Jabberwocky Ecology

I am a graduate student. I have fibromyalgia.

This is a guest post by Elita Baldridge (@elitabaldridge). She is a graduate student in our group who has been navigating the development of a chronic illness during graduate school. She is sharing her story to help spread awareness of the challenges faced by graduate students with chronic illnesses. She wrote an excellent post on the PhDisabled blog about the initial development of her illness that I encourage you to read first.

During my time as a Ph.D. student, I developed a host of bizarre, productivity eating symptoms, and have been trying to make progress on my dissertation while also spending a lot of time at doctors’ offices trying to figure out what is wrong with me. I wrote an earlier blog post about dealing with the development of a chronic illness as a graduate student at the PhDisabled Blog.

When the rheumatologist handed me a yellow pamphlet labeled “Fibromyalgia”, I felt a great sense of relief. My mystery illness had a diagnosis, so I had a better idea of what to expect. While chronic, at least fibromyalgia isn’t doing any permanent damage to joints or brain. However, there isn’t a lot known about it, the treatment options are limited, and the primary literature is full of appallingly small sample sizes.

There are many symptoms which basically consisting of feeling like you have the flu all the time, with all the associated aches and pains. The worst one for me, because it interferes with my highly prized ability to think, is the cognitive dysfunction, or, in common parlance, “fibro fog”. This is a problem when you are actively trying to get research done, as sometimes you remember what you need to do, but can’t quite figure out how navigating to your files in your computer works, what to do with the mouse, or how to get the computer on. I frequently finish sentences with a wave of my hand and the word “thingy”. Sometimes I cannot do simple math, as I do not know what the numbers mean, or what to do next. Depending on the severity, the cognitive dysfunction can render me unable to work on my dissertation as I simply cannot understand what I am supposed to do. I’m not able to drive anymore, due to the general fogginess, but I never liked driving that much anyway. Sometimes I need a cane, because my balance is off or I cannot walk in a straight line, and I need the extra help. Sometimes I can’t be in a vertical position, because verticality renders me so dizzy that I vomit.

I am actually doing really well for a fibromyalgia patient. I know this, because the rheumatologist who diagnosed me told me that I was doing remarkably well. I am both smug that I am doing better than average, because I’m competitive that way, and also slightly disappointed that this level of functioning is the new good. I would have been more disappointed, only I had a decent amount of time to get used to the idea that whatever was going on was chronic and “good” was going to need to be redefined. My primary care doctor had already found a medication that relieved the aches and pains before I got an official diagnosis. Thus, before receiving an official diagnosis, I was already doing pretty much everything that can be done medication wise, and I had already figured out coping mechanisms for the rest of it. I keep to a strict sleep schedule, which I’ve always done anyway, and I’ve continued exercising, which is really important in reducing the impact of fibromyalgia. I should be able to work up my exercise slowly so that I can start riding my bicycle short distances again, but the long 50+ mile rides I used to do are probably out.

Fortunately, my research interests have always been well suited to a macroecological approach, which leaves me well able to do science when my brain is functioning well enough. I can test my questions without having to collect data from the field or lab, and it’s easy to do all the work I need to from home. My work station is set up right by the couch, so I can lay down and rest when I need to. I have to be careful to take frequent breaks, lest working too long in one position cause a flare up. This is much easier than going up to campus, which involves putting on my healthy person mask to avoid sympathy, pity, and questions, and either a long bus ride or getting a ride from my husband. And sometimes, real people clothes and shoes hurt, which means I’m more comfortable and spending less energy if I can just wear pajamas and socks, instead of jeans and shoes.

Understand that I am not sharing all of this because I want sympathy or pity. I am sharing my experience as a Ph.D. student developing and being diagnosed with a chronic illness because I, unlike many students with any number of other short term or long term disabling conditions, have a lot of support. Because I have a great deal of family support, departmental support, and support from the other Weecologists and our fearless leaders, I should be able to limp through the rest of my Ph.D. If I did not have this support, it is very likely that I would not be able to continue with my dissertation. If I did not have support from ALL of these sources, it is also very likely that I would not be able to continue. While I hope that I will be able contribute to science with my dissertation, I also think that I can contribute to science by facilitating discussion about some of the problems that chronically ill students face, and hopefully finding solutions to some of those problems. To that end, I have started an open GitHub repository to provide a database of resources that can help students continue their training and would welcome additional contributions. Unfortunately, there doesn’t seem to be a lot. Many medical Leave of Absence programs prevent students from accessing university resources- which also frequently includes access to subsidized health insurance and potentially the student’s doctor, as well as removing the student from deferred student loans.

I have fibromyalgia. I also have contributions to make to science. While I am, of course, biased, I think that some contribution is better than no contribution. I’d rather be defined by my contributions, rather than my limitations, and I’m glad that my university and my lab aren’t defining me by my limitations, but are rather helping me to make contributions to science to the best of my ability.

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.

Crowdfunding for Science 101 [guest post]

Ethan and I have been watching the emergence of crowdfunding in science with great interest. We meant to blog about it, but our rate of blog idea generation is >> our rate of blog writing. So, when Mary Rogalski, a graduate student at Yale who is participating in #SciFund (one of the crowdfunding sites being run by ecologists) asked if we might be interested in blogging about this new phenomena, we thought this was an opportune time for us to recruit a knowledgeable guest blogger!  When you’re done reading her post, wander over to #SciFund and check out Mary’s project and the other intrepid young scientists experimenting with this new venue.

 Now, introducing Mary Rogalski….

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You may have heard of crowdfunding – it’s sort of a combination of venture capitalism and social networking.  Artists, musicians, and video game developers have netted thousands or even millions of dollars by gathering small donations from the interested public.  In fact, crowdfunding is now a multibillion dollar industry.

Until recently I was peripherally aware of this flurry of activity, but it was only after I heard of scientists using crowdfunding to support their research that I began to pay attention.   If you’ve ever applied for research grants you know how competitive the process can be.  This only seems to have intensified as we tighten our belts to deal with the ongoing recession.

Two students in my lab recently raised $7,000 for their master’s project by crowdfunding through the group Petridish.  Impressed with their success, I decided to investigate the possibilities.  A friend shared an article in Nature that discussed crowdfunding, featuring the #SciFund Challenge. #SciFund caught my eye for two reasons.  First, unlike some crowdfunding campaigns, participants receive funds even if they fail to reach their funding target.  Second, #SciFund’s mission to teach scientists to more effectively engage with the general public resonates with my own career goals.

I submitted a short description of my research to the #SciFund organizers, Jai Ranganathan and Jarrett Byrnes, and was deemed worthy of joining round 2 of the #SciFund Challenge!  I quickly found that crowdfunding requires a lot of time and energy.  Overall I would say that I have spent close to 40 hours creating my project description and video, and an hour or two per day over the past three weeks promoting my project.

A short video serves as the centerpiece of a #SciFund campaign.   In only 2-3 minutes I had a lot of information to convey.  I study ecological and evolutionary responses to pollution exposure over long time scales.  I work in lakes, using the sediment record to reconstruct changes in heavy metal contamination and cyanobacteria blooms over the past century.  Zooplankton resting egg banks in these same sediments provide a means of examining ecological and evolutionary trends over the same time scales.  I will hatch Daphnia from resting eggs to see which species were better able to tolerate polluted conditions.  Later I will examine evolutionary responses over time.

I struggled to explain my project in three minutes – not to mention, I had never made a video before!  I decided that people would be most interested in the fact that I can “resurrect” animals from the past to see how they were affected by environmental conditions that they experienced.  In focusing on the “how” of my research, I think I might have sacrificed a bit too much of the “why”.  Why do we even care about long-term effects of pollution?  (I can give you lots of reasons, but they didn’t end up in the video!)  Considering it’s my first attempt at making such a video, I do like how it turned out.

During the month of April, the 75 participants in the #SciFund Challenge created draft videos and written descriptions of our research.   We reviewed each other’s work, focusing on creating clear, compelling language.

When the Challenge launched on May 1, we were coached on how to best spread the word about our projects.  First I alerted my close friends and family about my crowdfunding campaign.  Once I received some traction, I reached out to my broader social networks, asking my friends and colleagues to spread the word.  From here, outreach is only limited by your own creativity and time investment.  Before beginning my crowdfunding adventure my exposure to the world of science media was limited.  I felt overwhelmed by the number and diversity of blogs out there, not to mention newspapers, journals, Facebook groups, and scientists that Tweet.  I also felt awkward promoting myself, especially before doing the research that I propose.  In the end I just jumped right in and did my best to wade through what for me represents a wealth of new opportunities to reach out to the public.

With the #SciFund Challenge coming to an end on May 31, I can reflect on my experience.  First, I have been overwhelmed and humbled by the support that my project has received from friends and family.  Crowdfunding also turned out to be a great networking opportunity.  I have connected with other ecologists through Twitter, a form of social media that I had completely avoided until now.  I even found out that there is another paleolimnologist in my own department at Yale!  We are going for a coffee next week to chat about our research.  These interactions began because of my search for research funds, but the end result has been so much richer.

So, will I continue to crowdfund my research?  Do I think it is the wave of the future for science funding?  Could crowdfunding ever replace NSF?  I think the answers to these questions are yes, maybe and probably not.  However, that elusive crowd of people interested in my research, outside of my friends and family, will take years to cultivate.   As I build my career as a scientist I will implement the lessons I have learned from crowdfunding and continue reaching out to audiences outside of academia.  My new blog is a start!

I think that crowdfunding may not be for everyone, and that some types of science might be a tougher sell.  Major research programs requiring hundreds of thousands of dollars will likely not be easily supported in this way.  But who am I to say?  Perhaps crowdfunding could take off and replace traditional sources of science research funding.  Only time will tell!

Mary Rogalski
PhD Candidate, 2014
Yale School of Forestry & Environmental Studies

Why PubCred is both easy to implement and better than real money [Guest post]

After posting about PubCreds I emailed the authors of the original article to invite a response because: 1) it’s only fair if you’re going to criticize someone’s idea to give them a chance to defend it; and 2) I think that the blogosphere is actually the ideal place to have these kinds of discussions because unlike journals it is actually designed to allow for… well… discussions. Below follows a guest post by Jeremy Fox & Owen Petchey. My thanks to Jeremy and Owen for taking the time to respond. Enjoy.

First, thanks to Ethan for a very thoughtful post on Pub Creds. This kind of constructive criticism is actually more welcome and valuable than unreserved praise. Thanks also to Ethan for inviting Owen and I to respond. Owen and I have chatted about our response, and I’ve taken the lead on actually writing it.
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