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
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:
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.
1)If you can afford to have your blood tested for everything available, do it quarterly so you have a baseline of your own personal health
— Mark Cuban (@mcuban) April 1, 2015
2) create your own personal health profile and history.It will help you and create a base of knowledge for your children,their children, etc
— Mark Cuban (@mcuban) April 1, 2015
3) a big failing of medicine = we wait till we are sick to have our blood tested and compare the results to "comparable demographics"
— Mark Cuban (@mcuban) April 1, 2015
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:
- Mark Cuban is a loudmouth who somehow made billions of dollars and now talks about stuff he doesn’t know anything about.
- 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.
- Performing blood tests on everyone is prohibitively expensive, so we’d end up with “elite” patients and non-elite patients.
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!
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.
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
Friday, March 20, 2015
Priority in science is mostly a mirage
It seems these days that there are a lot of CRISPR priority fights out there, with the biggest being the patent dispute between Doudna and Zhang. Got me thinking about why we place so much emphasis on priority.
As scientists, it is a deeply engrained goal to be first. First to think of an idea, first to work it out, first to publish the idea. And in our culture, the one who does it first typically gets all the credit, sometimes even if they just “win” by a couple of months (although sometimes other factors come into play). It is what separates those perceived as the most shiny stars from the rest of us.
But think about it. If you’re working on something and get there just a few months before someone else, are you really that much more shiny than the next person? If the goal is to win a footrace, sure, you win. But if the goal is to create knowledge, the world would essentially be unchanged if you had never existed. Sobering. And true for the vast majority of us.
I think a pretty rational definition of a really original advance is something that if the researcher had not existed it is likely to have taken a really long time before anyone else would have come up with it. Almost by definition, such an advance is much more likely to come from one person. Like maybe RNAi. Or PCR. Although who knows? Maybe someone would have figured out these same things a few years later. I’m consistently surprised at how often you think you’re working on something completely alone only to find someone else hot on your heels. I think there are two reasons for this. One is that as technology and knowledge develops, the time becomes ripe for some discoveries. Like once sequencing was around, the discovery of several new long non-coding RNAs was essentially an inevitability. The other reason is that there are just so many smart people out there these days. With so many scientists, it’s virtually impossible that nobody out there is thinking about the same things you are. Even in math, which historically has worshipped at the altar of the solitary genius, often has multiple names attached to many new theorems. Which makes the exceptions all the more remarkable, like Yiteng Zhang’s amazing theorem about bounded gap primes or the discovery that primes is in P by a small group in India working largely independently. Kudos to them!
This is not to say that “meat and potatoes” science is not important. In fact, I think the steady, cumulative effects of incremental advances of the entire scientific community mostly outweigh the contributions of those few geniuses, especially in biomedical sciences in the current era. Somehow, I find this very reassuring and in many ways freeing: if you realize that we parcel out winners and losers in this race based on essentially arbitrary factors–and probably our innate desire to create heroic narratives–then it’s okay to just continue doing what you’re doing and not worry about it. In the long run, nobody really wins or loses, and science will continue moving, regardless.
So what is the strategy if you want to do something really original? Well, if the goal is to make a discovery that would take a long time to happen if you did not exist, then you can either do something really original or something that nobody cares about. Often one and the same!
As scientists, it is a deeply engrained goal to be first. First to think of an idea, first to work it out, first to publish the idea. And in our culture, the one who does it first typically gets all the credit, sometimes even if they just “win” by a couple of months (although sometimes other factors come into play). It is what separates those perceived as the most shiny stars from the rest of us.
But think about it. If you’re working on something and get there just a few months before someone else, are you really that much more shiny than the next person? If the goal is to win a footrace, sure, you win. But if the goal is to create knowledge, the world would essentially be unchanged if you had never existed. Sobering. And true for the vast majority of us.
I think a pretty rational definition of a really original advance is something that if the researcher had not existed it is likely to have taken a really long time before anyone else would have come up with it. Almost by definition, such an advance is much more likely to come from one person. Like maybe RNAi. Or PCR. Although who knows? Maybe someone would have figured out these same things a few years later. I’m consistently surprised at how often you think you’re working on something completely alone only to find someone else hot on your heels. I think there are two reasons for this. One is that as technology and knowledge develops, the time becomes ripe for some discoveries. Like once sequencing was around, the discovery of several new long non-coding RNAs was essentially an inevitability. The other reason is that there are just so many smart people out there these days. With so many scientists, it’s virtually impossible that nobody out there is thinking about the same things you are. Even in math, which historically has worshipped at the altar of the solitary genius, often has multiple names attached to many new theorems. Which makes the exceptions all the more remarkable, like Yiteng Zhang’s amazing theorem about bounded gap primes or the discovery that primes is in P by a small group in India working largely independently. Kudos to them!
This is not to say that “meat and potatoes” science is not important. In fact, I think the steady, cumulative effects of incremental advances of the entire scientific community mostly outweigh the contributions of those few geniuses, especially in biomedical sciences in the current era. Somehow, I find this very reassuring and in many ways freeing: if you realize that we parcel out winners and losers in this race based on essentially arbitrary factors–and probably our innate desire to create heroic narratives–then it’s okay to just continue doing what you’re doing and not worry about it. In the long run, nobody really wins or loses, and science will continue moving, regardless.
So what is the strategy if you want to do something really original? Well, if the goal is to make a discovery that would take a long time to happen if you did not exist, then you can either do something really original or something that nobody cares about. Often one and the same!
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