Tuesday, 18 August 2015

Why I read the introduction and discussion of papers

Over the past year, I've heard several times the sentiment that introductions and discussions of papers are not worth the .pdf memory they take up. Most recently, it took the form of the following cartoon passed around twitter.

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Cartoon by Anthony Crocco
But I've had this discussion in person too, with assistant professors in our department. And I just don't get it. To me, a paper without the introduction and the discussion is almost literally nonsensical.
The intro, discussion, and conclusion have value because I don't view them as opinion, but as argument. The introduction should set up WHY the problem is interesting to the field, and why the approach chosen is relevant. This isn't just set up. It tells me a number of useful things: whether the person knows what they are doing with regard to the broader intellectual climate they are working in for one, but also, their thoughts on why the problem is important may not be my own. Their thinking, as detailed in the introduction, may modify, interrogate, change my own. And their thoughts about why the work is worth doing will guide 1) how they did it, and 2) what they intended to get out of it (which is important, because that set up will color how they present BOTH the methods and the results).
What is written in a paper is never just a simple narrative of the work done and the results obtained. That is a stylistic conceit. So knowing the set up is essential for critically assessing the "objective" parts (which are not so objective).
But it is the dismissal of the discussion that makes me saddest. The implication that the discussion can be discarded means that what the authors think of their results is irrelevant. There may be fields (particle physics perhaps) where the results are entirely unambiguous. I have yet to encounter a biological problem in which that is the case. Moreover, the non linear hierarchical interaction of biological systems (from molecules to cells to organs to organisms to behavior to ecology to evolution) mean that from an integrated biology perspective, I want to know about potential implications of the resultsfor connected elements of the biological hierarchy of organization. Again, a well crafted discussion is an argument, and a source of ways forward, not the spewing of opinion.
But perhaps what makes me saddest about the sentiment expressed in that cartoon is the solipsistic vision of science it produces. A focus on methods and results discounts the intellectual work, the scholarship done by your peers. It views others' work solely in light of how it might relate to one's own, and assumes that modes of thought about scientific problems are already so fixed, that nothing new will ever be found under the sun. This is not my experience of science.
In my field (evolutionary biology), one of the most important events that ever occurred was the Modern Synthesis. Over the course of ten to fifteen years, a disparate group of biologists came together to generate the modern understanding of evolution by natural selection, rooted in population genetics. The modern synthesis involved no ground breaking discoveries, and happened before we even properly understood the molecular mechanisms of heredity. The modern synthesis was the result of years of discussion and argument, culminating in, not a series of papers detailing new methods and new techniques, but in a series of books detailing a new way of thinking about biology. Crucially, it involved biologists from other fields understanding each other's work, despite being unfamiliar with each other's methods. If Mayr, Simpson, Dobzhansky, Huxley, and Stebbins had only engaged with their colleagues work through the schema of that cartoon, the modern synthesis would have been impossible.

Wednesday, 5 August 2015


I am currently writing a manuscript. It's the second first author manuscript to come from my postdoctoral work (a little under two years in), and hopefully it will be sent out for review in the next couple of weeks. Currently, my PI and I are sending it back and forth, querying the writing, clarifying the main points, realising (for me at least) some pretty large gaps in my knowledge of the litterature. But, at no point since I wrote the first draft have either my PI or I thought anything other than "this is a good manuscript, we just need to make it even better".
This is in many ways the paper I came here to write. It's the paper that shows that I understand how to do biological kinematics, that is how to study the movement of biological structures as organisms use them. As I've mentioned elsewhere, my background (which now seems quite far off) is in ecomorphology as applied to the fossil record. I correlated variation in mammalian bone morphology with known variation in broad categorical behavioral and ecological variables. But these broad classifications don't tell you about function, and so about the behavioral phenotype on which selection is acting. So I took this postdoc in part to learn how to ask those questions.
And here I am, writing a paper that does just that, yet also so much more than I had anticipated. The study we did was an experimental manipulation to see how a nerve lesion affected the movement of the tongue and oro-pharynx in our animal model. The work replicates a relatively frequent iatrogenic injury in premature human infants, and so it is clinically relevant. But the direction we have taken with this paper is so much more than that. We're using the changes we observe to make inference about the neurological control of these oro pharyngeal structures. My head has, for the past few weeks, been full of discussion of central pattern generators, afferent and efferent pathways.
With this paper, I feel like I have grown immensely as a scientist. I have become the integrative biologist I've always wanted to be. I'm not doing it in this paper yet, but I feel ready to connect my paleontological work and knowledge of mammalian evolution with my understanding of experimental organismal physiology.
I have an idea of the direction I want to head in as a paleontologist, as a evolutionary biologist, as a mammalian physiologist. And it's so much more than I thought it would be when I started this project hoping to learn about kinematics.
I'm heading out onto the job market this year. And my research statement will be nothing like the one I wrote three years ago when I was finishing my PhD. I think it will be so much more interesting. And I hope others will too.