Wednesday, January 13, 2021

Finding a Job in a Pandemic

Hello Eco-Evo Evo-Eco Blog readers! 

I've been a contributor for this blog since it started, and I'm excited to say that I'll be another co-host of the blog along with Andrew (@ecoevoevoeco) and Dan (@danielbolnick). Consider this my first official blog post as a co-host. I (@photopidge) look forward to contributing to the blog. Also, a reminder we happily take guest posts! Published a paper you are super excited about? Have an issue that you think needs addressing? Have advice? Any and all contributions are welcome so please tell us!

So who am I? My name is Kiyoko and I'm currently a postdoc with Dr. Fanie Pelletier at the Universit√© de Sherbrooke. Previously I was at the University of Cambridge and somehow, I've managed to find a job in the middle of a global pandemic. I'll be starting as an assistant professor at Brock University in Ontario, Canada in August of this year. Who would have thunk that would be possible? I certainly didn't. So here, I'll recount my job search chronicles. This isn't really a job advice post, more just a look back at my personal path to finding a job. We have many posts about finding a job (though I know many disagree with some of the advice!) such as:

How to Get a Faculty Position 1

How to Get a Faculty Position 2

Resolution: I Will Get a Faculty Position


So what was my path to getting a job in a pandemic? I finished my PhD in 2016, and then spent five years as a postdoc at the University of Cambridge. I know that academia isn't for everyone, and for those of you who want to pursue a non academic career, DO IT. but I knew I wanted to aim for becoming a prof. I limited myself geographically to Europe and North America because I have strong, personal ties to Montreal, so I wanted to be as close to Montreal as possible. I set myself a six hour flight limit (which is what Montreal-England was essentially). So, pretty much right out of grad school, I started applying for a few jobs. Job applications initially take a LOT of time. I figured this was my first foray into the job market, so I applied to just a few places. Didn't hear from them. After the first few applications, I realized I wasn't happy with my application because I was pushing a research program that didn't feel like it was MY research program.


So, I had to sit down and think about what exactly is MY research program. I work in multiple systems and ask multiple questions, so what was the link between everything? I mapped things out visually on a whiteboard (I miss my whiteboard. It's still in Cambridge and I wish I had it with me in Montreal/Sherbrooke), I looked at word clouds of my abstracts, and I asked lots of people for advice. I eventually convened on a job application package I was (relatively) happy with and felt represented me, my research program, and my teaching philosophy. I was also happy with my diversity statement as I am a big proponent of equality and diversity in STEM. With my re-vamped application package, I got my first interview about two years out of grad school. It was in North America so it was the full two-day in-person interview. I was SO nervous. I spent hours and hours on my presentation, practicing it with multiple people and thought through my answers for interview questions. The experience was fantastic. Though I didn't get an offer, it did instill in me a little tiny voice that said, 'you know what. Maybe, just maybe you can do this!' Don't worry, that voice quickly disappeared.

I continued my postdoc and fully launched myself on the job market for the 2018-2019 season. My first big season applying for lots of positions, I got a few phone interviews in North America, a few in person interviews, primarily in Europe. But I didn't get anything beyond those phone interviews, nor beyond the in person interviews. OK, I thought. I knew I was still sorting out the best way to answer interview questions. I knew I was getting hung up on certain questions, so I worked on figuring out a way to answer them. I knew the positions in some cases were going to people with established research groups (still can't figure out why I landed an interview!). But I learned things. I learned tricks to streamline the job application process. I thought more (and sought feedback) on how to answer the questions I knew I was having a hard time answering. One thing I did not realize until much later was that having experience interviewing in both North America and Europe was helping me because I had to learn to communicate effectively and be concise. In North America, you have a two day in-person interview, where you give a research talk (one hour), often a chalk talk (at least one hour), and you meet everyone. Everyone! Profs, teaching faculty, research associated, admin, facilitators, grad students, etc. You also have so called 'informal' times where you go for lunch and dinner with members of faculty. In Europe, you have a very different process. My experience was you give a research talk, which can range from 12 minutes to 45 minutes, you meet the committee (maybe 90 minutes), and you might have a tour of the facilities. It is a much shorter process than North America. Often, you are there with the other candidates. And for those in North America, it might seem odd and uncomfortable at first, but it's actually a lot of fun and even inspiring! I got to meet researchers who I've been following on twitter, met people that could lead to collaborations, and actually found the process much less awkward and more rewarding than I expected. While we were all competing for one or a handful of positions, we're all in the same boat! These group interviews were extremely collegial and inspiring! But I didn't get any offers.

 

I did get good feedback (ask for feedback after interviews, both phone/skype interviews and in person if you didn't get to the next stage). So I plugged on, attended conferences, conducted field seasons, collaborated, wrote papers, etc. For the 2019-2020 season, I started sending applications out again.  The season started decently enough. I was getting Skype and in person interview invitations, lots of rejections, etc. The usual. And then news of a novel, devastating virus emerging started to appear. However, it wasn't found in North America or Europe yet, and I continued to go back and forth between Cambridge and Montreal. I got to go to the University of Glasgow as the Darwin Day graduate student invited speaker (so much fun!) and to Barcelona to give a talk to researchers at the Centre de Recerca Ecol√≤gica i Aplicacions Forestals (CREAF). I had an in person interview in the United States at the start of March. My colleagues and I then headed off to the Galapagos for our annual field season. 

And then the pandemic was declared. For adventures on how to get from the Galapagos back to North America, you can read about it here: https://ecoevoevoeco.blogspot.com/2020/06/escape-from-galapagos-how-to-get-home.html. Well, this completely changed the job interview process (as one would imagine). The primary thing was all interviews went completely virtual. This was fine as we were all getting more and more Zoom experience, However, some things remained the same. In the UK, all the interviews are usually scheduled on the same day, with no exceptions. So if you can't make the interview on the scheduled day, you don't get to do it at all (I had to change a flight once to make an interview!). As it turned out, one of my interviews was on a travel day, and so I did my interview from the airport while waiting for my flight (directional microphone was one of the best pandemic investments I made!). This type of scheduling has also meant I've done interviews at 10pm EST (which was 3am by my body clock) at night after walking off a flight from London to Montreal (I was interviewing for a position in New Zealand. I had applied on a whim) as well as from the Galapagos. Virtual interviews do make it extremely difficult to get a sense of the department, but you can still pick up information based on the questions you ask them. The pandemic also delayed the job searches themselves. I also found out that many job searches were suspended or cancelled, and I also heard a few cases where offers were actually rescinded. One place I interviewed at had their job search suspended, which puts the department in a difficult position because they can't notify applicants that they had made offers to other people and they were no longer under consideration. Yes, they were a department that would notify all applicants once the position was filled! Anyways, the delays were difficult. I'd apply for a position in the spring with a starting date of August 1st, and after a few months, it became quite clear the job search could not proceed on the timeline the committee would have liked and the position would not be starting on August 1! For my position at Brock, it was a one day virtual interview. I gave a research presentation and a teaching demo and then had meetings with members of the faculty. I couldn't tour the university, but they did take videos for me so I could get a sense of what facilities were available. To my great surprise, Brock made me an offer, which I accepted!

So, lucky me, I managed to find a job in the middle of a pandemic. You'd think that'd be the end of the story. It is, but I want to mention one more thing. As soon as I signed, the first thing I thought was, they really don't know what a huge mistake they just made, do they? Why do they think that I'm going to be qualified to be a prof? The impostor syndrome is alive, well, and incredibly active, and I'm still having trouble dealing with it.

https://ecoevoevoeco.blogspot.com/2017/08/i-have-imposter-syndrome.html

So that's how I found a job in a pandemic. If you are curious, I applied to 56 positions/fellowships in 2018-2019 and 61 positions in 2019-2020. If I were to offer advice, it is to get lots of feedback on everything (application materials, presentations, answering interview questions, all of it!), have supporting colleagues and friends (rejections are hard. They can be really, really, really hard), and recognize your own imposter syndrome (and realize you DESERVE to be where you are and where you will go. I know easier said than done). Good luck to those pursuing jobs, no matter what sector. Also, wash your hands, wear a mask, and get vaccinated! 

Saturday, January 2, 2021

#TryHard Virtual Teaching. 2 - Place-based teaching

I have decided to release my online lectures from this fall as a "short" course on youtube HERE. This series of blog posts outlines how the lectures were developed.

#TryHard Virtual Teaching. 2 - Place-based teaching

 A critical part of my in-person teaching has always been generating a personal connection with the students - no matter how big the classroom. Underpinning those connections is a kind of "show-and-tell" conducted during and  after class. For instance, I always bring in exciting physical items to illustrate concepts discussed in the class. Highlights from my Introductory (Organismal) Biology classes over the year have been a real gorilla skeleton alongside a cast of a human skeleton, a meter tape stretched out across the room to illustrate the size of a whale shark, a (stuffed) platypus, and many more items, but especially my wife's pet ball pythons (see picture below). These physical items coupled with the lectures generated some of the most fun personal interactions with students. 


The shift to virtual online teaching was going to throw all of this out the window - the best parts of my lectures - gone. I spent months mulling how best to achieve some of this personal connection in the virtual lectures, and I settled on "place-based teaching." The idea was to pre-record a 10 min video for each lecture that showed me discussing content in a physical location where I was (or had been) present. My hope was that I could "take the students out with me" to particular locations, where I could embed concepts into a real setting with which I was intimately familiar.

I started this effort at my cabin in northern BC over the summer. I simply walked around and recorded myself making a variety of natural history observations in hopes that I would be able to inspire new content for my lectures - or illustrate existing content from past years. I did not have a pre-conceived notion of how these observations were going to fit together - I simply recorded as much as I could in hopes that I could piece together useful narratives.

When I got back to Montreal, I sifted through the various recordings to find useful aggregations - and  the first one to emerge was a group of observations involved organisms consuming other organisms: bears eating salmon, skunk cabbage, and red osier dogwood berries (from camera traps); leaf miners eating aspen popular and willows; bark beetles eating spruce trees; parasitoid wasps ovipositing in bark beetle larvae; mice eating nuts that we put out for them; wolves following moose (again from camera traps); and so on. Thus, my "introduction to ecology" lecture became centered on food webs. Here is the introductory video that I released in advance of the lecture as a way of generating a place-based connection between the students, myself, and the content. 


A lot of the footage from my cabin also related to various effects of climate change, and so the next lecture became "Ecology and Evolution Under Global Change." Here is the introductory video for that lecture assembled from recordings at my cabin combined with additional recordings from my home in Montreal.



A third place-based introductory video from my cabin centered on mammal behavior as seen through the lens of camera traps that we have deployed there.


Of course, I couldn't use my cabin for all of the "place-based" introductory videos (e.g., amphibians, reptiles, and primates) - and so I also used footage recorded in previous years from various field sites around the world. I won't show them all here - but below is the one for Galapagos (Evolution!), which was the very first one I recorded and released to the students. 


Overall, I think this "place-based teaching" approach was useful for generating a bit of a connection with the students. The next step was combining that approach with a call for "lecture collaborations" with the students. I will detail these collaborations in the next post but - in essence - at the end of each introductory video I asked the students to provide examples or pictures or videos from their local areas - and then I wove those into the remaining segments of the lecture. 

Stay tuned.

-------------------------------------------------

Here is the developing series of #TryHard Virtual Teaching

1. Promotion

2. Place-based teaching



Wednesday, December 16, 2020

#TryHard Virtual Teaching. 1 - Promotion

I have decided to release my online lectures from this fall as a "short" course on youtube HERE. This series of blog posts outlines how the lectures were developed.

#TryHard Virtual Teaching. 1 - Promotion

Like all Profs, it became apparent to me very early in the summer that all of my teaching would be online in the fall. I was teaching several courses but the most challenging was going to be Organismal Biology (Intro Biology), which has lectures and labs for 600 first-year students. This blog post is the first of a series about how we converted all labs and lectures to new content specifically for online virtual synchronous and non-synchronous teaching for - yes - 600 students. 

Some things worked and some things didn't, and we learned a lot. Although much has been written by many profs on the transition to virtual teaching, these posts might have some useful new information as we went "all in" #tryhard with our efforts. So - if you really want to go crazy - you can find some useful stuff here. 

1. Promotional videos

Early in the summer, the university administration was panicking for fear that students would - en masse - fail to "show up" as a result of perceptions that the learning experience wouldn't amount to much more than watching last year's lecture recordings. The result of dropping enrollment could be a massive budget deficit owing to lost tuition - especially from international students. So we were strongly encouraged to develop promotional videos to show prospective students that we were serious about developing new tailored-for-them online content that was exciting and engaging. I am really into making videos generally, and I teach about biology, so I figured I should "go out in nature" and record some promotional stuff to get them excited. So I produced four very short promotional videos in hopes of attracting, encouraging, and reassuring potential students that we were "on it" with respect to their education. Each video introduced some new approaches we would take - and here I will outline the basic idea for each.

1. A START. The first video was intended simply to reassure students that they would be getting exciting new content tailored for the virtual environment. So I grabbed a GoPro, hopped in my kayak, and brought the enthusiasm. I interspersed myself talking from the kayak with earlier videos/pictures of (a) me doing the "Drunkard's Walk" in a previous year's class (for an Evolution lecture), (b) my wife's ball python breeding room (from a Reptile lecture), (c) camera trap footage from my cabin (for lectures on Ecology and also on Mammals), and (d) iNaturalist (for brand-new virtual labs). The hope was to quickly (this was May 27, 2020) reassure students registering for the fall that we were going all out for them. Although I can't be sure how influential the video was in reassuring and recruiting students, it was certainly viewed a lot.


2. INATURALIST: In the second promotional video (June 4, 2020), I expanded the idea of using iNaturalist for the labs. The idea (which came from my PhD student Lotte Jensen Skovmand) was to develop labs in which the students would out into their local environments (since they wouldn't be coming to McGill and were all over the world) to make observations and share them in "projects" on this virtual free online environment. In making video, I developed some new techniques I would apply later, such as lecturing from "out there" (in this case from my dock), the use of multiple cameras recording simultaneously, screen recording on my phone and computer, editing and assembly strategies (I use Adobe Premiere Pro), doing live on-the-fly recordings, and including some "bloopers" for fun.


3. GREEN SCREEN. In the third video (June 26), I did a test-drive of green screen approaches, which ultimately proved to be exceptionally useful. The green screen set-up that I got was only about $200 CAD and it was AMAZING. The best value purchase I made for this year's effort. This test recording has a number of flaws that I gradually figured out and fixed in subsequently lectures - as I will later describe in another post.


4. PLACE-BASED TEACHING. The fourth promotional video (Aug. 19) was, I think, the most important for the teaching plan I had envisioned. My main approach to teaching when in person focuses on trying to convey enthusiasm and inspiration to the students. This approach is easy in person but very hard when remote over zoom. So I had cast about for how I might bring a personalized connection to the lectures. I decided to develop what I ended up calling "place-based teaching". The idea was to connect all of the lectures to physical places from which I could record new content directly related to the lectures I would develop later. The core focus of this place-based approach would be my cabin in northern BC. So this promotional video was of me talking to students from my cabin (where I was much of the summer) and telling them how I would use place-based teaching in my lectures.


Well, that's all for the promotional videos I recorded. In the posts that follow, I will explain how we developed this concept further, collaborated with students, refined my technological approaches, and the various mistakes and problems we encountered - and tried to overcome.

-------------------------------------------------

Here is the developing series of #TryHard Virtual Teaching

1. Promotion

2. Place-based teaching



Wednesday, December 2, 2020

When strong young people get COVID19 - twice

This post is by Chelsea Chisholm. I (Andrew) saw it on Facebook and felt it had important implications for us all. Hence, I asked Chelsea if we could tweak it for the blog.

This is a post I wrote on social media in order to try to address the rampant misinformation that I saw spreading throughout my networks back home in Canada. Full disclaimer- I'm not a disease expert, I'm a postdoc working in the domain of ecology and evolution based in Switzerland. This post was never meant as a commentary on research around Covid. It was meant to provide a personal example of my experience with Covid after being in one of the worst-hit zones in Europe two times now. The audience was people I know, particularly young people who are excellent at both ignoring health advice and being vectors for the pandemic. I hoped it would cut through the lies and confusion and convince a few people to start taking precautions while providing them with some resources they could look to for information. As far as Facebook rants go it's a long one. Nevertheless, I have had nothing but calm and generally positive comments in response, even from people who had previously posted conspiracy theories about this pandemic. So for once social media doesn't suck.


Covid update 2.0: Masks & Small Gatherings

This post was initially aimed towards my friends and family back in Canada, as I see a lot of confusion and anger running riot on social media back home. For those of you who don't know, Michael (my husband) and I contracted Covid back in February/early March. I wrote a social media post then, detailing what it felt like to go through it and asking people to consider others' safety during the pandemic. I experienced some fever and chest pain, which disappeared after a week. Michael had only a slight dry cough, but soon after developed a case of pericarditis, or inflammation of the pericardium, the sack that surrounds the heart. He spent a month with chest pain akin to a mild heart attack, a lot of this time in bed, and was then put on strict orders not to stress his heart for another four months after his inflammation kept returning. Our doctor's main concern was that he would develop myocarditis, an inflammation of the muscle of the heart which can cause permanent damage. We slow biked our way through spring and luckily his heart healed. Michael ran an ironman in September after his recovery. I say this not to show that you can bounce back from Covid, but simply to point out that the man was fit. He was not in an at-risk group for Covid. He had no pre-existing conditions. He was 34.

Fast forward 7 months to October. Throughout the summer Michael and I needed to socially distance as much as possible to prevent catching another cold or flu that could trigger his pericarditis. But as he started to feel better, and as the summer had seen such low case numbers in our region, we made the decision to start seeing a few more people. This was around the time that weather was cooling off, sending more people indoors and cases skyrocketing, so I would say this was a poor decision on our part. Keep in mind that "seeing a few more people" meant expanding our bubble from ~2 to 6. Because a few of those extra people were not limiting their interactions with others, our bubble actually went from 2 to many, and they showed up for dinner at our place infectious (but not yet showing symptoms). We caught Covid again, and for those of you who are wondering, it was not easier the second time around. Michael had a raging fever, was in bed for a week, and after eight weeks now his smell and taste are still gone. His heart rate has been all over the place, making normal things like a short run difficult. And as for me, I was diagnosed with pericarditis, the same thing Michael had during our Covid 1.0. I've been told to lay off strenuous exercise for 6 months and I've yet to go for more than a short walk/run since my diagnosis 8 weeks ago (it still hurts, and simple things like walking uphill are physically exhausting).

Cases this past week in Switzerland were in the top five worst in the world per capita, and we've now entered a second (soft) lockdown. Doctors will start triaging patients, choosing who gets to have an ICU bed and who is sent home because there simply isn't enough space. My family doctor has had to move to the hospital to assist the ICU doctors. This is in one of the richest countries, with one of the best medical systems, in the world. I've watched debates around the pandemic rage back and forth in Canada. It's the same thing that happened here and continues to happen through the lockdown. Cases are rising steadily in Canada, just as they did here. The funny thing about exponential growth is that things seem under control until they are not. It will get much worse in the coming weeks. I am not a medical doctor, but I am a scientist, and the stuff I do know a little about, the data, is troubling. I'm going to ignore the usual arguments, that this is the same as the flu (it is definitively not) and that it only affects the elderly (sorry grandparents?), and focus on the demographic that seem to vocalise the most around the pandemic. Studies vary but thus far suggest that 5-10% of people aged 18-50 who contract coronavirus will suffer long-term symptoms. This ignores other categories of people who are more at risk due to pre-existing conditions or age, in which case the probability would be higher. You might look at that and say that's quite a low risk. Think of it this way. If cases continue to rise, as they did in Switzerland, one or two (young) people who catch Covid out of every twenty are likely to experience long-term symptoms. That means someone in your friend group, a few people in your family, a few people at work. We've seen this happen already as a lot of our work colleagues and friends have been laid out with Covid, with some still not back to work or working at half capacity. A few of these people may even go on to have permanent damage that they will have to live with for the rest of their lives. It could be us. We don't know, and that's even scarier.

From what I read online, people are upset about the infringement on their rights and freedoms, either through the cancellation of social activities or the requirement to wear a mask inside. The worst is when I see people calling the pandemic a hoax. I don't want to get in a screaming match over social media, I've seen enough of that already, and honestly, it's heartbreaking (no pun intended). For those of you who have questions about what Covid is like, or whether it is real, or whether it is indeed worse than the flu (yes), I'd be happy to talk about our own personal experiences, if only to put a face to this. I am also happy to share resources about what measures appear to be working to reduce spread (see the bottom of this post).

The pandemic is hard, and some of us are luckier than others, as I'm sure a lot of struggling small business owners will attest. But I would say almost all of us reading this post are pretty well off compared to the rest of the world. We have access to medicine or live in a place where self-isolating is possible. And many of us are being asked to do our part through very simple actions, like limiting our gatherings and wearing a mask to the grocery store so that elderly people can feel more safe shopping for food. While masks are not 100% effective (neither is birth control, I might add), they help to reduce the risk of spreading the virus from you to others. These things are not that hard, and are the least we can do to help reduce the load on the many doctors and nurses who are working tirelessly to save others during this time.

And if this feels like too big of an ask, I'd suggest reflecting on how good you must have it, that wearing a mask in a store is your biggest hurdle in life right now...

 

For those of you who want resources, here's an excellent graphic on how masks can work to reduce spread: https://www.nytimes.com/.../wear-mask-covid-particles-ul...

Here's a dashboard created by Nat Geo which does a really nice job of illustrating your risk of Covid in different environments (public transport, bars, restaurants, etc.). This shows that mask-wearing during your day to day (transport, shopping) can really help to protect you and others. It also shows that the longer you are in a room with someone (public/private gatherings), the more likely you are to catch it, even if everyone is wearing masks, so limiting indoor gatherings is really important.

https://www.nationalgeographic.com/.../how-to-measure.../

A recent paper that suggests limiting small gatherings, shutting schools and increasing availability of PPE are the most effective measures that governments have taken thus far to reduce the spread of the virus.

https://www.nature.com/articles/s41562-020-01009-0).


Friday, October 23, 2020

Data Archiving (and 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.

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