People who are a fan of the khan academy might know about the concept of "flipping the classroom". The simple idea of this technique is having students watch lecture videos as homework and do problems in the classroom, rather than the reverse.
I wonder whether this same method could be applied to conferences, which often result in long, dull talks followed by interesting questions and discussions. One could imagine recorded talks made available to conference attendees a few days in advance followed by a conference entirely devoted to activities designed to promote interaction between researchers, such as poster sessions, discussion panels, small workshops and even debates. Why spend a day watching a big screen in front of the lecture hall in some convention center when we can just as easily do that in our bathrobe at home?
Friday, November 18, 2011
Thursday, November 17, 2011
TCGA Datasplosion
I'm at the TCGA meeting in Washington DC, and am being blown away by the enormous amount of data and complicated analysis of that data. It's phenomenal how much sequencing, morphometric and related data have been accrued in a wide variety of tumor types. The analyses are pretty interesting, but it's also surprising how much previously known biology comes out again and again. I can't tell if people are reporting results that we already know because it's safer, or because there's not much new in the data. Either way, it's clear that for these results to be useful we will need much more clinically relevant annotation and many more tumors. In a future where all patients have sequenced tumors, perhaps we will see much more clinically applicable conclusions.
Friday, October 28, 2011
Micro-Science-Blogging
Here's a crazy idea, what if scientists posted results of their studies for the year, month, week, or hell, even their exciting result of the day, to YouTube? What if we blogged our science?
Let's say, for sake of argument, that I have an interesting result, not yet ready for publication in a journal but certainly worthy of the attention and maybe comments from other researchers. On the one hand, I could work on that idea further until it's ready for a "real" publication. That would probably involve some missteps, maybe some time lost (open the door for scooping), but will also make for a more complete product when it is actually released.
On the other hand, I could open myself up for comments at a very early stage. Not only would the online "timestamp" validate my status as first to the result immediately, it would also give others a chance to comment, criticize, and potentially even initiate their own projects. When the project reaches a later stage I will have already incorporated "reviewer" comments into my manuscript, which will remain just as valuable as a formal report of the work.
Perhaps such a system could work on a by-lab basis. Labs could become, in a weird way, their own publishing houses. Weekly updates on results could feed into the RSS feed of other labs. Just a thought
Saturday, October 22, 2011
If anyone is wondering what regulation capture by industry interests looks like, this is it:
A Life in Energy and (Therefore) Politics (wsj)
The energy industry is mired with so many competing regulatory and industry interests that calling it an "energy market" is a complete misnomer. Note the intriguing comments made later on in the article about some "dirty: coal plants being used as bargaining chips by companies against state and local politicians who, having granted monopolies, are now beholden to those companies.
It's a real fine mess.
A Life in Energy and (Therefore) Politics (wsj)
The energy industry is mired with so many competing regulatory and industry interests that calling it an "energy market" is a complete misnomer. Note the intriguing comments made later on in the article about some "dirty: coal plants being used as bargaining chips by companies against state and local politicians who, having granted monopolies, are now beholden to those companies.
It's a real fine mess.
Wednesday, October 12, 2011
The Rational Optimist and Ricardo
I'm about halfway through The Rational Optimist and have to say that it's a bolstering case for the phenomenal power of markets and trade in human society. It's not exactly erudite, but it's a well versed look at the way trade and specialization have massively improved the lot of the average human in the past few million years and enabled us to grow to a population of several billion. Some of the points I like the most revolve around Ricardo's Law of Comparative Advantage, which the book describes as "the only result of social science that is both surprising and true". In honor of the recent free trade agreement between the US and several countries, I want to take a moment on this little law.
Briefly, the law states that if two individuals, nations, companies, whatever, have a different relative ability to produce a pair of different items, then one or both of the actors will be better off if they trade. So, for example, even if France is better at making both wine and cheese than England (probably true), both England and France will still benefit from trade if the relative cost of producing wine vs. cheese in the two countries are different.
What if France makes wine much more efficiently than cheese, and England does as well? It turns out, it doesn't matter. If the tradeoffs of wine vs. cheese are just different, that's all it takes for both countries to benefit.
What's marvelous about The Rational Optimist is that it couches these modern conceptions of economics in the ancient environment, before they were even realized. Let's say I make spears incredibly well, and I also run down and spear bison incredibly well (probably not true). I take a day to make a high quality spear, and a day to run down a bison. You, sadly, are terrible at both, taking 2 days to make a high quality spear, and 4 days to run down a bison.
Now we could both spend time in our own little spheres, making spears and running around all day. At the end of 6 days, you would have one spear, which you will have used bringing down a bison. I will have made 3 spears and brought down 3 bison.
After those 6 days, you have a brilliant idea. A brilliant idea that will keep you from running around all day and instead put my hands at work for you. Let's say that the next 2 days look a lot like the 6 days before. I make a spear, and go skewer a bison with it. You're just be polishing off that first spear when I bring the bison home.
But now you throw your incredibly brilliant plan into effect. "Ugg!" you say, (we're cave man, that's the my moniker) "I'll give you that spear for just 1/3 of your next bison!".
I think it through. 1/3 of my next bison? But I can have all the bison if I make the spear myself. But if I make my next hunting spear myself, I have to sit around all day making it, and won't be able to hunt until tomorrow. If I take this spear, I can hunt now. Let's see... 1 bison in 2 days, or 2/3rds of a bison in 1 day. I might not be able to figure out the fractions, but I know that I'm getting more. I take your spear, head out for the hunt, and that night I come back with my prize. You get 1/3 of a Bison, and never had to run around on the hot plains.
I won't belabor the point, but if you work out the math, over 6 days with the occasional spear trading hands, you still get your one bison by making 3 spears instead of 1 spear and one hunting trip. I am doing a lot more running, but I get 3 hunting trips without having to stop to make spears, and can make one hunting trip with my own spear and still have a day to spare. Calculated out, I get the same 3 bison, and a free vacation day!
Consider that this example is the most meager form of Ricardo's comparative advantage. Imagine that after a year of this arrangement, you get absurdly good at spear making. You've been doing it every day of the week after all, and you've had a chance to try some things out. Now, after figuring out how to use a rock to sharpen the tips and finding the best source of branches in the woods, you're turning out 2 or 3 a day! You're still only trading one for 1/3 of a buffalo, but now you can stock up on spears the first 2 days of the week and spend the rest of the time figuring out how to corral a buffalo calf and save it for later.
Clearly I've just sketched the barest bones of the argument here, and I highly recommend the book for a better treatment. The point, though, is that specialization and trade are massively powerful ways to improve our own lives and those of our trading partners. Imagine, in your own life, how difficult it would be to independently create all the wonderful artifacts of human productivity you enjoy. What you get out of voluntary trade makes possible the life you lead today.
Briefly, the law states that if two individuals, nations, companies, whatever, have a different relative ability to produce a pair of different items, then one or both of the actors will be better off if they trade. So, for example, even if France is better at making both wine and cheese than England (probably true), both England and France will still benefit from trade if the relative cost of producing wine vs. cheese in the two countries are different.
What if France makes wine much more efficiently than cheese, and England does as well? It turns out, it doesn't matter. If the tradeoffs of wine vs. cheese are just different, that's all it takes for both countries to benefit.
What's marvelous about The Rational Optimist is that it couches these modern conceptions of economics in the ancient environment, before they were even realized. Let's say I make spears incredibly well, and I also run down and spear bison incredibly well (probably not true). I take a day to make a high quality spear, and a day to run down a bison. You, sadly, are terrible at both, taking 2 days to make a high quality spear, and 4 days to run down a bison.
Now we could both spend time in our own little spheres, making spears and running around all day. At the end of 6 days, you would have one spear, which you will have used bringing down a bison. I will have made 3 spears and brought down 3 bison.
After those 6 days, you have a brilliant idea. A brilliant idea that will keep you from running around all day and instead put my hands at work for you. Let's say that the next 2 days look a lot like the 6 days before. I make a spear, and go skewer a bison with it. You're just be polishing off that first spear when I bring the bison home.
But now you throw your incredibly brilliant plan into effect. "Ugg!" you say, (we're cave man, that's the my moniker) "I'll give you that spear for just 1/3 of your next bison!".
I think it through. 1/3 of my next bison? But I can have all the bison if I make the spear myself. But if I make my next hunting spear myself, I have to sit around all day making it, and won't be able to hunt until tomorrow. If I take this spear, I can hunt now. Let's see... 1 bison in 2 days, or 2/3rds of a bison in 1 day. I might not be able to figure out the fractions, but I know that I'm getting more. I take your spear, head out for the hunt, and that night I come back with my prize. You get 1/3 of a Bison, and never had to run around on the hot plains.
I won't belabor the point, but if you work out the math, over 6 days with the occasional spear trading hands, you still get your one bison by making 3 spears instead of 1 spear and one hunting trip. I am doing a lot more running, but I get 3 hunting trips without having to stop to make spears, and can make one hunting trip with my own spear and still have a day to spare. Calculated out, I get the same 3 bison, and a free vacation day!
Consider that this example is the most meager form of Ricardo's comparative advantage. Imagine that after a year of this arrangement, you get absurdly good at spear making. You've been doing it every day of the week after all, and you've had a chance to try some things out. Now, after figuring out how to use a rock to sharpen the tips and finding the best source of branches in the woods, you're turning out 2 or 3 a day! You're still only trading one for 1/3 of a buffalo, but now you can stock up on spears the first 2 days of the week and spend the rest of the time figuring out how to corral a buffalo calf and save it for later.
Clearly I've just sketched the barest bones of the argument here, and I highly recommend the book for a better treatment. The point, though, is that specialization and trade are massively powerful ways to improve our own lives and those of our trading partners. Imagine, in your own life, how difficult it would be to independently create all the wonderful artifacts of human productivity you enjoy. What you get out of voluntary trade makes possible the life you lead today.
Monday, October 10, 2011
Minimum Publishable Unit
What the hell, I'll post again this year.
When is the right time to publish? Is it when you have an interesting result? Is it when your result is "complete", zipped up, lock-tight, slam-dunk? Is it when the result seems more likely true than not? Is it when you want to recruit others to the cause? Is it when you think it's good enough to impress people, and impress them in the amount that you need them to be impressed for your career to advance?
Sadly, I think the answer is often that last on my list. Publications are the the currency of science, and the only hard paper that demonstrates productivity on the public stage. Science is a big establishment, and our individual spheres are often tightly circumscribed, though they may seem vast from the inside. If I am applying for a job, and I have a Nature paper or a Cell paper (not happening any time soon, but let's just imagine for a moment), then I can put that on the desk and point to it. Say my competitor has a paper in PLoS Genetics. Still good, still the same paper, but different brand. I'd carry more weight with the Nature paper.
That brand seeking behavior is nothing new, and it's not actually the problem in itself. The problem is when the brand takes on a life of its own. If everyone buys Nike shoes because they are flashy and Nike, and not because the Nike brand speaks to quality, then where can you expect the quality to go? Similarly if Nature papers are sought because they are flashy, and hard to get, where does Nature go from there? Will Nature continue to speak to the quality of the underlying science?
My fundamental problem with the big name paper is that the results are often big and sweeping. They are rarely circumscribed, but elegant and well thought out. Imagine a demonstration that a single class of proteins perform some specific catalytic or signaling function. This in itself is worthy of being shared with the scientific community, as an informative work. But to get the Nature paper you need to show the protein is relevant in disease X, and that if you inhibit the catalytic activity you cure warts, cancer, and heart disease.
Of course inhibition of the protein won't turn out to actually cure warts, cancer and heart disease. Somewhere along the line a wrinkle will have been ignored. Some control, that in hindsight will be obvious, won't have been done. This is inevitable in the sort of expansive manuscripts that top journals demand.
I argue we should be more focused on rapid dissemination of our research, and broad feedback from the community early on in validating a result. I might run a smart, genome-wide screen, but you might have a better idea of how to interpret it. Someone else might recognize an important statistical error. Most importantly, someone else can *replicate* the experimental results early, before I truck on down the road with faulty assumptions.
The problem is not that the "minimum publishable unit" is too small, it's that it's too big, and that we focus on the papers and the journals and not on the results themselves. In the end, a Nature paper that's wrong is worth less than a small time journal article that's right. The Nature paper that's wrong may actually have negative value, having led labs down the wrong road. Next time you hear someone say that they have a Cell paper under their belt, ask next whether the result was replicated. Ask whether the result has, in fact, been important. Remember to value not the scientific articles, but the science itself.
When is the right time to publish? Is it when you have an interesting result? Is it when your result is "complete", zipped up, lock-tight, slam-dunk? Is it when the result seems more likely true than not? Is it when you want to recruit others to the cause? Is it when you think it's good enough to impress people, and impress them in the amount that you need them to be impressed for your career to advance?
Sadly, I think the answer is often that last on my list. Publications are the the currency of science, and the only hard paper that demonstrates productivity on the public stage. Science is a big establishment, and our individual spheres are often tightly circumscribed, though they may seem vast from the inside. If I am applying for a job, and I have a Nature paper or a Cell paper (not happening any time soon, but let's just imagine for a moment), then I can put that on the desk and point to it. Say my competitor has a paper in PLoS Genetics. Still good, still the same paper, but different brand. I'd carry more weight with the Nature paper.
That brand seeking behavior is nothing new, and it's not actually the problem in itself. The problem is when the brand takes on a life of its own. If everyone buys Nike shoes because they are flashy and Nike, and not because the Nike brand speaks to quality, then where can you expect the quality to go? Similarly if Nature papers are sought because they are flashy, and hard to get, where does Nature go from there? Will Nature continue to speak to the quality of the underlying science?
My fundamental problem with the big name paper is that the results are often big and sweeping. They are rarely circumscribed, but elegant and well thought out. Imagine a demonstration that a single class of proteins perform some specific catalytic or signaling function. This in itself is worthy of being shared with the scientific community, as an informative work. But to get the Nature paper you need to show the protein is relevant in disease X, and that if you inhibit the catalytic activity you cure warts, cancer, and heart disease.
Of course inhibition of the protein won't turn out to actually cure warts, cancer and heart disease. Somewhere along the line a wrinkle will have been ignored. Some control, that in hindsight will be obvious, won't have been done. This is inevitable in the sort of expansive manuscripts that top journals demand.
I argue we should be more focused on rapid dissemination of our research, and broad feedback from the community early on in validating a result. I might run a smart, genome-wide screen, but you might have a better idea of how to interpret it. Someone else might recognize an important statistical error. Most importantly, someone else can *replicate* the experimental results early, before I truck on down the road with faulty assumptions.
The problem is not that the "minimum publishable unit" is too small, it's that it's too big, and that we focus on the papers and the journals and not on the results themselves. In the end, a Nature paper that's wrong is worth less than a small time journal article that's right. The Nature paper that's wrong may actually have negative value, having led labs down the wrong road. Next time you hear someone say that they have a Cell paper under their belt, ask next whether the result was replicated. Ask whether the result has, in fact, been important. Remember to value not the scientific articles, but the science itself.
Saturday, October 8, 2011
Irritated in Chapel Hill
The scientific establishment is Democratic.
News to anyone? Probably not. After all, Democrats by and large promote increases in NIH and NSF funding, tout the importance of the scientific consensus, and so on. But when one is, oh, say, not a Democrat, and trying to do science within the field as it currently exists, there are bound to be frustrating moments.
Take, for example, two seminars in a year with national Democratic representatives. Let me add that these seminars are ambiguously mandatory, with a sign in sheet at many, though not all events, and that they are catered by the program. Imagine a room full of decidedly left leaning individuals with their representative on stage. These reps, so far as I can tell, have nothing to talk about but their political leanings and aspirations. And they'll have all the time in the world to tell you how important they think it is to support, Education and (National) Health Care. They'll also mention how they plan, at the Federal level, to fund Science, Education and (National) Health Care. Nevermind where the money is coming from...
Now I'm not saying no seminar has had a Independent, Republican, or otherwise non-democratically leaning individual who has weighed in, where asked, on political issues. It's just that I have yet to see such an individual given an open forum with a mandate to talk about politics. And perhaps I am being unfair, since I can't imagine any such speakers wanting to wade into the issues of a limited Federal role in that crowd. The Feds are our lifeblood, as it currently stands, and I am one of the few who bites the hand that feeds him. Hell, I have even applied for Federal grants, and benefit from State money given to our Cancer Center, so who am I to complain?
But of course that is exactly the ratchet of Federal authority, ever gaining constituents through patronage, that erodes limited government. I have to live within the system as it exists, even as I argue for its change, as I do here. I just wish that this group of ostensibly deeply thinking individuals were less overwhelmingly game to sign on with whoever holds the purse strings. And I wish they didn't strongly (though perhaps unintentionally) broadcast their inclinations from the top down.
I hate being a naysayer, and I hate biting back at a program that has given me a great deal. But in case people are suffering under the illusion that the MD/PhD program at UNC has built a scientific consensus that you should vote for David Price and Kay Hagen , I just want to make it clear that it has not.
News to anyone? Probably not. After all, Democrats by and large promote increases in NIH and NSF funding, tout the importance of the scientific consensus, and so on. But when one is, oh, say, not a Democrat, and trying to do science within the field as it currently exists, there are bound to be frustrating moments.
Take, for example, two seminars in a year with national Democratic representatives. Let me add that these seminars are ambiguously mandatory, with a sign in sheet at many, though not all events, and that they are catered by the program. Imagine a room full of decidedly left leaning individuals with their representative on stage. These reps, so far as I can tell, have nothing to talk about but their political leanings and aspirations. And they'll have all the time in the world to tell you how important they think it is to support, Education and (National) Health Care. They'll also mention how they plan, at the Federal level, to fund Science, Education and (National) Health Care. Nevermind where the money is coming from...
Now I'm not saying no seminar has had a Independent, Republican, or otherwise non-democratically leaning individual who has weighed in, where asked, on political issues. It's just that I have yet to see such an individual given an open forum with a mandate to talk about politics. And perhaps I am being unfair, since I can't imagine any such speakers wanting to wade into the issues of a limited Federal role in that crowd. The Feds are our lifeblood, as it currently stands, and I am one of the few who bites the hand that feeds him. Hell, I have even applied for Federal grants, and benefit from State money given to our Cancer Center, so who am I to complain?
But of course that is exactly the ratchet of Federal authority, ever gaining constituents through patronage, that erodes limited government. I have to live within the system as it exists, even as I argue for its change, as I do here. I just wish that this group of ostensibly deeply thinking individuals were less overwhelmingly game to sign on with whoever holds the purse strings. And I wish they didn't strongly (though perhaps unintentionally) broadcast their inclinations from the top down.
I hate being a naysayer, and I hate biting back at a program that has given me a great deal. But in case people are suffering under the illusion that the MD/PhD program at UNC has built a scientific consensus that you should vote for David Price and Kay Hagen , I just want to make it clear that it has not.
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