Cool Nature paper on how to predict success.

http://www.nature.com/nature/journal/v489/n7415/full/489201a.html

In the July issue of PNAS, Fawcett and Higginson argue, based on statistical analysis of citation rates, that a high density of equations will increase citation by theoreticians, but reduce citations by nontheoreticians even more. They advocate putting a minimum of equations in the main text, move everything else to the (online) appendix, and insert a maximum of verbal explanations of each equation.
This sounds trivial. Don’t we teach all our students to leave out unnecessary maths in presentations and manuscripts? Apparently this is easier said than done, as we still see very equation-rich papers in journals for the general ecological and evolutionary audience (such as Oikos). The reason may be that “necessity of equations” is subjective. For a thorough understanding, a full mathematical derivation seems indispensable, and hiding it from view by putting it in an appendix may also hide it from peer review. This may be good for the author (higher acceptance probability and more citations), but can be detrimental for science, and in the long run also for the author: there is nothing more terrifying for a theoretician than being confronted with an error in a derivation after publication, please let it be found during peer review!
Hence the theoretician faces a serious dilemma for which I have no full solution, only a couple of recommendations. To minimize errors, find collaborators that can check your derivations (so editors, be suspect of single author theoretical papers). A thorough verbal explanation of a model’s assumptions (and some of the derivation) may not only aid the reader, but may also advance the author’s own understanding of his/her work: when a theoretician has difficulty explaining what he/she is doing, the work is either unrealistic or incorrect. And, something Fawcett & Higginson did not analyse in detail, use simple equations: avoid Greek or curly symbols whenever possible, divide the equation in pieces where each piece has a clear meaning. Finally, when you’re really reluctant to banish your cherished formulas to an appendix, use a box. A box is really an inline appendix, and may represent the best of both worlds. Remember to think out of the box!

Rampal Etienne, SE Oikos

Each year, at the Oikos meeting, Oikos and Wiley/Blackwell together with the Per Brink Foundation, awards the Per Brink Oikos award in honor of Professor Per Brink. This year’s laureate, Prof. Tim Coulson from Imperial College London gives you below a short version of his paper entitled “Integral projections models, their construction and use in posing hypothesis in ecology”.

More about the award is found in the Editorial for the September issue 

At any point in their lives individual can be measured for a large number of characters.   These characters might be genotypes at a specific locus, age, body size, the ability to fight disease and behaviours.  Some characters might be continuous, some might be discrete.  Population level distributions of these characters can be constructed at each point in time.  Over time, a population level character distribution might change as individuals are born, die and develop.  Any population can consequently be considered as a temporally fluctuating character distribution.  Population biologists – be they life history theorists, quantitative geneticists, population geneticists or population ecologists – work with statistics that summarize aspects of the dynamics of character distributions.

Integral projection models provide a way of modeling the dynamics of character distributions.  Recently, a number of biologists including Steve Ellner, Mike Dixon, Mark Rees, Shripad Tuljapurkar, Dylan Childs, Jessica Metcalf, Peter Adler and I (to name a few), have worked on developing and applying integral projection models to address a number of questions in ecology, life history theory, micro-evolution and longer-term evolution.  A growing body of research has revealed that these models can be relatively easily parameterized for both observation and experimental laboratory and field studies, and that they can be analyzed to provide novel insight.  Given the utility of the models, many researchers, including me, believe that their use will increase in future.  For this reason I felt writing a paper showing how they can be constructed and used could be useful.  In the Per Brinck lecture I gave this year I described integral projection models, their parameterization and analysis.  The Oikos paper that accompanies this lecture develops this theme, and I hope it useful to researchers who want to learn how to construct and use integral projection models. I hope it proves of some use.

I was surprised, delighted and honoured to be awarded the 2012 Per Brinck award, and I’d like to thank the Oikos society for selecting me to receive it.  The Karlstad meeting of the Oikos society was one of the most enjoyable meetings I’ve been to, and I plan to attend many of these meetings in the future.  I do hope my paper generates some interest.

Why being a Subject Editor at Oikos? And what does it really mean? Wim van der Putten, who has been Subject Editor at Oikos for many years, and for several other journals as well, gives you his answers:

Why would you submit your research papers to Oikos and what would you expect to read in this journal? Those are key questions that each Subject Editor has to answer every time a new manuscript is ending up on the digital desk. Before that happens, however, the submitting authors had to answer the same questions, as did the Editor in Chief and the Managing Editor, and later on the anonymous referees. If somewhere in this chain a weak connection shows up, the submitted paper will not appear, at least not in Oikos. In spite of the high rejection rate at Oikos, my experience is that simply addressing these basic  why-what questions results in a balance between papers for which I proposed acceptance and rejection that comes close to the acceptance-rejection final rate of Oikos and official complaints are rare.

I am Subject Editor for Oikos since 2007. As in all journals that I was involved in as Subject, or Handling Editor, the atmosphere is nice, personal, involved, and, quite important, professional. The way how decisions are made may differ among journals. For example, in the case of the Journal of Applied Ecology, it was pivotal that the work presented should be both scientifically novel and practically applicable, which ruled out quite some submissions. On the other hand, in the case of Ecology Letters the question whether the paper presents excellent novel science that is of interest for a wide audience provides another sort of criterion and my experience is that reviewers often are quite outspoken on that issue.

My subject is terrestrial ecology, soil ecology, aboveground-belowground interactions, climate change and invasions. Quite wide and luckily I don’t get all papers in this area. All these papers get equal chance, provided that they are not narrowly focused. This may happen with for example soil ecological papers that are too obvious for specialists and not for a wider ecological audience. I think that Oikos is very suitable for soil ecological papers, provided that they are strongly conceptual. Those papers are, to my experience, very well cited in Oikos. Papers that deal with, for example, mesh sizes of soil sieving or a process in plant ecology that has already reported ten times, will not be sent out to reviewers. Also, papers that do not test clear hypotheses may not find their way through. Pleasantly, it is not too difficult to find referees, except in Summer or just before Christmas. I really don’t understand why authors submit their paper on the day before their Summer holyday starts. All potential referees may also be out for field work, hiking in the mountains, or whatsoever, which provides a hassle for the journals to find appropriate available referees.

Why would you be a Subject Editor? I see it this way. Progress in science depends on a peer review system and that depends on scientists who are willing to spend their time to handling and reviewing manuscripts for journals. When you wish to publish, but not to contribute to this process, you are capitalizing on time from others to keep the system running. That would be sort of cheating. I don’t get paid, so that my decisions will not depend on money, but on the question if I wish to make time available for this activity. The nice thing of being a Subject Editor is to send manuscripts out to who are the best experts in that field, ask their view and then weigh the outcomes. The difficulties are always in weighing contrasting views. It would be far more comfortable when all research would be published open access and I hope that we will gradually move towards that system, but there are many limitations and constraints as well.

For the near future, I hope that Oikos will be able to develop a strategy that facilitates easy availability of published work. It is very easy these days to send a request for a copy to the corresponding author, but that takes extra time and efforts, which is a real waste of money. Contents-wise, I think that Oikos is a great journal in the field of community ecology and that it might be developing even more profile into that area. Aboveground-belowground interactions and the rapidly developing area of analyzing the composition and functioning of networks in pristine ecosystems and those under (human-induced) global changes such as land use, climate change, and invasions are in my view perfect topics for Oikos and I hope to see some really great manuscripts in this area. I am ready for them!

Wim van der Putten

Here is a superb interview with Stephanie Hampton. She is the Deputy Director of NCEAS and one of the PIs on the DataOne project. Her talk at the esa 2012 meeting was very well received so I nabbed her for a chat.  The interview also includes suggestions for Oikos and journals in general. Also, she introduced me to some new terminology and thinking on the importance of data. I hope you enjoy it.

Hampton ESA 2012

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This project is cool, vibrantdata.org. Eric Berlow is one of the founders and is an ecologist with publications on food webs, interactions, alpine meadows, and the marine intertidal. This new project is bring together big data, designers, and Intel researchers to model and understand the dadta ecosystem they inhabit. Click on the research part and you will see the scope of data. Similar to the Ocean Health Index post below, this is another really nice example of ecological principles blending with social data. Here, they are using collective human input and network analysis to identify a few ‘under-nourished’ Grand Challenges for democratizing data. Wow, how can we help?

This is definitely novel synthesis. Here is the link to a really fascinating index that integrates both human and environmental condition estimates to provide a composite score of ocean health. It is also organized by public goals such as food provision, carbon storage, and provides a score for each. Canada beats Norway, Finland, and Belgium. Here is the link to the full details in Nature and the news reports.

I was wondering what ecofolks thought of this: http://bit.ly/cjlortie2. Oikos publishing a small data sample alongside each paper (when authors provide). This could be as simple as a small txt file or flat sheet showing the data structure with a few reps. Of course, an eml or link to the full dataset is preferable and should also be there, but it might be nice to at least have a little preview right there we could click on. In addition to this, we could publish a small file describing the meta-data, formally or informally, and could include a list of all factors and responses measured. This would be so fascinating. I don’t see this as impediment to full and open access to data. This would be a journal-level contribution to the process. It is also a teaser for readers to get the community wanting to see more data.

Here’s a quick interview about DataUp and how authors and journals can participate.

strasser DataUp

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Here’s a great interview from today at the esa about the open sci initiatives in eeb.

karthik ram – Broadband

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The 14th International Behavioral Ecology Congress is held in Lund on August 12-17 2012. Oikos is represented at Wiley’s stand, and I will be around from time to time.

http://www.isbe2012lund.org/

If you have questions about Oikos or issues you’d like to discuss with me, send a mail and we’ll set up a meeting.

Mail to oikos@oikosoffice.lu.se

Hope to se you in Lund!

Åsa Langefors

Managing Editor

A couple of weeks ago, the Oikos Editorial Office attended the conference “Editing in the Digital World”, organized by EASE (European Association for Science Editors) in Tallinn. Apart form giving us the opportunity to explore the midevial Estonian capital, it provided us with some really productive and creative inspiration.

It was especially two plenary talks that got us going on the new digital editing world. First, Deborah Khan from BioMedCentral, London talked about “Open Access and Digital Models”. We are heading there. Sooner or later. To Open Access. Yes, Oikos as well. The questions are just how and when? Deborah made it sound much easier than we had conisdered before, giving some answers to those questions. The answer to the second question is now: A bit sooner that we had counted on… The most tricky problem to solve first is of course the financial one (it’s always about money…). Who will pay?

The second inspiring talk was held by Alan J Cann from Annals of Botany, talking about “Social Media and Academic Publishing”. And here we are! In social media! The blog is a firts step already taken, but you can soon follow us on Facebook as well. What other social media should we be at? Where do you mingle?

Oikos’ former Managing Editor, now Director of the Editorial Office, Linus Svensson and Journal of Avian Biology’s Managing Editor Johan Nilsson. Herb beers served in medivial “glasses” at olde Hansa.

Big celebration with birthday cake for EASE turning 30! In City Town Hall.

We are very proud to have our own jazzsinger in the Oikos Editorial Board. I’m talking about our Subject Editor Lonnie Aarssen, Queen University, Kingston Canada.

When not holding the microphone in his hand, Lonnie is doing research within the field of Plant Ecology and Evolution. His special interest is in the development and testing of new hypothesis and conceptual models. These interpret adaptive strategies for growth, survival and reproduction, and how these strategies affect abundance, distribution, composition, diversity and productivity.

Lonnie has also started to bring evolutionary thinking to the area of Human Affairs, giving courses where students “apply Darwinian evolutionary theory to the interpretation of culture and human nature, and how these effects impact on civilization and the challenges it faces for
the 21st century.” Sounds really thrilling and interesting to me!

Lonnie is also Editor at the realtively new journal “Ideas in Ecology and Evolution”.

Read more about Lonnie here: http://post.queensu.ca/~aarssenl/

I have an announcement to make: I am leaving the Oikos Blog and starting my own blog, Dynamic Ecology. This was a difficult decision for me, and not one I took lightly. To understand my reasons for making this decision, you first need to know something about the history of the Oikos Blog and my involvement with it.

The Oikos Blog wasn’t my idea. The first I heard of the blog was when it was announced to the editorial board by Chris Lortie, the editor who was and remains in overall charge of the blog. The initial vision was basically that it would be a group blog: all the editors would post occasionally on whatever ecological topics interested them (here is a link to Chris’ video, introducing the Oikos Blog to the world). The hope, as I understood it, was that the blog would be a new way to promote the kinds of interesting conversations and new thinking that the journal had always tried to promote. Certainly, that was my own hope. I thought the blog was a great idea, a case of Oikos thinking outside the box and recognizing the potential of a new technology. There are lots of ideas in science that are worth sharing and discussing, but aren’t best shared or discussed via formal papers, or at least not only via formal papers. Besides being valuable in its own right, I had high hopes that the blog could help encourage its readers (especially students and postdocs) to take note of the journal’s content and support the journal as authors and reviewers.

At the time, I was reading a few blogs, but I’d never thought of blogging myself. But since the journal was starting a blog, I figured it might be fun to try it out. Plus, when colleagues ask me to do something, I try to default to saying “yes”.

So I started posting. I found that I enjoyed it, I seemed to be pretty good at it, and it didn’t take much of my time. But of course, everyone has to make their own time allocation decisions, and early on Chris and I were the only editors who chose to post with any frequency. I figured other folks might start posting once we built a bit of an audience, but that hasn’t happened. To be clear, I’m not criticizing my colleagues at all for this. Again, it’s up to each of us to choose how to allocate our time. I recognize that I’ve made an unconventional choice, and also that my circumstances (I’m a tenured professor in Canada) arguably make it unusually easy for me to allocate a bit of my time to blogging. But given the choices I and my colleagues have made, I don’t feel that the Oikos Blog is serving its original intended purpose as well as it could. Rather than functioning as an extension of the journal, I think the blog has become identified with me in the minds of many readers.

Which is something I find increasingly awkward. There are topics I would like to blog about, but which I avoid because they seem inappropriate even for a journal blog as broadly-defined as the Oikos Blog. There are also some new things I’d like to try that can’t really be tried on the Oikos Blog. I’ve also found that, in my own mind, I’ve started to think of the Oikos Blog as “mine”, which it isn’t. Over time, I’ve mostly stopped connecting my posts even tangentially to Oikos journal content, which is something I tried quite hard to do early on. And if someone at Oikos or Wiley were to (quite reasonably) suggest that the blog needs to develop some sort of tighter connection to the journal, I don’t know how I’d react. Which means it’s time for me to go.

I’m tremendously grateful to Chris Lortie, Dries Bonte, Tim Benton (our previous EiC), and other folks at Oikos and Wiley for coming up with the idea for the Oikos Blog, and for trusting me to run with it essentially as I saw fit (no one ever gave me any explicit or implicit instructions on posting, or exercised any pre- or post-publication review on my posts). I hope that I lived up to their trust. My decision to leave is entirely my own and in no way reflects badly on Chris, Dries, or anyone else at Oikos or Wiley. I’ve never had anything but positive feedback and support from everyone. Chris and Dries in particular (and Tim before Dries) have been enthusiastic about my blogging, and very understanding about my decision to move on, both of which I greatly appreciate. I continue to want to see the Oikos journal do well, and I’ll continue to support the journal.

I’ll also look forward to seeing what Chris et al. do with the Oikos Blog now that I’ve gone my own way. The Oikos Blog is not ending and you should definitely keep following it; I will. I’ve made some suggestions to my Oikos colleagues on cool new directions the Oikos blog could go, and I know Chris and other folks have their own ideas. Oikos Blog is going to change, but they’re going to be good changes. Right now, the blog and the journal are pretty independent. I think they can actually be greater than the sum of their parts, and I’m very much looking forward to watching that happen.

Finally, I hope you’ll check out my new blog, Dynamic Ecology. Initially, it’s going to be quite similar to my blogging for Oikos. Almost all of my old posts and the comments on them are archived over there. I already have some new content up, and I plan to try out what I think are some cool new ideas. Thank you very  much for reading my work on Oikos Blog, I’m tremendously flattered to have such a great readership. Looking forward to seeing you over on Dynamic Ecology.

Cheers,

Jeremy Fox

Evolution 2012 is over for me, couldn’t stay for the final afternoon. Highlight of the morning was watching my students talk, of course. They all did the Fox lab proud.

I enjoyed the meeting, and got out of it what I wanted to get out of it. I wasn’t blown away by the science the way I was in 2009, probably because I had a better idea what to expect, but it was still a very good meeting. It ran very well, a big thank you to the organizers, especially Howard Rundle and Andrew Symons, who I’m sure are glad to be getting their lives back in a few hours.

Time to get back to work–about which, more soon…

 

Susan Bailey’s discovery of synonymous beneficial mutations continues to be the talk of the meeting, or at least that portion of the meeting that I hear about.

Another good day for conversations. Had a good chat with Carl Simpson, a paleontologist who’s using Price equation-type approaches to quantify species selection and major evolutionary transitions. It’s a rare treat to talk to someone about something highly technical, but who comes at it from a slightly different perspective than you. So you totally understand and appreciate each other (so don’t have to work hard to make yourself understood), and you aren’t arguing with each other, but yet you each have something new to say to the other. Got to catch up with some old friends, and was flattered by multiple people coming up to say how much they like the Oikos blog (or just to ask my opinion on stuff!)

Saw Peter and Rosemary Grant talk; I’d never seen them talk before, so that was cool. Peter began with a (better translation of) this bit of verse from Lucretius.

A good day for talks by my collaborators. Rees Kassen was very good on the genetics of adaptation in microbes, he included some meta-analytical-type results from his forthcoming book. And Dave Vasseur was very good on eco-evolutionary dynamics in a spatial context, looking at how dispersal affects spatial synchrony of population dynamics on the one hand, and local selection and local adaptation on the other.

Had dinner at the Manx with Nick Rowe, an economist here at Carleton in Ottawa and a blogger for Worthwhile Canadian Initiative. Really enjoyed chatting with Nick about everything from Darwin’s life and times to the contrasting cultures of ecology and economics to how blogging makes you a better teacher.

Last day tomorrow, I won’t be here the whole day. Just long enough to see my students’ talks in the morning. Don’t know if I’ll be able to do a wrap-up post, or whether I’ll just end up skipping straight to the big announcement…

Fairly short tonight , I’m exhausted and I need to go to bed. Indeed, my exhaustion today caused me to embarrass myself when Elisabeth Pennisi, who writes for Science, asked me some questions about the meeting. I know who she is, I read her work every week, but I was so tired I just thought she was some random well-wisher. She was asking me questions about the meeting and I was just blathering semi-coherent responses. I realized what I’d done later and sent her an apologetic email with more sensible answers to her questions. But if anyone has somehow gotten the mistaken impression from this blog that I’m the slickest science communicator around, let me be the first to disabuse you of that notion.

The talk of the day for me was the very first one I saw. Susan Bailey talked about an extraordinary and totally unexpected result that cropped up in her work on experimental evolution of Pseudomonas fluorescens. She found not one but two synonymous mutations that increase fitness, by 6-8% (a quite non-trivial increase). The result is airtight: she transformed each of these mutations into the ancestral genetic background and showed that it increased fitness, despite being synonymous. Apparently “silent” mutations need not be so silent after all! She and her lab have some ideas as to how this could possibly happen, which they’re pursuing right now. Could be something like effects on rate of transcription or something. But even as it stands, just knowing what they know, it’s the most unexpected and potentially-important result I’ve seen so far.

Saw lots of stuff on evolutionary rescue today. Models and empirical work. Some of this stuff I’ve seen before, some of it was new to me. All of the experiments seem to work exactly as predicted. Always heartening to see real organisms behaving exactly the way theory says they should.

Also saw a really nice modeling talk extending Fisher’s geometrical model to the case of a directionally-moving optimum “chased” by an evolving population.  Actually had some relevance to the evolutionary rescue work. And made some predictions that would be totally straightforward (but a massive amount of work) to test with microbial evolution experiments. And I can’t remember who gave it as it wasn’t on my schedule until the last minute, and I’m too exhausted to look it up…

My own talk was today. Far from my best performance; I threw in some spontaneous jokes that ate up too much time. So I ended up running long, and the jokes didn’t even get very big laughs. The bit at the end that got cut off was just arm-waving speculation, so it’s not as if the audience missed out on too much, but still. Running long is a pretty amateur-hour thing to do for someone who’s done as many talks as I have. Hope I didn’t disappoint any readers who showed up assuming that my talks must be as awesome as my blog. I mean, I don’t think I was terrible or anything, and some folks were nice enough  to complement me afterwards, but I hold myself to high standards and I don’t really think I lived up to them today.

It was a good day for chats in the hallways with friends and colleagues, the sorts of conversations  that cause you to miss talks you were planning to see, but that’s ok because they’re good friends and good colleagues and good conversations. That sort of thing is why I love attending meetings like this.

And several people came up today and said how much they like the Oikos blog, which was really flattering. Thanks everybody! Keep watching this space, because I’m going to have a pretty big announcement to make in a couple of days…

Greetings from Evolution 2012 in delightfully summery Ottawa. My hometown of Calgary experienced an intense hailstorm centered on my house the day before I left for the meeting. I took this as an indication that it was a good time to get out of town for a few days.

The conference center is only about a year old and it’s great. Beautiful views of the canal and Parliament Hill. Just the right size for the meeting. Very easy to get back and forth between different rooms. Many of the seminar rooms are down short little hallways and so don’t open directly onto the main gathering spaces, which is good because it minimizes the noise from conversations outside the rooms.

And there are free boxed lunches! I didn’t know lunch was included. That was like the culinary equivalent of finding money in your pocket that you didn’t know you had.

p.s. In light of my deranged post about the chimes, I suppose you’re all wondering what I think of them. The answer is I don’t mind them as much as I thought I would, but I do mind them a little bit. I’d probably mind them less if they were having the intended effect more consistently. The first few talks I saw were very careful about using the chimes to time the talks as intended. But later in the day I saw many talks where one talk ended early, and so the next speaker started early, thereby defeating the purpose of the chimes. The presiders are presumably supposed to prevent this, but I think many presiders were just relying on the chimes and so not stepping in when speakers ignored the chimes. And as I expected, even when the chimes are adhered to, people are still coming in and out of the rooms while the talks are beginning and ending, simply because it takes more than 60 seconds to walk between even closely-spaced rooms. Please don’t get me wrong, I’m really enjoying the meeting, the chimes aren’t a big deal, and my opinion about the chimes is just my personal opinion. I’m sure many attendees think the chimes are great and many others don’t mind them at all.

Here are some highlights from what I saw today:

My colleague Sean Rogers did a great job summarizing his work on the genomics of ecological speciation in fishes. Very clear and very deft, compact and dense in a good way, without needing to resort to genomics jargon.

Tristan Long gave a great talk on a really clever experiment, selecting for fruit flies that can count. Yes, you can do this, apparently. You basically select for flies that, in response to an adverse stimulus, move towards a sequence of two light flashes rather than three, or three rather than four. And you have to be very careful about randomizing the properties of your flash sequences, to make sure the flies are “counting” the flashes rather than going by the total amount of time the lights are on, or the time between flashes, or the total time of the flash sequences. I envision a future in which math classes will be taught by highly evolved flies.

Anita Melnyk presented a nice series of experiments showing that Pseudomonas bacteria adapting to growth on xylose experience a more “rugged” fitness landscape than when adapting to growth on glucose. Which, as she noted briefly in the questions, is exactly the opposite of what you might have expected, given that these bacteria can metabolize glucose via two distinct biochemical pathways, but can metabolize xylose by only one. Predicting genotype-phenotype maps is hard, even for simple, well-known organisms; I’m curious if that’s something people will try to have a go at more frequently in the future.

Melanie Mueller talked about a very simple and elegant system using microbial colonizes growing on plates as a model system for studying selective sweeps in the context of populations undergoing spatial spread. Basically, it involves inoculating mixtures of different colored bacteria at a single point, and the resulting colony exhibits pretty, well-defined colored bands that change in size in predictable ways depending on the relative fitnesses of the different bacteria. Indeed, I actually wonder if the system is a little bittoo elegant, to the point of being too simple to really teach us anything new. It almost came off as engineering rather than science.

Andrew Furness talked about adaptive plasticity and bet-hedging in a really cool system, annual killifish that live in temporary ponds that dry every year. The timing of pond filling and drying is somewhat predictable (there’s a wet season, associated with reliable temperature and light cues), but somewhat unpredictable. And so as you’d expect, the fish lay diapausing eggs that initiate (and even pause!) development in response to cues, but that also develop and hatch somewhat randomly (thereby hedging their bets, rather than going “all in” in response to a possibly-unreliable cue).

Noah Ribeck explained how we’ve all been incorrectly estimating the strength of frequency-dependent selection (whoops!) The standard way to do it is to vary the initial relative frequencies of two different genotypes, then after some period of time measure their relative abundances again, and from that calculate what the selection coefficient was as a function of initial relative abundance. Which of course isn’t quite right, because you’re assuming that selection at any given initial frequency is constant over time, which it can’t possibly be in a system with frequency dependence (by definition, frequency-dependent selection coefficients change as relative abundances change). Noah derived the correct way to calculate selection coefficients for this sort of experiment, and showed that the resulting estimates differ substantially from those estimated via the usual method when frequency dependence is strong (so that relative abundances change a lot during the experiment).

Pedro Gomez did a nice poster asking how Pseudomonas fluorescens diversifies when grown under semi-natural conditions. In highly artificial lab conditions (unshaken, 6 ml batch cultures), P. fluourescens is a model system for adaptive radiation: it repeatedly diversifies into ecologically-distinct morphotypes, the two main ones being “wrinkly spreaders” and “smooths”, named for their colony morphologies when plated on agar. In nature, P. fluorescens lives in soil. And if you culture it in soil…wait for it!…it diversifies into the same frickin’ morphotypes as it does in batch cultures! Which is kind of amazing because the very specific spatial structure of batch cultures is thought to be what drives the repeatable diversification into these particular morphotypes, which occupy distinct spatial locations in batch cultures. Apparently this organism is a one trick pony! The match between the batch culture and soil diversifications is actually even tighter than that. In batch cultures you typically see a couple of different subtypes of smooths, and three or four subtypes of wrinklies–and you see all the same subtypes when you do the experment in soil! Now, it’s worth noting that in batch cultures you actually need rather specific culture conditions (e.g., specific growth medium) for the radiation to happen. And apparently those specific batch culture conditions are actually a really good analogue for this organism’s natural habitat! Who says laboratory microcosms are unrealistic?

Other notes:

“Eco-evolutionary dynamics” is hot. That kind of surprised me. I of course knew that it was hot in ecology, but I had thought that the proper evolutionary biologists would kind of dismiss it, since a fair bit of work by ecologists on “eco-evolutionary dynamics” treats the evolutionary side in kind of a weak way (a lot of it doesn’t, of course). But I’ve already seen a number of talks by people from proper evolutionary labs that sound just like the sorts of talks I’ve been seeing at the ESA meeting. Indeed, there’s a symposium on eco-evolutionary dynamics tomorrow that includes several speakers from a symposium on the same topic at the ESA meeting last year. I’m not complaining or criticizing this at all, it’s just something that surprised me a little.

Paralellism and convergence is hot. Under what circumstances is convergent evolution at the phenotypic level underpinned by the same mutations, or mutations at the same loci? But people mostly seem to be taking a case study approach to this. Maybe it’s just the brevity of the talks, but I haven’t seen any so far that have tried to place their results on this in a larger comparative or theoretical context. I don’t know, maybe we don’t yet have enough data or theory to make that worthwhile?

I saw a couple of talks on experimental bacterial evolution that pretty much came down to cross feeding (bacteria evolving to live off the metabolic waste products of other bacteria). That cross feeding evolves easily under certain culture conditions has been well-known for a long time, both experimentally and theoretically. I think it would’ve been nice to see recent work placed in the context of that literature–I wasn’t clear on if we’d learned anything really new about cross-feeding that we didn’t know before.

UPDATE: Post title corrected; it was late at night when I wrote it and for some reason I slipped into thinking I was at the ESA, where the first day of talks is always Monday.

A Canadian colleague has alerted me to a protest in Ottawa against the Canadian government’s suppression of scientific evidence, planned to coincide with the final day of Evolution 2012. Previously I’ve noted with dismay the government’s decision to cease funding the ELA; the protest organizers note that this decision can be seen as part of a larger pattern. The protest organizers (who have no connection to Evolution 2012 as far as I know) have set up a website which describes their motivation and plans. The protest will comprise a “Death of Evidence funeral procession” followed by a rally on Parliament Hill.

I emphasize that, in this as in all of my posts, I am speaking for myself, not for Oikos, its publisher, my employers, or anyone else.

I’ve talked in the past about how to network at scientific conferences–how to overcome any shyness you might have in order to talk to the people you’d like to talk to. The Evolution 2012 meeting is trying an interesting experiment on this. Poster presenters have been given the opportunity to browse the list of attendees and select a few to invite to their poster. Their chosen invitees then get an email from the conference organizers, listing the posters to which they’ve been invited and asking them to make every effort to accept the invitation.

This seems like a very creative idea to me, not something I’d ever have thought of.* I’ll be interested to see how it works out. I would think it would facilitate some interactions that wouldn’t happen otherwise. If someone looks through a list of thousands of people and invites you to their poster, that’s a bit hard to turn down (well, maybe not if you get a whole lot of invites, but I’m guessing nobody’s going to get more than a few invitations) And while some of those interactions might end up being brief or awkward–say, a student invites Dr. Famous to their poster purely as a way to meet Dr. Famous, even though Dr. Famous works on something totally different–I don’t see that as a big deal in the grand scheme of things.

On the other hand, I would encourage those who are using this system to consider whether it might not be more effective to email people personally if you really want them to come to your poster. Everyone’s busy and has lots of demands on their time. If you want someone to allocate some of their scarce time to come to your poster, it might be more effective to allocate some of your own time to sending them a personal email. Introduce yourself and your work, and briefly state why you’d like whoever you’re inviting to come to your poster. By putting in a bit of time and effort, you’re giving an “honest signal” that’s probably more likely to elicit a positive response, at least from people about my age and older.** Just a suggestion.

They’re only doing this for posters, not talks, and I think that’s the right call given that they’re trying this out for the first time. Most people already have lots of time conflicts when it comes to choosing talks, and so using the system for talks would probably result in many declined invitations. Don’t get me wrong, I think it’s great for people to invite each other to their talks, but for now that’s probably best done the old-fashioned way, via an email directly from the speaker to the invitee.

*Maybe it seems like a no-brainer to the younger generation, with their tweeps and their Bookface and their MySpace and whatnot. (MySpace is still a thing, right?)

**”Old farts”

Now up at Mousetrap. Includes a contribution from yours truly. Now you know what to read on the plane to Ottawa.

Here.

I swear by the techniques in panels 1 and 2. The techniques in panels 3 and 4 are totally beyond me.

It’s almost here: the biggest (~2400 attendees) evolution conference ever! I’m excited. I’ve only ever attended the evolution meeting once before, in 2009 in Idaho when it was much smaller because there were fewer societies involved. Evolution 2009 was the best conference I’ve ever attended in terms of the quality of the presentations, the standard of science on display was just incredibly high. I’m not sure how much of that was down to me knowing less about evolution than I do about ecology and so being more easily impressed than at ecology conferences, vs. me choosing talks well, vs. all the talks just being really good. But I think it was mostly the latter. So I’m psyched for this year’s iteration.

As with any big meeting (although this meeting actually seems a bit small to a regular ESA attendee like me), you can’t see everything and shouldn’t try. You need to have a focus. My focus reflects my goal to build up my currently-modest sideline of research in evolutionary ecology, using bacteria as a model system. I’m trying to identify some interesting questions I can address with experimental microbial evolution without doing genomics (as that’s still too expensive for me, and also very far from my training). I admit that it’s not entirely clear if this is still possible. One thing I took away from the 2009 meeting was that the genomics train hadn’t only left the station, it was more like a genomics rocket that was blasting into orbit, leaving people like me far behind (unless we collaborate with the people on the rocket, of course). My hope is that, even in the genomics era, there’s still a place for clever experiments describing and evolving interesting patterns of phenotypic and fitness variation across environments. The sort of experiments that would be cool to follow up with genomics–but that are also interesting in their own right.

So my focus for the meeting is experimental microbial evolution. That won’t fill my entire schedule, and so I’ll also be seeing talks by friends, a few talks by famous people who I haven’t seen speak (just to fill out my “speaker life list”), and some talks on other topics that just sound interesting. I’m also judging the student awards, so I’ve been assigned a few student talks. In order to maximize the amount of new stuff I learn, I’ll probably skip some talks by well-known folks who I think are mostly going to say things I’ve seen them say before.

I’ll also be looking to see if studies of “field model organisms” like Darwin’s finches, Caribbean anoles, and threespine stickleback are continuing to bear fruit. As David Hembry suggests,  the fact that we know so much about these organisms makes them powerful systems for asking questions that just can’t be asked elsewhere. But the fact that these systems are so famous and popular also increases the risk of bandwagony studies, and studies that just fill in minor details in a nearly-complete picture. Doing really original and important work in these systems is in some ways especially difficult, not especially easy.

So what am I going to see? I don’t have time to preview my entire schedule in detail, plus it wouldn’t necessarily be of huge interest unless your focus was similar to mine. But as a summary, I’ve scheduled pretty much everything on experimental evolution of bacteria, phage, and yeast. That includes a bunch of talks and posters from the groups of folks like Rich Lenski, Rees Kassen, Graham Bell, Mike Travisano, and others. Here are some talks on other topics that I’m planning to see, all of which should be very good, so I encourage you to check them out as well:

• Sat. 9:15, Canada Hall 2-3: Sean Rogers on Genomic approaches to studying speciation in postglacial fishes. You know how I said that genomics is taking off like a rocket? My Calgary colleague Sean Rogers is like the pilot of that rocket.
• Sat. 3:15, Canada Hall 2-3: Carl Boettiger on Detecting evolutionary regime shifts with comparative phylogenetics. Carl is super-smart, his talk at ESA last year on detecting early warnings of ecological regime shifts blew me away. Now he’s turning his attention to analogous problems in evolution. Looks like he has some really creative ideas in terms of both identifying the problem and on how to solve it.
• Sat. 3:45, Room 208: Andrew Furness on Adaptation to environmental unpredictability: phenotypic plasticity and bet-hedging in egg diapause. I think bet-hedging is cool (keep trying and failing to think of something I could do on it myself), so I want to see this.
• Sat. 4:00, Room 215: Leithen M’Gonigle on Sexual selection enables long-term coexistence despite ecological equivalence. I’m interested in coexistence, and results coming out of my own lab (see below) suggest that sexual reproduction combined with species interactions creates some novel effects on coexistence. This talk sounds like it might be broadly related. Plus, while I don’t know Dr. M’Gonigle, some of the co-authors (Sally Otto, Ulf Dieckmann) are among the best theoreticians going.
• Sun. 11:00, Canada Hall 2-3: Bronwyn Rayfield on Habitat connectivity and population dynamics in experimental networks. Bronwyn is sharp, she works with my friend and collaborator Andy Gonzalez, and like my students (see below) she works on spatial population dynamics using powerful lab-based model systems. So I really want to see this.
• Sun. 1:30, Room 201: Jeremy Fox on Local adaptation and maladaptation in space and time: aquatic bacteria as a model system. Yours truly will talk about what I think is a novel experimental approach, doing reciprocal transplants across time as well as space in order to test for local adaptation. Yes, you can do this; all you need is a “time machine” (to see what I mean you’ll have to come to the talk).  And I’ll be presenting what I think are some surprising results. And if that’s not enough incentive, there will be free beer.
• Sun. 4:00, Room 204: Ben Haller on Solving the paradox of stasis: Stabilizing selection and the limits of detection. Ben is a graduate student with Andrew Hendry. He won the “craziest thing you’ve ever done for science” thread by doing a simulation modeling study, the results of which required 2.5 billion regressions to analyze. I like to imagine Ben as Dr. Evil, putting his pinkie to his mouth and announcing that he plans to run one milllllllion regressions. Only to have a member of his committee clear his throat and whisper that one million regressions isn’t really all that impressive these days. To which Ben responds by going “Ok, two-point-five…[sidelong glance at committee member] billlllllion regressions!” (click the link if you have no idea what I’m talking about). In seriousness, this does sound like an interesting talk, independent of the whole “an-approach-so-crazy-only-a-grad-student-would-do-it” angle.
• Mon. 4:30, Room 210: Dave Vasseur on Local adaptation alters the impact of spatial population synchrony. David is a good friend and collaborator, but I’d go to this even if he wasn’t either. Because David is really sharp and gives a very good talk. This is a theoretical talk on eco-evolutionary dynamics, looking at the interplay of population cycles, dispersal, and local selection. Dispersal easily synchronizes population cycles over space, which you’d think would result in temporally-fluctuating but spatially-uniform selection pressures and hence lack of local adaptation. But it’s not as simple as that, because (if I correctly recall Dave’s summary of the talk) localized selection can alter the spatial synchrony of the system. I suspect every microcosmologist who sees this is going to rush out to try to be the first to test it.
• Tue. 8:45 am, Room 203: Stephen Hausch on Diversity, coexistence, and competitive ability: The effect of intraspecific diversity on invasibility and invadability in bruchid beetles. Full disclosure: Stephen is my student (co-advised with Steve Vamosi). Full honesty: this talk is really cool. In particular, if you’re into eco-evolutionary dynamics, you need to see this. Stephen has done a massive experiment looking at how intraspecific genetic diversity affects coexistence (mutual invasibility) in two competing species of bean beetles. The effects of intraspecific genetic diversity on species coexistence is an important, under-studied, and hot topic right now; the best current thinking on how it works was the subject of a major review in TREE recently. As far as we can tell, Stephen’s results can’t be explained by any of the ideas in that review.
• Tue. 9:00, Room 203: Colin Olito on The interacting roles of foraging biology, flowering phenology and trait evolution in determining pollination network structure. After you see Stephen’s talk, just stay where you are so you can see my second student, Colin Olito. It’ll be quite different than Stephen’s talk, but equally good. It’s a modeling talk, looking at how the structure of plant-pollinator interaction networks emerges from the underlying phenologies of flowering plants and pollinators and the foraging decisions of pollinators. A novel aspect of this model is incorporating eco-evolutionary dynamics. Pollinator foraging and species’ current phenologies creates selection pressures that shift plant phenologies (e.g., to avoid competition for pollinators), which feeds back to alter the pollinator foraging and thus the selection pressures. The model builds on previous work by Devaux and Lande, who radically simplified pollinator foraging and phenology. It is quite rich and complicated (as is necessary if you want to ground your model in reality rather than in mathematical convenience), but not intractably so. For instance, you can turn off different features of the model so as to ask how they affect the model behavior, particularly the long-run plant-pollinator interaction networks structure. If you, like Colin and I, are dissatisfied with theoretical studies of interaction networks that are disconnected from real plant-pollinator interaction biology, this is the talk for you.
• Tue. 11:00, Room 203: Geoff Legault on The threshold for dispersal-induced spatial synchrony in a model system. I can only assume that, in scheduling all three of my students for the final day, the organizers were trying to save the best for last. Geoff’s talk is on the latest results from my lab on spatial synchrony of population cycles. In previous work, we’ve shown in microcosm experiments that  dispersal between habitat patches “phase locks” the predator-prey cycles in those patches, so that prey populations in different patches all cycle  in near-perfect synchrony (i.e. in phase). This strongly suggests that phase locking may explain why cyclic populations in nature often are synchronized over vast areas. But it also raises a question: how does synchrony vary as a function of dispersal rate? In theory, the effect of dispersal rate on synchrony should be highly nonlinear, basically a threshold effect: you either have enough dispersal to produce phase locking, and thus very high synchrony, or else you don’t have enough, in which case you get no synchrony at all. We did an experiment to test that prediction, the first ever done in ecology as far as we know (analogous experiments have been done in fields like neuroscience, which deals with synchrony of neuronal firing).

Presenters at Evolution 2012 know about this, but I’m not sure if all attendees do: there’s a slick app for making your personal schedule. You can access if from any browser-equipped device. Its fully searchable as well as browsable, it auto-updates if there are cancellations (nice!), it includes profiles of all presenters and attendees (you can update your own profile to add all sorts of information). It also lets you take and email notes, but  I’m guessing most attendees already have their own preferred apps for doing that.

The ESA has had a browser-based scheduling app for years, and while I think it’s still pretty good, it’s not optimized for mobile devices and lacks some of the features of the Evolution 2012 app. Might be time for the ESA to look into upgrading.

The Dependent magazine wins the internet by estimating the population density of hipsters in Vancouver, using capture-recapture methods.

If they continue sampling and build up a time series, Ted Hart at UBC can show them how to estimate past hipster abundances.

HT Jeremy Yoder.

A mix of serious and silly advice on conferences, here.

HT American Naturalist, via Twitter.

FINAL UPDATE: The snark in this post is out of line, and for that I apologize to Howard Rundle and the other Evolution 2012 organizers. It was and remains true that I’m personally skeptical of the need for the chimes, based on my own experience over many years at an even larger meeting (the ESA). But as previous updates and Howard’s comment indicate, the organizers have good reasons for wanting to try the chimes. It was wrong of me to write a snarky post based on my own gut reaction to the idea without first checking in with the organizers.

As noted by Howard, myself, and others in the comments, it’s impossible to structure a large meeting in a way that will please everyone, so the only thing you can do is try to please as many people as possible. Which is exactly what the organizers are trying to do with the chimes. The chimes are an experiment, and the organizers deserve credit for carefully considering their options and deciding to give this experiment a go.

Evolution 2012 is going to be a great meeting, chimes or not, and it’s a massive amount of work to organize. Like all the attendees, I’m very grateful to Howard and his fellow organizers for putting this meeting together. And I appreciate him taking a bit of his very scarce time to stop by and clarify the reasoning behind the chimes.

In many elementary schools, a bell sounds throughout the building to indicate the end of one class, and a few minutes later another bell sounds to indicate the start of the next class. This practice is so common it’s given rise to popular slang, such as “saved by the bell“.

I have just received an email indicating that the Evolution 2012 meeting is going to work the same way (emphasis added):

You are scheduled to give a talk at the upcoming 1^st Joint Congress on Evolutionary Biology in Ottawa. The purpose of this message is to provide some additional information about timing. All talks in the general concurrent sessions are 14 min MAXIMUM, INCLUDING QUESTIONS. A building-wide chime system will be in place to help keep all concurrent sessions on time and in synch, and to allow 1 min  movement time for attendees to switch rooms between talks (as well as time for the next speaker to get set up ). Using the building PA system, a brief start chime will be broadcast every 15 min on the hour (i.e. at xx:00, xx:15,  xx:30, xx:45), and then a 2^nd slightly different ending chime at 14 min., 29 min, 44 min. and 59 min. past the hour. For example, if your talk is at 9:00 am, then it will begin with a start chime at 9:00 am and finish with an end chime at 9:14 am. 1 min later a start chime will indicate the beginning of the next talk (9:15 am). There will be a digital  clock in each room, situated so as to be visible to both the speaker and  the volunteer chair of each session, and it will be synchronized with the chimes.

It is unclear if attendees will also require hall passes to go to the bathroom.

I’m not looking forward to having my thoughts and conversations interrupted by chimes broadcast throughout the building every 15 minutes. Even if the chimes can only be heard in the seminar rooms (which I doubt), they’ll still be incredibly annoying. And no, I don’t think it will be worth it to avoid parallel sessions drifting 30-60 seconds out of sync with one another.

UPDATE: Just to be clear, the email also says that there will be a digital clock in each room, synchronized to the chimes and visible to both the presenter and presider. So the chimes are in addition to and not a substitute for clocks!

UPDATE#2: By the way, not all talks are 15 minutes–symposium talks and presidential and award addresses are longer. So those talks are going to have chimes sounding while the talks are going on! Correction: I am informed by the meeting organizers that the chimes will not sound in rooms hosting longer talks, with the exception of a small number of longer talks being held in one particular room that is also hosting shorter talks.

Hopefully, if enough people complain early enough, they’ll shut the chimes off. Peeps: start complaining on Twitter right now (#evol2012)!

UPDATE#3: And if you say “Well, we’ll get used to it”, my responses are (i) speak for yourself! and (ii) why the frick should we have to get used to it? If someone says to you, “I’m going to cause you discomfort twice every 15 minutes for no reason,” your response should not be “Ok, go ahead, I’ll get used to it.” (Plus, are you seriously claiming you’re going to get used to chimes going off during the longer talks?)

UPDATE#4: I have corresponded with some of the meeting organizers, who were gracious enough to reply very quickly to the concerns raised in this post. They said that the chimes are a response to complaints about parallel sessions getting out of sync in past years, they will be very short (2-3 seconds) and will serve only to indicate the time (as opposed to drowning out speakers), and now that the decision’s been made to use them it would cost $4000 to turn them off. (They also suggest that the chimes will be expected and therefore less bothersome than cell phones going off, but the relevance of this fact is unclear to me. You can’t justify deciding to disturb people by pointing out that other things disturb people even more).

So the organizers clearly had their reasons, and I certainly understand that it’s now too costly for them to change their minds. And I’m very glad to hear that longer talks (mostly) won’t be interrupted. I remain unconvinced that the cure is better than the disease here, but we’ll see–perhaps I and commenter Jeremy Yoder are in a minority on this. The reaction of attendees should reveal whether most folks prefer chimes to sessions drifting slightly out of sync.

It’s not why you think.

(warning: text a little NSFW)

Press release: The academic jungle: ecosystem modelling reveals why women are driven out of research. DOI: 10.1111/j.1600-0706.2012.20601.x
A large proportion of women and a growing number of men wish to work part-time in order to balance the demands of family and work.  However part-time employment in academia remains rare, and role models successfully balancing both teaching and research activities, are exceedingly rare.    There is a need to make part-time work more accessible and more viable in academia, in order to attract and retain more women in science and engineering research.   This paper identifies some of the most common and difficult issues faced by those working part-time in academia, and provides guidance about how to navigate around these.   It also identifies barriers faced by part-time academic staff which need to be addressed at a university level.

Assessing research performance of part-time staff is particularly difficult. Increasingly, research performance is assessed using metrics (such as number of papers, number of citations, h-index etc).   Application of these metrics can promote research output within an organization, however they can also undermine diversity.   In particular, research metrics are strongly biased towards full-time continuous employment, and penalize academics who take time off before becoming well established in their fields; e.g. women who part-time while raising their families.  This paper outlines the mechanisms by which metrics undermine the ability of women to participate in research if they work part-time.  This is done through an ecological analogy; just as a species is only sustainable if its population exceeds a minimum critical threshold, so too do researchers need to exceed a critical mass in order to attract more funding, students and high quality collaborators and so maintain their productivity.  In addition, the research production rate, analogous to the population birth rate, needs to exceed a critical rate if the population is to grow and survive –  these higher production rates are harder to achieve when part-time . A lower production rate is usually assumed to have a proportional effect on research outputs, but the ecological model suggests far more complex consequences on overall research productivity. If women have children before they are well established in their field, our model suggests that they will struggle to remain competitive.   This explains the observed drift of women from research to teaching, where performance is assessed on current rather than accumulated historical performance.

There are further analogies between ecosystems and universities: in both cases, diversity underpins resilience.  Optimizing a system, whether it be a forest or a faculty, to a narrow set of criteria is likely to undermine the ability of that system to respond to disturbance.   In the case of universities, over-reliance on research metrics could undermine the long-term quest for excellence by reducing the pool of talent from which our researchers are drawn.

The authors provide clear advice on how to address these issues:

• part-timers should be strategic and concentrate on either research or teaching; they need wise mentoring, and need to brave to be the “odd ones out” in a system overwhelming dominated by full-time continuous employment.
• university managers should use metrics cautiously, and implement schemes to ensure that part-time work and career breaks are not “one-way tickets” out of research.

This is pretty tangential, even for me, but I thought it might be of interest to some readers. Ecology, like many fields (including social science as well as hard science), is seeing a push towards data sharing becoming the norm rather than the exception (e.g., many leading ecology journals support the data sharing repository DataDryad). But in some areas, like politics, hard questions can be asked about whether Open Data is a good thing, or if it is a good thing, who or what it’s good for. Crooked Timber is going to be hosting a group discussion of Open Data, with a bunch of prominent and very sharp contributors, mostly from the social sciences. The focus looks like it will mostly be on Open Data in a government/politics context, but there might be something for those of you with more scientific interests. And of course, these two shade into each other, as I’m sure frequent commenter Jim Bouldin could discuss in the context of climate change politics and associated fights over access to raw climatological data.

If you can’t get enough of heavyweight intellectuals arguing about how to think about group selection, Steven Pinker has a lengthy post at The Edge, which has drawn responses from Dan Dennett and David Queller, among others (Queller’s response is particularly on point, I think).

HT Joan Strassman

 

 

I teach a graduate seminar on Darwin’s On the Origin of Species. We read and discuss the Origin and some related readings. It’s a lot of fun, for me and the students. If you haven’t yet read the Origin, or read it when you were too young to fully appreciate it, or haven’t read it in ages and don’t remember it that well, you really ought to (re-)read it. It’d be great choice for a graduate reading group–you could read a chapter a week and finish it in a semester. So here are a bunch of notes to help and encourage you to take the plunge.

Advice

• Read the first edition. Six editions of the Origin were published in Darwin’s lifetime. If you just go to a library or bookstore and pick a random copy of the Origin off the shelf, you’re probably picking up a copy of the sixth edition (if it’s got a whole chapter devoted to refuting the objections of a guy named “Mivart”, it’s the sixth edition). The sixth edition is mainly of historical interest, as the final statement of Darwin’s views. Those views were heavily revised from the first edition, in response to the many criticisms Darwin received. Unfortunately, most of those criticisms were off base, so the first edition actually is more correct than the sixth. So as a scientist who’s likely to be curious about how much Darwin got right, and who probably wants to be able to trace back modern ideas to their Darwinian roots, you’ll want to read the first edition. The first edition also is shorter, clearer, and more tightly argued, making it an easier read. It’s been aptly remarked that the sixth edition could have been titled “On the Origin of Species By Means of Natural Selection and a Whole Bunch of Other Things.” And the first edition is the edition that started the intellectual revolution–it’s the edition that changed the world. So why not read that?
• Consider which printing of the first edition you want. Darwin’s books have long since gone out of copyright, so you can read the first edition for free on various websites, such as this one. If you prefer a hard copy (and call me old fashioned, but I really think every biologist should own a hard copy), then I recommend The Annotated Origin. It’s a facsimile of the first edition, so it has the original pagination (helpful if you’ll also be reading scholarly articles about the Origin, as they all refer to the book using the original pagination). And as the title indicates, The Annotated Origin has extensive and very good marginal notes from biologist James T. Costa. This is the printing I plan to teach my class from in future. Another option, which I’ve used in my class in the past, is the famous Harvard facsimile edition first published for the Origin‘s 100th anniversary in 1959, which includes a famous and influential introduction by Ernst Mayr.
• Do a bit of background reading. The Origin is quite accessible. It’s not technical; it was written to be read by any educated person. And while the style may not be your cup of tea (though I actually like it, or at least don’t mind it), it’s not difficult reading. So you can get a lot out of the Origin without doing any background reading. But background reading can definitely help you get more out of it. I require my students to read Janet Browne’s Darwin’s Origin of Species: A Biography. It’s a short (readable in a few hours) introduction to the writing of the Origin, the social and scientific context, reaction to the book, etc. Browne’s mammoth two volume biography of Darwin is great too, but probably much more than you’d want to bite off for a reading group. And of course there are many other things you could read; it’s not for nothing that historians of science talk about the “Darwin industry”.
• Read it as part of a group. Read the Origin along with others so you can talk about your reactions as you go. Or just read along with John Whitfield, a science writer who back in 2009 did a nice series of blog posts called Blogging the Origin. He read the first edition and did a post on each chapter.

Food for thought

Here are a some suggestions for things to think about as you read the first edition of the Origin. Many of them reflect my own interests, of course, so just ignore them if you don’t share my interests. The Origin is a really rich book and there’s plenty in it for anyone.

• The quotations with which Darwin prefaces the book.  One is from William Whewell, an influential thinker of the generation prior to Darwin’s, and the other is from the “inventor of the scientific method”, Francis Bacon. Both quotes talk about how science, and scientific laws, don’t conflict with Christianity. These quotes are an attempt by Darwin not just to defend against charges of impiety or atheism, but also to defend against charges of being unscientific. At the time, the leading view on the origin of species was “special creation”, which actually had relatively little in common with the forms of creationism espoused (often in thinly-disguised form) by fundamentalists today. It’s important to understand that “special creation” was just one manifestation of the deep intellectual commitments of most senior scientists of the day. To those scientists, such as the geologist Adam Sedgwick (once a mentor of Darwin’s) the whole point of science was to read nature as the “Book of God”, to document natural order and patterns as a physical manifestation of God’s plan. To someone like Sedgwick, Darwin’s explanation for the origin of species wasn’t just wrong, it wasn’t even the sort of thing that counted as a scientific explanation at all. And conversely, Darwin argues in the Origin that “special creation” is not so much an incorrect explanation for the origin of species, as a non-explanation–it leaves all sorts of surprising patterns in nature “untouched and unexplained”. It’s difficult for a modern reader to really “get” the mindset of a special creationist, but it’s worth a try in order to understand the Origin as Darwin and his readers understood it.
  
• Darwin’s style. Note that the style is very cautious and modest (until the final, summary chapter, which is beautifully confident). Indeed, Darwin devotes a whole chapter to raising and then addressing objections to his ideas, and it’s clear from the way he writes (and from private correspondence) that he’s not just setting up straw men. He really does worry about these objections, perhaps even too much. It’s a far cry from the way most scientists write these days.
• Ordering of the material. Note that Darwin doesn’t start out with anything exotic (nothing about the Galapagos Islands, for instance, which are hardly mentioned in the book). Instead, he starts out talking about domestic animals. It’s an attempt to get readers on board, by talking about something ordinary and familiar. More broadly, note that in the first few chapters Darwin lays out his big conceptual idea–evolution by natural selection–and then in the remainder of the book discusses how that hypothesis fits with and explains the available data. One can ask, as philosopher Eliot Sober has, if Darwin wrote the Origin “backwards”. That is, he starts out with the mechanism of evolutionary change, and only then does he go on to argue for the fact of evolutionary change. Which seems a bit backwards, when put that way–shouldn’t you start by describing what needs explaining before you explain it? You may want to think about why Darwin ordered the material the way he did.
• What Darwin got right, and wrong, and the risk of mixing them up. Darwin gets a lot right in the Origin, including prefiguring almost every big idea in modern ecology (even trendy ecological ideas like biodiversity and ecosystem function!) My students are always shocked at just how much he gets right and how modern he sounds. He also gets some things wrong, of course (and not always because he was unaware of facts we’re aware of). But he gets so much right that it’s tempting to read into the Origin modern ideas that Darwin himself didn’t actually hold. Case in point: the book is infamous for not fully living up to its title because Darwin doesn’t really fully grasp how natural selection can generate new species from existing ones. That’s because he doesn’t really recognize the possibilities of spatially-varying selection (different variants favored in different locations) and frequency-dependent selection (relative fitness of different variants depends on their relative abundances). Instead, Darwin has what Costa aptly calls a “success breeds success” vision of how selection works–new, superior variants arise and then sweep to fixation everywhere they can spread to, replacing the previous variants. To get this “success breeds success” process to generate and maintain diversity, Darwin invokes what he calls his “Principle of Divergence”, which is the idea that parents will be fitter if they have divergent offspring (offspring that differ from one another in their phenotypes). The idea is basically to make the production of diversity itself a cause of evolutionary success. There are contexts in which this can work–but plenty of contexts in which it can’t (there are logical as well as empirical flaws to the idea as developed by Darwin). Now, I should note that I’m not an evolutionary biologist, and there are evolutionary biologists who read the Origin as presenting pretty much a fully-modern and correct theory of how selection affects speciation. All I can say is that I think they’re reading into the Origin, and in particular into the “Principle of Divergence”, something that just isn’t there. Read it and judge for yourself.
• Explanation and unification. It’s often said that Darwin’s great achievement in the Origin is to unify and explain many apparently-unrelated facts. The Origin links together and explains facts about everything from animal breeding to biogeography to embryonic development to the fossil record. Which raises many deep and interesting conceptual issues. For instance, is unification always a good thing in a scientific theory? Why? Is it because unification is a mark of truth? For instance, maybe unification is a sort of “indirect” or “circumstantial” evidence. If a theory seems to work well to explain facts A, B, and C, then perhaps we ought to take that as indirect or circumstantial evidence in favor of its explanation for fact D. But on the other hand, conspiracy theories also unify many apparently-unrelated facts–which is usually taken to indicate that they’re false, not true! Or maybe unifying theories are valuable because, true or not, they’re more productive as “working hypotheses”, guiding future investigations by suggesting what questions to ask and what data to collect. Darwin famously called his theory “a theory by which to work”. Then again, maybe not. For instance, progress on understanding the causes of variation and heredity (problems that famously vexed Darwin) came not just from the rediscovery of Mendel’s work, but from breaking the problem up and disunifying it. Muller and his followers figured out what we now call transmission genetics by explicitly setting aside and ignoring what we now call developmental genetics, regarding it as a separate problem. And what exactly does it mean to “explain” some fact or set of facts, anyway, and how are explanation and unification connected, if at all? For instance, do explanations have to be unifying if they’re to count as explanations at all? The intuition here is that every theory or hypothesis has to take something for granted. So if you produce a separate, independent explanation for every single thing you want to explain, then you’re effectively just changing the question, substituting one set of unexplained, taken-for-granted statements for another. At best, you’re just pushing the required explanations back a step (e.g., if you “explain” the origin of life on earth by saying “it arrived on an asteroid”, all you’ve done is change the question to “where did life on the asteroid come from?”) But if you have a unifying explanation, a single explanation for a bunch of different facts, you’re “killing many birds with one stone” and reducing the number of unexplained statements we just have to take for granted. See here and here and here for some longer posts I did on issues of explanation and unification for the class blog.
• Circular reasoning? Darwin developed his theory to explain lots of different facts about the world, and along the way he modified it in various ways as he discovered new facts. In light of that, isn’t it a bit (or even more than a bit!) circular to regard those facts as evidence for his theory, or as a test of his theory? Isn’t it circular (or maybe better, “double-dipping”) to use the facts to develop and inspire your theory, and then turn around and re-use those same facts to test the theory? After all, developing your theory so that it fits known facts guarantees that your theory will fit those facts! In philosophy of science, this is known as the “old evidence” problem: when does previously-known (“old”) evidence constitute evidence for a new theory? There are plenty of examples of the old evidence problem besides the Origin, so it’s a very general issue well worth thinking about (I emphasize I’m just throwing the issue out there as food for thought–I’m not saying whether I think Darwin’s argument is actually circular!)
• Comparative reception of the Origin. After you read the Origin, you’ll probably find yourself wanting to dig into all sorts of related topics. One related topic my class discusses is the comparative reception of the Origin in different cultures and religions. There are obvious reasons why North American and European biologists focus so much on how Christians, especially conservative ones, react to evolution. But it’s worth remembering that there are other strains of Christianity, and other religions, and it’s very interesting to compare and contrast the ways they reacted to Darwin’s ideas.
• UPDATE: Darwin is in the eye of the beholder. Darwin has been claimed as a model and even a hero by many groups. For instance, the Origin has been claimed as a biological justification for both communism and unregulated capitalism. John Whitfield astutely notes that Darwin has been claimed as a model by both the “lean and mean” school of evolutionary biology (theorists like Fisher, Hamilton, Maynard Smith, Dawkins, and Price, who focused on natural selection and its consequences using simple, elegant models) and the opposing “let a thousand flowers bloom” school (exemplified by Stephen J. Gould, with his emphasis on historical contingency and the complex interplay of many evolutionary forces). Darwin has of course been claimed as a model by naturalists, especially those who bemoan the perceived decline of field-based, observational natural history within biology. Even though Darwin himself did a lot of highly artificial greenhouse and lab experiments to which he attached great importance, wasn’t above collaborating with mathematicians (as in the section of the Origin in which he builds a geometry-based model of how honeybees can build perfectly hexagonal honeycombs), and was heavily criticized in his own time for engaging in ungrounded theoretical speculation rather than sticking close to the data and making inductive generalizations. Interestingly, many of today’s greatest naturalists, like E. O. Wilson and the Grants, achieved their greatness in a similar way, by seriously pursuing and integrating many different lines of work of which “natural history” was only one. So when you read the Origin and come to see Darwin as your hero (as you probably will!), pay attention to what you find heroic about him–it may well say more about you than it does about Darwin!

Over at Nothing in Biology Makes Sense, newly-minted PhD evolutionary biologist David Hembry reflects on the biggest changes in evolutionary biology and ecology since 2005. It’s a thoughtful piece, reflecting on some less-noted aspects of widely-noted trends. For instance, it’s not just the increasing availability of sequence data that makes synthesis and reanalysis of other people’s sequence data attractive, it’s also the fact that it’s cheap to do (particularly important in an era of rising fuel costs and increasing competition for funds). The same could be said of any database-based work, really, and also of theoretical work and laboratory microcosm work. It will be interesting to see how patterns of training, hiring, and publication shift in decades to come*, and if there aren’t frequency-dependent forces that will limit how far these directional trends can go (At some point, will really good field skills become highly prized precisely because of their scarcity, while good bioinformaticists/meta-analysts/theoreticians/programmers/etc. will be a dime a dozen?)

David also identifies some less-noted trends, such as the increasing focus of evolutionary biologists on “field model organisms” like sticklebacks and anoles, and how this poses problems of system choice for grad students who want to go on to academia. Do you choose the same model system as everyone else, thereby making it easier to ask big questions (after all, there are good reasons why sticklebacks and anoles are model systems!), but harder to stand out from the crowd? Or do you choose the road less traveled, which might make it harder to address big questions but also really impress people if you succeed? (sounds a bit like the handicap principle…)

Anyway, click through and read the whole thing.

*At least in ecology, there’s not yet much indication of a radical shift towards people publishing data collected by others.

I just tried to visit the Ecological Society of America website, and Google gave me this:

What the hell?! The diagnostic page says that over the past 90 days, a bunch of pages from esa.org resulted in malicious software being downloaded without user consent, including a bunch of exploits and trojans. I’m guessing this means the ESA website was hijacked sometime within the last few months?

UPDATE: Via the ESA Twitter feed, I see that the site was indeed hijacked within the last 24 hours. It’s been fixed, but it’ll take about 24 h for Google to recognize the fix.

As scientists, whether we’re reading a paper or listening to a talk, we often focus on the take-home message. The main conclusion. The key point. The bottom line. The gist. The summary.

But should we do that? Always?

Because the devil is in the details. And not just sometimes, but pretty much all the time. So if you don’t understand the details, if you don’t know how the “bottom line” was “calculated”, what good does it do you to know it? If you don’t know what the summary is summarizing, what’s the point of knowing the summary? Indeed, can you even be said to understand the summary?

Now, I actually think those questions have good answers–sometimes. Summaries do have their uses. There are certain times when it’s ok to ignore the details and just focus on getting the gist. But details have their uses too, and there are times when it is anything but ok to ignore them. In my experience, many of the most serious mistakes in ecology arise from insufficient attention to detail (see here and here for just two of many possible examples).

So here are some quite specific circumstances in which I think summaries have value even if you don’t know the details of what’s being summarized:

• The summary is only a starting point; you’re going to learn the details. For instance, you read the abstract of an interesting-looking paper, or read a live-tweet of a talk, and decide to go read some papers on that topic. Or, you read a bunch of abstracts, and decide to read whichever papers sound most interesting, thereby using the abstracts as a filter on what details to learn rather than as a substitute for learning the details.
• You’re only mildly interested in some topic and have no need to know very much about it.

Conversely, there are other circumstances in which you had better know the details, so that you know exactly what’s being summarized. Now, summaries are still valuable in these circumstances–but only because they help you understand the details, not as a substitute for the details.

• You’re going to work on the topic.
• You’re going to publish something on the topic.
• You’re going to apply for a grant on the topic.
• You’re going to present on the topic.
• You’re going to teach the topic.
• You’re going to cite a paper on the topic. Yes, I believe that you should read–carefully, critically, and in its entirety–every paper you cite (rule of thumb: read it as if you’re reviewing it). To cite something is to rely on it; you ought to satisfy yourself that you can rely on it. Doing otherwise is how mistakes get perpetuated. Yes, I admit to not always doing this myself. We are all sinners.

And here are some bad reasons and poor excuses for focusing on summaries to the exclusion of the underlying details:

• When reading a theoretical paper, skipping the math and any technical explanation and just focusing on the broad-brush summary, on the grounds that you don’t know math or don’t like math. No, you don’t need to rederive all the math, any more than you have to reperform every experiment you read about. But you can hardly claim to understand the math if you’ve skipped over the math entirely! Something similar could be said for any technical paper, of course, but in my experience “math phobia” is far more common than “natural history phobia” or “experimental design phobia” or “statistics phobia” or etc.
• Ignoring the details because you’re just looking for a way to get a quick paper. Many ecologists are understandably eager to find and use methods that seem easy to apply but yet promise great insight. This doesn’t just lead to bandwagons, it also leads to people rushing out to apply these methods without having thought about the details of how the methods work or how the results should be interpreted. In this context, focusing on “the bottom line” to the exclusion of details basically amounts to saying “I don’t want to have to think about this method, I just want to be able to ‘crank the handle’ and use it without thinking.”
• Ignoring the details because you think “the big picture” is what really matters. Hey, I’m a big-picture person too. I love the big picture. But if you don’t know the underlying details, then you don’t know what it’s a big picture of. You say you want to see “the forest for the trees”? Well, you’d better be able to tell if that green patch in your “big picture” (your “satellite photo”, if you will) is a forest and not grassland or farmland. Heck, you’d better be able to tell if your “big picture” is a satellite photo and not a child’s fingerpainting. (oops, that snapping sound you just heard was the sound of the whole “big picture/forest for the trees” metaphor being stretched beyond the breaking point…)

It occurs to me that this is connected to a really old post of mine on hand waving in ecology, in which I illustrated by example, but struggled to articulate, the difference between “good” and “bad” hand waving. One characteristic of good hand waving is that it starts from an appreciation of the details. When someone like Mathew Leibold argues that a very simple food web model “captures the essence” of what’s going on in some complex natural community, he’s starting from a thorough understanding of what the model assumes and what it predicts. But if you only “get the gist” of that same model, you’re in no position to judge whether it is, or is likely to, “capture the essence” of what’s going on in your study system.

p.s. Protip: if it’s not obvious where a link goes, it probably goes to something funny that’s related to the post. This is true of many of my posts.

PeerJ is a new open access publishing initiative which you join by paying a flat one-time fee, entitling you to publish as many open-access articles as you want for the rest of your life. Articles are peer reviewed for technical soundness. The initiative was founded by some serious scientific publishing bigshots.

But that’s not actually what I wanted to note. In passing, a recent Nature news article on PeerJ says that

To avoid running out of peer reviewers, every PeerJ member is required each year to review at least one paper or participate in post-publication peer review.

Hmm, wonder where I’ve heard that idea before? Wait, it’ll come to me…

p.s. Just to be clear, I’m not claiming that PeerJ got this idea from Owen Petchey and I. I just feel vindicated that something like our “PubCreds” idea would be incorporated into a serious publishing business venture. More than one, actually. This also vindicates a remark which scholarly publishing consultant Joseph Esposito made to me at a publishing conference: PubCreds will happen when someone figures out how to monetize it (or in this case, monetize a larger initiative, of which something like PubCreds is one component).

Here’s an intriguing little cognitive psychology experiment, which shows that highly educated people evaluate the truth or falsehood of statements less quickly and less accurately if those statements are ones that appear true under a “naive” theory, but which education teaches us are actually false (e.g., “Humans are descended from chimpanzees”, “The Earth revolves around the sun.”). This suggests that pre-existing false ideas aren’t “overwritten” by education, they’re merely “suppressed”.

I wonder if something similar can explain the persistence of certain zombie ideas. Is it just inherently difficult to unlearn the first thing we ever learn about a topic, as I suggested in this old post? So that, if the first idea you ever learn about a topic is false (say, you’re taught the IDH as an undergrad), you become a zombie and it becomes very difficult to cure you? And if so, what can we do about it (besides make sure that our undergrad curricula are up to date)?

Presumably there’s a lot of research on this I’m not aware of.

p.s. Depressingly, rates of correct responses were lowest, and speed of response slowest, for questions about evolution (questions fell into 10 different subject areas across the physical and life sciences).

UPDATE: Error in first paragraph now fixed.

The Ecological Society of America is encouraging bloggers to blog the ESA meeting. If you do a post on any aspect of the meeting, they’ll create a post on their EcoTone blog with your post title, an excerpt, and a link back to the full post on your blog. Details here.

Interesting idea. I’ll need to ask a few questions before I participate. Not sure if my daily previews and summaries of my experiences are the sort of thing they’re looking for. Those posts are really informal, and they’re written for the audience of this blog rather than the much broader audience of EcoTone. Plus, I sometimes include criticism of various aspects of the meeting. Even if EcoTone is just going to be doing brief excerpts and linkbacks, I want to make sure they’re ok with what they’re linking to.

And if you’re tweeting the meeting, the hashtag is #ESA2012.

Elinor Ostrom, the first woman ever awarded the Nobel Prize in Economics, has died. Ecologists, including me, mostly don’t know her work (I only know of it). But we should. She did hugely important work on the management of common pool resources, and argued that Hardin’s tragedy of the commons was in fact sustainably soluble (and, as a matter of historical fact, had been sustainably solved many times) via appropriate social norms and institutions, not just by privatizing the commons as Hardin argued.

Crooked Timber has a brief remembrance and (as always over there) a remarkably good comment thread full of thoughtful remarks and useful links.

 

I lived in Ottawa for four months a couple of years ago while on sabbatical. I’ve drawn on that experience to create an annotated map of suggested places to eat and drink for Evolution 2012.

Basically, everyone is going to be eating and drinking in the Byward Market area, as it’s the highest concentration of bars and restaurants close to the convention center and to major tourist attractions like Parliament. I’ve suggested a few places in that area, but also some places a bit further afield for folks who like to walk or who are willing to bike/drive/take a taxi. The other “main drags” in downtown Ottawa are Elgin St. and Bank St.

Bottom line: the best places to drink in Ottawa are The Manx (walkable from the convention center; hidden in a basement; great cozy, buzzy atmosphere; excellent, changing food menu; really popular) and Pub Italia (not walkable; has the only world-class beer selection in Ottawa; big draft list plus hundreds of bottles including lots of rarities and obscure Belgians; an essential stop for beer geeks like me).

See also this list of local pubs produced by the meeting organizers.

Over at Sociobiology Joan Strassman has a great post on how to choose talks at big conferences like the ESA Annual Meeting. This is something we’ve talked about on this blog before, but no one ever brought up Joan’s excellent suggestion: have a focus. That is, try to see as many talks as you can in a particular area that you want to learn more about. This is a great way to get up to speed on the current state of play in that area.

 

Patterns and processes of population dynamics with fluctuating habitat size by Fukaya K (Hokaido University, Japan), Shirotori W and Kawai M.

Competitive outcomes between two exotic invaders are modified by direct and indirect effects of a native conifer by Metlen KL (Nature Conservancy, Oregon, USA), Aschehoug ET and Callaway RM

Soon as Early View!

  Hi everybody

My name is Åsa Langefors, I’m the new Managing Editor at Oikos. After the two initial  months at the office, I have now started to learn the routines and to get aquainted with editors, authors and reviewers. i.e. with Oikos. And just as things started to  find their place in my brain, we switched over to ScholarOne for handling of manuscripts. New stuff to learn, new routines etc. But the new system has so far run smoothly and I hope everybody will have some patience for possible confusions that might arise in the beginning.

I have my background in Molecular Ecology, having studied MHC-genes in fish as a PhD-student and post-doc. During the last five years, I have combined a career as a freelance journalist with work at the university in a research school in Genomic Ecology (with a special interest in so called soft skills, including carreer development, personal development, how to deal with gender issues etc.) and in a EU-project in Soil Ecology. I am sure that several parts of my quite mosaic background will be useful in my work with Oikos.

When not working, I spend time with my family, consisting of a husband and two kids and also a lot of time in my garden. In addition, when life is good, I think we have a duty to enjoy it. So, good cappuciono, fine wine, good food, doing workout (preferentially outdoors, like running, walking, skiing or skating) are important matters to me.

A rant against live-tweeting talks, here.

I don’t tweet at all, so I don’t live-tweet. In particular, I don’t feel like I’d provide much of value to anyone by live-tweeting talks, or that I’d get a lot of value out of following others’ live tweets.* And while it doesn’t bother me much as a speaker–I just ignore people who are doing it, much as I ignore undergrads who text during class–I can understand how it would bug some people.

I do agree with the linked post that those who do it get less out of the talk. In particular, I try to make my talks as dense and fast-paced as possible without risking losing the audience. That is, I try to design my talks so that you have to pay close attention, and so that your close attention is rewarded. You’ll hopefully feel like you really got a lot out of the time you spent listening to me. I question whether you’ll be able to fully follow a talk, especially the sort of talk I try to give, if you’re live-tweeting. Studies show that even people who think they’re good at “multi-tasking” and have practiced it a lot actually aren’t good at it, by any measure.

So live-tweeting doesn’t really bother or offend me personally, though I can see why it would offend others. I think the people who do it are mostly hurting themselves, if only a little, and not for much benefit that I can see. But I’m an old guy, so I suspect some of our regular commenters are totally going to disagree with me on this.

UPDATE: Just to be clear, I certainly don’t think that the only people who ever pay less-than-full attention to a talk are the people who are live-tweeting. Far from it. And as a speaker, I personally am no more bothered by live-tweeters than I am by people who aren’t paying full attention for some other reason.

UPDATE #2: Perhaps not surprisingly, I’m not big on the way this post is being summarized on Twitter. The post isn’t really about whether “talks should be ‘tweetable’”, it’s about the benefits and costs of live-tweeting them. Anything is ‘tweetable’. But in truth, this probably says more about me than it does about Twitter or folks who use it. I tend to distrust other people’s short summaries of anything, whether tweeted or not. And just for the record, let me say that commenters here, and Joan Strassman in her own post, have articulated some good reasons why one might live-tweet (or tweet right after a talk), or follow the live-tweets of others. So while I personally still don’t see much value in live-tweeting, I can understand why others do. As with many things in life, it’s a question of doing what works for you.

*To be clear, I do see value in many other uses of Twitter.

I continue to find Zen Faulke’s “fighty crab” meme hilarious. I’m still realizing how versatile it is.

Written a confusing blog post? Fighty crab tells you:

Want to celebrate World Oceans Day? Fighty crab tells you how:

Want to win your One True Love back (assuming your One True Love was having a dalliance with, um, dolphins)? Fighty crab has you covered:

p.s. I didn’t come up with any of these.

Zen Faulkes (‘Neurodojo‘) has compiled his many excellent blog posts on scientific presentation tips into a short e-book (i.e. a pdf file). Recommended.

Billiards is all about sequences of causal events. Your cue strikes the cue ball, causing it to roll into another ball, causing that ball to roll into the corner pocket.

Falling dominoes are sequences of causal events. You knock over the first domino, which knocks over the second, which knocks over the third.

Rube Goldberg machines are sequences of causal events. The toy car is pushed into a line of dominoes, the last of which falls onto another toy car, which rolls down a ramp and runs into a ball, which rolls down another ramp…[skipping ahead]…which causes a piano to fall…[skipping some more]…which causes paintball guns to fire at a rock band.*

When humans think about causality, they find it natural to think in terms of sequences of events. That’s why colliding billiard balls are a paradigmatic example of causality in philosophy.

But ecology is mostly not like billiards, or falling dominoes, or Rube Goldberg machines. Like history, ecology is (mostly) not “just one damned thing after another.” But it’s hard not to think of it that way, and to teach our students not to think of it that way.

(UPDATE: I’m not saying that ecology, or dynamical systems in general, aren’t causal systems. They are! I’m just saying that the nature of that causality is such that it’s misleading to think about it as “Event A causes event B which causes event C which causes event D…”)

(UPDATE#2: Nor am I saying that ecological systems are “nonlinear” or “nonadditive”. They are, but that’s not my point here. For instance, you can have a sequence of causal events in which the magnitude of the effect is nonlinearly related to the magnitude of the cause. See the linked post from Nick Rowe, below, for further clarification. Sorry the original post wasn’t better, it’s clear that I did a lousy job of anticipating the ways in which readers might misunderstand what I’m trying to get at here).

Ecology is about dynamical systems. Stocks and flows, not falling dominoes. Inputs and outputs, not colliding billiard balls. Simultaneity, not sequences. Feedbacks, not one-way traffic.

Here’s an example. It’s a population ecology example, but not because population ecology is the only bit of ecology that’s about dynamical systems. It’s just a bit of ecology I know well. I could equally well have picked an example from physiological ecology (e.g., to do with individual growth), or from community ecology, or from ecosystem ecology, or from island biogeography, or conservation biology, or spatial ecology, or macroecology, or etc.

The example is predator-prey dynamics. You’ve got some prey that reproduce and die, and some of those deaths are due to predators. Predators convert consumed prey into new predators, and they die. Purely for the sake of simplicity (because it doesn’t affect my argument at all), let’s say it’s a closed, deterministic, well-mixed system with no population structure or evolution or anything like that, so we can describe the dynamics with just two coupled equations, one for prey dynamics and one for predator dynamics. And again for the sake of simplicity, let’s say it’s a constant environment and there’s no particular time at which organisms reproduce or die (e.g., there’s no “mating season”), so reproduction and mortality are always happening, albeit at per-capita and total rates that may vary over time as prey and predator abundances vary.

You cannot think about this dynamical system in terms of sequences of causal events. For instance, let’s say the system is at equilibrium, meaning that predator and prey abundances aren’t changing over time. That does not mean nothing’s happening! In fact, there’s a lot happening. At every instant in time, prey are being born, and prey are dying, and those two rates are precisely equal in magnitude but opposite in sign. And at every instant in time, predators are being born and predators are dying, and those two rates are precisely equal in magnitude but opposite in sign. Inputs and outputs are in balance. You cannot think about equilibria in terms of sequences of causal events, it’s like trying to think about smells in terms of their colors, or bricks in terms of their love of Mozart. What “sequence of events” keeps the system in equilibrium?

Or, let’s say the predators and prey exhibit cyclic dynamics. For concreteness, let’s say it’s a limit cycle in the Rosenzweig-MacArthur model. Why do the predators and prey cycle? This is a case where it’s sooo tempting to think in terms of sequences of events; I know because my undergrad students do it every year. “The prey go up, which causes the predators to go up, which causes the prey to crash, which causes the predators to crash.” In lecture, even I’ve been known to slip and fall back on talking this way, and when I do the students’ eyes light up because it “clicks” with them, they feel like they “get” it, they find it natural to think that way. And it’s wrong. Not “wrong in the details, but basically right”. Not “slightly wrong, but close enough.” Wrong. Births and deaths are happening instantly and continuously. There are no sequences of events here.

Now I can hear some of you saying, ok, that’s true of the math we use to describe the world, but it’s not literally true of the real world. In the real world one could in principle write down, in temporal order of occurrence, all the individual birth and death events in both species. But my point would still hold. A prey individual was born, which caused prey abundance to increase by one, which caused…what, exactly? What’s the next domino to fall in the sequence? Another prey birth? No. A prey death? No. A predator birth or death? No. What that increase in prey abundance did was slightly change the expected time until the next birth or death event, by increasing prey abundance and (in any reasonable model) feeding back to slightly change the per-capita probabilities per unit time of giving birth and dying. Now, you could try to drill down even further, down to the underlying physiological (or whatever) causes of individual births and deaths, and the underlying mechanisms linking per-capita birth and death probabilities to species’ abundances. But you’re never going to find something that lets you redescribe predator-prey dynamics in terms of sequences of events, each causing the next. (UPDATE #3: And to clarify further, no, I’m not trying to argue against the notion that population dynamics are ultimately a matter of individual organisms giving birth, dying, and moving around. I actually heartily believe that! My point is to do with how to interpret the causality of what’s going on, whatever level of organization (individuals or populations) we choose to focus on.)

Our deep-seated tendency to think in terms of causal sequences of events rather than in terms of rates of inputs and outputs (i.e. rates at which the amount of something increases or decreases) doesn’t just make it hard to teach ecology. I think it also makes it hard for professionals to do ecology. For instance, to preview a future post, much of the appeal and popularity of structural equation models (SEMs) that they let researchers take causal diagrams (variables connected by arrows indicating which ones causally affect which others) and turn them directly into fitted statistical models. That is, SEMs mesh with and reinforce our natural tendency to think about causality in terms of colliding billiard balls. Which I think makes them positively misleading in many circumstances (as I say, much more on SEMs in a future post).

This post was inspired by a post on the same topic by Nick Rowe. Nick’s post is about economics. His post is way better than mine. You should click through and read it (no training in economics required; stop when you get to the bit at the end about “concrete steppes”, which is where the post segues into technical economics issues).

*Click the link to see what I’m talking about.

The current distribution of species bears the strong stamp of “big, slow” historical events and processes–speciation events, continental drift, meteor strikes, ice ages, the rises and falls of mountain ranges and land bridges, etc. Which has often been taken to imply that, in the grand scheme of things, the sorts of “small, fast” processes that contemporary  community ecologists study don’t actually matter all that much.

In this old post, I argue that, to the contrary, “big, slow” historical processes only matter if contemporary community ecology lets them matter. What we ought to be asking is not whether community ecology is “important” (because it has to be), but why community ecology is “history preserving” rather than “history erasing”.

Intrigued? Click through and read the whole thing.

p.s. I know I said in a recent post that I was done talking about macroecology for a while. But the response to that post was so positive that I changed my mind. It’s gonna be all macroecology all the time now! (just kidding)

Here’s what it probably feels like for a strawberry flower to be pollinated and develop into a strawberry. With cartoons.

“The changes can be unsettling.” LOL!

HT Jeremy Yoder