Specifically, the status of methodological naturalism within scientific enquiry has been challenged by [Philip Johnson]?, a lawyer who has in a number of works (Darwin on Trial, Defeating Darwinism, Objections Sustained, and The Wedge of Truth) argued that methodological naturalism is a prop used by the Darwinian orthodoxy to ensure the exclusion of evidence for Intelligent Design Theory on a priori grounds. Johnson argues that a strong commitment to methodological naturalism on a priori grounds can blind researchers to the truth just as easily as a commitment to a literal reading of Joshua blinded the church to the evidence for Copernicus's heliocentric theory.
Johnson's position has been rejected by a some scholars, like [Robert Pennock]? who note that he often conflates methodological naturalism with philosophical naturalism. However, others note that the objection Pennock raises ignores the main thrust of Johnson's argument which a methodological assumption that excludes the possibility of looking at the evidence for a theory inevitably leads to a rejection of that theory.
Though many evolutionary biologists continue to reject Johnson's argument, it has been noted that [Richard Lewontin]? who has debated Johnson several times on the issue, seems to have adjusted his position to one which is compatible with Johnson's view. In a recent review of a book on intelligent design Lewontin argued that true science requires a prior commitment to both methodological and philosophical naturalism:
In this context it important to note that Lewontin seems to have changed his mind, in order to agree with Johnson's claim that evolutionary theory is based on an absolute or philosophical naturalism. However, it is also important to note that Lewontin's statement does not amount to a wholesale acceptance of Johnson's project, since Johnson is defending the right of the advocates of intelligent design theory to have their case evaluated on the merits of the current evidence, while Lewontin is claiming that rigorous scientific methodology requires an absolute commitment to natualism which rules out such evidence on a priori grounds.
Johnson's attack on MN has wider implications than just for the sciences; in Reason in the Balance (199x), he attacked naturalism in law.
Who is a leading defender of MN in the scientific community? Is there any more history to this?