Felsenstein posts at Panda's Thumb

The blog Panda's Thumb is the most important blog refuting scientific arguments (or ostensibly scientific arguments) by advocates of Intelligent Design and creationism.

I have made a series of guest posts there:

Note -- in 2016 Panda's Thumb migrated to a new software system for comments. For the moment, comments on old posts are missing. Some of the comments -- the first page worth for each post -- are visible if one looks up the page on archive.org (the Wayback machine, where the PT site archives will be found here). The old comments have been saved and will ultimately reappear at PT, once the necessary migration work can be done.

(5 May 2008) A population-genetic argument by creationist Sal Cordova argues for the ineffectiveness of natural selection. I pointed out that his calculation gives a misleading impression. (And here -- in comment no. 2 -- is a 2010 comment at Uncommon Descent showing that Cordova has learned nothing from that exchange).
(1 August 2009) Not about creationism or ID, but a happy birthday to Lamarck.
(21 August 2009) Theologian and mathematician William Dembski and electrical engineering professor Robert Marks have published a peer-reviewed paper which Dembski argues supports Intelligent Design. Why it is just as supportive of more mundane views of the world.
(24 August 2009) More on why Dembski and Marks's argument, which they believe shows intervention in the world by a Designer to make fitness surfaces smooth, does not refute evolutionary biology.
- (and here is a comment I made later at Dietmar Eben's blog summarizing my conclusions about the implications of Dembski and Marks's “Search for a Search” paper).
(12 December 2009) How Cornelius Hunter, a biophysicist and old-earth creationist, fails to put forward a scientific theory.
(February 18, 2010) How the weeds in our back yard show that if an argument by creationist mathematician Granville Sewell (published by the Discovery Institute) is correct, the Second Law of Thermodynamics is wrong.
(13 April 2010) How a Bayesian calculation of the posterior probability of evolution being correct, made by Cornelius Hunter, necessarily requires that he have some alternative scientific theory (which he refuses to put forward), and how the mathematical statistician Peter Olofsson rather thoroughly thrashed Hunter by making just these points in the comments at Hunter's own blog.
(1 August 2010) Happy 266th birthday to Lamarck.
(28 September 2010) Why a calculation at the Uncommon Descent anti-evolution blog supposedly showing that humans and chimps differ in DNA sequence by a lot more than 1% is totally wrong.
(27 February 2011) Oh no! It's Granville Sewell again. This time he has published a paper in Applied Mathematics Letters repeating his old arguments, without any acknowledgment that they are absurd and have been demolished. Here I once again make fun of him by pointing out that he has “proven” that weeds can't grow in your garden and for that matter, neither can flowers! (Apparently, AML rescinded its acceptance of Sewell's paper after some people complained and pointed out its fatuity. But here is a video he has since posted on 6 June 2011 repeating the same discredited argument. Sewell subsequently had a lawyer pressure AML, which agreed to pay him $10,000 for violating their own rules for publishing papers. It sounds as if AML had little valid review in the first place, accepted the paper on insufficient grounds, and then paid Sewell the $10,000 but without agreeing to reinstate the paper and publish it, perhaps because they know it is a silly paper.)
(27 March 2011) A commentary by me on Complex Specified Information (CSI) and whether it is important to get it formally defined in terms of information theory to understand William Dembski's argument about The Design Inference (I say not, the problem with his argument is elsewhere). This was in reaction to the article by "MathGrrl" at Uncommon Descent where, in spite of being an opponent of Intelligent Design, she was allowed to post there asking for the pro-ID commenters to define what they meant by CSI. They couldn't.
(25 May 2011) Oh no! It's “niwrad” again, over at Uncommon Descent, making the same argument that I criticized earlier. Now it's comparing two human genomes, and finding that they are much more different than people say. This done by (1) asking how many contiguous blocks of 30 bases are identical in the two genomes, while (2) keeping a straight face. I have pointed out the silliness in all this and suggested the use of blocks of 1000 sites instead, to make the degree of difference much greater.
(5 June 2011) At Uncommon Descent, the engineer Gil Dodgen once again posted the dramatic conclusion that “Darwinism” has collapsed but that evolutionary biologists are in denial about this obvious fact. That is not new -- he's always dramatically concluding that. But this time he got carried away and said that ID apologists “continue to mount what I perceive as increasingly indefensible assaults on the creative powers of the Darwinian mechanism of random errors filtered by natural selection”. Yes, I agree: these assaults are indeed indefensible!
(1 August 2011) The annual celebratory post for the birthday of Lamarck. The discussion in the comments starts out interesting but degenerates into trollery. The troll ends up putting forward a non-theory, misunderstanding Lamarck's theory thoroughly, and asserting that I am not an expert in behavior or biochemistry (both true but irrelevant to that discussion) but somehow seems to think he is an expert in those areas (very much not true).

and after that I became part of the Panda's Thumb "crew" so my posts were not guest posts. Posts after that are:

(23 August 2011) On Uncommon Descent, poster Eric Holloway had declared that even critics of William Dembski's 2002 book No Free Lunch admitted that his argument did apply to evolution. And declared that the critics had not refuted the NFL argument which showed that natural selection would be ineffective. So I showed how Dembski's argument has been refuted by many critics who all had the same powerful argument, one that Holloway ignored.
(9 September 2011) Denyse O'Leary (writing under the pseudonym "News") at Uncommon Descent quoted a passage from my 2007 paper while misunderstanding it thoroughly. To top things off she called me a "Darwin lobbyist" whose salary "is paid for under protest by people who dont believe it". So I put up a post pointing out how wrong she is. In the comments at their site, Gil Dodgen then calls more names (while misunderstanding the issues) and no one answers the reasonable questions of one commenter who wonders what they are talking about.
(13 September 2011) A post in memory of the late Peter H. A . Sneath, who died on 9 September.
(17 November 2011) It's Granville Sewell yet again! He posted another repetition of his Second Law of Thermodynamics refutation of evolution. I posted again at PT, pointing out my previous posts and the earlier ones by others thoroughly refuting them. I described his argument as unanswerable -- but only because at Uncommon Descent he had the Comments feature turned off (as he does on all his posts). So we did the answering in Panda's Thumb, instead. Sewell did not, alas, join that discussion. That led on to a very long thread on the Second Law of Thermodynamics and evolution.
(11 January 2012) An obituary of James F. Crow, a friend and mentor to many evolutionary geneticists, and a major figure in theoretical population genetics. This includes a couple of photos I took of Jim (one with Motoo Kimura) from 1972. If the pictures are not side-by-side, widen your browser window and they will be properly laid out and captioned.
(17 April 2012) An obituary of Robert R. Sokal, who cofounded numerical taxonomy with Peter Sneath. He was also, somewhat against his will, a pioneer of numerical methods for inferring phylogenies. With F. James Rohlf, he wrote the widely-used statistics textbook Biometry. The obituary quotes extensively from a good one written by Bob Sokal's colleague Michael Bell. If you cannot get the photos of Sokal to align properly, try widening your browser window.
(1 August 2012) The annual birthday post celebrating Lamarck, a great pioneer of evolutionary biology. In this case his 268th birthday.
(26 March 2013) It has been announced that Stephen C. Meyer, the leader of the Discovery Institute's Center for Science and Culture, is to publish a book, Darwin's Doubt, which starts with the Cambrian Explosion and uses this to explain "the theory of intelligent design" and deal with criticisms of it. I suggested we help him out, that we list some of the important issues that he might inadvertently overlook.
(7 April 2013) Writing at the Discovery Institute's site Evolution News and Views, William Dembski complained about our Panda's Thumb thread on what Stephen Meyer should say in his book. He set out to refute me on whether Complex Specified Information could be used to detect Design. This thread on Panda's Thumb is an extensive reply to Dembski, vindicating my argument against the CSI/Design method.
(1 August 2013) The annual birthday post celebrating Lamarck, pioneer of evolutionary biology. We had reached his 269th birthday. My remarks about celebrating with "Picardy calvados" caused some controversy.
(27 August 2013) Not a post about creationism or ID. I posted a recollection of the 1963 March On Washington. Includes a photo of the march pin that I bought there, and still have.
(July 23, 2014) I express astonishment at the dramatic conclusions of some engineers and physicists about the "evolution" of airplanes, and their ringing declaration that the study of evolution "belongs in physics".
(1 August 2014) The annual celebratory post of the birthday of Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck and pioneer of evolutionary biology. 270 candles on the cake!
(2 October 2014) William Dembski gave a talk on August 14, 2014 at the Computations in Science seminar at the University of Chicago, a seminar run in part by Dembski's thesis advisor Leo Kadanoff. It was subsequently made available on video. This post argues against the Search For a Search argument which was the basis of Dembski's talk, critiquing two of the papers by Dembski and Robert Marks that he cited for the points in his talk.
(30 January 2015) A new website, the Third Way of Evolution was established last year, and came to my attention by being publicized in a post at Uncommon Descent. It has statements by 43 scientists and engineers indicating their disagreement with the Modern Synthesis, and urging one or another alternative. I brought this to the attention of Jerry Coyne, who posted on it. This Panda's Thumb post The Third Way of Evolution announced, but fails to cohere calls it to the attention of the Thumb's readers, leading to a discussion. The main problem with the Third Way is that it seems to be 43 ways, not one.
(29 March 2015) William Dembski, Winston Ewert, and Robert Marks have defended their Search For a Search argument, arguing (correctly) that I misconstrued their argument. In this response at Panda's Thumb, I have been joined by Tom English. We pointed out that when my argument is corrected to deal with Dembski, Ewert, and Marks's actual model, it turns out that their argument becomes even weaker. Just having organisms that reproduce, and having the ordinary laws of phyics, makes evolutionary processes far more effective than they are in Dembski, Ewert, and Marks's mathematical model of "search".
(5 August 2015) The annual happy-birthday post for the birthday of Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck. But a few days late this time.
(8 November 2015) I finally posted a response to Winston Ewert's defense of the DEM paper. He had pointed out that in the 29 March post by me and Tom English we did not question any of the theorems in the Dembski-Ewert-Marks paper. Yes, we didn't, we said we didn't. What we did question was the conclusions DEM draw, that their Active Information requires Intelligent Design. In the 29 March posting we had showed it doesn't require ID. This post documents statements by all three of those authors that show that they want people to draw this invalid conclusion from their DEM paper.
(4 May 2016) A retired German plant breeding researcher (and creationist), Wolf-Ekkehard Lönnig, posted an argument at the Discovery Institute's blog Evolution News and Views, that random noise from deaths of the many offspring that organisms produce will be fatal to natural selection, creating a noise that will overwhelm modest differences in fitness. Actually we do know about that -- it is called genetic drift. And when you do the calculations, the results look bad for Lönnig, as I explain in a PT post.
(8 April 2017) A creationist blogger, Mark Champneys, commented on an old 2011 post where I made making fun of Granville Sewell's arguments that the 2nd Law of Thermodynamics ruled out evolution. He argued that Sewell was right, but Champneys's argument was actually different from Sewell's. He argued that the origin of photosynthesis was ruled out, not the operation of photosynthesis. To allow more discussion of Champneys's argument I posted this post. Alas, Champneys never showed up to join the discussion.
(7 November 2018) At the Discovery Institute's "Mind Matters" series of blog posts, Eric Holloway has declared that Intelligent Design can "be demonstrated mathematically through information theory", that this was shown by William Dembski, and that on reading criticisms of Dembski's work "I have not been able to discover a precise reason why they think Dembski is wrong" and that critics of Dembski "actually tend to agree with Dembski when the topic lies within their respective realms of expertise." So I posted a reply pointing out all the demolitions of Dembski's work that Holloway missed or misunderstood. Just as he did with critiques of Dembski's use of the No Free Lunch Theorem in 2011 (see above). A parallel post was made at The Skeptical Zone so discussion could occur there too (link in my PT post).
(11 March 2019) Holloway did it again. This time he declared that the main reason scientists were becoming "more skeptical of evolution" was that they saw that evolution could not explain consciousness. Once again I asked for clarification. And pointed out that he had not countered criticisms of his previous arguments about conservation of information.
(29 April 2019) Holloway subsequently made a comment on a post at The Skeptical Zone making the same dismissal of criticisms of Dembski's argument as before. So I replied to the dismissal again and linked to the previous Panda's Thumb post where links to all the criticisms of Dembski can be found. Just in case Holloway cannot find them.
(14 May 2019) In the preceding thread it was pointed out that contrarian computer scientist David Gelernter had published an article in the Claremont Review of Books declaring that he was "giving up" on Darwin's theory of evolution, which he justified mostly by citing a book by Stephen Meyer and a paper by Douglas Axe. I put up a thread on this to enable discussion without disrupting the discussion of Holloway's assertions.
(23 July 2019) The conservative think tank The Hoover Institution has put out a video showing two supporters of Intelligent Design, Stephen Meyer and David Berlinski discussing with David Gelernter (see the previous post in this list) why they don't give credence to "Darwinism". In spite of the title which mentions "Mathematical Challenges to Darwin's Theory of Evolution" only one mathematical argument is mentioned, one that is 50 years old. So I had to ask people to help me look for any valid argument in their hour-long discussion.
(2 August 2019) The annual Happy Birthday celebration of the Chevalier de Lamarck, the first evolutionary biologist, in this case his 275th birthday. This year's post describes his bravery as a soldier and his inability to provide for his family.
(19 August 2019) A post noting that The Evolution2019 meetings have just made videos of 369 talks available. That may help put to rest the creationist misconception that all we do at those meetings is sit around quoting Charles Darwin and swooning. Link to those videos in the post.
(22 August 2019) A post pointing out that the Catholic-tinged site First Things now has an article publicizing David Gelernter's announced dismissal of Darwin. I have some comments there giving links to other sites that have publicized Gelernter's announcement, mostly supporting it, but some critical of it.
(5 December 2019) Eric Holloway and others have been arguing that conservation theorems for Kolmogorov mutual information justified William Dembski's argument that Complex Specified Information cannot be achieved by natural selection. I have argued that this is wrong. Algorithmic Specified Complexity, put forward by Ewert, Marks, and Dembski, addresses how much unusually simple the description of a bitstring is. This has nothing to do with fitness or the achievement of adaptation. Dembski's CSI is at least defined in terms of adaptedness, but the whole Algorithmic Specified Complexity literature does not make any connection to fitness. I argue its total irrelevancy to what evolution can or cannot do.
(28 January 2020) I posted a guest post by commenter MaryKaye on "Complex information arising from random processes: the chess program AlphaZero", a really lovely example where information about how to play chess accumulates in a chess-playing program as it plays itself repeatedly
(3 March 2020) I made a post on "Evolutionary biology in real time" about the use of phylogeny programs to reconstruct the genealogy of SARS-CoV-2 infections in the Covid-19 epidemic and the Nextstrain project run by Trevor Bedford at the Fred Hutchinson Cancer Research Center here in Seattle.
(5 March 2020) A post about implementation of a new feature -- a Recent Comments widget -- at Panda's Thumb.
(25 March 2020) A post following onto the 3 March post, about An updated genealogy of SARS-CoV2 virus from the Nextstrain project.
(2 May 2020) I co-signed this post by Matt Young reporting on the online viewing for the excellent documentary on the Ark Park in Kentucky, which is available for a modest fee on Amazon Prime video. It featured the documentary makers and two of the people who they featured, Dan Phelps and David MacMillan, who were on the side of actual science.
(May 16, 2020) Discussion: Is William Dembski's CSI argument mistaken or merely useless? This continues a discussion at Josh Swamidass's blog Peaceful Science, between biostatistician Dan Eastwood and me. We differed on where the fundamental flaw was in William Dembski's argument for Design from Complex Specified Information and we agreed to move the discussion to Panda's Thumb. My position is of course the correct one.
(August 7, 2020) We are almost back The server that hosts the files for Panda's Thumb crashed on 16 June, 2020. Several of the PT "Crew" worked hard trying to get the configuration changed in readiness for the pages to be served by Github after the server was replaced. Some of this effort consisted of correcting each other. This describes progress four days before the pages were finally fully restored.
(August 30, 2020) A belated happy birthday to Lamarck The annual Happy Birthday post for Lamarck, the first major evolutionary biologist. This was delayed 29 days by the server crash. It discusses Lamarck's invocation of an inherent complexifying force in his theory of evolution.
(September 17, 2020) Are Evolutionary Biologists Ignoring Science? A reply to a video posted by Mark Champneys, one which had been promoted by Granville Sewell at Uncommonm Descent, and by Evolution News & Science Today, part of the Discovery Institute's website. Champneys joined the discussion in the comments, but although a number of people provided physical or biological counterexamples to his assertions, he refused to engage with these.
(October 25, 2020) Does approach to higher probability block natural selection? More in the debate with Mark Champneys. I discussed a simple case with mutation and natural selection in a large population, and showed that the move of the system toward equilibrium did not erase the effect of natural selection because it then moved to a different equilibrium. Champneys did not refute this.
(November 14, 2020) Counterexample to Mark Champneys’ argument about natural selection: more technical details More technical details about the counterexample case, including the equations.
(November 22, 2020) What are the most important misconceptions about evolution? An attempt to harvest some new misconceptions that creationists have. But there is little new under the sun.
(December 1, 2020) Are there any new ID arguments? A quick description of various ways that the notions of specified complexity have been used to try to show that it measures whether natural selection can explain adaptations. And why none of them work.
(December 27, 2020) Is natural selection a meaningless tautology? A more detailed examination of whether fitness is a tautological concept. It isn't at all if you can find an association of fitness with a phenotype or genotype, and then examine more individuals, other populations, or other generations. It is as meaningful as measuring the speed of runners in a test race, and then using it to put together a good track team. The "tautology" argument is itself useless.
(January 30, 2021) Report: ID experts mistakenly think evolutionary trees cannot be reconstructed In which it turns out that speciation and extinction rates inferred from evolutionary trees cannot always be distinguished. But the Discovery Institute's site Evolution News & Science Today, and the pro-ID site Uncommon Descent, mistakenly think that this means evolutionary trees cannot be inferred.
(February 19, 2021) Report: Are jellyfish so dumb that their evolution needed help? Jellyfish and pretty dumb, and that leads Uncommon Descent's "News" reporter to think that they cannot evolve to use a principle of physics as they cannot understand it.

Granville Sewell thinks it's obvious.

(May 15, 2021) We are the knights who say ... evolution The Discovery Institute's commenter "News" is upset because so many scientists describe themselves as in fields that start with the word "evolutionary", such as "evolutionary genetics". It is the unhearable word, very much like the Knights Who Say 'Nee' in Monty Python and the Holy Grail.
(August 1, 2021) Happy 277th birthday, Jean-Baptiste! As every year, Happy Birthday to the Chevalier de Lamarck, this time pointing out how present-day "Lamarckians" fail to address problems that Lamarck tackled.
(August 9, 2021) Denaming the Huxley College of the Environment, part 2 The controversy over whether Western Washington University's Huxley College of the Environment should be named after him, as he shared the racist prejudices of his day.
(August 20, 2021) All theories in science involving randomness are invalid In which Eric Holloway, at the Discovery Institute's "Mind Matters" site, seems to say that if a model involves random events, then it is not an explanation of the phenomenon. Uncommon Descent of course agrees. Physicists and chemists might beg to differ.
(September 6, 2021) Evaluating Alan Kleinman's arguments Alan Kleinman has published papers with probability calculations of successive beneficial alleles accumulating in a nonrecombining bacterial culture. He calls this calculation "the basic science and mathematics of random mutation and natural selection". This seems to imply that the outcome of these processes was unknown for 100 years, and has only been analyzed properly now, by him. Why he's wrong about that.
(October 22, 2021) Advertising bot solves the problems of early hominid by Joe Felsenstein.
(November 6, 2021) Is common descent untestable? by Joe Felsenstein.
(November 30, 2021) William Dembski on why ID has and has not succeeded by Joe Felsenstein.
(December 29, 2021) The worst ID or creationist argument of 2021? Let us know by Joe Felsenstein.
(January 29, 2022) Not really evolution? by Joe Felsenstein.
(March 24, 2022) Herschel Walker isn't the only one wrong about humans and apes by Joe Felsenstein.
(June 24, 2022) Predicting rough times ahead for teaching about evolution? by Joe Felsenstein.
(January 18, 2022) Removing James F. Crow by Joe Felsenstein.
(March 6, 2022) Is mutation nonrandom? If so, in what sense? by Joe Felsenstein.
(April 26, 2022) Methinks it is sort-of like two weasels by Joe Felsenstein.
(May 18, 2022) Jason Rosenhouse's book on mathematical anti-evolutionism is available by Joe Felsenstein.
(June 9, 2022) Has Michael Egnor shown that everything is intelligently designed? by Joe Felsenstein.
(July 5, 2022) Uncommon Descent tries to stay on topic by Joe Felsenstein.
(July 25, 2022) New Paradigm Of The Month: Silly-looking birds, and evolutionary theory renamed by Joe Felsenstein.
(August 1, 2022) Happy birthday, Lamarck by Joe Felsenstein.
(August 10, 2022) Lamarck rides again? by Joe Felsenstein.
(August 14, 2022) Meyer and Thaxton ask one question and answer another by Joe Felsenstein.
(August 31, 2022) ICR argues that science refutes junk DNA by Joe Felsenstein.
(September 12, 2022) A wrong analysis of information in evolution by Joe Felsenstein.
(October 18, 2022) How jellyfish prove Intelligent Design (according to ID advocates) by Joe Felsenstein.
(November 1, 2022) Science leads to stock photo entertainment by Joe Felsenstein.
(December 31, 2022) What didn't happen in 2022? by Joe Felsenstein.
(March 17, 2023) "P Hacking" and natural selection by Joe Felsenstein.
(April 18, 2023) Uncommon Descent is dead (or maybe undead) by Joe Felsenstein.

These are in addition to my numerous comments at PT on posts by others.

Incidentally, my article in Reports of the National Center for Science Education:

Felsenstein, J. 2007. Has natural selection been refuted? The arguments of William Dembski. Reports of the National Center for Science Education 27 (3-4): 20-26.

is available online (free) here.

In addition, I have been honored by having joined a most distinguished group of opponents of creationism and Intelligent Design, having actually met the famous Dr. Steve Steve. The good doctor's assistant, Reed Cartwright, photographed us together at the Portland Convention Center in June, 2010 at the Evolution2010 meetings. I was so excited that my hair stood on end! (At my age you're so happy to have any hair that you don't care which way it goes). Here is Dr. Steve Steve's account of this. Dr. Steve Steve's role in the debate can be examined here where all posts about him at PT are collected.