Can a physicist fix a cell?

I posted this the other day on the Amaral Lab blog, but if you didn't get a chance to see it:

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For those of you who haven’t read the article “Can a biologist fix a radio?” allow me to summarize: physicists and engineers are awesome, biologists are idiots. I could (and at some point, likely will) ramble on at greater length about the litany of problems that I find with the author’s entire premise and conclusions but here I’d like to focus myself a bit more. Of course, you can and should read the article yourself but my one sentence summary is sufficient prior knowledge for the current purpose.

I’m frequently annoyed whenever I hear people citing this editorial as insightful. The fact of the matter is that the author poses an extremely interesting question: how would individuals that were trained in different disciplines approach a novel problem such as understanding or fixing a strange new object (a radio)?

This thought experiment could be really interesting, but unfortunately in its published form this is not the case. Perhaps my real problem with this editorial is that I imagine the thought experiment as if the object of understanding were a strange foreign object – something that no one knows anything about a priori. The radio analogy serves merely as a nice way to ground this potentially esoteric thought experiment.

From this starting point, the author lays out/mocks the potential straw-man-biologist approach: a) get your hands on a lot of these radios, b) take them apart and catalog the pieces noting various qualities, c) remove components and see how the function of the radio is altered, d) shoot radios with a shotgun until they cease to function and try to determine why, etc. To this relatively simple list I would also add that a biologist would most certainly try to understand inputs and outputs. It appears this alien thing functions with electricity so lets send a pulse of electricity through it and maybe we can track where this electricity goes and how that is altered when components are missing. I could go on listing the types of experiment that a humble biologist such as myself would propose, but I would rather ask the question of how would an engineer or physicist approach the problem?

However, the author doesn’t specify in this regard and rather states “we know with near certainty that an engineer, or even a trained repairman could fix the radio”. Oh, we’re talking about actual radios. Literally, the kind of radios that engineers who are required to take electronics classes grow up building and diagramming as part of their training. Not a strange new object for which a radio serves as an analogy. An actual radio.

When the question is framed this way, I submit that an average electrical engineer would do a much better job at fixing the radio than an average biologist. Next you’re going to tell me that if you want to solve an unknown equation, the best people to ask would be mathematicians and not biologists! Or that a biologist wouldn’t be the best person to manage your stock market portfolio. I’d be on the edge of my seat in anticipation of the conclusions of “Can a biologist solve the middle-east peace process?”.

My point here is that this could be an interesting thought experiment were it phrased differently. Its not only that biologists and physicists learn different material in their classes. I believe that to some degree we also learn different ways of thinking and approaching problems, and that the biological education has many shortcomings and biology as a whole has and will continue to benefit from physical scientists. When I sit down with my boss (a physicist) and show him particular data, his mind goes in completely different directions from my own. To some extent this is knowledge of the field and experience publishing, but to another degree I’m sure that these differences are the product of ways of thinking which clearly differ between the two of us. I’m just not sure exactly how we think different, how these ways of thinking are related to particular parts of our education, and whether different means that something is unequivocally better or even better suited to certain types of problems or not.

So how would a physicist or an engineer understand or fix a strange foreign object for which we will use a radio as an analogy? As a lowly biologist, I don’t know the answer to that question, and would love for someone to articulate it. However, let me stop you right now before I’m swamped with comments that physicists and engineers think in “models” and “first principles” and rather than a naive reductionist approach a physical scientist would “think holistically” and blah blah blah. I have no need for this verbal display of scientific pseudo-speak. Give me concrete examples of how a physical scientist would go about understanding a strange foreign object like a radio via experimentation.

Perhaps physical scientists wouldn’t catalog parts and iteratively take out objects and assess the function the way a biologist naively would. But until I hear different, my on-going assumption is that a physicist would build a radio accelerator and hurtle 2 radios at each other at the speed of light to figure out how radios function based on the scatter of the resulting collision. I joke (kind of) namely to make light of the original authors condescending tone to biologists, but also because I wish to point out that the reductionist approach is not even remotely unique to biology. I’m not so sure that the answers I hopefully receive will differ that significantly from a biologist’s prescriptions.

I’m not sure that biology was ever the isolated discipline that some would have you believe, but at very least I wish to make it clear that a lot of physical scientists are currently making great biological discoveries. Of course, so are biologists. And – this is crucial – physical scientists and biologists alike are are failing together in countless areas. Think: every unsolved biological problem. If physical scientists think different, convince me this difference exists within the framework of our little analogy. And if you’re really feeling ambitious, convince me that different is better.
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Decoding dialects key to understanding the language of DNA

Check out the article that I wrote for the Northwestern Science in Society website

How applied is to applied?

First off, I want to say thanks for the education and the living stipend. I'm a graduate student currently funded by you thanks to all of your generous donations to the National Institue of Health by way of the IRS. It is in my best financial interest to tow the party line and say that there is no such thing as to much investment in research and development at the federal level. After all, I'm rather unlikely to convince Pfizer to fund my intellectual curiosity at the basic linguistic structure of DNA, and I firmly believe that scientific research is absolutely essential for economic growth and innovation.

The premise behind funding research at the federal level is that there is little incentive for private companies to investigate basic biological or physical phenomenon for knowledge sake alone. Private companies want to make drugs to cure diseases because they can sell those drugs for profit; elucidating the physical mechanism that a protein uses to bind DNA pales in comparison. In addition to the enriching our understanding of the world around us, which few would disagree is a laudable goal, basic research into the aforementioned mechanism might have unintended applications. The modern internet was born from physicists working at a particle accelerator whose purpose was to investigate the fundamental laws of physics at the atomic scale. No one anticipated it, but the plethora of data and the need to share it spawned the world wide web. This often cited example would likely never have been funded by any company because of the high costs and low odds of payoff.

But, like everything, research funding is far more subtle. The Economist recently held a small debate concerning the nature of public versus private research funding (see here, though the interface is unfortunately clunky to read now that the debate has closed). The first and clearest take home message is that there is no way to delineate basic from applied research.  Research falls on a continuum, and what one person would call basic another would call applied. Can we truly study plant genetics without uncovering applications that lead could lead to drought resistant Genetically Modified Organisms? I was fully convinced by this argument that basic versus applied is a false dichotomy and I was ready to go home with my tail in between my legs. But another debater briefly raised the issue of profit versus non-profit research and I realized this is the real underlying debate and the cause of my unease at funding particular research areas.

The first thing that you must know is that academic science is a very safe endeavor for scientists. Sure, becoming a professor is incredibly difficult and so to is procuring tenure. But compared to the alternative option of starting your own company to fund your research, the financial security of an academic job can't possibly be understated and I would love to hear any debate to the contrary. I don't doubt that a life as a consultant or in the pharmaceutical industry where you work on a research project dictated form above is far safer, but if you want to pursue your own research goals and intellectual curiosity there is absolutely no safer place to do it than under the umbrella of a university. As such, I'm continually baffled that taxpayer money can be used to fund research that is then taken to the private marketplace either by professors starting their own companies or by selling their discoveries to existing companies.

The Economist debate failed truly elucidate this issue, and to this day I can't see any economic justification behind why a professor should have their research funded by the government such that if they fail, they lose nothing but prestige. If they succeed, they can profit wildly and profiting wildly isn't as uncommon as you might think. At my own institution I know of countless professors with multiple spin-off companies or income generating patents. This absurd system is the very same paradigm as 'moral hazard' that banks operate under and that has proven so wildly unpopular (i.e. if a bank fails, the government will bail them out but if they succeed they reap rewards).

You could make the argument that financial incentives are the best way to encourage progress, and I would be the first to agree. But individuals who chose a life in academia have either done so out of intellectual curiosity or at very least out of safety. They could have founded their own companies, procured their own venture capital, profited if they succeeded and been forced into bankruptcy if they failed. This is the capitalist model that I so ardently support. But instead they chose the safety net of academia where they can study their own research whims as long as they can convince taxpayer funded agencies that there is some remote benefit to it.

My hope, is not that we decrease federal research funding for the sciences. Quite the contrary I think that research funding should be greatly increased. But the dirty little secret that any honest scientist will tell you is that a lot of research funds are poorly spent either on frivolous projects or on financing public risk for private gain. Developing better funding strategies that re-align incentives and payouts by keeping the taxpayer in mind will add to the pool of money available to non-profit driven scientists who will continue to produce ever-more novel and exciting research that benefits everyone.

Communicating complexity

I'm terribly lazy these days so here is yet another re-post of something that I posted over on my lab's website (which can be found here) a few days ago. Apparently self-plagiarism is all the rage these days anyway.  


Many of you know that I frequently tirade about the value of good presentation and writing skills, and the complete lack thereof in the scientific world, so here is a bit more to add on to that pile:

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I study cancer. Except, of course, that I don’t.

But if you’re a friend or family member of mine, there are pretty good odds that I’ve told you that I do. Before you judge me too harshly, let me assure you that I’m not a con artist using the prestige of a cancer researcher to attend gala dinners and pick up lingerie models. Rather, my reason for lying about what I study has a perfectly logical, age-old explanation: laziness.

What I actually study is the relationship between the coding sequence of a gene and its rate of translation by ribosomes into a protein product, as well as the evolutionary pressures that shape and constrain this relationship —worst elevator pitch ever.

The great majority of the population has no idea what a ribosome is. Or that proteins are the effector molecules that carry out virtually all of the vital processes of life. This poses a problem for me as a biologist, when in the middle of Christmas dinner or at a smoke-filled karaoke bar I get asked, “what do I do?”. Biology. Bacteria. DNA. How about them Yankees? Cancer.

Understanding your audience is one of the first rules of both writing, and speaking. Or if it isn’t, it should be. Most graduate students aren’t taught how to adapt their sales-pitch to a ‘general’ audience. Add in the constraint of brevity and most of us resort to superficial descriptions of our research that everyone will understand but that hardly begins to describe the actual work that we do. Hence: cancer.

Answering the question: ‘what do you do?’ without resorting to the extremes of jargon is a challenge that all scientists—and dare I say: people—should accept. Even short conversations in a crowded bar can lead to academic growth as we take the time to understand our research enough to communicate it clearly and concisely. The added benefit of course is that in doing so we also get to convince people, whose taxes we rely on, the breadth and importance of research.

So in case you were wondering:

I study the language of DNA.

I study how the language of DNA affects the production of molecules within the cell.

I study how the language of DNA can predict the production of molecules within the cell.

I study how the language of DNA developed over evolutionary time and how we can possibly exploit the grammar of this language to better target disease and and synthesize pharmaceuticals.

It’s not perfect, but I’m working on it. And I’m sure glad that a lot of other people are studying cancer in the meantime.
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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.