Monday, October 23, 2017

Biodiversity and contemporary evosystem services

Part 1

Bursting a thought-bubble

The Eco-Evo Evo-Eco blog site has had a number of interesting contributions (e.g. rapid evolution and big apple) about “evosystem services” – broadly defined as all the benefits to society from evolutionary processes (Faith et al 2010). Our bioGENESIS group introduced this term to set up a contrast with the conventional term “ecosystem services”. After all, why should we (we asked) refer only to benefits from healthy ecosystems, when we equally could be talking about the benefits from healthy evosystems?

That nice thought-bubble could be all there is to the story. But evosystem services critically adds something more. While every ecosystem service is also an evosystem service, “evosystem services” also captures the idea that the core product of evolution, biodiversity (the variety of life), itself is an evosystem service. As Faith et al (2010) argued, biodiversity has (typically global) “option value” – it provides a contribution to society in maintaining options – maintaining the potential for unanticipated future benefits. Thus, while global biodiversity is not an ecosystem service, it is perhaps the most fundamental evosystem service (for more discussion, see Faith 2017).

As an evosystem service, biodiversity and its option value therefore is a nice interplay of past, present and future. Past evolution creates a storehouse of “features”; presently we place some value on the benefit of having biodiversity’s maintenance of options, knowing that future generations then will continue to discover unanticipated benefits and uses.

The “past” does not have to be that long ago

Faith et al (2010; for discussion, see Faith et al 2017) also discussed evosystem services from rapid or contemporary evolution. Contemporary evosystem services then are all the benefits from rapid evolution. These benefits include option values from biodiversity. The evosystem services work of Bellon and colleagues (e.g. Bellon et al. 2015) illustrates this well. They describe the evosystem services in global food systems arising through “on-farm conservation”: management of crops to produce and maintain biodiversity and its option values, as a global public benefit.

The new home of bioGENESIS, Future Earth, focusses on human-earth system science and sustainability. We wondered initially how evolution and biodiversity conservation fit into conventional “earth system science” (for discussion, see e.g. Faith and Richards, 2012). It is clearer now that there is a good fit. Evolution is a key Earth System process, and one way to look at the human-earth system is that this system operates with a time-lag – evolution in the past has created biodiversity and, from humanity’s point of view, this is a rich heritage or “storehouse” that society now continues to harvest over time. Of course, humanity also is rapidly foreclosing its options through human-caused loss of biodiversity. How we deal with all that is central to sustainability.

This evolutionary perspective on human-earth systems is even more interesting because evolution can be rapid, it may well be directly or indirectly influenced by humans (Hendry et al. 2017), and it may or may not promote human well-being. Such contemporary evolution importantly not only may support ecosystem services, but also support global biodiversity option values, as illustrated by the work of Bellon and colleagues (and discussed in Faith et al 2017).

Biodiversity “option values” do not always get the attention they deserve (see below, and see my review in Faith, 2017). So, it is not surprising to see more discussion in the context of contemporary evosystem services. Rudman et al (2017a) provided useful perspectives, but provided a narrow definition of “contemporary evosystem services” as “the maintenance or increase of an ecosystem service resulting from evolution that occurs quickly enough to alter ecological processes”. As our bioGENESIS response paper in TREE (bioGENESIS members, Faith, Magallón, Hendry, and Donoghue, 2017) pointed out, this definition unfortunately implies that ecosystem services are the only benefits from contemporary evolution, overlooking the role for contemporary evolution in providing the “maintenance of options” contributed by biodiversity.

Wrapped up in that discussion (and in Rudman et al 2017b, which is a reply to our response) are two concerns about how our broad definition extends beyond ecosystem services to include biodiversity option values–

1. It could be claimed that our definition of “evosystem services” is so broad that it is intractable, and so a focus on ecosystem services, in the definition of contemporary evosystem services, makes it more measurable and operational.

2. It could be claimed that biodiversity option values can’t really be a contemporary evosystem service, because the benefits are in the future and not a product of contemporary evosystem

I’ll discuss these in turn.

1.  Reading Hendry labels

I can see why a more constrained definition of contemporary evosystem services might be tempting. Rudman et al’s blog contribution about their TREE paper (the “MS” below) presented more on their rationale. They found support in Andrew Hendry’s recollection that we:

 “intended specifically to make evosystem services synonymous with ecosystem services - to make clear the importance of studying evolutionary diversity even when interested in ecosystem services. [A Hendry 4/9/2017: Stated more correctly, ecosystem services ARE evosystem services.] Thus, the original intent of the term was exactly that which authors of the present MS criticize - that it is all inclusive and, as the authors argue, therefore unhelpful).”

As I noted above, synonymising evosystem services and ecosystem services might have been one useful way to increase appreciation of evolution, but our Faith et al 2010 paper promoted that idea that evosystem services critically adds something more:  

“‘Evosystem services’ provides us with a useful handle in reflecting values that are not very naturally accommodated by the concept of ecosystem services, including the capacity for future evolutionary change and the continued discovery of useful products in the vast biodiversity storehouse that has resulted from evolution in the past. In this sense, ‘evosystem services’ and ‘ecosystem services’ are complementary. Together, the two capture a wider variety of the values that we associate with ecosystems and biodiversity…..Because the pursuit of some ecosystem services can sometimes entail the loss of biodiversity, it is important to make sure that other uses arising from biodiversity also are measured. We think those other uses are extensive— they include not only known uses from known species, but also yet-to-be discovered uses from known and still unknown elements of biodiversity..”

I think the Andrew Hendry blog quote above therefore does not capture the whole story – in fact, in his early blog post here on evosystem services, Andrew noted that not only are ecosystem services a product of evolution but also that –

“evosystem services are so much more because they recognize that biodiversity has current or potential future values to humans that we don’t know about yet and can’t yet envision.”

So, all that supports the little diagram that appears in our TREE response (re-drawn below):

Rudman et al (2017a) had characterised our broad interpretation of evosystem services as “a concept too meta-scale to measure”. But the individual arrows in this figure are measurable. For example, the assessments of on-farm conservation sometimes measure the option values of contemporary evosystem services (blue dotted arrow). Similarly, the maintenance of options resulting from past evolution (blue dashed arrow) is measured using “phylogenetic diversity” (PD).

2. Definitions, and stories about definitions

In their reply to our response in TREE, Rudman et al. (2017b) defended their ecosystem service-focussed definition, arguing that our notion of biodiversity option value did not correspond to something produced by contemporary evolution. They properly referred to Faith 2017 as providing our definition of option value, but then quoted it this way:

“’option value refers not only to the unknown future benefits from known units of biodiversity, but also to the unknown benefits from unknown units.’ Using this definition, Faith et al. focus on the importance of maintaining genetic diversity to maintain ‘future options’ provided by living variation. …. we would not classify these option values as contemporary evosystem services because they are not the product of current rapid evolution”

Faith (2017) did not state that definition, which would on its own have given the impression that the benefits were in the future and so could not be a product of contemporary evolution. This can be cleared up by looking at the full paragraph in Faith (2017) from which Rudman et al’s quoted sentence was plucked:

“the best argument for what we call the option value of biodiversity is that we see many currently beneficial units, and maintaining a large number of units (biodiversity) for the future will help maintain a steady flow of such beneficial units (see also the “storehouse” analogy in Faith et al 2010).  In accord with this idea, the Millennium Ecosystem Assessment (MEA; 2005a: 32) described option value as: “the value individuals place on keeping biodiversity for future generations”. Option value refers not only to the unknown future benefits from known units of biodiversity, but also to the unknown benefits from unknown units. Biodiversity option value therefore links "variation" and "value": providing a fundamental relational value of biodiversity reflecting our degree of concern about benefits for future generations.”

Thus, the sentence prior to the one quoted by Rudman et al points to a version of the actual definition. Individuals (or society) gives some value to that benefit biodiversity provides in maintaining options for the future. As Faith (2017), and our response to Rudman et al (2017a), made clear, the value/benefit is now (“the value individuals place on keeping biodiversity for future generations”) and, as illustrated in Bellon’s work, this benefit may be produced by contemporary evolution.

Part 2

The pre-history of a term

The discussions about evosystem services and biodiversity option value, arising from the Rudman et al papers and bioGENESIS responses, have been constructive. But this also recalls for me the widespread resistance (reviewed in Faith 2017) to the idea that biodiversity has its own direct benefit, maintenance of options, that goes beyond any benefits through support of ecosystem services. Indeed, Faith (2017) traces a popular re-writing of the history of “biodiversity” in which the ecosystem services movement supposedly forged links for the first time from “biodiversity” to human well-being (with biodiversity supposedly only having intrinsic value prior to that).

Faith (2017) also laments that this story-line sometimes is propped up by re-casting “biodiversity” as practically any aspect of ecology that supports ecosystem services. A special case of that problem concerns PD (see above), proposed as a measure of biodiversity and its option value at the regional/global scale (Faith 1992). But now many ecosystem services papers state that Faith (1992) defined PD as the phylogenetic diversity of a community.

An antidote to what I call “the histrionics of a term” (roughly, the over-the-top re-written history of the term after it was invented) is to not only carefully trace the actual history, but also to examine what I call the “pre-history” of a term (“roughly, the history of the term before it was invented”; see Faith 2017).

For the term “biodiversity”, this pre-history exploration is not yet complete. But early papers (well before the coining of the term “biodiversity” around 1985), using terms like “biotic diversity”, reveal rich discussions of anthropocentric values related to the value of variety in maintaining options for the future (see Faith, 2017).

Unmarked landmarks 

Uncovering a “pre-history” can be fun. I have relied on Web of Science and also some previous excellent reviews (including Mazur and Lee, 1993 and Farnham 2007). It appears that a suite of uncovered papers collectively can document an emerging idea well, but any one of the papers may not have been cited much. Indeed, some of the early significant papers are “unmarked landmarks” that raise mysteries.

I really liked a little 1974 paper in Science that reported on an important discussion meeting where participants called for “an Ethic of Biotic Diversity” in which “diversity is viewed as a value in itself and is tied in with the survival and fitness of the human race”. The paper warned that extinction “threatens to narrow down future choices for mankind” (see Faith 2017).

The pdf of that “news and comment” page in Science only had the signature “C.H.”:

Based on Web of Science I attributed the paper to C Haskins (Web of Science now reports it as having exactly one citation - mine). However, I later noticed that Mazur and Lee (1993) referred to the same paper, but with attribution to a different “C.H.”, “Constance Holden”. This seemed plausible; a little detective work revealed that Constance Holden may have been the staff journalist for the “News and Comment” section. Back in Web of Science, I found no less than 15 “News and Comment” papers by Constance Holden in 1974 – all signed “C.H.”

Each paper had a title beginning with a subject:  e.g., “Sex therapy -”, “Ethiopia -”, “Cliometrics -”, “Methadone -”.  Of all of these, the most cited was: “Sex therapy – making it as a science and an industry”. But nowhere could I find a Constance Holden paper on anything like “Biotic diversity – making it as a science and an industry”, which would have been a great read in 1974.

I think I will stick with the C. Haskins attribution

(and raise this challenge to the reader – can you nominate other papers as “unmarked landmarks” that deserve to go from (say) 0 citations to 1 or more?).

Meanwhile, I noted recently that Mazur and Lee also cited another relevant paper for my pre-history of biodiversity - Iltis (1972). H. H. Iltis, who died this past year, was professor emeritus of botany at the University of Wisconsin–Madison. He was best known for his discoveries in the domestication of corn, but also wrote broadly about environmental matters. His 1972 paper called for society to “preserve sufficient diversity of species and of ecosystems” because “we will never reach a point where we shall know which organisms are going to be of value to man and which are not.” Again, we see an early paper that neatly captures the fundamental link between biodiversity and maintaining options for the future.*

*see also the Iltis (1967) Bioscience paper that is 50 years old this year. He argues “life's diversity is threatened with imminent destruction, that in 20 or 30 years it will be all but over for this exuberant biotic wealth”.

Iltis (1972) is another unmarked landmark paper -  Web of Science reports it has been cited only 6 times. In any case, while my pre-history task is not complete, we already can say that by 1972 (45 years ago), biotic diversity itself was promoted as a benefit to be valued by society, and the nature of this benefit to society was the maintenance of options.

I like the phrase “maintenance of options” as a reference to biodiversity’s contribution to people.. As our TREE paper (Faith et al, 2017) on contemporary evosystem services noted, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES 2017) recently recognised “maintenance of options” as a distinct category of “nature’s contributions to people” (NCP).   NCP is a useful shift from conventional ecosystem-services speak. While IPBES (2017) stated that its list of 18 NCP “are generally closely associated with the concept of ‘ecosystem services’”, the “maintenance of options” NCP is the important departure. I hope that IPBES assessments now will implement measures for both the blue-dotted and blue-dashed lines in our figure.

Some references

Bellon, M.R. et al. (2015) Assessing the effectiveness of projects supporting on-farm conservation of native crops: evidence from the high Andes of South America. World Development 70, 162–176

Faith, D.P. (1992) “Conservation evaluation and phylogenetic diversity,” Biol. Conserv.  61: 1–10.

Faith, D.P. (2017) A general model for biodiversity and its value. in The Routledge Handbook of Philosophy of Biodiversity (Eds. J Garson, A Plutynski, S Sarkar)

Faith, D.P. et al. (2010) Evosystem Services: an evolutionary perspective on the links between biodiversity and human-well-being. Current Opinion in Environmental Sustainability 2, 66-74

Faith D P and Richards Z T (2012) Climate change impacts on the tree of life: changes in phylogenetic diversity illustrated for Acropora corals. Biology 1(3), 906-932

Faith D. P., Susana Magallón, Andrew P Hendry, and Michael J Donoghue (2017) Future Benefits from Contemporary Evosystem Services. Trends in Ecology and Evolution Volume 32, Issue 10, October 2017, Pages 717-719.

Farnham, T. J. (2007) Saving Nature's Legacy: Origins of the Idea of Biological Diversity, Yale University Press, 276 pages.

Hendry A.P. et al. (2017) Human influences on evolution, and the ecological and societal consequences. Phil. Trans. R. Soc. B 372:20160028

Iltis, Hugh H. (1967) To the Taxonomist and Ecologist Whose Fight Is the Preservation of Nature. BioScience17, 886-890.

Mazur, Allan and Jinling Lee (1993), Sounding the Global Alarm: Environmental Issues in the US National News. Social Studies of Science, 23, 681-720

Rudman, S.M., M. Kreitzman, K.M.A. Chan and D. Schluter (2017a).  Evosystem Services: Rapid Evolution and the Provision of Ecosystem Services. Trends in Ecology & Evolution. Doi: 10.1016/j.tree.2017.02.019.

Rudman, S.M., M. Kreitzman, K.M.A. Chan and D. Schluter (2017b). Contemporary evosystem services: A reply to Faith et al. Trends in Ecology & Evolution. Doi: 10.1016/j.tree.2017.07.006

Monday, October 9, 2017

The secret lives of manuscripts

Everyone who has written and published a scientific paper has pondered the mystery: you send in your final version, then there’s this long silence. Suddenly you get an urgent email with your page proofs, insisting that you go through them with a fine-toothed comb and get them back within two business days.  “Hurry up and wait“, I’ve heard multiple authors remark, rolling their eyes.  For most scientists (myself included), our publishers are a cryptic “black box”. We know something is happening to our paper, behind the scenes. But we’re not really sure what happens out there,  why it takes so long, or why there’s suddenly such a rush when the proofs appear. Okay, the black box metaphor is boring and overused. How about we think of it as the mysterious years after young salmon (our paper) venture out into the wide ocean, out of sight, before suddenly returning to their natal stream for spawning (proofreading). Um, that’s not exactly a great metaphor either, but I’ll swim with it. So here’s a blog on the unseen part of your manuscripts’ life history.
            Last week I got to venture under the publishing ocean surface, visiting the journal office of The American Naturalist at the University of Chicago Press (UCP). I’m gradually transitioning into the role of Editor-In-Chief of AmNat. I officially start January 1 2018, but am ramping up my activity by starting to share some Editor tasks with Judie Bronstein, the outgoing editor. I visited the Press for a day to learn more about how the journal works, meet the people who make it happen, and talk about ideas for the future.

I started my day in Chicago with a visit to a Hyde Park institution, Valois, where Obama was a regular. I got to sit at the Presidential table. Then, well fed, it was off to the University of Chicago Press.

            When I walked into the UCP board room, the first thing that struck me was how many people were there.  I had expected to be meeting with Trish Morse (the public face of the journal at scientific meetings), Owen Cook (who works closely with authors during revisions and preparing final version), and Valerie Bajorat (the Publisher, who I’d corresponded with), and maybe a couple of other people. But the room had a dozen people in it, and they quickly apologized on behalf of a few people who were out sick or traveling. I was genuinely surprised that so many people had come. Over the next few hours, they took turns explaining to me what each person did, answering my questions, and charting the unseen stages of a manuscript’s  life-cycle.  By the time I surfaced from this dive into the publishing underworld, I had a much greater appreciation for the value-added that a good journal office provides. And by extension, a greater appreciation for why publishing costs what it does, and why that is worthwhile.
To pass on what I’ve learned, let’s track a hypothetical AmNat manuscript from submission onwards.  Let’s start with the part that is at least mostly familiar to authors, though perhaps not in detail. The first parts below will be familiar to most authors, though maybe not in the level of detail, the number of steps. That’s what I want to convey though, that there are many, many steps:
1. The first thing a manuscript encounters as it leaves its natal stream (your computer) is the Editorial Manager website. This is a shockingly complicated (but flexible) commercial system that the journal subscribes to (which costs money). The AmNat Editors and Staff have personalized many aspects of the system over years, building in an informative but imposing set of visual flags, messaging systems, auto-alerts, reporting tools. There is of course a staff member (Rob Blixt) dedicated to keeping this system operational, and optimizing it to make submission as quick as possible for you, but as informative as possible for us.
Owen Cook (left) and Rob Blixt (right)

2. Once your manuscript is submitted, the Managing Editor (Trish Morse) or Owen Cook check to make sure the basic requirements have been met. Unlike some journals, we don’t require a specific format for review (again, to make submission as easy as possible for you; though be forewarned that reviewers often get agitated if they think your paper doesn’t match journal style). If the paper passes this check, it gets moved into a folder where the triumvirate of Editors can see it.

Image result for Trish Morse
Trish Morse, who many readers may have met at conferences.

3. One of the three editors will claim a paper (sometimes after a bit of haggling amongst ourselves), then read it over. We may opt to send it back to the authors with a clear justification for why it isn’t suitable. These can be several-page reviews by the Editor; we don’t want to make such a decision lightly or arbitrarily. If we think the paper has a chance, we will check the list of Associate Editors: who is suitable to handle this paper’s subject, setting aside people who are unavailable, or already handling a full load of papers. We then post on Editorial Manager a list of the AEs we think would be good, and hope they take it. If not, we revisit the list of names.
4. The Associate Editor then looks over the paper to decide whether it is worth reviewing. We don’t want to waste authors’ time if their paper doesn’t have a chance (poor fit for the journal, or too clearly flawed), nor waste reviewers’ time. If the paper seems worthwhile, then the AE proposes a list of names of reviewers (see for some comments on this process). This involves looking through the manuscript’s references, searching on scholarly databases or Google for people with appropriate expertise, checking for conflicts of interest, and perhaps tracking down contact information if the reviewer isn’t in the Editorial Manager database. The proposed list (often  ~6 names) goes back to Trish Morse at the journal office. She or Owen checks the list for conflict of interest and availability, since AEs don’t always have the time. invite reviewers and process the responses until we hit the targeted 2 reviewers. Often, they go back to the AE to get more names until we hit the two-reviewer target. Unlike some journals, which blast out all the email invitations at once (thereby often getting an excess of reviews, which uses everyone’s time), AmNat sends out invitations until we get exactly two reviewers. That takes just a little more time, but it is better citizenship, I believe, to not draw on too many peoples’ time.
5. AmNat gives reviewers 21 days to review.  They are busy people, after all, and volunteering. Some journals demand faster reviews, but we want to give them enough time to do a careful job. Rushed reviews can be sloppy (missing a mistake, or misunderstanding a point) and cursory and are more likely to be grumpy. That Editorial Manager website proves its worth again with review reminder reports with the flexibility to respond individually to reviewer.
6. Once both reviews are in, they are checked for completion and problems by Trish or Owen and then routed to the Associate Editor, who typically reads the paper a second time and writes a substantive review in their own right. One of the things that we pride ourselves about at AmNat is that the AEs really work to fix any flaws that the reviewers happened to miss. Many of our AEs also go to great lengths to identify diamonds-in-the-rough; manuscripts that are flawed but contain the ingredients for a great paper. Some will take a paper through multiple rounds of revision, providing detailed feedback on writing, graphics, and pitch until the paper meets our standards. My favorite example of this is detailed in Meghan Duffy’s blog post about how our (then) AE Yannis Michalakis helped her ms (previously rejected at Ecology) improve until it won the ESA’s Mercer Award ( .
7. The AE sends the reviews and their own recommendation to the Editor, who typically reads the paper again, and adds their own insights as well in a decision letter. There are often Skype calls or email conversations at this stage to negotiate a mutually agreeable decision. Last week alone I ended up in three separate conversations with AEs who wanted some feedback on their recommendation. Once they submit a recommendation, my decision letter has to be written, then sent back to the Managing Editor (Trish) who checks it, formats it, and sends it. I usually give the paper another read-through before writing my decision. Speaking as an author, I can’t over-emphasize how valuable the feedback from AmNat’s Editors can be. Yannis Michalakis has (as Editor) greatly improved several of my papers with feedback that went above and beyond what the reviewers and Associate Editors provided (themselves giving very good feedback).
8. For each round of revision, the paper may or may not go out to reviewers (usually only  if the changes are substantial and the AE not able to evaluate themselves), but will be read by the AE and often the Editor, until it is clear that the paper is good enough to publish, or clear that the paper isn’t on a trajectory to reach that level.  Then a final decision is rendered, which brings up format issues for a smooth journey through Production,and the author makes any last changes and submits a “final” version to the office via Editorial Manager.

Let’s pause here. Everything up to this point is moderately familiar to scientists. But let’s put it in perspective. At the time the paper is submitted in its “final” form, it has been handled by Trish Morse or Owen Cook somewhere between 6 and a dozen times. There have been dozens of separate steps on Editorial Manager. The Editor has read the manuscript two or more times. The Associate Editor has read it two or more times. The two reviewers have each read it at least once, often twice. So it has been read through, on average, about nine times (assuming two rounds of review), and has involved six people. But so far, a large fraction of those people are volunteers (AEs, reviewers).  This is the point at which the manuscript leaves the natal stream and enters that unseen world.

9. Picking up where we left off: the submitted “final” version is checked over in detail by Owen Cook, to make sure all the parts are present and accounted for. Data is deposited, files are complete, appendices and supplements sorted out. Owen makes sure that figures conform to journal standards for size, font, resolution, and are converted into vectored EPS format for the highest quality online and in print. He’ll communicate with authors to fix any remaining problems, and clarify what is destined for print appendices versus online supplements.  Forms and agreements are gathered. When files, figures, and forms are complete in the journal office, the paper gets assigned to an issue (usually the next one headed to Production). Then the paper is sent from Editorial Manager to the UCP Production system. This process takes as long as it takes authors to bring the paper up to Production standards.

10. Once in Production, the Production Coordinator Jeannie Harrell checks it into the Production database, makes sure all the necessary metadata and elements have come through from the journal office. the paper has to be translated to a new file format (XML) for the next stages. To do this,  Jeannie sends it to a professional service. This way we can get LaTex and Microsoft Word and Open Office files into a single publication-ready version.  The service returns the paper within 48 hours, where it is checked for the necessary tagging and code by the Publishing Specialist and Production Editor Samanatha Tansino.
Jeannie Harrell

11. When she gets the file ok from Sam Tansino, Jeannie delivers the manuscript to the copy-editing team (“Editorial” led by Mary Nell Hoover).  The manuscript PDF now is printed on paper as the last word on the authors’ intentions, placed in a green folder, and brought downstairs. Editorial goes through the paper line by line, looking at grammar and phrasing. They convert your equations into XML-friendly format for the clearest presentation. They check that things are capitalized, or not. They check citations in the text and reference details at the end of the paper. They check that you are consistent in using symbols or abbreviations in the same way. In short, they go over the paper with the proverbial fine-toothed comb, with the Chicago Manual of Style close at hand on every copy-editor’s desk. Their goals are to ensure the writing is clear, readable, and conforms to journal style. As needed, they will change sentences, capitalization, punctuation (adding proof queries to the author about any changes in meaning). The editorial team also formats tables into journal style. They even check a lot of our numbers in tables, for instance making sure that sums add up. Just to get an AmNat manuscript ready for the quality control check can take an editor up to 36 working hours, depending on the size and complexity of a manuscript. Then the other team member -checks it, sending queries to the author as needed. Because our in-house copy editors are working on many papers (for many journals) at once, this can take roughly 20 days.

Mary Nell Hoover

12. When the copy editor is done, they hand the paper over to another team member for checking, When those changes are made and approved, the paper is sent to the typesetter, who has two days to return the proofs. These are not immediately sent to the author. Instead, the Editorial team checks the “pre-proofs,” especially the math, and either approves them or sends them back to the typesetter for corrections.  At this point the copy editor also makes sure all queries to the author are ready. This editing-typesetting-checking process is repeated until the copy editing team thinks the proofs are ready. All told, this step usually takes about 5 days more.

13. This is when the proofs get sent back to you, with a request that you return the proofs within two days with any last (minor) corrections.  Two days always seems rather demanding to authors, who are unaware of what’s been going on in the background, but as you have seen the paper has passed through many hands, many times.  And it’s not done. Problems with returning the proofs can be solved, but the deadline is to keep the issue as a whole on its monthly schedule.

14. When you return the pdf with corrections, it is received by the Production Controller, who sends it downstairs again to the copy editing team. They check your responses, which is at least the fourth time they are seeing your paper. Then the paper is sent back to the typesetter for re-typesetting; they have one day to return it.

15. When re-typesetting is done, office staff get a notification and download the zipped version. They print out a copy of the typeset pdf on paper, and send it back down to the copy editing team for one last check. All told, every single character in the math in every article has been checked against the author’s PDF at least three times. When they are satisfied the paper has no errors, it is returned and marked as finalized and ready to be posted online. At this point it goes back to the Publishing Specialist, who puts the HTML  version and the typeset pdf on the journal website. Now, your paper is posted as an Ahead Of Print (AOP) article. The digital version and its green folder are put in a pile to await a complete issue’s-worth of articles.

16. The articles then have to be sorted into an order by the Editor In Chief.  The articles must then be paginated, leaving room for advertisements, announcements, editorials, and the like, to form a complete issue. The whole issue is printed on the same kind of paper that forms the actual journal issue, for one last review by the copy editing team. Mary Nell makes corrections to the whole issue, sends it back to the typesetter if any corrections are needed. This cycle is repeated as many times as necessary to get a version that is approved by the UCP Editors.

17. A print-ready pdf is made by the type-setter for the whole issue, and sent to the printer. The printer returns a digital and a hard-copy version to be checked one last time, printed now on the same paper stock as a real issue.

18. After a last check-through, the issue is approved, sent to the printer, and published as an electronic edition and e-book, as well as printed and mailed to libraries and subscribers by the UCP Distribution Center.

19 Only after the paper is safely tucked into its issue does the Billing Manager take the page charge calculations from the Managing Editor to work out the invoices because the charges are tied to actual pages (unless an author requires a flat fee article processing charge)

Now, this team of people cannot operate without some other support. There are the electronic publishing experts, who solve the tough tagging and presentation issues. There’s the IT people who make sure the Editorial Manager database and website, and journal website, are operating smoothly. And fixing people’s desktop computers as needed. There’s the marketing staff who keep subscriptions coming in from institutions, and seek new institutions to work with. There’s human resources staff who pay everyone. There’s the janitorial staff, maintenance. Many of these people of course help with the whole University of Chicago Press, which handles a moderately large number of journals.  

So, why does this take so long?  Because careful publication takes time. The University of Chicago Press believes that scientific publications should be as accurate, readable, and professional as possible. As you’ve seen, that takes an incredible amount of behind-the scenes work to make sure that everything from the tables to figures to grammar to copyright permissions are perfect. Your paper passes through many people’s hands, with many iterations of corrections. The end result is a higher-quality product with fewer mistakes.  As an author, I’ve long been impressed with the detail and professionalism of the AmNat copy editing team, which finds many small details to query and correct, often far more than other journals pick up. Better still, let’s contrast this with PLoS One (not to name names), which makes authors do all their own copy editing, and doesn’t even do a round of proofs. Let’s face it, most of us just aren’t trained as copy editors. As a result, I’ve found PLoS One papers to be full of stylistic flaws, typos, and errors that a professional copy editor would catch.

Why does it cost a few thousand dollars per article (few authors shoulder that whole cost)? The income generated from our roughly 120 articles per year (and past papers) brings in the income that keeps these people employed to help your articles be as clean as they can be. The income also has to pay to use the Editorial Manager software, and contribute a bit to keeping the lights and water on in the UCP as a whole. Those page charges you pay are a very modest contribution towards supporting that behind the scenes staff, but by no means covers all the costs. The balance comes from institutional subscriptions, and individual subscriptions, and society memberships. Despite UCP’s reliance on subscription income, it gives away free journal access to institutions in over 100 developing countries, about 8,000 universities in total.

The end result is that AmNat produces a very high quality product, even though it is actually one of the cheapest journals to publish in or subscribe to.  A moderate number of authors pay nothing at all. That’s very important especially for early career researchers who may not have the financial resources to cover even regular page charges. Those who do pay regular page charges are covering a moderate fraction of the costs of producing their article. People who opt for open access pay various higher rates depending on the level of access. At the extreme, we offer the opportunity to cover the full costs of production for extreme levels of open copyright.

So when you balk at a bill for page charges, remember the hard work of the large team of people behind the scenes who are laboring to make your paper into a high-quality product. In the case of The American Naturalist, the journal is a not-for-profit (501c3) entity. The University of Chicago Press is a branch of the University of Chicago. Its primary task is not maximizing income for investors or an owner, but promoting academic pursuits. The building and offices are clean and well maintained, but not fancy.  I asked for directions to the room where you can roll around in big piles of cash, and the staff looked confused.

Occasionally on Twitter I read comments by people who basically want to shift to an all-BioRXiv publishing model. We self-publish, and “get rid of journals”. Cheaper. Faster. No annoying peer-review setting standards (just post-publication review).  Personally, I’m not on board with this.  I think the review process gives great value added, and that’s backed up by a totally unscientific poll I did on twitter: a vast majority agreed that reviews improve papers slightly (50%), or very substantially (40% of 88 votes).

So if ever someone advocates getting rid of journals, I have my canned response. GOOD journals can:
1)   help improve your paper through anonymous (and thus more frank) reviews

2)   improve your paper through Associate Editor and Editor comments that seek to bring out the best in your paper, or direct you to a journal where your paper will most readily reach its target audience

3)   help you produce a polished and professional final product that reads well, is easy to understand, and looks good. As a result it will be read more, and cited more.

4)   Distribute your paper to readers via their website, table of contents, subscriptions, and social media.

5)   Apply any excess income back to academic societies, which in turn support student research, travel, conferences, and the like, building a richer academic community.
These represent value-added to the scientific enterprise. That value added isn’t free, because it takes digital and personnel resources. So who pays? It either has to be the government (good luck asking Trump for that), the author, or the reader(s). Each has its flaws. Government payment is subject to political interference. Author-payment creates a barrier to entry for underfunded (especially junior) scientists, which hampers their career. Reader payment reduces readership access and citation (though remember we give away AmNat for free to thousands of institutions).

To conclude, repeat after me:

Journals provide value-added.

That value-added has a cost associated with it, which someone must pay.

Support your society journal (especially if not published by a big lucrative conglomerate).

Non-profit and open-access are not synonymous things.

The American Naturalist is awesome (though I am admittedly biased), both because of the great authors who submit interesting papers, the Editors and Associate Editors and Reviewers who work to improve those papers, and, let’s never forget, a large and hard-working editorial team that makes the high-quality final product.

A huge thanks to the staff of The American Naturalist at the University of Chicago Press, for the in-depth tour and education.

Saturday, September 16, 2017

Work-Life Balance or Work-Life Fusion?

We were in a remote area of British Columbia, having driven from our already remote cabin to the very end of an old logging road and then having hiked up a game trail for more than an hour. Cedar and Heather were out of sight a hundred meters or so away in the old growth timber, collecting information on obstacles that animals face while walking along the trail. Aspen and I were standing at a three-way split in the trait, setting up a camera trap to film animals as they selected one branch of the trail over the others. We had just turned on the GoPro for Aspen to walk the trail recording its obstacles, when just behind us we heard a loud WHOOOOSH , like a mix of a bark and a hiss (recorded [listen closely] in the video below). We spun around to see a big grizzly not 5 m behind us …


When I get back from a trip, which is exceedingly frequent these days, people I know outside of work – and sometimes even at work – often ask “Was it work or a holiday?” I always hesitate to answer because, for me the dichotomy is a false one. My personal interests (adventure, exploration, nature, diving, fishing, photography) are so closely relate to the things I do for work that every “work” trip involves some fun and every “holiday” involves some work. This might seem paradoxical to some who emphasize the need for work-life balance but, for me, it is instead a work-life fusion. I have chosen a job that I love – not just for the job itself but because I would do much the same even if I didn’t have the job.

Perhaps the most direct illustration of work-life fusion is research with your family, which I have found exceedingly rewarding – and I hope my family has too. In this post, I want to sketch little vignettes of the story behind research projects with my brother (Part 1), my kids (Part 2), my wife and kids (Part 3), and my wife and friends (Part 4). In doing so, I hope I can supplement the discussion of life-work balance with a recognition that life-work fusion is also rewarding. And, perhaps, along the way, I can inspire others to conduct research with their families.

Part 1. From fishing to fishery science

My brother (Mike) and I grew up with fishing being our primary passion. Much of this passion was concentrated at our cabin on the Kispiox River in northern BC, which my uncle Paul purchased in 1975 and my parents bought into in 1980. We, especially my brother and I, started fishing for coho salmon and then, in 1985 or so we transitioned to steelhead being our primary target. Soon this passion had spread beyond the Kispiox, with both of us choosing the University of Victoria so that we could fish for steelhead year-round.

Our first steelhead season, 1985.
In 1991, Mike started working at perhaps the most famous steelhead camp in the world – the Lower Dean River Lodge. (NOT coincidentally, my father had gone with Bob Stewart and Dick Blewett on their first scouting trip to Dean River 1961, a year before Bob started the lodge.) Soon after starting to work their, Mike was steeped in the lore and mythology of premier steelhead fly fishing.

Mike and I with a spectacular Dean River COHO salmon.
In 1995, I was a graduate student in the lab of Tom Quinn at the School of Fisheries at the University of Washington (UW), and Mike had just finished his undergraduate degree. I arranged for Mike to work for Tom on a variety of projects for which Tom’s students needed help. Being constantly surround by people conducing research on salmonids got Mike to thinking: “Hey, I should do this too” – so he hatched a plan to study the population structure of steelhead in the Dean River. 

Together, we planned a study in which Mike – and all the guides and clients on the Dean River – would collect life history information (size, scales for ageing) and genetic samples (small fin clips), and conduct mark-recapture sampling, of steelhead in the river. Mike wrote to all the Dean River fishermen telling them of his plans and asking for a small financial contribution to purchase equipment and do genetic analyses. To their credit, many of the fishermen chipped in and the study was a go.

Sampling over the summer of 1996 went very well, with 591 fish captured, measured, and tagged. In the fall, Mike brought the genetic samples back to UW and worked with John Wenburg in the lab of Paul Bentzen to analyze them genetically using DNA microsatellites – a cutting-edge technology at the time. The scales were analyzed for age by another researcher at UW, Kate Myers. Then – primarily over a Christmas at home with our parents – Mike and I analyzed the data and wrote the paper. Published in Transactions of the American Fisheries Society in 2002, the study provided the first evidence for population structure within this premier fishery.

While Mike hasn’t conducted additional formal studies, he has since helped me with my research in Alaska, Trinidad, Galapagos, British Columbia, Chile, and Uganda. He has also monitored fish in the creek that flows through the Hendry Vineyard, which he manages.

Part 2. Hendry Vineyard stickleback (excerpts from early post).

In 2009-2010, I completed my sabbatical at the University of California at Davis. In reality, however, much of my time was spent on my family’s vineyard in Napa, California, where I lived for that year. (The vineyard and winery are owned by my uncle, George, and the vineyard manager is my brother, Mike.)

Nearly every day, my kids (Aspen – 7 years old – and Cedar – 4 years old) and I would go for a stroll around the vineyard. A few weeks into our stay, we found ourselves walking along the creek that flows through the property. The kids got all excited about the small fish they could see rushing around in what little water remained in late summer. “Catch the fish Daddy, catch the fish.” Well, it is hard to resist the kids when they want to catch fish, and so we got some small nets and set to it. To my complete surprise, it turned out that the most numerous fish in these tiny pools were threespine stickleback, which I was studying in my own academic research.

A few weeks later, one of our walks took us past the two reservoirs on the property and I happened to look in and notice some small fish swimming around. I looked closer – stickleback again! Now fate just seemed too obvious to ignore – we were literally living between a reservoir and a creek, and my stickleback research focuses on lake and stream populations. Moreover, the two reservoirs had been created in the early 1970s by pumping water from the creek – and this would have been how the stickleback colonized the reservoirs. So not only was it a lake-stream stickleback pair in our backyard but it was also a potential “rapid” evolution scenario – one of my other major research interests. How could we not study it? 

The creek is shown in the white line and the reservoirs in the white circles.
Aspen and Cedar set and retrieved the minnow traps, Cedar “died” the stickleback, I photographed them, and Aspen labeled and preserved them. The next year back home in Montreal, we continued the project on rainy days and in the dead of winter. Aspen set the morphometric landmarks on the computer, Cedar took the fish out of the vials, I measured and dissected the fish (thanks to my Mom donating her dissecting microscope), and Aspen recorded the data in the computer and returned the stickleback to the vials. The next year it was back to the vineyard for a second round of sampling and then came another winter of fish processing.

Aspen checking traps.
Cedar searching (with Jake) for traps.
Our first major finding was the lack of noteworthy divergence between creek and reservoir stickleback. Although this was initially disappointing, it eventually became more exciting – because it represented a dramatic exception to many other lake-stream pairs and to the frequent evidence for rapid evolution in stickleback. Our second major finding was that morphological variation in Hendry Vineyard stickleback – in both reservoirs and in the creek – was extremely high. In fact, consultation with many stickleback biologists suggests that the variation at these sites was higher than that in any other known stickleback population.

 A really cool spin-off outcome from the paper we published in Evolutionary Ecology Research, and the blog post I wrote about it, was that several other researchers subsequently were inspired to conduct research and write papers with their kids. Here is one from Heather Gray and her son documenting some unexpected behavior in a tropical toad. Here is one from Steve Cooke and his kids studying the effects of “playing time” on the recovery of fish caught by hook and line.

Part 3. Walk this way.

In the remote area described at the start of this post, a very heavily used game trail meanders its way for several kilometers along a ridge between the river and a lake. As the trail winds along, it periodically splits into two (or even three) branches before reconnecting again just a few meters to a few hundred meters later. Why? Why should some animals go one way and others go another way? Do bears take one branch and moose the other? Do male moose with cumbersome antlers follow one route and female moose with calves another? Do animals take one branch going north and the other going south? Are some animals left-handed and others right-handed?

Aspen, Cedar, and Heather asking "which path would you take?"
I had often pondered these seemingly inconsequential questions when walking the trait and thought it would be a fun question to answer. So, this year, the whole family decided to find out. We set up 8 Reconyx game cameras to film animals at the various splits in the trail and, next year, we will pull the memory cards and analyze the resulting videos, which we can then relate to data on obstacles along the trails, which brings me back to that grizzly.

Working on a camera trap.
just behind us we heard a loud WHOOOOSH, like a mix of a bark and a sneeze. We spun around to see a big grizzly not 5 m behind us. For just a few seconds, we all just stood there looking at one other and then the bear wheeled around and ran 10 m or so back down the trail. At precisely the moment I realized “damn I forgot the bear spray,” the bear stopped and turned back toward us, sniffing the air and bobbing its head up and down. While I love watching bears unobtrusively, it struck me that this might be a good time to be more obtrusive, so I started to yell “Hey bear.” The bear continued to stare at us for another minute and then walked back the way it had come. “Whew”, I thought, “that was really cool” and then, just a second later, “Whoa, where are Heather and Cedar?” Off we went to find them and soon, all reunited we reminisced about the exciting adventure as we walked back toward the cabin.  

The video below records this entire sequence, with data collection starting seconds after the bear left. "Did it hiss at us?" Aspen asks. (Sadly, we never thought to point the camera at the bear - it happened too fast.)


Part 4. The Heir of Slytherin?

When our friends, Hans and Gemma, were renovating their house, we looked after their snake, which was great fun. When they took their snake back, they gave us another one as a way of saying thanks. The next year, we bought our first ball python. The year after that, we bought our second. These snakes became more and more a part of our menagerie and the first ball python, Nagini, has become a regular feature in the biology classes of both Heather (at Vanier College) and myself (at McGill).

Nagini helping me teach.
Now, a number of years later, we have more than 30 ball pythons and Heather has become obsessed with breeding them. The reason is that they show dramatic color variation and Mendelian predictions for the various morphs are well known, you can use the “genetic wizard” to plan your crosses to generate particularly rare or exciting morphs. Who wouldn’t want to breed an “emoji” ball python – as one breeder succeeded in doing.

Just a few of our snakes.
A couple of years ago, at the joint HenDRY-BARrett (DRY-BAR) Christmas party, we were all looking at the snakes and started talking about how great this system would be for studying the genetics of color. This, then, is our next big family (and friends) research project. Heather has been collecting shed skins from a number of cooperating breeders and we will use genomic methods in an effort discover the genes and causal mutations driving color variation.

The point of all this.

All of these projects are entirely curiosity driven. No funding body has made a “call” for proposals on them, no opinion papers in Science have pointed to a need for them, and none of them has (yet) become a citation classic. Nevertheless, each study has made (or will make) a small contribution to our understanding of the natural world that will aid and guide additional research. (Our steelhead paper has been cited 37 times and our stickleback paper 9 times.) Beyond that, the act of conducting these studies has helped to create a work-life fusion that makes the work more fun for everyone and the holidays more interesting at the same time. Perhaps it isn’t the right strategy for everyone – but it certainly is for us.

And, in closing, Cedar's moose trail obstacle simulation ...