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 https://dynamicecology.wordpress.com/2017/09/06/choosing-reviewers-recognition-not-recall-and-why-lists-like-diversifyeeb-are-useful/ 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 (https://dynamicecology.wordpress.com/2012/10/16/the-paper-that-ecology-rejected-that-later-won-the-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 …

video

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.)

video


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 ...


video




Wednesday, September 6, 2017

Descent with Modification: The Evolution of a Conceptual Figure

Almost every student talk – and many by postdocs and profs – starts with a conceptual diagram linking ideas and concepts. The simplest possible version of such a diagram for eco-evolutionary dynamics is two boxes, one for ECOLOGY and one for EVOLUTION, with arrows linking the two. This figure still leads many talks as a way of emphasizing the fact that researchers have long focused on the arrow from ECOLOGY to EVOLUTION but not the reverse, which has recently become the primary new emphasis of research in Eco-Evolutionary Dynamics.


Starting from this simplest framework, I developed an expanded – but still simple – version that sought to make several key points explicit. First, phenotypes are the true nexus of eco-evolutionary dynamics because it is PHENOTYPES (not genotypes) that are under direct selection and it is PHENOTYPES (not genotypes) that have ecological effects. Thus, arrows from ecology to evolution and back must flow through phenotypes. Second, the direct effects of phenotypes on one ecological level (e.g., populations) can cascade to indirect influence other ecological levels (e.g., ecosystems).


I tried to unearth out when I first came up with this figure and was unable to be definitive. However, it was first published in Bailey et al. (2009), a New Phytologist “Forum” describing a symposium on eco-evolutionary dynamics at the ESA meeting in Albuquerque, New Mexico, in August of 2009. I had used the figure in my talk at that symposium. Another early appearance was an F1000 Biology Report that I did with Eric Palkovacs in 2010. Since those uses, the figure has become widely used in various publications and talks (and my book) as a simple intuitive way of conceptualizing eco-evolutionary dynamics.

In short, the basic figure has stood the test of time, largely without revision for almost 10 years. However, almost every time I show it, I end up having interesting discussions with someone about how it could perhaps be improved. In nearly all such cases, I have convinced myself that no change was necessary but, twice now, I have been compelled to admit that it could be better. The first time came during a “the genomic of eco-evolutionary change” symposium and workshop in Monte Verita, Switzerland, in 2016. Victoria Stork pointed out during her talk that my use of “genes” at the top of the figure ignored other, potentially important, genomic changes that influenced phenotypes and could therefore have ecological effects. Epigenetic changes, such as DNA methylation, are perhaps the most obvious example. At this point, my book was basically done and at the printer but I was able to add “genomes” to “genes” at the last minute. My intent in doing so was be inclusive of people studying epigenetics.


The second time I have felt compelled to make a change came just last week at a “significance of sexual selection for population fitness” workshop, again in Switzerland – but this time in scenic Fafleralp and organized by Claus Wedekind. I gave a talk on the first night of the meeting and, afterward, several people – most notably Jacek Radwan – argued for the addition of an arrow directly from population dynamics to genes (bypassing phenotypes). The most obvious reason for such a pathway would be that small population sizes can lead to genomic changes through inbreeding or drift, which could then have phenotypic effects with ecological consequences. I had heard this argument before and had not been convinced, because I felt that the effects still had to flow through phenotypes. This time, however, the argument was clearer to me because I had been specifically talking (and therefore thinking) about the genetic effects of population size.


Specifically, I now agree that small population sizes can directly influence genomes without having to pass through phenotypes, with my apologies to those who made this point previously and I dismissed it. However, I still think that effects of genomes BACK to ecology must flow through phenotypes. That is, inbreeding and drift will change genomes but they will have ecological effects only if those genomic changes modify organismal fitness (leading to a phenotypic effect on population dynamics that could cascade to indirectly influence communities or ecosystems) or traits (a potential direct effect on communities and ecosystems).

Here’s hoping no more major changes are needed. Or, wait, maybe not. Keep ‘em coming – just realize it might take me years to agree! 



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Fafleralp: our workshop was held in the building in the lower left.

Fafleralp: looking back where I had hiked on my first day.

Fafleralp: looking back where I had hiked on my second day.

More photos from Fafleralp.

Wednesday, August 23, 2017

I have the Imposter Syndrome.

At a recent meeting, I had a long discussion with a student about their struggles with the imposter syndrome - not just having it, but even admitting they had it. I was moved and inspired. I asked the student if they wanted to post their story on my blog, anonymously if they chose. So here it is. I hope you find it as helpful, honest, and - indeed - inspiring as I did. (Andrew).

A few months back I was chatting with a friend and collaborator about my post-doc plans and options. He kept throwing what I felt were outrageous suggestions at me, funding that I wasn’t competitive for at all. I brushed the suggestions off. I told him that I would look into it, but needed to think more realistically, that I wasn’t in that league. He cut me off and said, “you need to get over this imposter syndrome thing.” To which I laughed and responded, “imposter syndrome? I think I have anti-imposter syndrome.”

I know anti-imposter syndrome is not a thing. But I really did not identify with the way that I heard imposter syndrome described. I had heard young PhD students talk about it as though it was an inevitable consequence of their genius. It was almost like humble bragging – “Oh of course I have imposter syndrome, I’m at _______“ (insert ivy-league institution of your choice here). I’ve never heard someone from a lesser esteemed school make such a claim. No, we know we are the academic scraps, having been rejected from far better schools for various reasons. Or at least that’s the mindset many of us have. I felt like people routinely under-estimated me. I don’t have imposter syndrome, I told myself. Quite the opposite, I was trying really hard to be accepted into a world I had longed to be a part of for so long. I knew that I would prove myself worthy if given the chance. I had so much confidence in myself and my abilities. I had an “I’ll show you who I am” kind of attitude, and it worked for me.



Actually, it worked really well for me. Doors opened. Connections were made. Suddenly I was receiving awards and praise from some well-known people. People not only accepted me once they saw what I was capable of, but for the first time in my academic career, people had expectations of me! Overnight it went from “who are you” and “you’ll probably fail but go ahead and try” (yes that was actually said to me), to “you always give such great talks” and “I can’t wait to see the results from your next project.”

And with that my friend’s words came storming back into my mind. Maybe I did have this imposter thing after all? For so long I believed in myself when few others did. I had felt like I belonged somewhere that I wasn’t being accepted into. I felt a need to prove myself. And now that things were finally falling into place and I was accepted, I couldn’t shake the thought that “maybe they were right all along, I don’t belong here.” I felt myself spiraling into an anxiety induced despair as I stressed over not having published enough. This was fueled by comments from mentors like “you know your reputation exceeds your publication record” and “you have so many publications on this topic, oh wait, you only have 2?” And the chasm between my metrics of success and people’s opinion of me seemed to grow at an ever-quickening pace.

But I was still not willing to accept that I had imposter syndrome. Things came to a head over a 72 hour period at a recent conference. Expectations were high, reinforced by nearly every conversation I had. “Please expect less of me” I found myself timidly asking people. This was not me. I am not timid. My self-confidence was shattered and I couldn’t put my finger on why. I ignored it. I tried to psych myself up. But my usual mantra of “I’ll show them” was no longer valid. Instead I was grappling with an internal monologue along the lines of “I have to show them again. And again. And again. And if I don’t, they’ll know they were right before, that I don’t belong here.” I was one talk away from people realizing I was a one-trick pony, one conversation away from people losing their confidence in my abilities, one failure away from the confirmation of “you don’t actually belong here.” I felt like I was caught in a storm of expectation and praise that was wholly unwarranted and that I couldn’t possibly live up to.  I wasn’t worried that I wouldn’t give a good talk. I know I give good talks, it’s one of my strengths. But I was paralyzed with fear that silently people would be thinking “oh this is crappy science” and “her previous work was so much better, what’s this nonsense?”. And maybe this is where the root of my imposter syndrome comes from. I perform well, but that doesn’t mean my ideas are good – maybe people are just blinded by the well-thought out presentation and pretty slides and not impressed by the science itself.

The night before my talk I sent a couple of text messages to trusted friends admitting that my confidence was gone and that I was struggling with expectations. The next morning I woke up to a flurry of messages reassuring me. Before my talk I spoke with a friend about what I was feeling in person and she reassured me that she often felt that way too, and that I had no reason to doubt myself. My confidence temporarily bolstered, I stood up and delivered a great talk that was well received. And I realized then that I could never let myself get that worked up about expectations again. More importantly, I realized I needed to talk to people about this. And so, the rest of the conference I talked to some of my conference buddies about this “imposter” feeling I’d been having. I was shocked at how many people responded by telling me that they were dealing with it too. People who I admire, consider successful and confident, and who I wouldn’t have guessed experience this. Sharing our experiences was cathartic for me. 



I’m sharing this story because I’ve been told it’s a unique perspective on imposter syndrome. Maybe it is, maybe it isn’t. My story isn’t meant to teach you about imposter syndrome, or to describe what everyone feels. It’s my story, that is all. I agreed to post this because I didn’t think my experience fit with what I understood imposter syndrome to be. But when I was able to give a name to it and talk about it with others, then I could start moving past it. Who knows, maybe someone out there is reading this thinking “Hey, that’s my experience too!” And maybe this will help them begin to deal with it. I hope that someday I’ll move past this entirely, and that self-doubt will be fleeting and merely a check of my humility. Until then, I’ve found a few strategies that keep me grounded when I begin to doubt myself:

1.     I re-assess my self-worth. I now keep a list of the compliments I get and screenshots if they are in digital form. I look at them to remind myself that I do belong and that the people I trust believe in me.

2.     I remind myself that I’m on track and re-assess my metrics of success. When I stress about my pace of productivity, I look up the CV of a young career scientist. Nine times out of ten, I’m right on track when I look at the pace and number of publications. Keeping my expectations and comparisons realistic is important. I’m right where I should be at this career stage, and I’m on pace to be where I should be at the next. More importantly though, I remind myself that everyone progresses at a different pace and there is no universal standard of success.

3.     I reinforce my accomplishments. I made a list of all of my awards, grants, invited talks, etc. When I need a little extra boost I look at the list to remind myself that so many people couldn’t possibly be wrong about my potential and my abilities.

4.     I talk about it. Not to everyone, but I have talked about this with a few trusted people and have been surprised to learn that they had similar feelings. This issue is far more common than we think it is. It is comforting to know that people I look at as confident and successful are dealing with this too. I can’t help but think if people were more open about this topic, then maybe I would have talked it through with my mentors instead of having a near meltdown over it. 

One final note, I have chosen to post this anonymously for several reasons. Feeling like this is a mental health issue that I do not want to be associated with is not one of them. On the contrary, I will gladly talk / commiserate with you in person. However, I did not want to open myself to judgement, assumptions, or personal attacks from people I do not know. I also did not want to invite personal compliments – this was not a humble brag and I don’t want you to tell me I’m awesome because you think I need to hear it. Actually, I think that would be counterproductive. To my friends, you probably know I wrote this, so thanks for being awesome. To those who don’t know who wrote this, I’m probably your student, post-doc, colleague, collaborator, or conference buddy – think about that.