Blog Archives
Pandas, Kitzmiller, and the frozen frog fallacy
By Paul Braterman
January 4, 2023 13:00 MST
Paul Braterman is Professor Emeritus at the University of North Texas and Honorary Senior Research Fellow in Chemistry at the University of Glasgow
This Kitzmas was different. For the first time, the Discovery Institute allowed the anniversary of Kitzmiller v. Dover Area School District to pass without complaining about the verdict. Perhaps they are hoping that we will forget about the incredible badness of the text that they were trying to foist on the District’s students. Of Pandas and People is carefully constructed to be as misleading as possible, and we shouldn’t let them forget this, as long as contributors and advisers responsible for it remain in position within the Discovery Institute1, while the Institute continues to promote works such as Denton’s Evolution – A Theory in Crisis, that perpetuate the same elementary errors of logic. But first, an apparent digression. When students first come across the use of molecular or DNA sequencing in constructing phylogenetic trees, they are sometimes puzzled. They have been told that mammals are descended from fish by way of amphibians. Therefore, as a matter of common sense, they might expect that frogs should be closer to fish in evolutionary terms than we are. This is another example of the Evolution as Progress error. While amniotes have progressed through synapsid to mammal to humans, the pinnacle of creation, the frog has remained a lowly frog and should, therefore, be closer to the common ancestor, as if the ineluctable processes of molecular mutation had somehow been suspended. We might call this the “frozen frog fallacy.”
At this point, a Table like the one shown below might help:
All the multicellular organisms shown are, apart from small random fluctuations, at the same distance from the bacterium, as expected if they share a common ancestor distinct from bacteria, which have of course, independently, been accumulating their own set of changes.
All the animals shown are, apart from small random fluctuations, at the same distance from wheat, as expected if they share a common ancestor distinct from plants. And the relative number of mutations shows that the split between plants and animals is more recent than the split between multicellular organisms and bacteria. More recent yet is the split between fish and tetrapods, leaving all tetrapods (including you and me, and of course present-day frogs) at the same distance from the fish. And so on. Most tellingly, humans share a common ancestor with monkeys, more recent than their common ancestor with non-simian mammals. There is a lot more detail in the Table, for example about how to birds relate to reptiles, and how the different orders of mammal relate to each other. And of course the construction of a phylogenetic tree is based on the specific differences found, rather than the overall number.
There are now numerous published studies of the phylogenetic relationships revealed by Cytochrome C, to say nothing of the vast recent literature using numerous molecular and morphological traits to develop detailed high-resolution phylogenies, and to explore the limitations of the concept of a unique phylogeny. What is interesting about the particular Table I have quoted is its origin, and the uses that its authors make of it.
This brings us back to our original theme. The Table actually comes from Of Pandas and People, 2nd edition, 1993, which by the time of the trial had gone through five printings. The book does not give a reference to the source of the data, but much (not all) of the information can be found in a classic 1967 paper [2], which also explains the reasoning behind the method, and critically examines the assumptions made. So there is no excuse for what the book does next, which is to repeatedly assert that the data refute claims of common ancestry:
one might expect analysis to reveal that the cytochromes in fish are most similar to the cytochromes in amphibians. But this is not the case.
And again:
To use the classic Darwinian scenario, amphibians are intermediate between fish and the other band-dwelling invertebrates. Analysis of their amino acids should place amphibians in an approximately intermediate position, but it does not.
(Note the use of Darwin’s name to denote the whole of evolution. In fact, the book is obsessed with Darwin, mentioning him on almost every page, and on some pages up to 10 times. In fact, by my count, and I may have missed a few, Darwin’s name or some variant of it occurs 262 times within the 144 pages of text. This emphasis on Darwin is of course found throughout the whole of the creationist literature, although by now evolutionary theory is almost as different from what Darwin proposed as atomic theory is from that proposed by Democritus.)
These are just two of five separate reiterations of the fallacy, leading up to the extraordinary statement that
Based upon the evolutionary series, we should expect some amphibians to be closer to fish (“primitive” species) and others to be closer to reptiles (“advanced” species).
And to make sure that the message sticks, we have this Figure, with the plain implication that the data point, not to evolution, but to separate creation:
The fallacy is not merely being stated; it is being repeated, rationalised, and reinforced. The kindest explanation is that the authors simply do not understand the science that they are presenting, seeing a hierarchical structure where none exists, and imposing on their biology a perspective in terms of “higher” and “lower” which do not belong in modern science, but have been carried over, such as the power of human vanity, from a worldview more akin to Aristotle and the mediaeval Great Chain of Being. The same fallacy also occurs in Michael Denton’s 1985 Evolution – A Theory in Crisis, and while he had by 1998 [3] quietly walked away from this, his 2016 sequel, Evolution – Still a Theory in Crisis, retains his preference for Aristotelian over phylogenetic classification.
And why should this matter? Because it reminds us, and we should not forget, that the Discovery Institute does not only deal in dis-information, but in dis-education.
I thank Maarten Boudry, Glenn Branch, Joe Felsenstein, John Harshman, Kim Johnson, Larry Moran, and Massimo Pigliucci for helpful comments and links to the literature.
Footnotes and citations:Permalink
(1) Dean Kenyon (co-author), Charles Thaxton (Academic Editor), and Stephen Meyer, Michael Behe, and Nancy Pearcey (contributors) all hold positions at the Discovery Institute, as do Raymond Bohlin, Walter Bradley, Robert Kaita, J.P. Moreland, and Paul Nelson, who are on the list of those thanked for being “critical reviewers”, as, also, are Meyer and Behe.
(2) Walter M Fitch and Emanuel Margoliash, Science 155(3760), 279, 1967; DOI: 10.1126/science.155.3760.279
(3) For a discussion of Denton’s revised position, see this 2006 post at Larry Moran’s Sandwalk blog
Repost of https://pandasthumb.org/archives/2023/01/Pandas-and-Frogs.html
Some Assembly Required, Neil Shubin (review) [Long]
Some Assembly Required, Neil Shubin, Pantheon/Penguin Random House, March 2020, ISBN 978-1101871331, publisher’s price HB $26.95, £20.72. Publication date March 17
A shorter version of this review has appeared on 3 Quarks Daily.
This book will be of interest to anyone who is interested in the way in which evolution actually proceeds, and the insights that we are now gaining into the genome, which controls the process. The author, Neil Shubin, has made major contributions to our understanding, using in turn the traditional methods of palaeontology and comparative anatomy, and the newer methods of molecular biology that have emerged in the last few decades. He is writing about subject matter that he knows intimately, often describing the contributions of scientists that he knows personally. Like Shubin’s earlier writings, the book is a pleasure to read, and I was not surprised to learn here that Shubin was a teaching assistant in Stephen Jay Gould’s lectures on the history of life.
Shubin is among other things Professor of Organismal Biology and Anatomy at the University of Chicago. He first came to the attention of a wider public for the discovery of Tiktaalik, completing the bridge between lungfish and terrestrial tetrapods, and that work is described and placed in context in his earlier book, Your Inner Fish. The present volume is an overview, from his unique perspective, of our understanding of evolutionary change, from Darwin, through detailed palaeontological studies, and into the current era of molecular biology, a transition that, as he reminds us, parallels his own intellectual evolution.
18 March 2020, this just in: https://edition.cnn.com/2020/03/18/world/fish-finger-fossil-scn/index.html Fish finger fossils show the beginnings of hands; 
If you are interested in evolution, get this book
EVOLUTION: What the Fossils Say and why it Matters, Donald R. Prothero (2nd edition)
If you are interested in evolution, get this book. And make sure that your library gets it. And your children’s highschool library. Incidentally, it’s incredible value; list price $35.00/£27.95 from Columbia University Press, with over 400 lavishly illustrated pages.
The book is a comprehensive survey of the fossil record, supplemented at times with other evidence, and framed as one long argument against creationism. It opens with a general discussion of the ideas behind current evolutionary thinking, moves on to a survey of specific topics in (mainly animal) evolution, from the origins of life to the emergence of humanity, and concludes with a brief discussion of the threat that creationism poses to rational thinking. The argument is laid out clearly in the seemingly artless prose of an accomplished writer in love with his subject matter, with plain language explanations that presume no prior knowledge, while the detailed discussions of specific topics give enough detail to be of value, I would imagine, even to a professional in the field. The author is an experienced educator and researcher, with thirty books ranging from the highly technical to the popular, some 300 research papers, and numerous public appearances to his credit, and the work is copiously illustrated with photos, diagrams, and drawings by the author’s colleague, Carl Buell. These illustrations are an integral part of the work, graphically displaying the richness of the data at the heart of the argument. Read the rest of this entry
Why I do NOT “believe in Darwin’s theory of evolution”
Fact not theory; 150 years on from Darwin’s watershed publication; evidence not belief. Words matter.
A recent Harris poll asked Americans “Do you believe in Darwin’s theory of evolution?” Others more eminent have commented on the answers; I would like to comment on the question.
Darwin, of course, never used the word “evolution,” but let that pass. As for the rest, it would be difficult to cram a larger number of serious errors into so small a space. Errors of presentation, of logic, and of scientific and historical fact, all of which play into the hands of our Creationist opponents.
Start with the obvious, the word “theory.” In common language a theory always involves speculation. In academic discourse, it means a coherent set of ideas that explain the facts. Calling something a theory in this sense tells you nothing at all about how certain it is. A theory can be wrong (phlogiston theory), known to be approximate from the outset (ideal gas theory), very close to the truth but since improved on (Newton’s theory of planetary motions), or as certain as human knowledge ever can be (number theory in mathematics). Of course you can explain all this, but you should not put yourself in such a vulnerable position in the first place. It wastes time in debate, or in the classroom. It puts you on the defensive, and thus, paradoxically, confers legitimacy on the attack. It allows the focus to shift from what we know about the world to the words we use to talk about it. This takes us away from science to the domain of the philosophers, lawyers, and expositors of Scripture who are fighting on behalf of Creationism.
And so it distracts from what you should be talking about, namely the facts. Evolution, whether we mean changes in the genetic make-up of populations over time, or the common descent of living things on earth, is a fact. It is supported by, and explains, innumerable more specific facts concerning the fossil record, molecular phylogeny (the same kind of evidence that is used every day in DNA paternity tests), the frozen-in historical accidents of organs that have lost or changed their function, the distribution of species throughout space and time, and much more besides. Creationism cannot explain these facts, except by appeal to the whims of the Creator.
Next “Darwin’s.” Darwin did indeed have a theory, as independently had Wallace, which was that different species had arisen gradually by natural selection operating on variation. This he supported by meticulous observation, but the range of evidence available to him was far more limited than what we have today. He lamented the poverty of the then known fossil record, laments that Creationists echo to this day as if nothing had changed. He knew nothing about mutations or even about the existence of specific genes, and so he had no idea how new variants could arise and spread. His assumption of gradualism is in contrast to later ideas such as punctuated equilibrium, and we now know that much if not indeed most variation arises through neutral drift. Thus not only do we know far more facts about evolution than Darwin could have dreamt of, but our theories, too, incorporate numerous additional concepts.
Finally, worst of all, “believe in.” Believing always carries with it the feeling that disbelief is an option. Some members of the jury believe the witness, others don’t. Some people believe that Hillary Clinton will be the next President of the United States, but no one would say they “believe” that Barak Obama is the current incumbent, because no sane person doubts it. I don’t “believe in” atoms, or gravity, or quantum mechanics, because I regard them as established beyond dispute, although our notions about them will no doubt continue to change as we learn more. And exactly the same is true of evolution.
Does it matter? Yes, it matters enormously. Creationists often maintain that evolution and Creation are both beliefs, whose respective advocates differ, not about observable facts, but about how those facts are to be interpreted. They obsess about Darwin, referring to evolution as “Darwinism,” and to those who accept this reality as “Darwinists.” The aim here is to bypass 150 years of experimental and intellectual discoveries, to bog us down in the day disputes of the late 19th century, or even (“Darwin’s doubt,” see here and here) to enlist Darwin himself as an unwitting ally. And they contrast evolution, as “only” a theory, with facts or even with scientific laws, in order to claim that it is far from certain and that different views deserve a hearing.
Most people have not thought long and hard about evolution. And in the US at least, much of what they have heard about it will have come from its theologically motivated opponents. These opponents, whether through “statements of faith” that make obscurantism a virtue, or through “academic freedom bills” that disguise telling lies to children as open intellectual debate, use carefully crafted words to stake spurious claims to the moral high ground.
We should not, ourselves, be using words that help them do this.
Bears, whales, God, Darwin, and Peter Hitchens (Part I)
Can bears turn into whales? Peter Hitchens (PH) asks this question in two successive instalments of an anti-evolution tirade of the kind that gives ignorance a bad name. Normally I would not have bothered with such nonsense, especially since Jerry Coyne at WEIT has already dismembered what with PH passes for reasoning in greater detail than it deserves. However, PH does raise an interesting question or two, and makes one assertion is so breathtaking in its combination of arrogance and ignorance that I cannot forbear from discussing it. Let me deal with these matters in turn.
The first question is, can bears turn into whales? The suggestion is based on a remark by Darwin, in the first edition of On the Origin of Species, which he dropped it in later editions as being too speculative. However, PH still chooses, over 150 years later, to cite it as evidence that Darwin’s whole research programme, and by implication the entire structure of the life sciences as they have developed since that time, is really very silly. As to why we all indulge in such silliness, PH’s answer, which I will analyse later, is as ridiculous as it is insulting.
The answer to the question, by the way, is no. Of course, no presently existing species is capable of evolving into another presently existing species, any more than PH is capable of evolving into his late lamented brother, nor would Darwin ever have suggested such a thing. If we rephrase the question a little more precisely, do bears and whales share a relatively recent common ancestor, the answer is still no. Bears do in fact share a relatively recent ancestor with seals and walruses, but their last common ancestor with whales was back in the Cretaceous.
The obvious question then arising is this: if whales are not related to bears then what are they related to? Forty years ago, we didn’t have a precise answer to that question. Now we do, and PH could have found it easy enough, just by looking up whale evolution in Wikipedia. And while PH is understandably concerned about erroneous assignments, since the only fossil he seems to know about is the Piltdown forgery, Wikipedia will also provide him with a list of 43 separate extinct families of precursors of modern whales. But perhaps PH is a Wikipedia snob, or perhaps these articles, replete as they are with terms like “artiodactyl” and “cladogram”, are above his technical reading level. In the latter case, I would refer him to an excellent National Geographic article; in the former to either of two recent but more technical reviews, here and here. I will be writing about whale evolution at much greater length elsewhere, showing as it does a beautiful coming together of three separate lines of evidence; from the fossil record sequence, from anatomical homologies, and from molecular phylogeny.
My point here is a rather obvious one. PH admits that he is ignorant about evolution. Nothing to be ashamed of there. After all, he is a busy man, and has his own priorities, and if he can’t find the time to learn what kind of place the natural world is, and how we fit into it, then that’s his own business. But what he should be most deeply ashamed of, is his decision to write, not once but twice, about such a subject without first bothering to inform himself.
Despite his self-proclaimed ignorance, PH claims to have penetrated the motivation of the scientific community in its acceptance of what he describes, in rather simplistic and old-fashioned language, as “the theory of evolution by natural selection.” What he tells us of this theory is that the motivation is fundamentally theological, or rather, anti-theological. To quote, “I will re-state it, yet again. It is that I am quite prepared to accept that it may be true, though I should personally be sorry if it turned out to be so, as its implication is plainly atheistical, and if its truth could be proved, then the truth of atheism could be proved. I believe that is its purpose, and that it is silly to pretend otherwise.” [My emphasis]
So this is a clear statement of what PH considers to be the purpose of the theory; not to make sense of nature, as we scientists pretend, but to prove the truth of atheism. Well, questions of motivation are always interesting, if difficult to settle, but in this particular case we happen to be in a position to decide the truth or otherwise of PH’s claims. The theory of evolution by natural selection was first clearly formulated by two separate individuals, initially working independently, Alfred Russel Wallace and Charles Darwin. We know a great deal, in both cases, about their attitudes to religion, and Darwin in particular has left us a detailed description of how his views changed over time, as a result in large part of the evidence that he collected while developing and testing his theory. Both these great scientists changed their opinions on religious and spiritual matters during their working lives. Neither developed their theories in pursuit of a theological agenda, and if they had done so, that would have amounted to professional malpractice. The reality is very different, much more interesting than anything PH could have imagined, and we will return to this in the next part.
Primate's Progress 