text: On Friday, July 13, 2001, Phil Johnson suffered a stroke. He is currently undergoing rehabilitation therapy, and hopes to return to his normal activities soon. The following Weekly Wedge Update was in preparation when Phil became ill. It covers recent correspondence between Phil and Richard Dawkins, and concludes with comments from Paul Nelson.
  The correspondence begins with Dawkins commenting on questions from the Weekly Wedge Update dated July 9, 2001. Dawkins then directs questions of his own to Phil, who replies. Dawkins then clarifies his position, and Paul Nelson comments.
  Thank you for answering my lobster question unequivocally and honestly. This really has clarified your position. You are commonly bracketed with Behe and Dembski. You have now shown that actually you have more in common with Duane Gish, Henry Morris and Kurt Wise. No wonder you are so indiscriminate in whom you welcome into your big tent.
  Do you accept that, if human ancestry and sea-squirt ancestry is followed sufficiently far back, they will meet in a single common ancestor? Or if not a yes to all five of these supplementary questions, is there some point along the series after which you would answer no, as you did for the lobster, but before which you would answer yes? e.g. Yes to chimpanzee but no to pig and all the rest? Or yes to chimpanzee and pig, but no to all the rest?
  When Phil Johnson sent me this correspondence for comment, I found Dawkins's last message puzzling. Dawkins writes that "the reason we know for certain that we are all related, including bacteria, is the universality of the genetic code." But the genetic code is not universal. Since the mid-1980s, dozens of variant codes have been discovered, so many in fact that the National Center for Biotechnology Information maintains a web page listing them:
  Now Dawkins might reply "Oh, don't be a pedant – the genetic code is nearly universal, and these are only minor variants," but of course that would give away the game. If the theory of common descent predicts that the code should be universal – indeed, Dawkins himself has called this a "near-conclusive proof" of the theory (1987, 270) – but non-universality turns out to be the case, then, by strict logic, something is wrong with common descent.
  Yet predictions, theories, and evidence can have a curious relationship with each other. As it happens, common descent sailed right past the discovery of the non-universality of the code. In a recent article (2001, R63-R66) the molecular biologist Niles Lehman surveyed the consequences for evolutionary theory of the discovery of non-universality:
  Once thought universal, the specific relationships between amino acids and codons that are collectively known as the genetic code are now proving to be variable in many taxa. While this realization has been disappointing to some – the genetic code was often hailed as the ultimate evolutionary anchor in that its universality was perhaps the indisputable piece of evidence that all life shared a common ancestor at some point – it has also opened up a rich field of evolutionary analysis, by forcing us to consider what sequence of molecular events in a cell could possibly allow for codon reassignment....Our ever-expanding list of nonstandard genetics is not serving to unravel the unity of biology. Instead they are strengthening our understanding of the mechanisms of evolution.
  The "unity of biology" (i.e., common descent) is still intact, mainly because it was never really at risk.
  Thus, it would be more accurate to say that Dawkins believes that all organisms share a common ancestor, despite the fact that they do not all have the same genetic code. In any case, he can't know that common descent is true because of the universality of the code. One cannot know something that isn't so.
  I also found puzzling Dawkins's claim that "the same hierarchy of cousinship appears with different molecules -- independent confirmations of the same tree." This brought to mind the old story about a railway stationmaster who announced that all the trains were running on time. When passengers complained that their trains were hours late, the stationmaster replied, "Actually, what I meant to say was that the trains all run on time – except when they don't."
  In evolutionary systematics, the evidence all runs on time, except when it doesn't. Nearly any issue of Systematic Biology, Molecular Biology and Evolution, The Journal of Molecular Evolution, or Taxon (not to mention the many other journals in the field) will carry at least one report of a new molecular study contradicting a traditional morphological tree. As I was preparing these comments, for instance, I read the paleontologist Michael Novacek's critical response to new molecular trees in mammalian systematics that (he writes) "suggest a radical shakeout of the placental tree, in ways not anticipated by morphological work" (2001, R573).
  Do these anomalous trains – to revert to the railway metaphor – count for, or against, the theory of common descent? I leave that question for the reader's reflection. Again, however, Dawkins cannot know that common descent is true because molecules confirm morphology. It would be more accurate to say that Dawkins believes that all organisms share a common ancestor, despite the increasingly equivocal signals from systematic data.