Jabberwocky Ecology

Experimental ecology is dead, long live experimental ecology!

I read a handful of experimental ecology papers the other day. I liked some of them and didn’t like some of them. It wasn’t that there was anything inherently wrong with the ones I didn’t like, they just didn’t fit in with my world view.

Yeah, this doesn’t make any sense to me either, but apparently that’s how we’re using this phrase these days.

P.S. I was going to let this one go until Ecotone used the original post to question “the reality (or not) of macroecology as its own discipline.” There’s nothing wrong with creative titles (we enjoy them here at Jabberwocky), but when contrasted with EEB & Flow’s other posts from ESA it’s not surprising that Ecotone took this as being a passive agressive critique of the state of the field. My main concern is that EEB & Flow seems to conflate an important methodological approach with particular interpretations of ecological process resulting from an application of that approach. Just because I disagree with a particular paper using an experiment doesn’t lead me to have “an unsure feeling about this field.” I mean really.

Frequency distributions for ecologists IIa: Data Visualization: Histograms

Well, I guess that grant season was a bit of an optimistic time to try to do a 4 part series on frequency distributions, but I’ve got a few minutes before heading off to an all day child birth class so I thought I’d see if I could squeeze in part 2.

OK, so you have some data and you’d like to get a rough visual idea of its frequency distribution. What do you do know? There are 3 basic approaches that I’ve seen used:

  1. Histograms. This is certainly the simplest and easiest to understand approach and most of the time for visualizing frequency distributions it is perfectly acceptable. A histogram simply divides the range of possible values for your data into bins, counts the number of values in each bin and plots this count on the y-axis against the center value of the bin on the x-axis. Any statistics program will be able to do this or  you can easily do it yourself. If all of the bins are of equal width (as is the default in stats packages) then your basically done. If you want to convert the y-axis into the probability that a value falls in a bin, just divide the counts by the total number of data points. If you want to convert it to a proper probability density estimate then you’ll also want to divide this number by the width of the bin (i.e., the upper edge of the bin minus the lower edge of the bin). If the bins are not equal width (which includes if you have transformed the data in some way) you should divide by the the linear width of the bin regardless of whether you are concerned about turning your y-axis into a probability density estimate or not. This is to make sure that you are visualizing the distribution in the way you are thinking about it (most people are thinking about the distribution of x). Of course there are good reasons for wanting to visualize the distributions of transformed data. Just make sure you have one if you’re not going to divide by the linear width of the bin.

Well, I’m out of time so I’ll go ahead and post this and come back with the other two options for visualization later.

Amen brothers: why stimulus funding for science was a good idea

We just read this great piece from the Huffington Post by Todd Palmer and Rob Pringle on why including funds for NSF and NIH in the stimulus bill was a good idea (thanks to Ecotone for pointing us to the article). The great thing about the piece is that it doesn’t just make a cogent argument for the stimulus funds, but for why funding basic science is economically beneficial in general. Probably the high point of the article was this little gem:

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.

Frequency distributions for ecologists I: Introduction

Dealing with frequency distribution data is something that we as ecologists haven’t typically done in a very sophisticated way. This isn’t really our fault. Proper methods aren’t typically taught in undergraduate statistics courses or in the graduate level classes targeted at biologists. That said, as ecology becomes a more quantitative science it becomes increasingly important to analyze data carefully so that we can understand its precise quantitative structure and its relationship to theoretical predictions.

Frequency distribution data is basically any data that you would think about making a histogram out of. Any time you have a single value that you (or someone else) has measured, for example the size or abundance of a species, and you are interested in how the number of occurrences changes as a function of that value, for example – are there more small species than large species or more small patches than large patches, then you are talking about a frequency distribution. Technically what we’re often interested in is the probability distribution underlying the data and you will often have more luck using this term when looking for information. Many major ecological patterns are probability/frequency distributions including the species-abundance distribution, species size distribution (also known as the body size distribution), individual size distribution (also known as the size spectrum), Levy flights, and many others.

Last year I wrote a paper with Jessica Green and Brian Enquist on one of the problems that can result from the approaches to this kind of data typically employed by ecologists and the more sophisticated methods available for addressing the question. As a result I’ve been receiving a fair bit of email recently about related problems; enough that I thought it might be worth a couple of posts to lay out some of the basic ideas regarding the analysis of frequency distribution data. Over the next week or so I’ll try to cover what I’ve learned about basic data visualization, parameter estimation, and comparing the fits of different models to the data. Along the way I may have a couple of things to say about some recently published papers that have the potential to cause confusion with respect to these subject.

Please keep in mind that I am not a professionally trained statistician and that this is not intended to be an authoritative treatment of the subject. I’m just hoping to provide folks with an entryway into thinking about what to do with this kind of data and I’ll try to point to useful references to help take you further if you’re interested.

Data scientists

Nathan over at Flowing Data just posted an interesting piece on the emergence of a new class of scientists whose work focuses on the manipulation, analysis and presentation of data. The take home message is that in order to fully master the ability to understand and communicate patterns in large quantities of data that one needs to have some ability in:

  • Computer science – for acquiring, managing and manipulating data
  • Mathematics and Statistics – for mining and analyzing data
  • Graphic design and Interactive interface design – to present the results of analyses in an easy to understand manner and encourage interaction and additional analysis by less technical users

His point is that while one could get together a group of people (one with each of these skills) to undertake this kind of task, that the challenges of cross-disciplinary collaboration can slow down progress (or even prevent it entirely). As such, there is a need for individuals that have at least some experience in several of these fields to help facilitate the process. I think this is a good model for this kind of work in ecology, though given the already extensive multidisciplinarity required in the field I view this role as one occupied only be fairly small fraction of folks.

The other thing that I really liked about this post (and about Flowing Data’s broader message) is the focus on the end user. The goal is to make ideas and tools available to the broadest possible audience and sometimes often the more technical folks in the biological scientists seem to forget that their goal should be to make things easy to understand and simple for non-technical users to use. This is undoubtedly a challenging task, but one that we should work to accomplish whenever possible.

Hurlbert’s unicorn

Over at EEB and Flow, Marc aesthetically pleasing details” to our figures. I’m a big fan of visually pleasing figures and the examples that Marc gives show how a little extra effort can really improve communication. The post made me think of one of the earliest examples of adding… a little something extra… to one’s figures – Stuart Hurlbert’s unicorn (Hurlbert 1990).
Part of Figure 1 from Hurlbert 1990

Part of Figure 1 from Hurlbert 1990

April fools for the statistically inclined

You can always count on Andrew Gelman for quality April Fools Day posts.

Speaking of starting young

This picture and caption of a young linux developer-in-training is hillarious. At least if you’re a bit of a computer nerd like me. Via Ubuntu Linux Tips & Tricks.

Starting young: getting ecologists to blog

Within the small community of ecologist bloggers much has been of the lack of blogging (and other odd pursuits like twittering) among ecologists (this is, afterall, EEB & Flow‘s raison d’etre), and I recently read over at academHacK that “in the future [academics] can be online or be irrelevant”. So, this semester I did what I could to get some future ecologists blogging. Instead of having traditional writing assignments for my Biogeography course I required students to set up a blog and post at least 3 EEB & Flow style posts about papers they read from the primary literature (I didn’t know about EEB & Flow at the time, but this was/is the spirit of the assignment). The response so far has been very positive and at least a couple of students (mostly of the graduate persuasion) have taken to blogging in a way that suggests to me that they’ll do this again in the future (i.e., they’ve already posted more posts than required even though they already know that they’ve locked down an A).

In my broader experience with introducing ecologists to new technology it’s really all about exposing folks to the potential of the new approach. Once they’ve seen the potential of something ecologists tend to embrace it pretty quickly. So, start your students young. Show them how easy it is to set up a blog, get them posting a little, and maybe soon we’ll all be clammering to be heard above crowd.

Evolution in the Multiverse

Today, I was watching a great episode of the History Channel show “The Universe“, which was exploring the concept of the nature of the universe. (On the off chance you are some type of physicist or astronomer who has stumbled on to this blog, you might want to skip to the next paragraph. It’ll be less painful for you that way). The episode explored the concept of whether there are alternate universes and, if so, what is their relationship to our universe. Apparently there are several different types of possible alternative universes. The two possibilities (of the four types of multiple universe scenarios) that I vaguely understood were a) parallel universes may coexist in the same physical space as ours or b) many universes may be floating along through “hyperspace” like soap bubbles. When I was a high schooler, I was torn between two career paths: ecology and astrophysics (yes, I know. I’ve always been a woman with broad interests). Honestly, if I had known that such wild theories about the universe were being studied, I might well have made a different decision. It would also have helped if I was better at math.

What caught my attention in this episode, however, was the assumption that, in alternative universes, not only would human beings exist, but I would exist. Having chosen the ecology path, this immediately got me to thinking about evolution. “Replaying the tape of earth history” has long been a thought experiment in the study of evolution. If we reran the history of life from the beginning, what would life look like right now – 4.54 billion years after the formation of the earth? The crux of the question is: how random is evolution? On the extinction side one could ask questions like: Would catastrophes that occurred in the past have the exact same impact on life on earth? Or would subtle differences in timing and conditions of the event or the activity of individuals lead to survival of species that otherwise went extinct – thus altering the web of species’ interactions and evolutionary potential of earth’s biota? On the evolution side: are key mutations and innovations inevitable (i.e. would they occur again if the tape was replayed) and if so, would they occur at the same instance as they did the first time? How would changes in the probability of a mutation occurring again and the timing (occurring sooner or later than it did before) affect how evolution played out? If certain types of mutations are more probable to occur than other types of mutations, and those mutations were key in evolution of life, then perhaps evolution is something more deterministic than a pure random walk through DNA space. Since microevolution is not my field of expertise, I’m not qualified to say. I don’t even know if anyone has tried to address the probability of  specific mutations occurring but I suspect that there is more that is random in evolution than predictable. If so, then if we were able to study Earth in the alternative universes, I think I would find that most of them were not populated with copies of me. (In addition to the issue of whether there are human beings on those alternative Earths, there is also the issue of whether all my ancestors actually hooked up again or decided to mate with someone else.) However, for those of you who are really bummed by this idea, I have a ray of hope. The physicists kept talking about an “infinite number of alternative universes”, and when you talk about infinity…well, a small probability multiplied by infinity is technically, I believe, infinity (have to admit that makes my brain hurt), so you probably do exist in alternative universes.

The high school sci-fi fan in me has obviously already imagined a branch of ecological and evolutionary study which uses alternative universes as independent experiments of evolution. Imagine what we could learn. Is DNA the only molecule that could code information stably? Or are their alternative universes where all life on Earth has RNA as its genetic code or even some other molecular structure? How important is the identity of species that go extinct to the overall history of evolution (does the loss of a specific small mammal during the K-T extinction prevent the Age of Mammals? Or does it only result in minor or even no differences in the overall diversification and dominance of mammals that occurred after the demise of the dinosaurs? Inquiring minds want to know. And who knows, maybe in an alternative universe we have already learned how to do this and I never had to make the choice between ecology and astrophysics and I’m currently busy using my knowledge of the multiverse to study ecology and evolution. I just hope that my alternative self is a little better at math!

Ecological Samuri

Data is the sword of the 21st century, those who wield it well, the Samurai.

Jonathan Rosenberg, SVP, Product Management, Google

Who are you calling Vermin?

imageLast week, I enjoyed Marc Cadotte’s post over at EEB and Flow on learning that he had one of the worst jobs in science: Triage Biologist. I thought both the post was funny and also the fact that I would never have thought about the work he does as being one of the worst jobs in science. I mean, many of us can think of much much worse things to do with one’s time than to have Cadotte’s research career. (Let’s just say that my time spent as an undergraduate marking with paint the thorax of a 2 mm long wasp is not remembered fondly). Imagine my surprise when I found out this morning that apparently one of those things that people would rather not do is “vermin handler” – i.e. rodent catching…i.e., my job! 

 

Unlike Cadotte, my work is not specifically mentioned in the article. I’m grateful for this because I already have some recruitment issues. It is not uncommon for me to have to reassure prospective graduate students that they are not automatically expected to work with rodents if they join my lab. And let’s face it, as the Popular Science article clearly shows, working with rodents – referred to as small mammals when you want it to sound better and never never ever as vermin – does have an image problem. Given the image problem, you may wonder why I was surprised that small mammal handling was listed as one of the worst jobs. Let’s just say that I don’t consider getting to go here:

Sarah picking up traps

 

And work with these:

Dipodpomysmerriami_Kurzius 

to be any kind of hardship. You may also be wondering right about now about those students who join my lab who perhaps were not initially thrilled with the idea of working with “vermin” – what happened to them? Through fair means or foul, I do encourage all my students to go down to the field site to “just gain the experience”. They don’t have to handle rodents, all that is done by the trained graduate research assistant. All they have to do is help set traps and record data. Unanimously, undergrads and grads, come back loving the experience. So far they’ve even all ended up developing research projects on small mammals. If you’re suspicious, well, you’re welcome to tag along sometime. We always have room for one more vermin handler down at Portal.