Saturday, April 7, 2018

Undergrad the Impaler

Editor's note (from Dan Bolnick): The following is a reflection written by Cole Thompson, who was an undergraduate at the University of Texas at Austin and worked in my lab from 2013 until his graduation in 2015. Cole is now a PhD student at the University of Texas. From his work in my lab, he produced a first-authored paper and was a co-author on two other papers.

I arrived on the University of Texas at Austin campus in August 2011 excited by the opportunities that college would provide me. I had chosen UT largely in part because of the excellent science departments. However, as sophomore I was still looking to find my place on campus. On a cool January day walking the halls of one of the building I had class in, I found a poster searching for students interested in doing biological field work in Canada. Excitedly, I sent my resume to Dr. Dan Bolnick. He shot me back an offer to meet him and discuss the summer work—an NSF funded project on the parallel evolution of three-spine stickleback in evolutionarily independent lake-stream pairs on Vancouver Island. At the meeting he offered me the summer position and I accepted, unaware of how great of an impact this would have on my life. 
As I learned later during my time in the lab and undergraduate studies, Vancouver Island is an ideal location for examining how parallel evolution has occurred. As most readers of this blog will know, stickleback colonized lakes and streams on Vancouver Island about ~12,000 years ago after the last ice age. The result is many replicate pairs of neighboring lake and stream populations.
Finally, the spring semester ended and we were slated for a May 21, 2013 departure, but I excitedly and mistakenly arrived for departure a day early. The next morning, arriving at the correct time I met Dr. Yoel Stuart, the postdoc running the parallel evolution project, as well as Dr. Travis Ingram, another post-doctoral researcher conducting field work on the assortative mating of stickleback on Vancouver Island. Our trip began with a four day drive from Texas to British Columbia, which showed the beautiful side of the western US, and as we approached British Columbia I disconnected from the grid and my excitement for the summer grew. Once we arrived at our cabin on Roberts Lake, the real work began--sorting through fish traps, labeling tubes for storage of fins and eggs, preparing tea bags to store fish, and learning the codes for assessing the habitat surrounding the trap as part of gathering the ecological data for each fish trap, and, most importantly, dealing with the constant rain. 
After a couple of days of preparing materials we went to the first site—Comida Lake. The process, which was to be repeated for 16 lake-stream pairs, began. After bushwhacking to the site, 50 traps to collect the fish were set, recording their GPS coordinates and marking the time placed in the water. Then the depth, trap habitat, and flow rate (if applicable) were measured while a couple members built a processing location where trapped fish could be sacrificed and then weighed, measured, and have their fin clips cut for DNA sequencing. After two hours, the traps were checked with the stickleback taken for processing. This was done until 80 fish had been collected. After all the fish had been collected, the four most productive traps were identified and samples of the substrate and zooplankton tows were taken at each of their location. Then we used a spectrophotometer to measure the amount of down- and side- welling light at water level and one and two meters below the surface. The first site proved that this summer was exactly what I had hoped, and as I stood in the 50 degree water in the pouring rain with my hands barely able to move I was thankful to be doing science.
After a week of working on lakes close to the base camp, we moved to the northern part of the island to begin collecting at a different watershed, heading out to Joe Lake on June 3rd, 2013. In the early afternoon, while transporting fish to the processing station, I impaled the bottom of my foot. A sharp branch edge sliced through the boots of my waders, my sock, and an inch into my foot. Surprised by this, I gingerly finished transporting the fish I was carrying and then calmly sat and irrigated the wound with sterile iodine solution. Luckily most members of the field team had been asked to take a weekend-long wilderness First Aid class before going to Canada, a time investment that paid off. . After initial first aid,  we headed to the Port McNeil hospital. The result of the injury was not so bad, just stitches and crutches. There goes my summer, I thought. 
Cole, after his injury
Fortunately not so. Dr. Ingram, with the assortative mating project, took me onto his project. His team needed a boater who would row around on a pontoon in support of snorkelers who were sampling nest sites. From the boat, I could transport fish and eggs and record environmental data more easily than the snorkelers. Luckily for me, I could row without applying too much pressure on my foot or risking getting it wet. I jumped at this opportunity to help the team’s data collection efforts, which were going to help understand if stickleback in each lake mated according to similarity in diet. This was done by checking the carbon and nitrogen isotope ratios from the eggs in the clutch; which served as a proxy for the female diet, against the isotope ratio in a muscle clip taken from the male stickleback defending the nest. I spent the rest of the summer field season passing the hours on the little pontoon inflatable rowboat taking in the beautiful Canadian landscape, which like the boating, continually took my breath away. 
From left to right: Yoel Stuart, Cole Thompson (the author), Andrew Doggett (a high school teacher), and Brian Lohman

Once the field season ended I continued working in the lab performing DNA extractions and morphometric analysis on the specimens collected on Vancouver Island until the end of the summer. During this time I became awed by being part of the scientific process. I was doing science. Not only had I helped collect specimens, but now I was generating data for analysis and I wanted to find out what the data said. To do that, I began volunteering in the lab after my summer contract ended.  I sorted through benthic samples, took pictures of the fish we collected, used these pictures to measure differences in morphological traits, dissected out gill rakers and gut contents, examined gut contents for parasites, and transcribed ecological data. I couldn’t get enough. I wanted to learn how the environment and evolution has shaped these fish. As we sorted through the data, our preliminary data from the pictures of the fish showed that some lake stream pairs are evolving in a parallel fashion but this could be entirely antiparallel to other lake stream pairs, showing that there is clustering in directionality, but no steadfast uniformly parallel direction of evolution that holds across all watersheds. Dr. Yoel Stuart worked tirelessly on this project, and with help from Dr. Bolnick, formalized his findings on parallel evolution in the lake and stream in a Nature Evolution and Ecology in May 2017 titled Contrasting effects of environment and genetics generate a continuum of parallel evolution, showing that the environment dictated the direction of evolution, but genetics dictated the extent to which evolution occurred. My field and lab work earned me co-authorship on this paper.
Invigorated by my experiences in the lab thus far, I wanted to work in the lab again the following summer and with help from Dr. Bolnick and Dr. Stuart, was awarded an undergraduate research fellowship and an NSF-funded REU (Research Experience for Undergraduates) fellowship for summer 2014 to work on my own independent project in the Bolnick Lab. This project, examining the parallel evolution of jaw morphology and biomechanical values such as suction index, would be an extension of the work I had helped with the previous summer. For this project, I would excise the jaws of fish I had previously processed and take pictures of the jaw to calculate different metrics related to jaw function. With this I got to further embody the scientific process---creating hypotheses and synthesizing the results into a manuscript in addition to data collection, processing, and analysis I helped with the year before.

I worked, and worked, and worked on this project from summer 2014 until the November 2017 Evolution publication titled Many‐to‐one form‐to‐function mapping weakens parallel morphological evolution(Thompson et al 2017 Evolution). The results from my data collection and functional calculations showed that there is increasingly weak parallel evolution for biomechanical systems in which there are a greater number of morphological combinations that can generate the same functional output. That is, systems that are one-to-one in form and function are more parallel to each other than systems that are many-to-one in form and function, as there are multiple solutions that generate the same value.  I also collaborated with a fellow undergraduate Newaz Ahmed documenting the not-so-parallel evolution of brain morphology in these stickleback (Ahmed et al 2017 Ecology and Evolution).
During this 3 year process, with lots of help from Dr. Bolnick and Dr. Yoel Stuart, I did things I never thought I could do, or would do, like using R, a statistical software, to test our data, and help write a formal manuscript for publication; which, even with lots of encouragement and help, sometimes felt like an impossible task. Even so, in parallel to this project, I filled my life with lab-related things. I helped assist two other major projects in the lab, made life-long friends in the lab, found a quiet study place in the lab, met my wife across the hall from the lab, and learned about evolution, immunology, statistics, and countless other subjects while in the lab. In short, I spent the rest of my time in undergrad in “my place” at UT: Dr. Bolnick’s lab. 
Cole and Lauren got married last summer!
And now, almost 5 years since my first trip, I am thankful for the opportunity to go to Canada, do field work, and be a part of the scientific process—which to this day, has been the most influential experience of my life. 

Papers cited (blue names indicate undergraduate or K-12 STEM teacher co-authors:
Ahmed, N., Thompson, C D.I. Bolnick, Y. Stuart. 2017 Brain morphology of the threespine stickleback (Gasterosteus aculeatus) varies inconsistently with respect to habitat complexity: A test of the Clever Foraging Hypothesis.Ecology and Evolution7: 3372-3380.
Stuart, Y.E., T. Veen, C. Thompson, T. Tasneem, N. Ahmed, R. Izen, B. Doggett, D. Hanson, B. Lohman, K. Peichel, A.P. Hendry, and D.I. Bolnick.2017. Contrastingeffects of environment and genetics generate a predictable continuum of parallel evolution. Nature Ecology & Evolution. 1, 0158.  

This final part of the post is a video. Cole liked to video himself when he was on the pontoon rowboat and no snorkeler needed himself. He would babble about nothing in particular. We found a bunch of these kinds of videos on our GoPro cameras after the field season. And he probably never thought these would resurface to embarrass him. Little did he know.

There are more where this came from...

Tuesday, March 27, 2018

The 17 Types of Graduate Student - by GRR Martin

The “16 types of graduate student by JRR Tolkien” was extremely easy to write, and the various characters Tolkien described very nicely matched with various supervisor types. The present post on the “17 types of graduate student by GRR Martin” was much harder to write - partly because characters in Game of Thrones don’t match so cleanly onto student types, and also because all the Game of Thrones characters seem fundamentally flawed. Stated another way, most Tolkien characters are inherently good, with perhaps a few temporary flaws; whereas most Martin characters are inherently bad, with perhaps a few temporary redeeming qualities. Thus, please read the following not as an attempt to describe actual graduate student types but rather to envision the various GRR Martin characters as if they were graduate students. In truth, graduate students have many more positive qualities than Game of Thrones characters.

The Khal Drogo

The Drogo is extremely capable in field situations, including managing huge field crews with difficult logistics in uncompromising environments for long periods of time. However, he isn’t very intelligent, doesn’t publish much, and – it seems – would prefer to just stay out in the field rather than having to deal with committees and reviewers and administration.

The Ned Stark

This student is a zealous advocate of open science, data sharing, pre-registration, systematic meta-analyses, data archiving, open access, and all forms of transparency in science. He is much admired by other students for these stances, even though they would never seek to emulate his puritanical approach. Unfortunately, this warts-and-all approach to writing papers leads to frequent rejections from major journals, which – curiously – only strengthens his resolve.

The Viserys Targaryen

The Viserys is the son of a famous Professor – and he never hesitates to remind everyone of it. He seems to think that his pedigree entitles him to success without much effort – and he is extremely annoyed by rejections from journals and, in fact, any form of criticism. Owing to his obnoxious sense of entitlement, this student could well be kicked out of the department if the Qualifying Exam or Defense committee are too irked by his attitude.

The Jon Snow

Jon Snow’s current Professor agreed to supervise him at the request of the Chair of the Graduate Training Committee when the Snow’s former supervisor retired pre-maturely. His new supervisor accepted this role on condition that the Jon Snow would fund himself and not take up space or resources used by the other students. Despite all of these constraints, the Jon Snow is very hard working, serious (perhaps overly so), and dedicated. He turns out to be an exceptional, if understated, student who will start his academic career at a tiny undergraduate college but will ultimately be recruited to an Endowed Chair at Harvard.

The Daenerys Targaryen

For the first part of her graduate degree, she shared an office with a Viserys and – as a result – suffered from a serious imposter syndrome. Once the Viserys was kicked out of graduate school, however, she really came into her own and, in fact, (re)discovered a new methodology (three of them, in fact) that have made her one of the most influential and sought-after graduate students for collaboration. She seems destined for a position at a major research university, although she will face considerable challenges imposed by jealous competitors.

The Walder Frey

This student worked for a long time in the lab of one Professor, who advised and funded all of the research. Then, just before submission of the paper, the Walder switched to the lab of a competitor, taking all of the data with him and dropping his original supervisor from all the papers.

The Tyrion Lannister

Supremely intelligent, the Tyrion sometimes seems to squander his abilities and talents in food, drink (lots of it), and various social activities. This joie de vivre is somewhat understandable as his previous supervisor was mean and condescending, never giving the Tyrion credit for any of his discoveries. With a more understanding and appreciative supervisor, however, the Tyrion will cut back on his socializing (if not his drinking) and generate extremely novel and inspiring ideas.

The Littlefinger

From day one (and probably well before that), this student has been relentlessly maneuvering everything and everyone in an effort to maximize his career advancement. He is extremely effective at twisting any given collaboration to his favor, such that he now has a very good publication record. However, as time as gone on, his manipulative tendencies have become more widely known and he runs the risk of being blacklisted by the academic community.

The Cersei Lannister

Deceptively clever, the Cersei is rising quickly within her field, collaborating with important people (although they don’t always seem better off for it) and publishing many papers (although some say the work isn’t really hers). Rumor has it that much of her success comes from stealing the ideas of other students and undermining the success of her colleagues by providing withering reviews of their papers and grant applications.

The Tywin Lannister

The Tywin has published many excellent papers and intends to keep doing so. He is smarter than most (perhaps all) of the people around him – and he knows it. He has a hard time concealing his contempt for others, even his supervisors. He will go far in academia – but no one will like him.

The Brienne (of Tarth)

Highly skilled and loyal (almost to a fault), the Brienne will do whatever her supervisor asks of her, quickly and efficiently, without any complaint whatsoever. It isn’t clear that she has the independence to run her own research program, but she is very good at improving the research of those around her. At the same time, her intensity and dedication to principles can sometimes off-put those around her.

The Brandon Stark

The Bran seems to think on another plane. It isn’t so much a book-smart type of intelligence but rather a more intuitive, gut-feeling approach to academic topics – or so it seems. When he asks questions in seminars, no one can understand them – but it is nevertheless clear they are extremely insightful. He sometimes seems to know the outcome of an experiment even before it starts and he has an amazing recall for past details of scientific studies – even unpublished ones in which he wasn’t involved. He will only publish once – but it will likely win him the Nobel Prize.

The Jaime Lannister

When the Jaime was a senior graduate student, he blew the whistle on misconduct by his supervisor, who was then censured by the university and has disappeared from academia. Although some laud the Jaime’s action in this case, other supervisors have been reluctant to take him on. As a result, he is a quite jaded and often makes acerbic comments about the whole process of graduate school. Deep down, however, he just wants to do good science – although he has some pretty weird relationships with other students.

The Robert Baratheon

You have never met a person who enjoys living quite so much as the Robert. He is the life of every party and this popularity has carried forward to many collaborations and supporters, generating some outstanding papers. It seems, however, that his hard-living ways might be getting the most of him and he could flame out soon.

The Arya Stark

The Arya applied for a series of international fellowships and has been away for much of her degree. On her return, she is much more mature and experienced, having picked up a set of extremely rare and exceptional research skills, although it isn't clear she always uses them for the best purposes.

The Davos Seaworth

This student came from nowhere and, through simple hard work and dedication, has risen to a place of influence within his field. He has exceptionally good advice for other students in the lab and will – occasionally – directly disobey the wishes of his supervisor. Yet, whenever, he does so, it seems he made the right decision after all. He is extremely humble, almost annoying so, and would probably turn down an academic position on the excuse that he isn’t really worthy.

The Sandor Clegane

Another very capable student, he suffers one major flaw – he is terrified of snakes, even though his research is conducted in tropical environments abounding in them. Ok, perhaps he suffers several flaws, another one being his taciturn and blunt criticism of ideas he deems uninteresting and experimental designs he considers flawed. It seems clear that, deep down, he would really like to be a Professor and has the skills to do so; yet his difficult personality might preclude this.

Thursday, March 15, 2018

The 16 types of graduate supervisor – by JRR Tolkien

(Genders match the original.)

The Gandalf
Extremely wise – if sometimes inscrutably so – and able to solve your biggest problems, the Gandalf is often absent for long periods of time. And these can often be the most inconvenient times for him to be away. In his defense, these absences are often for extremely important meetings or to deal with problems in his collaborative network. Don’t count on the Gandalf for much day-to-day help with minor tasks but, catch him at the pub, and he will be fun and a fount of wisdom.

The Boromir
He is very good at solving your day-to-day problems, yet he does so reluctantly and seemingly without enjoyment. He is very skeptical of your ideas and will only let you pursue them when your committee guilts him into it. Often brooding, you get the impression that the Boromir might not like you. Indeed, he might be stealing your ideas and publishing them separately – although he will feel extremely guilty about it.

The Faramir
The Faramir had a famous PhD supervisor who is still active, and he has a bit of an inferiority complex about it. He is very sincere and helpful but often tries to adhere to the ways of his previous supervisor, even though they don’t really work that well for his own students. Fortunately, a well reasoned argument can usually shift the Faramir around to your way of thinking.

The Galadriel
The Galadriel is a giant in her research field and, if you are hard working and enthusiastic, she will provide you with tons of resources and moral support. She designs and constructs her own laboratory and field equipment, which is exceptional. However, she doesn’t travel much owing to a dependent husband, and so you are on your own in the field and at conferences. Also, very occasionally, she has this intense look that is very intimidating.

The Saruman
Long past the normal retirement date and having won the most prestigious prizes in his field, the Saruman is not satisfied and wants more fame. He will take a lot of graduate students but will ruthlessly use them to advance his own career and fame. He has a huge lab but will make you work long hours in poor conditions, and yet still try to make you feel like he is doing you a favor.

The Denethor
Nearing retirement, the Denethor is at a famous university but is perceived as one of the lesser lights there. He knows people think this of him but won’t accept it and so routinely lashes out at his students and denigrates them as a way of feeling better about himself. He has a huge lab with tons of money, but he is constantly afraid that the university is trying to take it away from him. Don’t expect much understanding from this type of supervisor.

The Eowyn
A brilliant scientist, she doesn’t get the recognition she deserves. Yet she forges ahead in her research, publishing excellent papers that, sadly, don’t tend to get accepted at the best journals. She is a bit jaded now and, while supportive, seems not to pay much close attention to your project. All her focus is on that elusive first paper in Science.

The Samwise Gamgee
Working at a small liberal arts college, the Gamgee is the ultimate micro-manager, always looking over your shoulder offering help and advice. He has a good understanding of basic lab and statistical procedures but doesn’t seem to have many truly original ideas. Yet the Gamgee is always there for you, offering what (little) funding he has and supporting you in your success and your failures. You sometimes get the feeling that he has come to think of your success as his crowning career achievement.

The Aragorn
Quiet and reserved, this supervisor is the ultimate skill-master. If you need to analyze your data, he can write the scripts. If you need to find that rare species, he is the only one who can do it. He doesn’t publish very much, but the few papers he does publish are very good – so good in fact that they could probably all be in Science. However, he really doesn’t want the hassle and so usually submits to much lower journals – unless encouraged (pestered almost) repeatedly by his colleagues to shoot higher. Unfortunately, the Aragorn doesn’t seem to enjoy his job very much and would probably rather be off somewhere hiking or climbing mountains.

The Pippen
Like the Gandalf, the Pippen is often absent but, unlike the Gandalf, not for work-related purposes. He is usually surfing or fishing or just hanging out somewhere. He sure is fun though, especially when hanging out with his prof buddy from down the hall. Great lab parties, with tons of food and drink and lots of laughter and activities, some scripted and some impromptu. He really wants to be your buddy is constantly trying to get you to smoke weed with him. Unfortunately, the Pippen doesn’t really have any skills to impart and essentially never publishes. Don’t choose this advisor if you hope for a career in academia.

The Radagast
This supervisor is extremely absent minded and really doesn’t pay much attention to you, yet it is hard not to be inspired by his sheer enthusiasm for the world around him. You will be his only student – and, much of the time, he won’t even realize it.

The Sauron
His lab is dark and dirty, and it smells bad all the time. He is in constant conflict with pretty much every other person in his field. You would think no one would be in his lab, but he is so powerful and influential that many flock to work with him – although they don’t seem to be very happy about it. When visiting during your recruitment, he won’t let you talk to his students (save this one really weird guy), nor will he meet with you except by Skype – with the video turned off.

The Elrond
This guy has been around for ages and knows EVERYBODY, often initiating huge collaborative projects. He can really hook you up with the best and brightest people, whose respect he commands. But, having done so, he has seemingly impossible expectations for your project. He is quite aloof and rarely travels but, just when your need is direst, he can show up unexpectedly with a critical influx of cash or equipment.

The Theoden
Early in his career, the Theoden had some very influential papers – but his fame and fortune have faded owing to vindictive competitors in his field. Fortunately, you could be just the person to rejuvenate his career if you have the patience and self-motivation. If you can shake him out of his lethargy, he will invest all his resources in you and plan to finish his career in a last blaze of glory, thus resuscitating his career and showing he wasn’t a one-hit wonder.

The Grima
This advisor has risen to a place of influence not because of any concrete scientific skills but rather because he has a knack for flattering the right people. He is a real creep and seems to have all sorts of unsavory designs on his students. He might even be faking the data in the few papers he has published, which – to everyone’s surprise – are sometimes in very good journals.

The Smaug
He has tons of money but is extremely stingy about it. He expects you to obtain your own funding for everything and then he takes most of it from you. No students have successfully graduated from his lab, yet his arrogance could be his downfall.

Stay tuned for – the 16 types of graduate student – by GRR Martin

Monday, March 12, 2018

My graduate school turns 100 - reflections

The School of Aquatic and Fishery Sciences at the University of Washington is turning 100. I was asked by the Director, Andre Punt, to provide a short personal narrative of my time there. This blog post is a draft of that narrative.

When I walked out of my last exam in my final year of university, 1991 at the University of Victoria, I cold-called my intended PhD supervisor, Tom Quinn. I gave a long, reasonably well-prepared spiel about my passion for salmon and my desire to do graduate work in his lab. A modest silence followed my monologue and then a “Well, it sounds like you would make an excellent graduate student but, unfortunately, you missed the application deadline by 6 months.” Momentarily crushed, my enthusiasm recovered when he suggested that I come work for him over the fall. Thus began a 7-year stint with Tom at the School of Fisheries; starting with a fall working on chum salmon at Kennedy Creek in Washington, then a winter working with sockeye salmon fry exiting the Cedar River in Seattle, then a summer in Alaska working with the Fisheries Research Institute (FRI - of the School of Fisheries) camps Wood River – at that time lead by Don Rogers as well as at Lake Nerka and Iliamna Lake. FRI has now morphed into the Alaska Salmon Program

Me in 1992 at Iliamna, Alaska.
The next year I met the deadline for application to graduate school, applying at the same time for a graduate scholarship from the Natural Sciences and Engineering Research Council of Canada (NSERC). In the spring, I received a letter from NSERC denying me the option of taking my MSc scholarship to Washington University on the grounds that it didn’t have a very good fisheries program. I wrote back politely – but without much hope – to first agree with NSERC that Washington University indeed was not well known for its fisheries program but that the University of Washington was – and that it was the latter at which I wished to pursue my studies. All was well regardless as I received an H. Mason Keeler scholarship that enabled Tom to take me as a student and, a few months letter, I received a letter from NSERC saying, effectively, “Oops, sorry, our mistake. Here is your scholarship.”

Having just had a formative and inspiring set of field experiences in Washington and Alaska, I suggested to Tom that I do my MSc on topics similar to those the projects on which I had been working. Tom, as always, listened politely and then suggested I instead work on rapid evolution in Lake Washington sockeye salmon that were introduced earlier in the century. This suggestion turned out to be exceptional as it started my path to being one of the forerunners – along with my office-mate Mike Kinnison – in the study of rapid evolution. At the same time, I met the great – and ever enthusiastic – Fred Utter who helped me do my first genetic work with allozymes – and still, sadly, my only hands-on genetic work. Of course, all was not always smooth sailing, especially when the boat – the Nettie H – I had worked on for the FRI test fishery in Bristol Bay, sank a few months later while crab fishing, causing the death of all on board, including Blake Grinstein, the Captain for my two years working on the test fishery.

Blake Grinstein surveying the test fishery catch.
Having had my MSc project suggested to me by my supervisor, I decided I needed to do a PhD all my own. I therefore suggested to Tom a project at Pick Creek, Alaska, on the reproductive energetics of Pacific salmon. Then followed two extremely intensive summers of field work at the Lake Nerka camp, not only conducting research but also having a wonderful time experiencing – and photographing – nature. 1995 was particularly memorable for probably 50 bear encounters, most of them pleasant and inspiring but some of them rather scary. I continued to work at Lake Nerka until 2000, even after graduating, making it an even 10 summers of Alaska work with FRI. These years included the first research visits to Lake Nerka of Ray Hilborn and Daniel Schindler, both of whom still work there, as well as visits by crazy drunk Soviet fisheries biologists and crazy drunk Norwegian fisheries biologists.

The Lake Nerka camp, early 1990s.
The School of Fisheries at the University of Washington, now the School of Aquatic and Fishery Sciences, was an outstanding experience for me. I am especially appreciative of my supervisor Tom Quinn, who gave me some great ideas, who shaped my manic approach to manuscript editing, who encouraged me to explore collaborations with others independent of him, and who had a knack for filling his lab with an exceptionally synergistic and energetic group of students. Especially formative for me was having my desk directly beside Mike Kinnison, now a Professor at the University of Maine, for 7 years. Although we played Doom and then Doom II with a serial cable linking our computers between 10 pm and 1 am, we actually did research for at least as many hours before that.

While I worked on "rapid" evolution in Lake Washington sockeye,
Mike Kinnison worked on "rapid" evolution in New Zealand
chinook salmon. He helped me. I helped him. I got the better deal!

Thursday, February 15, 2018

To what extent is evolution predictable, and why?

<Posted by Dan Bolnick on behalf of Patrik Nosil>

Evolution is often portrayed as a descriptive science, rather than a predictive one. Nonetheless, time series data on ‘evolution in action’ can be used to quantify the predictability of evolution. In this week’s issue of the journal Science we published an analysis of the predictability of evolution in the stick insect Timema cristinae (Figure 1), using a 25-year longitudinal study of morph frequencies, experiments, and genomic analyses.

Figure 1. The focal species (T. cristinae) used to study the predictability of evolution. Credit: Moritz Muschick.

We find that the evolution of both color morph (green versus melanistic individuals) and pattern morph (striped versus unstriped individuals) frequencies is strongly influenced by selection, yet the two traits differ in the predictability of their evolutionary dynamics. Color morph frequencies are only modestly predictable through time, because they are driven by multi-faceted and complex selective regimes that are still poorly understood. In contrast, pattern morph evolution is highly predictable, being driven by a more understood process that causes consistent up and down fluctuations in morph frequency, namely, negative-frequency dependent selection. Thus, evolution might often be as predictable as the types of mechanisms driving it, and our understanding of these mechanisms – good understanding of natural history and selective environments can lead to greater predictability.

In this post, I’ll offer a brief historical perspective on the making of the study (rather than give a detailed account of our paper, for which I direct interested readers to the article itself). My own interest in the predictability of evolution dates back to when I was a graduate student, and read the now classic 2002 paper in Science by Peter and Rosemary Grant about unpredictable evolution in Darwin’s finches. It struck me then that the real problem here was predicting the weather, because if that could be done then subsequent effects on seed size distributions and the evolution of finch beaks might be predicted. My interest in limits on predictability was peaked, but I had to wait two decades to accrue the date required to publish on it (in terms of a temporal context like the finch study).

Figure 2. Collecting stick insects. Credit: Moritz Muschick.

From the years 2000 to 2017 inclusive I collated data on morph frequencies in T. cristinae in the hills around Santa Barbara, California (Figures 2 and 3), and Cristina Sandoval (who introduced me to the system) contributed data from the 1990s. I proofed the data and centralized it into a master database over a recent summer. When asked why I was doing this, my reply was ‘I don’t know, something will emerge’. Patterns consistent with the conclusions above emerged from the time series data. This was interesting, but not sufficient to establish causality. We thus used genomic analyses to bolster the evidence for selection, and experiments to test for sources of selection, such as negative-frequency dependent selection. The story was coming into place, but we still did not have the focus required to write a compelling paper. After reading Jonathan Weiner’s book ‘the Beak of the Finch’ and having pub discussions concerning the role of deterministic versus random events in evolution, we were finally ready.

The manuscript was then written, many years after the seed of interest was sown. It’s now published, and we conclude that our constrained understanding of selection and environmental variation (i.e., limits on data and analysis), rather than inherent randomness, can limit ability to predict evolution. In terms of eco-evolutionary dynamics, these limitations may affect our understanding of ecological processes, because to the extent that evolution can be predicted, perhaps so can its consequences for population dynamics, community structure, and ecosystem functioning. In T. cristinae specifically, changes in morph frequency affect bird predation, which in turn can affect entire arthropod communities and plant herbivory (e.g., Farkas et al. 2013 Current Biology). Thus, limits to predicting evolution within species may be data based, with far reaching consequences for interacting species.

Posted by Patrik Nosil, from the Horseshoe Canyon Ranch in Arkansas.

Figure 3. Typical habitat in which T. cristinae is collected. Credit: Aaron Comeault.

Monday, February 12, 2018

Gaia, cancer, and the “holobiont”.

I just got back from a trip to Dalhousie University, to which I was invited by grad students to speak in the Department of Biology. Among the many interesting conversations was one I had in which Gaia and cancer somehow came together. My host, Sarah Salisbury, and I were speaking with Dr. Ford Doolittle and Andrew Inkpen, about their ideas on how natural selection might act at the level of processes – as opposed to the “things” that generate those processes. I won’t spill the details as they will be outlined in a forthcoming paper of theirs. However, I did want to relate how we got from Gaia to cancer and, then, during the course of writing this post how I ended up at the holobiont. (Get ready for a lot of “scare quotes” as I try to extend terminology in each of these areas to the others.)

Dalhousie is 200 years old - how cool is that. 

According to Wikipedia, the Gaia hypothesis “proposes that living organisms interact with their inorganic surroundings on Earth to form a synergistic and self-regulatingcomplex system that helps to maintain and perpetuate the conditions for life on the planet.” One way of framing this hypothesis is that global ecology and the evolution of life feedback to one another in such as way as to facilitate and maintain life on earth. Taken to extremes, one could say that natural selection favors the self-regulating feedback itself as life would otherwise cease to exist – but how would we ever test this hypothesis?

Here is the top hit in a Google search for "Gaia". SOURCE

In group selection or “higher-level selection” arguments of this sort, one would normally need multiple entities with heritable traits influencing differential “survival” and “reproductive success”. In the case of Gaia, then, we would need life originating on multiple planets among which selection was then occurring – because it is impossible to have selection among things if you only have one thing. Of course, one might argue that selection has indeed acted in this way and that our planet (or others we can’t perceive) is the only one left – because life did not evolve synergistic self-regulation on other planets and therefore went extinct. Or one might argue that selection on our Earth has weeded out organisms that do not participate well in this synergistic self-regulating system. Any of these speculations could well be true, but it is impossible to study such processes in the real world because we only have the one world.

Or do we really only have one world? As we were discussing Gaia, I started to think that perhaps we could use cancer as a Gaia model. Consider the similarities. Cancer starts with a single cell than then proliferates into a great diversity of descendent cells; much as current life on Earth has proliferated and diversified from a single initial cell. Then, the cancer that proliferates on an individual “host” organism will (in most cancers) leave no descendants when that organism dies; just as we might expect that (barring colonization of new planets) life on earth will cease to exist when the Sun has run its course. In addition, cancer can kill its host and be the reason for its own extinction, as well as most other life occupying that host; just as some life – us perhaps –could severely damage the Earth and kill much of the life on it. Thus, perhaps we can view cancer as a lineage of organisms proliferating on its own finite planet that, should the cancer disrupt the synergistic self-regulation of that planet, the cancer itself and much of the life on that planet will cease to exist. Considered in this way, perhaps we can – at least for the sake of argument – speculate on how cancer and its proliferation in individual hosts might yield insights into the Gaia hypothesis.

An awesome book on cancer.

When I started this post, I was thinking that much of the analogy from cancer would seem to parallel ideas supporting the Gaia hypothesis: for instance, “nicer” (as opposed to “meaner”) cancers should leave the host alive longer, nicer cancers should enable the persistence of more life on the host for longer, and so on. Indeed, all of these things are true. However, it now seems to me that one fact runs directly counter to the Gaia hypothesis: cancer exists, is common, and routinely kills its host. This fact might be taken to mean that selection does not generally favor a synergistic self-regulating system in the context of cancer and its “planet”. Why might this be? I speculate it is because cancer (the non-heritable kinds) are never transmitted to other hosts – that is, to other “planets.” In this case, selection would never favor cancer being nice to its host because, no matter how long the host lived, the cancer would never be passed on: as opposed to infectious/transmittable diseases of hosts where selection can indeed favor reduced virulence. For this reason of non-transmissibility among hosts/planets, presumably selection cannot act among the cancer/life on different hosts/planets to favor synergistic self-regulating systems on those hosts/planets.

Ok, wait, you might say, cancer is actually nice to its host because it rarely strikes before reproduction: however, the reason here isn’t selection on the cancer but rather selection on the against alleles in the host genome that increase the chances of pre-reproductive cancers. That is, it isn’t selection on the inhabitants of the hosts that favors synergistic self-regulation, rather it is selection on the host itself. Unlike hosts, however, planets do not have genomes that can be selected to “punish” lineages (species) that are not nice to the overall system. Or is that true? What if we consider all life on the planet as its genome – in this case, the “genome” of a planet perhaps could be selected to eliminate parts of that genome that do not promote self-regulation. That is, life could self-police itself through elimination of non-cooperative life. Interestingly, even this analogy could perhaps be extended to the cancer scenario: all the genes in a host, including all genes in all species living on or in that host (the so-called “hologenome” or “holobiont”), could be selected to act against cancers that are detrimental to the host itself.

The top hit on Google for "hologenome". SOURCE

I am not sure if any of this is useful in anyway, but it sure is interesting – to me at least. I have no intention of actually studying or testing these ideas in any way, but I have certainly been interested in the evolution of cancer for some time. For instance, here is a previous post in which I speculated about the fundamentally different problem posed by cancer relative to other forms of life that are detrimental to humans. In addition, I have recently become very interested in the microbiome (a key part of the holobiont) as regulator of fitness and adaptation. Indeed, just today, my student Lotte Skovmand, had her qualifying exam, which she passed (Congratulations Lotte!), in which she will examine the drivers of microbiomes in plants and howler monkeys. Perhaps that is how I got from Gaia and cancer last week all the way – today – to holobionts. Nothing like colleagues and students to get you thinking about new things!

Monday, February 5, 2018

Why have a gatekeeper, and who should it be?

Let's face it: scientific publishing is changing, fast. Open access journals. Online-only journals. Preprints. Post-publication peer review. For-profit redistribution services like or Researchgate that siphon web traffic away from the original publishing journals, to their detriment. Predatory journals.  Accelerated peer-review. Double-blind peer review. Open Peer review. Et cetera, and then some.

There are, without a doubt, good ideas in there. And, there are ideas that are maybe utopian but impractical. Open to abuse, or just not likely to work well in practice. So, when a new idea pops up on the landscape, it is worth taking skeptical notice. This past week, the President of the Howard Hughes Medical Institute, Erin O'Shea, co-authored a policy essay, "Scientific Publishing in the Digital Age" with the HHMI Chief Strategy Officer Bodo Stern. This is worth taking notice of, because these are two very smart people, and because they run the largest private non-profit biomedical research program in the world. HHMI helped kick-start the PLoS journals. Later, they helped kick-start eLife. So when HHMI's leaders say scientific publishing should change, you can bet they will implement the policy they propose, and implement with gusto and deep pockets.

So, I'm going to take a skeptical read through their article, and write my reaction as I go. I want to emphasize a few things. The following is my personal opinion.  Also, the following is my knee-jerk reaction, which is risky to blog. So if you disagree with me on something, try reasoning me out of it rather than getting agitated. Because people are certainly getting agitated about the changing publishing landscape, or agitated because some of us are traditionalist sticks-in-the-mud.

Before I dive into Stern and O'Shea's article, let's see if we can agree on a few (almost) universally shared goals and values, just to help remind readers we are on the same team, aiming at the same goals, even if we disagree on how to get there.

Research Quality:
   Goal 1)  Do not publish papers that are fraudlent, logically flawed, technically incorrect, misinterpret or misrepresent results,  incomprehensible prose, and so on...  This is the analogue of "do no harm" in medicine. We don't want to promulgate false conclusions, or fraud. We don't want scientific publishing platforms to give voice to unsound anti-vax papers, unscientific young-earth creationist articles, or racist or sexist rants.

   Goal 2) Take flawed papers and, if possible, improve them through (iterative?) review and revision until they are good enough to publish (e.g., to not violate Goal 1).
   Goal 3) Maximize the readability of the paper. This spans both the technical veracity of the research, but also the quality of the scholarship and its presentation (compelling prose, clear figures, etc).

   Goal 4)  Get new ideas, methods, data, results, insights into the public sphere as quickly as possible, without violating Goal 1, and hopefully also meeting Goals 2 and 3.  There is a trade-off here. Meeting Goals 1-3 typically requires in-depth review.  Hurried review is often cursory. So if we are to get good quality independent reviews, we need to be willing to sacrifice time. If we are to revise thoroughly and properly, we need even more time. So, we often must balance Goal 4 versus Goals 1-3.  Also, good copy-editing is valuable (helps mostly with Goal 3), and copy-editing takes time.

Publishing costs money (e.g., see this earlier blog), so someone has to cover these costs.
 Goal 5) Make taxpayer-funded research freely available to taxpayers. Proponents of Open Access also argue that open-access papers will be read more, cited more, and thus have more impact all else being equal. Typically, this means the authors pay. As has been noted elsewhere, this creates a potential conflict of interest in which predatory journals benefit from selling authors the right to publish, leading to violations of Goal 1.
   Goal 6)  Let researchers with limited funding publish. Graduate students doing independent work. Postdocs operating on a shoestring budget. Labs between grants. They all have valid ideas, good data, things to say. But, an article in some top Open Acccess journals can cost upwards of >$5,000.  That's a huge barrier to entry into publishing. So, Goal 5 and Goal 6 pose a Gordian Knot of a trade-off. Personally, I prefer the American Naturalist's model in which those who can pay to publish open access, do, and those who can't, get cheap page charges (or even a waiver), with operating costs met by subscription fees.

Reaching a target audience:
  Goal 7) It should be easy for scientific readers to find the highest-quality articles that interest them most, without having to wade through a thicket of irrelevant papers. It's also nice to be steered to the papers that are most likely to change how we think about, or how we do, our own research. This was a problem with PLoS One: too much chaff compared to the wheat (and there are good papers there, to be sure), and poorly organized along conceptual themes. This goal is getting easier and easier with recommendations from software like SciReader, and social media (though the latter can fall into group think and can amplify cultural biases).

   Okay, I'm sure you can add other Goals (post a message!), but that'll do for now. We'll use these in my comments below on the Stern and O'Shea.

One more thing before I dive in: I have a few disclaimers. First, I am Editor-In-Chief of The American Naturalist, which is a smallish non-profit society journal. It is still printed on paper and sent to libraries. So, I'm part of the traditional "System". Second, the following is my personal opinion and not the stance of the journal nor its publisher.

So here we go. This'll be sort of like a live twitter feed as I read. If you want to read along with me, here's the link again: 

I've read but won't comment on the abstract. Presumably these ideas are all developed more below.


So the Royal Society started peer review in the 17th century? I wonder how that worked then. I know that The American Naturalist's editors in the 1860's through 1890's used a very informal review system at least sometimes, but that often involved showing it to the professor down the hall, who would write things like "it is one of the most miserable and inadequate things ever printed ". Formal peer review as we know it now seems to have started later, maybe as late as the 1950's, when the instructions for authors printed in the journal mentioned the need to submit two copies of a manuscript, for review purposes.

Stern and O'Shea write: "It made sense for publishers to charge consumers subscription fees in exchange for hard copies of journals and to establish editors as the gatekeepers of publishing, when printing and distributing scientific articles was expensive and logistically challenging. These limitations no longer apply" I want to point out that many journals are still in print, and there are benefits to print journals (seredipity of discovering something unlooked for when leafing through, for instance; and I retain info better from the printed page still, but maybe that's just me). Also, journals still cost money to run. There's a website to maintain, staff to handle communications with authors and editors, copy editors: there's a lot that goes on behind the scenes and that's not free. Still.

Next S&O'S are reiterating arguments for Open Access, but saying it isn't enough. They repeat the claim that paywalls are a barrier that slow science, and limit who can build on existing knowledge. True, to a point. For many journals (like AmNat), the large majority of universities have subscriptions. The University of Chicago Press gives away thousands of institutional subscriptions for free to universities in impoverished and middle-income countries. So more people have access than you might think. But it is true that you might not have access from home, which might stop you from downloading and reading my students' excellent AmNat papers, if you didn't want to take the time to log in remotely or from campus. And high-school teachers can't easily read paywalled scientific papers for their classes. There is a problem, for sure. Then there are new journals like Nature Ecology and Evolution which most libraries won't subscribe to for some waiting time. The University of Texas library won't subscribe for at least 5 years they told me, when I asked whether or how I could access my own publication there (Stuart et al 2017).

Now S&O'S are arguing that "The subscription price that publishers charge is inflated because it is not based on the specific value that publishers add. By imposing a toll for access to scientific articles that were created and evaluated by scientists for free, publishers hold these scientists’ products “for ransom,” charging for the whole product instead of for the publisher’s specific contributions to that product.". There's some truth to this, especially for many journals from commercial publishers. As the Editor of a not-for-profit journal, the cost we hand off to consumers covers the publisher's contributions, and that's it. So I do object to S&O'S stating this as a broad generality, painting us with the same brush as some journals from high-profit publishers you might name.

Ah, good, S&O'S do recognize the conflict of interest that Open Access creates, favoring a pay-to-play system where predatory journals and fake editorial boards can thrive (violating Goal 1). Their solution is to make the review process transparent: publish reviews, so that fake-review journals are exposed for the frauds they are. I agree that will help. But at the end of the day, an author who needs more lines of publications on their CV for promotion may still gladly pay to publish something shoddy at a journal that does half-hearted review. I'm not convinced this solution will fix the problem.

Wrapping up the section on Open Access. I agree with most of what they say here, even if they over-generalize a bit (in ways that directly concern the journal I Edit). But they totally ignore Goal 6 (cheap publishing for authors), as you might expect for people with a history of great research funding. HHMI started eLife which initially was free to authors AND readers. But no longer free to authors, sadly.

Now we are on to Impact factors and the academic incentive system.
"Journal name is used as ... an indicator of quality". That's mostly true, though we can all think of papers in Nature or Science where we thought "how did THAT get published?" - but maybe that's just sour grapes (more on that soon, I think). I totally agree with them here, that it would be nice if articles were judged on their own merits and not so much on the merits of the articles' neighbors. To use a personal example my 2003 AmNat paper is cited 10 times more than my 2001 Nature paper. But the latter is surely what got me my job interview at UT Austin as a finishing PhD student. Okay, so we should judge papers on their own merits. I don't think anyone disagrees in principle. But I can't read everything, and so I rely on someone (Editors, reviewers) to collate the things most likely to interest me into nice succinct tables of contents (that's meeting Goal 7).

Interesting point here: "the opinions of two to four peer reviwers... by chance [may] not be representative". Everyone with experience as an author knows this - things get published with a casual nod from someone who doesn't take the time. Or a great paper can be misunderstood and savaged by someone with an axe to grind or not enough coffee (though a reminder: if a reviewer misunderstands, it may be the author wasn't clear enough). But in the context of this essay, this made me think about the role of sample size: the more people who read and rate and comment on a paper, the more accurate the evaluation is. Let's imagine each paper has some 'quality' parameter. Sampling N=2 isn't really enough to estimate that parameter accurately, we have a high standard error. So it really is with many reads and ratings/comments by readers, that we converge on a high-confidence measure of its quality. We need an Amazon 1-to-5-star rating system? But would it be used?

S&O'S point out correctly that hyper-competition for high impact factor journals is creating an incentive system that can drive people to fraud (violating Goal 1).

Integration of peer review with the publishing decision.
On to the next section. Here, they take issue with the privacy of reviews. "nontrasparent". "Most journals keep peer reviews a confidential exchange among editors, reviewers, and authors, which gives editors flexibility to use their own judgement in deciding what to publish".   I don't quite see the link between this and impact factor, as they claim, but maybe I'm missing something.  This non-transparency is certainly true. Before I read on about why they dislike it, I'll mount a pre-emptive defense for sake of argument. Submitted manuscripts contain omissions, mistakes, and other potentially embarrassing flaws. Many are minor, but some are big. A young scientist is nervous enough submitting a paper for the first time, to expose themselves to the criticism of strangers. How much more horrifying if that criticism were broadcast for all to see? I suspect many trainees especially, but also senior scientists, when asked, would really rather have a chance to quietly correct mistakes outside the limelight. We always tell our students and postdocs when they write, speak, interview: "put your best foot forward first", or some variant on that. Public posting of peer review does the opposite. This may be a major disincentive to anyone with self-doubt or anxiety over their place in science. That's my guess, at least.

S&O'S write : "The main purpose of peer review should be to provide feedback to authors in order to improve a manuscript before publication. But, in service of the publishing decision, peer review has morphed into a means of assisting editors in deciding whether a paper is suitable for their journal. " This is obviously true, especially for top journals. At Editor at AmNat, I can't publish everything that comes in. We have a limited page budget and limited copy-editing staff. So I have to be picky. And I feel I have a duty to my readers, to bring them the papers that I and my co-Editors think will be most likely to interest them. That's not a decision I take lightly, and I am keenly aware that "whether a paper is 'novel enough'" (as S&O'S put it) is subjective and the hardest criterion to use. But that doesn't mean I totally agree with their characterization of peer review being a means for making this cut. Usually that cut is made without peer review, just me or me and an Associate Editor. When I do so, I explain my logic. I handle a few papers every day, and when I make an Editorial decline because something isn't suited to our journal I often write a page, sometimes several pages, of my own comments and recommendations. Our goal, as a journal, is to leave every paper better than when it came to us, whether or not we publish it. In this regard, the intense efforts of the reviewers, Associate Editors, and Editors, is very much focused on improving the papers. In this regard, I disagree with the  claim by S&O'S quoted above. At AmNat, review is still very much focused on helping the paper. If it weren't, the AE's and Editors wouldn't bother writing long and careful commentaries on papers we reject. The fact that we do sets our journal apart, to be sure. We are proud of that (and a bit exhausted).

"The intense competition for publication in high impact factor journ
als likely increases how often and to what extend [sic] scientific articles are revised before publication". Hm. That mistake might have been caught by a reviewer or copy-editor.

"While most papers are significantly improved through revisions suggested by reviewers and editors, there is a sense among scientists that a significant fraction of the time spent on revisions, resubmissions and re-reviews is not adding sufficient value and needlessly delays the sharing of findings" Maybe I'm just a crappy scientific author, but I consistently feel that my articles are improved by review and revision. I am always surprised by the sentiment in the quote above. So, about 6 months ago I did a totally unscientific poll. About half of the responses indicated they felt review greatly improved their paper. About half said it somewhat improved. And only about 5% (if I remember right) said review had no effect or negative effect. That 5% may be a very vocal minority.

"it is time to acknowledge that peer review before publication is just the initial step in scientific evaluation": Interesting. I don't disagree, but that's not a reason to water down peer review either, or change how publish / not publish decisions get made.

Now we hit the author's recommendations. This is where it gets fun, I bet.

Improvements to peer review.
- Publishing reviews along with the papers. My main problem is what I noted above: the disincentive arising from authors' fear of having their mistakes aired. Would reviewers get credit? Named? Can that go on their CV? That might create an incentive to do more reviews, and more careful reviews. Certainly when I became an Associate Editor, and knew my name would be listed at the end of a paper, I became more cognizant of doing a thorough job.

- Consultative peer review: conversations among reviewers and editor before a decision.  I like this idea. It gives everyone a chance to correct each other's misreadings. At present, AmNat's Editorial Manager web system isn't designed to do this in a way that would maintain mutual anonymity, which is a barrier. That's just a technical barrier. The other barrier is the extra time it takes. In another unscientific poll I did on twitter, it seemed most people would be okay with this as long as it didn't delay publication more than a couple extra days.

- Peer reviews should focus on technical quality: are conclusions warranted. I do often see reviewers commenting that they don't think the paper is suitable for our particular journal, though it would be fine elsewhere. Given that we have a constraint on how many pages we can publish, I find that slightly useful, but for the most part I reach that conclusion on my own based on the technical details. I rarely pay close attention to the 'suitability' comments, and sometimes override them.

- Ah, now they are saying 'Give recognition for peer review'. (see three paragraphs up here). Specifically they want reviews signed. I agree that recognition for good reviews is important (Maybe AmNat should come up with some sort of award for great reviewing). But objections are well known. When a reviewer is critical, being outed can create animosity that can hurt younger reviewers. There's an unrecognized flip side here: when a reviewer is positive and names herself, this creates a feeling of obligation / patronage. For instance I know now that Joe Travis and David Reznick reviewed my 2017 Nature paper. And that feels more awkward for me than if I had known they reviewed and rejected it. Because now I feel like I owe them something as a thank-you.

Next up: "Put dissemination of scientific articles in the hands of authors".
This is weird. They argue that funders trust scientists to do the research, so we should trust them to choose what when and how to publish. "why don't we ask independent parties to oversee experimental design and execution as well?". Um, two things. First, we do: they are called grant panels. Unlike at HHMI, at NSF and NIH you need to get your experimental design past a critical panel. Second, we do: manuscript review serves this purpose.

So here's what they are arguing for, this is the crux: Authors submit a paper, it gets reviewed. Authors can choose to revise (or not), then decide whether or not to publish. Its sort of like putting something on BioRxiv, but after getting reviews. You can heed the reviews or not, then post on BioRxiv or not. Up to you. The barrier to publishing is not an editor, but is your own self-respect: have you gotten enough feedback and done enough revision that you are comfortable posting it?

Okay, right away I have a problem with this. By this criterion, someone could go ahead and publish creationist rants and call it a scientific publication. You'd be really surprised what comes in the door to journals:  creationism, offensively sexist or racist, and so on. Heck, some people tried to publish the bigfoot genome. It wasn't until it was soundly rejected (with review!) from some respectable journals that the authors bought their own predatory journal and self-published in what they said was an open-access reviewed journal. As soon as you let authors be "the decider", I promise there will be bunk. And that bunk will inflame the creationist movement and intelligent design (the latter was smacked down by the judge in the Kitzmiller vs Dover court case specifically because they weren't publishing in scientific journals. Now we let to get them decide?)

That's my main knee-jerk objection, now let's see what S&O'S have to say in favor:

"Since authors have such a clear self-interest in publishing their own work, nobody would equate the author’s decision to publish with a stamp of quality. This stamp of quality has to come from elsewhere, including the published peer reviews and post-publication evaluations described below"  Okay, I can see that. But that means that newly published papers are not organized into batches of higher-quality articles that are more likely (on average) to be worth my very limited time. That is, this means that Goal 7 is set aside until papers have had time to develop a following, or not.

"the peer reviewers would direct their comments to the authors focusing their peer reviews on improving the manuscript as opposed to advising the editor on suitability for a journal." Yes please!  But actually, this is the standard way people review things, at least at AmNat, and at Evolution, and most society journals. I think this is mostly a problem if you are trying to mostly publish in Nature and Science and PNAS and Cell. At those journals, the reviewers have all had their own rejections. They then have sour grapes, and think "well if my paper wasn't good enough, neither is this". So I think S&O'S are right, but in a limited domain; more often for us publishing mortals we work with journals where reviewers already take this advice.

"the time and resource savings would be significant: authors wouldn’t have to perform experiments that they deem unnecessary; " Again, this is more of a Nature & Science problem, not so common in our fields.

"demanding revisions and multiple rounds of review": When revisions are cosmetic, Associate Editors shouldn't be sending things out to re-review anyway. When revisions are substantial (new data, new statistical analyses, substantially large chunks of new text), it is entirely appropriate to have that new material reviewed, which means another round of review to ensure quality (Goal 1). That's appropriate. To be sure, I've had papers sent out to re-review and thought "you're kidding me, this was cosmetic, just make the decision yourself and speed it up".

Now S&O'S are tacking possible objections. The first one is what I raised above as my knee-jerk reaction. I think I'm more cynical than they are. They write: "Few authors will knowingly want to put out poor-quality work."  I'm not so sure. As long as promotion is based on counting papers, this will be a hard sell. And as long as there are crackpots out there with pseudo-scientific ideas, their proposal will be an open invitation. (by the way, is any of that crackpot stuff showing up on BioRxiv?)

Here's the most compelling part: "The peer reviews themselves will be a powerful restraint on the author, since they will be published together with the paper (see above). An author may, for example, prefer to withdraw a paper submitted to a journal if the reviews reveal fundamental flaws that cannot be addressed with revisions. And if an author decides to publish a paper despite serious criticism from reviewers, at least those criticisms will be accessible to readers, who can decide for themselves whether to side with the author’s or the reviewers’ point of view." In a utopian world, I totally agree this is a great model. Most scientists are conscientious, careful, and will use reviews as a source of feedback to improve, then publish or not publish their work. But wait: do we REALLY think most people would say "oh, that's a great point, there was a mistake, I'll just delete this paper that represents a year of my life"? That's a hard thing to do (I can attest personally).

So "where does this leave journals and editors", they ask. They envision a hybrid model, part way between tradition and the open wild-west of BioRxiv or F1000Research. They suggest that papers go to to journals (still organized by theme, to meet my Goal 7). Editors assign reviewers, as we have done. But, Editors stop making the publish/don't publish decisions. Instead, that is up to the authors, once they get reviews.

Ah! Here we go: Here near the end they write: "In rare cases, editors may need to step in and stop publication of an article when the peer review process reveals that publication would be inappropriate – for example, in cases of plagiarism, data fabrication, violation of the law, or reliance on nonscientific methods."  So the Editor still does some triage to keep out the riff-raff.

And here's another nod to something I was objecting to: "At the moment, society journals are between a rock and a hard place. They can’t afford to switch to open access, since the open access fees required to replace their subscription income would be too high for readers. On the other hand, they feel considerable pressure from for-profit publishers who are launching competing journals at breakneck speed. Academic publishers risk becoming obsolete if they don’t adjust." That is a concern. The solution they propose is that society journals charge for peer review, then basically guarantee that authors can publish when they have received the reviews and feel ready to do so. They figure journal income goes up, reducing the per-article open access fee. Okay, but that assumes that the journal's costs are flat. In reality copy-editing and data-archiving fees and some other features are on a per-article basis, so cost per article will be less sensitive than S&O'S think, especially when most reviewed articles eventually get published. And of course this won't work for print journals, which wouldn;t be able to keep page numbers to within budget for the printer's.

The last part of the essay is about post-publication processing. They argue that after an author decides their paper is ready, the paper and its reviews go online. Then, the reviewers and/or subsequent readers can 'tag' the paper with various kinds of tags, for rigor, interest level, data sharing, code review, data downloads, citations, pdf downloads. This is crowd-sourcing the process of rating and ranking papers for my Goal 7. Its like going on Amazon and seeing a product has lots of positive reviews, though more multi-dimensional in the kinds of metrics. What could possibly go wrong giving people the chance to comment & review & tag things online????? (hint, read this Washington Post article on scientists posting reviews on Amazon if you haven't already)  

Now here's the interesting point where they start to back-peddle a little bit. They say, although the editor gave up the role of gate-keeper, the editor could place a warning tag on a paper basically saying the article was published by the authors against the reviewers' recommendations. A "read the reviews carefully & take this with a big grain of salt" tag. The Editor could place high general interest tags on the articles they would normally publish, and low general interest tags on articles they wouldn't usually touch.

Well, that's it. I really should have spent tonight doing some data analysis, but their essay was interesting to read and thought provoking. And I, for one, benefitted from writing my thoughts as I read it.

So, will AmNat implement this? No, not soon.'

Update: Based on a comment on their article, Bodo Stern shifted from "Tags" to "Badges". To which I must, in a fit of late-night infantile humor, respond:

Undergrad the Impaler

Editor's note (from Dan Bolnick): The following is a reflection written by Cole Thompson, who was an undergraduate at the University of...