Douglas Axe has posted a response to criticisms of his work from Arthur Hunt and Steve Matheson, regarding his 2004 JMB paper, on the Biologic Institute website.
In August of 2004 I received an email inquiry from plant biologist Art Hunt. He had written a draft for a blog piece aimed at reviewing a research article of mine that had just appeared in the Journal of Molecular Biology , and he wanted to know whether he had understood my work correctly. He clearly aimed to refute claims that were beginning to surface that my paper supported intelligent design, but he also wanted to make sure he wasn’t misconstruing my work in the process. He didn’t expect me to oblige—“I will understand if you decline; in fact, I would probably do the same…”—but I did.
His summary of the experiments I reported in the JMB paper was largely correct, though his understanding of my analysis was off in several respects. As a result, many of the conclusions he drew were, in my judgment, not well grounded. I gave him feedback to this effect, but since it was a blog entry rather than a peer-reviewed scientific publication, I wasn’t particularly concerned to see the final version, or to respond to it.
Two things have happened since then. One is that my 2004 JMB paper has, as Hunt predicted, been cited in support of intelligent design in several prominent places, and the other is that Hunt’s finished blog piece  has become the favored argument against using my paper in support of ID.
Here I summarize what appear to be the four most common objections to using my 2004 paper in support of ID, three of which trace back to Hunt’s blog entry, the fourth perhaps originating with Steve Matheson, who joined Art Hunt last summer for critical dialog with Steve Meyer in front of an audience at Biola University.