Monday, April 19, 2021

Is biological adaptation and publishing papers the same thing?

 

Guest post from Pim Edelaar:

Publish or perish ... You have probably heard this “advice” before. And while there are many alternative ways to be a valuable and contributing academic, if you do research then publishing your science is indeed an important responsibility. And at the same time a daunting task. There are many books and postings about how to write a good paper (e.g. Andrew´s entry “How to write/present science: BABY-WEREWOLF-SILVER BULLET”: https://ecoevoevoeco.blogspot.com/2014/10/how-to-writepresent-science-baby.html), but here I wanted to explore whether there are underutilised strategies to get your paper published where you want to get it published. I will intersperse this with some parallel observations on organisms that face a similar ordeal but then in the eco-evolutionary arena, and to what extent we, as researchers, may have some blind spots with respect to how organisms solve this.



Two years ago Dan Bolnick and I published a paper in Trends in Ecology and Evolution (Edelaar & Bolnick 2019: https://pimedelaar.org/publications/) where we presented a classification of the processes that can increase the match between an organism and its environment. Because the better that match, the greater its ecological performance and the higher its expected fitness. And in order to explain how to apply this classification to real life, in talks I sometimes use human examples, and ask the audience for strategies that can result in the desired match. Like the publishing of a paper in a good journal. This typically results in a long list of possibilities, and it turns out that these can always be nicely categorised and understood using our classification. Interestingly enough, the audience often does not mention some additional strategies that are also viable. So we proposed that the classification of our paper can help us to focus our attention on such under-recognised strategies, not only in publishing but in biology in general.

Our classification is composed of four processes (the paper goes into the derivation and justification of these, but I will not repeat that here). The first one is “good old” natural selection. In terms of publishing, that would perhaps be equivalent to sending a randomly generated paper to a random journal, and hope for the best. If you use this strategy, then keep reading because I think you can do better. (Although some predatory publish-for-pay journals or conferences might accept virtually anything, even near-random papers: https://pdos.csail.mit.edu/archive/scigen/). For the other three processes the organism (so you as writer!) takes an active role, and either changes its phenotype (your paper) or the environment (the journal). This second option may seem a bit odd at first sight, but if what is important is the match between a phenotype and its environment to perform well (the match between a paper and the journal to be published), then it really does not matter which of the two interacting components is changed in order to improve this match. So changing the environment is a perfectly valid, and sometimes under-recognised, strategy to achieve one’s goals. 

Still, let’s first look at the thing we tend to spend most time on, the development of our manuscript. This is what we have been taught to do as researchers, and what we could perhaps compare to the development of an organism, resulting in a phenotype. What strategies do we have to make the best paper? (Important note here: I am talking about the best paper in the eyes of the journal, since we are only focussing here on getting it published. Whether it in fact is a good paper depends on what readers think. And these views don´t always align, so we may need to take this into consideration and reach some compromise. Unfortunately this is even more relevant for research proposals: you need to convince the funders, virtually the only people who will ever read your proposal.) 

So, how do we nicely “develop” a good paper? We can look for an interesting or unresolved topic, design clever or ambitious experiments, use cutting-edge methods or materials, collect or analyse valuable data, make appealing figures, write a useful or provocative discussion, write clearly and engaging (see Andrew’s really useful entry again, if you didn´t do this before: https://ecoevoevoeco.blogspot.com/2014/10/how-to-writepresent-science-baby.html). To do this better, read and think, practice and edit, get feedback from other people, collaborate with other people, etcetera. 



 My technician Fatima working with our optogenetic fruit flies – cutting-edge materials, but not that you can see that ...

Those are the usual strategies. But if our only goal is to get a paper published, then alternative strategies do come to mind, some questionable and some outright rejectable. For example, adding names of famous people to your list of co-authors, hoping for better reviews or editorial preferences. Double blind reviewing (http://robertfeldt.net/advice/double_blind_reviewing/) hopefully puts the scope for this dubious practice to rest. Or selective citation, where you misrepresent what has been written before, or you ignore citations that counter your message (one of the hardest things to spot as a reviewer). Or only presenting the statistical analyses that resulted in significant results, while ignoring equally valid approaches or models or outlying data (https://en.wikipedia.org/wiki/Researcher_degrees_of_freedom). Or even fabricating data. Of course I am not trying to give you ideas of how to get your paper published using strategies that are not accepted by the scientific community, I simply want to show that conceptually they align with the strategies for producing a good paper – it is all about producing the product that matches best with what the journal is looking for. If we think about the development of a biological organism, then indeed there is no ethics and fairness involved and the most unpleasant appearances, weapons, toxins and behaviours might appear, as long as they get the job done. 



 

Assuming you stick with accepted practices (highly recommended, for the sake of good science and yourself), then one common and useful advice here is that it helps to write the paper with a specific journal or at least a specific audience in mind, since this will increase the probability that your paper will be a good match with your target journal or a similar one. So you do all of that ... and then comes that dreaded rejection. Now what? After we have dealt with this mentally (see Andrew’s entry on this: https://ecoevoevoeco.blogspot.com/2016/02/dealing-with-rejection.html), we look for another journal, and resubmit our manuscript. But before we do that, it of course would be wise to adapt our manuscript in order to improve the match. Whereas the previous section was more about the innate development of the first submission of the paper, this response of producing a changed submission is comparable to adaptive phenotypic plasticity, where the environment (the journals) rule, and the organism (the manuscript) responds. 

What strategies do we have to adapt our paper best to the next journal? Apart from adhering to journal requirements (oh, the joy of reformatting citations ...), it is often a good thing to take reviewer comments seriously, and improve your paper where you can. Never resubmit the same manuscript unchanged to another journal! The chances are that (1) you really could have made a better product (previously rejected papers are more cited: https://www.sciencemag.org/news/2012/10/scientists-may-feel-rejected-rejection-rare-publication-study-finds), and (2) one of the reviewers for your new submission is the same as for your old submission, setting yourself up for a nice rejection again. 

Now maybe somebody noticed, above I already mentioned a strategy that is actually not about the phenotype, but about the environment: “write the paper with a specific journal in mind” and “we look for another journal”. And of course you would be wise to carefully select your journal to improve your chances of acceptance! Again, if the challenge is to obtain the best match between your paper and the journal, you should not ignore this other side of the interaction! So check which journals might be interested in publishing your paper. Going through your references might give you some ideas, and if you have read many papers or browsed many journal issue indices, you might have a feel for what different journals tend to publish (both in terms of topics and in terms of quality). Advisors and colleagues can also help with identifying a good target journal. Journal editors and potential reviewers may hate me for this comment, but if you have time to spare, you may aim a bit high in terms of journal quality in the beginning, if you think your paper has a realistic chance of getting accepted there. But be warned that “going down the ladder” can take a lot of time, energy and perseverance (or what some call stubbornness, a waste of people’s time, or stupidity). I think my personal record is with Edelaar et al. 2019 (https://pimedelaar.org/publications/), which was submitted 9 times (Nature, Ecology Letters, Science, Nature Ecology & Evolution, Nature Communications, eLife, Nature Ecology & Evolution again, Evolution, and finally Proceedings of the Royal Society B), because I was (am) convinced it is a damn good paper that deserved (and got) a good place. But that took over 3 years, and a lot of reviewer effort (so let’s hope it gets read and cited). If you follow this strategy a lot (and I think most people do to some extent?), it would be nice if you also reviewed your fair share of the manuscripts seeking their spot in the light (read: you really should ... See “The Golden Rule of Reviewing”: https://www.journals.uchicago.edu/doi/full/10.1086/598847). (You can show your contributions to science as a reviewer on Publons, e.g. see my page: https://publons.com/researcher/1175333/pim-edelaar/metrics/)

Not ignoring the environment as a target is also true for organisms: the phenotype-environment match can be improved by tweaking both components, simultaneously or independently. Indeed, there is overwhelming evidence that organisms select aspects of their environment in order to increase their expected fitness: they select habitats, prey types, sexual partners, social partners, and so on. While selecting what to eat and with whom to mate might not appear to be comparable (and should not be confused – https://www.youtube.com/watch?v=ycuzVQmVj44), it all has to do with what we called in our TREE paper’s classification “selection of the environment”, in the sense of selecting the environment with which the phenotype then has to interact. And the outcome of this choice might depend on how the phenotype is, or in our case, how our paper is. So choose wisely ...



Choose wisely ...

There is one last process that organisms might employ to improve the environment they have to interact with, and we called that “adjustment of the environment”, since it does not involve the choice out of a set of available alternatives (as for selection of the environment), but the changing of the characteristics of the single option they work with. Together with selection of the environment, it is often not recognised as a distinct process of adaptation, and commonly treated as “just a behaviour”. Narrow-sense niche construction falls into this domain (making physical constructions like nests and burrows for example), but also somehow changing the characteristics of the organisms an individual might interact with: changing the perception and behaviour of a competitor or a (potential) sexual or social partner, changing the behaviour of an infected host, those kinds of things. Humans are masters in this strategy, and if you look around and compare what you see with what the undisturbed landscape and biological community would look like if there were no humans, then I hope it is clear what I mean. We adjust our environments to how we are and what we need to perform well (or at least, we think so).

Paradoxically enough, I think this is one of the more under-recognised “strategies” in publishing, where the aim is to change the journal such that its fits our paper. It is hardly ever suggested when I ask people for publication strategies in talks, so not only in biology but even with respect to our own lives it appears to be a bit of a blind spot. But the communication with the editor and reviewers falls under this umbrella: writing an appealing and convincing cover letter, responding well to editorial and reviewer comments (that does not mean doing everything they ask for, but at least politely explain why some changes have not been implemented), and perhaps even talking to an editor at a conference or via a pre-submission inquiry. One of the comments editors keep making in public, is that they want to work with authors to get the best paper possible, but I think this interaction also involves (perhaps unconsciously) movement (understanding) from the editor’s part on what the paper is about. Alternatively, the writer takes up the role of the journal: editing a special issue usually means that you can publish one or more of your own papers in that issue. I don´t think this is the main motivation for people editing special issues, but I do think people see that as a nice side effect for their hard work as editors, and it may swing the balance towards undertaking this endeavour. More questionable practices also fall under adjustment of the environment: proposing favourable colleagues as reviewers (how many people regularly suggest their worst critics?), excessive citing of papers written by the handling editor and reviewers, or even blunter types of bribing (for which I don´t know examples, but I am pretty sure it has been done or attempted) or threatening and bullying of editors or reviewers. (Please don´t do these things.) And again, for biological organisms nothing is out of bounds, so the most intricate ways to manipulate their abiotic and biotic environments have evolved. Like a parasite that manipulates an infected ant to swell up and change colour and to perch motionless at the top of a plant, such that it might get eaten by a bird that mistakes it for a juicy ripe berry – all of that so the parasite gets into the bird, its vector for dispersal (https://www.nationalgeographic.com/animals/article/parasite-transforms-ants-into-berries).



A normal and an infected ant

Where does this exercise of revising our goal of publishing our paper in a desired journal using the classification framework leave us? Perhaps you picked up an extra suggestion on how you can increase the chances of getting your paper published – in an honest way. Perhaps you know of a strategy that I missed, and it would be great if you could write these in the comments. My prediction is that it can always be classified as one of these three processes: somehow changing the paper to match with the journal, some sort of selective process regarding the journal to match with the paper, or some sort of adjustment of the journal to match with the paper. (What do you think, is this still true in a new world with Open Access, public repositories, Peer Community In (PCI) journals, self-publishing, etc.?). The same is true if we consider the phenotype-environment match in biology: I think that anything adaptive that individuals do can be classified by these three processes (changing the phenotype, selecting the environment, adjusting the environment). Likewise, I think that this classification can help us to recognise specific behaviours and strategies for what they are, and how they compare with other seemingly unrelated strategies (e.g. choosing what to have for breakfast, and with whom to have it, involve similarities in choice and constraint). And perhaps most of all (or at least I hope so), it can help us recognise that adaptation is not only about the organism adapting to its unmoveable and ever-demanding environment: organisms have tons of ways to adapt their environment to themselves. Even though we know this, it is not always something we take into account when designing research projects or interpreting results, so doing that more often in your papers should be interesting and valuable. And that happen to be two traits that help getting your papers published ...

 

Thursday, March 18, 2021

Admission essays rebooted


There is a lot of excellent discussion these days about how we diversify our organismal biology community (ecology, evolution, behavior, etc). One of the keys needs is to admit more students from more diverse backgrounds into our training programs, whether at the undergraduate or graduate level. But often applicants from diverse backgrounds have a disadvantage in the application process, because they may not be as well connected to people in our field who can advise them on *how* to apply. There is an art to applying for a graduate program, which involves knowing the many things that admission committees and professors are on the lookout for, and red flags we are tuned to avoid. Having a good network of well-informed and dedicated mentors is crucial to help students know what topics to cover and how to approach things like direct contact with potential mentors. If applicants from underrepresented groups are less likely to receive this mentorship, their applications aren't as strong. So an important step in diversifying our scientific community is to rethink the application process. 

Many graduate schools are engaged in application-reboots. I briefly describe one such reboot, which I have been involved with at two different universities - first the University of Texas at Austin, and then the University of Connecticut. I do this both to get feedback, and to perhaps inspire other departments to consider following suit, if you feel it is a good idea. 

Specifically, I want to focus on the admissions essay. Anyone who has reviewed graduate school applications in EEB is familiar with the formulaic application essay opening, in which an applicant waxes eloquent about how they love nature, or turtles, or biodiversity. The "I grew up searching the local stream for critters" style opening story may often be heartfelt for the author, but to the admissions committee it often feels trite - they've seen variants on that theme before many many times.  But what follows that opening statement is... variable, to say the least. Each applicant has their own guess as to what we want to hear about. Sometimes this is spot on and they weave an engaging story about their motivations, past research experiences, future research goals, career aspirations,  strengths (what they will add to the lab & program) and weaknesses (what topics they need to learn more of). But all too often we get a subset of these topics, and different subsets from different applicants. The result is an apples-to-oranges comparison problem for the admissions committee. Students who don't deliver on the full set of topics we'd like to know about (e.g., those from underserved backgrounds often) are put at a disadvantage. 

A solution I'm fairly passionate about is to replace the application essay (which is very open-ended) with a series of more precisely targeted short answer questions. These specify the topics that we want to know about, directly conveying to the applicant what they should tell us about. For specifics, see the templates at UConn EEB and UT Austin EEB. For example, at UConn we ask questions like:

  • Describe your reasons for going to graduate school and your long-term career goals. (approximately 100 words)
  • Describe your research interests, the scientific questions that you hope to address as a graduate student, and your motivations for choosing this topic. If you have ideas about specific hypotheses you would like to test, study systems you think might be suitable, or approaches you would take, please provide that information as well. The Admissions Committee recognizes both that not everyone will know these details when they apply, and that research directions often change once a student enters graduate school. (approximately 400 words)
  • Describe any prior research experience, including the research teams you worked with, the topics studied, your role in the research, the skills you gained, any math or computing skills learned, and any papers or other products that you were directly involved in creating. It is not necessary to repeat everything that is in your CV (see below); use this section to highlight the points that you think are most relevant to your planned graduate research. (approximately 400 words)
  • Describe any other relevant work or teaching experience that you believe has helped prepare you for graduate work. This could include non-academic work experiences, for example those that demonstrate commitment, a strong work ethic, ability to work in a team, ability to work independently, etc. Also use this section to describe non-research skills that might be relevant to your planned graduate work. (approximately 150 words)
  • Describe one obstacle you have faced in research, work, or life and how you either overcame it, or used the experience to inform your future outlook or actions. (approximately 150 words)
  • Describe any activities you have engaged in that demonstrate a commitment to enhancing diversity and inclusion in science. (approximately 150 words)
  • Please tell us anything else you would like the Admissions Committee to know. (approximately 200 words)

If a student has nothing to say on a topic (e.g., they never taught before in any context), we try to make it clear that its fine to leave some areas blank. For instance at UConn we specifically state: "Provide what information you can for each and note that the Admissions Committee recognizes that not everyone will have detailed answers to every question." 

The goal here is to lay out specific expectations, so the students aren't left to guess what we are looking for, and don't forget to leave out key elements we might wonder about. The result is a set of essays that are much more parallel between applicants, which helps to compare them more effectively and to better recognize the multi-dimensional nature of people's strengths. We might have some applicants with stellar research experiences, others with exceptional teaching, and still others who don't stand out as much in either area but had exceptional obstacles to overcome to achieve the things they have managed. Personally, at both UT Austin and UConn, after implementing these changes, I felt much better able to compare applicants. I get the sense my colleagues feel the same (at least, neither department has yet abandoned these formats).

So what are the drawbacks? For one, I worry that having an atypical application process might deter applicants. If many other departments we 'compete' with for applicants have a standard one or two page essay format, where the contents are up to the applicants, then a student might write an application once, and submit it to multiple institutions. Then they come to us and realize there's a whole other format, and decide maybe to not bother. So far I don't think we've seen a drop in application rates associated with this new format. And students who are genuine in their interest in coming here won't be deterred (I think). But, it worries me a bit. Luckily, there's a solution: the more institutions that shift to a comparable format, the less of a burden it becomes on the applicants. I'd love to see a variant of this become more common. Because I really do think it aids under-served applicants in knowing what we are looking for, and it aids the faculty in comparing candidates in a multivariate sense.

Another worry is that by making everyone shoehorn their lives into a few pre-specified questions, we actually obscure some of the diversity of perspective, approach, experience, and make it hard to really see a creative mind at play. I don't really buy that, because I've seen great and creative answers to these pre-fixed questions, and we make a point of leaving something open-ended (e.g., the last question from the UConn list above). 


This experiment in reframing application questions is recent, and I'll be interested to see how this plays out. I'd also welcome comments, ideas, and others' attempts to crack similar challenges in other ways.

Oh, and if you are wondering about whether we require GRE scores, UConn dropped those this year. That's a whole other topic, for another time.


_____

Added later:
Theresa Rueger commented and for some reason I couldn't reply directly so I'll write my reply here:

Great question. I honestly don't know. I can't speak for how members of underrepresented groups might or might not feel about this question, and would *greatly* appreciate feedback on that one in particular. Note, though, that even a privileged white cis-male 3rd generation college student such as myself can engage with diversity and equity issues in proactive constructive ways. Its not necessarily who you are, but should expand to include what you do. As a department, EEB at UConn is really devoted to DEI issues, and my colleagues felt strongly about including such questions in grad admission, as we also do in faculty applications (requiring a DEI statement that plays a strong role in distinguishing among otherwise equally excellent research applicants).


Tuesday, February 16, 2021

In praise of double-dipping from data.

 

There’s a widely held view in biology that one dataset should equal one paper. Using the same data in two papers is often viewed with suspicion. To readers, it may appear that the authors are trying to get twice the academic credit for a given amount of work. This even has a name, ‘double-dipping’.  (Note, this is distinct from publishers’ ‘double-dipping’ to get both author open access fees, and also institutional subscriptions).

 

I recently double-dipped. Triple-dipped, Quadruple-dipped, and more really. I was both very hesitant to do so, and yet happy with the result. I’m writing this post to explain what I did, why I did it, and why I think double-dipping can be an excellent choice for authors, readers, and funding agencies. So much so, that I think funding agencies should consider fellowships to support salaries of students, postdocs, and perhaps even faculty to revisit published data to squeeze more insights.

 

What I did.

In 2009, I obtained funding from the Howard Hughes Medical Institute to pursue a study of how stickleback immune genes evolved across complex landscapes of populations connected by varying degrees of gene flow (for hosts and parasites). The focus initially was meant to be on MHC.  Our very first order of business was to set the stage for the evolutionary genetics work by learning the basic natural history of the host-parasite system I intended to study. What parasites are present in the area I worked in on Vancouver Island? To what extent do they differ from one stickleback population to the next? To what extent is this parasite community variation attributable to abiotic variables, biotic communities, fish population traits, or fish genotypes? By answering such basic natural history questions, we get a foundation to choose the most interesting populations for evolutionary genetic contrasts. 

 




To collect such data, we conducted a field survey in May 2009. “We” included my graduate student Will Stutz (who helped conceive of the project to begin with), a grad student collaborator Travis Ingram, a new PhD student Yuexin Jiang, two undergraduates (Chris Thompson and Todasporn Rodbumrung), UBC graduate student Travis Ingram, and a high-school biology teacher Kim Hendrix (most of us pictured, above)
. Over the course of 4 weeks on Vancouver Island we sampled ~100 stickleback from each of 45 populations, a mix of lake and stream and estuary sites. Then from fall 2009 through 2013 I employed Julie Day then Kim Ballare as research technicians to count parasites, characterize stomach contents, measure ecomorphology for ~3500 fish specimens. From 2013-2014, Hollis Woodard worked as a technician in my lab to genotype a couple thousand stickleback for MHC, and Yoel Stuart helped her do ddRADseq on a subset of individuals to get neutral genetic markers. The result was an enormous natural history dataset on diet, morphology, infection, MHC, >100,000 SNPs, all set within a geographic context of varying lake sizes, elevations, etc scattered across watersheds on north-eastern Vancouver Island.




 

The resulting data set was enormous, and intimidating. I had all the data in had by sometime in 2014, and it took me nearly a year of on-and-off-again work just to organize and curate the data to check for errors, odd outliers, misspelled population IDs, and all those little things that can creep into a dataset that has been handled by many separate people. For several years in a row, the data would lie fallow for months on end, then I would find a bit of time to work on analyses, only to set it aside and start over half a year later. The problem was this was nobody’s primary dataset. It was meant to be exploratory (with some a priori predictions to be sure), and there was much to explore, and I was the sole person delving into these explorations for a long time. Each summer I’d spend a couple weeks on Cape Cod with my family and I’d sneak in some time at a great French Patisserie spending a few hours analyzing these data while my kids were in summer camp (photo below). Over time I built up a set of analyses that answered my a priori questions and went a step further to describing the spatial structure of the parasite metacommunity in great detail.

 

Thousands of lines of R code later, it was time to write. But I pretty quickly found that the writing built up to over 100 pages of text. I was writing a book, and not even I want to read a book-length document on the natural history of stickleback parasites on Vancouver Island. The trick was, there are so many distinct questions that can come from a dataset of this size. Do we analyze parasite species richness? Or multivariate composition? Do we analyze each species of parasite separately, or via ordination in one group? Do we include genetics, or host diet, or lake abiotic conditions? These all are interesting, all tell us something different, but to do them all simply took way too much text, it would strain the interest of any but the most dedicate readers.

 

At some point, in stepped Emlyn Resetarits (a PhD student with Mathew Leibold and myself), who helped convince me to split this up into bite sized parts. The result:


1)    A paper focused on parasite metacommunity composition – which species are found where, and which species are found together or apart, and what predicts this variation? We throw in a big GWAS study of many parasites in the appendix, which might have been a paper unto itself. Bolnick et al 2020 Ecology




2)    A paper focused on parasite metacommunity diversity – not so much who is found where, but how diverse they are, which revealed a richly different story than species composition alone. Bolnick et al 2020 Ecography


3)    A third paper set aside the parasite information to focus on the evolutionary ecology of stickleback diet and individual specialization. This was revisiting a topic that was core to my academic beginnings, which I hadn’t touched in a few years. But the dataset on stickleback diets (collected to understand infection patterns) was also exactly something I’d hoped to achieve for years. This turned out to give a beautifully clean and intuitive result that generalist populations (eating roughly equal mixes of benthic and limnetic prey, in mid-sized lakes) had the greatest dietary and phenotypic diversity. But, these functional variances were unrelated to genomic heterozygosity, which increased steadily with lake size. In short, neutral genomic diversity and functional ecological diversity were unrelated, and responded to entirely different features of the populations’ environments (Bolnick and Ballare, 2020, Ecology Letters).


4)    That Ecology Letters paper happened to include, in passing, a GWAS analysis of SNPs related to lake size. Are there loci whose allele frequency varies predictably between smaller versus larger lakes, and whose heterozygosity was largest in mid-sized lakes? Well, at an American Naturalist conference right around when this paper came out, Diana Rennison and I compared notes. I had this GWAS between benthic versus limnetic allopatric lake populations, and she had population genomic data for benthic versus limnetic species pairs in symatry. Why not compare these? Harer et al 2020 Molecular Ecology was the result. Remarkably, the benthic-limnetic species pairs show both more repeatable evolution, and greater divergence, than allopatric populations.


5)    Most recently, we finally got to the original motive for this data collection: Major Histocompatibility Complex genetic diversity. MHC (here MHC IIb) is among the most diverse genes in the vertebrate genome, frequently said to be under balancing or frequency-dependent selection to maintain this diversity. The whole point of this survey was to determine the diversity of MHC, and its association with parasite load and diversity. Well, with help from Stijn de Haan we finally ran the bioinformatics pipeline to identify alleles and genotype individuals (using a bioinformatics protocol developed by Will Stutz, the PhD student who first planned this study with me). Then Foen Peng adopted the dataset to run statistical analyses and write. The resulting paper just posted to Molecular Ecology a few days ago: Peng et al 2021 Molecular Ecology.  Disappointingly, (e.g., contrary to our starting motives) very little about the parasite community tells us anything about MHC. Instead, MHC diversity seems to be best predicted by neutral genomic diversity, not parasite diversity. And MHC divergence between populations is best predicted by genomic Fst, and not parasite or ecological differences. This only deepens the puzzle of MHC diversity for us, because it certainly is insanely diverse, yet we twice now have failed to find a clear adaptive explanation for this variation (see also Stutz et al 2017 Molecular Ecology, which used a different set of populations and different analytical approach).


6) Ultimately, I am glad to say we mostly moved away from the MHC focus, which seems to not matter for the parasite that engages us most, the cestode Schistocephalus solidus (pictured below), and instead started doing QTL mapping, expression, and GWAS analyses. The data set collected in 2009 for some basic natural history proved to be extremely useful in motivating and guiding our genetic mapping studies (manuscripts in prep, and also Weber et al 2017 PNAS).



 

Why I did it: the benefits of N-dipping

Now, apologies for what must seem like a lengthy advertisement for a facet of my lab’s recent work (okay, it sort of is an advert). But I have a broader goal with this post. Here we had one survey, one dataset, that has yielded five papers (and more in queue). That’s some serious data recycling. So is it ethical? Absolutely yes, indeed I’d say it is morally preferable. 

 

Here’s why. First, each of the papers cited above asks an entirely different question of the data. The biggest overlap is between Peng et al 2021, and Stutz et al 2017, but those used two different datasets, and different analytical approaches, to ask the same question. Stutz et al used parapatric populations to take advantage of gene flow, Peng et al used allopatric populations but far more of them, with the added bonus of ddRADseq genomic data.  And the MHC data analyses don’t really make sense until you have grappled with covariation between parasite species, and described their diversity, so we had to tackle that Ecology and Ecography paper first. So, the papers support each other, but they certainly aren’t redundant conceptually.

 

Second, we could have put all this into one paper but it would have been a 150 page behemoth. You don’t want to read that, and I don’t want to write it. In fact, I did write it. At least, the Ecography and Ecology and Ecology Letters papers were all mashed into one >100 page manuscript at one point, and the MHC data would have added another >50. And it was so hard to keep clear threads of which analyses when with which results. Breaking it up made it easier to read and understand.

 

Third, funding agencies put significant funding into this dataset, which required salary for four technicians and two postdocs to pull together. Aren’t we morally obligated to wring every bit of insight out of that hard-won data?

 

A call to funds

This last question leads me to a suggestion. Many of us accumulate datasets as our careers progress. Often these data sets have a rich multi-layered nature, but we publish the most exciting bit of information then move on. This is partly because we prioritize publishing the highest-impact work we can, and for career advancement are better off setting aside less exciting findings, to spend time on the splashiest stuff. But there is also a financial angle. Data analyses, and re-analyses, and writing, take time. Which takes money. Most Associate Professors and Professors have sedimentary layers of unpublished or incompletely published analyses. These took funds to generate. It is a shame to have their results only partly published, with important elements gathering dust. The reason is, when I apply for my next grant the review panel will want to see evidence of a new plan of action. What data will I collect next, what experiment will I conduct, what survey or model will I design? Revisiting older data to wring out more precious drops of insight? Not fundable. Well, it should be. Those data contain more insights. They are hard-won, costly to obtain, and carry more than one paper’s worth of knowledge and lessons. So I think it would be great if NSF or other funding agencies would support fellowships, whether for grad students, postdocs, or faculty, to revisit and repurpose existing data to achieve new ends. The data are there, we just need the time to delve deeper.


So to conclude, I think we need to encourage people to use their hard-won data more efficiently and thoroughly. That requires funds, and the social support for the practice. It also has the interesting side-effect that we end up with interconnected papers strewn across many different journals, that build a much larger holistic story when viewed together. I'm intrigued by the notion of bundling published papers to create a story arc that transcends a single paper in one journal. Consider the above description of a set of papers to be such a bundled set.

Saturday, January 30, 2021

Susan Foster - Memories

Susan Foster of Clark University passed away recently. Here we collate and compile memories of some Susan's contributions to science, education, and collegiality. She will be sorely missed. This is a living document - please add your own thoughts in the comments.


1. In Remembrance of Susan Adlai Foster (1953 – 2021), ABS Fellow and Past President. Written by Matthew A. Wund, with input from John Baker, Christine Boake, Zuleyma Martinez, and Dale Stevens. This obituary is modified from text that will be published in the March newsletter of the Animal Behavior Society.

Dr. Susan Foster passed away at her home in Petersham, MA from complications associated with cancer on January 16, 2021. She was in the company of her loving husband, John Baker, and their two children, Patrick and Dylan. Susan devoted her career to the study of behavioral plasticity and evolution, and is best known for her extensive work using threespine stickleback fish as a model to understand these processes.

Susan earned her B.S. in Botany and Zoology from the University of Wisconsin, Madison, and in 1984, earned her Ph.D. in Zoology from the University of Washington under the mentorship of Robert T. Paine. Her graduate work investigated group foraging behavior in coral reef fish of Panama. She is most well-known for her extensive research on the plasticity and evolution of behavior in threespine stickleback fish. She began her stickleback research as a postdoctoral fellow working with Michael A. Bell at Stony Brook University. From 1990-1995, she continued this work as an Assistant Professor of Biology at the University of Arkansas. In 1995, she moved with her husband and collaborator, Dr. John Baker, to Clark University in Worcester, MA, where she spent the remainder of her career until her retirement in 2020. She continued mentoring her students and conducting research until her final days. Susan served Clark University with as much dedication and enthusiasm as she served the ABS, including in her position as the Warren Litsky Endowed Chair in Biology, and in her leadership on a variety of institution-wide committees and councils. She was also instrumental in establishing Clark University’s very successful Environmental Science Program, in which she served in several capacities.

Susan served the scientific community in many capacities throughout her career. She was exceptionally fond of the Animal Behavior Society, which spanned her nearly four decades of membership. The highlights of her service to the ABS include multiple terms as Secretary (1993-1999), Second President Elect (08-09), First President Elect (09-10), President (10-11), and Past-President (11-12). Susan was elected an ABS Fellow in 2004. More recently, she served as Executive Editor of Animal Behaviour, and served for more than a decade as the North American Editor of Ethology. Susan also served on numerous NSF review panels, and participated in several working groups sponsored by the National Evolutionary Synthesis Center (NEScent).

Susan’s body of work is exceptional for its breadth and depth. In more than sixty peer reviewed articles and book chapters, as well as four edited volumes, her research beautifully married natural history, extensive field observations, exquisite laboratory experiments, and evolutionary theory. She did not view herself as either a field biologist, or as an animal behaviorist, or as an evolutionary biologist, but rather as all of these things simultaneously. She had a wonderful ability to comprehend the interplay among multiple scales of biological organization: appreciating how the nuances of individual behavior related to complex evolutionary processes. She was fascinated by threespine stickleback fish as an individual species, while simultaneously leveraging their value as a model system for studying general processes of behavioral evolution and adaptive diversification.

In addition to her brilliant mind, Susan was a loving wife and mother, an exceptional cook, an avid gardener, and had a wonderful, dry sense of humor. She also had a lifelong interest in the conservation of natural landscapes, and while at Clark University taught a course on the topic nearly every year. She was an unwavering advocate for the many students and postdocs she mentored throughout her career, many of whom came to know her as not only a mentor and friend, but as a member of their family. Susan was perhaps most in her element in her 250-year-old farmhouse in Petersham, MA, where, with her husband John, she would effortlessly move between writing research papers and grants, reviewing manuscripts for Animal Behaviour and Ethology, gardening, cooking, and entertaining guests. While home was her happiest place, Susan also enjoyed traveling, spending many field seasons studying stickleback fish behavior in Alaska and British Columbia, and traveling to conferences around the world. Her life was enriched by the many friendships she formed in her travels and through her research; indeed, news of her passing has resulted in an outpouring of love and respect from friends across the globe.

To commemorate Susan’s life and legacy, and the impact she had on her friends and colleagues, her dear friend and fellow ABS Fellow Dr. Christine Boake shared these sentiments:

“Susan and I first met due to our mutual interests in behavioral divergence between animal populations, which we recognized could lead to speciation. Her generous hospitality made it easy for us to become close friends. Our visits always combined our shared interests in science, cooking, and gardening. She had boundless energy; even after surgery imposed physical limitations, she kept up a strenuous pace both in research and at home. Her energy and enthusiasm allowed her to have her noteworthy professional success as well as having a multifaceted and rewarding life with family and friends. She had a full life.”

Susan’s professional and personal legacy includes the dozens of postdocs, graduate students, and undergraduate student researchers she mentored, as well as the hundreds of undergraduates she taught in her Evolution and Animal Behavior courses. The students and postdocs whose lives she touched were helped to be better scientists, but more importantly were inspired to be better people. She will be dearly missed by the many students and colleagues who will remember her as not only an exceptional scientist, but more importantly as a true friend.

2. From Bill Cresko to his lab members

Susan Foster passed away yesterday due a rapidly progressing cancer that was only diagnosed early in 2020. She was able to be at home in Petersham MA with her husband and lifetime research partner John Baker, as well as her children Dylan and Patrick. Susan loved her colonial-era home and garden with the snow and the fireplace and the after seminar parties and the pickling of vegetables. Susan was my and Cristin’s Ph.D. advisor. She has been a professor of biology and the chair of the Biology Department at Clark University for much of the past decade, and retired in early 2020 at the first diagnosis. Susan advised numerous postdoctoral scholars, graduate students, and undergraduates over the years.

Susan was a pioneer. After her Ph.D. on Wrasse behavior at the University of Washington with Bob Paine, she did her postdoctoral work with Mike Bell at SUNY Stony Brook. In fact, I came to work with Susan after contacting Bob and telling him about my interests and he said ‘you should work with Susan instead on this amazing system’. At Stony Brook Susan helped develop the stickleback systems in British Columbia and Alaska, and through many publications helped biologists appreciate that behavior - like morphological and life history traits - could exhibit significant geographic variation that was influenced by both environmental and genetic variation. In addition to her many journal articles, Susan published two books with Mike Bell and John Endler that are now classics in the field.

Susan was a leader and role model in the fields of ethology and behavior. She help several leadership positions in the Animal Behavior Society, and she was part of an early wave of women in biology fighting for gender equity in the life sciences. Susan was a fierce advocate throughout her career for achieving the goal of having people judged by their abilities, not their chromosomal composition, skin color, or socioeconomic background. She matched these professional efforts at equity and inclusion in her private life in ways that were truly inspiring. The impacts that Susan has had on the field through her students from these diverse backgrounds (including me) is deep and broad.

In December of 2020 David Hibbett and others from Clark University and I began making plans for a virtual conference to honor the work of Susan and John. Unfortunately Susan’s cancer returned quickly at the beginning of the new year. We will continue our work to highlight Susan’s and John’s life work and educational legacy. All of you who are or have been in my lab working on stickleback have Susan to thank, and I hope that you will be able to attend.

Sincerely, Bill

3. From Jun Kitano - email to Andrew Hendry

This sad news reminds me of my old days in Kyoto, when I came to know a series of Susan Foster’s excellent works on behavioral variation in natural populations of the threespine stickleback. When I almost finished my PhD thesis on molecular neuroscience in mice, I was wondering what to do next as a postdoc. I read several papers and books and finally found that I want to study wild animals rather than laboratory mouse. One day, I came across a paper by Katie Peichel, David Kingsley and their colleagues (Peichel et al. 2001 Nature). In that paper, they investigated the genetic architecture underlying morphological variation in the threespine stickleback. I thought that I could apply the same genetic method to behavioral variation. 

Then, I started to read many papers on the behavioral variation in sticklebacks, including those by Dr. Susan Foster. She has conducted extensive field observations and characterized behavioral variation in natural populations of the threespine stickleback. A series of her papers were so exciting that I perhaps spent more time reading her papers than reading papers directly related to my thesis. Reading her papers, I was convinced that behavioral genetics in sticklebacks would be an exciting direction of research. As I decided to work on Japanese populations in collaboration with Dr. Seiichi Mori (my long-term collaborator), I had no chance to work with Susan. But, Susan is definitely one of the persons who guided me into the stickleback research.

I met Susan at a stickleback conference in Alaska, and she kindly encouraged me. She invited me to her research fields in Alaska, although it did not happen due to several reasons. It is sad that we can no longer meet her, but her works will continue to encourage not only me but also many present and future young researchers. This would be a good timing to appreciate that our recent cutting edge genomic studies are based on the extensive works done by old researchers who spent a lot of time observing nature like Susan.

R.I.P.

4. From Jeff McKinnon - email to Andrew Hendry

I ran into Susan at various times over the years. My fondest memory was visiting her and John at their beautiful old house in Mass, probably in the early 2000’s. I remember their generous hospitality and lively conversations about stickleback biology, as well as about hockey. Susan was a great fan of Steve Yzerman, if memory serves.

5. From Tom Reimchen - email to Andrew Hendry

Gone before her time. As well as her obvious contributions to behavioural evolution in stickleback,  another substantial contribution of Susan was her novel observations on coral reef fishes , particularly the importance of  cleaning stations for the repair of wounds in coral reef fish  (Foster 1985,  Copeia 875-880). I have used this in my Ichthyology courses for many years as an example of co-evolution at a community level and as one of the first examples of self-medication in fishes.

6. #SusanFosterMemories














































Friday, January 22, 2021

Conferences in the After-Times

What will conferences be like when COVID is in the rear-view mirror*?

Just over a year ago, the three co-editors of this blog, Kiyoko Gotanda, Andrew Hendry, and Dan Bolnick, were chatting around a bonfire at the American Society of Naturalists' conference in Asilomar CA. Afterward, we added on a brief outing to see elephant seals, and then reconvened at the Hendry Winery in Napa for a wine tour, wine tasting, and brainstorming a grant proposal. It was scientifically productive, and an utter blast culminating in Rowan Barrett and I pretending to be elephant seals engaging in a contest.



A year later, this kind of social / scientific gathering seems far off. Conferences have been cancelled, like the Evolution 2020 meeting, or delayed a year or more (like the Gordon Research Conference on Speciation that Katie Peichel and Dan Bolnick were organizing for Feb 2021, now put off till 2023). Other conferences have emerged to fill the void, giving graduate students and postdocs a platform to disseminate their work and connect with peers via Zoom or other platforms. The American Society of Naturalists (which normally meets every other year) held an off-schedule Virtual Asilomar via Zoom in early January 2021, specifically to give PhD students and postdocs a platform to speak (the talks are now posted here). Unlike the usual Asilomar meeting, which is capped at 200 people due to the size of the venue and a desire to maintain a smaller scale where more drawn-out conversations are easier, Virtual Asilomar was open to all viewers. It drew 710 registered participants from around the world: 569 from North America, 66 from Europe, 27 from Asia (mostly India), 40 from South America, 9 from Australia and New Zealand. Some sessions had presenters sitting on 4 different continents - and this under-counts participation because many talks are continuing to accrue views on the ASN Youtube Virtual Asilomar video playlist.  A quick perusal of these videos suggest that many have accumulated 50 - 200 views in the 2 weeks after the conference. This highlights the fact that the virtual meeting broadened participation in ways that we will be loathe to abandon when COVID (hopefully) recedes into a mythical past. All of these contrasts led us (all slightly skeptical of Virtual Conferences before trying them) to ask:

What aspects of virtual conferences worked well?

What aspects didn't?

And, most importantly, what features of COVID-era virtual conferences should be folded into meetings in the After-Times when we are free to travel again? (artists' rendering below)

Frenzy on Fury Road: Mad Max faces a post-digital apocalypse


The following is a summary of our own thoughts on this issue, drawing also on responses to a Twitter query of Dan's, where this conversation may continue to unfold. Be aware when reading the thoughts below that there's no one-size-fits-all answer. For some people the weekend meetings were better, for some people they were worse, for example.


1. What aspects of virtual conferences worked well?



* Price Tag. (Most) virtual conferences are much cheaper than the in-person conferences from the Before-Times, although there were exceptions. The Ecological Society of America conference in summer 2020 was expensive enough to deter many people from engaging (hundreds of dollars to view pre-recorded videos). But even when registration is not free, virtual meetings don't require airplane/train tickets, hotel rooms, catered food, and ground transportation - and so will still be far cheaper than in-person meetings. If you have research funds, you save enough to pay your research staff a bit more, or do an extra lane of Illumina sequencing or whatever.

* Inclusivity. Virtual meetings can be attended from far away without travel, enabling participation by people from around the globe, including in places from which travel would be prohibitively expensive. Virtual meetings enable participation by undergraduates or graduate students who lack travel funds, and faculty at smaller institutions who lack conference support grants.

* Convenience. You can participate from the comfort of your own home in your pajamas. Dan left his laptop on to watch videos while baking, and the next day enjoyed the fruit of those labors with muffins and coffee while watching talks. You can knit, craft (Dan rewove the seats on a couple of ladderback chairs while watching talks), enter data (Andrew extracted data from his camera trap videos), clean up your references (Kiyoko cleaned up citations in her reference manager as she downloaded the cool papers mentioned in talks), and otherwise multitask while paying attention to the scientific content.





* Carbon savings from reduced travel. Admittedly, spinning the drives at Google or Zoom does generate substantial carbon - but much less than in the case of travel, or - at least - airline travel.

* New modes of speaker feedback and discussion. Many people commented that Slack channels, chat rooms, twitter, and other online tools gave opportunities for viewers to give speakers live feedback and questions during and after the talk in drawn-out conversations that were often more effective than might happen when you must rush off to the next talk. One good suggestion is that chat room tools should forward questions to speaker's emails so they don't have to keep checking for days afterwards to see if there are any questions arriving later. Caveat: although it could be distracting to viewers watching a talk to see ongoing conversations about previous talks. Commonly used online tools mentioned included: Zoom, Teams, Gathertown, Twitter, Slack, and Remo

* Concurrent sessions All conferences have to make a choice to either artificially limit who can speak, or else have so many speakers that there must be concurrent sessions. Viewers must then choose which talks to view, and which to miss. Most virtual conferences record the talks and post them for people to view after the fact, so you can see both of those simultaneously scheduled talks you were excited to learn from! Caveat: Many people said this is a great benefit but many also noted that they didn't actually avail themselves of the opportunities it affords.

* Relaxed format. Some online twitter respondents noted that virtual presentations feel more casual and relaxed, causing less anxiety, which in turn improves self confidence and speaking quality and clarity. And some speakers can further reduce anxiety by pre-recording talks that are then played during the relevant session.

* Pause and rewind. Want to linger on a detail? Need to take a call? Cat walking across your keyboard? Kid vomiting carrots all over the floor? Its okay, you can pause that recorded video, or rewind, and catch up or revisit a point. 

* Come one come all. Most meetings need to book a certain number of rooms and days, which constrains the number of presenters due to building constraints. And the audience size is capped by fire code limits on seats in a room. Neither apply to virtual meetings. As Mark McPeek wrote "The stated goal of ASN and the other societies during discussion last summer was to provide opportunities for early career researchers. Limiting the number of contributed paper slots is antithetical to that goal."

* Shorter day.  At physical meetings, senior folks often duck out for a half day at a time to catch up on emails, editorial decisions, grant writing, and so on; putting out the dozens of proverbial fires that seem to crop up every day. We always feel guilty about this because we traveled so far, and are paying good money, and should be meeting colleagues and students. Some virtual meetings just build this constraint into the schedule via half-day time lines. And its okay, because its not like you are paying for a hotel room. More generally, these meetings can achieve flexible schedules: one day per week for a month, three half days in a row, or 24 consecutive hours to serve all time zones around the globe.

* Posters by any other name.  For some, live poster sessions can be awful: crowded, hard to navigate, hard to hear, hard to read. And that's all the more true for people with disabilities affecting mobility: hearing in over-loud echo chamber rooms, navigating tight spaces with few places to sit, and seeing small font posters. Virtual poster sessions can fix these, but are the target of both strong positive and negative feelings. It seems there are some ways to do this well, and some ways to do this poorly. Many people complained that poster sessions are useless online, and should be replaced by 3-minute lightening talks. There were complaints of small font size, lack of interaction, and inability to see who if anyone is viewing your hard-work posters. Other people clearly had great experiences. The software likely makes a big difference. Some conferences used Slack and each poster had a channel in which attendees could ask questions asynchronously. For more synchronous experiences, "GatherTown is best for poster presentations" - Caitlyn Foster. 





* Networking in small interest groups /breakout rooms /chat windows came up a lot as a positive in people's comments.

* Good moderators matter, both to keep everything exactly on time (especially with concurrent sessions) and for managing Q&A sessions. For many conferences, the arrangement seems to be that people type in questions into a chat window which are then picked and read by the moderators. This encourages some shy people to ask questions, and lets a good moderator ensure more age/gender balanced sources of questions. 



Here's a review of a virtual conference that went well: https://ecologyforthemasses.com/2020/12/22/the-bes2020-festival-of-ecology-write-up/


2. What aspects didn't work - things that future virtual meetings should avoid?

A number of people on twitter commented that they just can't stick with a virtual meeting. For example: "Tried virtual conference twice, it just does not work for me" - Misha Matz.  This is a fairly common sentiment. 


* Lack of in person encounters. The number one sentiment seems to be that virtual conferences have their advantages, but are utterly lacking in the primary value conferences deliver to many of us: impromptu networking, accidental conversations that lead to collaborations, chance meetings, and so on. Then there's the cameraderie. Viewing the Virtual Asilomar meeting made many of us feel deeply sad at all the good friends we missed. The wine tours missed with old friends. The elephant seals not seen. We miss you folks!



* Zoom fatigue. Oh boy! Many of us just spent the last 3 months teaching on zoom and meeting with students and colleagues on zoom. Now you get to have more zoom! You know exactly what we mean. Zoom fatigue can be way worse than lecture hall fatigue.

* Distractions. It is too easy to get up and walk away from your laptop and get distracted at home; whereas, when you travel to a conference, and are in a room with other people, there's a helpful element of peer pressure to keep you focused. 

* Work/life time balance. Without travel away from home, it is harder for many of us to step away from our daily obligations. When we travel to a meeting, we miss our kids, our partner, but they understand we are away. When we watch a zoom meeting from home, we are right there in their midst, available for interruption. For some people, this means weekends are an absolutely impossible time to participate because kids aren't in school or day care. Further, weekends are sacred family time for many people when they are home. For others, by contrast, a partner can watch the kids during the weekend, but must be away at work during the weekday. There's no universally successful option here. Steve Cooke: "When conferencing from home, weekends are a hard NO."



* Participation drop-off.  Based on the Genetics Society of America conference in summer of 2020, which strung out talks over a longer time, we are told that participation trailed off over successive days, so stringing a meeting out over many days may be a disservice to the later presentations.

* Pre-recording loses 'live' feel. Mark McPeek writes:  "The idea of having all talks pre-recorded will undercut the feeling of actually being “at” a meeting, and make you feel like you are sitting on a youtube channel all day.  I think having live talks (and certainly with the option for a person to choose to pre-record) made Virtual Asilomar feel much more like a real meeting and human."

* Lack of social events. Virtual meetings that lack social events aren't really meetings, some feel. Virtual Asilomar had a few social events, most notably the natural history trivia night organized by heroic graduate students, but some comments on twitter expressed a desire for far more events. A few spur-of-the-moment Zoom Beer offshoot meetings were also held - and were great fun (although less so than in person).

* Time zones are rough. As one tweeter noted, when you travel to a destination in another time zone, you have the local sunrise/sunset to get you on track. Sure there's jet lag, but you adjust, especially if you go a day or two early. But when you are at home, an afternoon talk in the US is the middle of the night in India and there's no sunlight to help someone there adjust and stay awake. Andrew: Even people on the opposite coast of North America found the 3 hour time shift awkward - especially in relation to normal evening family activities. Better time zone accommodations are needed. Perhaps rolling 24-hour long meetings so everyone around the world has something at a reasonable time for them (and can view the youtube videos after for the talks in the middle of their night). In February, Kiyoko will be giving a keynote at 4am local time because of time zones. She might break her no-caffeine rule for this....

* No napkins to scribble notes on. Some of us think by drawing on chalk or dry erase boards, which should be present scattered around any conference venue. We need virtual dry erase boards to write on when conversing with far-distant peers in chat groups. These exist on a number of online meeting platforms.

* Technology problems. Many people complained that switching between different sessions can be difficult: you have to sign out of your zoom session, find the url for the other, sign in all over again, for instance. This may be one point where free cheap conferences versus expensive conferences that pay for fancier software may make a difference. 

* Where is everyone? When the audience all have the camera off, there's no feedback, no expressions of enthusiasm or puzzlement, no sense of community. If you can possibly manage, keep your camera on and smile and nod for the presenters. Of course, this makes some of the above "at-home" freedom disappear as you feel you can't just get up and walk away during a talk - perhaps listening still from the kitchen. The verdict is still very much out on this one.

* Lack of closed captioning. This is a tough one because the cost can be really high to do professional closed captioning. The cheap automated versions are junk for technical talks (although they might still be helpful for people struggling with the language), and the cost for professional ones gets passed on to the attendees. There are surely ways to do better.

* Internet accessibility. Virtual meetings are bad for people with poor/unreliable internet (e.g., rural area residents)

Bernie attending a virtual meeting


3. What features of virtual conferences should be folded into meetings in the After-Times when we are free to travel again?



It is abundantly clear that most of us want to resume in-person meetings for the networking and the personal conversations; but that we also want to see the low cost, inclusivity, and accessibility of virtual meetings persist in some form. Many people suggested they might go to one live conference per year, and attend a few virtual ones. (And it might be easier to engage more in a virtual conference when we are no longer on Zoom all day long for months on end.) It remains to be seen whether the future holds a mix of some all-in-person and some all-virtual meetings, or whether we see hybrid meetings that are in-person for people who can attend, and virtual for those who cannot. Such hybrid meetings have the negative implication that not everyone has equal access and equal participation; yet there's just no way to have the virtual participants have 100% the same experience as the in person attendees. But this means that those with funds and proximity can get benefits that the less-well-funded and farther-afield colleagues cannot afford or access. Really, that's always been the case with live meetings. But the virtual experience lately brings that fact into sharper focus for those of us privileged enough to be in the conference-attending crowd. Hybrid conferences seem likely to be the best available option that retains the possibility of in person experiences while doing our utmost to bring others into the experience as best we can. Conferences will not be the same in the After-Times: and the opportunity is there to make them better.




A few overarching rules seem to stand out for future in-person meetings:

* Record talks for non-attendees to view, and for people with concurrent session conflicts. Doing so improves access for people from far away, and for under-funded researchers that can't afford in-person meetings.

* Consider having talks pre-recorded, but the speaker active at answering questions live during the talk.


* Permit pre-recorded or live virtual presentations in in-person meetings, to enable people from the other side of the world to present. Live is generally better, it seems; but pre-recorded needs to be an option for someone 12 hours of time zone away. Sure, it isn't the same but it is still better than nothing.

* Create chat rooms with in-person and remote participants for scientific conversation, debate, Q&A sessions.

* Create social events that merge virtual and in person attendees

* Have discussion panels with both in person and remote discussants.

* Get a cadre of senior faculty / established scientists to circulate among chat rooms and find talks that don't have comments/questions, and post something to start an engagement with the neglected material to help build network and community.


* Conferences typically provide help with child care (at least, when they are big enough to provide economy of scale). Can societies do something to facilitate child care for at-home participants? No doubt this will take a lot of discussion and consideration as it clearly won't be simple and must be fair.


* Do better on accessibility



Co-authored paper accepted for publication!!🍾πŸ₯‚πŸ™Œ

* Jet lag is tough. Jet lag when you haven't gone to a new time zone is even tougher. If you want an international meeting, schedule it to work for people in all target time zones. Again, this won't be simple and will deserve careful consideration about how it will be done. 


More recommendations for future virtual conferences:

* To achieve separation from your distracting home life, consider getting an Air BnB to get away and focus on virtual meeting.  


* Spread out the meeting to reduce fatigue. Plan for a half day on same day every week for multiple weeks. It becomes easier to participate and less exhausting.

* There was widespread (but not universal) support for shorter talks (3 + 2 or 5+2 for a talk + questions). Or, to let the questions go entirely online.

* As a participant at home, make a coffee break experience (or have a beer!).


* Many twitter respondents argued for an end to concurrent sessions. The difficulty is that you must either extend a meeting over many weeks, or restrict the number of presenters which defeats the purpose of giving students and postdocs and junior faculty a platform to disseminate their work. The typical ASN Asilomar meeting for example had 5 concurrent sessions for 3 full days, so to accommodate the same number of presenters you'd need 15 full days of meeting - half a month! And that's with only 200 total attendees, some of whom aren't presenting. Personally, we don't think that creating artificial scarcity of talk slots is the solution.

Some other resources on networking and conferencing online: 

https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lob.10407


https://medium.com/@juniper.lovato/a-how-to-reflections-on-planning-virtual-science-conferences-eeb754ed404b

https://pubs.acs.org/doi/abs/10.1021/acs.jchemed.0c00833


Andrew's Favorite Idea: Regional Clusters

Create small regional groups that gather at an AirBnB or a local conference center or field station to view and present and participate in a big international meeting. Along with virtual connections to a larger group, these distributed regional "clusters" would have many of the best in-person networking, exchange, and debate opportunities. This regional cluster option also creates some separation from the distractions of a home setting, thus allowing better focus, without the cost and carbon emissions of long-distance travel. 

Dan's Favorite Idea

The most valuable element of in-person meetings for many people is the bit that cannot be compressed into bits and bytes. It is the opportunities for personal interaction and chance meeting and networking. Yet conferences are not usually designed to promote these, they emphasize sitting and listening, punctuated by 15 minute coffee breaks in which most people are focused on getting in the coffee line. So, what if we tried to promote the uniquely in-person elements of in-person meetings? Specifically, take the passive part of the conference (sitting and listening to talks), and make that more compressed and more virtual. Meetings should be a half day of talks with many concurrent sessions (yes, I know that's an unpopular opinion), with everything streamed online for far-away attendees, and recorded for those concurrent session complaints and people in distant time zones. Permit presentations by people from off-site as well, streamed into the conference center and online. Use the other half of each day for the real business of an in-person live meeting: talking with people. The things that can happen online, should be on line. The things that cannot happen as well on line should be enhanced and kept.


Kiyoko's Favourite Idea 

Virtual Reality conferences. Of course accessibility will be a problem as VR headsets are not that cheap, but it would come about as close as you could get to recreating that conference atmosphere of walking around and 'bumping' into people, standing in virtual lines while waiting for 'coffee', and running to make the next session (just don't run into your wall at home).
 

See y'all virtually and in person at a next meeting!













Is biological adaptation and publishing papers the same thing?

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