Category Archives: ecology
Oikos has a blog? [Blogrolling]
Thanks to an email from Jeremy Fox I just found out that Oikos has started a blog. It clearly isn’t on most folks radars (I represent 50% of its Google Reader subscribers), and Jeremy has been putting up some really interesting posts over there so I thought it was worth a mention. According to Jeremy:
I view the Oikos blog as a place where the Oikos editors can try to do the sort of wonderful armchair ecology that John [Lawton] used to do in his ‘View From the Park’ column. I say ‘try’ because I doubt any of us could live up to John’s high standard (I’m sure I don’t!). I’m going to try to do posts that will be thought-provoking for students in particular. Oikos used to be the place to go with interesting, provocative ideas that were well worth publishing even if they were a bit off the wall or not totally correct. It’s our hope (well, my hope anyway) that this blog will become one way for Oikos to reclaim that niche.
I think they’re doing a pretty good job of accomplishing their goal, so go check out recent posts on the importance of hand waving and synthesizing ecology, and then think about subscribing to keep up on the new provocative things they’re up to.
A GitHub of Science? [Things you should read]
There is an excellent post on open science, prestige economies, and the social web over at Marciovm’s posterous*. For those of you who aren’t insanely nerdy** GitHub is… well… let’s just call it a very impressive collaborative tool for developing and sharing software***. But don’t worry, you don’t need to spend your days tied to a computer or have any interest in writing your own software to enjoy gems like:
Evangelists for Open Science should focus on promoting new, post-publication prestige metrics that will properly incentivize scientists to focus on the utility of their work, which will allow them to start worrying less about publishing in the right journals.
Thanks to Carl Boettiger for pointing me to the post. It’s definitely worth reading in its entirety.
_______________________________________________________
*A blog I’d never heard of before, but I subscribed to it’s RSS feed before I’d even finished the entire post.
**As far as biologists go. And, yes, when I say “insanely nerdy” I do mean it as a complement.
***For those interested in slightly more detail it’s a social application wrapped around the popular distributed version control system named Git. Kind of like Sourceforge on steroids.
Postdocs Galore [Jobs]
Advertisements for three exciting postdoctoral positions came out in the last week.
Interface between ecology, evolution and mathematics
The first is with Hélène Morlon’s group in Paris. Hélène and I were postdocs in Jessica Green’s lab at the same time. She is both very smart and extremely nice, oh, and did I mention, her lab is in PARIS. Here’s the ad. If it’s a good fit then you couldn’t go wrong with this postdoc.
A postdoctoral position is available in my new lab at the Ecole Polytechnique and/or at the Museum of Natural History in Paris to work at the interface between ecology-evolution and mathematics. Candidates with a background in biology and a strong interest in modeling, or with a theoretical background and a strong interest in biology, are encouraged to apply. More information is available here. Potential candidates should feel free to contact me. The deadline for application is May 8th.
The other two postdocs are associated with Tim Keitt’s lab (which I consider to be one of the top quantitative ecology groups out there).
Mechanistic niche modeling and climate change impacts
A postdoctoral position is anticipated as part of a collaborative project to develop and evaluate mechanistic niche models that incorporate geographic variation in physiological traits. The post doc will be based in Michael Angilletta’s laboratory at Arizona State University, but will interact with members of Lauren Buckley’s lab at the University of North Carolina in Chapel Hill and Tim Keitt’s lab at the University of Texas in Austin. The post doc will be expected to engage in modeling activities and coordinate lab studies of thermal physiology. Experience with mathematical modeling in C++, MATLAB, Python or R is beneficial and familiarity with environmental data and biophysical ecology is beneficial. More here.
Ecological forecasting or statistical landscape genetics
The Keitt Lab at the University of Texas at Austin seeks a postdoctoral investigator to join an interdisciplinary NSF-funded project linking ecophysiology, genomics and climate change. The position requires excellent modeling skills and the ability to engage in multidisciplinary research. Research areas of interest include either ecological forecasting or statistical landscape genomics. More here.
So, if you’re looking for a job go check out these great opportunities.
Learning to program like a professional using Software Carpentry
An increasingly large number of folks doing research in ecology and other biological disciplines spend a substantial portion of their time writing computer programs to analyze data and simulate the outcomes of biological models. However, most ecologists have little formal training in software development¹. A recent survey suggests that we are not only; with 96% of scientists reporting that they are mostly self-taught when it comes to writing code. This makes sense because there are only so many hours in the day, and scientists are typically more interested in answering important questions in their field than in sitting through a bachelors degree worth of computer science classes. But, it also means that we spend longer than necessary writing our software, it contains more bugs, and it is less useful to other scientists than it could be².
Software Carpentry to the Rescue
Fortunately you don’t need to go back college and get another degree to substantially improve your knowledge and abilities when it comes to scientific programming, because with a few weeks of hard work Software Carpentry will whip you into shape. Software Carpentry was started back in 1997 to teach scientists “the concepts, skills, and tools they need to use and build software more productively” and it does a great job. The newest version of the course is composed of a combination of video lectures and exercises, and provides quick and to the point information on such critical things as:
along with lots of treatment of best practices for writing code that is clear and easy to read both for other people and for yourself a year from now when you sit down and try to figure out exactly what you did³.
The great thing about Software Carpentry is that it skips over all of the theory and detail that you’d get when taking the relevant courses in computer science and gets straight to crux - how to use the available tools most effectively to conduct scientific research. This means that in about 40 hours of lecture and 100-200 hours of practice you can be a much, much, better programmer who rights code more quickly, with fewer bugs, that be easily reused. I think of it as boot camp for scientific software development. You won’t be an expert marksman or a black belt in Jiu-Jitsu when you’re finished, but you will know how to fire a gun and throw a punch.
I can say without hesitation that taking this course is one of the most important things I’ve done in terms of tool development in my entire scientific career. If you are going to write more than 100 lines of code per year for your research then you need to either take this course or find someone to offer something equivalent at your university. Watch the lectures, do the exercises, and it will save you time and energy on programming; giving you more of both to dedicate to asking and answering important scientific questions.
______________________________________________________
¹I took 3 computer science courses in college and I get the impression that that is about 2-3 more courses than most ecologists have taken.
²I don’t know of any data on this, but my impression is that over 90% of code written by ecologists is written by a single individual and never read or used by anyone else. This is in part because we have no culture of writing code in such a way that other people can understand what we’ve done and therefore modify it for their own use.
³I know that I’ve decided that it was easier to “just start from scratch” rather than reusing my own code on more than one occasion. That won’t be happening to me again thanks to Software Carpentry
Ecology on the Web [Things you should read]
Jarrett Byrnes‘ first turn at the helm of the ESA Bulletin’s Ecology on the Web feature is now up. It’s definitely worth a look. I learned about Scratchpads, a really cool looking project which automatically sets up an “easy to use, social networking application that enable communities of researchers to manage, share and publish taxonomic data online.”
If you like to contribute information about your web-based efforts to further the field of ecology, check out Jarrett’s blog post on how to contribute. Thanks Jarrett.
UPDATE: Corrected the link to Ecology on the Web
Putting the first back in first author
UPDATE: As of April 2012 Wiley has now changed their feeds to include the full list of authors. Thanks to Brady Allred for letting us know.
An open letter to John Wiley & Sons Inc.
Dear Wiley,
I like a lot of things that you do, but a few months ago you quietly changed your RSS feeds in a way that is both disrespectful and frankly not good for your business. You started including only the last author’s name in the RSS feed. This is bad idea for three reasons:
- It shows a complete lack of respect for (or understanding of) a number of scientific disciplines that do not have a strong last author tradition (including ecology; a field in which you publish a large proportion of the journals). If you do this for a paper from my field then most of the time you are publishing the name of the least significant contributor.
- Even in disciplines (or labs) where there is a last author tradition, not including the name of the (often junior) person who did most of the work is just disrespectful. Yes, maybe you’ll attract more click-throughs with a more senior name, but the goal in scientific fields has always been to provide credit where credit is due and you are failing to honor that tradition.
- Finally (and worst of all from your perspective), you are costing yourself readers. One of the considerations that I make when deciding to read a paper is based on who the authors are. At least in fields like mine I will rarely see a name associated with a paper that is meaningful to me since the last author may well be an undergraduate or a tech.
In case you think this is just one person’s opinion we took a quick informal poll a little while ago. Of 37 respondents 100% agree that if you are going to list a single author’s name with a paper it should be the first author.
So please, either switch back to using the first author’s name or, better yet, actually list the entire author line. Seeing someone’s name whose work we respect will encourage us to click-through to the paper regardless of where that name occurs in the author line.
Regards,
Ethan White (and the readers of Jabberwocky Ecology)
P.S. Also, we know that the RSS feed includes the abstract. We don’t need it in large, bold, capitalized letters at the top of every feed.
Postdoc opportunity in macroecology, quantitative ecology, and ecoinformatics
Our truly excellent postdoc, Kate Thibault, is moving on to bigger and better things heading up the mammal work at NEON. So, we’re looking for someone to join our group to do research in the areas of macroecology, quantitative ecology, and ecoinformatics.
The short job ad:
Ethan White’s lab at Utah State University is looking for a postdoc to collaborate on research studying approaches for unifying macroecological patterns (e.g., species abundance distributions and species-area relationships) and predicting variation in these patterns using ecological and environmental variables. The project aims to 1) evaluate the performance of models that link ecological patterns by using broad scale data on at least three major taxonomic groups (birds, plants, and mammals); and 2) combine models with ecological and environmental factors to explain continental scale variation in community structure. Models to be explored include maximum entropy models, neutral models, fractal based models, and statistical models. The postdoc will also be involved in an ecoinformatics initiative developing tools to facilitate the use of existing ecological data. There will be ample opportunity for independent and collaborative research in related areas of macroecology, community ecology, theoretical ecology, and ecoinformatics. The postdoc will benefit from interactions with researchers in Dr. White’s lab, the Weecology Interdisciplinary Research Group, and with Dr. John Harte’s lab at the University of California Berkeley. Applicants from a variety of backgrounds including ecology, mathematics, statistics, physics and computer science are encouraged to apply. The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Applications will be considered starting on March 7th, 2011. Go to the USU job page to see the full advertisement and to apply.
UPDATE: This position has now been filled.
Thoughts on developing a digital presence
A while ago there was a bit of discussion around the academic blogosphere recently regarding the importance of developing a digital presence and what the best form of that presence might be. Recently as I’ve been looking around at academics’ websites as part of faculty, postdoc and graduate student searchers going on in my department/lab I’ve been reminded of the importance of having a digital presence.
It seems pretty clear to me that the web is the primary source of information acquisition for most academics, at least up through the young associate professors. There are no doubt some senior folk who would still rather have a paper copy of a journal sent to them via snail mail and who rarely open their currently installed copy of Internet Explorer 6, but I would be very surprised if most folks who are evaluating graduate student, postdoctoral and faculty job candidates aren’t dropping the name of the applicant into their favorite search engines and seeing what comes up. They aren’t looking around for dirt like all those scary news stories that were meant to stop college students from posting drunken photos of themselves on social networking sites. They’re just procrastinating looking for more information to get a clearer picture of you as a scientist/academic. I also do a quick web search when I meet someone interesting at a conference, get a paper/grant to review with authors I haven’t heard of before, read an interesting study by someone I don’t know, etc. Many folks who apply to join my lab for graduate school find me through the web.
When folks go looking around for you on the web you want them to find something (not finding anything is the digital equivalent of “being a nobody”), and better yet you want them to find something that puts your best foot forward. But what should this be? Should you Tweet, Buzz, be LinkedIn, start a Blog, have a Wiki*, or maybe just get freaked out by all of this technology and move to the wilderness somewhere and never speak to anyone ever again.
I think the answer here is simple: start with a website. This is the simplest way to present yourself to the outside world and you can (and should) start one as soon as you begin graduate school. The website can be very simple. All you need is a homepage of some kind, a page providing more detailed descriptions of your research interests, a CV, a page listing your publications†, and a page with your contact information. Keep this updated and looking decent and you’ll have as good an online presence as most academics.
While putting together your own website might seem a little intimidating it’s actually very easy these days. The simplest approach is to use one of the really easy hosted solutions out there. These include things like Google Sites, which are specifically designed to let you make websites; or you can easily turn a hosted blogging system into a website (WordPress.com is often used for this). There are lots of other good options out there (let us know about your favorites in the comments). In addition many universities have some sort of system set up for letting you easily make websites, just ask around. Alternatively, you can get a static .html based template and then add your own content to it. Open Source Web Design is the best place I’ve found for templates. You can either open up the actual html files or you can use a WYSIWYG editor to replace the sample text with your own content. SeaMonkey is a good option for a WYSIWYG editor. Just ask your IT folks how to get these files up on the web when you’re done.
So, setting up a website is easy, but should you be doing other things as well and if so what. At the moment I would say that if you’re interested in trying out a new mode of academic communication then you should pick one that sounds like fun to you and give it a try; but this is by no means a necessity as an academic at the moment. If you do try to do some of these other things, then do them in moderation. It’s easy to get caught up in the rapid rewards of finishing a blog post or posting a tweet on Twitter, not to mention keeping up with others blogs and tweets, but this stuff can rapidly eat up your day and for the foreseeable future you won’t be getting a job based on your awesome stream of 140 character or less insights.
*Yep, that’s right, it’s a link to the Wikipedia page on Wiki’s. †And links to copies of them if you are comfortable flaunting the absurd copyright/licensing policies of many of the academic publishers (or if you only published in open access journals).No peer review crisis after all?
We’ve had a bit of discussion here at JE about potential solutions to the tragedy of the reviewer commons, so I found a recent letter in Nature (warning – it’s behind a pay wall) suggesting that there may not actually be a problem interesting. The take home message is:
At the journal Molecular Ecology, we find little evidence for the common belief that the peer-review system is overburdened by the rising tide of submissions.
and the authors base this conclusion on some basic statistics about the number of review requests required to obtain a reviewer and the average number of authors and reviewers for each paper. It’s not exactly the kind of hard, convincing data that will formally answer the question of whether there is a problem, but it’s interesting to hear that at least one journal’s editorial group isn’t particularly concerned about this supposedly impending disaster.
these unified theories have arrived with relatively little fanfare… [Quote]
…in the last 10 years ecology, specifically macroecology, has produced not one, but at least half a dozen different unified theories of biodiversity. These theories broadly unify ideas of area, abundance and richness to produce from a few underlying principles such seemingly distinct patterns as the species–area curve and the species abundance distribution. With one exception (neutral theory), these unified theories have arrived with relatively little fanfare. Unlike physics, unification has not been heralded as one of the highest achievements in ecology. No doubt this is in part due to certain sociological tendencies in ecology which fail to appreciate theory in general and especially theory that greatly simplifies the natural world (Kingsland 1995; Simberloff 2004).
- Brian McGill (in McGill 2010 published in Ecology Letters)
Earlier this year we featured this great paper by Brian McGill in our first Things you should read post. I was rereading it for a graduate seminar tomorrow and couldn’t help but post this great, beautifully dry, quote.
