Monday, August 26, 2013

Everything you wanted to know about peer review (but no one mentions)

Since the British Ecological Society has published an introduction to reviewing successfully, here’s a short list of additional, less noted, observations about the reviewing process.

For example, excitement for reviewing is proportional to the number of reviews you have done
  • When you are first asked, reviewing feels like a great honour. It is one of the first signs that some group larger than your lab or department recognizes your existence. You will spend an unreasonable amount of time perfecting your review.
This plot would not survive peer review.
  • The novelty will wear off, and your enthusiasm upon receiving a review request will decline, usually in relation to your increasing workload. 
  • Sadly, the urgent need to complete a review may also wane. You will probably submit the first review early, but after that… 
Despite declines in enthusiasm, review quality usually increases with the number of reviews you have done. Practice and experience make a difference. It is also a confidence boost to see your suggestions actually instituted and valued by the authors or editors.

Manuscripts fall broadly into only a few categories. They might be deeply flawed and unpublishable, and therefore easy to review; or they might be uniformly excellent and therefore easy to review. But these are the least common types you will experience. Most manuscripts have both strengths and weaknesses and fall somewhere on the spectrum between “accept” and “reject”. These are the papers that take the most time, since you must weigh the flaws against the strengths, agonize over what changes to suggest, what suggestions might get them around the biggest issues, and what recommendation to give the editor. It’s also easy to fall into Monday morning quarterbacking and make impractical suggestions - why didn’t you design your experiment like this? Why didn’t you measure that? While these points might be reasonable and relevant, but it is important to be clear as to what is within the scope of a revision and what is a bigger picture problem.

Reviewing is of course an important service to ecology. It can also makes a number of subtle contributions to your own professional development. Once the novelty of someone caring about your opinion has worn off, the best part of reviewing may be things you don’t expect.
  • For example, one of the best parts of reviewing a paper in the same area as your research is seeing what literature the authors cite and how they cite them– some real gems you've missed can show up. 
  • Reviewing a paper that falls so exactly in your body of knowledge that you feel completely qualified is a great feeling. It’s nice to be reminded that you have (mostly) mastered a topic you care about.
  • When you are asked to review a paper that combines some topic or method you are well-versed in with ideas or systems or methodologies you are not familiar with, it can be truly eye opening. The funnest papers to review are the ones where you think “I never thought of that!”.
  • Reviewing can give you the clarity to recognize the weaknesses in your own work.

Thursday, August 22, 2013

Quotes that stick. #INT13

I'm back in Toronto now, and here are some quotes from talks that have really stuck with me. INTECOL was a great meeting, it was very interesting to hear about all the research from around the world. I hope all the attendees had a great time.


Sandra Diaz: “We just don't know enough to understand how functional diversity links to environmental change and ecosystem services.”

Erika Edwards: “big phylogeny, big trait data set analyses leave me feeling a little empty”

Erika Edwards: “carbon economy is part of the whole organism, not single traits.”

Joel Cohen: “Mathematics is like sex, you can talk about it but you shouldn't do it in public.”

Enrique Chaneton, Describing what happen during a study looking at the effects of grazing on ecosystem decomposition rates: “A volcano erupted during the study and sometimes shit happens, ….. the volcano killed many of the cattle.”

Carsten Meyer, Talking about global data availability in large databases: “Countries that under report are large emerging economies (china, India, Brazil, Russia) which could finance these efforts but for some reason do not.”


Ove Hoegh-Guldberg, ‘To get change we need to reach more than the brain, but the human heart”

INTECOL & the future of community ecology for infectious diseases – August 21st 2013 - #INT13

This year's conference has a strong focus on infectious disease which included today's symposium Community ecology for infectious diseases organized by Joanne Lello.

Throughout the symposium a great deal of interesting questions related to host-parasite interactions being addressed with a diverse set of methods ranging from the mathematical biology of Andy Dobson, to the experimental C. elegans / pathogenic bacteria systems of Olivier Restif and Gregg Hurst, the wild rodent systems of Heike Lutermann, Andy Fenton, and Owen Petchey, and the next generation molecular techniques employed by Serge Morand.

However, it was Robert Poulin the keynote speaker who set the theme of the symposium to which many of the speakers kept returning: What are the future directions of parasite community ecology? Dr. Poulin began the session with an overview of the recent trends in parasite ecology over the last few decades and Lawton's view that community ecology is a mess (Oikos 1999 – 84: 177-192). The initial research done on host-parasite interactions was centred within the one host – one parasite framework, often dealing solely with the effect of the parasite on its host. This was then expanded to the one host – multi-parasite level, often investigating drivers of parasite species richness among hosts via comparative analyses and occasionally extending to parasite-parasite interactions though the use of null models. Although the data were available beforehand, only recently has the field moved into the domain of multi-host – multi-parasite interactions, now focusing on questions of infection dilution, meta-analyses of parasite richness, and describing the networks of interactions within these communities.

Looking ahead into the future of this discipline, Poulin suggested that researchers should expand beyond simple topological networks of associations to include the strength of interactions, potentially via energy flow, and the use of network analyses on smaller scales using individual hosts. Serge Morand also highlighted the need to develop and incorporate parasite phylogenies into these multi-host - multi-parasite communities. His talk highlighted recent advances in next generation sqeuenceing and how these techniques can be applied to parasite communities. One obvious advantage is that through molecular phylogenetics researchers will be able to define and quantify a higher degree of parasite diversity, but additionally molecular markers can be used to uncover unexpected host diversity or identify species that may be difficult to distinguish through traditional taxonomic keys. Morand continued to press the application of new techniques in immunogenetics and the integration of methods in molecular epidemiology with the theory of transmission and community ecology.

Finally Andy Dobson posited that in addition to pressing forward with our research into infectious disease, it is imperative that contemporary researchers revist the “best hits” of the past and address important issues that have fallen to the wayside. Primarily Dobson pointed out that mathematically, aggregation and virulence of parasites have been shown as important factors for determining parasite co-existence. However, the concept of aggregation is often left out of contemporary discussions although it will be important to determine natural forms of the aggregation distribution and also to attempt to make the link between immunity and aggregation of parasites in a multi-host – multi-parasite community.

Whether incorporating novel molecular and statistical techniques, exploring previously unstudied model systems, or revisiting the context of contemporary research, it is clear that community ecology and infectious disease has a promising future and that it has progressed greatly from the mess Lawton made it out to be in 1999.

Tuesday, August 20, 2013

INTECOL day 2: Plenaries to rock you. #INT13


Today I had a number of journal related obligations (for the Journal of Applied Ecology -which is celebrating its 50th anniversary here at the conference) and I had time to attend just a few talks. I saw some great talks -especially by Tad Fukami on evolutionary priority effects, but I decided to only post my (inadequate) notes about two of the plenary talks today. They were great talks, and both of them really expanded my perception of human-caused effects on natural systems, in very different types of habitats. 

Ove Hoegh-Guldberg. Corals reefs and global climate change. Coral reefs occupy less that one percent of ocean area but one in four fish caught come from reefs, supporting 400 million people. In the Caribbean coral cover has drastically declined from 80 percent cover to about 10 percent. This has happened elsewhere too, Asia and Australia. In Australia, where coral reefs are well protected and financed, they are still declining. Human development, pollution from agriculture and over harvesting are the common local causes, but global warming and ocean acidification are major global changes. Marine systems are greatly warming, more than land, but very few studies in marine systems. Increases in sea temperature can result in mass coral bleaching and death of corals. Major bleaching events over the past two decades, killing significant proportions of coral. Even though temperature is the best predictor of bleaching, mortality is more variable and other factors may help corals recovery, and these other factors are what managers can influence. In the coming decades, warming temperatures will mean common widespread bleaching events, with some areas becoming too warm for corals. Based on large mesocosms that track local ocean temperature and co2 concentrations. With warming, the mesocosm reefs change into algal dominated systems, with fewer other types of species (e.g., sea cucumbers). Two scenarios to deal with climate change -mitigate or adapt. We need to mitigate within twenty years, reduce co2 emissions. To get change we need reach more than the brain, but the human heart. Partnered with Google to have street view for reefs (this is completely awesome -check it out here). This initiative is both science (mapping reefs) and important outreach, letting people experience diving. One billion people have visited with almost two million people 'dived' in the first week.

Nancy Grimm. Water systems in urban habitats. Populations around the world are moving to cities, and projections have over 650 cities with over a million people by 2025. Creates multiple stressors in urban ecosystems, and there is a new need to build knowledge capacity. Large proportions of people already live in urban areas with limited water supply, quality and delivery capacity. Eighty percent of the population lives in areas under threat of water scarcity, but some people have access to technological solutions that minimize this (e.g., arid USA). For others, ecological knowledge may help reduce this threat. Areas around the world are experiencing more heavy rainfall and flooding. The way municipalities deal with storm water is building hard channels and surfaces, but building ecological systems can better handle water and pollution. In the arid southwest, there are opportunities to retain storm water in semi-natural systems. Provides ecosystem services and denitrification.

Sorry for the brevity of the talk summaries -I'm working on a very full schedule!


Monday, August 19, 2013

INTECOL day 1: A day full of ecosystems #INT13

Note: These are some thoughts from the first day of INTECOL. –Sorry for the abruptness and lack of polish on these entries, there were many talks and I have little time for a proper composition.

*acronyms: BEF = Biodiversity and Ecosystem Function; GBIF = Global Biodiversity Information Facility

It is clear to me that INTECOL is the premiere ecological meeting. There are delegates from countries all over the world from 67 countries , with especially strong European contingents. The next INTECOL meeting will be in Beijing in 2017. This is a special INTECOL as this is the 100th anniversary of the British Ecological Society. The opening talk by Sandra Diaz was held in an immense auditorium at the ExCeL centre, with a couple of thousand in attendance.

Morning plenary:

Sandra Diaz: functional traits are at the core for understanding changes in biodiversity and how species contribute to ecosystem function. Theophrastus, Greek philosophers, created first functional groups. Looks at key traits for tens of thousands of species, only possible through TRY data base. Most variation explained by size ( height, seeds, etc.), second was leaf economy ( leaf N, Leaf area, etc). These traits define plant functional design. Densities low on the fringes of this trait space -physical challenges, and many of these species use human help for success (crops and weeds). Two dense areas in the trait space -big slow growing trees, and small species. Effect and response traits are important for linking environmental change to ecosystem services. These traits can be linked or decoupled, and could change management options.
Linking trait dispersion and values to ecosystem function is a new area, and so few studies. We just don't know enough to understand how functional diversity links to environmental change and ecosystem services.

 Sandra Diaz giving her plenary lecture


Tree of life in ecosystems symposium:

Lisa Donovan: how selective pressures influence evolution of biogeochemical cycling. Traits appear evolutionary labile, and reported on a common garden experiment to find genetic differences controlling traits. Nitrogen has phylogenetic signal but few differences between close relatives. Major differentiation within species and especially for different agricultural lines.

Erika Edwards: Need to move down to small scale to truly understand the evolution of traits that affect ecosystem function. She looks at the genus Viburnum. Need to think about whole organism traits. E.g., branching and growth pattern. This originates from tropics and reinvaded temperate regions repeatedly, and a mix of different and similar strategies emerged. growth patterns highly conserved, but leaf spectrum traits were not. Flowering time seems linked to carbon economy traits.

Amy Zanne: Evolution and biogeography of leaf and stem traits. Angiosperms originated in the tropics and understory woody species and spread everywhere and all types of morphologies. Most species are woody and not exposed to freezing, and lineages move back and forth in climate species but less so with growth form. lineages shift growth form first, followed by climate changes.

Cornwell. Evolution of decomposition. Differences in decomposition rates among different phylogenetic lineages. Did plant life go from fast cycling world to slow one during evolution. Experiment in common garden for decomposition rates. basal angiosperms (magnolias) has lower decomposition than eudicots, which has fast decomposition rates.

Afternoon plenary:

Joel Cohen. Taylor's law after half a century. Taylor's law has been verified but we don't understand it. Taylor's law states that the variance of a population is positively related to the mean population size. Further mean population size is correlated with body size. He showed that tree data supports a body size-variance relationship. Does it apply to food webs? Data from aquatic systems show this pattern across species. Why do we care about Taylor's law? Used for understanding fluctuations in epidemiology, conservation of endangered species and management of forestry resources. Can see the same variance-mean relationships in nonbiological data -computer data packets, weather data and stock market trades. No underlaying theory to explains these. Previous attempts, such as affects of competition, do not seem to affect pattern.


Biodiversity & Ecosystem function session:

Enrique Chaneton. Movement of large herbivores around the world, introduction of cattle versus reintroducing native extirpated herbivores. Little is know how these large herbivores influence forests. Multiple pathways of effect from changing plant composition and waste excretion, affects decomposition. Within an Argentinean park, sites on lake islands do not have introduced herbivores and compared to nearby mainland sites. Herbivores reduce vegetation cover by sixty percent. Trees and shrubs were particularly affected. Distinct composition shifts. Litter layer was substantially different. In dry sites, higher decomposition in ungrazed sites. Volcanic eruption during research 'sometimes shit happens' killed many of the cattle.

Carsten Meyer. Examined the completeness of species point data inventories. Looked at GBIF records and compare to known distribution maps. GBIF records are highly biased to North America, Europe and Australia. Species rich areas are almost absent from GBIF records. Not adequate for research or conservation. Funding, accessibility and human safety all at play for biases. These factors seem to differ among taxonomy, interestingly. Countries that under report are large emerging economies (china, India, Brazil, Russia) which could finance these efforts but for some reason do not.

Julia Koricheva. Tree species richness and genetic diversity on leaf miners. What is the relative importance of these two effects. Two experiments, one manipulating tree richness -up to five species, and another with up to eight clones of silver birch. Silver birch was in both experiments, so was the focus of leaf miner surveys. Tree richness affects miner richness, but not abundance. More leaf miner species with higher tree richness in first year, but not second. For genetic diversity, miner richness also increased with number of clones. Looked at effect sizes of two experiments and genetic diversity appeared to have a stronger effect on leaf miner richness.

Tommaso Jucker. Complementarity in functional groups enhances wood production. He noticed that there were eighty talks on BEF at INTECOL. Four species combinations two pines and two oaks. Biomass increased with richness, but looked at more detail, growth over the past ten years from wood cores. Both pines grew much better in mixture, but oaks only increase growth when other oak is present. Tree that benefit the most are small trees. For pines, wet year showed largest increase in growth, most room for complementarity.

Eric Allen. Direct and indirect effects of landuse on multifunctionality. Landuse intensity changes functions, it increases biomass but reduces bird diversity, flower cover, increases pathogens, etc. Used path analysis to compare landuse and biodiveristy as well as environmental variables. from this analysis, plant richness seems negatively correlated with multifunctionality. looked at groups of functions (e.g., production, soils, cultural). some plots shows strong indirect effects of richness for some functions.

Siobhan Vye. Responses to multiple stressor change. Examined stressors in coastal systems. Looked at how an invasive species affected community response to stress by experimentally combining species in mesocosms and manipulated nutrient enrichment and temperature. Invader increases productivity. The presence of the invader determined how the stressor influenced community functions.


Sebastian Meyer. BEF changes over time. A number of studies show that BEF experiments increase in strength over time. Examined how functions change over time using Jena experiment. How many different functions show changes over time? Over half of functions are influenced by diversity generally. He regressed the richness-function slopes across time, and about one third of functions showed increasing diversity effects over time. What are the mehanisms? The stronger relationships are driven by a combination of changes in high diversity treatments and changes in low diversity treatments.

Thursday, August 15, 2013

Everything you ever wanted to know about peer review, but were afraid to ask

The thing about peer review is that there isn't much of an education process. Maybe you've published a paper or two and experienced the process as an author, and then you're asked to start reviewing for other authors. It's a bit like the telephone game - you mimic the reviews you received, maybe noting what you liked and avoiding what you didn't like. But that's often all you have to go on, and when you're just beginning a little advice might come in handy. To that end, the British Ecological Society has just published a pretty useful Peer Review 101 text. This should be required reading for new reviewers.

http://www.britishecologicalsociety.org/wp-content/uploads/Publ_Peer-Review-Booklet.pdf

Monday, August 12, 2013

#esa2013 What ESA tells us about where ecology is going

The annual ESA meeting functions in a lot of different ways. There are the obvious: the sharing of ideas and work, the discovery of new ideas, methods or sources of inspiration, networking and job finding, social reunions. But it also functions as a kind of report on the state of the field (and that's not even considering sessions meant to explicitly do this, like the panel “Conversations on the Future of Ecology”). The topics and methods presented say a lot about what ideas and methods are timeless, what is trendy, and over many meetings, where ecology appears to be going. If you go to enough ESAs, you are participating in a longitudinal study of ecology (or at least your subfield).

I went to my first ESA five years ago in Albuquerque, NM. One of the things that struck me was that there were two Community Assembly and Neutral Theory sessions and many talks in those focused on tests of neutral theory, particularly looking at species abundance distributions (SADs) and various iterations of neutral models. There are usually still one to two sessions called Community Assembly and Neutral Theory, but five years later, I don't think I saw a single talk that looked at SADs for evidence of neutral theory (and only one or two talks that were named to explicitly include neutral theory). Instead, the concept first introduced by Hubbell has morphed from "neutral theory" in to something slightly more general, designated "neutral dynamics". This gets used in a lot of ways – most precisely, neutral dynamics are in the spirit of neutral theory, suggesting that population demographic rates are similar, allowing long-term co-occurrence. Sometimes this is cited with reference to equalizing fitness effects in a Chessonian framework, where similarity in fitnesses prevents exclusion despite overlap in species niches. But it also seemed to get used in a default sort of way, as the explanation for why niche differences between species weren't discovered by a study, or else "neutral" was used interchangeably with "stochastic". In any case, the pattern appeared to be a move from highly specialized and precisely defined usage of the term, to broader incorporation of the concept that had suddenly acquired several, often less precisely defined meanings. Instead of being the central focus of a few specialized talks, neutrality was commonly invoked as a minor theme or explanation in many more talks. It is not what I expected, but its continuing usage suggests that neutrality has developed a life of its own.

Other topics similarly seem to have taken on separate lives from their initial application; even over the short time I've been attending ESA. For example, sessions focused on simple applications of ecophylogenetics methods (overdispersion, clustering, using different systems) were relatively common 3-4 years ago, while there wasn't a single contributed session specifically named for phylogenetics this year. There was however many sessions in which phylogenetic work formed the backbone of talks that were about broader questions, including in the "Evolution, Biodiversity, and Ecosystem Function" session and the “Coexistence of Closest Relatives: Synthesis of Ecological and Evolutionary Perspectives”. In the best case scenarios, it seems like even over-hyped approaches may be used with more nuance in time, as people recognize what information these methods can and cannot provide.

Sometimes it did seem that there is a lag between when critiques of certain methods or ideas are expressed and when they actually get incorporated into research. I could be wrong, but it seems this is most common where the research is focused on particular study systems or species, and methodology may be driven more by precedent in the literature and criticisms may take longer to infiltrate (since they aren’t the main focus of the work anyways). And unfortunately, the topics and sessions which appear to be timeless are those on human-related applications (restoration, climate change, invasion). Those pressures are sadly unchanging.

*The great thing to do would be map out changes in keyword frequency over the ESAs that have archived programs. Unfortunately, I don’t have the time/motivation.

Friday, August 9, 2013

Thursday, August 8, 2013

#esa2013 Day4: Sisters getting along, and our variable world

The talks I saw today were uniformly good and a number were excellent. At least half of them focused on the many implications for ecology of nature's innate variability. It appears that community ecologists have decided that now is the time to start considering the fact that the environment is not stationary, which was long a default assumption in most theoretical and empirical work. Many of the talks I saw reflected this changing approach. The other half were part of a symposium organized by Sharon Strauss that looked at coexistence among sister species. This topic, combining as it did large-scale evolutionary and biogeographic processes with local competitive interactions made for a broad range of talks and some interesting attempts to reconcile different methodologies and scales.

Our variable world

Many of the past studies on environmental variability and coexistence involve desert winter annuals. Desert winter annuals are limited by available water, and the yearly rains vary greatly in the amount and timing of onset. The hypothesis is that variable germination (via prolonged dormancy in seedbanks) may allow desert winter annuals to reduce the variance in their fitness between years. Alejandra Martinez-Berdeja presented some tidy hypothesis testing using biogeographical gradients: if variable germination is an adaptive response to variable precipitation, she hypothesized that differences in germination variability might be expected where precipitation is more or less predictable. Looking at the three North American deserts, she predicted that variable germination would be greater where rainfall was more variable (bi-seasonal) compared to winter rainfall deserts. She measured the involucres (dispersal structures determining seed release) on collected seeds and found that indeed they were larger in more variable rainfall deserts, producing greater variability in seed release. Further, in winter rainfall deserts, variability in the size of involucres was correlated with variability in rainfall at a site, again suggesting a link between germination variability and rainfall variability. Her next step will hopefully be to expand the tests look at the effect of autocorrelation in rainfall likelihood on bet-hedging, since this should increase selection for bet-hedging type adaptations.

David Vasseur gave a great talk showing how extreme environmental conditions--which we are seeing as part of the changes in mean and variance of the climate--could have particularly detrimental effects on population growth rates. Species have temperature performance curves that reflect the relationship between their fitness and the temperatures they experience. Vasseur showed that in the tropics, species tend to have much narrower temperature ranges over which they can grow and survive than species in the temperature regions, and experts agree that these narrower curves give tropical species less ability to deal with increasing temperatures. But variability is rarely considered in this equation. When variability is present, long-term species fitnesses will be subject to Jensen's inequality (nonlinear averaging) mean that shape of these performance curves is additionally important: that in some situations (concave curves) variability is particularly detrimental, and in some situations (convex curves) it may have a beneficial effect. Vasseur then used models to show that as temperature variation increases, it is increasingly likely that its effect will be negative, and high variation will produce high extinction rates. In fact, on average Vasseur predicted that temperature variation would have negative effects, a concerning conclusion.

Sisters getting along

This organized symposium was advertised as: “Whether closest relatives coexist reflects the often opposing effects of limiting similarity, mode of speciation, reproductive isolation, niche conservatism, competition and facilitation, which may be strongest in sister taxa; using new phylogenies, niche models, and experimental approaches, we explore coexistence in closest relatives in both plants and animals.” It was an interesting and useful idea – sister species (species who are each other’s most recent relative) are an important tool to understand how evolution, biogeography, and ecological interactions determine coexistence. The content of the symposium provided a number of example systems, methods, and approaches that suggested this was an important but still far from cohesive area of work. Mark McPeek spoke about the damselfly work he has done over the last many years, which shows that sister species are sympatric and ecologically identical, co-occurring happily through neutral dynamics. In contrast, Richard Glor talked about his work with Hispaniola anoles, where biogeography is an explanation for radiations, close relatives use different microhabitats and rarely compete locally and traits are divergent among close relatives. Looking at California plant species, Brian Anacker’s talk suggested something in between these extremes. A broad survey showed that 80% of sister pairs were sympatric, range overlap was modest but not uncommon, but asymmetry in range size was high. Ecological differences between sister species were not particularly clear in the handful of traits he examined, not even for reproductive traits. Sister species can and do co-occur, although not in large portions of their ranges. Having established the current state of knowledge, hopefully the symposium will stimulate greater focus on the construct of sister species as a way of understanding coexistence at multiple scales.

Finally, not being willing to miss another talk with the word “derby” in the title, I attended Daniel Atwater’s talk, “Is competition among plants like a boxing match or a demolition derby? Why competitor suppression may not matter in plant communities”. Atwater argued that there were two ways to win at plant competition – be good at suppressing your competitors, or be good at tolerating them. When in competition with a single individual, being a strong suppressor should be favoured, but in competition with multiple species, tolerance may be a better strategy. That’s because resources spent on suppressing one competitor may also benefit any other species involved in the competition. In such cases, tolerance of your competitors may provide the greatest benefit. (Apparently this scenario is like a successful (but frowned upon) strategy (sandbagging) in a demolition derby). Atwater used experimental data from blue bunch grass grown in competition with spotted knapweed to parameterize a model in which he found the optimum strategy in single versus multi-species competitions. The model agreed with his hypothesis that tolerating competitors is favoured when multiple species are competing. Although I am not clear on whether competitive strategies are easily classified as tolerant vs suppressing it was an interesting talk, and left me thinking about new questions.

ESA 2013 Day 3: Bolkerisms

All the best quotes that I caught today were undeniably from Ben Bolker, who also gave an interesting talk.

"The hallmark of great theoretical ecology is that it is obvious in hindsight. When you explain it to someone, they say well, of course."

In relation to a philosophical issue: "That's a beer question, not a coffee question".

To explain the reason he and his coauthors chose to build a model to explore the question, Bolker showed a Dilbert cartoon illustrating the truism "When all you have is a hammer, everything looks like a nail".

Only one full day left to go, and it looks like it will be a good one!

ESA 2013, day 3: Like a kid in a candy store.

Sometimes there are moments in my career where feel truly fortunate. Today I was fortunate enough to be a speaker in a session on evolution, biodiversity and ecosystem function. The other talks in this session were outstanding, full of amazing insights into how historical evolutionary dynamics affect modern-day ecological patterns. The presentations were followed by a fantastic panel discussion stimulated by thoughtful questions from the audience. The talks covered a range of topics from including species interactions in models of evolutionary change to using traits to understand coexistence to trying to find patterns when close relatives do not coexist.

The first talk from Luke Harmon on finding phylogenetic signatures on species interactions was incredible. He is an entertaining speaker and included references to his kids finding leaf cutter ants.  He show us how one could fit phylogenetic models that include coevolution. The negative effects of coevolution should affect trait evolution and one should see this signature in variance-covariance matrices. Random evolutionary change generates covariance between species. Stabilizing selection will remove this covariance, while with competition there should be negative covariances apparent. From models we see an interesting signature where older species are able to diverge and fill niche space (thus diverging rapidly) while later species are constrained in their evolution (thus remaining similar). Older species can contribute more to ecosystem function because of historical competitive effects.

Next was Nathan Kraft talking about how traits can potential shed light on fitness and niche differences in coexisting species. In a plant experiment with focal species grown alone and at different densities with competitors, he showed that very few pairs met the conditions for coexistence. For those that do appear to be able to coexist, no traits were associated with fitness difference, but several traits appeared to be associated with fitness differences. Multivariate analyses  showed that an assortment of five traits collectively appeared to be associated with niche differences. Some of these traits appeared to also explain fitness differences, revealing the complexity in assigning traits to specific ecological effects.

In Jeannine Cavender-Bares’ talk, she examined how evolutionary transitions in seed dormancy helped explain modern day ecological patterns in the Fabaceae family (the pea and bean family). The Fabaceae includes species that have dormant and non-dormant  seeds. Dormancy should be favored in certain environments (e.g., less predictable and poor environments). Large seeds are much less likely to be dormant, as well as those occurring at lower latitudes. Historical transitions in dormancy seemed to be correlated with changes in temperature lineages experienced.

Finally, Sharon Strauss critically examine dhow to separate history form ecology. We need to be cognizant of scale effects, where larger scale observations will include more close relatives than we usually see at local scales. Communities contain ‘ghosts’ of past competition and assembly. If species originate allopatrically (in separate places), then we expect that close relatives should not coexist, which can skew our inference about how ecological differences have evolved. Within habitats we seldom see closely related species coexisting . She gave a number of great Californian examples of species appearing to co-occur at large scales but not locally. For example, Limnanthes plants occur in the same region but species never co-occur in the same vernal pool.


These talks represent the collective excitement about the fact that we are entering a new synthesis in ecology. Evolution is required to understand ecological patters and ecological interactions are need for understanding evolutionary change. These talks exhibited where the forefront of this synthesis is, and it was a great afternoon of talks.

Wednesday, August 7, 2013

ESA Day 2: The problem with statistics...

These are just my favourite quotes from talks on day two of ESA:

(All from great, but anonymous, speakers)

After showing the results of a spatial statistics test: "...But still I was worried because that would be using statistics to prove something and that feels wrong."

On being asked how the speaker quantified earthworm abundance: "I used a non-invasive electroshock technique".
(I'm sure this is normal procedure, it just sounds hilarious to the uninformed).

Tuesday, August 6, 2013

ESA day 2: The shampoo salesman and new questions.

Day two started off on a high note with Bernhard Schmid's talk on evolution in biodiversity-ecosystem function (BEF) experiments. He is one of the originators of the Jena biodiveristy experiment, for years they have been maintaining plant species in monocultures and in polycultures to assess how much more ecosystem function is produced by multi-species assemblages over single species monocultures. However, it occurred to Schmid that species in these two contexts face different pressures, which may have resulted in evolutionary changes. In monocultures, species face high intraspecific densities and thus competition is severe, as is negative indirect effects like pathogen sharing and herbivory rates. Within polycultures, intrraspecific interactions may involve niche differences, with opportunities for character divergence to further stabilize coexistence. He reported on an experiment that took seeds and cuttings from monoculture and polyculture populations and grew then in monoculture or polyculture. He showed that individuals originating from monoculture did better in monoculture and species originating from polyculture did better in polyculture. The implications are fascinating. If the rate of evolutionary change in performance are equivalent between monocultures and polycultures, the BEF relationships should remain constant. However, if the rates of change are greater for polyculture populations the BEF relationship should get stronger over time. Conversely, BEF relationships should became weaker if higher evolutionary change in monoculture. 

It was hard to top this talk, but there were several other impressive talks as well. Jacob Vander Laan used a country-wide dataset on aquatic insect diversity across the USA and showed that at larger scales, beta-diversity decreases with connectivity, but is seemingly unaffected by environmental heterogeneity.

Restoration is community assembly with management goals and Emily Grman gave an interesting talk on assessing the success of prairie restoration by accounting for management activities, landscape, historical and local abiotic factors. She showed that management activities were the most important, with species-rich sowings result in rich communities, even though many of the species are not those in the sown mixture. Sowing a high diversity of grasses did not increase diversity, but high diversity of forbes did. Other factors like landscape influences and local factors were not important.

Will Pearse examined plant diversity patterns and homogenization across six large urban centres. He showed that there has been little taxonomic homogenization, but substantial phylogenetic and moderate functional trait homogenization. Beyond the interesting questions about how urban centres may cause biotic homogenization is the new tools that Pearse created for these analyses, and that are available online. As a self described 'shampoo salesman', he created a general tool called Phylogenerator that creates a pipeline that makes estimating trees form sequence data more efficient -definitely a tool that ecologists should be using. He further created a way to quantify complex leaf shapes and has a tool available for that, called Stalkless.


All in all , this was a good day, one that has stimulated new questions and approaches. These talks got me thinking about some of my data and experiments and how I can extend them to new questions. 

Monday, August 5, 2013

ESA 2013 Day 1: Temporal variation, roller derby, and topics in between


With day 1 over, ESA 2013 was off to an excellent start. Minneapolis seems like a very friendly place, and I enjoyed perhaps the most chatty bus ride I've ever experienced. As always, I failed to determine the best point on the trade off plot between cherry-picking certain talks based on topic, speaker and friends, and staying put in a session with an interesting topic. Nonetheless I managed to see some really good talks.

Among them, I saw Lauren Shoemaker in the Theoretical Ecology section, who illustrated how to model the four metacommunity paradigms (I.e. species sorting, mass effects, neutral, and patch dynamics) with the Chessonian framework of equalizing and stabilizing forces. She illustrated how both deterministic and stochastic models could replicate dynamics from the four paradigms. This suggests that rather than the usual description of the neutral paradigm as stochastic and the mass effect and species sorting paradigms as niche-based and therefore deterministic, the terms niche and deterministic and neutral and stochastic should not be synonymous. Rather, in the Chessonian framework, fitness differences drive neutral-type dynamics and spatial niches structure the species sorting and mass effects paradigms. More importantly, the results show how the paradigms are just a few sets of points on the much broader set of parameter values that could describe metacommunity dynamics.

It must be funny for Peter Chesson to follow up a talk in which his name is used as an adjective. After the talk on the Chessonian framework, he spoke about the fact that environment is fluid and non-stationary, yet models of communities have almost always treated it as being at equilibrium. Since it is not, ideally models of community dynamics would begin to incorporate environmental variation, and ask questions more relevant to non-equilibrium systems. For example: when is long-term persistence expected, given this non-stationarity and can communities in a non-stationary system still be stable? He showed that including environmental fluidity into models doesn't mean that communities are necessarily unstable, for example, when spatial and temporal trends of environmental variation match, communities may be stationary.

In another of many good talks about temporal variation (seemingly a popular topic of late), Colin Kremer showed that altering the basic characteristics of abiotic temporal variation (amplitude, means, periodicity) changed the amount of diversity present as communities evolved over time. Temporal variation isn't a simple concept anymore than spatial variability is - it has different characteristics with different effects on ecological dynamics and needs to be considered in greater depth.

My biggest disappointment was that I had a time conflict and couldn't attend a talk titled "Significant changes in the skin microbiome mediated by the sport of roller derby".  No doubt I would have learned a lot.

Monday, July 1, 2013

Carnival of Evolution is up!

The latest Carnival of Evolution (#61 if you are keeping track) is up and running at Teaching Biology. It is the Crustie Lovin' Edition.

Friday, June 28, 2013

MacArthur's words still resonate 40 years on

I recently received an old library copy of “Geographical Ecology: Patterns in the Distribution of Species” by Robert MacArthur (1972). It’s the last book that MacArthur wrote before his early death to cancer. It is an ambitious book that connects repeated ecological patterns to mechanisms as broad as the earth’s rotations (producing climate as we experience it) and as focused as organismal behaviour.

But honestly, the thing that has struck me most so far as I read is the timelessness and wisdom in MacArthur's introduction. Issues ranging from focusing on questions versus systems, the value of repeated patterns, complexity, and what generality really means, aren't at all new.

“To do science is to search for repeated patterns, not simply to accumulate facts, and to do the science of geographical ecology is to search for patterns of plant and animal life that can be put on a map. The person best equipped to do this is the naturalist who loves to note changes in bird life up a mountainside, or changes in plant life from mainland to island, or changes in butterflies from temperature to tropics. But not all naturalists want to do science; many take refuge in nature’s complexity as a justification to oppose any search for patterns. This book is addressed to those who do wish to do science. Doing science is not such a barrier to feeling or such a dehumanizing influence as is often made out. It does not take the beauty from nature. The only rules of scientific method are honest observations and accurate logic. To be great it must also be guided by a judgment, almost an instinct, for what is worth studying. No one should feel that honest and accuracy guided by imagination have any power to take away nature’s beauty.

Science should be general in its principles. A well-known ecologist remarked that any pattern visible in my birds but not in his Paramecium would not be interesting, because, I presume, he felt it would not be general. The theme running through this book is that the structure of the environment, the morphology of the species, the economics of species behaviour, and the dynamics of population changes are the four essential ingredients of all interesting biogeographic patterns. Any good generalization will be likely to build in all these ingredients, and a bird pattern would only be expected to look like that of a Paramecium if birds and Paramecium had the same morphology, economics, and dynamics, and found themselves in environments of the same structure.”
--Robert MacArthur

It's interesting that an introduction written in 1972 is so relevant that it could have been written today. The pessimistic view is that ecology is just iterating through the same problems and solutions, or progress is slow. Or maybe classic books remain as classics because their authors understood and explored the issues at the core of the science and had the benefit of being there in the formative years. It's fun to see that when MacArthur thanks particularly four friends who influenced his work most, he means G. Evelyn Hutchinson, E.O. Wilson, Richard Levins, and Jared Diamond. I suppose any book influenced by the combination of all these scientists and written by MacArthur will always have something interesting to say. 

Wednesday, June 26, 2013

Evidence for the evolution of limiting similarity in diving beetle communities


In 2006, Marten Scheffer and Egbert van Nes published a very nice paper showing the outcome of simulated evolution of competing species. Their results showed how patterns of evenly-spaced clusters of species along a niche axis could evolve to minimize competition via limiting similarity. 
From Scheffer and van Nes (2006): Evenly spaced clusters of species along a niche axis (x-axis) evolved in response to competition.
Within any cluster along the niche axis, species tended to be more similar than expected. The results suggested that complex self-organizing clustered patterns might result from simple competitive limitations. Interestingly, although the original paper suggested that clustered patterns in size distributions are common, only now are these theoretical expectations about the evolution of limiting similarity being tested with data. In fact, though theory has long suggested that patterns of limiting similarity should evolve to allow coexistence between competing species, empirical evidence is rather lacking. Despite this, limiting similarity and competition are staples of ecological thought: for example, patterns of overdispersion in traits or relatedness are often used as evidence for the importance of competition.

The follow-up paper -Vergnon et al. (2013)- tests for the pattern predicted in Scheffer and van Nes (2006) using communities of subterranean diving beetles (Coleoptera, Dytiscidae) in Australia. These species have evolved for over 5 million years in isolated aquifers. If limiting similarity structured beetle communities, the authors predicted that there should be regularity in the spacing of species along a niche axis. If competitive interactions determine species' positions on the niche axis, then their absolute positions on the niche axis could vary between communities so long as their relative positions are evenly spaced. If, in contrast, niches are driven by environmental conditions, species in different communities/aquifers should have similar absolute positions along the niche axis.

The authors used a nice combination of statistics, modelling and observational data (34 communities of beetles representing 75 total species) to test for these predicted patterns. They used beetle size as the measure of niche position, since size is often an indicator of niche position and food availability and identity. For almost all aquifers, co-occurring beetles were significantly different in size. Further, species in different aquifers classified as occurring in the same size classes (small, medium, large), had different absolute sizes (i.e. the largest beetle in one 2-species aquifer was not similar in size to the largest beetle in another 2-species aquifer).  
From Vergnon et al. (2013): Absolute sizes of diving beetles in aquifers with 3 species present. The absolute size in a size class (large - black; medium - white; small - grey) varies between aquifers.
Although the absolute size of species differed between aquifers, the ratio of sizes (regularity of spacing on the niche axis) was highly consistent. Further, simulations of evolution of body size due to competition were capable of reproducing the observed size structure of the diving beetles.
From Vergnon et al. (2013): regularity of spacing between competing diving beetles (measured as the body size ratio). 

This paper does a nice job of integrating theory and data, and combining pattern and process. The focus is on testing contrasting predictions, and the authors use complementary approaches to test statistically for the presence of patterns and to demonstrate with simulations the relationship between the evolution of limiting similarity and the observed pattern. The evidence is suggestive that limiting similarity and not pre-existing environmental niches explains the size structure of communities of competing diving beetles. There are still questions about how far these inferences can be extended. For example, do we expect that predefined environmental niches are really the same across aquifers? How important is competition in these communities - at the moment, the authors only have minimal evidence of gut content overlap from a single aquifer. Further the low diversity of aquifer communities (~1-5 diving beetle species) means that the prediction of clusters of multiple similar species made in the original Scheffer and van Nes paper can't be tested. But the fact that aquifer diving beetle communities have low diversity and are very simplistic is beneficial for the authors. Patterns in diverse communities where multiple processes (predation, migration, etc) are important may be too complex to show clear evidence in observational data. Simple systems (including microcosms) are a good place to find evidence that a process of interest actually occurs. Whether or not that process is important across many systems is of course a more difficult question to answer. 

Friday, June 21, 2013

Movement patterns in populations of early academics

Sometimes of the perks of academic life are also the most difficult parts – frequent travel opportunities mean you are also frequently away from friends and family (and spend too much time in airports). The nature of the university job market provides global opportunities for work, but also means that in reality opportunities and circumstances can constrain you to places you wouldn't have chosen otherwise. Your friends will cover the world, but you will rarely be in the same room together. The apprenticeship-like nature of early academic positions means that you will move, probably many times, before you find a permanent position (if you do). 

I have a friend who grew up with diplomat parents, which meant her family moved to a new place in the world every few years. The result was that she often felt like she didn’t have a strong connection to any one place or group of people. Academia isn’t quite so extreme, but you can understand why after moving to one place for undergrad, another for a Masters and/or PhD, one or two more for postdocs, your interactions and place in the world can feel rather impermanent. It also means that, for better or worse, your social circle includes other academics, and they are also shifting from place to place. When I tell non-academic friends and family (who mostly have settled in a single place) about upcoming moves, they are often more excited than I am about the opportunity to pick up and go. No doubt this is a grass-is-always-greener situation, but I often think that the most notable and difficult aspect of academic mobility is that you end up saying goodbye a lot.

I wonder whether some of the academic ambivalence expressed is aggravated by this early, necessary transience. Certainly there is lots of evidence that residential mobility (i.e. moving) relates to higher mortality and lowered health indicators, though some studies suggest that this effect may be more true for introverts than extroverts (presumably because extroverts form new friendships more easily). Academics share this phenomenon with groups like military families and third culture kids. The commonality is that, with every move it becomes harder to define home as a particular place – it is more like an intangible connection to multiple places and people. And maybe that's not so terrible - a good friend who was raised by an academic suggested that the key is to redefine your life and friendships as being global rather than local. And eventually professors settle down (I can think of a few people who have been at one university for 30+ years). But in the interim there is always the not-insignificant tension between the costs and benefits of uprooting yourself every few years, and the slow loss of individuals who are not capable of this mobility, from the academic pipeline.

Felsenstein for SMBE president :)

A highly entertaining, somewhat relevant update to my post about Joe Felsenstein's 'dishonour roll'. Felsenstein is running for President of the Society for Molecular Biology and Evolution, and his personal statement is a must-read career retrospective. If you don't at least crack a smile, you might be taking science a bit too seriously...

For example: "[Felsenstein] has been President of the Society for the Study of Evolution, and imagines that he could be President of the SMBE, even though he has not yet learned the names of all 20 amino acids."

Honestly, I think it gives more insight than most bios into the person and their work.

Monday, June 17, 2013

Another round in Diamond vs. Simberloff: revisiting the checkerboard pattern debate

Edward F. Connor, Michael D. Collins, and Daniel Simberloff. 2013. "The Chequered History of Checkerboard Distributions." Ecology. http://dx.doi.org/10.1890/12-1471.1.

One of the most vociferous recent debates in community ecology started in the 1970s between Jared Diamond and Dan Simberloff (and colleagues) regarding whether 'checkerboard patterns' of bird distributions provided evidence for interspecific competition. This was an early and particularly heated example of the pattern versus process debate that continues in various forms today. Diamond (1975) proposed that the distribution of birds in the Bismark Archipelago, and particularly the fact that some pairs of bird species did not co-occur on the same islands (producing a checkerboard pattern), was evidence that competition between species limited their distributions. The issue with using this checkerboard pattern as evidence of competition, which Connor and Simberloff (1979) subsequently pointed out, was that a null model was necessary to determine whether it was actually different from random patterns of apparent non-independence between species pairs. Further, other mechanisms (different habitat requirements, speciation, dispersal limitations) could also produce non-independence between species pairs. The original debate may have died down, but the methodology for null models of communities suggested by Connor and Simberloff has greatly influenced modern ecological methods, and continues to be debated and modified to this day.

The original null model of bird distributions in the Bismark Archipelago involved a binary community matrix (rows represent islands, columns represent species) with 0s and 1s representing species presences or absences. Hence, all the 1s in a row represent the species present on the island. The original null model approach involved randomly shuffling the 0s and 1s, maintaining island richness (row sums) and species range sizes (column sums). The authors of a new paper in Ecology admit that the original null models didn’t accurately capture what Diamond meant by a "checkerboard pattern". This is interesting in part because two of the authors (E.F. Connor and Dan Simberloff) lead the debate against Diamond and introduced the binary matrix approach for generating null expectations. So there is a little bit of a ‘mea culpa’ here. The authors note that earlier null models captured patterns of non-overlap between species' distributions but didn’t differentiate between non-overlap between species with overlapping ranges compared to non-overlap between species which simply occurred on sets of geographically distant islands (referred to here as 'regional allopatry'). The original binary matrix approach didn’t consider spatial proximity of species ranges.

With this fact in mind, the authors re-analyzed checkerboard patterns in the Bismark Archipelago, but in such a way as to control for regional allopatry. True checkerboarding was defined as: “a congeneric or within-guild pair with exclusive distribution, co-occurrence in at least one island group, and geographic ranges that overlap more or significantly more than expected under an hypothesis of pairwise independence”. This definition appears closer to Jared Diamond's original definition and so a null model that captures this is probably a better test of the original hypothesis. The authors looked at the overlap of convex hulls defining species’ ranges and when randomizing the binary matrix, added the further restriction that species could occur only within the island groups where they were actually found (instead of being randomly shuffled through any island, as before).

Even with these clarified and more precise null models, the results remain consistent. True checkerboarding appears to rarely occur compared to chance. Of course, this doesn't mean that competition is not important, but “Rather, in echoing what we said many years ago, one can only conclude that, if they do compete, competition does not strongly affect their patterns of distribution among islands.” More generally, the endurance of this particular debate says a lot about the longstanding tension in ecology over the value and wealth of information captured by ecological patterns, and the limitations and caveats that come with such data. There is also a subtle message about the limitations of null models: they are often treated as a magic wand for dealing with observed patterns, but null models are limited by our own understanding (or ignorance) of the processes at play and our interpretation of their meaning. 

Monday, June 10, 2013

The slippery slope of novelty

Coming up with a novel idea in science is actually very difficult. The many years during which smart people have, thought, researched, and written about ecology and evolution means that there aren’t necessarily many easy openings remaining. If you are lucky (or unlucky) enough to know someone with an encyclopedic knowledge of the literature, it becomes quickly apparent that only rarely has an idea not been suggested anywhere in the history of the discipline. Mostly science results from careful steps, not novel leaps and bounds. The irony is that to publish in a top journal, a researcher must convince the editor and reviewers that they are making a novel contribution.

There are several ways of thinking about the role of the novelty criterion - first, the effect it has had on research and publishing, but also more fundamentally, how difficult it is to even define scientific novelty in practice. Almost every new student spends considerable effort attempting to come up with a completely "novel" idea, but a strict definition of novelty – research that is completely different than anything published in the field in the past - is nearly impossible. Science is incrementally built on a foundation of existing knowledge, so new research mostly differs from past research in terms of scale and extent. Let's say that extent characterizes how different an idea must be from a previous one to be novel. Is neutral theory different enough from island biogeography (another, earlier, explanation for diversity which doesn’t rely on species-differences) to be considered novel? Most people would suggest that it is distinct enough as to be novel, but clearly it is not unrelated to works that came before it. What about biodiversity and ecosystem functioning? Is the fact that its results are converging with expectations from niche theory (ecological diversity yields greater productivity, etc) take away from its original, apparent novelty

Then there is the question of scale, which considers the relation of an new idea to those found in other disciplines or at previous points in time. For example, when applying ideas that originate in other disciplines, the similarity of the application or the relatedness of the other discipline alters our conclusions about its novelty. Applying fractals to ecology might be considered more novel than introducing particular statistical methods, for example. Priority (were you first?) is probably the first thing considered when evaluating scientific novelty. But ideas are so rarely unconnected to the work that came before them, so then we evaluate novelty as a matter of degree. The most common value judgment seems to be that re-inventing an obscure concept first describe many years ago is more novel than re-inventing an obscure concept that was recently described.

In practice, then, the working definition of novelty may be that something like ‘an idea or finding doesn't exist the average body of knowledge in the field’. The problem with this is that not everyone has an average body of knowledge – some will be aware of every obscure paper written 50 years ago, and for them nothing is novel. Others have a lesser knowledge or more generous judgement of novelty and for them, many things seems important and new. A great deal of inconsistency in the judgement of papers for a journal with a novelty criterion results simply from the inconsistent judgement of novelty. This is one of the points that Goran Arnqvist makes in his critique of the use of novelty as a criterion for publishing (also, best paper title in recent memory). Novelty is a slippery slope. It forces papers to be “sold” and so overvalues flashy and/or controversial conclusions and undervalues careful replication and modest advances. And worse, it ignores the truth about science, which is that science is built on tiny steps founded in the existing knowledge from hundreds of labs and thousands of papers. And that we've never really come up with a consistent way to evaluate novelty.


(Thanks Steve Walker for the bringing up the original idea)

Thursday, June 6, 2013

Speaking the language: is jargon always bad?

You hear mostly about the evils of jargon in science. Undeniably jargon is a huge barrier between scientific ideas and discoveries and non-scientists. Translating a complex, nuanced result into a sound bite or recommendation suitable for consumption by policymakers or the public can be the most difficult aspect of a project (something Alan Alda, as part of his Center for Communicating Science, is attempting to assist scientists with). But sometimes the implication in general seems to be that scientific jargon is always undesirable. Is jargon really always a bad thing?

Even between scientists, you hear criticism about the amount of jargon in talks and papers. I have heard several times that community ecology is a frequent offender when it comes to over-reliance on jargon (defn: “words or expressions that are used by a particular profession or group and are difficult for others to understand”). It is fun to come up with a list of jargon frequently seen in  community ecology, because examples are endless: microcosm, mesocosm, niche, extinction debt, stochastic, trophic cascades, paradigm shift, priority effects, alternate stable states, or any phrase ending in ‘dynamics’ (i.e. eco-evolutionary, neutral, deterministic). Special annoyance from me at the usage of multidisciplinary, trans-disciplinary, and inter-disciplinary to all express the exact same thing. I don’t think, despite this list, that jargon is necessarily problematic.

If the meaning implied by the word or phrase is more than the sum of its parts it is probably jargon. Ideally, jargon is a shared, accurate shorthand for communicating with colleagues. A paper published without any jargon at all would be much longer and not necessarily clearer. Instead of saying, “we used protist microcosms”, it would have to say, “we used a community of protist species meant to encapsulate in miniature the characteristic features of a larger community”. (And arguably ecology is still relatively understandable for a newcomer, compared to disciplines like cell and systems biology, where an abstract might seem impenetrable: “Here, we report that, during mouse somatic cell reprogramming, pluripotency can be induced with lineage specifiers that are pluripotency rivals to suppress ESC identity, most of which are not enriched in ESCs.”)

Jargon is useful as a unifying tool: if everyone is using the same nicely defined label for a phenomenon, it is easier to generalize, contrast and compare across research. Jargon is many pieces of information captured in a single phrase: for example, using the term 'ecophylogenetics' may imply not only the application of phylogenetic methods and evolutionary biology to community ecology, but also the accompanying subtext about methodology, criticism, and research history. At its best, jargon can actually stimulate and unify research activities – you could argue that introducing a new term (‘neutral dynamics’) for an old idea stimulated research into the effects of stochasticity and dispersal limitation on community structure.

That’s the best case scenario for jargon. There are also consequences to developing a meaning-laden dialect unique to a subdiscipline. It is very difficult to enter a subdiscipline or move between subdisciplines if you don’t speak the language. New students often find papers difficult to penetrate because of the heavy reliance on jargon-y descriptions: obtaining new knowledge requires you already have a foundation of knowledge. Moving between subdisciplines is hard too – a word in one area may have completely different meaning in another. In a paper on conservation and reserve selection, complementarity might refer to the selection of regions with dissimilar species or habitats. In a biodiversity and ecosystem functioning paper, a not-very distant discipline, complementarity might refer to functional or niche differences among co-occurring species. Giving a talk to anyone but the most specialist audience is hampered by concerns about how much jargon is acceptable or understandable.

Jargon also leads to confusion. When using jargon, you can rely on understood meaning to delimit the boundaries of your meaning, but you may never specify anything beyond those boundaries. Everyone has heard a 30-second spiel so entirely made of jargon that you never develop a clear idea of what the person does. The other issue is that jargon can quickly become inaccurate, so laden with various meanings as to be not useful. The phrase ‘priority effect’, for example, has had so many particular mechanisms associated with it that it can be uninformative on its own. And I think most ecologists are well aware that jargon can be inaccurate, but it’s a difficult trap to get out of. The word “community”, essential to studying community ecology, is so broadly and inconsistently defined as to be meaningless. Multiple people have pointed this out (1, 2, 3) and even suggested solutions or precise definitions, but without lasting impact. One of the questions in my PhD defense was “how did I define an ecological community and why?”, because there is still no universal answer. How do we rescue words from becoming meaningless?

Something interesting, that you rarely see expressed about jargon is that linguists tells us that language is knowledge: how we understand something is not independent of the language we use to describe it. The particular language we think in shapes and limits what we think about: perhaps if you have many ways of finely delineating a concept you will think about it as a complex and subtle idea (the 100-words-for-snow idea). On the other hand, what if you have to rely on vague catch-alls to describe an idea? For example, a phrase like ‘temporal heterogeneity’ incorporates many types of differences that occur through time: is that why most researchers continue to think about differences through time in a vague, imprecise manner? Hard to say. It is hard to imagine where community ecology would be without jargon, and even harder to figure out how to fix all the issues jargon creates. 

Friday, May 31, 2013

Some ways you might not expect your research to be used

Most ecologists recognize that ecological knowledge is a tool, with useful applications to conservation and management, recreation, and ecosystem services and goods. Many of us have even written or said something suggesting uses for our work, no matter how likely. But few ecologists expect their research to be cited for military applications or support for the superiority of capitalism.

For example, a recent editorial in the New York Times detailed how conservation of biodiversity became part of American Cold War strategies. In those days, the American military was considering the role for ‘environmental warfare’, and the research of Charles Elton, who wrote of the dangers of simplifying landscapes by reducing biodiversity resonated. Strategists advocated maintaining biodiversity in food supplies and stockpiles (wisdom which transcends the military motivation). Ecological research into invasive species has also informed the US military in modern times. For example, the report "Invasive Threats to the American Homeland" considers the possibility of introduced species being used as terrorist weapons. Such introduced species might be crop parasites or vectors for human diseases, theoretically wreaking economic, structural, and human costs. 

Sometimes attempts to adapt research to other uses fall rather short of the mark. Evolutionary biology is not unfamiliar with this: for example, the misapplication of evolution to social Darwinism and some of the ideas touted in evolutionary psychology misrepresent evolutionary theory. This can happen in ecology too. A recent PNAS paper presented the result that evolutionary diversity increases ecosystem productivity. One writer in the Washington Post blogging community presented this finding as evidence that capitalist concepts like division of labour are found even in nature. It seems difficult to accept the link the writer attempts to make (the title is rather over the top as well: “Darwin’s free market wisdom: division of labor starts in the genes”). The writer states that nature wouldn’t exhibit a relationship between diversity and higher productivity if it wasn’t optimal, so “[t]he same findings would also appear to suggest that species, like humans, are not all created equal and some are more adept at certain tasks than others.” Therefore, apparently, capitalism is superior to communism. 

This kind of thing makes me think that Darwin was lucky that he did not live to see his words and ideas so frequently misquoted and misapplied (although he certainly suffered this during his own lifetime). This is the danger of sending an idea or result into the world: you no longer fully control how it is used and understood. A successful idea is one that, for better or worse, has an independent life. 

(There are probably many misapplications or unusual uses of ecology and evolution that I haven't thought of. If you think of other examples, feel free to mention them in the comments.)

Wednesday, May 29, 2013

Has academic advancement changed your point of view?


We regret to inform you that you paper has not been accepted
as a graduate student:
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as a postdoc:

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 as a professor:
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We are pleased to inform you that your paper has been accepted
as a graduate student:
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as a postdoc:

as a professor:
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