Who pays the publication fees for your papers, when there is a fee? What if it’s a collaboration?

Who pays the publication fee for your papers, when there is one?

When the authors are all members of the same lab, I assume the PI ordinarily pays the fee if there is one. That’s certainly what I do.

Just recently I published an author-pays open access paper with a grad student whom I co-supervised with a colleague, and there’s a second such paper in the works. I had been hoping to split the publication fees with my colleague. But it may come down to whoever has the most grant money.

What about papers by working groups or other big collaborations? Who pays the publication fee then? Does whatever funding source paid for the working group also pay the publication fee? Or does some working group member pay the fee from one of their grants, or from some other source available to them such as an institutional open access fund? What if more than one person in the working group has the ability to pay? In that case I guess the first author, or the first author’s PI, would pay?

Same questions for the data hosting fees charged by some depositories, when depositing data associated with a publication.

ht to a correspondent for suggesting this post idea.

Here’s the draft introduction to my book about ecology. Please tear it apart. (UPDATED)

If you’re a very avid reader of this blog, you need to get a life will know that I’m writing a book about ecology. It’s for University of Chicago Press. The working title is “Ecology At Work”, though that’s only one of several candidate titles. Other candidate titles include “Ecology Master Class”, “Re-engineering Ecology”, and the joke titles that I and others tweeted recently.

Anyway, I’m very excited by this new challenge I’ve set myself, and also very nervous that I can pull it off. Which is where you come in. Below the fold is a draft introduction to my book. Please tear it apart.

Ok, don’t just tear it apart; any and all feedback is most welcome. But critical feedback and suggestions for improvement are particularly welcome. If you think the style sucks, or that the book sounds boring, or whatever, you are not doing me any favors unless you tell me that!

Feel free as well to ask me questions about the book, suggest things I should read, etc.

I’ll of course be getting feedback from more traditional sources as well. But every little helps.

Since many readers prefer not to comment, at the end there’s a little poll for you to tell me what you thought.

UPDATE: The comments have already given me some good feedback: it’s not as clear as it should be up front what the book is about and who the target audience is. And for some readers it’s still not totally clear even by the end. So: the book will comprise comparative case studies of what works and what doesn’t in ecological research. It’s not an introductory ecology textbook, it’s not a methods handbook, and it’s not an “ecology grad student skills” manual like How To Do Ecology. If you think of it as “kind of like A Critique For Ecology, but with lots of positive bits to go along with the critical bits and without a single narrow prescription for how to do ecology properly”, you won’t be too far off. The target audience is ecologists and ecology grad students interested in fundamental research.

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Book review: The Theory of Ecological Communities by Mark Vellend


Earlier this fall I read Mark Vellend’s The Theory of Ecological Communities. I read it on my own, and also read it in a reading group with several ecology grad students. Here’s my review.*

tl;dr: It’s a very good book that fills a real pedagogical need. Whether it will also shape the direction of future research in community ecology is an open question, I think. Below the fold you’ll find me engaging with the book, which I think and hope Mark will welcome.

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Recommendations of popular science books that scientists would enjoy? (UPDATEDx2)

I like to read about science and scientists. I like books that get me thinking about science and how to do it. But I find it difficult to identify popular science and history of science books that I will enjoy. The problem is that I’m a scientist. Many popular science books are too basic/slow-moving for me, too familiar, or else too wildly speculative.*

That’s where you come in. In the comments, please share your recommendations for your favorite popular science and history of science books. Specifically, ones that you think that scientists would especially enjoy.

To kick things off, here are some of my favorite popular science books, books that I think readers of this blog would really like as well. I also threw in a book you’d probably think I would’ve liked, but I didn’t.

(UPDATE #2: You have GOT to read the comments as well. Our commenters came through big time, as they always do. I love our commenters!)

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I’m going to be speaking on blogging at a fisheries meeting. Tell me what to say!

So, I’m going to be speaking in a symposium on social media at the American Fisheries Society meeting in August. I’m talking about blogging, obviously, but I deliberately kept my abstract pretty broad so that I could decide later what exactly to talk about. So, if you were attending this meeting–or if you are!–what would you like me to talk about? If you were in my shoes, what would you talk about? Here are a few scattered but hopefully interesting ideas I’ve had:

(attention conservation notice: short post ahead)

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What makes for a great departmental seminar series? And how do you fix one that’s not great?

Note from Jeremy: this is a guest post by Peter Adler.


Is it important to have a well-attended, stimulating department seminar series? And if an existing seminar isn’t working well, can it be saved?

Here’s a totally, completely, absolutely hypothetical scenario: A large state university has a cross-campus ecology program with a great seminar series run by graduate students. That seminar series brings in a nationally-recognized speaker each month to give a pair of talks, accompanied by a reception, meetings with students, and organized discussions or workshops. The same university also has a College of Natural Resources (NR) that runs its own seminar series during the other three weeks of each month. The NR series isn’t so great: it does not have a big budget to bring in speakers from across the continent, the quality of the talks is inconsistent, and attendance by both faculty and graduate students is poor.

Should a hypothetical NR professor try to do anything to improve this seminar series?

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Using our posts as course material? Please tell us just so we know.

A request: if you’re using our posts as course material, please let us know in the comments (what post, what college or university, what course). Not because you need our permission (you don’t), but just for our information. It helps us make the case to our employers and funding agencies that our blogging is worthwhile. Thanks!

If you’ve let us know about this in the past, you don’t need to tell us again.

Can anyone help Jeremy specify an asymmetrical “distance” matrix for a partial redundancy analysis?

Trying something new for me: using the blog to get help with a technical issue.

Briefly, I did an microcosm metacommunity experiment in which inter-patch dispersal was experimentally controlled. So I know the rates at which species dispersed from any given patch (microcosm) to any other patch. Some of those rates were zero–not all pairs of patches were connected by dispersal. And dispersal was asymmetrical–the rate of dispersal from patch A to B wasn’t the same as the rate from B to A.

I’d like to code up up the dispersal rates in the form of a “distance” matrix. But the problem is, it wouldn’t be a metric distance matrix since it’d be asymmetrical. It’d just play the same role as a metric distance matrix in the analysis I have in mind. That analysis being a partial redundancy analysis, partitioning the variance in species abundances attributable to environmental variation from that attributable to “space” (here, dispersal). Basically, I want to do the same analysis as in Cottenie 2005 EcoLetts (and many subsequent papers by various authors), the difference being that the “distance” between any two of my patches isn’t determined by their geographic coordinates (since they don’t have any), it’s determined by the experimentally-imposed dispersal rates.

But I can’t figure out how to code up my asymmetrical “distance” matrix  in a form that works with the rda function in the vegan package in R. Note that I’m pretty sure partial redundancy analysis can be done with a non-metric distance matrix (right?), so I think my question here is just a matter of how to get R to do what I want it to do. But I’ve never done any sort of ordination besides PCA, and I only started reading up on redundancy analysis yesterday, and so maybe the problem is that I’m trying to do the impossible. Googling and searching Stack Overflow hasn’t helped, hence my resort to this post.

There’s a beer at the ESA* in it for you if you can help me out, whether in the comments or via email (jefox@ucalgary.ca). Thanks!

*Or equivalent reward