Archive for: May, 2011

Transformative Science

May 27 2011 Published by under Uncategorized

Senator Coburn from Oklahoma is now leading the latest Republican charge against science. In a recently released so-called exposé of wasteful spending at the NSF he shows his deep seated ignorance of how science is conducted and what its significance is. While several bloggers have already eloquently written about his report's misrepresentations and distortions of what he calls frivolous science (here, here and here), one thing that struck me is his view of what "transformative" science really entails. A few years back the NSF amended its grant review criteria to consider whether the proposal under consideration explored "potentially transformative concepts". Sen Coburn spends about 25 pages outlining projects that in his expert scientific opinion are not only not transformative, but also frivolous and wasteful. However if you read closely the descriptions of such projects many of the distortions become evident. He particularly picks on studies in the social sciences, as if studying the nature of race relations in America, or the best methods to disseminate science to kids, or the growing effect of social networks on the structure of society, or studying the democratic process, or the best way to involve the community in scientific discovery thus increasing science literacy, are not important issues that affect us all. Even studies which the potential implications for improved technology are evident such as teaching robots incredibly complex tasks such as riding a bike or folding laundry are ridiculed. Does Coburn really thing that scientists are designing a laundry-folding robot to help out with their housework? Is he THAT narrow-minded?

Furthermore Coburn's report shows an utter lack of understanding of the scientific process. It is very rare that a single study will be transformative on its own. Rather most projects work to solve little bits of the puzzle at a time, creating useful basic information which gradually becomes incorporated into the body of knowledge and ultimately leading to a transformative concept. One has to look at the entire portfolio of a funding agency or directorate within the agency to grasp the overall scope of the research, which when all put together it becomes transformative. Science funding agencies only fund a tiny percentage of proposals submitted to them, and these are reviewed by panels of experts and managed by scientific officers who keep an eye on the big picture. How does the senator claim to be more of an expert than the hundreds of scientists reviewing these proposals.

Finally, what most pissed me off is his call to eliminate (or consolidate) most of the education programs run by the NSF. The senator claims that there is too much overlap with other STEM programs run by other federal agencies. But the NSF has a long history of supporting STEM education, increasing scientific literacy, reducing achievement disparities in underrepresented groups and notably in integrating research and education. Unlike other federal funding agencies the NSF requires that proposals have a plan to disseminate their science as part of their broader impacts. Many of these educational activities serve as an important means by which scientists can communicate their science with the public and train the next generation of sciences.

I urge you to call your representatives in congress and ask them to support basic science and science education.


28 responses so far

Coordination School

May 23 2011 Published by under Uncategorized

Recently I watched my daughter try to kick a stationary soccer ball and miss. Or try to throw a basketball towards the hoop, only to have the ball shoot out backwards. Unfortunately, I think she's inherited her poor motor coordination from me. I always have sucked at most sports, and like my daughter. as a kid I would always prefer sports, like swimming, that did not require large amounts of hand-eye coordination. I feel pretty bad about this, and I keep encouraging her to keep trying since I don't want her to miss out on a lot of fun activities. And I know its pretty hard growing up as the 'uncoordinated kid' like I did. I even went to coordination school.

I actually had a lot going against me in addition to my innate lack of good coordination. For one I had four older brothers, all good at sports, who would continuously make fun of my clumsiness. My mom was somewhat clueless since she sent me to basketball classes when I was six wearing suede shoes and tube socks, but that's another story. In reality, I blame my second grade teacher for my aversion to participating in team sports. Back when I was in elementary school my mother decided to go back to college to study educational psychology. As she was learning about the different assessment tests used in the field she would test them out on me and then explain how she would evaluate them. At school, the school psychologist would occasionally come by and use these very same tests on us, and since I already had done them and knew how to skew their interpretation I would invariably decide to mess with the teachers. This would result in some fairly alarmed teachers and a call to my mother, who would then explain that I was just messing with their minds and that didn't they have anything better to do than to harass her son. I remember a pouty school psychologist finally telling my mother, "well maybe there's nothing wrong with him psychologically, but he's severely uncoordinated!"

This led to my mother asking my pediatrician(who happened to be my uncle) during one of my checkups whether he thought I was uncoordinated. My uncle said, "let's see" and he crumpled up a piece of paper and tossed it on the ground. Then he asked me to kick it. Being left handed, I usually kick things with my left foot. So as I went to kick the paper I was thinking, "hmm…maybe they want to know since I'm left-handed, whether I'm also left-footed – maybe I'll confuse them by kicking with my right foot!" This of course was just as I was about to kick the paper with my left-foot and as I attempted to quickly change to my right foot I somehow managed to trip and fall flat on my face. "Yup…definitely uncoordinated." So despite my protestations and explanations they sent me to what my mother called "special gym".  "It'll be fun", she said. But I knew where I was going: I was going to coordination school.

This supposedly fun thing, turned out to be classes for kids with motor problems. Some sort of occupational therapy where we had to walk in straight lines, practice clapping and standing on one foot. It was evident to me, even then, that the other kids were more worse off and had actual problems, unlike my fake ones. And after a month or so this also became evident to my mom, who took me out of the classes and instructed my brothers to teach me how to play soccer. I never did mess with the school psychologists after that. And I'm still bad at soccer.

17 responses so far

The Data Sink

May 19 2011 Published by under Uncategorized

Some people call it karma, others mojo. I call it the data sink. Not a sink as in a kitchen sink with a drain, but rather a sink in the sense of something towards which things  flow. I have a theory that on a given day, there is a finite amount of data to be had in a given research environment. And this data is not evenly distributed amongst the members of said research environment. Rather it is usually distributed between a handful of data sinks. These are the people in a lab who seem to be sucking up all the data while everyone else toils around fruitlessly. Fortunately, these data sinks are not stable and can rotate around from person to person over several days. And once you have a data sink you can keep it going by taking advantage of it, much to the chagrin of your lab mates. In my postdoc lab, this seemed to be certainly true, where someone would have a good run where they would get lots of data for several days, but eventually things started to falter and it would be someone else's turn to soak up all the available data. Occasionally a couple of people would be having good runs and then it would be truly dismal for everyone else. In the rare occasion where everyone was getting data at the same time –a mega sink–  we would hear cries and screams from the lab next door. They would knock on our doors demanding we give them back their data. Once you acquire a data sink, the way to keep it going is to work harder, to keep the data flow steady. As soon as you let up, your sink will dry up and go to someone else. So you should treat your data sink with love.

While not everyone will subscribe to my theory on data sinks, I think there are some valuable lessons to be learned from it. Probably one of the most valuable things I learned as a grad student, was learning to identify data sinks. The time when all of your equipment is working perfectly, all your experimental preparations are healthy, your mental state is groovy, and then it happens. Data starts pouring in. And if it does, it is important to fully ride with it, because you don't know when something is going to break, and the data flow will stop and you never know when you will get it back. During these times you really have to work extra hard, you can take a break when the data sink dries up. And I find this difficult to impart to my graduate students who will often go home, or to the gym, or to a two-hour lunch, or whatever in the middle of an experiment which has been giving them good data all day. They are basically losing their chance to acquire more data and making their life more difficult in the long run. I have no problem with people having a life, but science seems to work at its own pace and you just have to have a flexible work schedule. I'd rather they stay for an extra few hours and then take off the next day, than to stop a perfectly good experiment midway.

Have you ever experienced a data sink? If so, how have you kept it going, how do you get it back once it goes away? Good data sinks  are difficult to achieve, and if you find yourself lucky enough to experience one, good care and feeding of your data sink will ensure a most pleasant and long lasting experience. Let the data flow!


14 responses so far

Low volume

May 15 2011 Published by under Uncategorized

Listening to music at low volume is like going to a museum with the lights out.

That's why I want a really big stereo.

2 responses so far

Because she's supercool

May 09 2011 Published by under Uncategorized

Happy mother's day to all the mommas out there! I especially want to wish supercoolwife a happy mother's day. Throughout this whole time since I've been sick my wife has basically held our family together singlehandedly. When I was in the hospital she would rush from getting the kids to school to bringing me breakfast –since she knew I wasn't eating the hospital food– to getting the kids from school and giving them a nice dinner to restore some sense of normalcy in their lives, to running back to the hospital to spend the night by my side. She fed me when I was home to make me gain weight making several different foods to make sure there was something I would like, all the time organizing play-dates for the kids and attending school events. Oh, and all this time working. And she has been a pillar of support for everyone during these difficult times. I hope she knows how much we all love her and appreciate everything she does for us. None of us would be getting through this if it weren't for her generosity and love. She truly is a supercool wife and a great mom. I hope she had a good mother's day (despite the kids' getting into an epic mud fight as they "helped" her plant flowers in our garden). And we look forward to many more happy and great mother's days together.

I love you sweetie (and so do the kids), happy mother's day!!

Speaking of mommas, here's some "Big Mama" Thornton:


One response so far

A tale of two manuscripts

May 03 2011 Published by under Uncategorized

Recently, there has been some talk on the blogosphere regarding the role of editors in glamour scientific journals vs. journals affiliated with professional societies. In a glamour journal, the editors are professional editors who's job is basically to be an editor, while in society journals editors tend to be working scientists who are doing a stint as acting editor for a journal. Submitting papers to these journals can result in very different experiences, and much of it has to do to the level of editorial control over the process and the experience of the editor. I'm sure many readers are curious how the publishing and peer review process works in various scientific disciplines. This was our experience.

In my lab, we recently had the fortune of having a paper published in maybe not quite a glamour journal but one of the glamour journal offshoots, which still has a relatively high impact factor (~14) and is one of the top journals in my field. Also we had a paper published in the journal of my scientific society (IF ~8). Let's call the first, fancy journal and the second, society journal. So what were our experiences with the different journals?

The first paper was the work of my grad student who had worked on it for 3 years or so. I've written before about this paper. It was a novel finding with a new mechanism and model system by which to study a neurological disorder. Because it was medically-related and thus of potential general interest, we chose the more visible fancy journal. Mind you that my lab had already had some decent publications before sending this out. If I were panicking to get more papers out I would never chance the long delay that you can encounter with fancy journals. The second paper was also the work of a grad student, took about the same amount of effort and time as the first and the results were of equal quality. Although we had to develop some fairly sophisticated experimental techniques for this study, the findings were more phenomenological and more discipline-specific, and this kind of a thing tends to not interest fancy journals. We did send it to a fancy journal but they basically said "fuck you very much" and was returned without review. Fuck you too. So this paper went to society journal.

After about ten days after sending the first paper to fancy journal we received notice that it had gone out for review. This is good because most of the time they send it right back saying they are not interested. About 5 weeks later we received the reviews. It usually takes the journal a week or so to find reviewers, then the reviewers typically take 3 weeks to return reviews and then another week or so for the editor to read the reviews and decide on the paper. The paper was sent to two reviewers and both indicated that our findings were interesting and novel, but they each had suggested an extra buttload of experiments to strengthen our case. Since both reviewers were reasonable, and the experiments were doable, my student and I decided to just go for it and do everything they asked. I mean if they say, "if you do X,Y and Z we'll find your paper acceptable", they you do X,Y and Z. The editor asked us to substantially extend the study (which was already quite substantial) and resubmit. My student had to develop a few new assays but with the help of a couple of undergrads this was done as well as the other buttload of experiments. Everything worked well and fit together beautifully. We re-wrote the manuscript and resubmitted. This whole process took about 8 fucking months, but for a fancy pub it was worth it. Or was it?

Things were not so simple. About 6 long weeks later we get an email saying that our paper was rejected. Whatthefuck!?! When we looked at the reviews, the original two reviewers praised us for the good job we did and suggested the paper be published. But of course the editor sent it to a third reviewer who you could tell barely read the paper and dismissed the whole thing with a very short review suggesting basically a host of impossible and useless experiments. We were pissed. So we had to go through an appeals process. They basically make you fill out a bunch of tedious forms and write a rebuttal stating why they should change their mind. Since this needs to be written carefully, it took us a few weeks to get it right. You want to be diplomatic here. You want to convey that the reviewer is an idiot without quite saying so. They also tell you that appeals are their lowest priority business, and that they'll get to them whenever they get to them. For us was that about 10 weeks. What they did is send the whole thing to one of the original reviewers. Fortunately the reviewer agreed with us that reviewer 3 was out of line and somehow this convinced the editor who finally accepted the paper. In total, form initial submission to acceptance it took over a year. I really find this last minute third reviewer bullshit to be very backhanded. If they want three reviewers, then they should send it to three reviewers from the beginning. Not have you spend months pandering to the first two and then stick you with a third one. But in any case, at least we got that one through.

The second paper was submitted to society journal and we promptly received notice it had been sent out for review. About 4 weeks later reviews came in. Both reviews were very extensive, but ultimately positive and mainly had issues with one of the figures and wanted extra data. We were also asked to completely overhaul our discussion section. The editor asked us to revise the paper and resubmit. He also suggested doing the new experiment since it did not seem too difficult with the techniques we already had available in the lab. So we did, we removed the problematic figure, did a couple of extra experiments, which in fact were not that difficult, did a thorough revision of the text and resubmitted. This took only a few weeks of work. About four weeks later we get noticed that the paper is basically accepted but that one of the reviewers still had some issues with our conclusions. So we did a second round of revisions, only in the text and figure layout and resubmitted. At this point the editor usually makes a decision without sending it again to the reviewers, but in this case he did send it back. So we had to wait another 4 weeks for the paper to be finally accepted. All in all this was a much more pleasant experience than with fancy journal. And its not that the quality of one paper was better over the other, but in the glamour journals they really make a big deal about impact and novelty. Whereas a respectable society journal typically will publish any solid piece of science, although of late some society journals are starting to make a big deal about impact too.

So why publish in a fancy journal? For one it looks good in your CV, but more importantly you get tons more exposure. There are many people who only routinely look through fancy journals and basically ignore the rest unless it's in their immediate subfield. Whenever we've published in a fancy journal, I typically start getting random emails from people who read the paper and had questions or were interested in collaborating, etc. This never happens with society journals. Maybe my friends or immediate colleagues will write. It is always tricky picking a journal to submit your work to. You have to keep in mind your audience, the novelty of your findings and how much extra time and effort are you willing to sacrifice to get the thing published.

13 responses so far