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Essay:An opinion on the nature of the movement
So the Deep Rifts that Pharyngulites used to joke about? They really do exist.
The atheist/skeptical community is, to put it charitably, a big, blobby mess. It's an overlap of two somewhat related but very distinct concepts, and a fairly complex overlap at that; there are certainly skeptical believers (admittedly, mostly agnostics; Martin Gardner, during his lifetime, was the most prominent example), and there are atheists who aren't very skeptical at all. In fact, though I identify as an atheist myself (the "no evidence, no belief" kind), I'm of the opinion that atheism per se isn't as important as general skepticism.  I do get the sense that a lot of people simply don't have a clear view of what the whole movement is supposed to be about; while laughing at crackpots is always fun, it's my belief that the fundamental mission of the movement is educational, and that any other view of it is really missing the point.
A digression on geek pathologies
Here's a fundamental problem with the whole issue: most skeptics are geeks. Most geeks grew up on the wrong side of the social tracks, and many carry a well-deserved chip on their shoulders. And most geeks are pretty smart, although I'd argue that most of us are not nearly as smart as we think we are. The result is that there is a toxic streak that goes straight to the core of geek culture. The result is that way too much of geek culture has traditionally been built on in-jokes, lodge passes, and aggressive gatekeeping by whatever passes for graybeards in any particular context; where real life (and science) are often messy and given to side effects, practitioners of the geek arts (by and large, people who should know better) often display a terrifying degree of compartmentalized thinking. Geek culture has way more than its share of people who have believed too much of their own press and think they can think their way around anyone; among other things, this is how we got the explosion of scientists taking the side of woo during the Human Potential movement in the 60s and 70s, with people like Jack Sarfatti and Harold Puthoff falling for the weak-assed magic tricks of Uri Geller or Ted Serios because they believed that a professional magician had nothing to teach scientists.
The result: many geeks have become too bitter and angry to relate rationally with the rest of the world, and have actually become worse than the people that ostracized them; male geeks in particular seem especially inclined to direct this ire towards women, who they apparently associate with all the girls they wanted to fuck in school who paid no attention to them, as well as anyone they perceive as having had too easy a ride in life (which may explain why big-L libertarianism is so popular, despite its total lack of ability to deal with life being messy and full of side effects).
People come to learn, so we should teach
The widespread perception, of course, is that science is cold, technical, and emotionless. The whole concept is so ingrained that TVTropes, in its discussion of the concept, uses the term Straw Vulcan to describe it, acknowledging that emotion and logic aren't mutually exclusive at all; science, in fact, is driven by people who find the world outside their own senses to be fascinating and exciting in a deeply primal sort of way. (There is a saying some atheists like: "Your God is too small for my universe.") In fact, the universe is deeply, profoundly, and wonderfully weird, and science has been so successful at describing it that it's unreasonable to assume that given enough time and interest, that science can't describe literally everything about it. This, fundamentally, is where the intersection of atheism and skepticism lies: we don't need a God because what we think happened is way more interesting.  Perhaps counterintuitively to those encountering the concept for the first time having only known the term "skeptic" as someone resistant to change, skepticism is about defining what it really means to have an open mind. Our mission should be to make "question everything" more than simply a reflexive cry of rejecting authority, and treat it as a call to curiosity.
Now the question is, are we doing this? Certainly most skeptics will say they're doing this. The James Randi Educational Foundation is explicit about this in their name, and yet some of the JREF's brass were decidedly on the wrong side of Elevatorgate. (Randi himself never weighed in, although he was willing to admit error when his lack of expertise put him tentatively on the wrong side of the global warming debate. So he's probably okay himself.) But...
We have reached a strange point in history where geekery and science, traditional allies, seem to have started to diverge. Genre fiction (especially SF and fantasy) and comics of all sorts remain common themes, as do movies and video games. But we've reached a point where a political chasm has opened up in the last couple of years that roughly follows an orthodox science/center-to-left vs transhumanist/libertarian-to-right-wing divide, and it has gotten phenomenally ugly. Since this article is in essay space and represents an opinion, I don't mind stating that I'm firmly on the orthodox science side, as well as being decidedly to the left; this is a position that I seem to share with the overwhelming majority of working scientists, as well as the academic mainstream of economists, most of whom lean more or less Keynesian in roughly the same way that biologists are Darwinist. As such, I believe that history and science both show that it's smarter and more constructive to concentrate on peoples' similarities rather than their differences. I'd even argue that this is actually self-evident, but since so many people seem to have a problem with such things, I'm probably wrong about that.
I also think that history has shown that for someone who truly claims to be rational, humility is a very good thing indeed. Granted, science has its assholes, but the ones people remember tend to have been either correct or spectacularly wrong. The problem is that humility is sometimes treated as weakness, doubly so when assholes turn out to be right about their claims and are seemingly rewarded for their dysfunctional behavior. Consider Edward Teller; from a strictly objective point of view, Teller wasn't stupid, but his out of control ego proved something of a liability within the US nuclear weapons establishment, and it's generally agreed that without Stanislaw Ulam's help, Teller's work on the hydrogen bomb wouldn't have succeeded. But Teller's willingness to schmooze the most paranoid people in power proved to be incredibly toxic; he got Robert Oppenheimer railroaded out of the community on suspicions of communist sympathy, a move that most of his colleagues attributed to Teller's resentment of Oppenheimer's belief that the H-bomb was unnecessary, and he spent the rest of his career using politically-motivated FUD to shore up his position and forward increasingly strange schemes, which culminated in the probably-nonfunctional SDI x-ray laser warhead. If you want a prime example of what lack of humility can lead to, look at Teller's influence on the Cold War and the resulting billions of dollars spent on quixotic missile defense schemes and the like; I'm not a big fan of the monolithic concept of the "military-industrial complex", but if any one person embodied it, it was Teller.
Now take a bunch of social outcasts, feed them ego-boosting propaganda like Ayn Rand that convinces them that smart people can do no wrong in a culture that already depends way too much on dogma, and immerse them in black box thinking, as if everything in life is a module in a computer program... then tell them that there's no God. Yeah.
When you can't tell the difference between an open and closed mind...
The point here is that if you consider skepticism an end in and of itself, you're doing it wrong. Rationally-based empirical study is the best way we've found yet to examine the world; when you've found a way to explain love, you're doing pretty damn well, I should think. But it's still a tool, not an end; the end is to find answers to the highest degree of certainty we can, and use those answers to find other answers. Skepticism is part of that tool, and a tool in its own right. You can only claim the high ground if you're using that tool correctly, and using it to justify your preconceived views on society, as opposed to deriving said views from it, is doing it wrong. And yet, that's what a lot of skeptics seem to be doing, which is why so many alleged skeptics seem to cling so tightly to ideas like evo psych or Libertarian economics, despite the fact that both have been shown to come from a world view most charitably described as myopic.
One symptom of what we're dealing with relates to the perception of feminism. There are (as you should probably know) numerous strains of feminism. We're very harsh on some (especially that subset of radical second-wavers that tend towards isolationism and/or woo), but quite accepting of the baseline concept that hey, women are people who deserve respect and rights, and have the right to determine the direction of their lives on their own terms. (This, basically, is what third-wave/sex-positive feminism is about, by the way.) Of course, the problem is that the anti-feminist faction either can't or won't make the distinction. You can demonstrate the existence of male privilege till you're blue in the fingers and they'll still deny that it exists, and all the slutwalks in the world won't rid some people of the perception that if a woman asks for it once, she owes it to everybody.
I are stuck. What do?
Fortunately, in some ways, we're already doing it. RationalWiki is pretty well-known as a source for debunkery, at least outside the community of blinkered reactionaries that I was ranting against. One key message we've had some trouble getting across, though, is that while there really are no limits to what can be questioned, falling back on bullshit (like Forteans) or prejudice (like said blinkered reactionaries) does not qualify as skepticism; it's just juvenile self-delusion.
Now dealing with that... that's the hard part. The use of terms like "ftbullies" and the like is meant as a shaming tactic, as if to say that by embracing feminism and social justice issues while avoiding Libertarian thinking, transhumanism, and the like, we are selling out our fellow geeks and have become, essentially, the jocks.  I'm not convinced that such people can even be reached. 
- I'm not exactly sure where that puts me in relation to the whole debate, but it is what it is.
- See another essay of mine, Essay:Open Source and the insanity problem, for further points on the matter, and the rather horrifying outcomes thereof.
- The popularity of evolutionary psychology and the seduction community among geeks would seem to back this up.
- And if there was, in fact, a God behind all of it? Science wouldn't stop there. The next step would be to create and test a Theory of God.
- Thanks to Emo Philips for one of the great religion jokes of all time.
- As opposed to thinktank economists, who tend to make good livings telling the political Right what they want to hear.
- And still assholes either way; nobody honest is going to pretend that William Shockley wasn't a loathsome bigot, or that James Watson didn't screw Rosalind Franklin out of deserved credit for her X-ray work on DNA.
- See: every male geek who refuses to believe women -- even attractive ones like, say, Nixie Pixel, Adrianne Curry, or Alyssa Campanella -- can be geeks, and sometimes even be part of the cool crowd while doing it.
- And you know things have gotten bad when even PZ Myers gives up.