Tuesday, February 5, 2013

What is ecology, and evolution - the value of interdisciplinary collaboration?

What is ecology? What is evolution? Seems like a really simple question from an ecology or evolution perspective, until you bring a different field into the mix, e.g., transposon/genome biology. When we started the TE (formerly known as genome) ecology group, sometimes in March 2010, I had no idea we would end here, with a publication in a journal with a higher impact factor than Ecology.

Our starting point for this publication was the appeal of using ecological theory to explore the dynamics of transposable elements in the genome. But we quickly realized that what these genome biologists described as "ecology", did not correspond with my idea of ecology, and it seemed more like an evolutionary pattern/process. Luckily our collaborative group consisted of a combination of ecologists, evolutionary biologists, philosophers, and computational biologists, which provide the necessary background information to study this interdisciplinary problem. We thus ended up defining, in very general terms, ecology and evolution:
"A strictly evolutionary approach investigates change (or the lack thereof) in some focal entity over successive generations. The focal entities can range from genes to traits or from populations to higher taxonomic units. 
A strictly ecological approach assumes no change in the focal entities themselves, but focuses instead on the relationships between these entities and their environment. Here we use ‘environment’ in a broad sense potentially to include any of the factors with which an entity interacts."
Not exactly rocket science, you would think, but writing this publication has been an eye opener (in a positive way) to me on the importance of clear and exact definitions. I think that we have literally discussed every term we wrote in this manuscript.

Moreover, because of our interdisciplinary group, we could actually provide a proof of principle analysis, with some actual, very promising, results:

The predictions arose directly from our philosophical definitions and applying general ecological and evolutionary principles, the data from available genome sequences obtained and handled with bioinformatics, the actual tests from standard ecological multivariate practices.

And this is also the only manuscript I have worked on that received these completely positive (anonymous) reviews:
"This is a brilliantly organized and beautifully written paper that provides a closely analysed conceptual framework and strong evidential support for several key claims made by the authors. The paper draws on, clarifies and expands existing literature, and provides suggestions for how findings about the system of focus (TEs in genomes) have much broader implications and potential applications. The authors set out clearly and thoroughly a case for why transposon ecology is interesting, and are very convincing in their treatment of potential confusions and conflations. The figures are illuminating, and the results of the empirical analysis strongly supportive of all the distinctions made with such care by the earlier part of the paper. The ideas the authors develop are novel and thought-provoking, and are likely to gain a lot of attention from the biology community and beyond. I can only recommend acceptance with no changes at all, apart from a few typos to do with spaces, italicization, redundant commas, and the occasional missing ‘that’ or ‘the’. I expect this paper to be read and cited abundantly."
Since this type of accolade is very rare, I decided to put it here, and thank the anonymous reviewer again (I hope s/he doesn't mind me putting it out there). This would be the perfect blurb that often comes on the dust cover of a book, and it provides a better summary and critical praise for our work.

Finally, to stress again the importance of the collaborative nature of our truly interdisciplinary group, during our discussions I came across this publication: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004803, that looks at how different types of sciences are linked to each other (by following the surfing behaviour of users of scientific websites):

There is a lot of fascinating information in this figure, but without access to the raw data (and given my limitations due to daltonism), I get the impression that 1) ecology/biodiversity seems to be this bridge between the social and natural sciences (with Ecology, a very specialized journal in ecology, identified as a "connector[s] between various domains"), 2) philosophy is surprisingly far away from ecology.

I think that our publication explicitly and successfully bridges that gap between these disciplines, and benefited greatly from collaborations with researchers from these disciplines.

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