Jabberwocky Ecology

Postdoc position available with Weecology

I’m happy to announce that we’ll be hiring a postdoc starting this summer to work on research in the areas of macroecology, quantitative ecology, and ecoinformatics. The complete description follows below. Please forward a link to this post to anyone you know who might be interested or post a link to it on your blogs. Thanks!

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Journal Article 2.0

Cell Press has recently announced what I considered to be the most interesting advance in journal publishing since articles started being posted online. Basically they have started to harness the power of the web to aggregate the information present in in articles in more useful and efficient ways. For example, there is a Data tab for each article that provides an overview of all figures, and large amounts of information on the selected figure including both it’s caption and the actual context for its citation from the text. Raw data files are also readily accessible from this same screen. References are dynamically expandable to show their context in the text (without refreshing, which is awesome), filterable by year or author, and linked directly to the original publication. You’ll also notice an comments tab where editor moderated comments related to be paper will be posted (showing the kind of integrated commenting system that I expect we will see everywhere eventually).

I have seen a lot of discussion of how the web is going to revolutionize publishing, but to quote one of my favorite movies “Talking ain’t doing.” Cell Press is actually doing.

I’d strongly encourage you to check out their blog post and video and then go play around with one of the articles in the new format. This is really exciting stuff.

Drug Monkey on comprehensive exams

I have never been a big fan of comprehensive exams. In my opinion being able to perform on a test (of whatever form) has very little to do with what it takes to be successful as a scientist and most of the exam systems that I am familiar with have serious structural problems above and beyond this basic objection. I started a post on the problems with the comprehensive exam system at my university some time ago and will hopefully finish it one of these days, but for the time being I thought I’d point you over to Drug Monkey for his recent thoughts on the matter. The crux of his argument is:

Maturing through the career arc, I care less for this [the ability of the exam to protect the university’s reputation by preventing the graduation of incompetent hacks]. Mostly because I’ve come to realize nobody that is judging me now gives a rat’s patootie what University or Department of -ology appears on my doctorate. They care about the papers I have published. Period. Full freaking stop.

So if I were dictating a graduate program, I’d be looking to enhance the ability of the students to publish papers. This would pretty much rule out the examination approach.

While you’re over at his pad I’d recommend browsing around a bit. He and co-blogger Physio Prof aren’t ecologists but they are very sharp thinkers when it comes to life in academia. Plus, they introduced us to this, so what more can you ask for.

All truth passes through three stages [Quote]

All truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident.

—Arthur Schopenhauer, German philosopher (1788 – 1860)

Via Signal vs. Noise.

Rise of the neoFisherian statistical paradigm

I’ve been meaning to get around to posting about Stuart Hurlbert and Cecilia Lombardi’s recent paper (2009; Ann. Zool. Fennici 46: 311–349) on the use of p-values in drawing scientific conclusions… but thankfully Jarrett Byrnes over at i’m a chordata! urochordata! wrote such a great post about it that all I need to do is point you over to his place. Just so you know what you’re getting into, Hurlbert & Lombardi provide a convincing argument against the sanctity of the canonical alpha value of 0.05 and against the use of alpha values and ‘statistically significant’ in general. Instead they recommend (quoting Jarrett):

1) Report a p-value for a test. 2) Do not assign it significance, but rather refer to the level of support it gives for rejecting a null – strong, weak, moderate, practically non-existent. Make sure this statement of support is grounded in the design and power of the experiment. Suspend judgement on rejecting a null if the p value is high, as p-value testing is NOT the same as giving evidence FOR a null (something so many of us forget). 3) Use this in accumulation with other lines of evidence to draw a conclusion about a research hypothesis.

Go check out the full post. It’s well worth the read.

American Naturalist Adds Online Forum

American Naturalist (one of the top journals in ecology and evolution) has just announced that they are rolling out a forum system to allow for online discussions about their published papers.

The American Naturalist is testing a new online forum, starting with the March issue, which allows readers to post comments about a particular article.  The forum is in its beta phase as we work out the best configuration that serves the community.  Please help test it out and start the conversation!

The idea of rapid, open dialog about published papers is certainly exciting, and the possibility that whole community review and feedback could take the place of the necessarily more restricted peer review and publication process is a regular topic of conversation at places like Scholarly Kitchen and academHack.

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New Masters Program in Quantitative Biology at Imperial College London

Imperial College London is offering a new masters degree program in quantitative biology. It sounds like a great opportunity to get some good quantitative training via an intensive 1 year MS program. The best part of their pitch follows below. If you’d like to see the whole ad check out the flier that Dan Reuman sent me.

Over the past 10-20 years, biology has become increasingly quantitative, and mathematical sciences have in turn been increasingly influenced by biology. It has been said that “mathematics is biology’s next microscope, only better” (Cohen, J.E., PloS Biology, 2004) because mathematical, statistical, and computational sciences will continue to reveal unsuspected and entirely new worlds within biology, just as the microscope revealed previously unseen worlds following its invention. It has also been said that “biology is mathematics’ next physics, only better” (Cohen, J.E., PloS Biology, 2004) because biology will in turn continue to spur major new developments in computation, mathematics and statistics, just as physics has done in the past several hundred years.

Recognizing this integration, the MSc in Quantitative Biology provides students of life sciences with the quantitative skills they will need to thrive in the modern discipline of biology, and provides students from a more quantitative background with the biological insight they need to apply their technical skills. The course is unique in integrating important current research questions in biology with data from ecosystems down to cells and state-of-the-art quantitative methods. Graduates will be highly trained scientists prepared for employment in any of several settings, including as PhD students in universities and institutes worldwide; in the research departments of multinational industries concerned with the environment (e.g., pharmaceuticals, biotechnology); in conservation, management and agricultural agencies; and in local and national governments.

Blogrolling graduate student ecology blogs

We’ve recently been following a couple of blogs by graduate students studying ecology and have been enjoying them enough that we thought we’d point folks in their direction.

Transient Theorist is a first year PhD student interested in quantitative and interdisciplinary approaches to ecology. How could we not love his blog. Particularly good recent posts include Ups and Downs and Intimidating questions.

Karina at Ruminations of an Aspiring Ecologist is a third year PhD student who travels to remote foreign lands for field work (we love her use of – Ukenzagapia – to pseudonymize the location). Good recent posts include Timescales in graduate school and Even more of my life in comics: writing to professors.

We are glad to see graduate students blogging for a variety of reasons. First, graduate school can sometimes be an incredibly isolating experience in that it can feel like some of the difficult situations are unique to you, when in fact hundreds of students are going through exactly the same thing. Having a cadre of students writing about these experiences helps their readers feel less alone in their struggles. As faculty we also appreciate the opportunity to be reminded of the graduate student perspective on academia. We’re not too far out of graduate school, but it is already difficult to recall what a committee meeting was like from a student perspective. Reading students thoughts, especially the sort of honest presentation of internal thoughts made possible by pseudonymous blogging, helps remind us that things often look very different to students than they do to us, which (we hope) helps make us better advisers, committee members, and teachers. Third, it provides opportunities for mentoring and interaction beyond the traditionally defined boundaries of one’s own department or university. Finally, and most importantly, it helps to build the nascent community of ecological bloggers. If you know of other good blogs by students studying ecology let us know in the comments.

Getting things done in academia

In a couple of days I’m participating in a panel to help young faculty be ready for their 3rd year review (the halfway step to tenure, which is kind of a big deal at my institution). This is the sort of thing that I normally say no to, but I’ve been to a couple of these things and I just couldn’t bear the thought of another group of young faculty being told that what they really needed to do to get tenure is to have a really spiffy tenure binder… so I’m going to talk about what they actually need to do to get tenure – get stuff done – and I thought it would be worth posting my thoughts on this here for broader consumption. This advice is targeted at assistant professors at research universities, but folks in other situations may be able to adapt it to their individual circumstances (e.g., if you’re at a small liberal arts college or other teaching centered school try swapping research and teaching below). Since the goal of the workshop is getting through the first phase of tenure, this is about what you need to do to accomplish that goal, not what you should be doing in any sort of broader philosophical sense. This advice is built on the lessons that Morgan (my wife and co-blogger for those of you new to JE; in fact she was so instrumental in developing these ideas that even though I’m using the first person singular this will be listed as a co-authored post) and I have learned during our time as assistant professors.

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Faculty position in experimental conservation ecology

The Community and Conservation Ecology group at the University of Groningen in the Netherlands, has a job opening for a tenure track assistant professor in Experimental Conservation Ecology (details below). This is a very impressive group that is headed by Han Olff and includes Rampal Etienne and David Alonso. I’ve worked with all three of these folks and I have no doubts that working in this group would make for a very intellectually stimulating environment. So, if you’re interested in moving to the Netherlands, check out the ad below and put in an application.

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MacArthur on generality in ecology

I just came across this great Robert MacArthur quote on Allen Hurlbert’s website:

Ecological patterns, about which we construct theories, are only interesting if they are repeated. They may be repeated in space or in time, and they may be repeated from species to species. A pattern which has all of these kinds of repetition is of special interest because of its generality, and yet these very general events are only seen by ecologists with rather blurred vision. The very sharp-sighted always find discrepancies and are able to say that there is no generality, only a spectrum of special cases. This diversity of outlook has proved useful in every science, but it is nowhere more marked than in ecology.

–Robert MacArthur, 1968

It seems to me that one of the real challenges for us as scientists is to make sure that even if we don’t understand what others see when they look at the ecological world, we need to consider the possibility that they simply have an alternative, and equally valid, perspective. As MacArthur notes, ecology will move forward most rapidly with a diverse set of approaches and perspectives, not by having a single viewpoint dominate how we address ecological research.

Ideas in Ecology and Evolution

I just read the excellently forward thinking year end editorial of the new journal Ideas in Ecology and Evolution. The editorial was written by Lonnie Aarssen and Christopher Lortie and is filled with Aarssen’s trademark,creative, outside the proverbial box, thinking. In this case it applies to the field of scientific publishing, the things they’ve tried to change with their new journal and those attempts that have failed and required rethinking. There are a lot of great ideas embodied in this editorial and that from the launch of the journal the previous year.

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