Tag Archives: chemistry

A Linkspamination unto Nuggan (9 Aug 2013)

You can suggest links for future linkspams in comments here, or by using the “geekfeminism” tag on 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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Want to highlight a geek woman? Submissions are currently open for Wednesday Geek Woman posts.


Wednesday Geek Woman: Maud Menten, medical researcher

This is a guest post by Ingrid. Ingrid looks at the entire world from an evolutionary perspective and sometimes remembers to post stuff to Dreamwidth.

Submissions are currently open for Wednesday Geek Woman posts.

Photograph of Maud MentenMaud Menten was one of the first Canadian women to receive a medical doctorate, in 1911. Women could not do research in Canada in those days, so she sailed alone across the Atlantic to work at Leonor Michaelis’ lab in Berlin. During her year there, they developed the first model and equation to describe enzyme kinetics, the Michaelis-Menten equation. She worked for many years as a teacher and researcher at Pittsburg, making more important discoveries – she was the first to separate proteins by electrophoresis, and altogether, could lay claim to being the mother of biochemistry.

She was hard-working, determined and persistent, despite lack of recognition – her contributions to medical science exceed that of many Nobel laureates, and she was only made full professor a year before she retired. She also studied languages, music and painting, and did mountaineering. Today, she is surprisingly unknown, even by biochemists (I learnt the Michaelis-Menten equation early in my undergraduate biochemistry courses but only found out that Menten was a women significantly later), and I’d like to rectify that a bit.

Wikipedia: Maud Menten
Rebecca Skloot (2000) Some called her Miss Menten
Canadian Medical Hall of Fame: Dr. Maud Menten (includes 4min YouTube documentary)

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Photograph of Branca Edmée Marques

Wednesday Geek Woman: Branca Edmée Marques, Portuguese scientist, and collaborator with Marie Curie

This is a guest post by Jennifer. Jennifer is a feminist and actuary who is travelling the world with her family and profiling notable women of history on her blog.

This entry is cross-posted from Jennifer’s blog.

Submissions are currently open for Wednesday Geek Woman posts.

Photograph of Branca Edmée MarquesBranca Edmée Marques was a Portuguese scientist, who studied and worked with Marie Curie. She was born in Lisbon in 1899, and studied chemistry at the University of Lisbon. In 1925 after completing her degree, she was invited to be an Assistant by the Chemistry Professor. He was concerned about whether she would maintain discipline in her classes, being female, but she must have succeeded as in 1930 she was awarded a scholarship to study with Marie Curie at the Sorbonne, in Paris.

Marie Curie was by then very famous, having won two Nobel Prizes. Curie liked her work so much that she gave her one of her most interesting research projects to do, and wrote a letter to the Portuguese government asking them to renew her research grant.

Unfortunately the combination of Marques being a woman, and the Portuguese government being in a state of flux (transforming from military to civilian dictatorship) meant that her grant wasn’t renewed. Curie managed to finagle a continuing scholarship for her anyway, and her doctorate on “new research on the fragmentation of barium salts” was awarded with the highest possible rating of tres honorable. In 1936, the Portuguese Universities recognized the degree, and awarded her an equivalent doctorate.

On returning home, however, she was unable to get an appropriate post at University. This, from all my sources, does appear to be fairly simple sexism, even if the lack of financial support in France might not have been. Instead, she lectured and started up the Laboratory of Radiochemistry and only in 1942 was she awarded the title of First Assistant, which meant that the University was recognizing her contribution more significantly.

Photograph of Branca Edmée Marques
She continued to lecture and work towards building up a new department, which eventually became the Department of Radiochemistry and Nuclear Chemistry. She published regularly throughout her professional life, researching many aspects of peaceful application of nuclear technology. In 1966, her contributions were finally recognized with a full professorship at the University of Lisbon.

She died in 1986, at the age of 87.

This post is based on Portuguese language sources (linked below) so anyone who can read the original Portuguese, please feel free to comment if my interpretations were wrong!

Marcas das ciências e das técnicas: Professora Branca Edmée Marques
A ciência em Portugal: Branca Edmée Marques
Maxima: Sancha Sanches

Wednesday Geek Woman: Marie Curie, Nobel Prize winning physicist

The Wednesday Geek Woman series is mostly on hiatus. Remaining WGW posts will appear sporadically over the next few months.

This is a guest post by Jennifer, an Australian actuary and feminist who blogs at Penguin Unearthed. She is currently travelling the world with her family and is blogging about notable women of history as she travels. This post originally appeared on her blog.

Photograph of Marie Curie, ca 1898

Photograph of Marie Curie, ca 1898

Marie Curie has been a hero of mine for as long as I can remember. She was the first woman to win a Nobel Prize (for Physics), and then went on to win another Nobel Prize for Chemistry, for discovering two different new elements – polonium and radium.

Marie Curie was born Marie Skladowska in Warsaw, in 1867, which at the time was part of the Russian Empire (the country that had been and would become Poland was split between three different empires at the time). Her parents were schoolteachers, and quite poor, with the family having lost much money supporting various Polish patriotic causes over the years. So after she finished school, she and her older sister agreed to fund each other through University. Her sister went to Paris first, and studied to become a doctor, and then after a few years as a governess, Marie travelled to Paris in 1891, at the age of 24, to study at the Sorbonne.

After finishing two degrees, she married Pierre Curie, and they devoted themselves to science. They were very poor, and spent long hours experimenting in a very basic laboratory. They studied the phenomenon of radioactivity (a word with Marie Curie coined) and realized that it was did not come from molecular interactions, but from inside the atoms themselves. They also realised that pitchblende, a uranium rich mineral, was more radioactive than could be accounted for by its uranium, but that there must be some other radioactive element or elements emitting more radiation. They spent long hours chemically analysing tonnes and tonnes of pitchblende in order to separate out first polonium, and then, after Pierre was killed in a tram accident, Marie continued alone to separate radium.

Marie and Pierre won the Nobel Prize for Physics in 1903, shared with Henri Bequerel, for their discoveries and descriptions on radioactivity. And then Marie won the Nobel Prize for Chemistry on her own in 1911, for discovering Radium. Despite the two Nobel Prizes, the French Academy of Sciences refused to elect her as a member, as she was a woman.

Marie Curie's Birthplace At the time, nobody knew how dangerous radioactivity was. Marie Curie died of leukemia in 1934, probably because of her exposure to radioactivity. Her notebooks remain too radioactive for safe use even today.

She and Pierre had two daughters, both also extraordinary. Irène, the older, won a Nobel Prize of her own (shared with her husband Frédéric Joliot-Curie), and Eve was elected an officer of the French Legion d’Honneur for her work with Unicef.

Marie Curie was a driven woman; driven by her devotion to scientific discovery. She won her second Nobel Prize one hundred years ago this year. To do what she did, she was in almost completely unchartered territory to be a woman in science. But she didn’t just succeed. She surpassed. She is still the only person to have won two Nobel Prizes for two different sciences.

Wikipedia: Marie Curie

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Ever tried explaining science using dance?

Some of my fellow Women in Science and Engineering are finalists in this fun contest called “Dance your PhD.”

The dreaded question. “So, what’s your Ph.D. research about?” You could bore them with an explanation. Or you could dance.

That’s the idea behind “Dance Your Ph.D.” Over the past 3 years, scientists from around the world have teamed up to create dance videos based on their graduate research.

I’m sure they’d love some more votes, and I just wanted to share their creative way of explaining chemistry, so here’s the video:

Selection of a DNA aptamer for homocysteine using SELEX from Maureen McKeague on Vimeo.

McKeague’s Ph.D. dance, based on her research at Carleton University in Ottawa, Canada, is about a technique called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The target is a small molecule called homocysteine. SELEX uses natural selection to find the small strands of DNA called aptamers (the other dancers) that bind specifically to the target. Watch for the hilarious Taq Polymerase scene in the middle of the dance.

When you’re done watching, you can check out the other entrants and vote for your favourite on the sciencemag website. I think the Da Rosa lab video does the best job of really explaining the research so they’ve got my vote, but I’m biased, and the other entrants are pretty impressive too. The results will be announced on October 19th.

And here’s a question to all of you: what’s the weirdest way you’ve explained what you do, be that research, code, your favourite game or show, etc? Anyone inspired to try some dance now?

Quick hit: Ada Yonath

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.