Category: Science

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Linkspam: academic rat race edition

A few links have been floating around among PhD comrades:

End of an ERA: journal rankings dropped:

[Australian Innovation, Industry, Science and Research Minister Kim Carr] chastised the research community, saying: There is clear and consistent evidence that the rankings were being deployed inappropriately within some quarters of the sector, in ways that could produce harmful outcomes, and based on a poor understanding of the actual role of the rankings… One common example was the setting of targets for publication in A and A* journals by institutional research managers.

Why is the Impact Factor still around?:

But even if these flaws were all fixed, the Impact Factor is of course entirely unsuited for ranking anything other than journals on principle grounds. Because the distribution of citations to the articles in a journal is so skewed, the actual correlation of the citations any individual article gathers with the Impact Factor of the journal it was published in, is very weak…

The case against double-blind peer review:

How well does it work in practice? You would expect double-blind reviewing to favor people from outside academia. Yet Blank (1991) reported that the opposite is true: authors from outside academia have a lower acceptance rate under double-blind peer review.

(As a counterpoint, note the results of Budden et al, via the Geek Feminism linkspam.)

Free Science, One Paper at a Time:

The current publishing regime, [science publisher Mark Patterson] argues, locks up these functions too closely in the current, conventional version of the scientific paper — even though some of these functions can be met more efficiently by other means.

So what are these functions?

Registration is essentially a scientific claim of discovery — a marker crediting a particular researcher with an idea or finding. The current system registers these contributions via a paper’s submission date. Certification is essentially quality control: ensuring a paper is solid science. It is traditionally done via peer review. Dissemination means getting the stuff out there — publication and distribution, in printed journals or online. And preservation, or archiving, involves the maintenance of the papers and citations to create a breadcrumb trail other researchers can later follow back to an idea or finding.

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Open thread: parthenogenesis in Komodo dragons

This article originally appeared on Geek Feminism.

A baby Komodo dragon born by parthenogenesis, photographed at Chester Zoo (CC BY-SA 3.0, Wikipedia user Neil)
A baby Komodo dragon born by parthenogenesis, photographed at Chester Zoo (CC BY-SA 3.0, Wikipedia user Neil)

What the hell. It’s geeky. And this is a fairly new (published 2006) finding about komodo dragons. To quote from Wikipedia:

On December 20, 2006, it was reported that Flora, a captive Komodo dragon living in the Chester Zoo in England, was the second known Komodo dragon to have laid unfertilized eggs: she laid 11 eggs, and 7 of them hatched, all of them male. Scientists at Liverpool University in England performed genetic tests on three eggs that collapsed after being moved to an incubator, and verified that Flora had never been in physical contact with a male dragon. After Flora’s eggs’ condition had been discovered, testing showed that [London Zoo dragon] Sungai’s eggs were also produced without outside fertilization…

Komodo dragons have the ZW chromosomal sex-determination system, as opposed to the mammalian XY system. Male progeny prove that Flora’s unfertilized eggs were haploid (n) and doubled their chromosomes later to become diploid (2n) (by being fertilized by a polar body, or by chromosome duplication without cell division), rather than by her laying diploid eggs by one of the meiosis reduction-divisions in her ovaries failing. When a female Komodo dragon (with ZW sex chromosomes) reproduces in this manner, she provides her progeny with only one chromosome from each of her pairs of chromosomes, including only one of her two sex chromosomes. This single set of chromosomes is duplicated in the egg, which develops parthenogenetically. Eggs receiving a Z chromosome become ZZ (male); those receiving a W chromosome become WW and fail to develop.

The Nature article is Phillip C. Watts et al (2006) Parthenogenesis in Komodo dragons, Nature 444, 1021–1022 (21 December 2006), doi:10.1038/4441021a.

This is an open thread, for a discussion of biology geeking, great nerdy events and, of course, anything else you want to discuss!

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The latest essentialism go-round: do we dare to discuss?

This article originally appeared on Geek Feminism.

Showing up on our Linkspam radar this week is John Tierney’s article for The New York Times, Daring to Discuss Women in Science, which is another round of “I am going to challenge the groupthink and be the one person who dares to make gender essentialist arguments about women in technical fields [well, me and that army over there]”. It argues from a finding among very high performing high school students, the top 0.01 percent of the population as sorted by the SAT and ACT standardised tests in the US, from which the researchers concluded that there’s distinct gender differences among students with that sort of performance.

Tierney writes:

The boy-girl ratio has also remained fairly constant, at about three to one, at the right tail of the ACT tests of both math and science reasoning. Among the 19 students who got a perfect score on the ACT science test in the past two decades, 18 were boys.

Meanwhile, the seventh-grade girls outnumbered the boys at the right tail of tests measuring verbal reasoning and writing ability. The Duke researchers report in Intelligence, “Our data clearly show that there are sex differences in cognitive abilities in the extreme right tail, with some favoring males and some favoring females.”

Here’s a roundup of feminist/women-in-science-o-sphere responses, many via SKM at Shakesville:

  • Anna N., 3 Problems With The “Women In Science” Debate: If boys and girls, men and women had truly equal opportunities, we might be able to conclude something about their “innate abilities” ”” or at least stop worrying about gender inequality in various fields. But we’re still very far from that point. Tierney finds fault with programs to eliminate bias at the university level, and says, female scientists fare as well as, if not better than, their male counterparts in receiving academic promotions and research grants. But girls may be implicitly or explicitly discouraged from pursuing science long before they actually become scientists…
  • Caroline Simard, “Daring to Discuss Women in Science:” A Response to John Tierney: The problem with the biology argument that “boys are just more likely to be born good at math and science” isn’t that it’s not “politically correct” — it’s that it assumes that we can take away the power of societal influences, which have much more solid evidence than the biology hypothesis. Tierney makes the point himself in his article…
  • Christina Agapakis, Adventures of Women in Science: The irony here being that this article is a very clear example of some of the social biases women in science face every day, just one of the countless attacks and indignities that make it that much harder for women to get up and go to lab every day, to achieve great things in math and science.
  • Janet D. Stemwedel, John Tierney thinks he’s being daring: On the general subject of claims for which there does not does not exist relevant empirical evidence, are there any published studies (or any research projects currently underway) to explore the connection Tierney, Summers, et al. seem to assume between being in the extreme right tail of laboratory measures of mathematical and scientific aptitude (like the math section of the Scholastic Aptitude Test) and having the chops to to get a doctorate in science or to win tenure at a top university?
  • SKM, Daring to Discuss Women and… *Yawn*, which also includes several links from the Larry Summers debate and earlier: For that matter, I think the “daring” idea that women are innately inferior to men at various Important Things–and indeed the preposterous notion that the idea is “daring” to begin with–has been answered quite competently in the past
  • Gretchen Keller, Women in Science: 2+2=?: …one of my least favorite, yet thought-provoking questions is “How does it feel to be a woman in science?”. Usually I reply that it feels the same as it does for a man: frustrating, time-consuming, invigorating and mostly like a bird flying repeatedly into a window desperately hoping that one of these times that pane of glass will turn into thin air.
  • Amy E. Slaton, Erring on the Side of…Exclusion: I know, I know: sarcasm is petty and unattractive. So before I lose any remaining credibility, let me defer to Troy Duster’s brilliant historical discussion of biological understandings of intellectual capacity. For almost 20 years, editions of his book, Backdoor to Eugenics, have laid out the very worrisome political and cultural implications of our pursuit of biological bases for intellectual and behavioral differences.
  • Clara Raubertas, “daring” to draw unscientific conclusions from statistics: Of course, his conclusions aren’t very scientific. Here are a few of the unfounded assumptions he has to make to draw the conclusions he draws… The assumption that science is so hard that it’s really only suited for people with extremely high scores (in the top fraction of a percent among a group of students who are already in the top fraction of a percent among their peers)
  • Melissa, The never-ending discussion: biology or bias?: What I find most frustrating is that there are myriads of studies, and everyone can cite their favorite study to support their viewpoint ”” be it that bias is the dominant factor keeping women out of sciences or that biology accounts for the paucity of women… I found what may currently be the best, though still imperfect, antidote to the never-ending, go-nowhere discussion of this topic, namely Stephen Ceci and Wendy William’s book, The Mathematics of Sex: How biology and society conspire to limit talented women and girls.
  • FemaleScienceProfessor, But I Don’t Want to Write about John Tierney Again: Thanks for all the e-mails and comments with links to the New York Times commentary by John Tierney, but what he wrote is just more of the same of what he’s written before: i.e., many women don’t want to be scientists or engineers, others can’t because they aren’t as good at math as the guys. Oh yeah, and Larry Summers made some reasonable statements in a speech that was misunderstood by hysterical females.
  • Hannah (in reply to FemaleScienceProfessor), Daring to Discuss: While I do understand this fear, how else are we going to convince the scientific establishment, many of whom likely share Tierney’s views, that gender bias is real and actually does keep women from succeeding in science careers? Clearly, just waiting for the old guard to pass on isn’t working, because I’ve met plenty of young male scientists who are just as biased as the old ones: they just hide it better.
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Ethics of Free Software community research

Most of this entry is exactly a year old today and it’s just sat around in draft form all that time. Since I posted something similar on Geek Feminism about research into women in tech and similar topics, I thought I’d get it out there.

In January 2009 a researcher named Anne Chin of Monash University Law emailed the chat list for the linux.conf.au 2009 conference asking for research subjects to be interviewed about licencing and Open Source software. There were several responses criticising her use of HTML email and Microsoft Word attachments. I’ll leave the specifics of this alone except that people should be (and probably are) aware that this is almost always an unknowing violation of community norms.

I did, though, think about making some notes on research ethics and Free Software research. A bit about my background: I am not a specialist in ethics. I’m somewhat familiar with ethics applications to work with human subjects, but not from the perspective of evaluating them. I’ve made them, and I’ve been a subject in a study that had made them.

For people who haven’t seen this process, the ethical questions arising from using human subjects in your research in general covers the question of whether the good likely to arise from the outcomes of the study outweighs the harm done to the subjects, together with issues of consent to that harm. (There are many philosophical assumptions underlying this ethical framework, I don’t intend to treat them here.) Researchers in universities, hospitals, schools and research institutes usually have to present their experimental designs to an ethics committee who will determine this question for them and approve their experiment. Researchers who work across several of these (eg, a PhD student who wants to interview schoolchildren) will need to do several ethics applications, a notable chore when the forms and guidelines aren’t standardised and occasionally directly conflict. Researchers working for private commercial entities may or may not have a similar requirement. Researchers who use animals also have to have ethical reviews, these are done by animal ethics committees, which are usually separate.

At my university, essentially any part of your research that involves measuring or recording another person’s response to a research question and using it to help answer that question needs a human ethics application.

The good/harm balance may include very serious dilemmas: is there a health risk to subjects? how will the researcher manage the conflict between maintaining subject confidentiality and research integrity and the good of her subjects or the requirements of the law if she uncovers, say, episodes of abuse or violence? But it also involves less immediately obvious and serious ethical questions. Is this study a giant waste of subjects’ time? is considered a question of ethics by ethics committees, and is in fact the most serious problem for linguistics research, since there’s very seldom an outcome of particular interest to the subjects themselves.

The study in which I took part a few years back was towards the serious end actually: it was a study into the psychological profiles of people who have an immediate family member who had cancer as a child and involved both questionnaires and a phone interview with a psychologist. Both because the study explored memories of the illness and because the profiling included evaluating depressive episodes, suicidal ideation and so on, it came with a detailed consent form and with information about a counselling service that had been informed of the study and was prepared to work with its subjects.

In the case of the Free Software community the ethical questions are often more towards the waste of time? end of the spectrum than the more immediately serious end. It’s important to understand that this isn’t necessarily the case though. Here are some more cutting ethical problems:

  • getting findings that expose your subjects and/or their employers to intellectual property claims; or
  • revealing that your subjects are breaching employment contracts in some way (generally also related to IP) and thus exposing them to job loss and possible civil action.

Getting ethics approval to carry out workplace studies can be fairly hard precisely due to problems like these. But in the rest of this post I will treat the waste of time problem.

Firstly the basics: are your subjects going to be identifiable in your final reports or to the general public? If not, who will know who they are? Can a subject opt to have their responses removed from the study? When and how? All this should be explained at the start. (Usually if an ethics committee has been involved, there’s a consent form.) If doing a survey look into survey design, in order to construct non-leading questions and such.

Now, for specifics. Most of them arise from this principle: there are a lot of researchers working, in various ways, on the Free Software community, possibly making it a slightly over-studied group if anything. This places the onus on the individual researcher to demonstrate to the community that their project is worthwhile and that they’re going to do what they say. Thus:

  1. demonstrate some familiarity with the background. Depending on your research level this could mean anything from demonstrating a knowledge of existing anthropological work on Free Software (say, if the research project is for your anthropology PhD) down to at least understanding the essential concepts and core history (say, a project at high school level). This can be demonstrated by research design, eg asking sensible well-informed questions, but actually mostly requires a bigger time investment: making appearances in the community, either virtually or physically, ideally for a little time before asking the community to help you get your PhD/A-grade/pass.
  2. don’t get the community to design your experiment for you. Have a specific goal, more specific than get people to write me lengthy essays about Free Software, and get ideas from that and write about them. In the general case, the ask people incredibly vague stuff and hope they say something interesting technique fails the waste-of-time test.
  3. give your results back to the community. The most common problem with the various surveys, interviews and questionnaires sent to the Free Software community is that responding to them is like shouting into a black hole. It is not unheard of, of course, to see the thesis or essay or roundup that comes out of these, but it is unusual, relative to the number of requests. Most of the time the researcher promptly disappears. Researchers should come to the Free Software community with an explanation of when and where they will make the results of the study available. They should explain the aims in advance unless this would compromise the results. (On that note: Anne Chin is giving a linux.conf.au talk this year.)
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Menstrual geeking: getting started

This article originally appeared on Geek Feminism.

I was surfing around on Vagina Dentata which I stumble across periodically (most recently in our last linkspam) but have not quite got to feed-reader-adding yet. This is poor form I admit”Š”””ŠI’ll go right off and add it after writing this”Š”””Šbut does mean that I can enjoy a number of posts at once. Today I spent some time on periods. Periods. PERIODS. P.E.R.I.O.D.S. and Time to talk periods and thought other folks of the menstruating kind and/or the geeky kind might enjoy a bit of related geekery.

My official menstrual cycle education essentially boiled down to, if I recall correctly, that there was a time when one bled, a longer time when one didn’t and that at some point during the longer time ovulation occurred. And there were was certain amount of practical information regarding pads and tampons, which largely came down to a few diagrams and “beware Toxic Shock Syndrome”. Only in my mid-twenties, looking only to fill, I think, idle geek time, I found out about the follicular phase and the luteal phase, about fertilisation taking place in the Fallopian tubes and implantation occurring only around a week later, about the fairly short lifespan of the ovum and the fairly large corpus luteum cysts that ovulating women develop each cycle. (I had an early ultrasound of my current pregnancy, while the cyst was still presumably secreting progesterone, and it was a fairly big black circle on my ovary.) As best I understand, and I’m very much a layperson when it comes to the science of menstruation, Wikipedia’s article on the menstrual cycle is a good place to start reading for your menstrual geeking initiation.

I learned this when on the recommendation of another woman geek I picked up Toni Weschler’s book Taking Charge of Your Fertility. It’s a Fertility Awareness guide, about using a combination of basal body temperature, cervical mucus and cervical position to identify fertile times in your menstrual cycle in order to either get pregnant or avoid it. (This is not necessarily a religiously inspired practice, and it’s more effective as a contraceptive than you’d expect: much of the dubious reputation of cycle-based methods of contraception comes from use of strictly calendar based methods. Fertility Awareness requires a fairly good working knowledge of the signs and the use of either barrier methods or abstinence at fertile times though, with failure modes you can imagine.) I can’t get as excited about the idea of taking my temperature every morning of my fertile life as Weschler can, and I’ve never charted a cycle to the extent that would satisfy a Fertility Awareness educator, but I have tracked my temperature through a couple of cycles in order to observe the basic signs. I’d recommend this book if you’d like to do some serious observing of your menstrual cycle from, as it were, the outside.

Vagina Dentata also has a promising pointer to the re: Cycling blog of the Society for Menstrual Cycle research, and you might be interested in (note: photos of cervixes at link… as you’d expect) the Beautiful Cervix photos taken throughout various people’s cycles.

If you have a geeky interest in menstruation and related things, what are the coolest facts you know, and what are your favourite sources of info?

Someone is going to make a bingo card about my notes to commenters some day, aren’t they? Today’s note is: remember that not all women menstruate, and not all people who menstruate are women.

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Geek culture stereotypes and women’s responses

This article originally appeared on Geek Feminism.

Links to Lisa Grossman’s Of Geeks and Girls have been turning up everywhere. She’s recounting work by Sapna Cheryan asking women about their interest in computing, in their case rooms that are decorated such that “Star Wars posters adorned the walls, discarded computer parts and cans of Coke clustered on a table” and showing that they are much less likely to agree that they have any interest in computer science. (Grossman does not report how men responded: surely Cheryan’s work used male subjects as well?)

The article goes on to caution though that while geek culture stereotypes seem to alienate women to some degree, dismantling the whole culture is not the solution:

But what about the women who do think like computer scientists? What of the girl geeks?

Cheryan has given talks where the audience doubted the existence of girl geeks. She’s also given talks to girl geeks. There, she has received responses such as, “I’m a female engineer, and I like Star Trek! What are you trying to say?” She explains that her studies aren’t supposed to give a picture of what computer scientists are actually like. The geek room is a caricature. “We couldn’t have found a room in the CS building that really looked like that,” she says. But the perception it captures is real.

It’s a fairly frequent response to geek feminism to argue that it’s an attempt to destroy geek culture, or at best that it’s a zero sum game: the number of women who would join a more feminist geek culture would be equalled by the number of men who would leave; occasionally this argument essentially boils down to “I’m here to get the hell away from women” but more commonly it’s along the lines of “I’m here to get the hell away from mainstream social norms, I like the social norms in geekdom, you’re trying to turn them into mainstream social norms, ew.” This reminds me of that response, but from women. We’re here for the geekdom. We talk about what we want to change; we should also talk about what we want to keep.

You’re welcome to discuss Cheryan’s work and Grossman’s take on it in general in comments here (worth remembering though that we generally don’t have perfect insight into our prejudices, so you may or may not be more turned off by discarded computer parts than you think), but I specifically wanted to ask women who see themselves as part of geek culture, or a geek culture, what are the parts of it that you enjoy and that you’re hoping to open up to more women?

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Quick hit: Ada Yonath

This article originally appeared on Geek Feminism.

Per Meli in comments, with the announcement of the Nobel Prize in Chemistry for this year another women laureate has been named: Ada Yonath, with Venkatraman Ramakrishnan and Thomas Steitz, “for studies of the structure and function of the ribosome”. I didn’t know that the announcements were staggered, my apologises for implying that Elizabeth Blackburn and Carol Greider were the only women laureates. Thanks for the update Meli.

Women in Science has a profile of Yonath, here’s an excerpt:

After receiving her bachelor’s degree in chemistry and master’s degree in biochemistry from the Hebrew University of Jerusalem, she entered the laboratory of Wolfie Traub at the Weizmann Institute of Science in Rehovot, Israel. She earned her Ph.D. for X-ray crystallographic studies of collagen in 1968. After brief postdocs at Carnegie Mellon and MIT, she returned to the Weizmann Institute to establish the country’s first protein crystallography laboratory in Israel.

Despite her expertise in X-ray crystallography, many scientists were skeptical that the technique could be used to determine ribosome structure, only they apparently didn’t express it quite so tactfully.

[…] she was able to count on the support of “a few individuals, including several distinguished scientists and my own group of young and highly motivated students. They encouraged me even when my project met with rigorous skepticism from most prominent scientists all over the world, even when I was called ‘a dreamer,’ ‘crazy’ or the ‘Village Fool.'”

Even her initial successes weren’t immediately recognized by her colleagues:

[…] with the techniques then available, it took Yonath months of trying different solutions and crystallization procedures to get tiny crystals of the larger, or 50S, subunit of the ribosome from a Bacillus bacterium, and more than a year to get the first very fuzzy x-ray crystallographic images. But when she showed colleagues her results at an August 1980 meeting, “everyone laughed at me,” Yonath recalls.

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Quick hit: Elizabeth Blackburn and Carol Greider

This article originally appeared on Geek Feminism.

A couple of days ago Skud linked to the Women in Science introduction to women potentially eligible for Nobel Prizes. Now the awards have been announced and there are two female laureates this year: Elizabeth Blackburn and Carol Greider. They, with Jack Szostak, are sharing the Physiology or Medicine prize “for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”.

Blackburn is Australian and so has received a lot of Australian press. Here’s an excerpt of a Sydney Morning Herald story:

Professor Blackburn, 60, who now works in San Francisco, pioneered the study of telomeres, caps that protect chromosomes in cells, and is a discoverer of telomerase, an enzyme that does the protecting.

…

… Professor Blackburn is a vocal advocate of independent scientific thought who fell out with the Bush administration over cloning and stem cells.

She was dropped from George Bush’s Council on Bioethics in 2004 after questioning its bias.

A colleague and friend, Melbourne University’s dean of science, Rob Saint, said Professor Blackburn, who graduated in 1971, chose her career when women were starting to become more involved in the sciences.

“I think she would be representative of a change in that gender balance,” Professor Saint said. “It’s wonderful that here we’re seeing the fruits of opening up the system.

…

Dr Blackburn’s career path wasn’t easy. Early in her tertiary education, she returned to her birthplace, Hobart, where according to her biography a family friend said: “What’s a nice girl like you doing studying science?”

Her interest had been sparked by a likeable chemistry teacher at Launceston’s Broadland school. There, biographer Catherine Brady said, she used the new chemistry lab to try to make touch powder fireworks.

She completed her schooling at Melbourne University High School, topping the state in three matriculation subjects, before completing a biochemistry masters, and moving on to Cambridge and Yale.

Women in Science has an extensive introduction to the work of both Blackburn and Greider.