Tuesday, November 27, 2018

I spent WHAT?

Journals today are much maligned. We all want to publish our work for free, and read papers without paywalls. Many of us also want to have nicely typeset and carefully copyedited articles. These are incompatible goals. Until we get governments that fund all journals' expenses (good luck with that!) or we get a Paul Allen or Howard Hughes to fund publication (ditto!), we need to make two choices.

1) Do we want the value that journal editorial staff add to the production of a snazzy final version? Journals provide website support, database management, and staff that enable careful anonymous peer review. They provide copyediting that (*if done well*) catches errors (rather than introduces them) and improves the final product, and typesetting that makes it all look good. And, if you publish in a traditional print journal they put it on nice archival paper so it'll still be readable after the Zombie Apocalypse, unlike those e-articles that'll be forever lost.

For more detail on the value added by journal office work, see this previous blog post of mine on "The Secret Lives of Manuscripts". I did a very informal (e.g., unscientific) twitter poll on this question: of 500 respondents to my (certainly poorly worded) question, 92% prefer the typeset journal version. The other 8% were all named Andy Kern, I think (kidding).

Today on twitter, my grad school friend Andy Kern suggested maybe we need a hybrid approach where authors can choose to pay for all these services, or can have their raw manuscript posted. Interesting idea. I wonder how many authors would opt to pay for the services. And, would the decision have any impact on how widely our papers are read and, eventually cited? I don't know.

2) If the answer to (1) is yes, then who pays for the value that journals add and that we desire? There's a lot written about this, and disparate strongly held opinions. Both have their drawbacks: author open access fees can pose insurmountable barriers to low-funded labs or students (*A STORY ABOUT THIS AT THE END*). Traditional journals can be inconvenient to access: if you don't have an institutional subscription access you either need to pay (few people do), or contact the author (long lag times or no answer), or go to SciHub, or read another article entirely. I'm not going to delve into that here. There be dragons.

Instead of tackling those dragons head-on, I want to address a point that Andy Kern raised in our twitter conversation today. He pointed out that I had published 8 papers in 2018, and estimated I probably spent $20,000 on the page charges (2500 per article) plus the indirect costs my university charges on those expenses for a total of (he estimated) $40,000.  What, Andy asked, could I have done with that money instead?

It is a fair question. I always budget for some page charges, but I had never specifically tallied up my page charge total across all grants and projects. So, that's what I did. The table below shows all my papers from 2014-2018 (a 5 year period), where they were published, who paid, and how much. I should note (before you read the table too closely) that I couldn't find all of my page charge invoices from the whole 5 year period, having switched computers twice in that interval. So some of the numbers are estimates derived from the journal websites. Others (marked with asterisks) are from memory because I know the APCs (Author Page Charges) were lower a few years ago than the websites indicate today.

2018American NaturalistBronstein and Bolnick1000Open Access (voluntary)
2018Annual Reviews of Ecology Evolution and SystematicsBolnick et al0
2018Animal BehaviorStockmaier0
2018Ecology and EvolutionBrock et al1,560
2018PeerJFrench et al1095
2018ScienceKuzmin et al0
2017Frontiers in ImmunologyLohman et al2950
2017Molecular EcologyLohman et al0
2017Molecular EcologyStutz and Bolnick0
2017MsystemsDhielly et al1200Lead author paid
2017EvolutionBrock et al700
2017Molecular EcologyVeen et al0
2017Frontiers in ImmunologySteinel and Bolnick2950
2017PNASWeber et al1640
2017NatureBolnick and Stutz0
2017Nature Ecology & EvolutionStuart et al0
2017Ecology and EvolutionAhmed et al1,560
2017Biol J Linn SocStuart et al0
2017American NaturalistLohman et al975
2017Journal of Evolutionary BiologyJiang et al0
2017Medical Science EducatorBolnick et al2000
2017EvolutionWeber et al700
2017American NaturalistWeber et al1050
2016Proceedings of the Royal SocietyPruitt et al1600Lead author paid
2016Molecular Ecology ResourcesLohman et al0
2016Biology LettersBolnick et al0
2016Evolutionary Ecology ResearchIzen et al0
2016Journal of Evolutionary BiologyOke et al0
2015ISME JSmith et al3300* Estimate
2015EvolutionJiang et al350
2015Molecular EcologyStutz et al0
2015Ecology and EvolutionIngram et al1,560
2015PLoS OneBolnick et al1595
2015EvolutionBolnick et al500
2015OecologiaSnowberg et al0
2014Molecular EcologyPuritz et al0
2014Ecology and EvolutionParent et al1,560
2014Trends in Ecology & EvolutionWarren et al0
2014Molecular EcologyBolnick et al0
2014Ecology LettersBolnick et al0
2014Nature CommunicationsBolnick et al2000* Estimate
2014PloS OneStutz and Bolnick1595
2014American NaturalistStutz et al1125
2014Trends in Ecology & EvolutionRichardson et al0
2014EvolutionStuart et al0

The 46 articles listed above added up to a whopping $35,115 over a five year period (of which I paid $32,315 plus roughly 56% overhead for a total of $50,411.  That's $10,000 per year. Ouch.

But let's put this into some perspective. First, I have been exceptionally lucky to be well- and continuously funded. For much of the time period covered here I was supported by the Howard Hughes Medical Institute, which paid for open access fees. Come to think of it (as I write this), my 2014 & 2015 papers with $0 APCs were probably wrong, as I almost certainly had HHMI pay for open access fees. That lifts up my per-article average and 5-year total above what I report here, but I don't have the details on hand. That said, the open access fees mandated by HHMI didn't come out of my research budget, but out of separate HHMI funds. That supplemental publication funding disappeared in 2016 and after, when I ceased to be an HHMI Early Career Scientist (but was still publishing work from my HHMI time). So, the grand total listed above is a lot, and is an underestimate, but I actually paid less than what is listed above (thanks Uncle Hughes!) and it was a modest fraction of my very generous HHMI funding.

 Next, lets look at this another way. That total translated to an average of $702 per article (not including overhead), with a standard deviation of $921. That's a lot of variation:

The point is, there were just a couple of boutique journals that charged an arm and a leg. All were open access and for-profit. Then there is a set of mid-range articles that were expensive, but between $1500 and $2000 (usually closer to 1500), mostly society open access journals. But the majority of my publications cost under $1000 each. A number of journals were free of page charges, because they gain all their income to cover expenses from subscriptions. Some readers I know will object, but given my research output it was frankly either that or not publish these papers at all, if I can't afford to pay OA fees for them all. Maybe some of you will suggest I take that latter approach, in which case see that story at the end, which I promised (in all caps) up above.

Let's return now to Andy's radical suggestion: what if we lived in a world where we skipped copyediting and typesetting and distribution and archiving, and we just posted our (reviewed and revised, I hope) manuscripts on servers. Its then up to us to format our papers, proofread them super carefully, and typeset them as best we can. An interesting notion. I would have saved roughly $50,000 over the last five years. Save that up and its a year of graduate student support, or a year of postdoc salary (but not enough for fringe & overhead on that salary). Tempting. So what's the downside? First, I'd need to learn how LaTeX or something to make my manuscripts look better. Second, the copyeditors at (some of) the journals I publish in are excellent and help nit-pick to fix the last few items in every paper that I inevitably miss. That's an expensive service. To put it another way, my cumulative output of scientific writing in the last 5 years is well over 500 pages. That's a long book. If I were to copyedit that myself, and typeset that myself... ugh. I'd pay for a professional (again, I know some journals' copy editors are know for messing things up more than they help, but that's not always true. This is where I make a plug for AmNat's excellent team).

As an Editor I can also attest to the fact that many manuscripts come in poorly written and in desperate need of copyediting, more than the reviewers and Associate Editors and I have time to do. So I have a pretty good idea of what the scientific literature would look like if we all skipped these (costly) services, and it's not pretty. Copyediting is especially valuable to authors for whom English is a second (or third, or...) language. We do sometimes have articles that are excellent science but need a fair bit of word smithing to be up to standards.

So, my conclusion? I'm really torn about this. Once I added it all up, I've spent a lot on publication in the last half decade. That's paying for a service I appreciate and value (especially because I see the process from the journal perspective as well). But, its a lot of money. Considering the cumulative totals I am spending, there's more science I could do with that money. But, doing all the copyediting and typesetting in house takes us away from doing science. And there's still the issue of archiving on paper for the Zombie Apocalypse.  Now that I've seen the totals I am spending, I will certainly choose my target journals even more carefully based on financial and policy concerns, which is a shame because it steps away from my scientific ideals. And maybe I'll hesitate about that extra little paper, and wonder 'is it worth the APCs to write this'?

I promised you a closing story, so here it is. When I was a graduate student some friends and I got together to discuss some papers we read together, and it turned into a reading group and a Synthesis paper (Bolnick et al 2003, American Naturalist). It was an all-student group of authors, self-organized, with no funding. When we finally got it accepted (after 2 revisions, at least), we reckoned with the cost of publication. It had become a really long paper with extensive tables. I was an ASN member, which got me 10 (?) free pages, but the article was way longer. Page charges for those excess pages rang up something like $1500. And not one of us had the funds to spare. It almost stopped there, but Michael Turelli offered to pay the APCs. None of us were Turelli students. He's just that kind of generous*. We accepted his offer, the paper was published, and it became my most cited article by a long shot. So, I am very sensitive to the barriers that APCs impose on unfunded authors. This is why I am such a proponent of mixed publishing models (like The American Naturalist uses), where people can opt in to pay for Open Access, or can pay less for regular page charges, or can get waivers if they are members ($20 for students!) who lack funds for APCs. That's a powerfully flexible model. But, one that is threatened by the EU's Plan S.

*Turelli had one condition: that we list him in the acknowledgements of our paper using a humorous phrase that he specified.

Wednesday, November 21, 2018

Am I an OLD prof?

One of the weirdest feelings when you first become a new professor is that students and postdocs view you differently – you have instantly transitioned from being “one of them” to being “separate from them.” I suppose this shift seems natural from the external (to you) perspective, but it is extremely weird from the perspective of the person who just became the professor. That is, you aren’t a different person overnight just because someone bestowed a job on you. You are that same stupid, procrastinating, goofing-off, incompetent, flawed, and so on, person that you were before you accepted the job offer. This feeling persists for years – in the sense that you don’t feel qualitatively different from graduate students. You just feel a bit older. And it makes sense. After all, you likely spent 6 years as a graduate student and 3 years as a postdoc – so you will need to be a prof for 9 years before you have as much experience at it as you already have at being a trainee. Sure, I felt a growing difference between myself and grad students - but it has been very gradual, not abrupt – that is until recently. 

Earlier this year, I received an email from Steve Young that read: As editor of the Paper Trail section in Ecological Society of America¹s Bulletin, I am writing to ask if you would be willing to contribute a short piece to an upcoming issue. You may be familiar with this section, but if not, it is a recent addition that was part of the 100th anniversary of ESA in 2015. … I have made some changes to the ¹old¹ format to try and reach a wider audience by showing how ecology has connected generations starting with those who are just beginning their careers as graduate students or junior faculty members all the way to those well advanced … the guidelines are simple: 1) less than 500 words or so and 2) include picture(s). The picture should show you or is symbolic in some way of your work. I have already asked an arising ecologist to contribute to this section and she has graciously agreed. This person is Dr. Emily Lescak, who is an up and coming researcher at the University of Alaska ... She has identified you as an established researcher who has had a significant influence on her career through a scholarly paper.

Wait, what? I am being identified as an established researcher who has had a significant influence on someone’s career through a scholarly paper. How can that be? Sure, I suppose I am someone who contributes to science in ways that shape RESEARCH, but not RESEARCHERS! How is it possible that people whom I haven’t worked with are identifying my work as shaping their career development? It was at this precise moment, receiving that email, that I no longer felt at all like a graduate student or postdoc.

I am not sure how I feel about this. Of course, I am flattered and humbled that Emily felt my work had influenced her career, and that Steve had supported her suggestion. And I really enjoyed writing the two-part essay with Emily. At the same time, I still want to feel like a graduate student, brimming with new ideas and embarking on new projects, not some “old” professor whose big influence here-on-out will be in supporting and inspiring the next generation of researchers. Perhaps it means that I am about to be over-the-hill and, in fact, I am in some ways. I don’t write first-authored data-based primary research papers anymore. I don’t know how to do statistics in the R environment. (My first ever plot - below - was also my last.) I write books – and am even planning to write a trade (“popular”) book. I run from meeting to meeting and idea to idea and student to student without sitting down and thinking long and deep about any one specific thing. And I think that new professors in our department are starting to think of me not as a collaborator but as a mentor – and I might even be accepting that.

Perhaps it is only coincidence, but I did turn 50 this year. And I have been a prof for 15 years, which would be half of my career assuming (incorrectly) that I will retire at 65. I just received a Tier 1 Canada Research Chair that, with renewal, could last until that time. Can it be that a career is divided into equal portions, with a first half where you simply feel like an old graduate student and a second half where you can’t remember what it is like to be a graduate student? Is this the moment where I should start planning my exit seminar, my scientific memoir, my retirement? Have I passed the tipping point leading to a regime shift that generates an alternative state from which I can never recover? “Chill out” I hear you saying, “You are a mid-career scientist.” OK, sure, but, if you HAD to divide each career as a prof into two states (emerging versus established, young versus old, new versus old, developing versus old, etc.), which state would I be in?

I am not saying my career is winding down – far from it. I have more students than ever before, more collaborations than ever before, and more papers than ever before. We are just embarking on three huge new long-term collaborative “eco-evo in nature” projects that will likely last for decades. I still actively avoid major administrative roles. I still thing about the big questions, the big papers, and the new topics that might be emerging.

But that doesn’t mean that I am not transitioning to a new state without (until now) formally realizing it. I actively encourage my students to engage in projects that motivate them instead of those that build my research program. In fact, I am doing the same for myself, recruiting students to work on camera traps and eDNA and “micro-oases” and whatever seems fun and interesting, as opposed to projects that represent the next logical step in my existing research program. I have students who work on howler monkey microbiomes and dolphin behavior, and I support other students who are working on ball python genomics and many other diverse projects. I no longer care (much) about where my name is on an author list, even if it is my student or “my” project. I (sometimes) don’t even care if I am an author on such papers. In short, maybe I really am in a qualitatively different career state where I am no longer worried about building my career but rather in building fields and developing the next generation of scientists.
I look forward to how my approach and perspective will change into the future. 

Some of our ball pythons

Will I age gracefully as a professor – in my own eyes and in the eyes of others? Who knows. But – for the moment – I love where I am and how I got here, and I am excited to see where I am going. Long live the “old” professor.

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