Monthly Archives: February 2009

Things to listen to

I’m juggling a lot of different little projects at the same time right now, so apologies for once again linking to one of my other blogs. Actual original content is forthcoming, promise!
I interviewed some people about connections between science and music when I was at Science Online 09. They were research interviews for the documentary I’m working on at the pace of a snail/sloth (whichever is slowest). That means I’m not going to give everything away, and I’m holding back on the good stuff, but I do want to give people something to listen to, so I’m posting snippets of the interviews, with permission of the interviewees.
The first interview I posted was with Victor Henning. We talked about the connections between Mendeley and the music industry. I was unable to cull this any shorter than 5 minutes, because he told a very long interconnected story. My interview with Nature’s own Henry Gee, on the other hand, yielded so many short, usable, sound bites that I need to think about which to post. Those are not up yet, though, but you know now to keep an eye on this blog (maybe add it to your feed readers). Other interviews that are ready to go up are with Cathy Davies and Cameron Neylon. I won’t post those two back to back, because they’re kind of similar in terms of the type of music and science they both do, so one of them is the next one to be posted, then Henry, then the other of the latter two. I’ll be starting Skype interviews in a few weeks, probably, and won’t post the last of the edited interviews until I have another one in the works. How is that for a peek behind the scenes?

Jennifer’s Malaria Song

One group of people that I sadly did not get to talk to when I was at the Science Online 09 conference last month was Miss Baker’s Biology Class. Stacy Baker’s interactive teaching methods were recently profiled in The Scientist, and she brought a few of her students to Science Online 09, where they were the life of the party. I missed their session, but everyone who did go there later mentioned that as their favourite session of the conference!

Today I found the class online again, when one of the students, Jennifer, put up a video of herself performing a song she wrote about malaria:

Interview with Victor Henning

I have started doing research interviews with people who are somehow involved in both music and science. My first set of interviews was carried out at the Science Online 09 conference in North Carolina last month. I interviewed four people there, and only just got around to editing the interviews into little snippets. I don’t want to give away all my info, and am deliberately holding back the most interesting bits, but I do want to share some bits of the research interviews I recorded, and will be posting those as I go along.

Zoom H2The interviews are recorded with the Zoom H2, which looks like a cross between a 1930s jazz club microphone and something out of an old science fiction movie. I guess that’s a science/music connection in itself.

The first interview I’m going to put up is the one I did with Victor Henning of Mendeley. It is also the longest audio file I have. Everyone else I managed to shorten to one or two minute soundbites, but Victor’s stories were too long and interconnected to do that with, and I could not trim it down any further than 5 minutes.

Mendeley is a reference manager tool that can be used to store and organize academic papers. Interestingly, it is developed, run, and supported by people with a background in the music business. Listen what Victor has to say about his own past in the music industry, about the similarities between Mendeley and LastFM, and about the music connection of one of Mendeley’s new investors (Their funding deal was reported today in Tech Crunch).

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Mammoth in the “news”

Something in the news today reminded me of Jenny’s science-vs-sports reporting idea.
I blogged about it on my other blog , because that’s where I originally reported on my Tar Pits trip, but it’s cool enough to mention twice.
In 2007 the LACMA museum started expanding its parking garage. The museum is right next door to the La Brea Tar Pits. (That city block consists of only the Tar Pits park and the museum). This means that the museum is built on the exact same interesting ground that yields all those fossils at the pits, so the museum got all the ground that was excavated. When I visited in August 2008, I saw lots and lots of crates full of parking garage soil that they don’t even have time to go through. I also saw mammoth tusks , still in plaster! And in the fishbowl of the museum I saw more plastered things from underneath the garage.

A mammoth from underneath an L.A. parking garage is incredibly cool and I was very excited about this. But science news reporting is slow, and it wasn’t officially announced until…today .
I am fascinated by the intermediate process I saw, where everything was plastered up. How did they get the tusks out? What did they do in between August and February to go from these white blobs I saw in the fish bowl to the picture in the NYT article . (Is that even the same jaw?) Yes, these are the things you can see in the museum itself, and ask the scientists there – the La Brea Tar Pits Page museum is extremely interactive and open about what is going on – but how can you possibly in good conscience call this “news” anymore?

Trendy flu

ResearchBlogging.org Playing with Google Trends is a favourite pastime of geeks .
You can look at searches that are more popular in certain locations compared to others, and you compare the popularity of searches over time. For example, if you look at the trends for searches for “christmas”, “easter”, “valentines”, and “halloween” you’ll see that they are more popular in the days leading up to those holidays, peak on the day itself, and then abruptly drop again as people immediately lose interest.

People only look for info on holidays close to the date
In certain search words you can clearly see the pattern of the Northern hemisphere school vacations:

Nobody cares about math in summer or around Christmas.
Other keywords don’t have that as much.

Everyone always cares about coffee and chocolate.
Hey! Look at those peaks for chocolate! Don’t they look familiar? I overlapped the chocolate graph with that for Easter and Valentines Day to be sure (the Christmas peak was too high – it made the chocolate graph look like noise), and there it is: people search for chocolate around the holidays! It’s most clear in 2007 and 2008. You can also see the peaks around Christmas.

People search for chocolate around the holidays
This is all pretty mundane stuff, but Google can also be used to plot relevant trends. A team of researchers from Google and the Centers for Disease Control and Prevention showed that Google is faster at predicting when and where a flu outbreak will pop up than current methods.
The traditional way to spot an epidemic is to go by reported physician visits. If more people start seeing their doctor with flu-like symptoms, that is often the first sign that something is wrong. Physician visit stats are collected and published by agencies like the CDC, but that takes a few weeks to process. Epidemics can spread fast, so the earlier such trends can be spotted, the better they can be fought.
Now, a lot of people, when feeling unwell, look up their symptoms or medications in Google before (or even instead of) visiting a doctor. Fever, tired, headache, cold, Nyquil, vomiting, Tylenol – you name it. The researchers on this study followed trends of people searching for such keywords, and compared them with past data from the CDC that were based on physician visits in the corresponding areas. With certain keywords, analysis of Google data was able to detect the same local flu epidemics as the CDC had plotted. And not only that, Google could do it faster. Because it takes a while for people to visit the doctor and for the doctor to log the visit and for the CDC to collect these data and analyze them, Google was actually about one to two weeks ahead by grabbing the data immediately from the search logs.

(From the paper but also available as video ) The model based on CDC data (red line) follows the same trend as the model based on Google search info (black line) did earlier. (ILI = Influenza-like illness)
This could be a pretty useful tool. Pandemics become much harder to fight once they spread further, and knowing that you’re in the early stages of one is incredibly valuable. With a two week delay in information, you’ll realize that you were in the early stages of a pandemic two weeks ago which means that you could be in the middle of one right now!
Google set up a separate website for this: Google Flu Trends
You can select a US state to see the current pattern of flu-related searches, and if you’re in that area, know if other people are experiencing the same symptoms. It’s not specific to smaller areas, so I doubt this would be of use to individuals. Still, if this is able to pick up emerging outbreaks faster than current tools, it could be useful for the CDC.
But above all, it’s just incredibly cool that someone got a Nature paper out of Google statistics. Can I publish the chocolate-holiday correlation, too?

Continue reading

Soup, beautiful soup

_“Soo—oop of the e—e—evening,
Beautiful, beauti—FUL SOUP!”_
Are scientists generally good cooks? asks Sarbjit.
Not this one, I can tell you that ! But I’m learning…
As I wrote before , my resolution for 2009 was to learn to cook five awesome dishes. Three people kindly left recipes in the comments of that post, and a few weeks ago I decided to give Åsa’s soup a try. It seemed more simple than Henry’s recipe, and Steffi suggested something with ginger, which is the one food item I sometimes find really gross (especially when it’s chopped in pieces) so I went with the safest recipe.
Potatoes, onions, and leek were on my shopping list, but when I wandered through the store there was no leek to be seen. They recently rearranged the vegetables, and the organic ones are now separate from the rest, so I looked at both sections. No leek. I looked again, and again, until I found a sign that said “leek” next to an empty compartment. Huh. Disappointment. I lacked the culinary creativity to come up with a whole new dish right then and there in the supermarket. Couldn’t I make it without the leek? Could I maybe substitute something else? Onions are kind of like leek, and chives taste very similar, so I decided to jump off the deep end and experiment.
I should remind you that, despite being a lousy cook, I’m an above average baker. I have made pumpkin pie twice, both times using this recipe but never doing what it said and rambunctiously adding apple or too many spices or whole wheat flour.
Replacing leek with onion and chives in a non-dessert food, however, was a whole new kind of scary. That’s like using the wrong TRIS buffer, and that can be absolutely devastating to your experiments! But the soup turned out fine! It was a bit mashed-potato-textured, so I knew to add more water next time, but it tasted just fine.
Did it taste the right kind of fine, though? I had to find out. There’s the scientist attitude! So today I made the soup again, with leek this time, and with more water. It tasted… pretty much the same! If there was any difference, it was the amount of onion. I only had a small onion this time, and it didn’t even make me cry when I cut it, so it wasn’t as strong as the one I had before. The chives as leek replacement, though, were uncanny.
Conclusion: I experimented in the kitchen and it worked!
Discussion and Suggestions For Future Work: I have one dish down, four to go! This dish was vegetarian if you add the sour cream and vegan if you leave it out so I’ll see what the tally is at the end of the year to see where it counts. For now, I’m just very proud that I cooked something with total disregard for protocol and still made it taste good.
Thanks, Åsa!

Mr. Darwin, you make me blush

My birthday this year was somewhat overshadowed by Darwin’s 200th in the same week. But both Darwin and I are victims of the yearly creep of that Hallmarkest of Holidays – Valentine’s Day.

Well-meaning friends might step into Ye Olde Card Shoppe, looking to purchase a birthday card for Darwin or me, and BAM Pink! Teddy Bears! Hearts! Heart-shaped balloons! Teddy bear-shaped balloons with heart-shaped confetti! Chocolate hearts! Giant pink heart-shaped cards with saccharine poems!
What were we here for again? Oh well, let’s just buy some chocolate.


This might as well be Hallmark around Valentine’s Day

And what’s the point of Valentine’s Day anyway? A yearly reminder to tell someone you love them? I thought you’re supposed to say it more often than that. But what do I know; I’m far from an expert on the expression of emotions…

Darwin, on the other hand, wrote a book about it.

Expression of the Emotions in Man and Animals was published in 1872 and sold a decent 5267 copies on the first day. He originally intended for the topic to be just a chapter in his book Descent of Man but when he looked at his notes he realized he had way too much for just a chapter. Darwin had been taking notes on the topic since 1839, when he started writing down details of the facial expressions of his newborn baby.

The book is a far cry from current scientific literature, full of anecdotes and phrases that would not be printed in psychology papers these days. We’ve come a long way, and the field of the study of emotions has advanced to controlled studies and statistics, but it’s just so much fun to look at old texts.

What does Darwin have to say about Valentine’s Day customs?

“No doubt, as affection is a pleasurable sensation, it generally causes a gentle smile and some brightening of the eyes. A strong desire to touch the beloved person is commonly felt; and love is expressed by this means more plainly than by any other. Hence we long to clasp in our arms those whom we tenderly love.”

Oh, Darwin, you make me blush.

“It is plain to every one that young men and women are highly sensitive to the opinion of each other with reference to their personal appearance; and they blush incomparably more in the presence of the opposite sex than in that of their own. A young man, not very liable to blush, will blush intensely at any slight ridicule of his appearance from a girl whose judgment on any important subject he would disregard. No happy pair of young lovers, valuing each other’s admiration and love more than anything else in the world, probably ever courted each other without many a blush.”

Really, Darwin? What about the barbarians of Tierra del Fuego?

“Even the barbarians of Tierra del Fuego, according to Mr. Bridges, blush “chiefly in regard to women, but certainly also at their own personal appearance.”“

I probably also blush at my own personal appearance, like when I fall down stairs, or maybe when people see me naked. That happens less often than the falling down stairs, sadly. Sadly for several reasons…

But never mind that, Darwin. Let’s talk about nearly naked men!


Nearly naked men

“With Europeans the whole body tingles slightly when the face blushes intensely; and with the races of men who habitually go nearly naked, the blushes extend over a much larger surface than with us.”

Darwin, I don’t think this is even correct. But thinking about blushing is, itself, making me blush.

“No doubt a slight blush adds to the beauty of a maiden’s face…”

Aww, thanks.

“…and the Circassian women who are capable of blushing, invariably fetch a higher price in the seraglio of the Sultan than less susceptible women.”

Wh-what?

Darwin? Where are you taking me?

I…I even got you a birthday card! Or, well, I tried to get one, but there were teddy bears, and they were pink, and….chocolate. Hey, how am I only worth one camel? I’m capable of blushing! That’s at least a camel and a half…

Beam me up

After 6.5 years in Canadaland, I forgot that I learned some new words while here. Not many – about 2 per year – and most of them Canadian or otherwise local expressions that English-speaking folks from other parts of the world might not know, such as tuque or Zamboni . The expression “pencil crayon” that I used in a previous entry was also Canadian, apparently . I didn’t even realize that. I’m just absorbing words here and there.
I also had to relearn a few lab words when I moved, because Dutch lab-English is not the same as lab-English in other places. I learned “erlenmeyer” for “(erlenmeyer) flask” and “eppie” (as anglification of “epje”) for “Eppendorf tube”.
These little buggers have a different name according to every single person I’ve asked, in five different countries and even more labs:

My most recent lab had no name for them. When I needed one (because mine were always lost) I had to walk around with a glass pipette, making pipetting gestures while asking for the “rubber thingie for the glass pipette” to express what I needed. Bulb, balloon, pear, rubber thing, or a range of made-up words (I learned “fiepje” in Amsterdam, but a Google image search for the word only brings up people’s pets) all for this little thing.
And then there’s the matter of the projector, of course…
Two friends from Holland recently moved to Canada, and brought up something I had completely forgotten: “It’s so weird that it’s not called a beamer.”

(photo by libraryman )
Beamer! I hadn’t heard that word in ages, but that is also what I called a projector when I arrived, and so did the fresh-from-Zürich Croatian postdoc who started a few months later. But nobody else did. “Why do you call the projector a beamer?” my supervisor asked. That’s…what it’s called? It’s an English word! Like “computer” and “laptop”, “beamer” was just one of those English computer words that are used everywhere, right? Wrong. Apparently, a projector is only called a beamer in Dutch and German. It’s tricky, because it’s an English word, spelled and pronounced the English way.
“Beamer” for a projector is not English, as most of you knew well before me. It’s pseudo-English, and there is a whole list of these words on Wikipedia. Words like this are hard to unlearn when switching to English, because you automatically assume they are English. “Sheets” for overhead transparencies is also on the list of Dutch pseudo-English words. To give a presentation, you either need “sheets” for the “overhead projector”, or “powerpoint” for the “laptop” and the “beamer”. See how much English is in there? It’s very confusing that some of those words are not English after all!
Where does the word “beamer” come from? I have no clue.
I just deal with knowing different words for the same thing. Much like how, in the lab, I wrote “glucose” on the jar labeled “dextrose”, filed the IGEPAL bottle under the “N” for NP-40, and was somewhat confused in undergrad physiology when the textbook kept saying “epinephrine” where I knew it to be “adrenaline”.
It’s enough to make you want to break out the Tylenol/paracetamol.

Look at my cat

I previously spotted a blogger in an early twentieth century neurophysiologist, based on his love of writing and his consistent weekly letters to his mother. In thinking it all through, I thought there might be certain tell-tale signs that someone is bound to be attracted by the concept of blogging. Diaries and letters are one thing, but there might be other clues.
When I was a kid (age 9-14) I took tremendous pleasure in writing for an invisible unknown audience. At age eleven I wrote two parody essays at school. I forgot one topic, but the other – the funniest one – was about invisibility. It contained a section written in invisible ink (just skipped a few lines) and a newspaper picture of the (at the time) Minister of Internal Affairs with an invisible man (just a picture of the Minister). It was written in the style of a general informational piece for a wide audience, but only my teacher and my friends read it, of course.
At home, I sometimes made little booklets. I made my own comic books, puzzle books, and information booklets about my pets. I had my parents look for the latter, because I remembered that one in particular to be so extremely blog like. It was a small booklet about my guinea pig and our cat that I made it when I was ten or eleven.
This is the cover:

Neel and Snoopy
The entire booklet was full of anecdotes and facts about the pets. Here is something I thought was a very interesting fact about my guinea pig:

Snoopy is often outside in the yard. Snoopy has a roll to run in. Snoopy also has hay to lie in, but he always eats it all.
[Ed. – it’s the cardboard inside of a toilet paper roll. I just called it a “roll” for short.]
If you thought that was fascinating, wait ‘til you hear about the cat!

We have a glass stand for the TV. Neel always sits under it and looks up at the underside of the TV.
See, it’s such a blog. Nobody read this but my parents, who were already familiar with our pets and their quirks, but it was written as if it was for strangers, with vital stats on both animals (bit of a lab book there) and talking about them as if you did not know them.
It was inevitable that once I heard about a thing called internet that I’d immediately put stuff up there myself. I went online for the very first time when I started university in the fall of 1996, and by the time the 1997 calendar went up, I already had a website, hand-coded in html that had to be e-mailed to the server. My first “blog”-like thing was a manually updated page to describe four months I spent working in Quebec in 2000. My first blog software was installed in 2001, and I went through a couple of “look at my cat”-style personal blogs before settling into science blogging in 2005.
But my first (b)logs were those little stapled-together booklets, written in pencil-crayon, and elaborately illustrated. My mom kept them on the living room book shelf for an embarrassingly long time, in between the other non-fiction books. I also have a collection of personal diaries that I kept from age 7 to 18 or 19. The first one contains an entry (age 8) in which I was really excited about two things: one was that my friend came over and I got some gift or other, and the other was that my sister was born. Next to that entry I stuck in a sticker of a horse and the birth announcement card. It’s pretty cute. (The age 16-17 diaries, on the other hand, are an existential, Adrian Mole-like train wreck, and we should all be thankful that I hadn’t discovered the internet yet at that time.)
Now, like the teenage version of me, I’m once again wondering whether I’m in any way special and crazy, or if there are many others like me. If you blog now, did you ever make little info booklets as a kid? Or keep diaries? (Or still keep a diary? Or even still make little info booklets that only your parents read?)
Let me know, and look at my cat doing a handstand in a trash can:

Bloggers

Many congratulations to Shirley Wu and Russ Altman , who won the Science Blogging Challenge and have secured a spot at SciFoo this summer! (They’re also getting all expenses paid from Stanford to Mountain View – just down the Caltrain line – but lest you think Nature is being cheap, they’re using the money they saved by awarding the prize to Google’s next-door neighbours to allow people from developing countries to be able to make the trip.)
But, honestly, other than the prize incentive, why should more senior scientists blog?
That was what was in the back of my mind when I wrote my previous post about Penfield and Cone. One of them would have made a great blogger, but the other one would have certainly refused if asked. I didn’t ask anyone to start a blog as part of the challenge, no matter how badly I would have wanted a chance at the prize, because most of the scientists I know are of the Cone-type. Great at research, but hate writing.
The 1920s didn’t do much active science outreach, but there’s that as well. Most scientists I know hate outreach, and probably wouldn’t like blogging either. Why do they hate outreach? The same reason they hate teaching. I have observed someone go from the most eager student ever to the kind of professor who complains about teaching. Creepy. That’s one reason I don’t ever want to be in that position. I love teaching and writing and talking about science, and do not want a job that could turn me into someone that complains about all these things.
So, why do PI’s hate outreach and teaching? It takes valuable time away from research, and research is what brings in the funding, and funding is what keeps the lab afloat. There is no incentive to do anything on top of that. They reluctantly teach to fill contract requirements. They’ll do outreach to please a higher-up. They write, because they have to. There is no way I’m influential enough to tell someone to sacrifice their valuable spare time to write a blog about science. I can’t tell anyone why it would be good for them to blog, I can only say what good it has brought me, and those things are all in the area of science communication – the thing I love that most PI’s hate. They wouldn’t think my writing gigs and contacts in science communication were anything desirable at all. They’d see them as just more wastes of time!
Most scientists simply aren’t bloggers. In a literal sense, that seems to have been the drive behind the challenge: there are more non-blogging scientists than blogging ones; let’s get more to blog.
But, most scientists simply aren’t bloggers in the sense that they aren’t the blogging type. And is that a bad thing? Should they be bloggers? Or: should they be bloggers, as opposed to the enthusiastic writers who already are?
I’m not asking rhetorically, or even sarcastically. I really would like an answer: Why do (more) senior scientists need to blog?