I quote: "There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference."
Here's the article.
His argument is an argument that I have heard before (I think it's his standard argument); that religion - any religion - is out of keeping with science, and as such the battle has to occur. Tolerance on the part of either side will simply end with that side being taken advantage of. Namely, in Sam Harris' case, the atheists have to take a strong view espousing reason at all costs - and particularly at the cost of God - in order not to be abused. To be utterly honest, it is a tempting view especially after seeing atheism blasted in various forums, and being told that I am not a good person or am going to Hell. Of course not all of my religious friends have told me that, and in fact a few of them have told me that they don't believe it, but it is a striking statement that the fact that some of my religious friends have told me that or things like it does not mean that I am not friends with those people anymore.
(P.S. Please don't read this as a plea to have my religious friends tell me I am not a bad person. It isn't. After a lot of deliberation I have decided that I couldn't care less what someone else thinks of my actions. At this point in my life, I can honestly say that I regret none of my actions, and that I do not think I behaved poorly in any major occasion and did not at least try to make up for it. Except that time I shot four men in Vegas. But you know what they say; what happens in Vegas stays in Vegas.)
In any case, the man brings up some good points; basically amounting to the fact that at least in a scientific journal, we don't have to lower ourselves to the kind of politically correct "Of course there are no contradictions between science and religion" that we do in other forums, and that since we do not have to stoop to that sort of, well, lying, we shouldn't. For example: "In his Commentary, Sardar seems to accept, at face value, the claim that Islam constitutes an "intrinsically rational world view". Perhaps there are occasions where public intellectuals must proclaim the teachings of Islam to be perfectly in harmony with scientific naturalism. But let us not do so, just yet, in the world's foremost scientific journal."
I think a nicer way to phrase his point, in general, is that religion never constitutes a rational world view, but that it doesn't even attempt to. It is impossible for religion to be rational because its agents are by their very definition arational or superrational. And perhaps there shouldn't be a value judgement attached to that.
The problem is where to draw the line. If you let someone believe something of which there simply cannot be any evidence or something which is simply a personal opinion (such as the existence of God or when life starts, respectively), you aren't saying that when faced with contrary evidence they should deny it. The existence of God or a Universal soul or merely something cannot really be proved or disproved, and so there is nothing requiring someone to deny reason and evidence simply because they believe in God. So we can say that the belief of God is perfectly in harmony - or could be perfectly in harmony - with the practice of science.
Then you get to things that we simply don't know yet. They are potentially knowable, but we don't know them. I'd put things like the physical cause of "the soul" (will and consciousness), here. There are a lot of people trying to figure it out, and it's possible that in the future some religious belief will be contradicted by evidence and reason. But at the present time, we don't know - all anyone has right now is a belief or a hunch or a gut feeling. In this case, perhaps, most people who lean towards atheism lean towards one answer and most people who lean towards religion lean towards another. But that's all there is - a lean - there isn't a clean line and there isn't a clean disharmony between the two views, at least in principle.
Of course, there are quite a few things that we do know, and that are hard to contest using reason and evidence, but are still contested issues simply because religious people make them so. For example, evolution. We've seen evolution take place in petri dishes (see here) and the paleontological and genetic evidence of relation between humans and other primates is huge, but there are still crackpots and religious nutters saying that all of that means nothing, because of a passage in the Bible or the Koran or whatever that says God created man in his image, period, end of story. Or who are masquerading as scientists saying that life is "too complex" to have developed through a process of natural selection (something which is, it seems to me, complete bullshit). This one, in my opinion, comes down pretty clearly to religion versus science. Either you believe what is written in the Bible or you believe in what we have learned and theorized and figured out. You can't believe both. Here, religion and science are directly at odds. There are religious people who believe in Darwin's theory of Evolution through Natural Selection, but they are choosing which parts of their religion to believe. And that's a slippery slope, because if you only believe some parts of the Bible literally, then why should you believe any of it? If you don't believe the Bible when it tells you that the ratio between a circle's circumference and its diameter is 3, why do you believe the Bible when it tells you that homosexuality is a sin, and why do you believe the Bible when it tells you that Man was Created in God's image?
But the point is that it's a continuum. There are plenty of things that the scientific community isn't quite certian of and religious views push you one way or another on. There are all sorts of intermediates. And you have to draw a line somewhere, except there's absolutely no clear place to do it. And so 44% of Americans say they judge atheists harshly, and people like Sam Harris say that the "forces of unreason" are attacking science, and we have to fight back or we will be defeated.