outlook than that of Darwin – once they do and I am still around, feel assured that I will read and consider such with a great deal of interest.

Lou Jost - #77954

March 29th 2013

I didn’t say theology mocks reality, I said it should not mock reality. Some theologies do mock it, and others don’t. Choose wisely.

GJDS - #77955

March 29th 2013

Do you think Augustine, Athanasius, Barth, Thomas Aquinas, Calvin and perhaps Polkinghorne, mock reality? Or is it the Bible that does so?

Lou Jost - #77957

March 29th 2013

Yes to most of the above, but some of them can be excused due to lack of knowledge at the time. Augustine tried to tell you not to mock reality…

Lou Jost - #77959

March 29th 2013

GJDS, here are some quotes from Augustine. In response to someone who wrote that god is not to be sought by reason:

“You say that truth is to be grasped more by faith than by reason … Heaven forbid that God should hate in us that by which he made us superior to the animals! Heaven forbid that we should believe in such a way as not to accept or seek reasons, since we could not believe if we did not have rational souls.”

This is his best-known quote, which I am sure you have seen:

“Now, it is a disgraceful and a dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics [of the natural world]; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. …

“If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods and on facts which they themselves have learnt from experience and the light of reason?”


GJDS - #77975

March 29th 2013

How does Augustine ‘mock reality’? Your quotes show the opposite. You need to read Anastasius on intellectual questioning of all knowledge, and get some understanding of Thomist thinking.

Lou Jost - #77984

March 29th 2013

I said “Augustine tried to tell you NOT to mock reality…” (77957). I did not say that he was one who mocked it.


melanogaster - #78298

April 8th 2013

Lou, it’s hopeless.

Lou Jost - #77960

March 29th 2013

Regarding my 77957, the Bible and the Quran do seem to be the primary reasons why so many people nowadays do mock reality. That was not necessarily the intention of the writers, though.

GJDS - #77976

March 29th 2013

It is one thing to read these books and another to understand them - this something you should be able to grasp - the simpletons are found both in theistic and atheistic camps. Nonetheless they are just that, simpletons who place their lack of understanding on these (and I suggest) many other books.

Lou Jost - #77964

March 29th 2013

Eddie, when you have time to come back to our discussion of Shapiro and the mechanisms of evolution (above), would you like to go over to the following post with me and continue the discussion there regarding Shapiro’s teleology?
The immune system is one of Shapiro’s major examples.

Eddie - #77970

March 29th 2013


No, I’m out of time.  I have deadlines to meet.  But you know my position now.

Lou Jost - #77973

March 29th 2013

Eddie, one quick comment here. You said above that “I do know, however, that Shapiro has more qualifications as an evolutionary biologist—both in terms of his formal position at the University of Chicago and in terms of his publications of peer-reviewed articles, and his new book (which Karl Woese, a world-class theorist, calls a “game-changer”), than either you or Venema. ”

I have to correct you. First, as I am sure you would agree, it is important to engage the arguments and not be satisfied with credentials. Second, Shapiro’s papers and books on evolution have not been influential, as measured by number of times they have been cited. You can tell a lot by these citation numbers as measures of actual scientific impact. His book has been cited only 42 times. An older book, “Mobile Genetic Elements”,  has been cited 314 times, which is quite good. But even my own little paper on genetic divergence has been cited 500 times, more than any article on evolution that Shapiro has written.  (source: Google Scholar, searching {James Shapiro evolution} and {Lou Jost evolution}, using first 100 results). (For comparison, Michael Behe’s peer-reviewed paper citation rate on evolution is near zero, though his books have very many citations.) Not that this is a good reason to believe me, but at least don’t insult me (or Dennis).

Anyway, Shapiro’s many critics are right that he misrepresents even basic evolutionary concepts (especially natural selection) and that his “teleology” is not really what it seems. So let’s go over to the link I gave in my last comment and talk about it, if you have time. To me, his “revolution” is mostly verbal flourish, and the neo-Darwinian vision of evolution is much broader than you think.

Eddie - #77977

March 29th 2013


I did not mean to insult you.  I genuinely thought, based on what you told me, that your scientific field was “the measurement of genetic diversity” or something like that, not “evolutionary biology”—which I take to be “the debate over various mechanisms of evolution.”  Obviously there would be an area of overlap between the two fields, but I thought they were two distinctive fields, with their own distinctive journals, conferences, etc.  And it struck me that, while you would doubtless know something about some of the evolutionary mechanisms that Shapiro talks about, you would not have spent as much time as he has spent thinking about evolutionary mechanisms overall.

I also, not long ago, viewed a podcast on the web where Shapiro was interviewed about his book and his ideas by a panel of leading evolutionary biologists.  Not all of them agreed with his views, of course; but the fact is that they thought his challenge to evolutionary theory was significant enough that he deserved an interview and a grilling.  They didn’t invite Behe or Dembski or Venema or Falk and grill them on their view of evolution.   They would only have interviewed someone who, even if he was wrong, was competent enough in the field to be thought to offer a conceivably useful view.  I was assuming—perhaps wrongly, and I will gladly retract if I am—that you have never been invited by a panel of leading evolutionary biologists and grilled on your views on evolutionary mechanisms.  

My point was not that Shapiro was right; my point was that he is recognizable as one of the significant contemporary evolutionary theorists.  And maybe you are, too; and if so, I apologize for not ranking you as his peer in the field.

But you are right that I should not turn comments to the person.  I let myself get irritated because you seemed to be standing in judgment upon Shapiro, as if you knew more evolutionary theory than he did.  So I wanted to know on what basis you arrived at that conception.  But maybe you weren’t claiming more knowledge than Shapiro, but were only objecting to certain of his ideas.  If so, I apologize for overreacting.

To tell the truth, I get a little frustrated in these debates.  Critics of Darwin who are creationists will mention Duane Gish as their champion, and then are told Gish was an incompetent scientist driven by fundamentalism.  Then they mention Mike Behe, who is not driven by fundamentalism (he’s not even a Protestant!), and who makes no arguments from the Bible, all from biochemistry; and they are told he is not competent in genetics or evolutionary theory.  Then they mention Margulis, who is not even Christian, and who has an impressive record in evolutionary biology, and they are told that she was good on the mitochondrion, but a “one-trick pony” and not really a good source for evolutionary biology.  Then they mention Shapiro, and who is also non-religious, and he is dismissed as well.  It seems that the rule is:  criticize neo-Darwinism, and the establishment will jump to find something wrong with your qualifications, your knowledge, etc.  Anyone who criticizes it is automatically wrong, and if religious motivation can’t be pinned on them, something else will.  (Actually, Coyne, who very rudely sneered at Shapiro, has apparently accused Shapiro of being a closet creationist, which is ludicrous.)

When I see this kind of defensiveness, I sense dogmatism.  Hence my bristling.  Sorry for giving in to temptation.

Lou Jost - #77980

March 29th 2013

Eddie, thanks for the explanation. You were doing to me what you accuse others of doing to Shapiro. And you seem to do it again here when you say “I was assuming—perhaps wrongly, and I will gladly retract if I am—that you have never been invited by a panel of leading evolutionary biologists and grilled on your views on evolutionary mechanisms..” For what its worth, I get invited to give talks all over the world, and last year was invited to Barcelona to interact with other experts in ecology and genetics for not just an hour or two but for an entire month. Shortly I’ll go to the Santa Fe Institute, invited to discuss (for a whole week) the application of my pop gen work to subjects like the evolution of altruism. Scientists like to discuss things with each other; these kinds of events are not that unusual.

I actually know very little about Shapiro’s subject, molecular biology; my beat is macroscopic evolution, natural selection, and pop genetics. However, I think he makes serious mistakes in those areas, making the rest of it more or less moot.

I hope we can  just discuss the ideas, not whether I or he have sufficient credentials. I did buy Shapiro’s book when it came out, and that says a lot about how interesting it sounded (I can only buy three or four books per year). I was disappointed. I’ll tell you why when we both have more time. I also have deadlines now…

Eddie - #77990

March 30th 2013


I never doubted your competence in your area of biological science, and never meant to imply that I did.  Nor did I mean to imply that you were inferior as a scientist to Shapiro.  I just honestly (and perhaps mistakenly) thought that you would not be described as an “evolutionary biologist” by other scientists who regard themselves as full-time evolutionary biologists.  I thought you would be regarded as a geneticist or an ecologist or something of the sort.  But possibly the subject “evolutionary biology” has fuzzier borders than I’ve been assuming. 

In any case, I don’t deny overlap between different biological studies, and I have no problem with your assertion that your knowledge allows you to criticize parts of Shapiro’s work.  But then, by the same token, Shapiro’s knowledge of molecular biology should enable him to criticize parts of the work of those evolutionary theorists who are not strong in molecular biology, and think that evolutionary theory is little more than an extension of population genetics.  It seems to me, then, that what is needed is dialogue between biologists who tend to overrate their own specialization and underrate the specialization of others.  That is certainly the case in academic disciplines of which I have more expert knowledge.  For example, sociologists of religion have an annoying habit of reducing religion to a sociological phenomenon, philosophers of religion tend to think of religion as a set of abstract theoretical propositions disconnected from the lived practice of actual religion, etc.  You don’t get a credible picture of the phenomenon “religion” where any single approach is allowed to run the show.

So I’d say—if you think Shapiro makes mistakes, by all means point them out.  But unless those mistakes destroy his central thesis—which is that organisms have a certain capacity to self-engineer their own genomes and therefore do not always have to wait for variation or mutation to throw up something useful—you can’t declare his work to be without value.

It’s an old academic trick, one I’ve seen in many disciplines, for critics to point out some error that someone has made, and make out that, because of this error, the person is too incompetent to be taken seriously—while in the meantime the main contention of the person has not been disproved.  On this site, for example, melanogaster, about a year or two ago, alluded probably a dozen times to two alleged errors in biochemistry and/or genetics in Steve Meyer’s book, generally throwing in insinuating remarks that these errors indicated incompetence, or dishonesty, or both; but when asked to show that these two errors (one of which was apparently little more than a slip in nomenclature) were so central to Meyer’s thesis as to invalidate the entire 500-page book, or even an entire chapter, he would not reply.  So all I ask is that you distinguish between “Shapiro should do a major rewrite of Chapter 3 to fix up the theoretical errors in his account of population genetics” and “Shapiro’s thesis is wrong; it has been proved that organisms do not have the capacity to re-engineer their own genomes.”

But on the point of dialogical method, I agree with you; I’ll try to stick to ideas and not qualifications in the future.

Lou Jost - #78001

March 30th 2013

Thanks. Like I said, I don’t know much about molecular biology, and I learned a lot from Shapiro’s book about that. So I agree with you that ““Shapiro’s knowledge of molecular biology should enable him to criticize parts of the work of those evolutionary theorists who are not strong in molecular biology”

I do think he makes mistakes that are central to his thesis, though, and I also think both of you may have an overly narrow view of the “standard” version of evolution.  Some of the things you have said suggest you might also have too narrow a view of population genetics. But we can talk about that later…after our deadlines….

Lou Jost - #77974

March 29th 2013

Eddie, just saw your #77970, which crossed my last post in the ether…Sorry to hear that, but good luck with your deadlines.

Roger A. Sawtelle - #78021

March 31st 2013

Lou wrote:

I can see why someone would believe in a higher power, a “lawgiver”. Personally, I don’t see that this idea actually helps as an explanation of why the universe follows laws; to me it seems like it just pushes the problem into the more familiar sphere of personal agency, giving the illusion of solving it. But I wouldn’t argue much if someone disagreed and thought a “lawgiver” was a good explanation.

Thank you for your response.  For a number response I was unable to respond earlier, burt I will now although I realize that it will probably get lost in the shuffle. 

Again the question is “Is the universe rationally structured?  Yes or No?”  Monod based on his belief that the universe is made up of matter/energy says No.  You and I seem to agree that the answer is Yes.

What we can say, though, is that many of these mathematical laws follow from some very simple characteristics of space and time.

Most people seem to think that the laws of physics are not that simple.  I have the book The Road to Reality by Roger Penrose (on relation) which is more than 1000 pages long and not simple.  Also as you know the Antropic Prinsiple indicates that many basic relationships found in the universe are calculated to allow and permit life as we know it on the planet earth. 

Humans can think, but nature cannot.  Doesn’t that make humans supernatural, above nature.  We know that particles cannot think, but we know that we can design machines whereby we can make things do what we want them to do.  We do the thinking, the machines do the work. 

Non-believers sometimes say that Christians create God in their image.  However we know that God is much better in every way than we are, even though we are created in God’s Image.  It would be a shame is non-believers created a world like Stalin and Mao did where human life is devalued.

Now you say that saying that God is the creator of natural laws does not solve anything.  Now if a crime has been committed and the criminal is identified and convicted, most people would say that the crime has been solved.

That does not mean that we know exactly why the crime was committed.  That is the task of theology to explore why God created the universe.  I do not claim that Christianity has the only answer to this issue.  I am speaking from what I know best which is Christianity.  I do believe that it is the best explanation, but I am willing to consider others. 

(animate objects follow the laws of physics).

I wonder if you really believe this statement.  I mean, Do the laws of physics make some people Republicans and others Democrats?  What laws of physics was Einstein following when he discovered his Theory of Relativity? 

The fact is organisms use the laws of physics to survive and flourish, not the laws of physics govern the actions of organisms such as ourselves.

If humans (as well as bees, ants, and termites) can create homes and farms and factories, why can’t God have created the universe.  It makes much more sense than stupid matter and energy creating order, space, and time out of nothing.        



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