Tag Archives: biology

Linkspam is the mind-killer (1 July 2014)

Facebook’s emotion study and research ethics:

  • Facebook Manipulated 689,003 Users’ Emotions For Science | Kashmir Hill at Forbes (June 28): “Facebook’s data scientists manipulated the News Feeds of 689,003 users, removing either all of the positive posts or all of the negative posts to see how it affected their moods. If there was a week in January 2012 where you were only seeing photos of dead dogs or incredibly cute babies, you may have been part of the study. Now that the experiment is public, people’s mood about the study itself would best be described as ‘disturbed.'”
  • Facebook unethical experiment : It made news feeds happier or sadder to manipulate people’s emotions. | Katy Waldman at Slate (June 28): “Facebook’s methodology raises serious ethical questions… ‘If you are exposing people to something that causes changes in psychological status, that’s experimentation,’ says James Grimmelmann, a professor of technology and the law at the University of Maryland. ‘This is the kind of thing that would require informed consent.'”
  • Facebook and Engineering the Public | Zeynep Tufecki at Medium (June 29): “I’m struck by how this kind of power can be seen as no big deal. Large corporations exist to sell us things, and to impose their interests, and I don’t understand why we as the research/academic community should just think that’s totally fine, or resign to it as ‘the world we live in’. That is the key strength of independent academia: we can speak up in spite of corporate or government interests.”
  • Did Facebook and PNAS violate human research protections in an unethical experiment? | David Gorski at Science-Based Medicine (June 30): “As tempting of a resource as Facebook’s huge amounts of data might be to social scientists interested in studying online social networks, social scientists need to remember that Facebook’s primary goal is to sell advertising, and therefore any collaboration they strike up with Facebook information scientists will be designed to help Facebook accomplish that goal. That might make it legal for Facebook to dodge human subjects protection guidelines, but it certainly doesn’t make it ethical.”

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You can suggest links for future linkspams in comments here, or by using the “geekfeminism” tag on Pinboard, Delicious or Diigo; 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.

Quick hit: “A quantitative analysis of gender bias in quantitative biology meetings”

Plenty of us have scanned down the list of speakers at a conference and wondered why there appeared to be so few women, but when Jonathan Eisen saw the numbers at Q-BIO, he started by taking note: “Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome b/c they don’t take a XX” [1]:

That is a 25:1 ratio. Pathetic. Embarrassing. The sponsors – UC San Diego’s Division of Biological Sciences and BioCircuits Institute, San Diego Center for Systems Biology, the University of Hawaii and the Office of Naval Research – should all be ashamed.

He notes in a previous post that the ratio of men and women in biology is close to 1:1, so a ratio so far off that suggests something could use some work. But for Q-BIO, he’s taken it a step further and submitted a very appropriate abstract.

UPDATE – I have now submitted an abstract to the meeting. The abstract I submitted is available here and posted below

The probability of having one out of twenty six participants at a scientific meeting be female
A quantitative analysis of gender bias in quantitative biology meetings
Jonathan A. Eisen
University of California, Davis

(Note – new title suggested by John Hogenesch)

The title alone made me laugh. You can read the full abstract at his blog, including equations and graphs!

[1] See Tim’s comment below

Cells shown on a microscope slide

Wednesday Geek Woman: Esther Orozco, cell biologist and politician

This is a guest post by Cecilia Vargas, a retired software developer living in Vancouver, Canada.

Esther Orozco is a Mexican cell biologist, winner of the 1997 Pasteur medal, and a 2006 laureate of the L’Oréal-UNESCO Awards for Women in Science.

Esther Orozco was born and raised in a small rural town in northern Mexico, where she became a school teacher. I admire her because she overcame all the social expectations for women that exist in such conservative environments and became a successful scientist. She also found time to raise 2 kids. In 1998 she ran for governor of Chihuahua state, Mexico. Last year she became president of the Autonomous University of Mexico City.

The UNESCO/Pasteur medal is awarded by UNESCO and the Paster Institute for “outstanding research contributing to a beneficial impact on human health and to the advancement of scientific knowledge in related fields such as medicine, fermentations, agriculture and food.”

Orozco received the L’Oréal-UNESCO award for her discovery of the mechanisms and control of infections by amoebas in the tropics.

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Pillar covered by colourful advertising bills

A long time ago in a linkspam far, far away… (10th December, 2011)

  • The Wikimedia Foundation’s paid 12 month Community Fellowship positions are open for application until January 15. This time the proposals are encouraged to focus on improving editor retention and increasing participation across Wikimedia Projects, a perfect focus for people interested in increasing women’s participation.
  • Tired of outlandish requests on your time to review every half-baked project a man thinks of? Try the wiki’s new Free feminist consulting form letter (at least for a laugh).
  • The Problems With Geek Girl Con – And Some Solutions: For the last few years, I’ve artfully dodged involvement in a number of geek feminist movements and events because of my severe allergic reaction to second-wave feminism.
  • Inspirations in science: It’s very, very personal. On the public television channel, though, I found the real magic. Sesame Street, only a year younger than I. Electric Company. And Jane Goodall.
  • Jailbreak the Patriarchy: Jailbreak the Patriarchy genderswaps the world for you. When it’s installed, everything you read in Chrome (except for gmail, so far) loads with pronouns and a reasonably thorough set of other gendered words swapped.
  • She’s Just an Attention Whore: The conversation was going well until my friend (who I always considered a pretty not sexist guy) said this: There are two types of female gamers: ones who actually like games, and ones who are just trying to get attention.
  • Racism And Meritocracy: What accounts for the decidedly non-diverse results in places like Silicon Valley? We have two competing theories. One is that deliberate racisms keeps people out. Another is that white men are simply the ones that show up, because of some combination of aptitude and effort… The problem with both of these theories is that the math just doesn’t work.
  • Lynn Margulis, Renowned Evolutionary Biologist and Author at UMass Amherst, Dead at 73: Margulis was best known for her theory of symbiogenesis, which challenges central tenets of neo-Darwinism.

You can suggest links for future linkspams in comments here, or by using the “geekfeminism” tag on delicious or pinboard.in 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.

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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Photograph of Jill Bolte Taylor giving her TED talk

Wednesday Geek Woman: Jill Bolte Taylor, brain scientist and stroke survivor

This is a guest post by Kelly Seiler. Kelly blogs at Undercover Feminist. She is an electrical engineer working on the avionics for an unmanned airplane.

Submissions are currently open for Wednesday Geek Woman posts.

I first heard of Jill Bolte Taylor as a result of watching the free entertainment (which happened to be TED talks) on a Virgin Flight. I was rivited by her story. She recounts her experiences including the moment where she realizes she was having a stroke (10:35 mark):

“Oh my gosh! I’m having a stroke! I’m having a stroke! Wow! This is so cool. This is so cool. How many brain scientists have the opportunity to study their own brain from the inside out? But, I’m a very busy woman! I don’t have time for a stroke!”

Photograph of Jill Bolte Taylor giving her TED talk

Jill Bolte Taylor's TED talk, by Steve Jurvetson

Jill is an inspiration to me in so many ways. While still recovering her memories she taught a highly technical class. She stayed just ahead of the students in learning the material. Amazing!

If you haven’t heard of Jill, check out her TED talk where she recounts the morning of the stroke and it’s aftermath. She also spreads a wonderful message of letting go and living in the moment… she asks that we “Step to the Right” of our left hemisphere brain chatter – a reference to the profound peace and nirvana she experienced as she lost the function of the left half of her brain.

Her TED Talk: My Stroke of Insight
On the web: My Stroke of Insight
For an in depth look at Jill’s story check out her book: My Stroke of Insight: A Brain Scientist’s Personal Journey

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Photograph of Charlie McCord, with her reflection

Wednesday Geek Woman: Charlie McCord, student of biomechanics and fish feeding

This is a guest post by Maya. This entry originally appeared at the Project Exploration blog.

Charlie McCord is a PhD candidate in biology at the University of Chicago. Her research focuses on biomechanics in fish feeding and the morphology of fish jaws. She works in the Field Museum’s Biodiversity Synthesis Center.

Photograph of Charlie McCord, with her reflection

Charlie McCord © C. McCord, used with permission

Charlie grew up in Ojai, California. As a child, Charlie says she was “a bit of a tomboy” who loved being outside. She was always interested in science, but she initially leaned more towards writing and the performing arts. She credits her high school AP Physics teacher with inspiring her by emphasizing the creativity inherent in science.

After graduating from high school, Charlie went to UCLA to study ecology, behavior, and evolutionary biology. It was a big change for her; the university was almost eight times larger than her entire hometown. Getting involved with community service projects such as peer counseling and mentoring helped her “gain the confidence I needed to succeed.”

Charlie is currently studying organismal biology and anatomy at the University of Chicago. She has completed her master’s degree and is now a PhD candidate. Her research focus is primarily biomechanics, and she studies “the evolution of jaw form and function in triggerfishes and filefish.” Spending time with the collections of the Field Musem allows her to study the morphology of a broad range of fish jaws. Charlie works closely with the Field Museum, and as part of their “ongoing effort to better understand the biodiversity of life,” she has had the opportunity to travel with museum staff on several specimen collecting missions. “I’ve become quite the experienced SCUBA diver and spear fisherwoman!” she says.

Charlie finds the independence of doctoral research both challenging and rewarding. “You are coming up with experiments and questions that no one has ever done before, which can be very frustrating,” she says. She describes her committee of advisors as “wonderful,” but adds that “at the end of the day, what work I put in parallels how much data I can produce and how quickly my research progresses. This aspect is also the most rewarding, though. I know that whatever results I find are my own; it was the combined effort of the experiments I designed and the data I analyzed that produced them.”

Travel is another part of work that Charlie enjoys. In addition to going on expeditions with the Field Museum, she is spending the summer in Taipei, Taiwan as part of her National Science Foundation East Asia and Pacific Island Summer Institute Fellowship. Charlie was one of around 200 American students to receive the fellowship, and she says she feels very honored. While abroad, she is working on a project of her choice at the Academia Sinica.

Charlie also likes sharing science with young people. She has been working with Sisters4Science for three years and appreciates the variety of science subjects covered. “I don’t think I’ve given the same program twice since starting!” she says. Charlie has also worked with the Junior Paleontologist program and IGERT Explorers. She enjoys the opportunity to introduce her research to high school and middle school students in ways they can relate to. But the students aren’t the only ones learning. “I’ve also tackled various subjects that are not my expertise,” Charlie explains. “Learning new things to a degree that I can teach them is good practice for me.”

Asked what she’d say to an aspiring scientist, Charlie had this advice:

“Ask questions and be observant! Ther are so many exciting fields in science and SO so many unanswered questions that need fresh, young minds to ponder them. When you start thinking scientifically, it fundamentally changes the way you perceive the world around you. I think this is especially true for biomechanists and functional morphologists. You see the way things move, the way they interact with other organisms and their surroundings, and it is truly inspiring. You want to know how and why animals do what they do, and these fields give you the tools to be able to figure it out.”

Charlie is still putting together her website, but you can read about the lab she works in at http://biosync.fieldmuseum.org/users/mwestneat.

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jane-goodall-institute-tanzania

Jane Goodall: a little girl who loved animals and grew up to teach us all

The post about smurfs and animals got me thinking about little girls who love animals, and thus got me thinking about Jane Goodall, renowned chimpanzee expert who made her start as a little girl who really loved animals.

I got to see her speak at the Ottawa Writer’s Festival last year (which is when I took the picture at the top of this post — it was a packed house!) and loved hearing her story of how she went from being a little girl who loved animals to a field naturalist who hugely expanded our knowledge of animal behaviour. She’s an amazing speaker, and I was sad that I didn’t have any way to have you all experience the lecture I attended…

But thankfully, technology comes to the rescue! There’s a really great recording of Jane Goodall speaking at University of San Diego. It’s pretty long for a youtube video, but absolutely worth it — put it in on in the background while you’re doing something else and hear her incredibly inspiring story. I particularly enjoyed hearing her story of how she went to get her PhD (there wasn’t time for a BA) and was told she was doing everything wrong and how she knew it was they who were wrong (It starts at 28:08 and runs a minute or two.)

One of the lovely things about her latest tour is that rather than talking about the doom and gloom environmentalism of the 80’s, she’s promoting a message of hope by talking about the amazing ways in which the world has bounced back with our help. She’s telling some really fantastic stories!

Open thread: parthenogenesis in Komodo dragons

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!