Monthly Archives: November 2011

Head and shoulders photo of Margaret Dayhoff

Wednesday Geek Woman: Margaret Dayhoff, quantum chemist and bioinfomaticist

This post appeared on my blog for Ada Lovelace Day 2011.

Head and shoulders photo of Margaret Dayhoff

It’s become kind of a cliché for me to claim that the reason I’m happy working on ACPI and UEFI and similarly arcane pieces of convoluted functionality is that no matter how bad things are there’s at least some form of documentation and there’s a well-understood language at the heart of them. My PhD was in biology, working on fruitflies. They’re a poorly documented set of layering violations which only work because of side-effects at the quantum level, and they tend to die at inconvenient times. They’re made up of 165 million bases of a byte code language that’s almost impossible to bootstrap[1] and which passes through an intermediate representations before it does anything useful[2]. It’s an awful field to try to do rigorous work in because your attempts to impose any kind of meaningful order on what you’re looking at are pretty much guaranteed to be sufficiently naive that your results bear a resemblance to reality more by accident than design.

The field of bioinformatics is a fairly young one, and because of that it’s very easy to be ignorant of its history. Crick and Watson (and those other people) determined the structure of DNA. Sanger worked out how to sequence proteins and nucleic acids. Some other people made all of these things faster and better and now we have huge sequence databases that mean we can get hold of an intractable quantity of data faster than we could ever plausibly need to, and what else is there to know?

Margaret Dayhoff graduated with a PhD in quantum chemistry from Columbia, where she’d performed computational analysis of various molecules to calculate their resonance energies[3]. The next few years involved plenty of worthwhile research that aren’t relevant to the story, so we’ll (entirely unfairly) skip forward to the early 60s and the problem of turning a set of sequence fragments into a single sequence. Dayhoff worked on a suite of applications called “Comprotein”. The original paper can be downloaded here, and it’s a charming look back at a rigorous analysis of a problem that anyone in the field would take for granted these days. Modern fragment assembly involves taking millions of DNA sequence reads and assembling them into an entire genome. In 1960, we were still at the point where it was only just getting impractical to do everything by hand.

This single piece of software was arguably the birth of modern bioinformatics, the creation of a computational method for taking sequence data and turning it into something more useful. But Dayhoff didn’t stop there. The 60s brought a growing realisation that small sequence differences between the same protein in related species could give insight into their evolutionary past. In 1965 Dayhoff released the first edition of the Atlas of Protein Sequence and Structure, containing all 65 protein sequences that had been determined by then. Around the same time she developed computational methods for analysing the evolutionary relationship of these sequences, helping produce the first computationally generated phylogenetic tree. Her single-letter representation of amino acids was born of necessity[4] but remains the standard for protein sequences. And the atlas of 65 protein sequences developed into the Protein Information Resource, a dial-up database that allowed researchers to download the sequences they were interested in. It’s now part of UniProt, the world’s largest protein database.

Her contributions to the field were immense. Every aspect of her work on bioinformatics is present in the modern day — larger, faster and more capable, but still very much tied to the techniques and concepts she pioneered. And so it still puzzles me that I only heard of her for the first time when I went back to write the introduction to my thesis. She’s remembered today in the form of the Margaret Oakley Dayhoff award for women showing high promise in biophysics, having died of a heart attack at only 57.

I don’t work on fruitflies any more, and to be honest I’m not terribly upset by that. But it’s still somewhat disconcerting that I spent almost 10 years working in a field so defined by one person that I knew so little about. So my contribution to Ada Lovelace Day is to highlight a pivotal woman in science who heavily influenced my life without me even knowing.

[1] You think it’s difficult bringing up a compiler on a new architecture? Try bringing up a fruitfly from scratch.
[2] Except for the cases where the low-level language itself is functionally significant, and the cases where the intermediate representation is functionally significant.
[3] Something that seems to have involved a lot of putting punch cards through a set of machines, getting new cards out, and repeating. I’m glad I live in the future.
[4] The three-letter representation took up too much space on punch cards

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Anne McCaffrey

In memory of Anne McCaffrey

Anne McCaffrey

We lost Anne McCaffrey this week, to stroke. Yonmei remembered her gloriously at FeministSF (and if you don’t know her inspiration, reading that makes it even better.)

I was nine years old when my frenemy Claudia (precociously elegant with her hair in a glossy pageboy) read aloud to me: “Lessa woke, cold.” Dragonflight was my first contraband, and F’lar one of my first crushes. In a corner of the high school playground, determinedly ignored by the kids with friends, I was comforted by my flight of fire lizards, or hurtling through space as an embodied ship. When my text adventures in CPM/BASIC actually executed, it was like the black crystal picking up and amplifying my voice. I was young enough to extract maximum escapist value from McCaffrey’s worlds before her writing started to pall.

I hadn’t thought of her in years when I chuckled over Liz’s fierce and righteous takedown of gender (and race and disability) politics on Pern. McCaffrey was a product of her time, no question, and not the worst by any means. Ursula Le Guin works strenuously to re-examine and correct her older work, and with mixed success, but that’s part of what makes Ursula Le Guin so very full of awesome. We can’t expect it of every writer. Now, as we mourn McCaffrey, we have to find some way to honor both the worlds she gave us and the ground we’ve covered since.

Our foremothers fail in myriad ways, and we will doubtless look like hypocritical assholes to future generations too. Re-examining assumptions is good and important work (and might help us avoid our own worst excesses.) But without foremothers like McCaffrey – and the other writers of sexy, problematic contraband, like Marion Zimmer Bradley and Jean Auel – we wouldn’t even be having this conversation.

Thank you, dragon lady, for teaching us to sing.

Wednesday Geek Women: Mary Whiton Calkins and Elizabeth Spelke, psychological scientists

This is a guest post by Shauna, a psychologist, programmer, writer and blogger. This post appeared on her blog for Ada Lovelace Day 2011.

For Ada Lovelace day I thought I’d go back to my roots and write about a psychological scientist. Being as I am prone to digressions, I ended up writing about two – one historical, one current. We’ll go chronologically.

Mary Whiton Calkins was born in the 1860s in Connecticut who studied classics and philosophy at Smith College. She took a job teaching Greek at Wellesley College after graduating, where by a combination of luck and talent she caught the eye of a psychology professor. He asked her to come teach psychology, but requested she spend a year studying it first. It was in this way that Calkins started taking classes at Harvard, and with William James himself among her tutors and mentors, it’s maybe not surprising that her interest in the field grew. She spent the next two years taking classes at Harvard and doing research into dreams with collaborator Edmund Sanford. Though their research would soon be eclipsed by Sigmund Freud (who did acknowledge and cite their work), their discovery that dream content could be influenced by external stimuli is much in line with our current theories of dreams.

In 1891 she returned to Wellesley to teach, and established there an experimental psychology laboratory, the first of its kind at any women’s college and only the twelfth in the United States. Over the next ten years, she trained hundreds of women in experimental psychology, putting out articles on subjects such as child development, aesthetics, and synesthesia. Hoping to continue her studies at Harvard, she also petitioned the university to become a graduate student, but the college did not allow female graduate students at the time and she was refused. Nevertheless, she continued to take classes, and three years later an unsanctioned committee of six Harvard professors awarded her an unofficial doctorate. Despite numerous petitions over the last 100+ years, Harvard has never awarded her an official one.

Calkins’ biggest research contribution is probably her work on paired association, a memory technique that is still used today. My favorite work of hers, though, is Community of Ideas of Men and Women, an article she published in 1891 in Psychological Review in response to one Dr. Joseph Jastrow. Jastrow had looked at lists of words generated by women and men, and claimed then men showed greater variety in word choice. This, he said, was evidence for the “Variability Hypothesis” – the theory that men have a greater range of abilities than women, with more men than women falling at the high and low ends of any given spectrum. Calkins and her student Cordelia Nevins replicated Jastrow’s study but not his results, and in their paper called into question the fundamental assumptions of his research:

[Jastrow et al] by the expression “masculine and feminine mental traits,’ attempt a distinction between masculine and feminine intellect per se, and this seems to me futile and impossible, because of our entire inability to eliminate the effect of environment. Now the differences in the training and tradition of men and women begin with the earliest months of infancy and continue through life. Most of the preferences which have been substantiated by both experimenters, for instance that of women .for the surroundings of a home, are obviously cultivated interests… The question of the essential difference between masculine and feminine mind seems to me, therefore, untouched by such an investigation.

Unlike the good scientists of that era, the Variability Hypothesis is not dead and buried. You may remember back in 2005 a controversy breaking out when Harvard’s then-president Larry Summers speculated in a speech that underrepresentation of women in science in general, and in tenured positions at top-tier universities such as Harvard in particular, might be due to innate differences between men and women. Specifically, he suggested that men have greater variability in mathematical ability than woman, leaving them overrepresented at the highest echelons (as well as in the lowest mathematical gutters.)

In response to this controversy, the Harvard psychology department set out to debate that claim on its merits. Summers’ claims were defended by Steven Pinker, a well known linguist and evolutionary psychologist, who faced off against Elizabeth Spelke, a developmental psychologist whose done a great deal of research on gender differences in children. From the debate:

Let me take you on a whirlwind tour of 30 years of research in one powerpoint slide. From birth, babies perceive objects. They know where one object ends and the next one begins. They can’t see objects as well as we can, but as they grow their object perception becomes richer and more differentiated.

Babies also start with rudimentary abilities to represent that an object continues to exist when it’s out of view, and they hold onto those representations longer, and over more complicated kinds of changes, as they grow. Babies make basic inferences about object motion: inferences like, the force with which an object is hit determines the speed with which it moves. These inferences undergo regular developmental changes over the infancy period.

In each of these cases, there is systematic developmental change, and there’s variability. Because of this variability, we can compare the abilities of male infants to females. Do we see sex differences? The research gives a clear answer to this question: We don’t.

I recommend reading or watching the whole thing, and/or reading Spelke’s more formal review of the literature in American Psychologist. I particularly like Spelke’s point at the end, when she talks about the role of competition in science:

You’ve suggested, as a hypothesis, that because of sexual selection and also parental investment issues, men are selected to be more competitive, and women are selected to be more nurturant. Suppose that hypothesis is true… What makes for better motives in a scientist?

What kind of motives are more likely to lead to good science: Competitive motives, like the motive J. D. Watson described in The Double Helix, to get the structure of DNA before Linus Pauling did? Or nurturant motives of the kind that Doug Melton has described recently to explain why he’s going into stem cell research: to find a cure for juvenile diabetes, which his children suffer from? I think it’s anything but clear how motives from our past translate into modern contexts.

Calkins went on to teach psychology for forty more years and in 1918 became the first woman president of the American Psychological Association. Spelke continues her child development research as a professor of psychology at Harvard University.

Information on Mary Whiton Calkins was gathered from Feminist Voices, Webster’s Women’s Contributions page, and of course, Wikipedia.

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Stylised atom, showing nucleus and electrons

Wednesday Geek Woman: Mahananda Dasgupta, nuclear fusion researcher

This post appeared on Lecta and Hoyden About Town for Ada Lovelace Day 2011.

Mahananda Dasgupta is a professor in the Department of Nuclear Physics at the Australian National University. Dasgupta’s research takes place at the heavy-ion accelerator facility and investigates quantum tunnelling when heavy nuclei collide. Her Pawsey Medal award in 2006 cites cutting-edge contributions includ[ing] precision measurements of unprecedented accuracy.

Dasgupta moved to Australia from India for a postdoctoral position in the 1990s, and eventually was appointed to a tenured position in 2003. She became the first woman to hold a tenured position in the Research School of Physical Sciences and Engineering at the ANU in its entire 50+ years of existence! (I was very surprised to find this, the School must be enormous in terms of academic staff, it comprises nine research departments.)

How do we retain that female workforce [in science]?

By strong and meaningful mentoring, which doesn’t just mean a quick meeting once a month or web-based mentoring, but real mentors who encourage women or younger people to devise strategies about how best to use their time, and what roles to apply for to advance their career.

Every person at that early stage needs support. We need to champion women scientifically – not “she’s a good person”, but “she’s an excellent physicist who’s done this great work”… Equally, the employers’ responsibility to provide childcare is very important… If we are expanding and building infrastructure – why are we not building childcare facilities?

I was educated in India where, if a student is sharp, they’re encouraged to show it through participating in discussions or taking on extra-educational activities… It does strike me that in Australia we give a lot of kudos to those who excel in sports, but if you excel in studies you are a dork, particularly among other students… Sometimes, following talks I give in schools, students come to the carpark to ask me science questions, rather than asking them in front of the class… How do we get away from that? I believe that to make real long-term progress we must respect and encourage intellectual achievements.

Mahananda Dasgupta, The Conversation: So seriously, why aren’t there more women in science?

Dasgupta is active both in advocating careers in science in general, volunteering herself as a science careers lecturer at schools, and in speaking on behalf of women in science. In 2004 she was the Woman in Physics Lecturer for the year, and in 2011 she represented the Group of Eight universities (the eight universities that consider themselves Australia’s best research universities) at a Women in Science and Engineering summit at Parliament House. Her 2011 Georgina Sweet Australian Laureate Fellowship from the Australian Research Council calls upon her to increase the profile of Women in Science through outreach activities, and work towards advancing early career researchers as well as facilitate leadership pathways for senior women researchers.

Recognition Dasgupta has received for her work includes:

  • the Australian Academy of Sciences’ Pawsey Medal in 2006, for outstanding work in physics by a scientist under 40
  • her election as a Fellow of the Australian Academy of Science in 2011
  • an Australian Laureate Fellowship in 2011

I can’t embed them in the post for licencing reasons, but David Hine has a couple of photos of Dasgupta with her experimental equipment: Dr Mahananda Dasgupta and Dr Mahananda Dasgupta and Dr David Hinde.


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Wall of Spam, by freezelight on Flickr CC BY-SA 2.0

Linkspam as portrayed by an actress from a younger generation

Yes, that’s right, linkspams are back! Rebooted! New director! New continuity!

No, not really. Same people. Same style. We’ve just been a bit collectively discouraged by the Delicious disaster, the Google Reader implosion and the neverending outage. Talk about making bookmarking unfun. But we’re going to try again, right now supporting pulling bookmarks from Delicious, Pinboard and Twitter. In order to not have to have 200 bookmarks, we’re just going to start afresh with some recent-ish links and go from there. Apologies to people who submitted things in the interim, post them in comments for others to catch up on.

You can suggest links for future linkspams in comments here, or by using the “geekfeminism” tag on delicious or or the “#geekfeminism” tag on Twitter. Please note that we tend to stick to publishing recent links (from the last month or so).

Thanks to everyone who suggested links.

Multiple small broken window panes, through which greenery outside can be seen.

Quick hit: #mencallmethings

Trigger warning for quoted harassment and threats in the entry and links.

On Twitter, Sady Doyle has created a #mencallmethings tag:

The thing is, name-calling DOES have an impact. It’s a continual message that your voice is not legitimate & using it will only hurt you.

Threats are scary and all, but we’d have a field day if every woman and anti-sexist person online listed the names they were called.

AND THUS, I SHALL NOW DO SO. Shrieky. Screechy. Hysterical. Professional victim. Pathological victim. Hypersensitive. #mencallmethings

Feminist writers are thus tweeting some of the abuse they have received on the #mencallmethings tag. As Jill of Feministe puts it:

Have you ever wondered what it’s like to spend a day in the glamorous life of a feminist blogger? Check out #mencallmethings on Twitter… (Trigger warning for rape, violence and misogyny).

xx your favorite lesbian hambeast

Further commentary by Sady Doyle is up at Tiger Beatdown:

And yet, a sadness comes upon me. Now that I have regenerated, Whovianly, into my current form — all serious-faced and irritable and SAD TIMES ABOUT SEXISM — I find myself missing her carefree ways. Moreover, I find myself wondering how she pulled it off. How the Hell did she stay in such a good mood all the time? And I think I’ve found my answer: In 2009, I genuinely believed people were going to change their minds about being sexist, because they read my blog

I hate to tell you this, friends. But I think my plan, it had a minor flaw. Which is: Misogynists don’t like women. It doesn’t matter how uniquely charming and witty and acquainted with various fine bourbons you are. Are you a woman? Then they don’t like you. And they especially don’t like you telling them what to do. By, for example, asking them to cut it out with the misogyny.

In fourteen hours, it’s already made it to the Australian mainstream media, where I actually learned of it. I am clearly off my blogger game here.

Quick Hit: Sexism In Games Bingo

Tired of hearing the same arguments regarding sexism in games? Here’s a sexism in games bingo card by @fireholly99.

Trigger Warning: Includes mention of violence against women.

Additional Warning: This card has been copied verbatim and includes slurs and other derogatory language that we wouldn’t normally allow here because I felt it was more effective when allowed to parrot inappropriate comments than it would be if I reworded. This is not going to be extended to the comments, however, so please adhere to our comment policy there.


But men are all super-buff, they’re sexually objectified too! But it’s not FOR women. If they can’t deal with it, they shouldn’t be here. She might play games, but she’s not a REAL gamer, she’s just attention whoring. Chainmail bikinis are unrealistic, but’s not realistic for a woman to be fighting anyway. YOU’RE the one who hates women – you’re saying they can’t be both sexy AND tough.


But they call her a ‘bitch’ because they’re the bad guys. No-one gives a shit about this sexism stuff, I’m just here for the review scores. I am a feminist and love women because they are inherently too nurturing and responsible to play video games. The only reason a guy could have to care about sexism is so women will think he’s sensitive and want to fuck him. But we have equality, there are nonsexualised female characters, like… Samus except when she takes off her Suit…


But there are sexualised male characters, like… uh, Marcus Fenix is sexy, right? I don’t know, I’m not a fag. Men want to WATCH desirable women and women want to BE desirable women, so no-one wants sexy male characters except gay guys. GET BACK IN THE KITCHEN AND MAKE ME A SANDWICH There are women who get their genitals ritually mutilated and you’re complaining about video game boobies? So you think all female characters should be ugly and dress in burqas.


Girl who likes video games? You only have interests because you’re not thin enough to have a real boyfriend. Yeah, the story, dialogue and character design is all sexist, but everyone can enjoy the amazing gameplay. As a woman, it doesn’t bother me, so no-one else is allowed to be bothered. Why should I care about this so-called ‘unfair’ depiction of women when women have more rights than men nowadays and feminists are trying to destroy capitalism? But trash talk is normal on XBL. Women are just too sensitive to rape threats and feigned masturbation.


How can it be sexist when women in REAL history were their husband’s property? How can it be sexist when women in REAL life are weaker and wear less clothing than men? If you didn’t want attention for being a girl you wouldn’t be using a female name in your tag or speak with a female voice. Everyone knows ‘sex sells’, and the developers are just making things they think will sell. But I’ve suffered oppression too, as a black/ poor/ gay/ nerdy/ girlfriendless MAN! What about my feelings? It’s just a game. No-one cares.


Stata computer science building on the MIT campus

Wednesday Geek Woman: Anne Street, president of the MIT alumni association

This is a guest post by kim. This post appeared on her blog for Ada Lovelace Day 2011.

I met Anne back in the ’80s, when we both worked for an engineering firm specializing in infrastructure. She has a dazzling technical background, with multiple degrees from MIT, at a time when women MIT graduates were few and far between. Her specialty then was business development for applied engineering, and she took me under her wing as she made her rounds of the nuclear industry and associated Government and research entities.

Anne taught me a lot. There’s the obvious – how to read and answer Government requests for proposals. And there’s the not-so-obvious. How to engage engineering vision. How to distill the musings of the stratosphere-inhabiting set and transmit their thoughts to non-tech folk, without being didactic or condescending. How to be the only (or almost only) woman in a field dominated by men; taking neither nonsense nor prisoners, but doing so by subverting from within rather than wasting energy on pointless direct confrontation. How to lead the unwilling. How to build a team of people who might not be happy about putting in after hours and weekend work; shaping them so that in the end they were damned proud that their output was of the highest quality, because that way all the overtime was a badge of honor, and not wasted effort.

Through all of this ran a wicked sense of humor. She held a wake when a particularly large and desperately desired potential opportunity came in as a loss – complete with black balloons, a model coffin, and wilted flowers. The telephone play of her convincing the florist that she WANTED dead, droopy flowers was priceless. Her parties were legendary: Tinkertoys as icebreakers; mystery role playing gatherings; just the things to make totally unconnected creative folk from many walks of life unwind together, even though they had just met as strangers. I still have the glass lampwork beads and jewelry we made. Three houses and 20 years later – her daylilies still bloom in my yard. And I’m still writing engineering proposals.

But most of all Anne was always the epitome of encouragement. There was no field, no technical arena, no bit of knowledge too arcane to tunnel into and to share. She taught me to step aside and engage the brain when I read, to assess not only face value content, but possible sub rosa influences; and to always look for the proof or the root cause. And that in the end, everything can be researched because there is no priesthood. Women and men without tech degrees can through curiosity, enthusiasm and perseverance, always find meaningful and substantiated data.

Anne today is president of the MIT alumni association, where I am sure she’s using connections and influence to further the cause.

Way to go, Anne!

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GF classifieds: wiki edition

This will probably be another very occasional series.

As you know, we have a wiki as well as a blog (in fact the wiki is more than a year older than the blog), and it only has a few (3 to 5 at any given time) regular editors. There’s also a lot of attention paid to the Incidents relative to the rest of the wiki. That’s not a bad thing, but the rest of the wiki could use some love too.

Hence, every so often we’ll point out areas of the wiki you could help out with. At any given time, this list will be hugely incomplete, so you can also go over there and do what suits you.

If you need a hand, drop in on the Community portal and ask for help.

Getting articles ready for feature article status! Getting a featured article on our wiki is nothing like the arduous Wikipedia process: we simply want articles about a geek woman or group of geek women doing awesome stuff! They should be several paragraphs long, in the correct categories, and have a picture. Fixing up our proposed feature articles to bring them up to scratch would be a good task if you know your way around Mediawiki wikis a bit.

Improving our coverage of the Science field! You can see the base article: it covers all of science in about a screenful of content. Obviously that could be massively expanded in several directions: into the subfields, expanding the writeup of the issues, and documenting sexist incidents in science more fully.

Groups and events for younger women! There are lots and lots of outreach programs for younger geeks, and some autonomous groups run by teenagers for teenagers. But we don’t have a lot of coverage of them on the wiki. I just started categories today for Young women’s organizations and Young women’s events. Please add to them! (Click ‘Add a Page’ to add a new page to the wiki and start writing! If you don’t know wikis yet, someone will add the right categories for you, so don’t worry about that.)

GF wiki editors or readers, what would you like to see more work on?