Jabberwocky Ecology

How technology can help scientists with chronic illnesses (or Technology FTW!)

This is a guest post by Elita Baldridge (@elitabaldridge)

I am currently the remotely working member of Weecology, finishing up my PhD in the lower elevation and better air of Kansas, while the rest of my colleagues are still in Utah, due to developing a chronic illness and finally getting diagnosed with fibromyalgia.  The relocation is actually working out really well.  I’m in better shape because I’m not having to fight the air too, and I’m finally making real progress toward finishing my dissertation again.

I ruthlessly culled everything that wasn’t directly working on my dissertation.  I was going to attend the Gordon Conference this year, as I had heard fantastic things about it for years, but had not been ready to go yet, but I had to drop that because I wasn’t physically able to travel.  I did not go to ESA, because I couldn’t travel.  There are working groups and workshops galore, all involving travel, which I cannot do.  Right now, the closest thing that we have to bringing absent scientists to an event is live tweeting, which is not nearly as good as hearing a speaker for yourself, and is pretty heartbreaking if you had to cancel your plans to attend an event because you were too infirm to go.The tools that I’m using to do science remotely are not just for increasing accessibility for a single chronically ill macroecologist.  They are good tools for science in general.  I’m using GitHub to version control my code, and Dropbox to share data and figures.  Ethan can see what I’m working on as I’m doing it, and I’ve got a clear record of what I was doing and what decisions that I made. While my cognitive dysfunction may be a bit more extreme of a problem, I know that we’ve all stayed up too late coding and broken something we shouldn’t have and the ability to wave the magic Git wand and make any poor decisions that I made while my brain was out to lunch go away is priceless.

Open access?  Having open access to papers is really important when you are going to be faced shortly with probably not having any institutional access anymore.  Also, important for everyone else who isn’t at a major university with very expensive subscriptions to all the journals.  Having open access to data and code is crucial when you can’t collect your own data and are going to be doing research from your home computer on the cheap because you can’t rely on your body to work reliably at any given point in time.

Video conferencing is working well for me to meet with the lab, but could also be great for attending conferences and workshops.  This would not only be good for a certain macroecologist, but would also be good to include people from smaller universities, etc. who would like to participate in these type of things too, but can’t otherwise due to the travel.  I did my master’s degree at Fort Hays State University, and I still love it dearly.  This type of increased accessibility would have been great for me while I was a perfectly healthy master’s student.  Fort Hays is a primarily undergraduate institution in the middle of Kansas, about four hours away from any major city, and it does not have some of the resources that a larger university would have.  No seminar series, no workshops, not much travel money to go to workshops or conferences, which doesn’t mean that good science can’t still be happening.

Many of my labmates are looking for post-docs, or are already in postdoc positions at this point.  I’m very excited for all of them, and await eagerly all the stories of the exciting new things they are doing.  Having a chronic illness limits what I am capable of doing physically.  I am not going to be able to move across the country for a post-doc.  That does not mean that I do not want to play science too.  I’ve got my home base set up, and I can reach pretty far from here.  I still want to be a part of living science, I don’t want to have to get to the party after everyone else has gone home.

And I wonder, why can I not do these things?  Is it not the future?  Do we not have the internet, with video chat?  I get to meet with Ethan and talk science at our weekly meetings every week.  I go to lab meetings with video chat, and get to see what my labmates are doing, and crack jokes, and laugh at other people’s jokes.  It wouldn’t be hard to get me to conferences and working groups either.

With technology, I get to be a part of living, breathing science, and it is a beautiful thing.

Unifying Ecology Across Scales: The role of nutrients, metabolism, and physiology [Announcement]

As some of you may know, I’ve been working with Michael Angilletta for the past year on organizing a Gordon Research Conference. I announced the mentoring program that is affiliated with the conference last week, but here is the official info on the conference itself. Please forgive a little repetition from the mentoring program post.

Application Deadline: June 22, 2014

When and Where: July 20-25 2014 at the University of New England, Biddeford Maine

Conference Topic: Many of the impacts humans have on nature affect patterns and processes at multiple spatial, temporal, or organizational scales. Thus predicting the response of nature to human impacts is challenging because changes in one scale can have profound impacts on patterns and processes at other scales of nature. Because ecology has traditionally been focused on patterns and processes at single scales, we have few approaches that allow us to understand cross-scale feedbacks that can influence the patterns and processes we are interested in predicting. The Gordon Research Conference on ‘Unifying Ecology Across Scales: the role of nutrients, metabolism, and physiology’ is a small conference focused on exploring how the availability, acquisition, and transference of energy and nutrients can link patterns and processes across spatial, organizational, and temporal scales. Our goal is to provide a venue for people interested in this topic to discuss the current state of the field and discuss how to promising avenues of future research. Research interests of participants span the diverse areas of ecology, evolution, and physiology, but are united in an interest to use energy and nutrients to unify different areas and approaches to ecology.

What is a Gordon Research Conference?: Gordon Research Conferences (GRC) are well known in some fields, but the number of ecology related GRCs is low, so many of us haven’t heard of one before. A Gordon Research Conference is a small conference ( < 200 people) focused on a specific topic. In our case, the topic is trying to link patterns and processes across scales using nutrients, metabolism, and physiology. Speakers at GRCs are by invite only, but there is a poster session almost every afternoon for attendees to present their research. The poster session is not just for the junior people to present. Well known senior people tack up posters and stand by them too.

The structure of a GRC is also pretty unique. Talks occur in the mornings and evenings, leaving the afternoons free for informal discussions, formation of collaborations, and recreational activities (our conference site has kayaking as well as other organized opportunities). Attendees all sleep in the same dorm and eat at the same cafeteria, further creating opportunities for interactions and discussions.

Applying to attend: Registration is now open.

GRC’s have a unique approach to the application process. You have to submit an application which the conference chairs (that’s me and Michael Angilletta) can then decide to accept or reject. Then you’ll get an ‘invitation’ to actually register. Don’t let the fear of rejection stop you from applying though. We have historically had space for everyone who wants to come.

Special events for graduate students and postdocs: We have a Gordon Research Seminar (GRS) associated with our conference focused on “understanding the drivers of biological systems by integrating metabolism, physiology, and macroecology”.  Gordon Research Seminars provide opportunities for graduate students and postdocs to present their research and network with their peers and a small number of senior scientists mentors before the main conference. Feedback from people who have attended these has been universally positive. In fact, when we didn’t have these one year, there was a huge outcry to bring them back. You have to apply for the GRS separately from the GRC. The conference chairs for the GRS are Sarah Supp and Sarah Diamond. The GRS registration process is also currently open. Dates for the GRS are July 19-20, 2014.

This year we are also excited to announce we have a mentoring program at the conference that graduate students and postdocs who plan on attending the conference can apply for. We have limited slots for this (approximately 20). Details can be found here.

Who is Speaking?: To (hopefully) get you even more excited about attending, here is the list of session topics, speakers, and discussion leaders for the conference. UPDATED: We’ve added a number of lightning talks (short talks). Those speakers have now been added below. If you want titles as well, the full schedule for the conference (with talk titles) is available here

Day 1:

Session Topic 1: Developing Unified Theories of Ecology

Leader Name:  Pablo Marquet

Speaker Names:  Michael Sears / John Harte

Day 2:

Session Topic 2: Macrophysiology Meets Macroecology

Leader Name:  Lauren Buckley

Speaker Names:  Piero Calosi / Amy Angert

Session Topic 3: Biogeography of Environmental Tolerance

Leader Name:  Jennifer Sunday

Speaker Names:  Sarah Diamond / Hans Otto Portner

Lightning Talks: Lacy Chick / Richard Feldman

Day 3:

 Session Topic 4: Metabolic Adaptation to Changing Environments

Leader Name:  Craig White

Speaker Names:  Daniel Naya / Carla Sgro

Session Topic 5: Mechanistic Basis of Macroecological Patterns

Leader Name:  Brian Enquist

Speaker Names:  Ethan White / Sally Keith

Lightning Talks: Nika Galic / David Harris / Xiao Xiao

Day 4:

Session Topic 6: Linking Organismal Traits to Community Dynamics

Leader Name:  Elena Litchman

Speaker Names:  Catherine Graham / Stephanie Dutkiewicz

 Session Topic 7: Using Stoichiometry to Link Organisms and Ecosystems

Leader Name:  Susan Kilham

Speaker Names:  Elizabeth Borer / Phil Taylor

Lightning Talks: Angelica Gonzalez / Catherine Hulshof

Day 5:

 Session Topic 8: Predicting Diversity across Scales

Leader Name:  Brian McGill

Speaker Names:  Maria Dornelas / Jessica Blois

 Session Topic 9: Integrating Ecological Processes at the Macroscale

Leader Name:  James Brown

Speaker Names:  Michael Kearney / James Brown

Lightning Talks: John Grady / Rebecca Trebilco / Joshua Rapp

Ignite Talk: Big Data in Ecology

Slides and script from Ethan White’s Ignite talk on Big Data in Ecology from Sandra Chung and Jacquelyn Gill‘s excellent ESA 2013 session on Sharing Makes Science Better. Slides are also archived on figshare.

Title slide

1.  I’m here to talk to you about the use of big data in ecology and to help motivate a lot of the great tools and approaches that other folks will talk about later in the session.

Photos of field work

2.  The definition of big is of course relative, and so when we talk about big data in ecology we typically mean big relative to our standard approaches based on observations and experiments conducted by single investigators or small teams.

Image of Microsoft Excel

3.  And for those of you who prefer a more precise definition, my friend Michael Weiser defines big data and ecoinformatics as involving anything that can’t be successfully opened in Microsoft Excel.

Map of Breeding Bird Survey

4.  Data can be of unusually large size in two ways. It can be inherently large, like citizen science efforts such as Breeding Bird Survey, where large amounts of data are collected in a consistent manner.

Images of Dryad, figshare, and Ecological Archives

5.  Or it can be large because it’s composed of a large number of small datasets that are compiled from sources like Dryad, figshare, and Ecological Archives to form useful compilation datasets for analysis.

Dataset logos

6.  We have increasing amounts of both kinds of data in ecology as a result of both major data collection efforts and an increased emphasis on sharing data.

Maps and quote about large scale ecology from NEON

7-8.  But what does this kind of data buy us. First, big data allows us to work at scales beyond those at which traditional approaches are typically feasible. This is critical because many of the most pressing issues in ecology including climate change, biodiversity, and invasive species operate at broad spatial and long temporal scales.

Map and results of general analysis

9-10.  Second, big data allows us to answer questions in general ways, so that we get the answer today instead of waiting a decade to gradually compile enough results to reach concensus. We can do this by testing theories using large amounts of data from across ecosystems and taxonomic groups, so that we know that our results are general, and not specific to a single system (e.g., White et al. 2012).

The most interesting man in the worlds says: I don't always analyze data, but when I do, I prefer a lot of it

11. This is the promise of big data in ecology, but realizing this potential is difficult because working with either truly big data or data compilations is inherently challenging, and we still lack sufficient data to answer many important questions.

Bullett points: 1. Training, 2. Tools, 3. More data.

12. This means that if we are going to take full advantage of big data in ecology we need 3 things. Training in computational methods for ecologists, tools to make it easier to work with existing data, and more data.

Logos of groups running training initiatives

13. We need to train ecologists in the computational tools needed for working with big data, and there are an increasing number of efforts to do this including Software Carpentry (which I’m actively involved in) as well as training initiatives at many of the data and synthesis centers.

Logos for DataONE, Dryad, NEON, Morpho, and DataUP

14. We need systems for storing, distributing, and searching data like DataONE, Dryad, NEON‘s data portal, as well as the standardized metadata and associated tools that make finding data to answer a particular research question easier.

Screenshot of Ecological Data Wiki

15. We need crowd-sourced systems like the Ecological Data Wiki to allow us to work together on improving insufficient metadata and understanding what kinds of analyses are appropriate for different datasets and how to conduct them rigorously.

rOpenSci and EcoData Retriever logos

16. We need tools for quickly and easily accessing data like rOpenSci and the EcoData Retriever so that we can spend our time thinking and analyzing data rather than figuring out how to access it and restructure it.

Map of Life, GBIF, and EcoData Retriever logos

17. We also need systems that help turn small data into big data compilations, whether it be through centralized standardized databases like GBIF or tools that pull data together from disparate sources like Map of Life.

Screen shot of preprint, and Morpho, DataUP, and CC0 logos

18. And finally we we need to continue to share more and more data and share it in useful ways. With the good formats, standardized metadata, and open licenses that make it easy to work with.

Dataset logos

19. And so, what I would like to leave you with is that we live in an exciting time in ecology thanks to the generation of large amounts of data by citizen science projects, exciting federal efforts like NEON, and a shift in scientific culture towards sharing data openly.

River Ernest-White saying "Aw Dad, Big Data s sch a buzz word"

20. If we can train ecologists to work with and combine existing tools in interesting ways, it will let us combine datasets spanning the surface of the globe and diversity of life to make meaningful predictions about ecological systems.

Metabolic Basis of Ecology Meeting [Announcement]

Are you interested in stoichiometry? Energy flow through individuals, communities or ecosystems? Implications of organismal physiology? Do you like macroecology? Field experiments? Lab experiments? Theory? Are you particularly interested in integrating various combinations of the above? Every four two years, people with a general interest in talking about metabolism and how it impacts various aspects of ecology and evolution get together at a Gordon Research Conference focused on the Metabolic Basis of Ecology. The topic is broadly defined and this year is organized around the theme: The Metabolic Basis of Ecology and Evolution in a Changing World. One of the nice things about the meeting is that its typically small ( < 150 people) and includes a lot of broad thinkers. If you’ve never attended a Gordon Conference before, they are organized around invited speaker sessions, small poster sessions, and scheduled time for meeting and interacting in between. You have to apply for the conference before you can register, but the deadline for those applications is imminent (June 24th). The meeting is July 22-27, 2012 at the University of New England (Biddeford, ME). The list of speakers and other information about the conference can be found here.

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.


Getting things done in academia

In a couple of days I’m participating in a panel to help young faculty be ready for their 3rd year review (the halfway step to tenure, which is kind of a big deal at my institution). This is the sort of thing that I normally say no to, but I’ve been to a couple of these things and I just couldn’t bear the thought of another group of young faculty being told that what they really needed to do to get tenure is to have a really spiffy tenure binder… so I’m going to talk about what they actually need to do to get tenure – get stuff done – and I thought it would be worth posting my thoughts on this here for broader consumption. This advice is targeted at assistant professors at research universities, but folks in other situations may be able to adapt it to their individual circumstances (e.g., if you’re at a small liberal arts college or other teaching centered school try swapping research and teaching below). Since the goal of the workshop is getting through the first phase of tenure, this is about what you need to do to accomplish that goal, not what you should be doing in any sort of broader philosophical sense. This advice is built on the lessons that Morgan (my wife and co-blogger for those of you new to JE; in fact she was so instrumental in developing these ideas that even though I’m using the first person singular this will be listed as a co-authored post) and I have learned during our time as assistant professors.

Read More

Biological Diversity in a Changing World – Royal Society Discussion Meeting

I’m going to be participating in a Royal Society Discussion Meeting and they’ve asked us to advertise this to interested parties so I figured I’d just post about it here. The meeting is on Biological Diversity in a Changing World and (other than your humble narrator) has a pretty impressive list of speakers. Here are the key bits of information (straight from the meeting’s web page).


We live in a world in which biological diversity is under threat as never before. This meeting will draw insights from organisms ranging from microbes to mammals to show why a deeper understanding of temporal processes in ecological communities is essential in coping with the changes that the natural world – and the humans that inhabit it – will experience over the next 50 years.

Speakers and chairs

Speakers and chairs include Professor John Beddington CMG FRS, Professor Mike Benton, Professor Anne Chao, Professor Andrew Clarke, Professor Rita Colwell, Professor Robert Colwell, Dr Maria Dornelas, Professor Anne Glover, Professor Nicholas Gotelli, Dr Jessica Green, Professor Jeremy Jackson, Dr Kathleen Lyons, Dame Georgina Mace FRS, Professor Anne Magurran, Lord Robert May FRS, Dr Rebecca Morris, Professor Marian Scott OBE, Professor William Sutherland and Dr Ethan White.


This meeting is free to attend, but pre-registration (online) is essential. Click here to register.
The online registration form and programme information can be found at royalsociety.org/events-diary.