Jabberwocky Ecology

How scientists see Climate “Gate”

Steve Easterbrook over at Serendipity has three recent posts that do a pretty solid job of capturing what I think when I see the ongoing coverage of the fallout from the CRU email hack (if you’ve been living under the proverbial rock for the last 6 months you can start here).

Here’s one quick highlight from the most recent post

The argument that scientists should never exhibit human weaknesses is not just fallacious, it’s dangerous. It promotes the idea that science depends on perfect people to carry it out, when in fact the opposite is the case. Science is a process that compensates for the human failings of the people who engage in it, by continually questioning evidence, re-testing ideas, replicating results, collecting more data, and so on. Mistakes are made all the time. Individual scientists screw up. If they don’t make mistakes, they’re not doing worthwhile science. It’s vitally important that we get across to the public that this is how science works, and that errors are an important part of the process. Its the process that matters, not any individual scientist’s work. The results of this process are more trustworthy than any other way of producing knowledge, precisely because the process is robust in the face of error.

but you really should head over to Serendipity and check out the following three posts:


Creativity = Science + Writing

A group of 5th and 6th graders where asked to define either “science” or “writing” and when the answers were combined this definition of creativity was the result. In scientific education, and as we conduct scientific research, we often lose track of the fact that creativity is critical to the scientific process. This is a great reminder of its importance.

Getting your own domain name: a recommendation, justification, and brief tutorial


I have been very encouraged of late to see more and more ecologists embracing the potential of the web for communication and interaction. I’ve recently blogrolled some graduate student blogs and in the last few weeks I’ve come across American Naturalist’s trial run of a forum system, Ecological Monographs’ blog, and a blog soliciting feedback on a new initiative to digitize existing biological collections.

Read More

Post-doctoral fellowship in ecology and/or natural resource management

It’s probably not really to our benefit to be advertising competing positions when we’re currently looking for a post-doc ourselves, but this is a great opportunity so I thought I’d pass it along. The Department of Wildland Resources at Utah State has a post-doctoral fellowship available to work with one (or more) of it’s faculty. It is available to work with anyone in the department, but I would recommend checking out the labs of Peter Adler (plant community ecology) and David Koons (population ecology). I’ve worked with Peter and interact regularly with both Peter and Dave. They are both smart, young, enthusiastic faculty and you couldn’t go wrong working with either of them. Here’s the full ad:

The Department of Wildland Resources at Utah State University is offering a post-doctoral fellowship in ecology and/or natural resource management. Applicants must contact a sponsoring scientist from within the department’s faculty (http://www.cnr.usu.edu/wild/htm/faculty-staff) and then jointly develop a one-page research proposal. Applications are due April 1, 2010. Duration of funding is one year, renewable to two years subject to satisfactory performance and continued availability of funds. The salary is $40,000 in addition to the standard benefits package for USU employees. Contact Johan duToit (johan.dutoit@usu.edu) for more details on the application process.

Spring Break = Think Week for academic scientists

Transient Theorist is planning on doing something with his Spring Break that most of us don’t do often enough – take a week to think. In the rush to do all of the things that have to be done, we often lose track of doing the things that are really important to our core mission – advancing scientific knowledge as quickly as possible. A large part of accomplishing this mission is taking the time to think, explore ideas, consider the broader contexts in which one’s interests lie and develop linkages beyond the narrow confines of one’s discipline. It also includes taking the time to develop new skills, be they in the lab or on the computer. These activities rarely have short-term benefits and they practically never have meaningful deadlines. As such, it is easy for them to be sacrificed for things that need to be done now. So, I’d suggest that you go read Theo’s post for inspiration (and check out some of the posts in the Study Hacks Primer), start saying no so that you have a chance to assign time to bigger things, and try to find at least a few days over this Spring Break to really think about where your science is going over the next year.

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!

Read More

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.

Read More

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.