NIH is the new Pirate Bay, and its about time

This week, congress officially shelved the 'Research Works Act'. This bill was proposed late last year and its main point was banning federal agencies from mandating that federally funded research be made publicly available. This bill stands in direct opposition to the recent trend of open access publications and prior mandates from the National Institutes of Health (NIH) that all research funded by them be made freely available to the public. From the taxpayers' perspective, it is logical that federally funded research should be made publicly available to those that helped to fund it. Imagine a different scenario where the Centers for Disease Control and Prevention paid 100 million dollars to produce 'Contagion', gave it away to Warner Bros, and allowed them to charge $12 a ticket for viewers to go see the film in theaters. It is a ludicrous proposition, and precisely what the NIH mandate is tries to prevent.

So why would anyone want to limit access to research? Its entirely obvious, but this is where parallels to copyright infringement, media piracy, and SOPA/PIPA emerge. One of the major headlines to come out of this relatively short debate was the 7,500 strong researcher boycott of Elsevier - a journal publishing company that initially sponsored the bill and was subsequently pressured to withdraw support, thus ending the bills hopes of proceeding. As a company which publishes scientific research at a considerable cost, it is in Elsevier's interest to prevent their content from being distributed freely. Even as a child of the internet age that has come to expect that all of my media content be free, I can sympathize with this concern.

Creating and distributing music costs money and so to does creating and distributing research. It's not to say that garage-band musicians who independently distribute can't make a profit, and scientists who publish on sites like arXiv can't readily distribute their research. But big journals, like big record labels and film studios, clearly distribute research broadly. More importantly, they also add value to the research by facilitating the peer review processes at a considerable financial cost. In the same way that musicians and film-makers have to deal with increasingly open access to their content (though it doesn't mean many have not tried, and failed, to fight this) so too must the publication companies. Their efforts should thus be focused more on how to change their business model to adapt to this ideological shift, which clearly journals can clearly do - other publication groups including Nature and the PLoS are doing just that and came out in opposition to this bill.

Lastly, a powerful lesson to take home from this kerfuffle is that we scientists, in our own nerdy way, are  just like musicians (I like to think of myself as the Jay-Z of systems biology). We are the producers of content and we have the power to choose where we publish - and it need not always be the highest impact factor journal. When publishers do something that we disagree with, we can and should choose not to support those decisions and thus not publish with them. Their prestige is little more than a product of our collective perception of their prestige. Boycotting journals, like boycotting artists, record labels, banks, or stores whose policies we disagree with can lead to real change. This case is a perfect example of that.

--Adam Hockenberry

Sources:
Slate here and here
Nature here 
Scientific American here,
and the NY Times here.

Benefits of higher education

So I try to avoid re-posting as much as possible but this chart is just to good to pass up. One of the most common-threads that runs through pretty much every scientific discipline/department/university at the graduate school level that I have been exposed to is that of complaint. No matter where you are, you can never seem to lose points by talking about how flawed the academic system is in terms of how much graduate students and post docs get paid, length of working days, shortness of vacations,  how small our chances of finding gainful employment are, etc. 

While I'm all for making improvements to a system that I see as being far from perfect, I never quite understand the jaded graduate student trope and more frequently get annoyed at it. At some point in their education, everyone seems to feel like they were lied to and that they didn't sign on for x, y or z. I'm sure most of those individuals are people who didn't necessarily think through the choice of graduate school adequately, and my sympathy is non-existent for them until convinced otherwise. 

Yet, there are undoubtedly others who took their time and made a career decision to continue their education rather then doing so simply out of inertia/apathy. For those individuals, I hope this chart is a pleasant reminder. 

Feel free to call me out when I come whining to you in a few more years time, but until then look at the numbers. High school education pays. Undergraduate education pays. Graduate education pays. All the terrible sacrifices that we make now and make us question our life decisions should be contextualized at least every now and then by the fact that education is a rational economic decision in addition to the numerous difficult-to-quantify benefits. 

Of course, business majors undoubtedly drag these numbers up but humanities and liberal arts majors probably drag them down (sorry guys) leaving scientists and engineers somewhere in the middle.

While I made this post about graduate school in particular, the benefits for graduating high school and attending university are even more striking. So for those individuals whom the graduate school argument seems a bit esoteric, I hope there is a take home message in here for you as well. 

I couldn't possibly argue for the intangible benefits of higher education enough, but take solace that if your sole goal is increased income and job security you will find both with increased education. 

It's a bit of a side issue but I can't seem to throw a rock without hitting a journalist/blogger/academic complaining about the sky rocketing costs of undergraduate or professional education. While I'll never make the argument that our system is perfect and that we couldn't/shouldn't make adjustments to control costs and make education more accessible, I will make the argument that the benefit that can be gained over a life time is substantially more then the cost you'll pay upfront or with loans. 

Even an absurdly expensive $50,000/year education will likely pay itself off several fold over a lifetime. Does that mean it should cost $50,000/year? Or be free? Or cost substantially more? These are arguments for another day but I'd love to hear them.

see the original posting at: http://www.bls.gov/emp/ep_chart_001.htm

Fact finding and conspiracy mining

Well it has been > 3 months since my last posting, and still I'm 13 days late on what I wanted to write about. But here goes:

If, like me, you read copious amounts of news, then you couldn't have possibly avoided reading numerous articles about the 10th anniversary of September 11th. "This is supposed to be a science blog" you may be telling yourself, and you'd be right to do so. I have no intention of turning this into a political blog/post/argument, but the two most interesting articles I read (at Slate and Popular Mechanics) were of scientific relevance so I thought it worthy of discussion. 

Plain and simply, the articles that I cited lay out the arguments against 9/11 conspiracy theorists. I think that we're all by nature susceptible to conspiracy theories (Moon landing, JFK, etc.) and perhaps that susceptibility stems from the fact that some of them are actually true. Perhaps. But how do we uncover the real truth? Therein lies the scientific question.

Think what you may about the facts of the 9/11 conspiracy theorist case, either for or against U.S. government involvement and/or prior knowledge. I don't aim to convince you either way. What I do aim to convince you of, is a gigantic flaw in the conspiracy theorist way of thinking. Namely, by refuting facts that support the predominant opinion, you strengthen the case for the minority opinion. 

Allow me if I may to generalize the case so as not to break down the minutiae of 9/11. A historical event occurred, and A and B represent multiple narratives as to how it unfolded. The best route to the truth would be to lay out all of the facts, and to conclude the most probable course of events. What conspiracy theorists do, however, is start with the assumption that B must be true. And rather than strengthen facts supporting B, casting doubt on the facts that support A must automatically lead you to conclude that B is indeed correct. Refutation of null hypothesis, however, is only useful when you have carefully enumerated all the null hypothesis (C, D, E, ...). In a complex system such as 9/11, this would be impossible and rather than refute explanations, the only way to 'prove' a historical truth is to bolster your hypothesis with facts. 

Another great flaw of conspiracy theorists is that they know their opinion before looking at the facts and are thus able to support their opinion against any mountain of facts by casting doubt. Scientifically, this is unacceptable. Medical trials for instance, are predicated on the fact that individuals do not know whether they have received treatment, and those who analyze the data are also blind as to who received a drug and who didn't. While this system has its own flaws, the crucial point is that people who analyze data evaluate facts without prior knowledge. If the doctor analyzing data on whether his drug worked knew the identity of who received the drug and who didn't, it would be tremendously easy to spin the data to prove the result that he wanted to see, most likely that the drug he discovered works wonders! 

We find this unacceptable scientifically, and it should be unacceptable logically. Of course, its impossible not to have an opinion on matters of political importance. So we all approach facts with a certain bias, but those whose opinions I trust most are those who clearly try to limit their bias and be as objective as possible. Sometimes its not so obvious to tell the difference, but sometimes its glaringly obvious.

Perhaps the truest test is to envision what amount of facts it would take to convince someone to change their mind. If all of those facts, purely imaginary at this point, could be twisted and refuted to fit the opinion that they purport to refute, it becomes obvious that nothing will change some people's minds; their opinions, are thus, of little significance to me. 

A healthy dose of skepticism is a fantastic thing, and I'm always glad that people are digging for truth and not accepting what their government tells them. I just hope they can recognize that truth when they find it, even if it doesn't support their preconceived opinion. 

Of cartography and biology

I recently became aware of a strange micro story/poem by Jorge Luis Borges called "On exactitude in Science". Seeing how I've quite recently completed a few courses on scientific modeling, and have also now officially joined a lab dedicated to modeling and understanding complex systems, I found this story to be incredibly witty and think at all scientists (if not all people) would benefit from taking a minute out of their day to read it over.

A map that is the same size of the country which it intends to map is clearly a ludicrous proposition. Yet, in many fields, it seems to be what many people ask for from those who do computational modeling and theory. While I know little about cartography, I do know about biological modeling. And the little bit that I do know is enough to make me plainly see the resistance that people have to any model which attempts to describe a complex system based on a small number of parameters.

In any model, the number of tweaks that can be made to make it a bit more realistic are nearly endless and  on the surface, all are equally deserving of being implemented. I say nearly endless, because all models do have an end which occurs when they contain each and every bit of information about the system which they are attempting to explain. But at that point, the model and the subject are one and the same and our map now spans the nation.

Where we define a 'minimal' explanation is of course the great question. Nevertheless, I hope we can all agree that if 90% of a phenomenon can be explained with 5 parameters and it takes another 47 to bring that total to 91%, perhaps our map has begun to outgrow its use. In physics, cross talk between theory and experiment has been instrumental in nearly every major discovery of the last century. On the other hand, in biology, theory is relegated to fringe academic journals and at best one individual per department. I'm not sure why these two fields have such drastically different dynamics, but I am sure that biology has a lot to learn from the physicists in this regard.

the Nature of failure, redux

Well, if you thought that last column was deservedly denied, it's because it was a first draft that I mistakingly copied and pasted without actually reading. So now to waste more of your time, here is the final. At very least, I'll call this a lesson in editing and let my first post up rather than delete it. My apologies, but seriously: I'd love to hear what people think about the drastic differences between the two. I think this version is orders of magnitude better in terms of making a cogent argument and hopefully you do too.


"In the academic world, the coming of spring brings more than migrating birds and warming temperatures. We can also count on seminars filled with faculty candidates, and prospective graduate students flocking to elaborate departmental recruiting events. Little time has elapsed since I was an interviewee in the latter category, but seeing things from the departmental side this time around has shown me the importance of recruitment events for everyone involved.


It is easy to see why potential students should take the process seriously, but it’s harder to grasp the large impact that these events can have on current graduate students, post-docs, and faculty members. Scientists rely heavily on professional and social connections for future positions, advice, critiques and collaborations. For many, the foundation of these important networks are laid during graduate school. Interviewing and recruiting potential students is essentially vetting the composition of our future social and professional networks - a task not to be taken lightly.


As a student, I have a vested interest in my program’s ability to select the top candidates and to convince those candidates to enroll. Their aptitude and productivity will ultimately affect the value of my institution and, by extension, my degree. Far more importantly, these individuals will have an effect on me because a portion of them will be my future friends, collaborators, and reviewers. Faculty should likewise concern themselves with graduate student selection; these students compose the front-lines of research, share bylines, and likely also comprise a considerable portion of scientific connections years down the line. And, of course, everything that I mentioned both for faculty and current students applies equally to post-docs, the vast majority of whom are conspicuously absent from recruitment events.


During these formative events, the more personal interaction we get with students the better. After all, we don’t choose our friends based on transcripts, essays, and GRE scores, and choosing friends is at least part of what we are doing. Surrounding ourselves with people that we respect scientifically, and get along with socially allows for productive and informative conversations to take place outside of the lab. These social connections unite people across labs and disciplines, providing fresh perspectives on our own research as well as informing us about diverse areas of research that our colleagues are working on.


Though it may sound exhausting and futile to converse with a litany of students in order to get a fair picture of both their aptitude and amiability, time with recruits need not be intellectually taxing. As a recruit, I found even casual conversations with professors and current students to be more informative than hours spent with web-pages and journal articles. These encounters were relatively brief in nature, but I am nevertheless continually amazed about how accurate my initial sketches proved to be. Most of us are busy with research and other obligations, but surely everyone can spare a small amount of time for our own sake as much as the potential students.


Of course, if students attend the highest ranked school that they get into regardless of their interviewing experiences then we have little incentive to bother. However, I still believe that student decisions are not quite so rigid. Ask a few of your close colleagues about their graduate school choices and recruitment experiences. While you’re at it, give a thought to where you met those colleagues; you might be surprised to find how many of your scientific friendships started during graduate school. When you’re finished, get out there and recruit a few more."

the Nature of failure

While this is a bit of an esoteric topic, I've been quite busy and I was happy with the final product so I decided to post this entry: a failed submission for the Nature Careers Columnist competition that I wrote a month ago (see this link for background). My apologies for the lazy recycling of material. I'll hopefully get time to write a bit more soon.

"The skies of the northern hemisphere are cluttered each spring with birds returning to their thawing homes and graduate school applicants hoping to find a home of their own. It was only a short year ago that I traversed the United States as an interviewee, and now that it’s my turn to entertain the potential incoming class I realize just how important these weekends are for everyone involved.

As a student, I have a vested interest in my programs ability to select the top candidates and to convince those candidates to enroll. Their aptitude and production will ultimately effect the ‘name brand’ of my degree, but far more important than benefits to the program and institution as a whole is the direct influence that these individuals will have on me; a portion of them will undoubtedly be my future friends, collaborators, and reviewers.

Faculty also have reason to concern themselves with graduate student selection; these students will make up the front-lines of the research, share the bylines, and most likely make up a considerable portion of scientific connections years down the line. And of course, everything that I mentioned both for faculty and current students applies equally to post-docs who are too often conspicuously absent from recruitment events though their research and connections still rely heavily on students.

In our capacity as members of the department, the more face-time that we get with students the better. Exhausting as that may sound, it need not be so intellectually taxing; indeed, sometimes less science is even better. As a recruit, I found even casual conversations with professors and current students to be far more informative than hours spent with web-pages and journal articles, and it amazes me to this day how accurate these initial sketches were even with a year of new knowledge to build on.

I recall two different interview weekends, both of which went reasonably well, but following my string of thank you emails I received responses from all five professors that I met with at one university and zero from another; they practically made the decision for me. The important thing to remember is that these impressions aren't just about graduate school, my opinion of certain departments and individuals has been likely shaped for years to come.

Face-to-face meetings are a two way street, and I still firmly believe that a conversation is worth as much as GRE scores, essays, transcripts, and reference letters combined. While these other methods may importantly measure past aptitude, conversations are where we can get a sense for a persons intangibles that are difficult to teach such as confidence, enthusiasm, presentation skills, etc. Try as we might to quantify and objectively view a person with essays and test scores, determining graduate school success may never be so algorithmic.

And of course, we must keep in mind that while the nebulous 'department' may be trying to judge graduate school success, as individuals in that department, we are trying to judge far more. We're making decisions about who we surround ourselves with, which will have implications perhaps decades down the line.

If students attend the highest ranked school that they get into regardless of their interviewing experiences then we all have little incentive to bother. But I still don't believe that student decisions are quite so rigid, and the data would be relatively easy to gather. Start by thinking of yourself and your close colleagues, and while your at it, think about how many of those close colleagues you met while either one of you were in graduate school."

South of the border, sans fireworks

I'm trying to keep this blog broadly science oriented, as it is my primary area of study and expertise, but it's nearly impossible for me to not inject some political and economic commentary every now and again; especially since the scientific industry, like all others, is heavily reliant on political policy.

Two weeks ago, President Obama visited South and Central America for the first time in his presidency. This baffles me.

Think of 10 humanitarian causes or images of plight and suffering across the world. Then think of 10 images of successful global cities or centers of industry. Chances are that with the exception of Haiti in the former category, you won't give a thought to the western hemisphere (sans U.S. / Canada) and who could blame you.

I wish I knew why this was, aside from the obvious fact that our education system doesn't teach us about Latin America and our media doesn't cover it. We have stronger ties with Thailand, Saudi Arabia, and Poland than we do with Peru, Uruguay, or Costa Rica. Our hispanic population is growing immensely and, with a clear majority, the best known second language in this country is Spanish. Yet still our ties with these countries and their greater than 600 million residents are feeble at best.

The best explanation that I can come up with is that the highest performers still underperform compared to western europe, and the lowest performers are considerably better off than the poorest nations of Africa and central Asia. These countries are stuck in the middle ground where NGO's care little about the poorest (Nicaragua, Bolivia, Honduras, etc.) and, with a few exceptions, our government ignores possible strategic alliances with the wealthiest (Chile, Argentina, Panama, etc.).

Aside from brutally obvious political (security) and economic (natural resources, labor markets, trading markets) advantages that relationships with our southern neighbors will foster, I'm also interested in the science. Intelligent and entrepreneurial people are being educated and doing research in the higher performing countries of this region, and I can't help but think that the economic might of the U.S. can help further the growth of science and technology industries here. Indeed, these industries already exist (see: Chile and Panama) but few people realize it or give them much merit.

Instead, the rising scientific and technological powers are emerging in Asia (think: India, China, Singapore, Korea). While I support increasing scientific proficiency and investigation everywhere, it seems that many of the countries of Latin America would produce a far greater return on investment. With GDP per capita in multiple countries doubling that of China and quadrupling that of India, they are simply better poised to enter the global marketplace of ideas and develop policies conducive to scientific investment.

In what will inevitably be a predominant theme of this blog, and of my future research: I firmly believe that scientific discoveries and technological innovations are to a large extent numbers games.  More people actively pursuing discovery will result in more discoveries but meeting the challenges of a more diffuse scientific network will require smart policies to cope with the infrastructural needs of knowledge dissemination and trust. Businesses, educational institutions, and individuals can start by fostering collaborations but eventually our government must set a clear precedent of allegiance based on mutual interests and our increasingly shared cultural heritage.

As it stands, most of the well performing countries in Latin America are politically far to the left of the U.S. (Colombia and Chile being two notable exceptions) and would likely prefer an invite to dinner with Hugo Chavez and Raul Castro over Barack Obama. This is tragic, and for the sake of political security, economic growth, and scientific discovery, it must be redressed.