I don’t really know what to say about this morning. There are large number of suicides on the suburban trains around Paris every year and it’s nearly impossible to avoid getting caught in a transportation disaster when one happens on the line. They tend to close up to six stations and trains running on the rest of the line are often disturbed. It happens enough that people have a pretty blasé attitude about it, maybe even being angry that their day was so drastically disrupted.

I can’t ever quite seem to muster up that level of indignation because it mostly just makes me sad. I’ve dealt with depression before and I feel fortunate that I have had the resources and support to get help while I struggle through my dark times.

This morning it was closer than ever. The train moved slowly away from the station where I board and eventually pulled slowly to a stop two stations later. Something was wrong. They announced over the loudspeaker that there had been an incident and we would wait. A minute later they ordered us all out of the train and started evacuating the station. Out of the corner of my eye I saw a fellow passenger point something out to an RATP agent. It didn’t click what they were referring to and as I walked past the gap between the cars on my way out I glanced down and saw her lying there.

I couldn’t see her whole body, but what I could see was broken and unmistakably lifeless. She had olive skin and was wearing jeans. She was either wearing gray knit boots over her jeans or socks pulled up over her jeans. I can’t get over that I don’t understand her footwear. Maybe they were socks and her shoes came off? They must have been boots. I also won’t forget how the line of her boots (I’ll go with boots) was broken by where the train had run her over. Her tibia had punctured her skin. Either this was a later injury or she had been moved down the track; probably both.

The humanity of her life and struggle was gone. What I was looking at was basically a pile of meat. Someone’s broken body after life that had been so hard. There really isn’t anything left and there’s no meaning except what the people she left behind assign to it. There’s a tragedy in that, because it seems like our struggles should mean something more.

I didn’t know her. I don’t know what happened. But I will spend today mourning her, because life is senseless and sometimes cruel. Because we all do our best with what we have. Because you never know what someone else is going through. Just because.

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It’s taken me a little while to be able to write a response to the article “Who’s Afraid of Peer Review?” Every time I sit down to write something, I begin coherently and slowly devolve into angry writing. The article asks, “Who’s Afraid of Peer Review?” and then proceeds to only talk about the peer review, or lack thereof, in open access journals. Because the open access that the article portrays is shoddy and corrupt and seemingly should present no major threat to the vaunted, subscriber-based journals. Somebody should let PLoS ONE know.

The major, fundamental difference is who can access the articles and for how much. The decision about what makes it into which journal is not based on–however much scientists want to believe it is–based on the quality of the science. Nature and Science (where this particular article appeared) have the highest retraction rates of any journal. Knowing that, it’s hard to argue that they publish The Best Science. No, they try to publish good science, but they are also concerned with the sex appeal of the article; they only want the high impact science. So that begs the question: What happens to scientifically solid work that the editors don’t think is sexy enough? Maybe the hypothesis was wrong, or the results were interesting but not game changing, or it’s a less well-known field. Well, in that case, it goes to lower impact journals, maybe along with some stuff that wasn’t as well-done. What if there was an alternative? A journal that only accepts stuff based on scientific merit, publishes it, and then leaves it up to readers to decide whether it gets more or less views. Well it exists: all the PLoS journals.

When I hear people talk about “open access” they’re usually talking about three phenomena–alternatives to subscriber-based journals that seek to remove some of editorializing in paper selection; those subscriber articles that will automatically go open access if they were funded by the US or the UK; and, what this article deals with, a lax, grey market designed to get people publications.

So back to the article itself. It commits some of the same sins that we monitor scientists for:

1) Conflict of interest. Did anyone have a problem with the fact that this was published by a subscriber-based journal with skin in the game (so to speak)?

2) Or, how the article targets potentially notorious open access journals without including a sample set of subscriber journals? (No controls? that’s just bad science.)

Stop with the outrage about author fees–it’s not like publishing in PNAS is free. Servers cost money and current article fees pay to keep all the older articles accessible.

My biggest issue, and perhaps the hardest to explain, are some of the assumptions that the author made. If were were talking about a different field, the term we use would be “microaggression.” A lot of detail was given to the description of the author’s “experimental” set up–how he engineered the names of the authors to look authentically African, how he purposely wrote in poor or grammatically incorrect English, how he included blatantly incorrect data and interpretation, to the point of approaching misconduct. I fully understand wanting to test the limits of whatever review these journals were purporting to offer and how including some factual and grammatical errors would check to see if anybody was reading whatsoever. But why did he, an Oxford-educated white dude feel the need to play up the ‘otherness’ of his fake scientists? Did he think that some of these open access journals would blatantly target scientist from developing nations? What would have happened if he submitted with a different name? I just think it’s really problematic to implicitly tie poor work with scientists from developing nations, even if he wasn’t consciously doing that.

There are plenty of problems in science, but I don’t think open access is one of them. I think the emphasis on “publishable results” (read: positive) and peer review is a much bigger part of the problem. A recent release by Elsevier editors estimated that around 10% of the papers they receive have some evidence of misconduct. That’s a staggering number. So yes, there’s obviously problems in science publication, but I don’t think these open access journals are the cause, although they are perhaps a symptom.

EDIT: A lot of people have been talking about this. One of my favorite responses can be found here, although I hesitate to pile on over the Ar DNA thing:  http://www.michaeleisen.org/blog/?p=1439

I recently had the opportunity to attend a conference that is completely outside of my field of study. I study bioinorganic chemistry and do most of my work on small metalloproteins, so I spend a lot of time thinking about fundamentals like inorganic spectroscopy, biophysics, and biochemistry.  I managed to have some interdisciplinary experiences early on and these likely influenced my choice of a Chemical Biology program over the more traditional programs that I was also admitted to.

This past week I saw some talks at the Goldschmidt, which is one of the largest geochemistry conferences. While there, I spent most of my time at the bio-geochemistry talks, since that’s what’s most interesting to me, and stuff like vulcanism (it’s a thing, I swear) and mantle chemistry is totally out of my reach. I have long had an interest in applying some of my skills to environmental problems and questions, but outside of reading some papers, haven’t had the opportunity to get a good idea of what’s been going on in the field. This experience got me thinking a lot about specialization in science and how, without having finished my Ph.D., I feel that am already very specialized.

While it’s true that what our group does is pretty interdisciplinary and what my project has entailed has been particularly broad, I worry about being able to broaden my horizons even more. Most people will tell you that the most important thing you learn in a Ph.D. is learning what you don’t know and how to get that information, but it’s still hard to imagine beginning a in a completely different field whether that be policy, publishing, or just a different scientific field, without knowing what’s there and what isn’t. Understanding the state of the field and the perspectives from which a lot of people in the field work are important to be able to work productively and push limits.

Modern society selects for specialization. We all know this–from the advent of agriculture and tradesmen, people have been specializing. Science is no different. Lots of progress has been made by people specializing and developing more and more powerful techniques, just think of protein NMR. So obviously expertise is rewarded and sought after, but the important questions and research that will be done will (in part) require synthetic skills. Meaning being able to bring together multiple fields of study, a breadth of background and conversation, and unique skill sets (in a person or a team).

How well are most scientists trained to work in such a situation? My gut answer would be that the oldest scientists are great at this. Peruse the notebooks of Linus Pauling if you don’t believe me (it’s online here). He was a polymath with a voracious appetite for knowledge. Richard Feynman is another person who comes to mind. But there’s definitely a cadre of people in younger generations that have thrived off of specialization. Perhaps in response to this, interdisciplinary fields, journals, and programs are springing up. The NIH and NSF are looking into funding groups of scientists for a single project, rather than single labs. From where I am within the system it’s hard to tell whether this will favor broader interests or whether we’ve just reached another level of specialization.

For myself, I am interested in having a broad perspective, and so choosing how I decide to approach my career post-graduate school seems very significant. Finding an appropriate post-doc that allows me to learn a different field/technique and poises me for progress in a new area is difficult and daunting. I’m looking to find a way to break outside my (self-) imposed boundaries and do something that I care about; that pushes me creatively, and that matters, and I have a sneaking suspicion that for me, the answer lies in between disciplines.

Cross-posted at ACS Chemical Biology

I often get asked, “what is Chemical Biology, anyways?” I’m sure we all get asked this question as it’s a relatively new field. The University of Michigan’s program in Chemical Biology is the first or one of the first free-standing programs in Chemical Biology and it was influenced by U of M being one of the first recipients of the NIH’s Chemistry-Biology Interface Training Program. 

 

One of my favorite things about my doctoral program (and the NIH training program) is how cohesive we are, despite our research diversity. We have people who do small molecule inhibitors, FRET on ribosomes, protein NMR, and even bioinorganic chemistry (like me!). I’ve often felt like an outlier in my program not only because I am probably the only person who spends any time thinking about inorganic chemistry the way an inorganic chemist would, but also working on some of the most basic research. But aside from that, I think one the things that brings us all together is the interdisciplinary techniques and training we have. Take me: I am academically-trained as a bio(inorganic)chemist, lab-trained as a microbiologist, but my current research requires not only biochemistry, but small molecule synthesis and a not insignificant amount of inorganic chemistry and spectroscopy. I’m practically the definition of a “jack of all traides, master of none.” And, perhaps I’m projecting here, but I feel like many of the pioneers of this field have felt that at one time or another, since many trained in one field and then crossed into another as they straddled the line and defined a new discipline. In fact, I’ve heard both Laura Kiessling and Dennis Dougherty say these types of things in talking about how they went from total organic synthesis to carbohydrate biosynthesis or physical organic chemistry to neuroreceptors. Now, we are beginning to see a new group of scientists, one who looked specifically for “Chemical Biology” programs when they applied for graduate school. How will this new generation of scientists change the field wither their thinking? I look forward to see how the field develops as people who explicitly trained in it for their PhDs graduate and begin their own research programs. I think people like these will bring a very different perspective, they will reside intellectually in the interdisciplinary rather create it. 

 

But I digress. Going back to the original question: “What is Chemical Biology?” I think most people would say, “applying chemistry (or chemical principles) to problems of biology.” But I like to use a slightly different framing, perhaps because I worry that it sounds like we’re mostly talking about organic synthesis. So I usually say, “a bottom-up approach, based on chemical principles and tools, to questions in biology.” I like this framing because it talks more about the methods than the questions, which is a major distinction. All scientists want to figure out how the world we live in works; the difference is sometimes more in how we answer the questions that we have rather than what questions we have. 

The other day I was wandering around the Internet and I ran across this insightful and well-written blog post: When the Village Doesn’t Need You Anymore. It relates work vs. leisure and academia in a discussion about the American model for productivity and MOOCs (massive open online courses). Academia already justifies its relevance, in part, through teaching and if teaching is “outsourced,” then what happens? We find ourselves in an interesting time where getting a college education is basically a requirement for any sort of decent job, this demand is driving up the cost of a college education, cutbacks in education and research funding has academics up against the wall, and the changing global landscape is forcing us to go in a different direction economically, socially, and scientifically.

In the blog post, there’s an imaginary exchange between a professor and an interviewer where the professor has to defend their stance:

Interviewer: “So what do you do?”

Professor: “I take the information from the texts and give it to the students.”

I: “Oh.  Well why couldn’t the students just go to the texts/lectures/forums themselves, since they are on the internet?”

P: “I have finely honed teaching skills!”

I: “So does Dr. UberAwesome from Harvard … in fact, I suspect he’s better.”

P: “… you … you don’t understand! See, the internet is not interactive like I am!  I have office hours from 2-3pm on the second Monday and third Thursday of every month by appointment!”

I: “But our forums are monitored 12 hours a day by teaching assistants …”

P: “… but the internet isn’t … good … with …”

So, the question is: Should academics be worried about their livelihood? Are MOOCs threatening academia?

Academia is feeling its own obsolescence in some senses. The way the system has worked doesn’t work as well any more. But are MOOCs a true threat? Or are they just forcing people to consider changes that might need to happen anyways? Let’s be honest, tuition fees keep rising disproportionately to the cost of instruction as infrastructure costs keep going up. There are too many highly educated unemployed people. There are even more minimally employed highly educated in huge amounts of debt who studied something in college that they didn’t love just so they could get a job afterwards. The truth is, most professors aren’t looking to make sweeping changes across the whole system; for one, it’s benefitted them, and two, they’re myopic by nature. Most academics spend their whole professional lives studying one or two things–when many of us are now looking at having an average 6 careers in our lifetimes, professors can still make a go at just having one. 

That being said, I think there are really two separate issues here surrounding MOOCs and education:
1. The issues from the post: the skills you learn to be a professor are in less demand and with technology you can educate more people for less. I think what academia does is necessary and important, but you can’t link it directly to economic output. Ideally, we as a society should hold that the pursuit of knowledge and education are inherent goods. Either way, any development fostered by academia is necessarily long-term and more about sustaining economic development through knowledge capital than triggering it or contributing directly.
2. The issue that MOOCs strive to address is the inherent classism in higher education. Many people not only cannot afford university, even more will never be able to qualify for it because of their disadvantaged educational and economic background. Regardless of how you feel about the quality of education gained via MOOC vs. traditional schooling, MOOCs not only challenge the status quo by challenging the utility of professors/academia but also by challenging our views on who “should” or can have access to this type of knowledge/schooling and how.

But the other truth about MOOCs is that only about 10% of people actually finish the courses. Most of the people who sign up for them are from economically developed countries and already speak English. So are they radically changing education? No, not really. Maybe one day they will, but for right now, academics you can relax.

 

I mentioned briefly in a different post an idea that’s been floating around in my head for a while: the pure capitalism can’t drive science. Or rather, that it can’t be the only driver. In making the case for basic science, I argued that government funding is necessary, because while the benefits of basic science are tangible, they’re often long-term and thus not attractive for profit-based investment.

When I wrote that I thought to myself, “I should probably cite that.” I know I’ve read it in several places, that basic science has tangible benefits. At the time, I was on a roll with thinking about open access and didn’t find the source. But now, serendipitously, an article in PLoS ONE popped up on my radar. It was just published last week and it has some interesting conclusions about science research and economic development.

As an aside, I’m a filthy idealist and I think that basic science is worth pursuing just increase our level of knowledge about the world we live in. I’m not religious, but what better way to celebrate our wonder at the amazing world we live in, than to try to understand it? Anyways, I also acknowledge that idealism doesn’t make the best argument, especially when many people don’t share your idealism. Also, research costs a lot of money, so some justification is needed for how we spend that money–we can’t just fund everything!

But this article came out in PLoS ONE, just in time for me to think about how I should better justify my statement that basic research has tangible benefits. The article links scientific research to economic growth and examines the utility of using one to track the other. Now, they don’t claim that investing in scientific output will trigger economic growth, rather they suggest that economic growth allows sustained, long-term economic development. One surprising conclusion is that applied research (such at agriculture, medicine, and pharmacy) is not the best indicator for economic development, but rather physics, chemistry, and materials science research. Specifically, countries who had higher relative productivity* in basic sciences had higher economic growth in the following five years. The authors suggest that mid-level economic countries would do best by investing in basic sciences, because as they note, “technology without science is unlikely to be sustainable.” Another tidbit that I found to be quite interesting was the idea that “individual specialization begets diversity at the national and global level.” It totally makes sense, but it also provides a good incentive for national or federal science programs to encourage training people in a variety of fields.

I’ll leave the authors themselves to summarize their conclusions:

  1. For historical periods with no global financial catastrophes, the economic growth of middle income countries can be predicted with high accuracy by looking at their relative academic productivity in physical sciences and engineering.
  2. Academic productivity is a much better predictor of future economic growth than economic complexity as measured in [16]. Scientific productivity is more accurate in predicting economic growth and wealth, than economic complexity. If we accept that “science is the mother of technology”, i.e. supports technological development, then science affects other aspects of live such as services, governability, rational thinking, attitudes, etc. and of the economy besides technological development[12][23]. This result is congruent with other statistical analyses comparing the information content of statistical models using ECI with those using scientific productivity to predict economic growth [24].
  3. No country with exclusive preferential investment in technology, without investment in basic science, achieved relatively high economic development. Thus, technology without science is unlikely to be sustainable.
  4. The effect on the economy of scientific development is long term. It can be observed in 5 years’ time. This time period is very short in terms of the process by which science creates new technology. Thus, we might be measuring the effect of science in preparing new technology leaders and in instilling rational thinking in the leaders of a country rather than the production of novel technology in middle income countries.
  5. No direct correlation between development in basic science and economic growth, or vice versa, exists. We suggest that the effect mentioned in point 1 is possible the outcome of the fact that relative investment in basic science is a reliable indicator of a rational decision making atmosphere, and if other factors allow, promotes economic growth.

Number 5 is really, really important. Blind investment in science isn’t what we want, but we want to foster an environment where investment in science is supported and encouraged. Getting more people who are more scientifically literate involved in government and decision-making processes is one way to help this; another is improving our educational system in the STEM fields.

So the next time I get asked, “what is the application of your research?” I can just answer: “economic growth.”

*calculated as a percentage of the country’s total scientific output

Jaffe K, Caicedo M, Manzanares M, Gil M, Rios A, et al. (2013) Productivity in Physical and Chemical Science Predicts the Future Economic Growth of Developing Countries Better than Other Popular Indices. PLoS ONE 8(6): e66239. doi:10.1371/journal.pone.0066239

There are several interesting paradigms in how science is practiced today. I can really only speak to the US, but since international science is based on the American model, we can say that some of these particularities are generally true. There are three main ways that scientific discoveries are reported and all are subject to some level of peer review: articles in journals, conferences, and patents. The first two are far and away are much more important in terms of discoveries and knowledge acquired.

Now, most research is federally funded, especially non-applied research. You just can’t rely on capitalism to fund basic research; the pay off isn’t consistent enough or on a short enough timescale, although the rewards are demonstrable down the road.

So, that being the case, the most prestigious journals are a pay to play sort of thing. A subscription to Science, on of most prestigious (and highest retraction rate–d’oh!) journals costs the individual $146 per year. And that’s if you’re a scientist. If, God forbid, you are an interested civilian, a yearly subscription to Science is $310. To stay abreast of all the federally funded research that gets published, you would have to pay quite a lot of money per year, and yet it’s your tax money that is going into this enterprise. Seem fair? No? You’re right, it’s not. It sucks, actually. I’ve even had collaborators at other universities ask me to send them PDFs of articles because their institution can’t afford the subscription.

Now, there have been various efforts to rectify this. One of the more revolutionary ideas is open access journals, like PLoS and the Frontiers series of journals. They put all the burden to publish on the authors (to be fair, PNAS does this too). Not meaning that there’s no peer review, but rather, the cost of publishing is borne by the authors, not the readers. NPG (Nature Publishing Group) recently acquired the Frontiers journal series, which perhaps lends some more legitimacy to the whole enterprise, or at least an indication that open acces is here to stay. An even greater indication of this is that the Obama administration released a memo via the OSTP, which calls for all agencies that fund more than $100 million in extramural research to make all publications available within a year of publication along with any unclassified, federally-funded research. This is pretty huge, and reflective of greater cultural changes, I think. We have been increasingly insistent on greater transparency in government and science. Obama was practically elected on a platform of greater transparency and then WikiLeaks happened (along with Manning and Snowden), not to mention the plagiarism suspicions/instances that are now rampant in the scientific community (there’s a whole website dedicated to retractions!).

Policy changes like this are part of a greater shift towards transparency that was, in part, brought about by the internet and all the data that anybody can access. There are a group of scientists that are dedicated to opening up science in general–making lab notebooks available, encouraging citizen scientists, and overall increasing transparency. I actually think this is a great idea. I know that in highly competitive fields, this level of transparency is anathema to getting to be the first one to publish something, but nobody says you can’t delay publicizing your lab notebooks. Maybe if more of the day to day grind of science were made available, we wouldn’t have so many drugs getting pulled off the market, and people might appreciate how difficult doing science actually is. Or I’m a total idealist and opening up data will just result in a kerfuffle like publication of some of the climate science data did. If you’re interested in this idea of opening up lab notebooks, the folks over at scifundchallenge.org are hosting a free online course/discussion group to get this going.

So is there a happy ending with the OSTP memo? Actually, yes. The American Association of Publishers has announced CHORUS, which stands for ClearingHouse for Open Research of the United States. It basically takes advantage of existing infrastructure via CrossRef and puts all of those publications that are federally funded under a 1 year embargo, after which the article goes open access. This is the publisher’s solution the the memo, but doesn’t necessarily reflect its final form, which will require some changes in the federal agencies themselves (especially after some recent debate in Congress). Overall, I think it’s a revolutionary step forward. What remains to be seen is also what happens with publishers (like NPG) who have not signed on to CHORUS and are not US-based.

As a trainee on the NIH’s Chemistry Biology Interface Training Grant, I recently had the opportunity to attend the 1st Annual Career Development conference, which was held in Urbana-Champaigne, Illinois, and featured representation from all the Midwestern CBI programs. Given the changing scientific environment, (training) programs in general need to focus more on the post-graduation outcomes of their students. To this end, conference organizers arranged for five panels focusing on  entrepreneurial, industrial, academic, post-doctoral, and non-traditional careers. Additionally, there were two keynote speakers, Laura Kiessling and Peter Senter, and two poster sessions. 

Probably the most important lesson I learned from the conference was not networking, but rather, that it’s never too early to start planning your career. For most post-docs and many jobs you need to start thinking as early as two years ahead, but more like a year and a half for most positions and places. And that’s where networking comes in. If you’re a graduate student–get yourself to conferences! Start meeting people and making connections. And if you’re an advisor of graduate students–get them to conferences! It’s hard for many of us to ask to go to conferences, but it’s the second-best thing you can do to help your students succeed (making sure they finish their Ph.D. being the first). 

But more on this conference: to put it bluntly, the conference was fantastic. I would consider myself to be relatively well-informed about the post-doc job search process. That being said there were a lot of things that I had no idea about, like industrial post-docs. However, for me the most informative and striking career panel was the non-traditional careers panel. I’ve always planned on a post-doc, but have been a bit agnostic about my career prospects after that. Or rather, not so much agnostic as closeted. I love science; it’s been a huge part of my childhood, adolescence, and adulthood. I read journals for fun and popular science magazines for light reading. But what I’m most passionate about is sharing that love–communicating science to non-scientists, advocating for more money for research, thinking about the best structure for our education and research systems, and encouraging as much diversity in science as possible. So I’m coming out of the closet: I want a non-traditional science career. Or at least to have these aspects be a large part of my professional life in the future. 

In part, this has spurred my participation in blogging. I spend a lot of time thinking about these issues, but I need more practice actually writing them. Almost all of the writing I do these days is personal or scientific, and finding the sweet spot in between personal communication and scientific communication is a skill that most scientists (including myself) need to develop. I’m planning on using this medium to keep up to date with current events in these fields, do some background reading, and writing about it. Hopefully, I can learn a lot about myself in the process and make some good connections that will aid me in the future. 

Working on some more elaborated thoughts on the conference, but for now a few quick thoughts/highlights:

  • Anything Laura Kiessling has ever said. Seriously. She’s hilarious. And while she didn’t explicitly talk about it, she has an amazing story of being a high-powered woman in science at a time when there weren’t many. She went into an interview and actually said that she wanted a group of about 20 people and didn’t listen when people were incredulous.
  • Getting to be creative with my TED talk. A note on the student TED talks…they’re a fantastic idea. We put such a premium on being the MOST accurate, MOST precise, and MOST data-filled, but in an interdisciplinary conference this gets you almost nowhere. While we scientists should get familiar with other fields, we also need to take on the challenge of making our ideas more communicable. Forcing scientists, especially students, to think outside the box and focus on how to communicate their ideas is important and this idea of a TED talk is a way of doing that.
  • All the meals. And not just for the food, which was significantly above average, but also for the interesting conversations at the table. 
  • Non-traditional careers panel. Fantastic.
  • Miles Fabian. What a character.
  • Jeff Peng. If you are at Notre Dame, you should make an effort to get to know this guy. Totally irreverent for a professor (I have a soft spot for irreverent professors), which is refreshing, and with an interesting range of experience.
  • Peter Senter and pharmaco-economic distress.
  • Industrial post-docs are a thing. Yup. And you’re pre-cleared for publication.

What I cannot create, I do not understand.

Richard P. Feynman