Most of the time, The New Yorker deserves every bit of its lofty journalistic reputation. But there are some subjects on which it regularly falls flat, and none more so than religion, coverage of which often sounds like it's written by a badly trained anthropologist studying the inexplicably primitive population of an alien civilization.

Take cosmologist Lawrence Krauss' bluntly titled essay ''All Scientists Should Be Militant Atheists.'' It's hard to know where to begin in enumerating its philosophical superficialities and elementary confusions.

There is, to begin with, the way Krauss slips so quickly from criticizing Kim Davis' recent act of civil disobedience in the name of her faith, with which very few Americans sympathize, to a sweeping denunciation of religious freedom in general.

In religious freedom cases, the law typically treats different kinds of claimants very differently: individual believers working (like Davis) for a government office or agency; individual believers working for private companies; private businesses owned by believers (as in the Hobby Lobby case); organizations owned or run by private citizens but affiliated with churches; churches themselves — each of these is held to different standards and granted, in the name of religious freedom, different kinds of accommodations and exemptions from laws and regulations.

But Krauss treats them all as interchangeable and flatly asserts that ''religious ideals'' shouldn't be ''treated differently from other ideals'' or ''elevated'' above them. Maybe so. A few scholars and even a judge or two hold something like that stridently secular position. But it's hardly the consensus view of American jurisprudence, it seems to run roughshod over the opening clauses of the First Amendment, and Krauss doesn't even begin to substantiate or defend it. He just blithely assumes its truth and then moves on.

Then there's Krauss' seeming inability to distinguish between social norms of civility that sometimes persuade atheists to refrain from attacking the religious beliefs of their fellow citizens and laws that officially ''endorse, encourage, enforce, or otherwise legitimize the suppression of open questioning in order to protect ideas that are considered 'sacred.'" Surely informal public politeness and theocratic despotism backed by law are very different things. Yet Krauss appears not to notice the difference.

But those are minor problems compared with the ones embedded in Krauss' core defense of scientists acting as ''militant atheists.''

To be clear, Krauss isn't making the limited, and defensible, point that scientists should criticize the assertions of fundamentalists. He's not saying, for example, that scientists should teach forthrightly that the universe is 13.82 billion — and not 6,000 — years old. No, Krauss has gone much further — to take his stand against all appeals to ''the sacred'' as such: ''In science, of course, the very word 'sacred' is profane. No ideas, religious or otherwise, get a free pass.''

The problem is that ''the sacred'' has far wider scope than Krauss appears to realize. Moral — and not just religious — experience is unthinkable without the idea or feeling of sacred restraints. Such restraints are what ground our intuition that certain acts are intrinsically right and wrong. They are what keep us from engaging in injustice when we would personally benefit from it and there is no reasonable threat of legal detection. They are, in part, what fills us with furious indignation when we are victims of injustice, especially when the injustice goes unpunished by the legal authorities. In such cases we feel that some higher (sacred) law or moral standard has been transgressed.

Now Krauss might respond that this feeling of intrinsic rightness or wrongness is just a holdover from monotheistic religious traditions that we can and should dispense with. But this gets the causality backwards. The sense of sacred restraints has roots independent of religion, in morality itself. It is our moral convictions and hopes that have led most people who have ever lived to presume that some kind of deity or other providential force will ensure that the righteous are rewarded and the wicked are punished for their actions, in this life, in the next, or in the fullness of cosmic time.

Krauss might also insist that the belief in intrinsic right and wrong — and the sense of sacred restraint that accompanies it — is just a product of our internalization of legal strictures, which are always a human creation. But once again, the reverse is true: Law is founded on and acquires its perceived legitimacy in part from the sense that it codifies, backs up, and enforces the sacred restraints we perceive even in the absence of law. Rights may be the most obvious contemporary example. Most of us believe that individuals have rights prior to or apart from the institution of government, that government exists to protect these pre-political rights, and that a government that fails to do so (or that transgresses them itself) has forfeited its legitimacy and may rightly be deposed.

The consequences of Krauss' failure to clarify these matters can be seen most clearly in the least coherent paragraph of his essay, where he attacks critics of Planned Parenthood by writing that many of them "are opposed to abortion on religious grounds and are, to varying degrees, anti-science.'' I have no idea where Krauss got the idea that critics of Planned Parenthood are ''anti-science.'' Because he cites no polling data on the matter, we must presume he thinks it follows from the fact that ''many'' of them are ''opposed to abortion on religious grounds.''

But it's unclear how he knows this either. Critics of Planned Parenthood haven't been quoting scripture or appealing to church authority in their writings and public statements. Moreover, to oppose the lethal violence of abortion — and the conducting of medical experiments on tissue acquired without consent from its victims — one need only believe that the creature killed in the procedure is a human being and that all human beings have an intrinsic right to life. The first is a judgment call based on genetics and backed up by ultrasound technology; the second is a moral conviction shared by nearly all Americans, religious and secular alike.

So what exactly is Krauss' problem with critics of Planned Parenthood? Could it be that he merely disagrees with them, doesn't want to bother arguing against their position on its own terms, and prefers to delegitimize that position by calling it "religious"?

If you already view "religion" with contempt and relish the prospect of brandishing the term as a weapon to vanquish moral and political opponents, then Krauss' "militant atheism" is for you. As for everyone else, they will see it for what it is: a dogmatic counter-faith that resembles the fundamentalism it professes to despise far more than it does the genuinely open-minded, scientific pursuit of truth in matters moral and religious.