Matzke has written many in-depth pieces and has made frequent posts online, including regularly blogging at The Panda's Thumb. In 2003, he wrote a lengthy paper about the evolution of flagella[M 9] and has continued to challenge claims from intelligent design proponents that flagella are irreducibly complex.[M 10][M 11][M 12] He co-authored a critique of Stephen C. Meyer's paper that became important in the Sternberg peer review controversy.[M 13][4] He also wrote a chapter-by-chapter critique[M 14] of Jonathan Wells' book Icons of Evolution,[5] which he described as a "travesty of the notion of honest scholarship" that is "shot through with misrepresentations." In addition to "a bevy of its own errors," Matzke stated that the book contained "numerous instances of unfair distortions of scientific opinion, generated by the pseudoscientific tactics of selective citation of scientists and evidence, quote-mining, and 'argumentative sleight-of-hand,' [by which Matzke means] Wells's tactic of padding his topical discussions with incessant, biased editorializing."[M 14] While still with the NCSE, he collaborated with Paul R. Gross to contribute a chapter on the use of critical analysis by antievolutionists[M 15] to their 2006 book Not in Our Classrooms.[M 16] In less serious or formal work, he co-authored a research parody based on NCSE's Project Steve.[M 17] He first made a name for himself posting on talk.origins as "Nic Tamzek".[6] He has also written articles on such topics for the popular press.[M 8]
He is the author of the 2013 R package BioGeoBEARS,[M 18] which enables statistical comparison of probabilistic models of how the geographic ranges of species evolve on phylogenies, such as models that include or exclude founder-event speciation,[M 19] geographic distance,[M 20] or dispersal-influencing traits.[M 21] He also authored a 2015 paper in the journal Science conducting a dated, Bayesian phylogenetic analysis of antievolution legislation proposed or passed in the United States in the decade following Kitzmiller v. Dover.[M 22][M 23]