Saturday, April 11, 2015

Gregg Popovich studied astronomical engineering

I was just reading this SI.com piece about Gregg Popovich, legendary NBA coach of the San Antonio Spurs, and found this line to be really interesting:
By his senior year he was team captain and a scholar-athlete, still the wiseass but also a determined cadet who loaded up with tough courses, such as advanced calculus, analytical geometry, and engineering—astronomical, electrical and mechanical. [emphasis mine]

Now, I'm pretty sure they meant aeronautical engineering, but that got me wondering if there is such a thing as astronomical engineering. Well, Wikipedia says there is something called astroengineering, which is about the construction of huge (and purely theoretical) objects in space. I wonder if Pop is thinking about Dyson spheres during timeouts.

Thursday, April 9, 2015

Dr. Padovan-Merhar!

Olivia is now Dr. Padovan-Merhar! Just defended on Tuesday–second student to graduate from the lab. And her paper just came out in Molecular Cell!


Saturday, April 4, 2015

Interpretive drawing of the lab


Why not test your blood every quarter?

Lenny just pointed me to a little internet kerfuffle emerging because of Mark Cuban’s twittering about saying it would be a good thing to run blood tests all the time. Here's what Cuban said:







Essentially, his point is that by using the much larger and more well-controlled dataset that you could get from regular blood testing, you would be able to get a lot more information about your health and thus perhaps be able to earlier action on emerging health issues. Sounds pretty reasonable to me. So I was surprised to see such a strong backlash from the medical community. The counter-argument seems to have a couple of main points:
  1. Mark Cuban is a loudmouth who somehow made billions of dollars and now talks about stuff he doesn’t know anything about.
  2. Just as whole body scans can lead to tons of unnecessary interventions for abnormalities that are ultimately benign, regular blood testing would lead to tons of additional tests and treatments that would be injurious to people.
  3. Performing blood tests on everyone is prohibitively expensive, so we’d end up with “elite” patients and non-elite patients.
I have to say that I find these counterarguments to be essentially anti-scientific. On the face of it, of course Cuban is right. I’ve always been struck by how unscientific medical measurements are. If we wanted to measure something in the lab, we would never be as haphazard and uncontrolled as people are in the clinic. There are of course good reasons why it’s more difficult to do in the clinic, but just because something is hard does not mean that it is fundamentally bad or useless.

I think this feeds into the most interesting aspect of the argument, namely whether it would lead to a huge increase in false positives and thus unnecessary treatment. Well, first off, doing a single measurement is hardly a good way to avoid false positives and negatives. Secondly, yes, in our current medical system, you might end up with more unnecessary treatment–with many noting that getting into the system is the surest way to end up less healthy. That is more of an indictment of the medical system than of Cuban’s suggestion. Sure, it would require a lot more research to fully understand what to do with this data. But without the data, that research cannot happen. And having more information is practically by definition a better way to make decisions than less information, end of story. To argue otherwise sounds a lot like sticking your head in the sand. I'm also not so sure that doctors wouldn't be able to make wise judgements based on even n=1 data without extensive background work. Take a look at Mike Snyder's Narcissome paper (little Nature feature as well). He was able to see the early onset of Type II diabetes and make changes to stave off its effects. Of course, he had a big team of talented people combing over his data. But with time and computational power, I think everyone would have access to the interpretation. What's sad is for people to not have the data.

Leading to another interesting point from the medical research standpoint. If it were really rich people making up the primary dataset, I don’t think that’s a bad thing. Medicine has a pretty long history of doing testing primarily on non-elite patients, after all.

Friday, April 3, 2015

Theorists give great talks

We just had Rob Phillips come visit Penn and give a talk in the chemistry department. It was great! A few months back, we also had Jane Kondev come give a talk in bioengineering that was similarly a lot of fun. Now, Jane and Rob have a lot in common (both are cool, interesting people), but I think one common thread that links them is that they are both theorists by training. (Both do have strong experimental work happening in their group now, by the way.) I think theorists (at least in our sort of systems biology) give some of the most engaging talks, and I think the reasons why are illustrated in some of the best features of both their presentations.

The first departure from business as usual is in the amount of data presented. In Rob’s case, he presented almost no data from his own lab. Jane’s talk also had a lot of background from other people’s work, and the work he did present always came with heavy references to other literature and findings. This allows them to set up the conceptual issues well, as well as their place in the context of science. I think that some people feel like bringing up other work distracts from their own work, and that they don’t have time for it because they have so much of their own to present. I think that Rob and Jane’s talks prove these concerns to be overblown. Rather, I think that their talks feel rich with history and thus significance. Those are good things.

The other main thing I’ve noticed in talks by theorists is that they emphasize the conceptual. Most talks suffer not from a lack of data but an overabundance of data. Here’s a simple rule: if you’re not going to explain a piece of data, don’t show it. If it’s impossible for the audience to truly grasp how the data you show proves your point, then you may as well not show it and just tell them that it all works out. Often times in bad talks, it’s hard to tell that this is happening because people haven’t even set up the question well.

Which brings me to another nice thing about theorists: they aren’t afraid to delve into what might be called philosophy. For some of us, I think there is maybe a fear that people won’t take us seriously if we muse about the big picture in our talks. I think those fears are ill-founded. Overall, I think biomedical science could do with a little more thinking and a little less doing. Another nice thing about this is that for trainees, it can be very inspiring to think about deeper problems. Isn’t that what got us all into this in the first place?

On a related but peripheral note, I was at a conference a couple years ago and was shocked by what I was hearing from the students and postdocs. I asked one student what they thought about some fundamental question about the field, and they responded with a blank stare as though they had never been asked that question before. Another postdoc I met, when asked about some underpinnings of the field, literally responded with “I just want to get an assay that works and get a bunch of data”. If that’s you, go see a talk by a theorist and get back in touch with your inner scientist!

Wednesday, April 1, 2015

Feeling dated

Conversation in the lab:

Andrew: "Isn't there some song that the CIA plays to prisoners to get them to talk?"

Arjun: "Probably some crazy pop songs. There was this one from grad school that used to play on the radio in the lab that drove me nuts. I can't remember it, though."

Olivia: "What was it? I want to know–I feel like it would date you."

Sara: "Was it by John Lennon?"

Ouch.

Thursday, March 26, 2015

Kepler ate with chopsticks?

Check this picture out from Wikipedia:


(Yes, I know it's a compass.)