Tuesday, December 30, 2008

Review or publish; the curse of the commons

ResearchBlogging.orgNeed we be concerned about the volume and quality of manuscript reviews for journal submissions? In a recent editorial published in Ecology Letters by Michael Hochberg and colleagues, they answer yes, we should be concerned. They argue that manuscript reviewing is suffering from a tragedy of the commons, where growing submission rates to top journals is overburdening potential reviewers. This overburdening has two causes. First, that researchers tend to send their manuscripts to journals based on impact factors, regardless of the appropriateness of the manuscript for the receiving journal. Second is that authors view negative reviews as stochastic happenstance and in the rush to resubmit do little to improve their manuscript.

While the concerns are real, and the authors do suggest common sense approaches to publishing (i.e., choose appropriate journals and get colleagues to review drafts -something most of my colleagues do), there is little discussion of what incentives could be offered. The curse of the commons is when individual motives do not benefit the greater good, thus incentives could be used to alter motives potentially benefiting the larger community.

A number of journals now offer free access or free color figures in future publications for reviewing or even offering payment. Perhaps the move towards reduced length rapid turn around publications is part of the problem and that we should be valuing longer, more detailed papers (the classic quantity vs. quality problem). Whatever the potential solutions, it is promising to see journals, especially top-ranked ones like Ecology Letters, discussing these issues.

Michael E. Hochberg, Jonathan M. Chase, Nicholas J. Gotelli, Alan Hastings, Shahid Naeem (2009). The tragedy of the reviewer commons* Ecology Letters, 12 (1), 2-4 DOI: 10.1111/j.1461-0248.2008.01276.x

Friday, December 26, 2008

How to plan an experiment that could last 99 years

ResearchBlogging.orgFor a number of reasons, including the fact that most grants only allow for research over a time span of 1-3 years, ecologists and evolutionary biologists usually plan experiments that last few years (with notable exceptions, such as the LTER). A usual approach to study long term phenomena is to take advantage of “natural” experiments. This allows us to understand about processes over long time periods, but usually with limited control on the initial conditions.
In a recent paper by Thomas Bruns and collaborators I learned about another way. They study spores viability of an important genus of ectomycorrhizal fungi, symbiont of Pinaceae: Rhizopogon. Pinaceae (the family of pines and other conifers) need ectomycorrhizal fungi to survive and usually spores and seeds are dispersed independently. It was not known how long their spores can last, which has very important implications, for example for colonization of areas not previously colonized by Pinaceae, or colonization after large scale disturbances, since if seeds cannot find mycorrhizae they have really few chances of survival. Now we know, based on this research that spore banks can be build and last probably decades.

What they did is really interesting, and was inspired on a previous study on seeds. They planted known number of spores of several species of Rhizopogon in terracotta pots, that were later planted into the ground (to mimic natural conditions). They planted 16 replicates, and they plan to open and analyze them later in the century based on the spore viability (for example, if in a few years most spores seem to be not viable that may reduce the expected length of the experiment to increase resolution). This paper found that after 4 years the inoculum potential of these spores seems to be increasing with time. I found the approach used in this experiment really fascinating and I look forward to see what happens in the next years!

Thomas D. Bruns, Kabir G. Peay, Primrose J. Boynton, Lisa C. Grubisha, Nicole A. Hynson, Nhu H. Nguyen, Nicholas P. Rosenstock (2009). Inoculum potential of
spores increases with time over the first 4 yr of a 99-yr spore burial experiment
New Phytologist, 181 (2), 463-470 DOI: 10.1111/j.1469-8137.2008.02652.x

Monday, December 22, 2008


Keeping up with scientific literature is a challenge. Even though is it possible to do a descent job in your super specific area of expertise, it is almost impossible to keep up with literature in general areas of science, such as ecology or evolution, given the hundreds of papers that are published each week. There are many tools that can be used to stay (kind of) updated. One of those are podcasts. If you are reading this blog (and if you frequently read blogs) it is likely that you know a lot about podcasts, but I found remarkable the few people that profits from this awesome resource in academia. There are many nice podcast on science, but few on ecology. The new podcast of Frontiers in Ecology and the Environment is an awesome one, and I hope that other journals start doing the same thing (let me know if they are more!). This ESA podcast, with music by Nick Gotelli (excellent choice by the way, click here for more of his music), is surely one that you want to have in your mp3 player when you go for walk.

Other nice ones (but not specific on ecology or evolution) are the Nature podcast and the Science podcast, and my preferred one, the Scientific American podcast.

Saturday, December 20, 2008

Ecology's romantic period

As an ecologist of the 21st century, I often think about the early ecologists from the period between 1900 and 1920 (Clements, Forbes, Warming, Spalding, Grinnell, etc.) and wonder what it was like for them to do their science. Being a scientist today usually means being a technophile. Amazing advances are made through technology, from new and larger genomes to running mind-bogglingly complex computer simulations with a scale and scope that would have been simply incomprehensible a generation ago. We also have a vast foundation of ideas, theories, hypotheses and observations that drive our current quest for knowledge.

Ecologists of 1900 did not have access to our level of technology, they did not have this huge foundation of knowledge informing their science. In fact the totality of human knowledge of the ecological world, from Aristotle to Darwin to Haeckel to Warming, could fit on a single bookcase. And for this I envy them. Every observation was something new and exciting. Hypotheses created to explain observations were novel and creative. I may be romantic, but the idea of a wide open frontier of ideas seems so exciting to me.
Being an ecologist today means competing in a crowded market of ideas. Much of our creative work involves revising and fine-tuning existing hypotheses or finding new technological and computation methods to better test existing hypotheses. Sometimes it feels like the scientist who yells the loudest in this crowded market will be heard. And so I wonder, would it be worth giving up the technological advances to simply stick your head in a hole and describe a brave new world.

P.S. I love both the photos of Frederic Clements shown here. The first is of him near Santa Barbara, CA were he would spend his winter months researching plant communities. The second is of him (head in hole) and his wife Edith, also an ecologist, apparently studying below ground interactions among plants.

Friday, December 19, 2008

Why this blog?

I decided to start The EEB and flow because I think this blog is needed. While there are some great science blogs dedicated to evolution (Dechronization and Evolutionary Novelties, for example) there is conspicuously little blogging of recent advances in ecology and evolutionary ecology. My short term plan is to highlight recent important papers, discuss ecology and conservation news and post thoughts on life in academic ecology and evolution. My long term goal will be to host a community generated blog where new papers and findings are discussed. Given that the only real community generated discussion of recent papers is a paid subscription (Faculty of 1000) the time may be right for a community blog. But stay tuned.

Thursday, December 18, 2008

Whence diversity?

ResearchBlogging.orgIt is a truism to say that ecological communities are diverse. They often contain dozens or hundreds or thousands of species that represent many of the deep origins in the tree of life. A recent paper by Prinzing and colleagues published in Ecology Letters tested the hypothesis that communities of plants that include more of the ancient divergences from the evolutionary tree of plants should also contain a greater diversity of physical traits. They examined over 9000 plant communities and found that those that contain fewer evolutionary lineages actually had greater trait diversity than those randomly assembled from more lineages. This result reveals that when communities are assembled from a few lineages (likely due to strong environmental selection -e.g., drought tolerance) those members tended to have evolved large differences. That is, while species may be constrained to certain habitat types due to their evolutionary heritage, successful coexistence depends on maximizing differences.
Andreas Prinzing, Reineke Reiffers, Wim G. Braakhekke, Stephan M. Hennekens, Oliver Tackenberg, Wim A. Ozinga, Joop H. J. Schamine, Jan M. van Groenendael (2008). Less lineages more trait variation: phylogenetically clustered plant communities are functionally more diverse Ecology Letters, 11 (8), 809-819 DOI: 10.1111/j.1461-0248.2008.01189.x