Jabberwocky Ecology

Four basic skill areas for a macroecologist [Guest post]

This is a guest post by Elita Baldridge (@elitabaldridge), a graduate student in Ethan White’s lab in the Ecology Center at Utah State University.

As a budding macroecologist, I have thought a lot about what skills I need to acquire during my Ph.D. This is my model of the four basic attributes for a macroecologist, although I think it is more generally applicable to many ecologists as well:

  • Data
  • Statistics
  • Math
  • Programming

Data:

  • Knowledge of SQL
  • Dealing with proper database format and structure
  • Finding data
  • Appropriate treatments of data
  • Understanding what good data are

Statistics:

  • Bayesian
  • Monte Carlo methods
  • Maximum likelihood methods
  • Power analysis
  • etc.

Math:

  • Higher level calculus
  • Should be able to derive analytical solutions for problems
  • Modelling

Programming:

  • Should be able to write programs for analysis, not just simple statistics and simple graphs.
  • Able to use version control
  • Once you can program in one language, you should be able to program in other languages without much effort, but should be fluent in at least one language.

General recommendations:

Achieve expertise in at least 2 out of the 4 basic areas, but be able to communicate with people who have skills in the other areas.  However, if you are good at collaboration and come up with really good questions, you can make up for skill deficiencies by collaborating with others who possess those skills.  Start with smaller collaborations with the people in your lab, then expand outside your lab or increase the number of collaborators as your collaboration skills improve.

Gaining skills:

Achieving proficiency in an area is best done by using it for a project that you are interested in.  The more you struggle with something, the better you understand it eventually, so working on a project is a better way to learn than trying to learn by completing exercises.

The attribute should be generalizable to other problems:  For example, if you need to learn maximum likelihood for your project, you should understand how to apply it to other questions.  If you need to run an SQL query to get data from one database, you should understand how to write an SQL query to get data from a different database.

In graduate school:

Someone who wants to compile their own data or work with existing data sets needs to develop a good intuitive feel for data; even if they cannot write SQL code, they need to understand what good and bad databases look like and develop a good sense for questionable data, and how known issues with data could affect the appropriateness of data for a given question. The data skill is also useful if a student is collecting field data, because a little bit of thought before data collection goes a long way toward preventing problems later on.

A student who is getting a terminal master’s and is planning on using pre-existing data should probably be focusing on the data skill (because data is a highly marketable skill, and understanding data prevents major mistakes).  If the data are not coming from a central database, like the BBS, where the quality of the data is known, additional time will have to be added for time to compile data, time to clean the data, and time to figure out if the data can be used responsibly, and time to fill holes in the data.

Master’s students who want to go on for a Ph.D. should decide what questions they are interested in and should try to pick a project that focuses on learning a good skill that will give them a headstart- more empirical (programming or stats), more theoretical (math), more applied (math (e.g., for developing models), stats(e.g., applying pre-existing models and evaluating models, etc.), or programming (e.g. making tools for people to use)).

Ph.D. students need to figure out what types of questions they are interested in, and learn those skills that will allow them to answer those questions.  Don’t learn a skill because it is trendy or you think it will help you get a job later if you don’t actually want to use that skill.  Conversely, don’t shy away from learning a skill if it is essential for you to pursue the questions you are interested in.

Right now, as a Ph.D. student, I am specializing in data and programming.  I speak enough math and stats that I can communicate with other scientists and learn the specific analytical techniques I need for a given project.  For my interests (testing questions with large datasets), I think that by the time I am done with my Ph.D., I will have the skills I need to be fairly independent with my research.

Graduate student opening with Weecology

We’re looking for a new student to join our interdisciplinary research group. The opening is in Ethan’s lab, but the faculty, students, and postdocs in Weecology interact seamlessly among groups. If you’re interested in macroecology, community ecology, or just about anything with a computational/quantitative component to it, we’d love to hear from you. The formal ad is included below (and yes, we did include links to our blog, twitter, and our GitHub repositories in the ad). Please forward this to any students who you think might be a good fit, and let us know if you have any questions.

GRADUATE STUDENT OPENING

The White Lab at Utah State University has an opening for a graduate student with interests in Macroecology, Community Ecology, or Ecological Theory/Modeling.  Active areas of research in the White lab include broad scale patterns related to biodiversity, abundance and body size, ecological dynamics, and the use of sensor networks for studying ecological systems. We use computational, mathematical, and advanced statistical methods in much of our work, so students with an interest in these kinds of methods are encouraged to apply. Background in these quantitative techniques is not necessary, only an interest in learning and applying them. While students interested in one of the general areas listed above are preferred, students are encouraged to develop their own research projects related to their interests. The White Lab is part of an interdisciplinary ecology research group (http://weecology.org) whose goal is to facilitate the broad training of ecologists in areas from field work to quantitative methods. Students with broad interests are jointly trained in an interdisciplinary setting. We are looking for students who want a supportive environment in which to pursue their own ideas. Graduate students are funded through a combination of research assistantships, teaching assistantships, and fellowships. Students interested in pursuing a PhD are preferred. Utah State University has an excellent graduate program in ecology with over 50 faculty and 80+ graduate students across campus affiliated with the USU Ecology Center (http://www.usu.edu/ecology/).

Additional information about the position and Utah State University is available at:
http://whitelab.weecology.org/grad-student-opening

Interested students can find more information about our group by checking out:
Our websites: http://whitelab.weecology.org, http://weecology.org
Our code repositories: http://github.com/weecology
Our blog: http://jabberwocky.weecology.org
And Twitter: http://twitter.com/ethanwhite

Interested students should contact Dr. Ethan White (ethan.white@usu.edu) by December 1st, 2012 with their CV, GPA, GRE scores (if available), and a brief statement of research interests.

Postdoc in Evolutionary Bioinformatics [Jobs]

There is an exciting postdoc opportunity for folks interested in quantitative approaches to studying evolution in Michael Gilchrist’s lab at the University of Tennessee. I knew Mike when we were both in New Mexico. He’s really sharp, a nice guy, and a very patient teacher. He taught me all about likelihood and numerical maximization and opened my mind to a whole new way of modeling biological systems. This will definitely be a great postdoc for the right person, especially since NIMBioS is at UTK as well. Here’s the ad:

Outstanding, motivated candidates are being sought for a post-doctoral position in the Gilchrist lab in the Department of Ecology & Evolutionary Biology at the University of Tennessee, Knoxville. The successful candidate will be supported by a three year NSF grant whose goal is to develop, integrate and test mathematical models of protein translation and sequence evolution using available genomic sequence and expression level datasets. Publications directly related to this work include Gilchrist. M.A. 2007, Molec. Bio. & Evol. (http://www.tinyurl/shahgilchrist11) and Shah, P. and M.A. Gilchrist 2011, PNAS (http://www.tinyurl/gilchrist07a).

The emphasis of the laboratory is focused on using biologically motivated models to analyze complex, heterogeneous datasets to answer biologically motivated questions. The research associated with this position draws upon a wide range of scientific disciplines including: cellular biology, evolutionary theory, statistical physics, protein folding, differential equations, and probability. Consequently, the ideal candidate would have a Ph.D. in either biology, mathematics, physics, computer science, engineering, or statistics with a background and interest in at least one of the other areas.

The researcher will collaborate closely with the PIs (Drs. Michael Gilchrist and Russell Zaretzki) on this project but potentiall have time to collaborate on other research projects with the PIs. In addition, the researcher will have opportunties to interact with other faculty members in the Division of Biology as well as researchers at the National Institute for Mathematical and Biological Synthesis (http://www.nimbios.org).

Review of applications begins immediately and will continue until the position is filled. To apply, please submit curriculum vitae including three references, a brief statement of research background and interests, and 1-3 relevant manuscripts to mikeg[at]utk[dot]edu.

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.

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.