Jabberwocky Ecology

Upcoming meetings on metabolic scaling and ecology

There are a couple of upcoming meetings (or sessions of meetings) related to metabolic scaling and it’s relationship with/to ecology that I thought might be of some interest.

The first is  a symposium at the 2010 Society for Experimental Biology conference in Prague on the relationship between the scaling of metabolic rate with body size in organisms and the ecology of those organisms. According to the flyer that one of the organizers (Shaun Killen) sent me

The scaling of metabolic rate with body size has been a central research theme in biology for over a century. Recently there has been a particular interest in how patterns of metabolic scaling at the individual level may affect ecological phenomena and, in turn, how environmental factors may influence changes in metabolic rate with body size. The purpose of this symposium is to review recent evidence of these relationships, and to exchange ideas regarding the underlying factors that cause the observed patterns of metabolic scaling both between and within taxa. The scaling of metabolic rate with body size has been a central research theme in biology for over a century. Recently there has been a particular interest in how patterns of metabolic scaling at the individual level may affect ecological phenomena and, in turn, how environmental factors may influence changes in metabolic rate with body size. The purpose of this symposium is to review recent evidence of these relationships, and to exchange ideas regarding the underlying factors that cause the observed patterns of metabolic scaling both between and within taxa.

The meeting is June 30th – July 3rd in Prague and registration is now open.

The other is the biennial Gordon Research Conference on the Metabolic Basis of Ecology and Evolution, schedule for July 18th-23rd in Biddeford, Maine. If you haven’t been to a Gordon Conference before, these are really amazing conferences. The number of participants is limited (I think it’s about 100-150 people) and the format is specifically designed to engender discussion and interaction among the participants (every one eats meals together, stays in dorms together, etc). This year our own Morgan Ernest will be giving a talk in the section on Regulation of Metabolic Systems Across Scales. You’ll have to apply and be accepted in order to participate and the talks are invite only so posters are the only general option for presentation (both of which are a little strange in ecology circles), but it’s definitely the best conference I go to so it’s well worth the effort.

Some things just shouldn’t be hidden behind pay walls

I have nothing against journals charging for content. While I like the open access model I think that there are upsides to both systems. But seriously, there really are some things that should not be hidden behind a pay wall.

  1. Corrections of any kind: Errata, Corrigenda, etc. Assuming that I don’t have access to The Journal of X through my institution and I choose to purchase a paper from said journal that ends up containing an error, should I really have to pay again to find out what that error is. It’s like buying a new car that breaks down 6 months later and having to pay for a whole new car to get it fixed.
  2. Society business: Announcements, calls for nominations, etc. Presumably the goal of this sort of thing is to reach as wide an audience as possible… right?
  3. Acknowledgement of Reviewers: And now we come to the thing that triggered this post. PNAS’s Table of Contents showed up in my feed reader last night, and there, right at the top, was their annual Acknowledgement of Reviewers. I review for PNAS on occasion and thought I take a brief moment and go look at my name for a little boost during the grind of grant writing season. But no, sorry, I was working at home and so ran firmly into a pay wall. Seriously. So if I review for your journal, but don’t have a subscription then I can’t even look at an acknowledgement of my own, volunteer, activities. Sigh.

Now I know that in many cases the journals don’t intentionally put these sorts of things behind their pay walls. They just don’t think about it, but if you are going to have pay walls in place, isn’t it really your job/responsibility to think (ever so briefly) about what content you hide behind them?

UPDATE: Theoretical Population Biology’s Reviewer Acknowledgment just showed up in my reader. If you don’t have a subscription to TPB you can check out this document for the low, low, bargain price of $31.50.

Biological Diversity in a Changing World – Royal Society Discussion Meeting

I’m going to be participating in a Royal Society Discussion Meeting and they’ve asked us to advertise this to interested parties so I figured I’d just post about it here. The meeting is on Biological Diversity in a Changing World and (other than your humble narrator) has a pretty impressive list of speakers. Here are the key bits of information (straight from the meeting’s web page).

Synopsis

We live in a world in which biological diversity is under threat as never before. This meeting will draw insights from organisms ranging from microbes to mammals to show why a deeper understanding of temporal processes in ecological communities is essential in coping with the changes that the natural world – and the humans that inhabit it – will experience over the next 50 years.

Speakers and chairs

Speakers and chairs include Professor John Beddington CMG FRS, Professor Mike Benton, Professor Anne Chao, Professor Andrew Clarke, Professor Rita Colwell, Professor Robert Colwell, Dr Maria Dornelas, Professor Anne Glover, Professor Nicholas Gotelli, Dr Jessica Green, Professor Jeremy Jackson, Dr Kathleen Lyons, Dame Georgina Mace FRS, Professor Anne Magurran, Lord Robert May FRS, Dr Rebecca Morris, Professor Marian Scott OBE, Professor William Sutherland and Dr Ethan White.

Registration

This meeting is free to attend, but pre-registration (online) is essential. Click here to register.
The online registration form and programme information can be found at royalsociety.org/events-diary.

Blogrolling Scientific Programming Blogs

I’ve recently started reading two scientific programming blogs that I think are well worth paying attention to, so I’m blogrolling them and offering a brief introduction here.

Serendipity is Steve Easterbrook’s blog about the interface between software engineering and climate science. Steve has a realistic and balanced viewpoint regarding the reality of programming in scientific disciplines. The blog is well written, insightful, etc., but I think the thing that really won me over were his sharp witted responses to the periodically asinine comments he receives. For example:

I’d care a lot less about seeing all the source and data if I could just ignore climate scientists and shop elsewhere. But since I’m expected to hand over $$$ and change my lifestyle because of this research, your arguments ring hollow…

[You can shop elsewhere – there are thousands of climate scientists across the world. If you don’t like the CRU folks, go to any one of a large number of climate science labs elsewhere (start here: http://www.realclimate.org/index.php/data-sources/). An analogy: Imagine your doctor told you that you have to change your eating habits, or your heart is unlikely to last out the year. You would go and get a second opinion from another doctor. And maybe a third. But when every qualified doctor tells you the same thing, do you finally accept their advice, or do you go around claiming that all doctors are corrupt? – Steve]

Software Carpentry is the sister blog to an excellent online (and occasionally in person) course on basic software development for scientists. I strongly recommend the course to anyone who is interested in getting more serious about their programming and the blog is a nice complement pointing readers to other resources and discussions related to scientific programming.

Laying the Groundwork for Change [Quote]

How then is it possible to modify and improve upon an academic culture populated by smart, creative individuals who are motivated by ideals more than by money, who have deep, intense interests, value substance over form, have little patience for conformity, think for themselves, do not defer to authority, and see their work not as a job but as a calling? Clearly the challenge is to find the incentives and rewards that will motivate this unique workforce to buy into desired changes and work willingly toward implementing them. But the first step is to explain clearly why change is nececessary and, even more important, why change does not mean abandoning core academic values. To win the hearts of academics, one first has to educate them.

– James C. Garland, Saving Alma Mater

This is just one of many brilliantly reasoned (and worded) arguments from Saving Alma Mater. If you are an academic, or an administrator at an academic institution, you really should read this book.

PhD opportunities in Theoretical Ecosystem Ecology with Ford Ballantyne [PhD Position]

I went to graduate school with Ford and would strongly recommend that those looking for PhD opportunities on the quantitative side of ecosystem ecology consider the opportunity below. Ford is a smart guy, doing cool work, and he knows an awful lot about math, so it’s probably pretty hard to go wrong (and yes, we’re still friends so I’m totally biased).

The Ballantyne Lab at the University of Kansas is looking to recruit up to two graduate students for the fall of 2010. Current research is focused on modeling ecosystem stoichiometry, nutrient dynamics, microbial decomposition of soil carbon, systems-level regulation of metabolism, spatially explicit populations and the trophic structure of communities. Although most of our experiments are performed with phytoplankton and bacteria in the lab, the KU field station, 20 minutes from campus, is a great resource that is home to long-term studies of community assembly. Please direct inquiries to Ford Ballantyne (fb4 [at] ku [dot] edu). For more information about graduate study in the lab and EEB at KU please look at http://www.people.ku.edu/~fb4 and http://www2.ku.edu/%7Eeeb/graduate/ and http://www.kuerg.ku.edu/.

Another opportunity to change the way we collaborate – G o o g l e W a v e I n v i t e s for ecologists

The current model of writing up collaborative research in science is that a single individual “takes the lead” and writes a complete draft of the manuscript, which is then sent on to coauthors for comments, corrections, etc. This means that even when the development of the ideas and the work of research and analysis has been conducted in a truly collaborative manner (which, I suspect is actually not all that common, at least for the research and analysis parts) that the writing is really more of a one writer – multiple critics system.

This is in part due to the legacy of technology. Up until a few years ago most people simply couldn’t easily work on the same document together. In sophisticated environments the official copy of the manuscript could have been stored on a central server and individuals could “check it out” to work on it for a while, upload it when they had finished, someone else could check it out, lather, rinse, repeat. This required enough coordination that I’m not sure it was much better than just emailing the manuscript from one person to another. There was of course better tech, but scientists didn’t typically know about it, let alone use it.

These technological limitations have now been largely overcome (though there are certainly still some kinks to work out). Wikis represent the first, easiest, step to move beyond these constraints. Most wikis still only allow one person to work on a document (in this case a page) at any given time (but see this recent announcement by weecology’s prefered wiki host, PBworks), but by having the document stored on the web and editable via the browser there is no dead time for the document. You are either working on it actively or you’ve saved it and it’s available to others to work on. This reduces the size of the steps that need to be made on a paper because it wasn’t “you’re turn” to make progress and you didn’t commit to making a real contribution by checking out the paper. Even better than wikis are online collaborative editors like Google Docs or Zoho. These allow multiple individuals to work on a single document at one time. This might seem extravagant, but if two people happen to have a spare 30 minutes at the same time of day, not getting in each others way can make a big difference. Better yet, it allows you to intentionally work simultaneously. At weecology we will actually schedule writing meetings, where two or three of us will sit down in the same room with separate laptops (or an equivalent remote setup) and go to work on a paper. It’s amazing how much easier it can be to sit down and write when your whole team is doing it at the same time and it facilitates active interaction on the paper – “Hey, what do you think we should do about this part of the section I’m working on right now?”

And now, there is a new exciting set of technologies that provide yet another opportunity to move beyond the old system of collaboration – Google Wave. You can think of Wave as combining email, instant messaging, and collaborative document editing. This combination is cool enough on it’s own, but the seamlessness of the collaborative editing goes beyond anything currently available, thus removing some of the hiccups and frustrations of the current options (NB: don’t expect wave to run this smoothly yet as they are still scaling up the system).

This post was motivated by the fact that I just received my long awaited invite to try out Google Wave, which is still in private Beta. I logged in last night and did a quick search for public waves with the word ecology in them. There weren’t any. So, I am happy to announce that I have five invites to give away to practicing ecologists (that’s scientists who study ecology, not environmentalists) who want to give Google Wave a try. Leave a comment with an email and (ideally) something (like a link to a website) that demonstrates that you are an ecologist in case the swarm of folks looking for invites finds JE.

UPDATE: Two things. First, I started a public wave – Any ecologists on wave yet? – which you can find with a quick search of either ‘ecologists with:public’ or ‘ecology with:public’. Second, I forgot to warn the folks who get invited that according to Google “Invitations will not be sent immediately. We have a lot of stamps to lick.”. So it might take a while for your invitations to show up. When they do, stop by and leave a comment so that others know about how long they can expect it to take.

UPDATE 2: I’ve been reloaded with invites, so there are plenty to go around. Just leave a comment if you want one.

[Ph.D. position] Graduate student opening in Ethan’s lab

The White Lab at Utah State University has an opening for a graduate student with interests in Macroecology, Community Ecology, or Ecological Theory/Modeling.  Active areas of research in the White lab include broad scale patterns of biodiversity and body size, dynamics of ecological communities, and the use of sensor networks for studying ecological systems. We use computational, mathematical, and advanced statistical methods in much of our work, so students with an interest in these kinds of methods are encouraged to apply. Background in these quantitative techniques is not necessary, only an interest in learning and applying them. While students interested in one of the general areas listed above are preferred, students are encouraged to develop their own research projects depending upon their interests. Graduate students in the White lab are funded through a combination of research assistantships, teaching assistantships, and fellowships. Students interested in pursuing a Ph.D. are preferred, though exceptional students interested in a M.S. will be considered. Utah State University has an excellent graduate program in ecology with over 50 faculty and 80+ graduate students across campus affiliated with the USU Ecology Center (http://www.usu.edu/ecology/).

Additional information about the position and Utah State University is available here.

Interested students can find more information about the lab at our website.

If you are still interested after checking out the website you should contact me directly at epwhite@biology.usu.edu. Please send a CV, GPA, GRE scores (if available), and a brief description of your general research interests.

DEADLINE: For full consideration, formal applications should be submitted by January 1st, 2009.

GRADUATE STUDENT OPENING

The White Lab at Utah State University has an opening for a graduate student with interests in Macroecology, Community Ecology, or Ecological Theory/Modeling. Active areas of research in the White lab include broad scale patterns of biodiversity and body size, dynamics of ecological communities, and the use of sensor networks for studying ecological systems. We use computational, mathematical, and advanced statistical methods in much of our work, so students with an interest in these kinds of methods are encouraged to apply. Background in these quantitative techniques is not necessary, only an interest in learning and applying them. While students interested in one of the general areas listed above are preferred, students are encouraged to develop their own research projects depending upon their interests. Graduate students in the White lab are funded through a combination of research assistantships, teaching assistantships, and fellowships. Students interested in pursuing a Ph.D. are preferred, though exceptional students interested in a M.S. will be considered. Utah State University has an excellent graduate program in ecology with over 50 faculty and 80+ graduate students across campus affiliated with the USU Ecology Center (http://www.usu.edu/ecology/).

Additional information about the position and Utah State University is available at:

http://whitelab.weecology.org/grad-student-opening

Interested students can find more information about the lab at our website:

http://whitelab.weecology.org

If you are still interested after checking out the website you should contact me directly at epwhite@biology.usu.edu. Please send a CV, GPA, GRE scores (if available), and a brief description of your general research interests.

DEADLINE: For full consideration, formal applications should be submitted by January 1st, 2009.

[Quote] You can recognize a pioneer by…

You can recognize a pioneer by the arrows in his back.

– Beverly Rubik

You can recognize a pioneer by the arrows in his back

[Quote] Nilsson on credit for scientific work

Some years ago, someone wrote a book called “The Seven Laws of Money.” One of the “laws” went something like this: “Do good work and don’t worry about money; it will come along as a side effect.” Whether or not that’s true of money, I don’t know, but in my experience, it’s true of credit for scientific work. Just make sure you keep working at important problems, enjoying a life of science, and don’t worry so much about credit. You will probably get what you deserve — as a side effect.

Nils Nilsson (via Vladimir Lifschitz)

[Postdoc and PhD positions] Danish Center for Macroecology, Evolution and Climate

Positions available to work within an integrated terrestrial and marine research program addressing fundamental questions on the origin, maintenance, conservation and future of life and biological diversity on Earth. Candidates should have a strong publication record, relevant analytical and data handling skills, and an ability to communicate within a research team. Competitive salaries are offered.

Themes where we seek postdoctoral and/or PhD applications:

THEME 1 – MACROECOLOGIST/BIOGEOGRAPHER. Postdoc applications.

THEME 2 – SPECIES DISTRIBUTION MODELER. Postdoc applications and PhD stipends.

THEME 3 – PHYSICAL OR PALEO OCEANOGRAPHER . Postdoc applications.

THEME 4 – PLANKTON ECOLOGIST/BIOLOGICAL OCEANOGRAPHER. PhD stipends.

THEME 5 – CLIMATE CHANGE BIOLOGIST. Postdoc applications.

THEME 6 – FISHERIES ECOLOGIST/FISHERIES OCEANOGRAPHER . Postdoc applications and PhD stipends.

THEME 7 – FISHERIES/BIOLOGICAL OCEANOGRAPHER. Postdoc applications and PhD stipends.

THEME 8 – EVOLUTIONARY BIOLOGIST. Postdoc applications.

THEME 9 – HISTORICAL BIOGEOGRAPHER. Postdoc applications.

THEME 10 – BIOSTATISTICIAN/STATISTICAL BIOLOGIST. Postdoc applications.

THEME 11 -MIGRATION BIOLOGIST / ORNITHOLOGY. PhD stipends

THEME 12 –MACROECOLOGY OF VECTORBORN DISEASES . Postdoc applications.

THEME 13 – ENVIRONMENTAL ECONOMIST). PhD stipends.

THEME 14 – CONSERVATION ECOLOGIST/COMPUTATIONAL BIOLOGIST. Postdoc applications.

THEME 15 – NATURE RESERVE SCIENTIST. Postdoc applications.

THEME 16 – CONSERVATION SCIENTIST. PhD stipends.

Fuller descriptions of individual positions within 16 themes are at http://www.bio.ku.dk/om/jobs. Application must be based on the full description of the positions, and submitted before 31 of October 2009. For enquiries about the program, contact Professor Carsten Rahbek, crahbek@bio.ku.dk.

[Postdoc position] Effects of elevated carbon dioxide on ecosystem C and N dynamics in the Mojave Desert

If you’re looking for a quantitatively oriented postdoc in ecology this position with Kiona Ogle is a great opportunity.

Ecosystem C and N Dynamics and Synthesis: A two-year post-doctoral position is available to work on a multi investigator, DOE-funded project that examines the effects of elevated carbon dioxide on ecosystem C and N dynamics in the Mojave Desert. The post-doctoral research associate will be responsible for synthesizing and modeling existing data from the 10-year Nevada Desert FACE project in a collaborative project between Washington State University, the University of Wyoming, University of Nevada Las Vegas, and the University of Nevada Reno. A primary goal of the synthesis work is to explore the combined effects of elevated carbon dioxide and precipitation variability on the functioning of arid ecosystems. Data are to be synthesized within a hierarchical Bayesian framework that facilitates simultaneous coupling of diverse data sources and mechanistic models. To apply please email an application letter with professional interests, research experience and goals, CV, reprints, and names, addresses, and E-mail addresses of three references to Dr. R. Dave Evans (rdevans@wsu.edu) and Dr. Kiona Ogle (kogle@uwyo.edu). Review of applications will begin 1 October and will continue until the position is filled.

I can’t vouch for her collaborator, but I’ve worked with Kiona and she is smart, has a good scientific philosophy, and is a patient & hard working collaborator – all goods signs for a postdoctoral mentor.