Jabberwocky Ecology

Ecology Letters now allows preprints; and why this is a big deal for ecology

As announced by Noam Ross on Twitter (and confirmed by the Editor in Chief of Ecology Letters), Ecology Letters will now allow the submission of manuscripts that have been posted as preprints. Details will be published in an editorial in Ecology Letters. I want to say a heartfelt thanks to Marcel Holyoak and the entire Ecology Letters editorial board for listening to the ecological community and modifying their policies. Science is working a little better today than it was yesterday thanks to their efforts.

For those of you who are new to the concept of preprints, they are manuscripts, that have not yet been published in peer reviewed journals, which are posted to websites like arXiv, PeerJ, and bioRxiv. This process allows for more rapid communication of scientific results and improved quality of published papers though more expansive pre-publication peer-review. If you’d like to read more check out our paper on The Case for Open Preprints in Biology.

The fact that Ecology Letters now allows preprints is a big deal for ecology because they were the last of the major ecology journals to make the transition. The ESA journals began allowing preprints just over two years ago and the BES journals made the switch about 9 months ago. In addition, Science, Nature, PNAS, PLOS Biology, and a number of other ecology journals (e.g., Biotropica) all support preprints. This means that all of the top ecology journals, and all of the top general science journals that most ecologists publish in, allow the posting of preprints. As such, there is not longer a reason to not post preprints based on the possibility of not being able to publish in a preferred journal. This can potentially shave months to years off of the time between discovery and initial communication of results in ecology.

It also means that other ecology journals that still do not allow the posting of preprints are under significant pressure to change their policies. With all of the big journals allowing preprints they have no reasonable excuse for not modernizing their policies, and they risk loosing out on papers that are initially submitted to higher profile journals and are posted as preprints.

It’s a good day for science. Celebrate by posting your next manuscript as a preprint.

Email subscription now available for Jabberwocky Ecology

After writing about the importance of good RSS feeds for a particular subset of the academic community it occurred to me that part of the reason that we have such hit and miss implementations of feeds by journals is that most academics don’t even know what a feed is let alone actually use a feed reader. If this is you then we still want you to be able to get regular updates from JE, so last night I setup a new feed using Feedburner. What this means to you is that you can now subscribe to JE using email. If you follow the link in the upper right hand corner you will get a single email each morning that we post new content. If you’re curious about using our RSS feed instead, I’m going to try to put up a post in the next few days to explain the benefits of this approach over email for keeping track to Tables of Contents, so you may want to wait to see if you’re convinced to start using a feed reader.

Those of you who are already subscribed to our WordPress feed have nothing to worry about. It’s not going anywhere.

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

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!

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.

Blogging the Origin

Unless you’ve been living under a rock (or are a new assistant professor), you are surely aware by now that Darwin’s 200th birthday is this week. However, unless you’re a certified blog-crawler, you may not be aware of Blogging the Origin. In honor of Darwin’s bicentennial birthday, John Whitfield (a freelance science writer and author of In the Beat of a Heart, a must read for those of us with a weakness for metabolic ecology) has been blogging his way through each chapter of On the Origin of Species. It is quite a treat to read – it is both insightful and funny….and much quicker than trying to reread the original in time for Darwin’s big day. Whitfield both summarizes Darwin and puts him in a modern context. Here are a couple of excerpts for you to whet your appetite:

From Chapter 1:

And, as evidence of ancient artificial selection, he mentions that “from passages in Genesis, it is clear that the colour of domestic animals was at that early period attended to.”

The. Irony.

From Chapter 2 (how can you not love something that quotes one of my favorite people):

More useful in such cases is the phylogenetic species concept — a species is a group of populations that shares a common ancestor, and is distinct from any other similar group. Although, again, seeing as we all share a common ancestor sooner or later, it’s tricky to know where you draw the line between groups. The microbial ecologist Jessica Green once pointed out to me that microbiologists typically put two cells in the same species if their ribosomal DNA is 97% identical. Applying the same criterion to primates, she says, and you’d be sharing a species with the ring-tailed lemur.

From Chapter 14 (not to ruin the ending for anyone):

This relentless piling, sorting and re-arranging of evidence can make Darwin seem a little OCD, like an intellectual version of Wall-E. But he also knows that beneath all the case studies, there’s a logical core to evolution by natural selection, even if he can’t put it in an equation.

So roll on over and check it out! I promise you won’t be disappointed*

*from the legal department of weecology: this is in no way a legally binding guarantee and does not imbue the reader with any legal rights such as refunds, exchanges, or restitution for lost wages for time spent reading said blog. The reader does have the right to leave nasty comments, however, if they did not enjoy reading Blogging the Origin – though the author thinks if you don’t enjoy reading Blogging the Origin it just indicates something is deeply wrong with you.

Lazy reviewers and whiny AEs

Those of you who attend conferences will be familiar with the standard – walk up to someone you know, who is talking to someone you don’t, get introduced to new person – conference interaction. Following the introduction at one of these the other introducee looked knowingly at me and said something like, “oh yes, you just turned down a request to review from me.” He then proceeded to complain to the assembled group about how hard it was to find people to review manuscripts. At this point another young AE who was part of the conversation jumped in and expressed similar frustrations. Both of them proceeded to make it clear that in their opinion the problem stemmed primarily from one cause – lazy reviewers. In other words, if everyone would just agree to do a reasonable number of reviews (defined in the conversation as doing enough reviews to match or exceed the number of reviews that are performed on your own papers) then there wouldn’t be any problems.

Now, both these people seemed like they were very nice individuals, and I’m sure that difficulty in finding reviewers is a common frustration among AEs, but as an active member of the reviewing community who not only pulls their own weight, numbers wise, but also spends the time to produce detailed high quality reviews, it really bothers me when either in person, or in print, editors and associate editors whine about lazy reviewers. It’s not that I don’t believe that there aren’t self-centered scientists out there who aren’t in a big rush to do something that can be quite time consuming, that they get effectively no credit for, for free (but that’s a subject for another time). It’s that it is hard to imagine serious people who are paying attention to the state of scientific publishing believing that this is the primary source of the problem.

The real issue is that the number of papers being published on an annual basis has been exploding. Here is a plot of the number of papers with the keyword ‘ecology’ indexed in ISI (note that the growth in this figure is conservative due to the way in which ISI chooses to include journals for indexing).

Now I don’t have any data on the number of regularly utilized reviewers, but I’m pretty sure that if we could get it that the numbers wouldn’t be increasing anywhere nearly as quickly. So the problem is simple – too many papers, too few reviewers.

Who is to blame for this situation? I don’t really know. We could blame publish or perish systems (I don’t, but you could), we could blame corporate publishing houses for the rapid proliferation of academic journals in pursuit of profit, or for that matter we could blame the whiny AEs for not rejecting enough of the poorer submissions without sending them out for review. Whatever the cause/solution this is clearly something that we need to address, and we need to address it now before we break the system.

Funnily enough, in preparing to write this post I went back through my email from the last six months and I couldn’t find a single review request from a journal on which the offending individual served as an AE. Maybe he had me confused with another lazy reviewer…