Friday, October 23, 2020

Open Access

 The following is a guest post by Bob Montgomerie, Queens University, written with input from Dan Bolnick. This was first posted on the American Naturalist Editors blog, and is cross-posted here for more visibility as the issues span far beyond The American Naturalist.




As you may know, this is Open Access Week (19-26 October) celebrating the progress made so far with making science open and accessible to all, but reminding us that there are still some challenges. One key feature of open science is providing free access to the data underlying published reports.  To that end, The American Naturalist requires that all authors make their data available either on DRYAD (free to authors), on another public repository, or as a supplement published along with their paper. My own experience seeking data from work published in a wide variety of journals has been, shall we say, mixed in recent years. So, it seemed like a good time to assess the availability and quality of recent data made available with American Naturalist papers. 
 
To evaluate the quality of data archiving with The American Naturalist, I looked at 100 papers published in 2020 (the first 50 and most recent 50). Of those 100 papers, at least 78 were based on data that should have been made available—the others were reviews, commentaries, or model-based (though some of those models seem to use data). The good news is that all but four of those papers had made data available either on DRYAD (56 papers), on other public repositories (3) or as appendices/supplements available with the paper as supplementary material (12). Three papers have data embargoed for a while, and only 4 papers made none of the data available. This is, in my experience, a remarkably high level of compliance.
 
The downside is that only 7 of those 56 of those papers with datasets on DRYAD have provided data in such a way that I, and I assume most users, would find convenient or even comprehensible. Here are the main issues:
•         no README (or any other) file explaining the variable names in data files
•         data files in EXCEL and other formats that are not easily read by statistical software. Yes, I know that R can read Excel files but only if they are set up properly, and many of those were not
•         odd file extensions that are not explained. I counted more than 30 file extensions in those 58 repositories, a few of which I had never heard of, and many of which are unlikely to be accessible without expensive or eventually obsolete software
•         not all data made available—I did not check every paper, as that would have taken too long, but I did check a few and could not find the data supporting a couple of figures and tables. Sometimes authors provided summary data (means, SDs) and not the raw data from which those summaries were calculated.
•         no R, Python or other scripts or notebooks to replicate the analyses
•         analysis code not well-enough annotated to be comprehensible
•         code that does not run, presumably created in earlier versions of the software with unknown packages and package versions
 
None of this is unexpected as (i) this whole idea about making data available is relatively new and not often part of our formal training in graduate school, (ii) journals rarely (ever?) provide guidelines for authors that detail what they consider to be best practices, and (iii) most journals have nobody checking to see if authors have actually complied with their requirements. There are many excellent reasons for all of us to want data to be freely available for every published study and I feel that we should take pride in doing as good a job with that as we do with our published papers. Good data will always be useful, whereas most papers have a short half-life if citation metrics are any indication.
 
The American Naturalist is now publishing guidelines for best practices in data archiving (see author instructions) and will have a small team of data editors checking each paper’s data repository to make sure that it is complete, comprehensive, and adequately documented. We are probably the first biology journal to fully embrace the value of open data in this fashion and we welcome your comments as we put this policy in place.  We also now encourage authors to submit private Dryad data links upon submission, so reviewers and editors have the option of checking compliance before manuscript acceptance (see Author Instructions for Submission for details). We will be asking authors resubmitting revisions to provide data links for checking prior to final acceptance.

If you find a published paper's Dryad or related archive that is unusable (incomplete, or unclear), please contact the author and ask that they fix the deficiencies, with a cc the editor . Since 2011, The American Naturalist has made complete data archiving (sufficient to reproduce the analyses and results) a condition of publication. Authors that have not done so are failing to live up to their side of the bargain that led to their publication. 

It is now the Editorial policy that the American Naturalist reserves the right to publish Editorial Expressions of Concern when we are made aware of grossly deficient data archives that are not amended in a reasonable amount of time. In extreme cases, we reserve the right to retract papers that are not supported by appropriately archived data, or to hold up an author's future submissions until past deficiencies are amended.  However, we also recognize that new policies entail growing pains and that compliance is understandably imperfect as we adjust to a new culture of more rigorous and complete data sharing.

Friday, August 7, 2020

How to Write a Thesis

 [ This piece is, supposedly, originally by one A. W. James, who seems to have been a professor in the Dept. of Biology at Canisius College in Buffalo, N.Y., perhaps as much as a century ago; I didn't put much elbow grease into tracking down his history.  My mother recently found it in her files; she says it was a source of great amusement for her and her fellow graduate students at Cornell some fifty years ago.  I am retyping this from a copy that my mother suspects she herself typed back then (on a typewriter, not a computer!).  I guess I'm viewing retyping it as a sort of passing on of the torch.  Enjoy!  –B. ]

On Selection of a Research Project

Be sure to select a topic which has been thoroughly explored by previous graduate students in your department, so that characteristics of your organism will be well known and basic procedures fully established.  Also, you can borrow reagents, ideas, and perhaps data from your colleagues.  Select a very limited, circumscribed, orthodox aspect of this topic for your investigation – preferably one where you don't have to believe the results of your work, certainly not one in which you will become emotionally involved.  Don't attempt to discover anything new – you can do that later on a higher salary – concentrate simply on obtaining data, quickly and in quantity.

Experimental Approach

Set up experiments which will give meaningful results regardless of whether data are positive or negative; once you set up a procedure, never, ever alter it or you will have to explain how and why and what difference it made.  Restrict your study to a single variable so that you don't have to concern yourself with complicating factors and there will be no necessity for a comprehensive discussion.  Avoid experiments which must be presented in the form of figures or graphs and, by all means, exclude photographs.  If all data can be summarized in typewritten tables you will save yourself time, money, and frustration.  (It's even better if you don't need tables!)

The Literature Review

If you've followed the advice above, your review will have been written for you by a former student and all you need to do is paraphrase it slightly and bring it up to date.  If you should work on a topic which hasn't been reviewed recently, depend exclusively on Chemical and Biological Abstracts for information for your own review.  Thus you will avoid the problem of trying to track down journals which were hidden away at the bindery all the time; you'll also save yourself many hours of reading and trying to organize experimental details which only make those lovely, sweeping generalizations more difficult.  It goes without saying that you should have made sure there is no significant foreign-language literature on the subject.  Remember to document thoroughly every statement you make.  It really doesn't matter that the idea is now out of date or that the author turned out to be an idiot – just so it's been published.  One thing you don't have to worry about is punctuation; trust your committee to put in any commas you have omitted and to delete most of those you have used; it salves their consciences for failing to understand or for not caring about what you have to say.

General Principles

Be sure that the organization of your thesis follows established, accepted, orthodox, conventional, recognized, approved, hallowed precedents.  Whenever questions of form arise it is safest to check with the graduate school, though this may require a lot of hiking.  Never, never do anything new, even to improve clarity of presentation, unless you can cite an established, accepted, orthodox, conventional, recognized, approved, hallowed precedent.  Always keep in mind the basic purpose of a thesis: to satisfy the graduate school.  Unequivocal presentation of data is far more important than unequivocal data.  But most important of all is that the margins are correct.

Sunday, July 26, 2020

Advice to young academics like myself: Be resilient.


Guest Post by Romain Villoutreix



Who am I?

I am currently holding a postdoctoral position in Patrik Nosil's lab at CEFE (Montpellier, France). I am interested in the origin and maintenance of intraspecific phenotypic variation over long evolutionary time. I am in the critical stage of my career were I need to secure a permanent position and funding of my own (7 year past PhD), and hope that the recent publication of a first author paper in Science is a good step in that direction.

Context, the paper.

The existence of multiple morphs of the same species co-existing in natural populations is a common feature of many taxa. These morphs often show discrete variation for multiple traits, all associated with a single chromosomal inversion. Because chromosomal inversions impede recombination between sequences with opposite orientation, it is often assumed that inversions shield multiple selected genes from recombination (supergene hypothesis). But inversions can also harbor adaptive mutations at one of their breakpoints, leading to their rise in frequency without any role for recombination suppression (breakpoint hypothesis). Therefore, a role for recombination suppression in inversion evolution needs to be demonstrated rather than assumed.



Color variation of Timema. Photo credits: Roman Villoutreix

In this paper (here), we show evidence for both hypotheses (supergene and breakpoint) in the cryptic body coloration of a genus of stick insects (Timema). Most species of the genus show intraspecific discrete variation for body color, with green and brown morphs. Green morphs are cryptic on the leaves and brown morphs on the bark of the host plants these stick insects live on. We showed that body coloration is associated with a genomic region of reduced recombination (likely an inversion) both in Timema cristinae and Timema bartmani. Given the size of the genomic regions identified (~10 Mega base-pairs and ~1 Mega base-pairs, respectively) it was nearly impossible to identify the number and identity of genes involved in this polymorphism. Fortunately, a species in the genus (Timema chumash) displayed more continuous variation for body coloration. The study of T. chumash thus allowed us to fine map color and demonstrate that multiple genes are involved in body color variation in this species. Interestingly, these genes are clustered in a ~1 Mega base-pairs (Mbp, hereafter) region of the genome. This region is deleted in the green allele of Timema cristinaeand located at one edge of the 10 Mbp region of suppressed recombination (a putative inversion breakpoint). In Timema bartmani this 1 Mbp region is the sole region of the genome associated with body color variation and, as mentioned above, shows reduced recombination and no sign of deletion in both morphs. This suggest that in Timema cristinae, the mutational event that generated a chromosomal inversion also generated the deletion of body coloration genes at one of the inversion breakpoints and contributes to the evolution of this inversion polymorphism. 

Since the news of acceptance in Science spread, I have had many discussions with PhD and postdocs about the journey leading to the eventual acceptance of this paper. Many told me they would not have had the patience for this endeavor. This pushed me to share this journey to a broader audience, as I think it is a common one for papers published in high profile journals.





The making of the paper.

I started collecting samples for this project, with the help of colleagues, in April-May 2015. We collected and photographed in a standardized manner around 2500 individuals from 10 Timema species. Library preparation and sequencing followed, along with more sampling and sequencing for a new reference genome in April-May 2016. By the end of 2016, I had ran GWAs for all species sequenced and was struck at how strong and clear the results were. Body color always maps to the same linkage group (LG8). The signal is different for each species but the only region always associated with color in this linkage group is the 1 Mbp region which is deleted in green Timema cristinae. We had not yet at this point placed the results in a broader context or understood their significance, but I am already convinced of one thing: I won't often come across results that clear; they deserve patience and special treatment. 

October 2016, Patrik's ERC grant runs out. I am out of a job but am still working on this data. Despite my finances running low, I am really having a blast analyzing it. April 2017, I start a second postdoc in Liverpool with Ilik Saccheri on recent adaption in different species of Lepidoptera in the UK. The project is big and challenging, but I still keep working on the Timema data to some degree at least half of my days. I remember being really uneasy and ashamed doing so, but am very grateful to Ilik for being so kind with me.

October 2017, we 'crack' the story. We understand the difference between Timema chumash and the other species. The results are placed into context and we have a narrative. I start reading like crazy on supergenes and inversion breakpoints (review to come) and we start writing a manuscript. I move to Montpellier in October 2018 to work with Patrik again. Possibly not a very good way to show independence, but I really enjoy working with him and I think this will make my life (and Patrik's) easier in order to get this story out. The 'easy' fun part is over, now starts the long and painful process of submissions followed by rejections...

Resilience in the face of rejection. 

...October 2018. Submission to Science followed by a rejection without review. November 2018. Same story at Nature and Nature Genetics. Submission to PNAS. The manuscript is sent for reviews... but rejected. We revise the manuscript accordingly to make multiple points clearer. February 2019. Submission to Current Biology. The manuscript is sent for reviews... but rejected again. March 2019. Submissions to PLoS Biology and PLoS Genetics followed by rejections without review. This is a huge blow for me. I really start having doubts. Was my feel about the awesomeness of these results right? Is it not enough of an advance in the field? But I never previously had results that clear in my short career, so I decide to keep trying, accepting the potential consequences of this decision: Publishing less papers, and having an article I spent years to publish possibly go unnoticed.

The end of the rejection tunnel

We start revising the manuscript again. The previous version was too dense. We remove the whole ecological side of the story to focus solely on the genetics of color. A meeting with our colleague and friend Mathieu Joron is crucial for our revision. Discussing with him, we understand the breakpoint mutation angle is the most interesting aspect of our results. We remove further results to center the story on this find. September 2019. The manuscript is ready and so different that Patrik is confident we should try Science another time. Rejection… but with encouragement to resubmit! February 2020. We resubmit, adding another reference genome and whole genome re-sequencing data to answer the reviewers’ points (not a small feat… long live the ERC!). May 2020. Final acceptance... I can't believe it, we actually made it! With the Covid-19 lock-down, the epic party I promised Patrik upon acceptance will have to wait... until public release, haha!

Things I learned 

Having a clear paper with limited points (one or two maximum) is key! At the end of the day, we (myself included) are all extremely busy reading enormous amounts of emails and papers. It is not surprising that we find heavy papers very challenging to read. We just don't have the time and mental energy available for many of them. While it certainly sucks on an academic and scientific perspective, I think it is part of the Science landscape nowadays...

Resilience is key! When you really believe in a set of results or a project, just go for it and expect rejection. And expect a lot of rejection. It is part of the publishing/grant process of course, but of life in general. Nothing really good is given easily! When I look at the final print of this paper, I see my resilience in the face of years of struggle and doubts. It is a positive and empowering feeling.

Friday, July 10, 2020

Unravelling little mysteries in the genome of Atlantic salmon

Salmon have always been part of my life. I grew up along the Miramichi River in New Brunswick, Canada, which is a river that is famous for its Atlantic salmon fishing. Even my high school mascot was a salmon named Samoo the Plamu (Mi’kmaq for Atlantic salmon). People travel from far and wide for the opportunity to catch a salmon on the Miramichi, and I have been lucky enough to catch at least one grilse (a salmon that spends only one winter at sea) when fly fishing with my dad. Although my grad studies took me to the west coast to study Pacific salmon, I was glad to have had the opportunity to move back to the east coast and work on a species that has always been close to my heart.


Catching my first salmon on the Miramichi River.


In 2017, I moved to Halifax, Nova Scotia, and started a postdoc with the Bradbury lab. I was excited to get some experience in genomic projects involving Atlantic salmon. Although, I was quickly reminded that Atlantic salmon are complicated. They exhibit a wide range of life history strategies (see Fig. 1), and unlike Pacific salmon, they don’t die when they spawn (they are iteroparous), making things even more complex (in my opinion). Nonetheless, the amount of diversity that exists makes them an exciting species for exploring never ending evolutionary questions. 

Fig. 1. The wonderful and complicated life of Atlantic salmon (Fig. 1 from Gibson and Haedrich, 2006)

 

One interesting part of the Atlantic salmon story is that Atlantic salmon occupy rivers on both sides of the Atlantic Ocean – in Europe and North America. Salmon from these continents diverged >600,000 years ago, and this divergence has occurred primarily in allopatry, although opportunities for gene flow have occurred. In one of my recent papers, we investigated genomic differences between Atlantic salmon from these two continents.


  

Atlantic salmon returning to a river to spawn. Copyright: Nick Hawkins Photography


As populations begin to diverge from each other, the genome can start to show variable levels of differentiation, resulting in peaks and valleys of differentiation. Regions of high differentiation between populations can occur through different mechanisms, one being divergent selection acting in opposite directions in each population. These regions often called ‘genomic islands of speciation’ have attracted a lot of attention as these regions may be important for initiating speciation. 


But some question whether these islands of speciation are real…

 

It is now clear that other mechanisms can produce the same signals of differentiation without divergent selection (Wolf and Ellegren, 2017). This can include purifying background selection, which acts to remove deleterious mutations. In regions of low recombination, this type of background selection can reduce diversity and lead to signals of increased differentiation between populations.

 

This means that two very different processes can lead to similar signals, so it’s important to consider what mechanisms might be operating in the genome to better understand the speciation process. In our study, we attempted to do just that with Atlantic salmon.

 

I will admit that the role of purifying background selection is not something that I had given much attention to before this paper. Luckily, another postdoc in the lab at the time, Tony Kess, had spent some time thinking about it already. Tony and I spent a lot of time drinking a lot of coffee and discussing the role of background selection in salmon. Admittedly, as I read more papers and became more caffeinated, I sometimes got more confused. One question that I kept coming back to is ‘how will we know if it’s divergent selection or if it’s just background selection?’. One answer we seemed to settle on was maybe we won’t know for sure, but by using multiple approaches, we can provide evidence that is more consistent with one of these processes.

 

Tony and me at Moominworld for ESEB 2019 asking Moominpapa about his thoughts on background selection. 


Fortunately, a lot of other scientists have focused their efforts on understanding and identifying the signals associated with background selection, and their work has been a tremendous help for understanding how such processes can shape the genomic landscape. For a nice example on the role of linked selection and recombination in driving regions of high differentiation, I suggest Burri et al. (2015), which investigates this across flycatcher species.

 

To try to disentangle these different mechanisms in Atlantic salmon, we took note of methods used in other studies. We expected regions under divergent selection (rather than just background selection) to show: 

1) high differentiation

2) high linkage disequilibrium

3) no reduction in recombination rate

4) no increase in gene density

5) signals of positive selection

 

The question about these differences between European and North American salmon is interesting from an evolutionary perspective, but also important for conservation and management. Atlantic salmon are moved all around the world for aquaculture purposes. The historical use of European salmon for aquaculture in eastern North America has posed problems to some recent conservation efforts in Canada (see CBC article).

 

In our study (recently published in Molecular Ecology), we utilized genomic data for 26 populations in North America and 54 populations in Europe, which cover a wide range of latitudes within each continent (Fig. 2). The study was ‘spawned’ partly out of curiosity when my postdoc supervisor, Ian Bradbury, asked if any loci were fixed between Europe and North America in our dataset. Upon a quick inspection of the genome, I found over a hundred loci that showed almost fixed differences between continents. But what really got our attention was that a large number of these loci (almost 40%) were localized in one large genomic region. This was news to us, and this led to a more formal investigation of where these large regions of differentiation were located in the genome, and what processes were shaping them. Identifying these regions would also be useful for developing markers that can be used to detect salmon of European origin (or with recent European ancestry) in Canadian waters.

 

Fig. 2. Location of Atlantic salmon sampling sites in (A) North America and (B) Europe.

In our study, we first found large genomic regions (>1 to 3 million base pairs) showing consistent signals of high differentiation across multiple methods. These were found on four chromosomes in the salmon genome.


Next, for these four chromosomes, we went back to our check list to see if these regions showed patterns consistent with divergent selection. With these data, we confirmed in these regions (see Fig. 3):

1) high differentiation: yes, we found highly divergent regions

2) high linkage disequilibrium: yes, we showed high linkage disequilibrium 

3) no reduction in recombination rate*: yes, we found no significant reduction in recombination rate relative to the rest of the chromosome

4) no increase in gene density: yes, we found no significant increase in gene density

5) signals of positive selection: yes, we found signals of positive selection


Fig. 3. Example of one region showing high differentiation (high FST) between continents on chromosome Ssa06. This region showed no significant reduction in recombination rate and no significant increase in gene count relative to other regions of the chromosome, lending support to the role of divergent selection in driving these differences

Together, these results support that differentiation is not likely due to background selection alone, which is more likely to produce signals of differentiation in regions of low recombination.

 

*Side note: Originally, I may have calculated recombination rate incorrectly. Before the paper was published, I uploaded my R scripts for the analyses to my GitHub. Arne Jacobs (postdoc at Cornell University – who I’ve met a few times at conferences) kindly reached out to let me know that my calculations were wrong. Turns out, it is not as simple as just centimorgans divided by base pairs. Who would have thought? (probably everyone else!) But, to be fair, there are many different ways to calculate recombination rate. While this was a bit embarrassing, I was happy to have the chance to correct this mistake before the paper was officially published. I was even more happy to find out that this did not change the results/interpretation of the paper. So thank you to Arne for reaching out in a kind and respectful manner, we can always use more kindness in academia! 

 

Overall, our results were consistent with the role of divergent selection acting to drive patterns of differentiation between continents rather than just purifying background selection. One question remains as to what traits/genes may be under selection at the continental level. As I think about salmon from each of these continents, I think about the diverse landscapes that they live in and the different conditions that they encounter. But we know salmon from Europe and North America are not morphologically distinct, and generally populations are expected to be adapted to local river conditions rather than at a large scale. So one question that weighed on me was ‘what could be showing adaptive signals across such a broad scale?’. We found genes and biological processes that could potentially relate to differences in ocean navigation/migration and immunity. One hypothesis could be that while salmon from each continent migrate to shared feeding grounds in the ocean, they have to travel in different directions to get there, so perhaps differences in ocean navigation may have evolved. I think this is a cool idea that would be interesting to study in the future.

 

Of course, there are caveats to any study, and we address these limitations in our paper. Future studies using genome sequencing and experimental work would help to better understand the adaptive differences between continents. 

 

Our study found differences between European and North American Atlantic salmon that may be contributing to early stages of speciation. These differences may explain some partial incompatibilities that exist between continents, and highlight the potential risk associated with the trans-Atlantic movement of salmon provided the currently limited data, high genome-wide differentiation, and largely unknown consequences. More focus on understanding these differences may help inform management decisions in the future as more plans develop to move salmon across the ocean. Luckily, I have recently started a job as a scientist with Fisheries and Oceans and can continue to concentrate on questions related to Atlantic salmon management and conservation.

 

Our recent paper:

Lehnert, S.J., Kess, T., Bentzen, P., Clément, M. and Bradbury, I.R. (2020) Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar). Molecular Ecology 29:2160-2175.


References:

Burri, R. et al. (2015) Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Research 25:1656-1665.

Gibson, J. and Haedrich, R. (2006) Life history tactics of Atlantic salmon in Newfoundland. Freshwater Forum 26:38-45.

Wolf, J.B. and Ellegren, H. (2017) Making sense of genomic islands of differentiation in light of speciation. Nature Reviews Genetics18:87-100.

Thursday, June 25, 2020

"I want to work but I can't"

So here I am, 9 PM, trying to get a few decision letters written. There were 6 waiting for my attention when I woke up this morning. I've written four decisions, and now there are four still waiting for me to look at the manuscript, reviews, and Associate Editor's recommendation.  I want to get these off my plate, and back to the authors.  But I'm tired, haven't had my run today, and am stressed, and so I just stare at the screen, check the news, check twitter, and stare at the screen again. As one of my graduate students said in a meeting earlier this week, "I want to work, but I can't".

This is a sentiment I've heard a fair bit lately. Last week, I had multiple members of my lab explain some permutation of why they hadn't gotten as much done in the previous week as they had wanted to. Social isolation is taking its toll. There's the stress of seeing COVID numbers rising again.  Folks are taking time to participating in protests for the Black Lives Matter movement, which is great. Everyone is stressed.

Now is a good time to cut people slack, given them the chance to deal with the complicated stresses of being stuck at home during national and global turmoil. As a mentor to my students and postdocs, and as an Editor working with Associate Editors and reviewers,  now is a good time to be understanding and give people the time that they need.

But, that does not mean it is healthy to lounge around obsessively checking twitter and the news ('doomscrolling' as someone colorfully put it on twitter), or compulsively make your fifth sourdough loaf of the week. Inaction itself can feed anxiety and other forms of stress, generating feedback loops: I can't work because I'm stressed, and I'm stressed because I haven't gotten any work done. As one person I spoke to said, "I'm getting in my own way". Sometimes, a bit more work can be a relief, a distraction and escape from the news cycle and its concomitant anxiety and depression.


Then, there are still some deadlines. Many have gotten pushed back or softened, but grant proposal deadlines still exist. So do deadlines for submitting reviews, or revisions to your manuscript (though these are pretty much always negotiable on request). There are still classes to teach, lectures to prep by specific days, grant annual reports due. The world has not come to a standstill around us, even when we wish it had. And this means that paralysis at your work desk can be scary and frustrating and unwelcome.

This post, then, is for the people who *want* to get more done than they are. What are some tricks to get yourself out of the intellectual doldrums and catch fresh wind in your sails to write, plan a lecture, analyze data, or whatever it is you feel you need to do professionally, but haven't been able to do.

In several conversations with students last week, who wanted help refocusing, we discussed various ways of helping yourself make progress on your own work goals. I then broadened my search for ideas with a tweet asking for others' ideas and strategms. The following is a list in no particular order, of the ideas that arose in conversation and over twitter.

* Before some readers get angry at me, I'm not advocating that anyone pressure anybody else unduly. The following should not be a tool to force others to work, but an aid for those individuals who wish to help themselves meet their own goals and self-imposed expectations.

Also, it is crucial that everyone recognize that the strategies that work well for one person can be useless or even counter-productive for someone else. We each have our own motivating compass and fuel:  for instance some are motivated by pressure, others find that oppressive. Find what works for you.

Here we go, with "50 ways to leave your procrastination"

1. Talk to a physician or therapist.  I'm putting this first for a reason. It's okay to not be okay. For many people, isolation during COVID has brought out unknown or previously-controlled mental illness of varying degrees. If you may be suffering from depression, anxiety, PTSD, or any of a number of mental illnesses, seek medical advice and help. This is common, acceptable, and likely not something you can just push on through without help. I'll openly say I saw a therapist for a block of time recently and it was immensely helpful. Do it, if you think it might possibly remotely help.

2. Create a timed schedule. Pretend you are taking solid blocks of classes this week, and create an hourly schedule in advance. Set defined blocks of time for different activities and set alarms for the transition between them. Check off the ones you complete with decent focus. The ones you don't remain focused on, ask yourself if you are really interested in doing them, and do you have to do them. If the answer is no to both, push it to your back burner to-do-list. The advantage of a timed block is that if you are on a roll working on something, you can just ignore the alarm and not switch tasks; keep plugging away while you have good momentum. But if you wander onto the interwebs and start reading some silly advice blog like this one, that alarm is a good book-end that prevents your diversion from eating up too much time.

3. Keep a journal, hour by hour, of what you spent your time on. You may surprise yourself by discovering you have done more than you give yourself credit for.

4. Set yourself a set of very small tasks, and do them. Get that permit application in the mail, fill out that form, search for that article you meant to look up. Completing a bunch of rapid to-do items in the space of a few minutes each gives you a tremendous feeling of accomplishment, cutting your to-do list down greatly.

5. In the spirit of (4):  really big to-do items like "Write that NIH R01 grant" are intimidating as hell. And it takes weeks to months to get it done, so the whole time the same to-do-list line is staring you in the face making you feel more and more guilty for not checking it off. But you can't check it off quickly because it is a gargantuan task.  I'm imagining a paleolithic hunter-gatherer shaming themselves for not eating the *whole* mammoth today. So, don't put a whole mammoth on your to-do list. Cut it up into well-defined edible chunks. That results in a very long to-do list. But you create specific achievable goals so that you can truly cross off items (multiple items) every day. And somehow that feels much more productive.

Don't eat a whole mammoth in a single day.


6. Set a timer and tell yourself to _______ for X minutes (Meghan Duffy suggested 30 minutes) and then you get to stop and do something pleasant for yourself.  This mixes well with the mammoth-bites idea above, if you can generate to-do list items that are short units of time worth of work (write one paragraph). Mike Kaspari noted this is the "Pomodoro Method" where 25 minutes of focus earns you 5 minutes of goofing off. Repeat 3 times, then you get an hour of distraction as a reward. 25 minutes feels less ambitious than half an hour.

7.  10-15 minutes of mindful meditation, followed by 1-2 hours of focused work.

8. Go for a walk or run (with your mask on, and if you are allowed to). You are taking time away from work, but you may get more work done as a result.

When working in Vermont a couple weeks ago, I would take an hour break each day to go do some nature photography.


9. Here's a big one many people suggested: get a work buddy and hold each other accountable for your bite-sized achievements. Many people have even been getting on zoom (or whatever web video conference tool you like), and quietly working on your own stuff in a virtual common room.  That way you have some of the casual chit-chat and sounding ideas off each other, but can still each do your own thing. Group meetings don't have to be meetings! Leave the video on, mute yourself (or not). Here's a description of the Online Co-working Partnerships:

10. Copious tea breaks. Sebastian Schreiber recommends golden orange pekoe black, and second flush darjeeling.

11. Start small. Write one sentence. Just one little wafer-thin sentence. One line of code. Then try a second, if you can. You might just start rolling.

12. A change of scenery. Move from the study to your living room to your dining room to your porch to your hammock, or whatever you have. Even moving from a desk to a chair in the same room can help surprisingly well.

13. Get a 'Focus Keeper' app.

14. Stack your zoom/Skype meetings into a tight set of short meetings, to free up blocks of space without interruption to get you room to get into the 'zone'. Many of us work best with large blocks of time to focus without interruptions, so schedule accordingly.

15. Plan your morning around something fun, with a bit of work, rather than vice versa.

16. Go play with your kids for a bit, if you have them. Or a spouse, partner, dog. Someone who makes you happy and distracted.

17. Eat an entire cheesecake.

18. Come to terms with guilt-free exercise, fun, cooking, social time, and pleasure reading.

19. Go outside. And don't come back for a while.
Going outside for a paddle


20. Read escapist books. But be forewarned: someone else's advice may not be your escapism. When Trump was elected I asked twitter for recommendations on a good escapist book. Ben Haller suggested I read "The Sheltering Sky".  Great prose, but not pleasant escapism.

21. Do something productive fun. Learn a new trick in R that you don't need right now, but were curious about. Go see a virtual seminar from a conference or online seminar series. Read a random paper from a journal. Something that isn't your work goal, but is helpful in the long run, pleasant in the short term, and feels enough like work to be guilt-free while enjoying yourself. Personally, I find solving coding puzzles for data analysis to be immensely enjoyable. But I'm kinda a nerd.

22. Have a weekly planning meeting alone with yourself to outline your daily list and create a schedule with bite-sized tasks. Helps get through triage paralysis (what to work on first). April Wright noted she does this Sunday night with a cup of tea and its a highlight of the week.

23. Well, you aren't traveling anywhere for work or vacation. So create days of vacation where you are obligated to NOT work and go do something fun (but stay off your computer!). Then you'll return to work reinvigorated.

24. To the extent it is allowed and ethical in COVID times, go for a trip. I drove to Vermont to my family's cabin on a lake (yes, I see my privilege)  and didn't stop anywhere en route up or back, and didn't go in a building with anybody else up there. Sure, I lost 7 hours round trip driving that I might have used for work. And I went kayaking twice a day and jumped in the lake a lot. But I got more done in my three days up there alone than I achieved in two weeks normally.

25. Smite people who are productive, and keep a list of the people you have smote.

26. Self-forgiveness. Jenalle Eck wrote "I tell myself 'I forgive myself for not making progress on X'", then does the smallest unit task towards X.

27. Aim to write one sentence every hour. If a second sentence flows naturally, don't stop it.

28. Tak hours away from your computer.

29. Take a break from your usual social media

30. Eat a snack, drink a glass of water regularly.

31. Get up from your chair ever 15 min and move your body.

32. Regular yoga, runs, etc.

33. Get a dog.

34. A daily dream: a to-do list with feelings. In the morning, write what you hope your evening journal entry would be and how you felt about it then work to achieve that aspiration.

35. Treat daily tasks-not-completed as not failures, but as lessons in setting more realistic daily goals.

36. Working from home is a marathon, not a race, endurance is more important than speed, so do what you need to to endure.

37. Put off email till later in the day, in well-defined blocks of time, so your mornings aren't distracted.

38. Play music regularly, perhaps as the 5 minute reward every half hour.

39. Figure out what you enjoy most about your work and focus on that. Rather than maximize productivity, maximize work-associated-happiness. If you love coding, do that and less writing for a while.

40. Go read other people's papers for a bit. Not even in areas directly related to your research. Go learn something new and see what inspiration strikes.

41. Develop SMART goals. Specific. Measurable, Achievable. Relevant. Timely

42. Fanny Pouyet wrote: "Write the big issue I would like to solve tomorrow. Then spend 30 min detailing every single step of that task. The next day's to-do list is ready"

43. Figure out what motivates you. Do you work well under a deadline, or not? Are you motivated to fulfill someone else's expectations of you, or your own goals? Is pressure good for your productivity, and if so from what source?  Find strategies to maximize that source of simulation or pressure or whatever helps, and minimize the things that stress you out in counter-productive ways. Personally, one of my biggest motivations is the feeling I owe people comments on manuscripts. My students and postdocs' paper drafts always come first, because if I get them comments then they can proceed to work on it (if they are able and willing), whereas if I sit on a manuscript draft then I slow everyone down. That feeling of duty to them, and to the authors in the journal I Edit, keeps me focused.

44. Quaranteam: create a small group of people who are socially distanced and vigilant about COVID from outside sources, but willing and able to meet together.

45. Start a new hobby:  I've done 1000-piece puzzles, cooked new recipes (an amazing Tacos al pastor was the winner so far), and done far more running than ever before.

46. Take a summer course. I'm very tempted to take an American Association of Immunologists online summer class, and there are some on population genomics I'm keen to try as well.

47. Get two dogs.

48. Take something off the back burner you've not gotten to work on in far too long. You might find that re-prioritizing is helpful. I have a history of science paper that's been awaiting revisions by my co-author and I for >500 days. That's right, over a year and a half since we got the reviews, and this paper just hasn't been top priority. Always something more important. But on Monday I dusted it off and did 95% of the revisions we needed, in a single day. It was intense, and I barely left my desk fo the day. But I was able to work with a focus I've mostly lacked recently, because it felt so good to work on this long-overdue task.

49. Here's my favorite for today. Reach out and contact a fellow scientist who you haven't met, but whose work you admire. Set up a time to talk by Zoom. They can be anyone, anywhere in the world. Chances are, in the COVID-times, they aren't traveling, they aren't doing field work, and they aren't out at a fancy restaurant or going to the pub with friends. Chances are, they are home wishing they had someone new to talk to. I did this today with Chelsea Wood, after seeing her EcoEvoSeminars talk. We had the most amazing hour and a half science conversation, despite never having met before. I left that zoom room energized and excited to have a new collaborator on the horizon. If there's any hidden blessing in all this, its that many scientists are ready and willing to meet colleagues from around the world and have new conversations that will expand all our social networks and academic networks in creative new ways unconstrained by the usual set of conference attendees and geographic limit. Go talk to someone a half continent away, or better yet continents away, and find a new friend and collaborator, and return to your work with a fresh set of eyes and new excitement.

50. When you are stretched too thin to work, go write a preachy blog post telling others how to get work done more efficiently. At least I feel I have achieved something productive, and come away with interesting ideas, even if I still have four - wait, no it's five now - manuscripts awaiting my decision.

Monday, June 8, 2020

Escape from Galapagos: How to get home in a pandemic


So briefly, my colleague and collaborator, Dr. Sarah Knutie and I, along with Sarah's field technician, got stranded on San Cristobal in the Galapagos. The Ecuadorian government suddenly shut down air travel mid-March. Ecuadorans were given two days to get home or they wouldn't be allowed back except on repatriation or humanitarian flights. The government grounded all incoming international flights, and all domestic flights, which meant those on the Galapagos were stuck there. The government did coordinate some special flights to get tourists off the Galapagos, but with all the confusion we feared that we might get stuck on the mainland and decided if we were going to be stuck in Ecuador, relatively isolated San Cristobal would be a better place than on the mainland. We ended up staying on the Galapagos for six weeks. We got in one week of data collection but then the park shut down and all research had to stop. Within a week of the park closing, we were only allowed out of the apartment twice a week for essential supplies, and only at limited times because the whole island was on a curfew from 2pm to 5am. In mid April, the government announced a flight going from the Galapagos to the mainland (Quito and Guayaquil), and that they would allow two commercial flights from Quito to Houston. We knew commercial flights in the US were still operating, and for me, I needed to first get to the US because that was the only country from where I could get to Canada as Canada had long grounded almost all international flights. For some great summaries of our adventures on the Islands and getting home, check out Dr. Knutie's Instagram stories here: https://www.instagram.com/saknut/

The travelers before the lockdown on San Cristobal and when curfew started at 9pm (curfew ended up being 2pm-5am everyday. Photo: Sarah Knutie
By far the most frustrating part of this experience was not knowing when we would go home. Life on San Cristobal during lockdown was fine given we had access to supplies, decent internet in the mornings (for Galapagos), and a sort-of schedule that included Pop Sugar dance workouts in the late afternoon. However, not knowing if and when we could get back to North America wore on us. The second most frustrating part was that we couldn't do any research. We had a fantastic opportunity to track in real time what happens when tourism stops and how this might affect the organisms. What will happen with the finches when restaurants and tourists are no longer around? What happens to their microbiome? What rapid changes in behaviour might happen? And not just finches, but the sea lions, and other organisms. But we weren't allowed to collect any data. And so it goes - research during a pandemic.

My partner wrote a summary of it that's much more entertaining to read than if I just recap it, so here it is (NB comments and photo captions are mine):

"ESCAPE FROM THE GALAPAGOS" has just wrapped up production. It was filmed on location in Ecuador, the USA, and Canada. (NB: Alternative title: How to get from the Galapagos to Montreal in eight days). By Chris Rush

Plot line:
Starring Kiyoko and her two fellow researchers, Sarah and Gabby, who have been quarantined due to a "zombie virus" causing a disease known as COVID-19, locked up in a 3 room apartment in the Galapagos, only being allowed out of their restrictive dwelling twice a week for whatever food they could source (NB: the cargo ships were still coming so we had food, and importantly, beer and caña), enduring a 2pm-5am daily curfew, and having to dodge the insidious, potentially infected unnatural clones (humans!) that have infested the Islands since the 19th century.

Then, at last!

The American consulate sent word that one of their Capitalistic Airlines would send a special plane on April 29th into the maelstrom of infection on the mainland of Ecuador, aka the "epicenter" of the pandemic in South America, to rescue stranded American citizens for a special "PANDEMIC one way fare" of only $1,442USD, to Houston. Luckily the beleaguered few realized that they could then fly to any city in the United States after that on the same fare as Houston if they booked it at the same time (thanks to some super-sleuthing by an un-named guardian angel safely squirreled away up in Canada).

But, wait, first they would have to escape off the "Malefic Island of San Cristobal" where they were quarantined, requiring a flight to Quito.  Thank goodness a local airline opened a flight from the main airport on "Ground Zero Island Baltra" to Quito! But booking the local flight to the mainland was turning out to be a disaster as the local airline company, TAME, would not accept foreign credit cards!  What to do?! An emergency skype call to the guardian angel in Canada did not help as his credit card was also refused. Thank God the intrepid souls managed to book the flights through an American travel agency instead, thanks to Sarah (NB: this took three days)! With the tickets safely booked  they had only one day to make their way to the local hospital for a medical inspection to get medical clearance (no fever!) to actually travel. 
Waiting for our medical examination to be able to board the flight from Baltra to Quito Photo: Sarah Knutie

The next day the hapless crew had to scramble to get from Malefic Island to Baltra on a ferry, requiring special curfew breaking passes to allow taxi passage to the ferry dock, being able to board the ferry, and then undertake the treacherous trip to Baltra on a boat amongst possible infected zombies. 
6am waiting for the ferry from San Cristobal to Baltra Photo: Sarah Knutie

Waiting for the ferry Photo: Sarah Knutie
The ferry ride Photo: Sarah Knutie
By the time this is all sorted out Kiyoko manages to get one of the last three tickets on the Pandemic rescue plane from Quito to Houston via her contact in Canada, as her internet kept crapping out. A chance to make it onto the North American rescue plane by the skin of the teeth!

Next obstacle, and this is a quote from one of the victims:
"We land in Quito after curfew. Which means we have to hire a taxi driver to take us to the hotel, but you need all these special permission slips to be able to get the taxi driver. We went to the website we were told to go to, and nobody could get on - Paola (our Ecuadorian friend back in Canada, who thank God was able to negotiate all the Spanish), Sarah, and I were trying to get on. I ended up opening three different browsers. When I got on the website, they said it was full and put you in a virtual waiting room for ten minutes. But then at the end, it just reset the timer. I finally managed to get on, and we got to a part that said the authorization was only for medical emergencies, so clearly this wasn't right. After a while, we figured out that we had the wrong site, Paola managed to fill in the proper form and so now we're good (NB: this took all day to do). They wouldn't even let us on the ferry if we didn't have proof that someone was coming to pick us up. So, we have all the necessary paperwork. Getting the approval to drive during curfew was extremely stressful."

Next will be a harrowing stay in the local "Fleabag" motel near the airport where they hope to scavenge food even though all restaurants are closed.  (NB: The hotel is actually quite nice)

Update from the travelers: Getting to Quito everything went fine, but it was just super long.   We had to show our medical forms to get ferry tickets. The ferry was full,  there was social distancing to get onto the boat, but once on all the seats were filled. It did have individual seats, so we weren't squished but we were still very close. There was social distancing at the airport. 


Our luggage baking in the equatorial sun
Social distancing while waiting to board the plane in Baltra 


Social distancing in the line to get on the plane in Baltra
I had to pay seventy bucks for my second suitcase which was surprising and annoying, but whatever. I'll be paying for it on almost all my flights. The flight was full, but there was no food or drink service, so I slept the flight to Guayaquil. A good chunk of people got off there, hopefully they will be able to dodge the rotting bodies thrown onto the streets in cardboard boxes as apparently no-one is picking up the dead in the city.  Then on to Quito. We were lucky  to be in the first group of people who had to be examined again before being allowed entry. 
Social distance waiting room for our medical examination upon landing in Quito photo: Sarah Knutie
Medical test in Quito before we could leave the airport
When we left there, the queue to be allowed into the exam room was really long, so we were happy to be through. The cab drive to a hotel is normally 8 bucks, but because of everything, Paola (our contact in the Galapagos) said the cab would be 20, and we should tip. We were fine with that, but we ended up giving him 40 because he helped with getting the Salvoconducto  (yes that’s what it sounds like, our salvation passage!), and then he was waiting for us for a long time, and came to where we were  very quickly when we said we were done and ready for pickup. He was very nice, wore a mask, and pulled over to look at my phone when we were trying to figure out where to go. The hotel is actually OK.  We brought food with us, we have access to a kitchen, and we can go to a tienda several kilometers away tomorrow for a few groceries. We each got our own room, and since I have the most bags, Sarah gave me the largest room. So, now in Quito at a hotel close to the airport so well away from zombies roaming the city center. No other guests on the property except us. Lots of room and we're allowed to be outside, so we're looking forward to that!!
The grounds of the hotel we stayed at near the Quito Airport
Is that our plane?!?!
Then 5, yes FIVE days later, unless the local mayor decides to blockade the airport runway with police and fire vehicles as happened last month to stop Dutch rescue planes from landing, the American rescue flight will indeed land and whisk our heroes back to the safety of the United States.  Ooops, sorry, to the zombie infested mess (thanks to a brainless president that the zombies therefore cannot eat) that is currently the United States.
Social distancing to check in at the Quito airport

An empty Quito airport

Update:  The plane actually landed at Quito as scheduled.  However more drama ensued, an email from Kiyoko while at the Quito airport describes what happened:  “Turns out this is a humanitarian flight and not a commercial flight so you have to be a US citizen to get on. They let me on only because I was able to explain that I was a dual citizen, luckily I had a scan of my US passport printed out, and was able to convince them why I did not have my US Passport (I flew direct from Canada to Quito and not through the US), plus I had proof I was leaving the US for Canada. There are two couples trying to get on the flight who were moving and one or both were not US citizens and they were being denied boarding. I have no clue what will happen to them (NB: They got on somehow). So, I might run into problems in Houston. I'll put my SIM card in and text/call you if I need you to do something like FedEx my passport. It shouldn't come to that, especially since I have things like Global Entry, but I'll keep you posted. Plane should be landing now but all the windows are frosted so I can't see out them and the gate has loads of barriers and stuff so I can't get close to the one window near the gate.  Wish me luck!”
Kiyoko with the piece of paper that let her get on the Quito to Houston flight photo: Sarah Knutie
Full fight from Quito to Houston. Masks were mandatory and a few folks had full PPE
Then they will have to brave a potentially infected hotel in Houston overnight before parting ways in the morning (NB: It was fine, but after coming from a flight where masks were mandatory, it was a bit unnerving seeing the shuttle driver and receptionists in Houston not wearing masks).
An empty Houston arrivals area
Kiyoko will then (hopefully) fly to Philadelphia, supposedly the city of brotherly love, where unfortunately, despite that city's reputation, she will not be able to interact with anyone as she hopes to dodge zombies in yet another airport hotel, for yet another possibly fateful night, in yet another infested city (thanks to the Donald - "We have it under control...one day soon it will be a miracle...it will all just disappear").

Update:  Kiyoko did make it to Philly, but it was touch and go.  Big stress the morning of the flight. Kiyoko arrived at the airport to find it "a zoo" with snaking long lines of people packed together wearing masks. I can't believe the photo she emailed me.  
The ridiculous mess at the United terminal in Houston (nobody to provide information, free for all lines everywhere, and no social distancing)
She called me to try and get a seat upgrade to be able to get thru the line and check her baggage. But no upgrades were available.  Next email:  "They apparently closed a terminal so domestic and international are in same one. Some big international flight was checking in. Once that went through it was a little better, a little less stressful.  Finally made it thru check in.  Now in security".  
I wonder if you can put adults on the TSA tables?
Next email: "Made it thru security. I really thought I was not going to make it. Closing door. Will message when in Philly".
If all goes well, she will overnight in Philly and fly out of Philly and land in Montreal on Friday, May 1st.
The five (yes five) people it took to check me in at the Philly airport
Update:  A relatively stress free flight to Montreal.  On landing, to her surprise there was no medical check or other hassle, just some questions regarding whether she had any symptoms and if she could quarantine for 14 days. It was surreal wandering through the deserted Montreal airport during the normal rush hour. This virus has really changed things!
An empty immigration area at the Montreal airport

HOME!
And then began a government mandated 14 day quarantine at home. This involved me sleeping in the spare bedroom, having room service from my partner, and wiping down with alcohol or bleach anything that I touched that was communal. But symptom free after 14 days!


Open Access

  The following is a guest post by Bob Montgomerie, Queens University, written with input from  Dan Bolnick. This was first posted on the Am...