In praise of difficult questions.

There were a lot of people at my graduate institution who weren’t afraid to ask probing, thoughtful, difficult questions. They asked them seemingly without any concern about making the recipient feel bad, although students were more likely to receive kinder versions, and they asked them at departmental talks, committee meetings, student seminars, and at faculty interviews. I’ll admit there were times when this made me uncomfortable, and it certainly contributed no small amount of anxiety before giving talks there (and I’m sure I’m not the only person who felt that way).

These days I find myself missing those tough questions, not because I enjoy confrontation per se, but because they made an important contribution to my education.

To be clear, bullying questions or competitive questioning meant to highlight the questioner’s intelligence are a waste of time (e.g. two minutes of talking about your research followed by "what do you think about that?"). Critical thinking, while one of the most important aspects of a post-graduate education, can't be taught. But tough questions and questioners model critical thinking for students in the most direct way. Being at the front of the room talking does not automatically grant expert status: the speaker's ideas must be clear and robust to debate. 

Difficult questions benefit a speaker too - they are the clearest demonstration that the audience has engaged with their work. The most useful talks are those in which the questions are thought provoking for both the speaker and the audience. 

And finally, it can be refreshing when a questioner holds a person to actually answering the question. Science is built on debate and some times disagreement. Hard questions made me feel that the people asking them were expressing a preference for good science, even if the cost was some discomfort or social unease. And that feels like an important thing to express.

The four types of failure, or how to fail in science

As scientists, we’re all wrong, at least sometimes. The question is, how are we wrong?

The arsenic bacteria saga, which we’ve discussed on this blog before, is turning out to be a very public example of failure in science. First announced by NASA press conference in December 2010, authors lead by Felisa Wolfe-Simon shared their discovery of a bacterium capable of replacing phosphorus in its DNA with arsenic, suggesting the possibility of life in phosphorus-limited conditions. This apparently momentous discovery was published in Science, and met with disbelief and severe criticism. Critics throughout the blogosphere and academic departments began to compile a comprehensive list of failings on the part of the paper—8 technical criticisms were published in Science—and as the result of the intense focus on the paper’s lead author is no longer associated with the lab group where this research was carried out. This is failure at its worst—the science was flawed and it drew immediate and intense censure. This is the kind of failure that most young scientists fear: judgment, intense criticism, career-long repercussions. But it’s also probably the least common type of failure in science.

However, it’s arguable that the saddest form of failure is the opposite of this: when a paper is right—innovative, ahead of its time—but somehow never receives the attention it deserves. There are lots of famous examples of scientific obscurity, with Gregor Mendel being the poster child for scientists who toil for years in anonymity. In ecology, for example, papers that considered species as equivalent (a la neutral theory) to explain coexistence were around in the 1950’s-1960s, but received little attention. Other papers suggesting variation in environment as a possible mechanism for plant coexistence were published prior to Chesson and Huntly's influential paper, yet essentially uncited. Most researchers can name at least one paper that foreshadows the direction the field will take many years later, yet is unacknowledged and poorly cited. There are many reasons that papers could be under recognized—they are written by scientists outside of the dominant geographical areas or social networks, or who lack the ability to champion their ideas, either in writing or in person. In some instances the intellectual climate may not be conducive to an idea that, at a later time, will take off.

If that is the saddest type of failure, then the best type of failure is when being wrong inspires an explosion of new research and new ideas. Rather than causing an implosion, as the arsenic-bacteria paper did, these wrong ideas reinvigorate their field. Great examples in ecology include Steve Hubbell’s Unified Neutral Theory of Biodiversity, which although criticized rightly for its flaws, produced a high-quality body of literature debating its merits and flaws. When Jared Diamond (1975) proposed drawing conclusions about community assembly processes based on patterns of species co-occurrence, the disagreement, led by Dan Simberloff ultimately led to the current focus on null models. Cam Webb’s hypothesis that there should be a relationship between phylogenetic patterns in communities and the importance of different processes in structuring those communities sparked a decade-long investigation into the link between phylogenetic information and community assembly. Although Webb’s hypothesis proved too simplistic, it still informs current research. This is the kind of failure on which you can build a career, particularly if you are willing to continually revisit and develop your theory as the body of evidence against it grows.

However, the most common form of failure occurs when a paper is published that is wrong, yet no one notices or worse, cares. For every paper that blows up to the proportion of the arsenic bacteria paper, or inspires years of new research, there are hundreds of papers that just fade away, poorly cited and poorly read. Is it better to fail quietly, or to take the chance at public failure, with all its risks and rewards?

Who is a scientist, I am a scientist: the bees of Blackawton

In discussions of the larger societal implications of scientific findings, the question of who is a scientist is frequently asked. I've talked with with creationists who invoke the authority of someone who has a PhD in a scientific discipline and happens to share their belief of supernatural origins, as a scientific authority. Does the fact that I have a PhD in ecology and evolutionary biology make me scientist or is being scientist something more?

This is an important question. It goes to the core of whose authority we believe for public discussion of such issues as climate change, evolution, risks of vaccines, and so on. Regardless of how we define 'scientist', a scientist participates in science by publishing peer-reviewed research articles in scientific publications. This notion of who is a scientist has been enjoyably stretched by the publication of a paper in Biology Letters by a group of elementary school children from Blackawton, UK. In consultation with a academic scientist and under the supervision of teachers, 25 8-10 year olds devised and carried out an experiment on bee visual perception and behavior, and wrote up their results into a publishable manuscript.

The students trained bees by offering them nectar rewards in different color containers. They then allowed these trained bees to forage in multicolored arenas and they conclusively show that the bees unambiguously select the colored containers they were trained on. Bess learn and adapt their behavior based on previous experience.

Publishing a paper by a group of children may sound like a gimmick, but the study is very interesting. The commentary from the journal says it best: "The children's findings show that bees are able to alter their foraging behaviour based on previously learned colours and pattern cues in a complex scene consisting of a (local) pattern within a larger (global) pattern . As there has been little testing of bees learning colour patterns at small and large scales, the results can add considerably to our understanding of insect behaviour."

The paper is extremely enjoyable to read and will have you chuckling to yourself. Sincerity pours from the words and I was left wondering if I could have reasoned so well at that age. The children develop hypotheses using information available to them, such as watching Dave Letterman's 'Stupid Dog Tricks'. Reading this article made me realize why I love being scientist. The students note that "This experiment is important, because, as far as we know, no one in history (including adults) has done this experiment before" and because they were given the opportunity to carryout this study they "also discovered that science is cool and fun because you get to do stuff that no one has ever done before". Too true. I could not have said it better myself.

Being scientist can mean a lot of things, it can mean knowledge (which the Latin origin, Scientia means), it can mean training and acquired skills, but at its core, being a scientist means conducting research, testing hypotheses and writing publications that are deemed acceptable by other scientists. Therefore the children of Blackawton are scientists, I am a scientist.

Blackawton, P., Airzee, S., Allen, A., Baker, S., Berrow, A., Blair, C., Churchill, M., Coles, J., Cumming, R., Fraquelli, L., Hackford, C., Hinton Mellor, A., Hutchcroft, M., Ireland, B., Jewsbury, D., Littlejohns, A., Littlejohns, G., Lotto, M., McKeown, J., O'Toole, A., Richards, H., Robbins-Davey, L., Roblyn, S., Rodwell-Lynn, H., Schenck, D., Springer, J., Wishy, A., Rodwell-Lynn, T., Strudwick, D., & Lotto, R. (2010). Blackawton bees Biology Letters DOI: 10.1098/rsbl.2010.1056

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Science 2.0 - science comes of age on the Internet

by Marc Cadotte, Nicholas Mirotchnick and Caroline Tucker

The Internet is not just for lolcats and porn anymore, scientists have begun using it in constructive ways. The past few weeks’ controversy about the ability (or lack thereof) of bacteria to incorporate arsenic exemplifies how the relationship between science and the Internet is changing. If you’ve missed the debate over the recent Science paper, researchers funded by NASA’s exobiology/evolutionary biology program published experimental results suggesting that a Halomonas species could incorporate arsenic into its DNA in the absence of available phosphorus. This paper received extensive attention in the mainstream media, but also vocal criticism, which was expressed primarily through postings and comments on scientific blogs. Until recently, for scientific communication the Internet has functioned primarily as an electronic source of published journal articles. Earlier attempts to take advantage of the Internet’s potential (immediacy, accessibility, and ability to connect individuals, organizations, and ideas) in scientific discourse have been mixed (e.g. Nature Precedings versus PLoS ONE). The use of blogs as a forum for scientific debate suggests that this is changing: posters tended to be active scientists and the comments were similarly knowledgeable. In contrast to this online approach, the authors of the Science paper stated that they would only respond to peer-reviewed critiques and would not engage in discussions on the blogosphere.

The story of the arsenic-utilizing bacteria highlights an emergent tension in the transition to internet-based scientific discourse. Traditional communication in science has been primarily unidirectional, from the authors of a study to the readership of a journal. Any discourse transpired on the pages of a journal, regulated by editorial and peer review. This gatekeeping meant that this discourse was technically sound and kept personal grudges and tangential discussions to a minimum. This also meant, however, that only a few voices were heard, the discussion was slow (occurring over months) and only happened for one back and forth (journals will not devote precious page space to on-going discussions and debates).

This method of discourse is changing. Journals have experimented with online discussion or commenting features on their websites. Methods in Ecology and Evolution, for example, has a correspondence page with discussion threads for each paper they publish, and PloS ONE allows for comments to be posted to every paper they publish. While, in concept, these are positive developments for scientific communication, commenting features are seldom, if ever, used. The main obstacle to their success is that they are only available on the publishers’ websites, but scientists access articles in many different ways, from database searches to library links. Few scientists actually go to individual journal websites to access papers. This is not to say that there are not discussions about scientific papers occurring online. As highlighted by the arsenic bacterial episode, blogs are an important avenue for discussing and disseminating new ideas in science. Blogs may not, however, actually foster conversations very well. One person or a few people usually run them and there is little discussion among blogs (a comment on a blog post at blog X will not be part of the discussion of the same story at blog Y). Rather, the greatest potential to foster discourse is through virtual networks where people are linked together either through friendships or professional self-identification (e.g., as fisheries biologists), with Google Reader being a particularly powerful communication tool.

It’s exciting to think about what the future of science will look like, given the changes that we’ve already started to see. The major upside of new channels of communication is that they give us the potential to quickly reach thousands of readers, instead of the handful that usually read any given journal article. They also let us communicate in both directions, and in real time. The pitfall, of course, is that they’re free-for-alls; anyone can blog about science.

But here’s what’s unexpected: these free-for-alls have been amazingly reliable at filtering out the bad and promoting the good. Inaccuracies are pulled from Wikipedia faster than anyone had predicted, the social news site Reddit is “astonishingly” altruistic, with users eliminating offensive or erroneous comments from the site and promoting other users’ questions and problems, and the reputations of blogs are shattered if their content becomes unreliable. Social networking has revolutionized the way we consume news, with sites like Facebook and Twitter launching the best articles into viral webspace. The open-access world has evolved self-regulating mechanisms that work surprisingly well so far and if these media are to continue to grow, we will have to ensure that these mechanisms remain built-in.

Seems like an easy task, right? Apparently not. For some reason, academics are slow and conservative when it comes to adopting new media. A letter to Nature two weeks ago scolded scientists for not contributing their share to Wikipedia pages. Various facebooks for academics, like Mendeley and ResearchGATE have emerged, but last week, another Nature article complained that researchers aren’t jumping on the bandwagon. These sites are potential collaborative goldmines, but we seem to be incapable mastering what tweens can do with two thumbs.

It’s not so hard to imagine a world where anyone with a broadband connection can contribute creative ideas to science, the good ideas get automatically filtered to the top and the information is all free to anyone. In this world, children count ants (or bees!) in their backyards and upload their data to global networks. Revolutionary discoveries are published instantly on blogs and thousands of scientists get to decide if they’re valid. Every gene ever sequenced and every tree height ever measured can be readily downloaded in an Excel (or OpenOffice) spreadsheet. In this world, the report on our little arsenophilic friends might never have been published in Science, because instead of being reviewed by two referees, the thousands of readers on the blogosphere would have filtered it out, if was in fact porous.

Academics should be the first, not the last, to adopt new communication tools. We are no longer limited by the postal service, email or PDFs; the web has gone 2.0 and we should follow suit. So go forth, young researchers, and blog, edit and share. And then go tweet about it all so your eight year-old kid knows how hip you are.

The Nobel prize and the grandeur view of life

As news of the latest Nobel prizes in physics and medicine were announced, science became a central story for many news outlets. Numerous stories and interviews were held about the discoveries that earned the laureates their just rewards. I’ve heard interviews with medicine winners, Elizabeth Blackburn and Carol Greider (2/3 of the prize, the other being Jack Szostak), about their discovery of telomeres and telomerase, and with Willard Boyle (for physics) on inventing an imaging semiconductor circuit (i.e., digital recording of light). The media play up the applications to humanity. Telomeres and telomerase offer a deeper understanding of cancer and potential treatments. The digital recording of light gave us digital cameras (among a plethora of other technologies).

However, in the interviews with these great scientists, there was a common thread in what they said. They reiterated the need to support basic science and that the pursuit of curiosity-driven science is a worthy and valuable enterprise. I found the fact that they found it necessary to reiterate this to be interesting and something that interviewers thought worthy of reiterating themselves. I know that news stories need to relate to a person’s everyday experience, but, I think, basic science offers something more. To quote Darwin “There is grandeur in this view of life”. That is, while the products of science have surely improved our quality of live, science has given us something deeper and more meaningful. Basic curiosity-driven research has changed our understanding of the world and our place in it. We now look up at the stars and have a pretty good idea of what they are. We know what causes thunder and lightening. We understand why our pet cat looks kinda of like a lion and gorillas like people. We no longer look to superstition and myth to explain these aspects of nature. To me, this is the fundamental contribution of science to humanity, and I wish this were as celebrated as technological advances. Though being able to take 2 gigabytes of photos and movies when my daughter is doing something cute is pretty cool too, I guess.