So researchGate is kind of an interesting idea. As is this this New York Times article on the future of science publishing. I happen to agree that science publishing is due for a major makeover, but I don't think its replacement is out there yet. PLoS One has a lot going for it, as do other open access journals, but they don't bring us closer to the thing I really want to see: real time science publication.

I'm not totally sure that it's a desirable end, since a lot of what gets done in paper writing (careful description of methods, bringing together disparate data into one story, filling in logical holes with supporting experiments) only gets done because of the hurdle of publication. But imagine how many small, interesting, positive results never get published because they don't fit in with such a complete narrative required by a paper. Or, for that matter, the number of negative results.

What if, at the end of the day, everyone just blogged their science. You'd put a blurb about your methods, a blurb about your results, maybe a picture of your gel, sequencing results, graph, whatever, and let it run free on the internet. I can think of 2 or 3 figures that I plan to put into a forthcoming paper that I wish I didn't have to wait to share.

What are the down sides? Well a blog is less permanent than a publication, which gets archived and saved in about a hundred different places. It also is hard to put on your CV. Moreover, do people really want to go to someone's blog to learn what their lab is doing, or would they much prefer a scientific paper, which is sort of a digest version? Finally, does it actually advance science if everyone can know what everyone else is doing at all times? Would people continue to have the drive to publish first to avoid being scooped? Would there be even less reward for replicating past results, since you could in theory check to make sure you were the only one working in your area?

The expanding ecosystem is not without problems, but it's interesting to see what is created in the years ahead.

Well intentioned mediocrity?

Opposing the bill that started the National Cancer Institute, James Watson, the loose cannon co-discoverer of DNAs structure said: … we must reject the notion that we will be lucky. … Instead we will be witnessing a massive expansion of well-intentioned mediocrity. (credit: The Emperor of all Maladies) Can we say, truthfully, that he was wrong? Or has the cure for cancer been a long road that will soon bear its full fruit?

Flip the Conference

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?

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.

A Tripartite Ethic (way off topic)

It's my personal belief that we probably have never read the work of the most brilliant philosophers. That is, no one has read their work, because they never wasted their time writing it down. The most knowledgeable philosophers were probably smart enough to pursue happiness on their own, outside of the public light, and never felt the need to have their ideas validated by others. The most wise philosophers don't need blogs.

Which all just comes as a preface to say that I write the following post with some hesitation, and that by the very act of committing it to words probably proves that it is wrong. With that preface, here are my thoughts:

It strikes me that we have a very confused conceptions of ethics in this country. I don't know who the culprit is, but I just want to state the problem. The fundamental confusion lies in unifying or scrambling the elements of what are most properly thought of as three different fields of ethics into a single mishmash. This is almost impossible to explain without first describing what the three separated fields are, as I see them. 

The Tripartite Ethic:

1) What you should do

2) What you should motivate others to do

3) What you should enforce others to do

Since that simple description is probably not crystal clear, I'll clarify. Field number one of ethics is what you should do. It consists of systems of rules or guides for your own behavior and a method for answering questions in your own life. It's what I think most people think of when they think of "ethics" writ large. This can be as mundane as "should I go to the store" to as broad reaching as "should I dedicate my life to the poor and helpless?" This is the broadest group.

The second sphere is really a subset of the first, in that it is still a set of rules that govern your own actions. This group of ethics, though, govern the way you react to others actions. That is it answers the question: "How should I respond in my actions to the actions of others?" In a manner of thinking, it is a set of rules that you apply to others' behavior to determine how you should react. For example, "Should I lend money to someone I know to be dishonest?" or "Should I associate with someone who dedicates her life to the poor?" or even "Should I invest my earnings in a cigarette company?" This is a set of ethics applied to others, but viewed through the lens of your reactions.

The third is probably the most frequently confused of the ethics. It answers the question: "When should I resort to applying force or threats of force to others or sanction the use of force in my name?" Few people, day to day, find many situations in which they should apply force, barring of course soldiers and police. Frequently when we believe it is proper to apply force we delegate that duty to police and soldiers rather than ourselves. However in the end it is force, applied by handcuffs, jail cells, bats and guns, that constrain the the thief, tax evader, or political dissident.

My point is not to propose an ethic, but point out that each of these is distinct, and deserves its own attention. For example, you might believe that all that are capable should give their lives to the poor (Sphere #1). You might, moreover, believe that when you observe others that are giving their life to the poor, you should respond positively to them and help them in turn (Sphere #2). However you probably don't believe that you should call the police or physically restrain those in the street who aren't helping the poor (Sphere #3). Then again, you might! However it certainly doesn't go without saying.

The problems seem to lie most frequently in blurring Sphere #1 and Sphere #2. Our philosophers, priests and politicians are full of ideas about what "we" should do. This amounts to their sphere #2, what they think that others should be encouraged to do. We have a name for the fact that sphere #1 and sphere #2 are not usually equivalent, it's called hypocrisy.

For all of the moralizing about how terrible hypocrisy is (perhaps it is also in the interest of sphere #2 to bemoan that others aren't practicing what they preach), I think it remains a universal element of human nature. The fact that our interests conflict with others' is just an unavoidable fact of a world with finite resources. We aren't naturally inclined to do unto others whatever they would have us do unto them. There are limits to our kindness. There will always be dissonance between what we'd like to do and what others would like us to do. In the end, the enticements and confinements created by others do shape our choices, as they must. But it is these enticements and confinements, not others' desires alone, that shape our actions.

To go way out on a limb (am I out on one already?), I think that the confusion has most likely been driven by the tendency to follow the person in the pulpit or square who has been invested with authority. We consume their Ethic #2 and try it on for our Ethic #1. They would have us give unto others, or maybe unto the pulpit, so we give unto others, or maybe unto the pulpit. Perhaps we shouldn't be quite so surprised when this borrowed morality becomes hard to follow, and even personally arduous. It is an ethic not our own.

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

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.

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.