Jabberwocky Ecology

MacArthur on generality in ecology

I just came across this great Robert MacArthur quote on Allen Hurlbert’s website:

Ecological patterns, about which we construct theories, are only interesting if they are repeated. They may be repeated in space or in time, and they may be repeated from species to species. A pattern which has all of these kinds of repetition is of special interest because of its generality, and yet these very general events are only seen by ecologists with rather blurred vision. The very sharp-sighted always find discrepancies and are able to say that there is no generality, only a spectrum of special cases. This diversity of outlook has proved useful in every science, but it is nowhere more marked than in ecology.

–Robert MacArthur, 1968

It seems to me that one of the real challenges for us as scientists is to make sure that even if we don’t understand what others see when they look at the ecological world, we need to consider the possibility that they simply have an alternative, and equally valid, perspective. As MacArthur notes, ecology will move forward most rapidly with a diverse set of approaches and perspectives, not by having a single viewpoint dominate how we address ecological research.

Ideas in Ecology and Evolution

I just read the excellently forward thinking year end editorial of the new journal Ideas in Ecology and Evolution. The editorial was written by Lonnie Aarssen and Christopher Lortie and is filled with Aarssen’s trademark,creative, outside the proverbial box, thinking. In this case it applies to the field of scientific publishing, the things they’ve tried to change with their new journal and those attempts that have failed and required rethinking. There are a lot of great ideas embodied in this editorial and that from the launch of the journal the previous year.

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Upcoming meetings on metabolic scaling and ecology

There are a couple of upcoming meetings (or sessions of meetings) related to metabolic scaling and it’s relationship with/to ecology that I thought might be of some interest.

The first is  a symposium at the 2010 Society for Experimental Biology conference in Prague on the relationship between the scaling of metabolic rate with body size in organisms and the ecology of those organisms. According to the flyer that one of the organizers (Shaun Killen) sent me

The scaling of metabolic rate with body size has been a central research theme in biology for over a century. Recently there has been a particular interest in how patterns of metabolic scaling at the individual level may affect ecological phenomena and, in turn, how environmental factors may influence changes in metabolic rate with body size. The purpose of this symposium is to review recent evidence of these relationships, and to exchange ideas regarding the underlying factors that cause the observed patterns of metabolic scaling both between and within taxa. The scaling of metabolic rate with body size has been a central research theme in biology for over a century. Recently there has been a particular interest in how patterns of metabolic scaling at the individual level may affect ecological phenomena and, in turn, how environmental factors may influence changes in metabolic rate with body size. The purpose of this symposium is to review recent evidence of these relationships, and to exchange ideas regarding the underlying factors that cause the observed patterns of metabolic scaling both between and within taxa.

The meeting is June 30th – July 3rd in Prague and registration is now open.

The other is the biennial Gordon Research Conference on the Metabolic Basis of Ecology and Evolution, schedule for July 18th-23rd in Biddeford, Maine. If you haven’t been to a Gordon Conference before, these are really amazing conferences. The number of participants is limited (I think it’s about 100-150 people) and the format is specifically designed to engender discussion and interaction among the participants (every one eats meals together, stays in dorms together, etc). This year our own Morgan Ernest will be giving a talk in the section on Regulation of Metabolic Systems Across Scales. You’ll have to apply and be accepted in order to participate and the talks are invite only so posters are the only general option for presentation (both of which are a little strange in ecology circles), but it’s definitely the best conference I go to so it’s well worth the effort.

Some things just shouldn’t be hidden behind pay walls

I have nothing against journals charging for content. While I like the open access model I think that there are upsides to both systems. But seriously, there really are some things that should not be hidden behind a pay wall.

  1. Corrections of any kind: Errata, Corrigenda, etc. Assuming that I don’t have access to The Journal of X through my institution and I choose to purchase a paper from said journal that ends up containing an error, should I really have to pay again to find out what that error is. It’s like buying a new car that breaks down 6 months later and having to pay for a whole new car to get it fixed.
  2. Society business: Announcements, calls for nominations, etc. Presumably the goal of this sort of thing is to reach as wide an audience as possible… right?
  3. Acknowledgement of Reviewers: And now we come to the thing that triggered this post. PNAS’s Table of Contents showed up in my feed reader last night, and there, right at the top, was their annual Acknowledgement of Reviewers. I review for PNAS on occasion and thought I take a brief moment and go look at my name for a little boost during the grind of grant writing season. But no, sorry, I was working at home and so ran firmly into a pay wall. Seriously. So if I review for your journal, but don’t have a subscription then I can’t even look at an acknowledgement of my own, volunteer, activities. Sigh.

Now I know that in many cases the journals don’t intentionally put these sorts of things behind their pay walls. They just don’t think about it, but if you are going to have pay walls in place, isn’t it really your job/responsibility to think (ever so briefly) about what content you hide behind them?

UPDATE: Theoretical Population Biology’s Reviewer Acknowledgment just showed up in my reader. If you don’t have a subscription to TPB you can check out this document for the low, low, bargain price of $31.50.

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).

Synopsis

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.

Registration

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.

Laying the Groundwork for Change [Quote]

How then is it possible to modify and improve upon an academic culture populated by smart, creative individuals who are motivated by ideals more than by money, who have deep, intense interests, value substance over form, have little patience for conformity, think for themselves, do not defer to authority, and see their work not as a job but as a calling? Clearly the challenge is to find the incentives and rewards that will motivate this unique workforce to buy into desired changes and work willingly toward implementing them. But the first step is to explain clearly why change is nececessary and, even more important, why change does not mean abandoning core academic values. To win the hearts of academics, one first has to educate them.

– James C. Garland, Saving Alma Mater

This is just one of many brilliantly reasoned (and worded) arguments from Saving Alma Mater. If you are an academic, or an administrator at an academic institution, you really should read this book.

Another opportunity to change the way we collaborate – G o o g l e W a v e I n v i t e s for ecologists

The current model of writing up collaborative research in science is that a single individual “takes the lead” and writes a complete draft of the manuscript, which is then sent on to coauthors for comments, corrections, etc. This means that even when the development of the ideas and the work of research and analysis has been conducted in a truly collaborative manner (which, I suspect is actually not all that common, at least for the research and analysis parts) that the writing is really more of a one writer – multiple critics system.

This is in part due to the legacy of technology. Up until a few years ago most people simply couldn’t easily work on the same document together. In sophisticated environments the official copy of the manuscript could have been stored on a central server and individuals could “check it out” to work on it for a while, upload it when they had finished, someone else could check it out, lather, rinse, repeat. This required enough coordination that I’m not sure it was much better than just emailing the manuscript from one person to another. There was of course better tech, but scientists didn’t typically know about it, let alone use it.

These technological limitations have now been largely overcome (though there are certainly still some kinks to work out). Wikis represent the first, easiest, step to move beyond these constraints. Most wikis still only allow one person to work on a document (in this case a page) at any given time (but see this recent announcement by weecology’s prefered wiki host, PBworks), but by having the document stored on the web and editable via the browser there is no dead time for the document. You are either working on it actively or you’ve saved it and it’s available to others to work on. This reduces the size of the steps that need to be made on a paper because it wasn’t “you’re turn” to make progress and you didn’t commit to making a real contribution by checking out the paper. Even better than wikis are online collaborative editors like Google Docs or Zoho. These allow multiple individuals to work on a single document at one time. This might seem extravagant, but if two people happen to have a spare 30 minutes at the same time of day, not getting in each others way can make a big difference. Better yet, it allows you to intentionally work simultaneously. At weecology we will actually schedule writing meetings, where two or three of us will sit down in the same room with separate laptops (or an equivalent remote setup) and go to work on a paper. It’s amazing how much easier it can be to sit down and write when your whole team is doing it at the same time and it facilitates active interaction on the paper – “Hey, what do you think we should do about this part of the section I’m working on right now?”

And now, there is a new exciting set of technologies that provide yet another opportunity to move beyond the old system of collaboration – Google Wave. You can think of Wave as combining email, instant messaging, and collaborative document editing. This combination is cool enough on it’s own, but the seamlessness of the collaborative editing goes beyond anything currently available, thus removing some of the hiccups and frustrations of the current options (NB: don’t expect wave to run this smoothly yet as they are still scaling up the system).

This post was motivated by the fact that I just received my long awaited invite to try out Google Wave, which is still in private Beta. I logged in last night and did a quick search for public waves with the word ecology in them. There weren’t any. So, I am happy to announce that I have five invites to give away to practicing ecologists (that’s scientists who study ecology, not environmentalists) who want to give Google Wave a try. Leave a comment with an email and (ideally) something (like a link to a website) that demonstrates that you are an ecologist in case the swarm of folks looking for invites finds JE.

UPDATE: Two things. First, I started a public wave – Any ecologists on wave yet? – which you can find with a quick search of either ‘ecologists with:public’ or ‘ecology with:public’. Second, I forgot to warn the folks who get invited that according to Google “Invitations will not be sent immediately. We have a lot of stamps to lick.”. So it might take a while for your invitations to show up. When they do, stop by and leave a comment so that others know about how long they can expect it to take.

UPDATE 2: I’ve been reloaded with invites, so there are plenty to go around. Just leave a comment if you want one.

[Quote] You can recognize a pioneer by…

You can recognize a pioneer by the arrows in his back.

– Beverly Rubik

You can recognize a pioneer by the arrows in his back

[Quote] Nilsson on credit for scientific work

Some years ago, someone wrote a book called “The Seven Laws of Money.” One of the “laws” went something like this: “Do good work and don’t worry about money; it will come along as a side effect.” Whether or not that’s true of money, I don’t know, but in my experience, it’s true of credit for scientific work. Just make sure you keep working at important problems, enjoying a life of science, and don’t worry so much about credit. You will probably get what you deserve — as a side effect.

Nils Nilsson (via Vladimir Lifschitz)

Frequency distributions for ecologists V: Don’t let the lack of a perfect tool prevent you from asking interesting questions

I had an interesting conversation with someone the other day that made me think I needed one last frequency distribution post in order to avoid causing some people to not move forward with addressing interesting questions.

As a quantitative ecologist I spent a fair amount of time trying to figure out the best way to do things. In other words, I often want to know what the best method is available for answering a particular question. When I think I’ve figured this out I (sometimes, if I have the energy) try to communicate the best methodology more broadly to encourage good practice and accurate answers to questions of interest to ecologists. In some cases finding the best approach is fairly easy. For example, likelihood based methods for fitting and comparing simple frequency distributions are often straightforward and can be easily looked up online. However, in many cases the methodological challenges are more substantial, or the question being asked is not general enough that the methods have been worked out and clearly presented. This happens in the case of frequency distributions when one needs non-standard minimum and maximum values (a common case in ecological studies) or when one needs discrete analogs of traditionally continuous distributions. It’s not that these cases can’t be addressed, it’s just that you can’t look the solutions up on Wikipedia.

So, what is someone without a sufficient background to do (and, btw, that might be all of us if the problem is really hard or even… intractable). First, I’d recommend trying to ask for help. Talk to a statistician at your university or a quantitative colleague and see if they can help you figure things out. I am always pleased to try to help out because I always learn something in the process. Then, if that fails, just do something. Morgan and I will probably write more about this later, but please, please, please don’t let the questions you ask as an ecologists be defined by the availability of an ideal statistical methodology that is easy to implement. In the context of the current series of posts, if you are trying to do something with a more complex frequency distribution and you can’t find a solution to your problem using likelihood then use something else. If it was me I’d go with either normalized logarithmic binning or something based on the CDF as these methods can behave reasonably well. Sure, people like me may complain, but that’s fine. Just make clear that you are aware of the potential weaknesses and that you did what you did because you couldn’t figure out an appropriate alternative approach. That way you still get to make progress on the question of interest and you may motivate people to help work on developing better methods. Sure, you might be the presenting the “right” answer, but then I very much doubt that we ever are when studying ecological systems anyway.

The broken peer-review system: a reviewer’s opinion

Many of us have had the feeling that something is not right these days with the peer-review system in science. Whenever I chat with colleagues about the peer review system, two issues consistently crop up: an increasing number of review requests that we cannot possibly keep up with and/or reviews that seem to indicate a reviewer did not spend much time with the manuscript they were reviewing. So, when Ecology Letters published an article in 2008 (Hochberg et al), written by a group of its editors, titled “The tragedy of the reviewer commons”, I read with great interest. However, I was dismayed to see that apparently the entire fault for the current sad state of affairs lay with people like me: reviewers and authors. I was slightly peeved at the tone of the article that implied that things would improve if only reviewers/authors behaved better. Where was the responsibility of the journals/editors in this mess? I thought, “I really need to write a blog post on this”. I never got around to it. Since then, at conferences and in additional publications (e.g., McPeek et al 2008), I have heard the same refrains:  Scientists need to review faster, better, smarter.  I began to wonder if I was alone in this world in my feelings that reviewers/authors are only half of the equation. Then I read a blog article over at the Chronicle for Higher Education. This article was also about the problems with the peer-review system, but from the perspective of a reviewer/author. And I realized not only was I not alone, but that we needed more voices demanding real dialogue on this issue. So here we go: a reviewer/author’s take on how journals/editors can help reviewers/authors make journal/editors happier.

1) Better reviewer databases: I say no a lot to reviews because I say yes a lot to reviews, not because I lack a sense of scientific responsibility. The Chronicle blog (by a sociologist) points out that the number of members in the American Sociological Association is more than enough to support a reasonable number of reviews/person. However, a much smaller number of people seem to be shouldering the load. I suspect the same is true for ecology. So why is this? Undoubtedly the journals are right that there are curmudgeons who simply refuse to review. But I also suspect that editors are busy people like the rest of us and when we are busy we go with the names of people who come to mind quickly; these “go-to” people are “the most obvious people” to review a paper or give a talk.  However, those go-to people are often the same for many people – resulting in the smaller number of people getting a higher load of review requests. As a reviewer I try to help with this situation by recommending people I think are not yet “in the system” (post-docs, young assistant professors, etc), but I might humbly suggest that journals invest in better reviewer databases to help editors come up with a better diversity of names.

2) More editorial control: My next two suggestions are not going to make me popular with either authors or editors. And I know (if they got implemented) I would occasionally get hoisted in my own petard, but I strongly believe that with the demands journals are making on reviewers theses days (thorough reviews, lots of reviews, quick reviews) journals have a responsibility to protect reviewers from superfluous reviews (i.e. unnecessary review requests).

a)  Better pre-review vetting. Many authors will hate this because this means one person is probably deciding whether or not to send something out for review. A bad draw on an editor (who has a strong personal opinion on the validity/novelty of your work) can kill your submission. However, I am not alone in having received manuscripts for review that are so poorly written that they are in effect incomprehensible or so far from the journal’s standard that clearly no editor looked at the manuscript before sending it on to me. I’m not talking about borderline cases but manuscripts so bad I barely know how to review them. As a reviewer this just makes me mad and takes up valuable time that could have been dedicated to a manuscript that actually deserved consideration. As the Chronicle post, points out: manuscripts do not have a fundamental right to be reviewed.

b) Stop looking for reviewer consensus. I have noticed a trend at certain journals: manuscripts keep being sent back to the reviewer until the reviewer “signs off” on the manuscript. This is consistent with the idea in the Ecology Letters article that authors are needlessly lengthening the review process by ignoring reviewer comments. As much as we may all wish otherwise, not all reviewer comments reflect absolute truth. We all have our opinions on things that (if we’re being honest with ourselves) actually are in gray areas. Sometimes reviewers just flub things. And, journals are right, sometimes reviewers give shoddy reviews. As both a reviewer and an author I recognize this. As a reviewer, I assume the editor will read my review (and the paper) and decide for his or herself whether they agree with my opinion. As an author, I assume that the editor will read my response to a reviewer and decide whether my objections to a certain critique have merit. As a reviewer, the only time I want to re-review a paper is if I have labeled my concern as “fatal” and the editor is uncertain whether the authors have either dealt with that concern or have a valid argument for why it is not a concern. In a world where reviewers are scarce, manuscripts should only go back to reviewers when absolutely necessary. This requires editors to insert themselves more into the process than perhaps they have been accustomed.

Maybe journals and editors already feel like they do these things. I don’t know. I do know I feel like I already do the things they want me as a reviewer to do! However, given how widespread concern over the strain on the peer-review process is, it seems to me that perhaps it’s time for a real dialogue – and that involves both sides talking about their perspectives and  making suggestions about how to improve things. Anyone out there have additional ideas for things that could be done?