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:

• (May 5, 2008) A population-genetic argument by creationist Sal Cordova gives a misleading impression of the ineffectiveness of natural selection. (And here -- in comment no. 2 -- is a 2010 comment at Uncommon Descent showing that Cordova has learned nothing from that exchange).
• (August 1, 2009) Not about creationism or ID, but a happy birthday to Lamarck.
• (August 21, 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.
• (August 24, 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).
• (December 12, 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.
• (April 13, 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).

• (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.

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.

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.