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.

—
  (@weecology) December 28, 2011

folks 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 Some of it is unpublished, or not published in enough detail for us to include.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.

• 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!

(via, appropriately enough, @gvwilson and @TEDxWaterloo on Twitter)

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.

We think this is a cool idea, but currently it is a relatively ineffective way to find interesting papers; primarily because there simply aren’t enough folks in ecology discussing what they’ve read. EEB and Flow does a great job of this and a few other blogs by practicing scientists make occasional contributions in this regard (e.g., I’m a chordata, urochordata), but there certainly isn’t a critical mass yet. Part of the reason for this is that putting together full posts on articles one has read can take quite a bit of time, and time isn’t something most of us have a lot of lying around. Here at JE we have half a dozen Research Blogging style posts that we keep planning on writing, but finding a couple of hours to reread the paper and a couple of related works and put together a full post just doesn’t seem to happen.

So, today Jabberwocky Ecology announces a new kind of post – Things you should read. The idea behind these posts is to reduce the activation energy for posting about papers that we like. As such, these might be as short as the title of the paper and a link. Most of the time we’ll try to contextualize things a bit with a few sentences or a paragraph to help you figure out if the linked material is relevant to you, but these won’t be full blown summaries because these are things you should read, not things you should read about.

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.

Say NO!

You could easily spend your entire life as an assistant professor doing some combination of serving on departmental committees and student committees, going to seminars and workshops, checking email, sending email, meeting with students outside your group to “talk about their research”, reviewing for journals, etc. While much of this is technically within your job description no one really cares if you do any of these things. Seriously, they don’t. They will say that they do, they may ask you why you weren’t at the meeting on such and such, but when push comes to shove at the vast majority of research universities none of this matters. So learn to say No. This is hard for a lot of people, but it is critical to your success (and for me at least, happiness).

My approach to this challenge is that my default response to any request for me to spend time on anything other than research and teaching is No. This means that the activity has to be important enough to me to overcome the default response. A lot of professors that I know have the opposite default – they say yes unless there is a particular reason that they can’t participate. This typically ends up meaning that the only reason they don’t do something is because they already have something scheduled when it would occur. This is a great way to end up with a calendar that is chock full of things that having nothing to do with succeeding in the tenure process. A very successful senior colleague of mine once told me that every time someone asks him to be involved in something new he thinks about what he isn’t going do if he chooses to participate in this new activity. So, when someone asks me to do something my default response is no and if I then bypass the default because this new thing sounds worthwhile I then ask myself if I’d rather do it than the things that are already on my list.

Schedule time for your actual work

Most people will agree to schedule something as long as they don’t have a direct conflict on their calendar. The problem with this approach is two fold. First, it means that the only time you have to work on what really matters – conducting research, writing papers, and, to a lesser degree, preparing high quality classroom experiences (lectures, exercises, etc.) – is whatever’s left over after everything that doesn’t matter is scheduled. This is obviously a bit… backwards.

The second problem is that even if you have enough total time left over to dedicate to your primary interests/responsibilities that time will be chopped up into little blocks. The vast majority of scientists and other knowledge workers that I know do not work well with short chunks of time. That is because the real work of science and other intellectual pursuits requires serious thought and that often cannot be accomplished in thirty minute chunks.

My answer to this is to schedule large blocks of time on my calendar for research and teaching. I do all of my teaching during the spring semester so this means that in the fall I typically block out Tue-Thur mornings from 8-12 and all day Friday for research. In the spring I block out those same three mornings for class preparation and keep Friday reserved for research. When someone wants to schedule a meeting with me I give them a list of available times that does not include these reserved periods. It can be hard to stick to this system when someone is having a hard time scheduling a meeting, but I rarely make an exception and then only when the person who is trying to schedule the meeting has completely run out of options and isn’t trying to schedule things at the last minute (and frankly this combination is quite rare).

Hide

Even if you follow all of these suggestions, life will find a way to interrupt your efforts. Other faculty will stop by your office for a few minutes to chat, your graduate students or the staff or your department head will have a quick question or need a signature on something, a valued colleague will send you an email that you’d like to respond to quickly, a book vendor will stop by to tell you about their latest and greatest text book, and the next thing you know you’ve spent an entire day dealing with little things that have almost nothing to do with getting tenure. The only method that I have found for dealing with this is to hide. That can mean closing (and locking; seriously) your office door and not answering it under any circumstances, it can mean working in a remote corner of the library or some other hidden nook on campus, or it can mean working at home if the distractions there aren’t worse than those at the office. I aim for eight hidden hours a week, typically by working at home one day.

Prioritize your efforts (by focusing on your CV)

Of course in order any of this to work you need to know what is important when it comes to getting tenure. This can be difficult to determine because most institutions will basically tell you that everything is important. Research is important, teaching is important (and not just actually teaching well, but going to workshops on teaching, having a teaching philosophy grounded in cutting edge pedagogy, documenting your teaching, and your efforts to improve it, and your efforts to improve your documentation of it), service is important (and not just on committees, but educating the general public, visiting K-12 classrooms, helping the department recruit students at job fairs, and helping put together departmental packets for university awards). So, basically everything you can imagine is important… Except, of course, it really isn’t. If you are in position with a research role that is greater than or equal to your other roles (faculty positions have role statements associated with them that are typically broken out as percentages of research, teaching and service; e.g., 50% research, 40% teaching, 10% service) then what matters most is your research (and by a greater margin than your role statement indicates). I have a simple rule for prioritizing things when it comes to promotion and tenure considerations:

Things only matter if you put them on your CV and their importance is in proportion to the amount of space you dedicated to them on your CV.

Your CV is the document that you use to characterize your accomplishments in your job. As such, things that you include on it are the things that really matter – publications, grants, some (generally brief) indication that you have taught classes and perhaps that your students didn’t totally hate you. You probably have a small section on service, but that probably has more to do with service outside the university than within it. From what I’ve seen promotion and tenure hinges almost exclusively on your CV so this is the right strategy. If you don’t believe me try asking your department head when the last time someone didn’t get tenure primarly due to their teaching or service. This strategy also has the nice ancillary benefit that if your university really is more interested in how many committee meetings you’ve gone to than how many papers you’ve published, then you’ll be able to use your spiffy new vitae to get a job someplace that’s a little more serious about research, or teaching, or whatever it is that you actually got into academia to do.

UPDATE: I forgot to add the credit for the title of this post that is of course due to Mike Kaspari’s excellent blog on the topic and that there is some other excellent related advice on this subject over at The EEB & Flow.

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.

Truthfully, the return on our relatively modest investment in basic research over the last half-century is so astronomical that it’s impossible to calculate. Science hasn’t just stimulated the economy; it has revolutionized the economy, and our lives along with it.

which seems like it must be hyperbole, but at least from our perspective it certainly is not. However, if we had to pick our favorite moment in the article it would definitely be the paraphrase of Paul Baskin’s concern about the utility of this funding:

Aren’t we just subsidizing a bunch of nerds who already have cushy academic jobs and buy fancy Japanese-made instruments? No.

This is definitely one of the clearest, best, and funniest explanations of why funding basic science is critical to the economy and to society in general. Go check it out.