There are many factors that lead to the troubling DiversityImbalance that we find in the software community. Some of these, like the problems in teenage education that discourages girls from STEM subjects is a long term problem where our profession can't play a central role in fixing . But one factor that comes down directly to us is the alienating atmosphere that hangs over the tech community.
One of the hardest things about talking about this alienating atmosphere is that it's something that's experienced very differently depending on who you are. For most middle-class white guys like me, it's something we've rarely experienced. Yet for many people in HistoricallyDiscriminatedAgainst populations it's a constant indication that "you're not welcome here".
One of the sharpest technologists I know is a woman who has been in the industry for a long time, much of it in technical leadership roles. There's nobody I'd rather have at my side in an important architecture meeting or reviewing a draft of mine that's veering into deep language theory. Yet she still says that she feels a reaction as she walks into a gathering of techies where nearly every face is different to hers, a little voice saying "this place is not for you". If such a reaction still strikes someone as accomplished as this, we shouldn't be surprised to see it elsewhere.
That basic reaction is set off just by the disparity in numbers, which is a long term problem to solve - but it can amplified by things within our short term influence. Sexually-oriented jokes tend to reinforce a men-only locker-room atmosphere which many women do find alienating. Many women have had real incidents of harassment, such jokes remind them of that. And although the chances of a serious incident are slim, they are not zero. 
If you have any doubt about how ugly this can get, just peruse the comments on a blog or news entry whenever this kind of thing comes up. The bile that falls on people who criticize alienating incidents is both vile and sadly predictable. Ironically the bilers often complain about censorship infringing their right to make sexual jokes, but not acknowledging that fear of the intermobs imposes its own censorship. I know several articulate women who will not post their opinions because they don't want to have to deal with this inevitable backlash.
There's an important asymmetry here. I've occasionally been on the receiving end of some nasty satire, but that's not such a big issue for me because I'm in a position of relative influence in the software world as well as part of a historically powerful group. For people from historically-discriminated-against (HDA) populations the dynamic changes. Such attacks reinforce the history of exclusion and oppression, and trigger fears of physical attack. Merely the fact that people think it's ok to make such attacks makes it clear that "your kind is not welcome here".
Trying to clear internet atmosphere of this feels like trying to deal with global warming - what can we do?
A first start is just to be aware that different people will react differently to the same things. One person might not find a remark offensive while it really hurts someone else. A phrase I've found useful in the past is I can't choose whether someone is offended by my actions. I can choose whether I care. If someone reacts in an hurt way to something I say, I don't get to say "you can't be offended by that". Their reaction is a result of their life experiences, which will be different to mine. Often HDA people gets lots of these small hurts, individually they don't mean much - but the sheer quantity has a big cumulative effect.
While I can't tell someone if they should be hurt or not, I can choose whether I care about the hurtful feeling. And it is a choice. I have offended some people when I've said we should treat gay people equally. In that case say I don't care very much. It's my choice that I'm not concerned about hurting the feelings of homophobes and I accept responsibility for that decision.
I do care, and think we as a profession should care, about this kind of thing with HistoricallyDiscriminatedAgainst groups. Correcting these long-term discriminations takes time, and can't be solved by just saying "we're all equal now". An alienating atmosphere against women, both in our profession and on the wider internet, reinforces an injustice that's been perpetrated for thousands of years. While I cannot be responsible for what my ancestors did, I can take responsibility to play what small part I can in cleaning up their mess.
I don't find it straightforward to learn about what causes alienation and how to avoid contributing to it. I try to pay attention to incidents when they come up and to listen to those who feel attacked. Not all women are alienated by an act, so I have to make a judgement about what proportion of people are going to react - is it just this one person, or is this individual the only one of many who felt brave enough to speak out?
I've found it valuable to find people who I can confidently talk to about these issues, and I certainly recommend searching out a few people who can act as guides. It's important to get a variety here, as different people react differently - it's easy to miss things by generalizing from opinions that are too few or not diverse enough. I feel that these steps have increased my awareness over the years, but it's far from being a territory I can be confident in.
Once we can begin to sense the alienation in the atmosphere the next step is to try to create environments with cleaner air. An example is how many conferences now have code of conduct policies designed to spell out that certain behaviors are not good manners. They can (and must) reinforce this by making it easy for people to make complaints and dealing with them swiftly and fairly. Yes, there is a risk that specious complaints will be made, and these are frustrating, but in practice the problems due to these are much smaller than the problems that never get reported. 
One question is what people in the majority groups should do when they detect some miasma in the air. If I hear a bunch of guys making sexual jokes in clear earshot, should I intervene? I don't find this an easy question to answer. I don't have high confidence in my ability to detect whether a group I care about is going to be offended by things that I personally don't find offensive, so I'd be reluctant to overreact myself.
But I agree with the notion that the standard you walk past is the standard you accept. Many women are sick of complaining about this kind of behavior because these complaints often only lead to more trouble. So I think it's important for all of us to battle against this miasma, to intervene when someone is fueling the bad air and to support someone's right to speak up and say they are feeling excluded.
So I believe I have the responsibility to act when such things happen but I say this with trepidation, I have that British thing about wanting to avoid fuss-and-bother, so my natural inclination is to let things go when I'm feeling offended. I know that even in the last few years I've missed opportunities to speak up when I should, but I know that I should not let that stop me from doing better in the future . We must change this culture of silence.
In particular we must avoid supporting this alienating atmosphere. Sadly such support appears when people attack those who are trying to fight it. Often women who complain about alienating incidents are told to "grow a thick skin". I find this kind of support for NetNastiness deeply annoying.
I value people with good ideas and don't consider the thickness of their skin. Anyone driven away from expressing innovation or writing excellent code is a loss to all of us, however unoffended we think they should be.
Amanda Hess gives a sad but worthwhile summary of attacks against women online. These are wider than just within the tech community, but are typical of what women have to deal with here too.
Ashe Dryden writes about the risks and rewards of speaking up to oppose the alienating atmosphere in tech. The post includes responses to common misconceptions and suggestions of how to help.
Often it's seemingly tiny things that contribute to the alienating atmosphere - things that are just one droplet of miasma on their own, but form a big cloud when you run into them every day. Do read Kat Hagan's excellent post describing them. Derrick Clifton has a similar piece on common reactions to racism.
2: Fear of physical attacks
Physical attacks are rare, but do sometimes happen. Recent statistics in the US indicate that 2 per thousand women suffer rape or sexual abuse each year (4 per thousand for younger women). Another survey focusing on college women found 35 women per thousand per year suffered sexual victimization in college.
It's also important to note that the fear of an attack, even if irrational, is still a factor. As one reviewer commented "I once had a rather unpleasant experience with a male colleague, I spoke up and took a stand and pretty much held my own. But after that, I couldn't shake off the fear for days together, that he might turn around and physically harm me! This was probably the farthest thing from a possibility - but that thought was with me with an annoying amount of conviction. And every time I take a stand I feel a pinch of that."
Someone can be very sure intellectually that there isn't a threat of a physical attack, yet the debilitating emotion is still there. These reactions come from triggers that are deeply ingrained in our culture.
3: The best study into this that I could find indicated that false report rate was somewhere in the range of 2-8%
4: It's difficult talk about what to do because different cases are so varied. Even with a specific example, I frequently find myself at a loss. I've often thought about what action I should take if I found myself in an audience for a talk that uses sexual imagery to illustrate its concepts. I know I should do something, but I confess that I'm unsure what it should be - which gives me little confidence that I'd do the right thing.
Pink and Blue
When preparing the illustrations for the article, I puzzled a good bit about whether to use the pink and blue colors you see here. Many people, including me, object to the gender stereotyping of these colors and I don't like to reinforce it. But in the end I felt that using the gender associations of these colors helped the illustrations communicate better (as opposed to using more neutral colors). I also tried using light and dark brown in a similar way (as the alienating atmosphere is true of race too) but pink/blue scheme provides more striking color.