Assorted thoughts

This page is constantly “under construction.” It contains an assortment of links on science, education, and society. Joel takes responsibility for its content, although his thinking on all of these subjects has benefited conversations with other lab members (as well as many others!).

Thoughts on mentoring and lab environment:

My own thoughts on running a lab and “personnel management” (urgh). Mentoring resources at Duke. An interesting article on power dynamics and communication. My guides/mentoring statements/compacts for undergraduate and graduate students and postdocs.

A nice essay on advice to graduate students.

Advice, most of which I agree with, on picking (and being?) a good graduate school mentor.

General thoughts on science:

An interesting article addressing both the discovery of cool science (mitochondrial antioxidants!) and how easy it is(n’t) to identify scientists’ likely future contributions at an early point in their careers. A series of publications by the National Academies of Science on how important discoveries began as basic science.

A great article on the importance of stupidity in scientific research.

And another, on the relative importance of effort as opposed to test-taking ability in succeeding in science. “The students who thrive are not necessarily the ones who come in with the perfect scores. It’s the ones who love what they’re doing and go at it vigorously.” Which raises an important question–what motivates us to work hard? Here is an article arguing for the importance of internal (love of learning, desire to improve the world) and *not* “instrumental” (eg, fame and fortune) motivation. You might think that both would be helpful, but in the study they describe (looking at the long-term success of cadets at West Point), instrumental motivations were actually harmful. Interesting!

Fun podcasts and movies and other resources on science in general available at radiolab and

A really interesting post on statistics and data analysis (with a cool interactive visualization tool), retractions and fraud, bad science, and why “science is hard:”

An important blog by Elisabeth Bik on scientific fraud, including the roles of AI in generating and detecting bad science:

Science and society:

Is science anti-religion? Is religion anti-science? Joel thinks this is interesting; some thoughts here. And here is a fun take on interpretations of the bible, with analogy to genetics and epigenetics.

“Science is the poetry of reality.” Richard Dawkins.

The role of universities in society, by Andrew Maynard.

An interesting article arguing that antiscience beliefs jeopardize US democracy.

An important effort to connect scientists to non-scientists in society: Get Out the Science.

Should scientists advocate for science in our society? There is a lot on this right now; here is a statement from AAAS supporting the March for Science, and here is a good blogpost from Scientific American on “How to defeat those who are waging war on science.”

Check out the great Carolina Science Café: Beer and science!

A cool tool to see if the words you use are easily accessible to the nonspecialist, by the writer of xkcd (awesome sciencey humor)!


On the value of a liberal arts education, by Duke’s former president Nan Keohane.

On why a college education should not be treated as a commodity. Relatedly,

Our best universities have forgotten that the reason they exist is to make minds, not careers, by William Deresiewicz.

On the complementary functions of liberal arts and STEM education.

On the power of patience.

Some great teaching tips in this article.

Should professors use trigger warnings, and when, and why? Kate Manning wrote a great article that changed my thinking on this: “Why I use trigger warnings.” It is a NYT article, so in case you can’t access it, I’ll summarize what most struck me: the argument about using them or not has tended to be framed as a trade-off between protecting emotions and stifling the open exchange of information and ideas that universities strive for. Dr. Manning points out that by *both* issuing a trigger warning *and* nonetheless expecting everyone to to be present and participate, she gets a win-win: Students are given time to prepare themselves for what may be an emotionally challenging exchange–and because they will have had a chance to prepare themselves, they can engage better in that exchange intellectually, because they will be less distracted by the emotional response. (Maybe a win-win-win or more actually: this also serves to model both empathy and high expectations regarding intellectual engagement, to students who may not be affected by those triggers.)

Another teaching topic: Why should we ever teach anything other than natural science in a natural science class? Eg, why do we even mention Watson’s and Crick’s names (or Franklin’s, for that matter) in discussing DNA—they are irrelevant to understanding the structure of DNA. I think the answer is that while most science students will enjoy natural science for its own sake if it is taught well, many will be more engaged if we tell interesting stories about how those aspects of science were discovered, how they are relevant in the real world, etc. So—WHICH stories do we choose to tell? this is always a fair question, and there is always a trade-off because we don’t have time to include everything. Here is a nice podcast on including stories of diverse individuals.

Reviewing manuscripts, peer review, and openness of data and review:

  • Useful starting places for how to review are here, here, and here. eLife has posted a nice article on assessing statistics.
  • Here is an interesting story on the growing phenomenon of open peer review and open posting of data (something that my colleague Alex Francisco and I have also advocated in the realm of toxicology data: Meyer and Francisco 2013). eLife has a very nice, detailed policy on this as well.
  • And here is one on the growing movement towards open-access journals, something that I like a great deal. But beware! as almost anyone with an academic email address realizes, there are also a lot of fake journals publishing junk, proliferating under the guise of the open access movement. Yet this costs money, since there is no subscription fee. Here is an interesting article on an extreme case of the role of money in publication even in a legitimate journal; this despite the exceptional profit margins of many such publishers (in part because we scientists review for free…); the reasons for this are explored in this interesting history.
  • The PLoS journals are well-known and outstanding examples of open access publication, and I like in particular PLoS ONE’s choice to explicitly not consider “impact” and likelihood of being cited in deciding whether or not to accept manuscripts. Others include PeerJ and eLife. Non-open access journals are responding with hybrid models, as reported here. Duke is supporting the Compact for Open Access Publishing, which encourages publishing only in fully open access journals.
  • Interesting further experiments along these lines are being carried out elsewhere; one reason I served on the editorial board of BMC Pharmacology and Toxicology is that this journal has chosen to experiment with posting early versions and reviews of manuscripts, and of giving the reviewers the option of not being anonymous (open, as opposed to single- or double-blind, review). Here is a recent assessment of by the BMC editorial board, and here is a related blog.
  • As reported here, the even more novel approach of “prepublishing” (prior to peer review) data and papers online has apparently taken off in Physics and Mathematics, as an alternative to the current peer review system; venues such as arXiv are beginning to include biology papers, and venues such as bioRxiv are being developed specifically for biology. an update on this movement is here.
  • The same article discusses two other areas of great concern in current science–the very large percentage of high-impact findings that turn out to be irreproducible (eg, only 6 of 53 important cancer paper findings were reproduced), and the need to find a venue for publication of negative results. Further reporting of the reproducibility issue here, and two more reports of the same problem here and here. But note this more recent analysis:
  • Speaking of negative results, here is a report on an interesting idea for how to encourage journals to accept negative data papers.
  • Here is a nice article by Alicia Kowaltowski addressing these issues as well as impact factors (below).

Impact factors:

In my opinion, these are a small step away from useless. Some interesting takes on the subject:

  • Here is a formal evaluation of misuse of such data (fun quote: “While numbers appear to be ‘objective,’ their objectivity can be illusory.”)
  • Here is a nice summary of several of the major technical issues with the impact factor; here is a response.
  • Here is a more philosophical discussion of the issues with focusing too much on where our papers are published.
  • A formal statement on issues with impact factors, from the Cell Biology community, addressing how this metric should(n’t) be used for promotion and other decisions and processes. Choice quotes: “The impetus for the meeting was the consensus that impact factors…do not accurately reflect the value…of the work published in these journal…;” Researchers should “Challenge research assessment practices that rely inappropriately on journal impact factors.” And a more recent assessment.
  • Evidence is growing that the more “newsworthy” studies are the most likely to be wrong: Publish and be wrong. Top journals arguably publish the least reliable data.
  • Finally, here is a humorous take–but also one that makes an important point. Why did we choose this career, again?

So…I think we need to evaluate the work we read on a case-by-case basis. Here is an attempt to measure impact of specific articles by citation, normalized to “field.”

Thoughts related to an academic career:

First: I am writing this from the academic career perspective because it is what I know best, not because I think academia is what all PhD students or other students should aspire to. I sort of stumbled into this career myself, and especially in a field like environmental science,  a lot of people want the knowledge for reasons very different than an academic career–and that’s great! Some of this may apply to other areas as well, I think. That said, here are some thoughts:

On how I chose this career: I have written a piece on this, but because it is somewhat personal have not posted it. If you are interested, email me with an explanation of why you are interested, and I will (probably) be happy to share it with you.

Lee Smolin’s great commentary on the apparently growing disillusion among grad students with the idea of an academic career.

On the importance of introspection and quiet thought. And another! And another!

Interesting advice on an academic career.

Concerns about biomedical research and education in the US; more at this website.