The current spat in the "atheist movement" is a cause for some glee in certain theistic quarters, with suggestions that if a reconciliation of the "schism" (currently exemplified between "new atheist" blogger PZ Myers and atheist YouTuber Thunderf00t) cannot be achieved, then the "movement" is doomed.
This, I think, misunderstands the nature of the split. The "atheist movement" was never a cohesive body, and likely never will be. Some Christians are suggesting that the movement's leaders need to make a stand, issue some decrees and whip the dissenters into line, or else the movement will fragment and disintegrate. But atheism as a movement has never been integrated. There's no doctrinal dogma to which atheists are required to subscribe, no articles of faith. The only thing that all atheists have in common is a disbelief in gods. Beyond that, they are as disparate as any random collection of individuals. That such a group could even begin to consider itself a "movement" is, to put it charitably, optimistic.
There are no atheist leaders, just some atheists who tend to be more vocal than others. It is in the nature of freethought not to take things on authority alone, so any calls for prominent atheists to grab the movement by the scruff of the neck and shake some sense into it will be for the most part ignored. Atheism will not fragment as a result of this latest hoo-hah because it's already fragmented, by definition.
The current controversy over sexism in the skeptical/atheist movement is, as far as I can see, merely an extension of the well established conflict over non-overlapping magisteria (NOMA). With regard to potential incompatibilities between religion and science we have two factions: on the one hand those who claim that science and religion are fundamentally incompatible — and the source of a great many problems in today's culture — and on the other those who claim that it's possible to find an accommodation between science and religion because they deal with different realms of enquiry. Atheists on each side of the NOMA debate will be forever opposed, because each side has a different way of dealing with religion. Arch-accomodationists will take a pragmatic approach to working with theists, on the basis that theism doesn't deal with scientific matters. Extreme anti-accommodationists will simply refuse to work with theists on scientific matters on the basis that theism does deal with scientific matters, but in an unscientific way.
In the sexism debate, views divide down the middle in a manner similar to the NOMA split. On one side are those who say that sexism is a problem that needs to be addressed (by, for instance, talking openly about it rather than sweeping it under the rug, and by implementing clearly stated harassment policies wherever these might be appropriate), and on the other are those who say that though sexism certainly exists, it isn't a particular problem in skepticism/atheism — any more than elsewhere — and that the current disagreement is a molehill that has blown up into a raging volcano.
I've no idea if what I'm about to write will alienate some of my readers, but I feel I must be open about my own biases on these matters.
Taking NOMA first, though I can see the value of making nice with theists in order to get things done (and because they are people — and therefore deserving of respect and consideration), I see no merit in pretending that science and religion are compatible when even a superficial examination shows they are anything but.
Second, on the question of sexism in general and the problem of sexual harassment at skeptic/atheist events in particular, some women have reported that there is a problem. Are we to ignore this? Certainly not. As a man I don't experience the types of unwelcome attention that are being reported (and have been reported in "the movement" for over a year now) so I can only go by the reports. The fact that some other women have said that in their experience it isn't a problem is insufficient reason for not doing anything.
It seems to me that in both the NOMA debate and the discussions (I use the term advisedly) about sexual harassment, PZ Myers has got it right. His stand on this and other matters speaks of an intellectual integrity that is to be admired rather than dismissed. His uncompromising attitude may well alienate many, but that's because he will not accommodate. Often I find his views quite unpalatable, but as far as I'm aware he always gives his reasons, and I find I usually agree with them.
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