Let's be clear about what the real issue is: Why does Sam Harris oppose President Obama's appointment of Francis Collins to be the Director of the NIH? Harris had the privilege of putting his case before the public on the OpEd pages of the New York Times (linked to above). In his editorial Harris conceded that Collins' "credentials are impeccable", but nevertheless Harris insisted that Collins' religious beliefs should "be of concern". Harris went so far as to say that Collins is "a man who is sincere in his beliefs. And that is precisely what makes me so uncomfortable."
But apparently the meanies at the NYT didn't give Harris enough space to make himself perfectly clear. So now Harris has "written a longer essay on the subject", which he has posted on his own website. While it is true that v2.0 of Harris' attack on Collins is over 6.5 times longer than his first attempt, nothing new is added because Harris still does not provide a single example of any time in Collins' career of over three decades as both a scientist and an administrator in which Collins' religious beliefs have interfered with his work.
Harris' whole argument revolves around his theoretical claim that there is "a perfect contradiction between reason and faith." Without ever suspecting it, though, Sam Harris actually ends up having no choice but to argue against his own position. You see, he must contend that this "perfect contradiction between reason and faith" exists in spite of the fact that the personal religious beliefs of scientists quite obviously do not interfere with their scientific work!
After all, if Harris could produce concrete examples (also known as "evidence") of personal religious ideas interfering with the work of accomplished scientists, well, then wouldn't he? But not only can Harris not point to any time in Collins' life when his own personal beliefs interfered with his science, he cannot point to any examples of this ever happening to any scientist!
What Harris is doing, then, turns out to be the exact opposite of science: he is demanding that the facts fit his theory! His theory, as he never tires of repeating, is that religious beliefs are incompatible with the ability to "think like a scientist", and especially with the ability to be an able administrator of a large scientific institution like the NIH.
I am not sure how far along Sam is in his scientific studies (he does hope some day to be a scientist himself) but apparently he has not yet learned about what biomedical scientists (like the ones who work at NIH) call a "dose-response relationship".
You see, if exposure to something, like religious ideas for example, has a certain effect, like a diminishing of one's capacity to reason, then the more one is exposed to measured doses of the substance in question, the more observable effect it should have.
According to Harris' own assessment Collins' religious views are of an especially egregious nature. In fact, Harris labels Collins' religious beliefs "simply astounding". But if we plot religiosity versus (observed) scientific ability, using Harris and Collins as data points (see figure above), we find the opposite of what Harris' theory predicts! A trained scientist knows what to do in such a case - but Sam Harris hasn't a clue. Let's hope someone on his thesis committee makes sure he figures this out before he gets his PhD!
The new essay, posted by Harris last Wednesday, begins with an "author's note" in which Harris explains that he felt the need to revisit and expand on this issue because "many of Collins’ defenders do not seem to be fully acquainted with his beliefs." But the real problem is that Sam Harris does "not seem to be fully acquainted" with the basic democratic principle of religious freedom, according to which, in the words of Thomas Jefferson
"all men shall be free to profess, and by argument to maintain, their opinions on matters of religion, and that the same shall in no wise diminish, enlarge, or affect their civil capacities."When the Virginia legislature finally, after eight years of rancorous debate (the measure was strongly opposed by Christians who felt it threatened them!), approved Jefferson's bill on religious liberty, he wrote to his friend James Madison (who had also worked hard for its passage): "it is honorable for us to have produced the first legislature who had the courage to declare that the reason of man may be trusted with the formation of his own opinions."
Nowhere in either his original editorial or in the bigger, longer, uncut version does Harris ever address the question of religious freedom. One wonders what Harris' views on that subject really are. Does he believe that the idea of religious freedom is now just a quaint relic of the past? If all religion by definition is the enemy of reason and science then what possible merit could religious freedom have? Doesn't Harris at least respect freedom of thought? But how could one claim to support freedom of thought if one does not support freedom of religious thought? If Harris had hoped to exonerate himself from the charge that he is proposing nothing less than narrow-minded bigotry, he has spectacularly failed.
[The Calvin and Hobbes cartoon was found online at the cooperativeindividualism.org (whatever the frak that is) website as a result of doing a google image search on "calvin hobbes science" (without quotes). The cartoon appears in Bill Watterson's timless classic Scientific Progress Goes 'Boink'.]