Carnival time.

The 34th edition of the Carnival of Evolution is hosted at Quintessence of Dust. Everything from the evolution of perfection to the evolution of small importance will be found there.

White-nose syndrome and wind turbines: why biodiversity matters

Linking ecosystem services to economic benefits is a vital step in connecting ecological research to policy and political action. The UN Environmental Programme’s The Economics of Ecosystems and Biodiversity (TEEB) initiative represents a concerted effort to draw attention to the economic benefits of biodiversity and cost of ecosystem degradation, and to bring together scientists, economists and policy-makers.

Accordingly, Boyles et al. (Nature, 2011) paint a troubling picture about the value of economic benefits that insectivorous bats provide to the North American economy, and the degree of extinction risk they currently face. The authors point out that bats are “among the most overlooked, yet economically important, non-domesticated animals in North America”, and their loss would cost North Americans more than 3.7 billion dollars/year. Given rapid declines in populations due to white-nose syndrome (over 1 million bats killed) and wind turbine fatalities (projected to reach up to 30,000-100,000 fatalities/year as wind turbine installations increase), the authors suggest action can't wait.



Hopefully using the universal language of money helps translate scientific knowledge into political action. After all, bats are only one group of species: imagine the true cost of current rates of biodiversity loss and ecosystem destruction, from the smallest microorganism to the largest megafauna. The total must be staggering. And so, it seems, is the scale of action required to halt this decline.

The regional community, maximum entropy, and other ideas in ecology

Looking through my feed of community ecology papers this month, I couldn’t help but notice that while most tested well-established concepts–density-dependence, niche partitioning, metacommunities, competition, dispersal limitation–there was also–as I suppose is usually true–a subset of papers championing newer, less established ideas.

For example, the article “Applying a regional community concept to forest birds of eastern North America” by Robert Ricklefs, furthers the regional community concept he introduced in 2008. Ricklefs is uncomfortable with how ecologists typically define local communities – i.e as spatially and ecologically discreet entities – and the predominant focus in community ecology on local coexistence. He argues that communities make sense as entities only at a larger scale, taking into account that local communities are not isolated, but instead interact as a function of overlapping ranges and species dispersal. In this paper he applies this concept to Breeding Bird Survey data to examine the distribution and abundance of birds in eastern NA.

Partel, Szava-Kovats, and Zobel are also critical of the predominant focus on local diversity. In their paper “Dark diversity: shedding light on absent species”, they pitch the idea of “dark diversity” as a valid diversity metric. Dark diversity accounts for the number of species which belong to the species pool for a particular habitat in a region but are not actually present in a local community of that habitat type. The resulting value can be used to calculate a dimensionless ratio of local to dark diversity, suitable for comparison of diversity components in dissimilar regions.

Lastly, in “A strong test of a maximum entropy model of trait-based community assembly”, Shipley et al. further test Shipley’s model of Entropy Maximization, using it to predict the composition of communities in the South African fynbos. The model predicts community composition (species identity and relative abundances) through an assumption of random assembly (or entropy maximization) within environmental constraints on species traits.

New ideas are a constant in ecology, but they face stiff competition in an already crowded field. The possible mechanisms of local coexistence, for example, are already a long list. What determines which of these–or any–ideas become entrenched in ecology? The likelihood of a concept becoming established must be a complex function relying on a cost-benefit analysis–what does applying this idea cost compared to the gain in understanding it produces?–further adjusted by intangible variables like timing and the skill and prestige of an idea’s advocate. After all, some ideas require decades to establish properly, requiring changes in the theoretical climate or technical capabilities, for example, neutral theory or spatial ecology. Others seem to catch on immediately. Philosophers have written more cogently on how scientific ideas change and paradigms shift, but as participants in the process, we have a rather unique perspective. After all, as scientists we play an active role in driving these shifts in thought and action. You might argue that the merit of the ecological ideas that become established are as much a reflection on those who accept and institute them, as on those who propose them.

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awesome infographic by Caroline Tucker

(click to go large)

There exists a problem in science so complicated that decades of work have yet to solve it. Its causes and consequences make some of the toughest questions in complex analysis or astrophysics look like child’s play. And yet when we consider this problem, the conclusion is immediately obvious and simple: it should not exist.

I am talking about the fact that today, in 2011, female scientists are punished solely because they are female scientists.

In theory, this problem doesn’t exist anymore. Multiple waves of feminism should have chipped away whatever glass ceilings once capped our ivory towers. Women are receiving more PhDs than men in many fields and they are earning such a high proportion of bachelor’s degrees that we may have to rethink that name.

But in the last several weeks, some disturbing realities have resurfaced in the science media. At the end of January, Nature reported that women earn fewer scholarly awards than they should, based on the proportion of their respective fields that they represent. That same week, Science published a graph showing the number of European Research Council grants awarded to women in its last funding round – 9.4%.

Stats like these are nothing new; they pop up all the time. What is new, however, is the article that followed in Proceedings of the National Academy of Sciences a few days later. It turns out that there is no longer much evidence for overt discrimination against women applying for jobs or grants in quantitative fields. Instead, disparities in available resources are causing many of the differences between women and men’s scientific careers.

Yes, there are discrepancies in publication acceptance rates and grants, but the authors attribute these to factors like women occupying more positions at teaching-intensive schools rather than research institutions. When they compared men and women with similar resources, the biases disappeared, or in some cases, favoured women. (If you don’t want to read the whole article, there’s a nice summary of it here.)

Ok great, the science community isn’t explicitly discriminating against women. But this leads us to a much more troubling conclusion; the culprits are actually deeply engrained societal expectations and constraints that likely extend well beyond the sciences, and certainly beyond the scope of this blog post, though a few of them are highlighted in this thoughtful opinion piece.

Here’s what I will say: it’s not written in our DNA. How many times have you heard lines like, “Men and women are just different, they always will be, our brains aren’t wired the same”? This kind of just so statement is rarely backed up with evidence. For a good debunking of these misconceptions, check out two new books, reviewed here.

Now it’s possible that I, as a young male grad student, do not hold the most valuable two cents on these issues. I could keep rambling about things that I don’t fully understand, but my perspective is limited, and I think maybe the most constructive thing to do at this point would be to hear about other people’s ideas and experiences in the comments section below. So I’m cutting this short and leaving it incomplete in favour of a more open forum. In particular, it occurred to me that we in the ecology and evolution community have a unique opportunity to shed light on many gender issues. The PNAS article focuses on the underrepresentation of women in math-intensive fields, but comparing mathy fields to less-mathy fields entails a lot of confounding factors. In ecology and evolution, however, we cover the whole spectrum, from the completely mathless and descriptive, to the suspender-wearing, calculator-toting quants. We generally all come from relatively similar biology backgrounds, eliminating many of those confounding factors, and it would be great to hear how you all think these issues play out in E & E. So go for it blogosphere, do your thing.

Documenting the sacrifice

Whether working in remote regions or with poisonous animals, biologists often put themselves in peril in the name of discovery. The first organized expeditions of naturalists sailed to exotic lands, their bravery supplemented by their curiosity, were threatened by storms while at sea, new and deadly diseases, unfamiliar animals, and new cultures. Add plane crashes and paramilitary groups to this list and not much has changed.

In a great New York Times piece titled 'Dying for Discovery', Richard Conniff recounts several stories of naturalists, ecologists and conservation biologists killed while pursuing their passion for discovery. But just how many field biologists have died while working to understand life's secrets? This is an interesting question, and begs the further question, are they adequately memorialized?

Gary Polis (1946-2000) desert ecologist, drown with four other biologists during a storm in the Sea of Cortez.

In an attempt to tell the stories of the fallen naturalists, Conniff hosts an interactive list, called the Wall of the Dead, which lists all biologists killed in the field and that he has a record of. People are able to add names, and I've visited this list several times over the past month and it has grown substantially. I've known a few field biologists that have died -and added one to the list, and know several that survived near-death experiences, and this list is a great and important monument to their memories.

Further studies of the decline effect find decline of the decline effect

“The Truth Wears Off: Is something wrong with the scientific method?”

The Decline Effect explored in an article by Jonah Lehrer in the New Yorker refers to a temporal decline in the size of an observed effect: for example, the therapeutic value of antidepressants appears to have declined threefold since the original trials. Based on the cases presented, this effect is not limited to medical and psychological studies. One example in evolutionary biology is the relationship between physical symmetry and female choice: initial studies consistently found strong selection for symmetry in mates by females, but as time passed, the evidence grew increasingly smaller.

This may be a result of selective reporting – scientists focus on results that are novel and interesting, even if they are in fact simply statistical outliers, or worse, the result of unconscious human bias. This sentiment is troubling; humans – scientists or not– are proficient pattern finders, but our subconscious (or conscious) beliefs influence what we search for. Lehrer argues that replication – the process of carrying out additional, comparable but independent studies – isn’t an effective part of the scientific method. After all, if study results are biased, and replications don’t agree, how can we know what to trust?

I don’t disagree with most of the article’s points: that scientists can produce biased results, PhD not withstanding, that more effort and time should be invested in data collection and experimental methodology, that the focus on 5% statistical significance is problematic. For one, it’s not clear from the article how prevalent the decline effect is. However, I wonder whether Lehrer, similar to the scientists he’s reporting on, has selected specific, interesting data points, while ignoring the general trend of the research. In 2001, Jennions and Moller published evidence of a small negative trend in effect size over time for 200+ studies, however, they suggest this is due to a bias toward high statistical significance, which requires either large effect sizes (the early studies published), or small effect sizes in combination with large sample sizes (a scenario which takes more time).

Even if the decline effect is rampant, does it represent a failure of replicability? Lehrer states that replication is flawed because “it appears that nature often gives us different answers”. As ecologists though, we know that nature doesn’t give different answers, we ask it different questions (or the same question in different contexts). Ecology is complex and context-dependent, and replication is about investigating the general role of a mechanism that may have been studied only in a specific system, organism, or process. Additional studies will likely produce slightly or greatly different results, and optimally a comprehensive understanding of the effect results. The real danger is that scientists, the media, and journals over-emphasize the significance of initial, novel results, which haven’t (and may never be) replicated.

Is there something wrong with the scientific method (which is curiously never defined in the article)? The decline effect hardly seems like evidence that we’re all wasting our time as scientists – for one, the fact that “unfashionable” results are still publishable suggests that replicability is doing what it’s supposed to, that is, correct for unusual outcomes and produce something close to the average effect size. True, scientists are not infallible, but the strength of the scientific process today is that it doesn’t operate on the individual level: it relies on a scientific community made of peers, reviewers, editors, and co-authors, and hopefully this encourages greater accuracy in our conclusions.

Carinval #32 and still going strong

Want to know what people are talking about? The 32nd Carnival of Evolution is online, hosted by Denim and Tweed. Check it out, pass it along.

Trend in ecology, 2010

Sciences are always in a state of ebb and flow (sorry), and topics of study fall in or out of fashion in response to paradigms shifts, methodological advances, and to support necessary ecological applications.
For the sake of curiosity, I've compiled the top keywords from ecology publications in 2010. Obviously there are many covariates, but it should come as no surprise that the top words were "biodiversity" (667 times), "climate change" (293), and "conservation" (274); other popular keywords were "evolution" (277), "population (ecology)" (273), and the rather vague "patterns" (196).

(click image for larger view)

The evolutionary story of ecosystem function

Twenty years of research has repeatedly shown that communities with greater diversity result higher functioning -namely greater production of biomass. One of the major mechanisms producing this relationship is that different species use differing resources, such that their complementary use of resources uses the total resource pool more thoroughly, thus converting more resources into biomass. Resource preference is the product of evolution and how organisms have adapted to using various resources can influence the strength of the diversity-function.

In a recent paper in Nature, Dominique Gravel and colleagues test how the evolution of specialization versus general resource use affect the strength of the diversity-function relationship. They use bacteria strains that have undergone evolution on diverse resources (generalist) versus on a singular resource (specialist). The resources in their case are different carbon substrates.

Assemblages of generalists were able to use many available resources and generally had greater productivity than specialist assemblages. Generalists also show an increasing relationship between diversity and productivity, because no generalist used all resources and they still showed some preferences. Combining multiple such generalists meant that more of the total resource pool was consumed. Specialists also resulted in the positive relationship, but a much steeper one. Because specialist use many fewer carbon substrates, additional specialists meant that new resources were tapped into. Thus increasing specialist diversity resulted in more new resources being consumed than with the generalist species.

While these results are logical, they are important for two reasons. First is that the strength of the relationship between diversity and function is mechanistically determined by the resource use efficiency of individual strains, and how many of the total substrates they can use. The mechanisms producing different relationships in previous experiments were hypothesized after the results analyzed, as opposed to being predicted. Second, recent work has shown that evolutionary history seems to be a better explanation of community function than the number of species. These results show how the history of evolution can have important consequences for function.

Gravel, D., Bell, T., Barbera, C., Bouvier, T., Pommier, T., Venail, P., & Mouquet, N. (2010). Experimental niche evolution alters the strength of the diversity–productivity relationship Nature, 469 (7328), 89-92 DOI: 10.1038/nature09592

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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