For a place with a reputation for innovation and modernity, Silicon Valley remains in many ways an old boys’ club. Sure there are women like Facebook Chief Operating Officer Sheryl Sandberg and Yahoo Chief Executive Officer Marissa Mayer. But by and large, there are few women in leadership positions in the hotbed of entrepreneurship.

Twitter, which recently filed for an initial public offering, has no women on its board, which prompted Stanford’s Rock Center for Corporate Governance Fellow Vivek Wadhwa to tell the New York Times in early October, “This is the elite arrogance of the Silicon Valley mafia, the Twitter mafia.”

The lack of women is not a problem isolated to startup boardrooms. Women are significantly underrepresented in Congress as well, and nationally, they still earn less than 80 cents for each dollar men earn.

Clearly, there’s work to be done.

But the problem is especially pronounced in Silicon Valley, where just a fraction of executives are women.

Here are three reasons the number of women in leadership positions in Silicon Valley remains stubbornly low:

1. “Brogrammer” Culture

Sure computer programming conjures an image of geeky guys in dark rooms banging away at their keyboards that does little to invite consideration, but it goes beyond that. Female junior level programmers are leaving the industry and many say its because of a “bro” culture at the office.

As VentureBeat pointed out earlier this year, “One quote from [a National Science Foundation] report is particularly troubling, especially as it reflects the experience of many women: ‘At my last engineering job, women were fed up with the culture: arrogant, inflexible, completely money-driven, sometimes unethical, intolerant of differences in values and priorities. I felt alienated in spite of spending my whole career trying to act like a man.’”

Most women in the industry won’t talk publicly for fear of professional retribution, but there are plenty of public stories. Startup founder (he created payment company Celery) Peter Shih posted a list of what he hates about San Francisco and named 49ers his number five.

“No, not the football team, they’re great,” he wrote. “I’m referring to all the girls who are obviously 4’s and behave like they are 9’s. Just because San Francisco has the worst Female to Male ratio in the known universe doesn’t give you the right to be a bitch all the time.”

Programmers Jethro Batts and David Boulton recently joked at a hackathon about a parody app they created that uploads photos of guys ogling women’s boobs.

“I think this is the breast hack ever,” Batts quipped.

Companies can throw as many free meals and perks at employees as they want, but few women will stay if the environment continues to be so toxic.

2. Few Women Major In Computer Science

It’s pretty hard to get women into Silicon Valley boardrooms when they’re not entering the appropriate classrooms in the first place.

As the Los Angeles Times noted, “Women say the problem begins in computer science classes where they are marginalized and persists throughout their careers as they are passed over for jobs and promotions.”

The number of women graduating from computer science classes has actually declined in recent years. In 2010, only 17 percent of computer science graduates were female. In 2000, that figure was 28 percent.

There are efforts to get more women into those majors but word about the “brogrammer” culture also spreads among potential candidates. Those who do choose such majors have trouble finding female mentors and professors do little to encourage them to pursue advanced studies in the field.

3. The Old Boys’ Club of Venture Capitalism

Venture capitalists hold the purse strings in Silicon Valley and those strings are firmly attached to male hands.

According to the National Venture Capital Association, nearly 90 percent of them are (mostly white) men. That’s not to say that men can’t invest in startups pitched by women, but so far, funding has gone mostly to men that look a lot like the venture capitalists who gave it to them. That’s a problem because the harsh reality is that funding can launch a winning company and brilliant ideas can flop without it.

A junior partner at one of the most renowned firms, Kleiner Perkins Caufield & Byers, filed a sexual discrimination lawsuit against the company and colleagues last year, alleging retaliation after spurned sexual advances.

So what can be done?

Sexism doesn’t have to be inevitable.

As New York Times columnist Nick Kristof wrote recently, “Companies sometimes protest that they can’t find qualified women. Rosabeth Moss Kanter, a professor at Harvard Business School, said that the real problem is boards trying to replicate themselves and that plenty of women would add value to the Twitter board. ‘I could come up with 30 names without thinking too hard,’ she said, adding that the challenge is to ‘look more broadly for talent, and be more welcoming to people not identical to those in power.’”

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