Category Archives: ecology
Why I will no longer review for your journal
I have, for a while, been frustrated and annoyed by the behavior of several of the large for-profit publishers. I understand that their motivations are different from my own, but I’ve always felt that an industry that relies entirely on both large amounts of federal funding (to pay scientists to do the research and write up the results) and a massive volunteer effort to conduct peer review (the scientists again) needed to strike a balance between the needs of the folks doing all of the work and the corporations need to maximize profits.
Despite my concerns about the impacts of increasingly closed journals, with increasingly high costs, on the dissemination of research and the ability of universities to support their core missions of teaching and research, I have continued to volunteer my time and effort as a reviewer to Elsevier and Wiley-Blackwell. I did this because I have continued to see valuable contributions made by these journals and I felt that this combined with the contribution that I was making to science by helping improve the science published in high profile places made supporting these journals worthwhile. I no longer believe this to be the case and from now on I will no longer be reviewing for any journal that is published by Elsevier, Springer, or Wiley-Blackwell (including society journals that publish through them).
Why have I changed my mind? Because of the pursuit/support by these companies of the Research Works Act. This act seeks to prevent funding agencies from requiring that the results of research that they funded be made publicly available. In other words it seeks to prevent the government (and the taxpayers that fund it), which pays for a very large fraction of the cost of any given paper through both funding the research and paying the salaries of reviewers and editors, from having any say in how that research is disseminated. I think that Mike Taylor in the Guardian said most clearly how I feel about this attempt to exert legislative control requiring us to support corporate profits over the dissemination of scientific research:
Academic publishers have become the enemies of science
This is the moment academic publishers gave up all pretence of being on the side of scientists. Their rhetoric has traditionally been of partnering with scientists, but the truth is that for some time now scientific publishers have been anti-science and anti-publication. The Research Works Act, introduced in the US Congress on 16 December, amounts to a declaration of war by the publishers.
You should read the entire article. It’s powerful. There are lots of other great articles about the RWA including Michael Eisen in the New York Times, a nice post by INNGE, and a interesting piece by Paul Krugman (via oikosjeremy). I’m also late to the party in declaring my peer review strike and less eloquent than many of my peers in explaining why (see great posts by Michael Taylor, Gavin Simpson, and Timothy Gowers). But I’m here now and I’m letting you know so that you can consider whether or not you also want to stop volunteering for companies that don’t have science’s best interests in mind.
If you’d like to read up on the publisher’s side of this argument (they have costs, they have a right to recoup them) you can see Springer’s official position or an Elsevier Exec’s exchange with Michael Eisen. My problem with all of these arguments is that there is nothing in any funding agency’s policy that requires publishers to publish work funded by that agency. This is not (as Springer has argued) an “unfunded mandate”, this is a stake holder that has certain requirements related to the publication of research in which they have an interest. This is just like an author (in any non-academic publishing situation) negotiating with a publisher. If the publisher doesn’t like the terms that the author demands, then they don’t have to publish the book. Likewise, if a publisher doesn’t like the NIH policy then they should simply not agree to publish NIH funded research.
To be clear, I am not as extreme in my position as some. I still support and will review for independent society journals like Ecology and American Naturalist even though they aren’t Open Access and even though ESA has made some absurd comments in support of the same ideas that are in RWA. The important thing for me is that these journals have the best interests of science in mind, even if they are often frustratingly behind the times in how they think and operate.
And don’t worry, I’ve still got plenty of journal related work to keep me busy, thanks to my new position on the editorial board at PLoS ONE.
UPDATE: The links to the INNGE and Timothy Gowers post have now been fixed, and here are links to a couple of great posts by Casey Bergman that I somehow left out: one on how to turn down reviews while making a point and one on the not so positive response he received to one of these emails.
UPDATE 2: A great collection of posts on RWA. There are a lot of really unhappy scientists out there.
UPDATE 3: A formal Boycott of Elsevier. Almost 1000 scientists have signed on so far.
A new database for mammalian community ecology and macroecology
There are a number of great datasets available for doing macroecology and community ecology at broad spatial scales. These include data on birds (Breeding Bird Survey, Christmas Bird Count), plants (Forest Inventory & Analysis, Gentry’s transects), and insects (North American Butterfly Association Counts). However, if you wanted to do work that relied on knowing the presence or abundance of individuals at particular sites (i.e., you’re looking for something other than range maps) there has never been a decent dataset to work with for mammals.
Announcing the Mammal Community Database (MCDB)
Over the past couple of years we’ve been working to fill that gap as best we could. Since coordinated continental scale surveys of mammals don’t yet exist [1] we dug into the extensive mammalogy literature and compiled a database of 1000 globally distributed communities. Thanks to Kate Thibault‘s leadership and the hard work of Sarah Supp and Mikaelle Giffen, we are happy to announce that this data is now freely available as a data paper on Ecological Archives.
In addition to containing species lists for 1000 locales, there is abundance data for 940 of the locations, some site level body size data (~50 sites) and a handful of reasonably long (> 10 yr) time-series as well. Most of the data is restricted to the particular mode of sampling that an individual mammalogist uses and as a result much of the data is for small mammals captured in Sherman traps.
Working with data compilations like this is always difficult because the differences in sampling intensity and approaches between studies can make it very difficult to compare data across sites. We’ve put together a detailed table of information on how sampling was conducted to help folks break the data into comparable subsets and/or attempt to control for the influence of sampling differences in their statistical models.
The joys of Open Science
We’ve been gradually working on making the science that we do at Weecology more and more open, and the MCDB is an example of that. We submitted the database to Ecological Archives before we had actually done much of anything with it ourselves [2], because the main point of collecting the data was to provide a broadly useful resource to the ecological community, not to answer a specific question. We were really excited to see that as soon as we announced it on Twitter
We just published a new data set of 1000 mammal communities esajournals.org/doi/abs/10.189… Check it out and do something cool with it.
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(@weecology) December 28, 2011folks started picking it up and doing cool things with it [3]. We hope that folks will find all sorts of uses for it going forward.
Going forward
We know that there is tons more data out there on mammal communities. Some of it is unpublished, or not published in enough detail for us to include. Some of it has licenses that mean that we can’t add it to the MCDB without special permission (e.g., there is a lot of great LTER mammal data out there). Lots of it we just didn’t find while searching through the literature.
If folks know of more data we’d love to hear about it. If you can give us permission to add data that has more restrictive licensing then we’d love to do so [4]. If you’re interested in collaborating on growing the database let us know. If there’s enough interest we can invest some time in developing a public portal.
The footnotes [5]
[1] We are anxiously awaiting NEON’s upcoming surveys, headed up by former Weecology postdoc Kate Thibault.
[2] We have a single paper that is currently in review that uses the data.
[3] Thanks to Scott Chamberlain and Markus Gesmann. You guys are awesome!
[4] To be clear, we haven’t been asking for permission yet, so no one has turned us down. We wanted to get the first round of data collection done first to show that this was a serious effort.
[5] Because anything that David Foster Wallace loved has to be a good thing.
Weecology at ESA
If folks are interested in seeing what Weecology has been up to lately we have a bunch of posters and talks at ESA this year. In order of appearance:
- Tuesday at 2:30 pm in Room 9AB our new postdoctoral researcher Dan McGlinn will be giving a talk on looking at community assembly using patterns of with- and between-species spatial variation.
- Tuesday afternoon at poster #28 Morgan will be presenting research on how the long-term community dynamics of the plant and rodent communities near Portal, AZ are related to decadal scale climate cycles. She’ll be there from 4:30 to 6:30 to chat, or stop by any time and take a look.
- Wednesday at 1:50 pm in Room 19A one of our new members, Elita Baldridge, will be giving a talk on her masters research on nested subsets.
- Wednesday at poster #139 Ethan will be presenting on our two attempts to make it easier to find and use ecological data. He’ll be there from 4:30 to 6:30 to chat, or stop by any time and take a look (or grab a computer and check out EcologicalData and the EcoData Retriever).
- Thursday at 1:50 pm in Room 10A another of our new members, Zack Brym, will be giving a talk on his masters research on controls on the invasion of an exotic shrub.
- Thursday at 4 pm in Room 8 Sarah Supp will give a talk on her work looking at the impacts of experimental manipulations on macroecological patterns (highlighted as a talk to see by Oiko’s blog)
- And last, but certainly not least, bright and early Friday morning at 8 am in Room 8 Kate Thibault (who has now moved on to fame and fortune at NEON) will be presenting on our work using maximum entropy models to predict the species abundance distributions of 16,000 communities.
Enjoy!
Some meandering thoughts on the difference between EcologicalData.org and DataONE
In the comments of my post on the Ecological Data Wiki Jarrett Byrnes asked an excellent question:
Very cool. I’m curious, how do you think this will compare/contrast/fight with the Data One project – https://www.dataone.org/ – or is this a different beast altogether?
As I started to answer it I realized that my thoughts on the matter were better served by a full post, both because they are a bit lengthy and because I don’t actually know much about DataONE and would love to have some of their folks come by, correct my mistaken impressions, and just chat about this stuff in general.
To begin with I should say that I’m still trying to figure this out myself, both because I’m still figuring out exactly what DataONE is going to be, and because EcologicalData is still evolving. I think that both projects goals could be largely defined as “Organizing Ecology’s Data,” but that’s a pretty difficult task, involving a lot of components and a lot of different ways to tackle them. So, my general perspective is that the more folks we have trying the merrier. I suspect there will be plenty of room for multiple related projects, but I’d be just as happy (even happier probably) if we could eventually find a single centralized location for handling all of this. All I want is solution to the challenge.
But, to get to the question at hand, here are the differences I see based on my current understanding of DataONE:
1. Approach. There are currently two major paradigms for organizing large amounts of information. The first is to figure out a way to tell computers how to do it for us (e.g., Google), the second is to crowdsource it’s development and curation (e.g., Wikipedia). DataONE is taking the computer based approach. It’s heavy on metadata, ontologies, etc. The goal is to manage the complexities of ecological data by providing the computer with very detailed descriptions of the data that it can understand. We’re taking the human approach, keeping things simple and trying to leverage the collective knowledge and effort of the field. As part of this difference in approach I suspect that EcologicalData will be much more interactive and community driven (the goal is for the community to actually run the site, just like Wikipedia) whereas DataONE will tend to be more centralized and hierarchical. I honestly couldn’t tell you which will turn out better (perhaps the two approaches will each turn out to be better for different things) but I’m really glad that we’re trying both at the same time to figure out what will work and where their relative strengths might be.
2. Actually serving data. DataONE will do this; we won’t. This is part of the difference in approach. If the computer can handle all of the thinking with respect to the data then you want it to do that and just spit out what you want. Centralizing the distribution of heterogeneous data is a really complicated task and I’m excited the folks at DataONE are tackling the challenge.
a. One of the other challenges for serving data is that is that you have to get all of the folks who “own” the data to let you provide it. This is one of the reasons I came up with the Data Wiki idea. By serving as a portal it helps circumvent the challenges of getting all of the individual stake holders to agree to participate.
b. We do provide a tool for data acquisition, the EcoData Retriever, that likewise focuses on circumventing the need to negotiate with data providers by allowing each individual investigator to automatically download the data from the source. But, this just sets up each dataset independently, whereas I’m presuming that DataONE will let you just run one big query of all the data (which I’m totally looking forward to by the way) [1].
3. Focus. The primary motivation behind the Data Wiki goes beyond identifying datasets and really focuses on how you should use them. Having worked with other folks’ data for a number of years I can say that the biggest challenging (for me anyway) is actually figuring out all of the details of when and how the dataset should be used. This isn’t just a question of reading metadata either. It’s a question of integrating thoughts and approaches from across the literature. What I would like to see develop on the Data Wiki pages is the development of concise descriptions for how to go about using these datasets in the best way possible. This is a very difficult task to automate and one where I think a crowdsourced solution is likely the most effective. We haven’t done a great job of this yet, but Allen Hurlbert and I have some plans to develop a couple of good examples early in the fall to help demonstrate the idea.
4. We’re open for business. Ha ha, eat our dust DataONE. But seriously, we’ve taken a super simple approach which means we can get up and running quickly. DataONE is doing something much more complicated and so things may take some time to roll out. I’m hoping to get a better idea of what their time lines look like at ESA. I’m sure their tools will be well worth the wait.
5. Oh, and their budget is a little over $2,000,000/year, which is just slightly larger than our budget of around $5,000/year.
So, there is my lengthy and meandering response to Jarrett’s question. I’m looking forward to chatting with DataONE folks at ESA to find out more about what they are up to, and I’d love to have them stop by here to chat and clear up my presumably numerous misconceptions.
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[1] Though we do have some ideas for managing something somewhat similar, so stay tuned for EcoData Retriever 2.0. Hopefully coming to an internet near you sometime this spring.
Distributed Ecology [Blogrolling]
I’ve been waiting for a while now for Ted Hart’s blog to get up enough steam to send folks over there, and since in the last two weeks he’s had three posts, revamped the mission of the blog, and engaged in the ongoing conversation about Lindenmayer & Likens, it seems like that time has arrived.
The blog is called Distributed Ecology because, as Ted describes,
I chose distributed ecology as a title because I like the idea of ecological thought like distributed computing. Lots of us scientists like little nodes around the web thinking and processing ideas into something great.
Sounds like what I’m hoping to see (and am increasingly witnessing) from the ecology blogs. So, head on over, check it out, click on the RSS button, and welcome Ted to the ecology blogging community.
A Plea for Pluralism
As you may have seen earlier either on Jabberwocky, EEB and Flow, or over at Oikos‘ new blog, the most recent piece about how some branch of ecology is ruining ecology has caused some discussion in the blogosphere. Everytime one of these comes out, I tell myself I’m going to write a blog post but then I think, “that’s just one cranky person,” and i get distracted doing science that is killing ecology (Given the plethora of opinions about what is ruining our field, odds are you too are killing ecology, regardless of what type of science you do). But as these opinion pieces keep emerging, I have increasingly come to feel that these debates on the ‘best’ approach reflect a very limited view of the scientific endeavor. Every approach (field ecology, microcosms, theory, meta-analysis, macroecology, insert your favorite approach that I’ve missed here) is fundamentally limited in its scope, focus, and ability to divine answers from nature, yet has unique strengths in what it allows us to do. Theory is abstracted from nature, but can also provide a concrete set of expectations and processes for empiricists to work with. Microcosms, while similarly critiqued for their abstraction from reality, can also give the clearest indication about whether ideas and theories work (or don’t) under the most ideal scenarios. Field ecology (particularly experimental manipulation) has been considered the gold standard for its ability to show cause and effect in ‘real’ ecosystems, but it is also messy, expensive, time-consuming (I say this thinking of my own field site, perhaps yours is less so) and in a natural setting it is impossible to have control over all of the important (and potentially confounding) variables. Macroecology and meta-analysis allow us to step back from individual systems and taxa to ask whether patterns and processes are general across nature, general within certain subsets of systems, or unpredictably important (and unimportant). However they lack the ability to manipulate nature directly to tease out cause and effect more definitively. Because all approaches have limitations, the exclusive use of any one approach is guaranteed to give us a limited and possibly flawed view of reality. In the scientific utopia that lives in my head, these different approaches to addressing scientific questions live together harmoniously, results from one approach generate questions best addressed with another approach and the cumulative evidence from all approaches give us a more complete understanding of nature. When I read opinion pieces that advocate for a particular approach above all others, I worry that this utopia only exists in my head. After all, those opinion pieces never seem to be balanced by a counter argument for plurality. But then sometimes I read things – often on the internet – and I think: it may be in my head, but maybe my head is not the only one that dream resides in.
Bridging, not building, divides in ecology [Things you should read]
There is an excellent post over at EEB & Flow on the empirical divide,inspired by an editorial by David Lindenmayer and Gene Likens in the most recent ESA Bulletin, titled “Losing the Culture of Ecology”. It was great to see some thoughtful and data driven consideration of the idea that we should choose to emphasize one broad area of ecology over another. I really like their conclusion that these “divides” are really driven by other things:
The tensions between “indoor ecology” and field ecology have been conflated with changes in the philosophy of modern ecology, in the difficulties of obtaining funding and publishing as a modern ecologist, and some degree of thinking the “grass is always greener” in the other field. In fact, the empirical divide may not be as wide as is often suggested.
This post motivated some discussion in the comments, and on Twitter,
Awesome post by @EEB_Flow on one of the many false divides in ecology. Why can't we just appreciate great science? evol-eco.blogspot.com/2011/07/empiri…—
Ethan White (@ethanwhite) July 26, 2011
Dear senior luminary ecologists,
Please stop writing papers about how your pet research area is discriminated against.
Seriously.
Ethan—
Ethan White (@ethanwhite) July 26, 2011
Change is needed for ecology to move forward->RT @ethanwhite: Dear senior luminary ecologists, Please stop wri… (cont) http://deck.ly/~eRoTC—
Scott Chamberlain (@recology_) July 26, 2011
And a nice follow up post by Jeremy Fox at the Oikos blog.
It’s all pretty short and well worth the read.
Postdoc position in Jim Brown’s group studying the major patterns of biodiversity
There is a new postdoctoral research position available in Jim Brown’s lab at the University of New Mexico to study some of the major patterns of biodiversity. We know a bit about the research and it’s going to be an awesome project with a bunch of incredibly bright people involved. Jim’s lab is also one of the most intellectually stimulating and supportive environments that you could possibly work in. Seriously, if you are even remotely qualified then you should apply for this position. We’re both thinking about applying and we already have faculty positions 
. Here’s the full ad:
The Department of Biology at the University of New Mexico is seeking applications for a post-doc position in ecology/biodiversity. The post doc will be expected to play a major role in a multi-investigator, multi- institutional project supported by a four-year NSF Macrosystems Ecology grant. The research will focus on metabolic processes underlying the major patterns of biodiversity, especially in pervasive temperature dependence and requires a demonstrated working knowledge of theory, mathematical and computer
modeling skills.Applicants must have a Ph.D. in ecology or a related discipline.
Review begins with the first applications and continues until the position is filled. Applicants must submit a cover letter and a curriculum vitae along with at least three phone numbers of references, three letters of recommendation and PDF’s of relevant preprints and publications to be sent directly to ecohire@unm.edu attn: James Brown. Application materials must be received by July 25, 2011, for best consideration.
Questions related to this posting may be directed to Dr. James Brown at ecohire@unm.edu or to Katherine Thannisch at kthannis@unm.edu.
The University of New Mexico is an Equal Opportunity/Affirmative Action Employer and Educator. Women and underrepresented minorities are encouraged to apply.
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.
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*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.
