Check your (taxonomic) biases at the door

Many of us like to believe that we are conceptually-oriented researchers; our particular study organism(s) are just means to an end, the end goal being to answer broad questions about how evolution or ecology works. But our citation patterns suggest otherwise. We are more likely to read, and hence more likely to cite, papers about organisms of direct relevance to our own work. That results in some unfortunate conceptual balkanization. Case in point: I’m writing an Annual Reviews paper on (non)parallel evolution, with several co-authors. Collectively, we have all studied sticklebacks (though we have some other study organisms in our history). So we tried very hard to diversify our citations (taxonomically; I must admit I haven’t gone through and checked the gender of first authors, for instance).

            In one section of the manuscript we discuss Langerhans and Dewitt’s 2004 AmericanNaturalist paper on Shared and Unique Features of EvolutionaryDiversification.  In that paper’s appendix they lay out a multivariate statistical approach to measure the extent to which evolution has occurred in parallel across multiple replicates, or in a unique direction in each replicate. That’s a very useful approach, that is very conceptually general and widely applicable (hence its great fit to The American Naturalist). So, I wanted to find a plant paper that cited this article, to use as an example illustrating their analytical approach. The problem is, I found only three plant papers out of the 200 that cited Langerhans and Dewitt (2004) according to Web of Science (as of December 1 2017). That’s 1.5%.  On the other hand, I noticed a suspicious number of fish citations. So I went back and noted down the taxonomic focus of each of the 200 papers citing their article (a few were reviews that had no particular taxonomic focus, so I didn’t tally those). Here’s the breakdown (sorted by # of citations):

Taxonomic group	Subgroup	# citations to L&D 2004
Fish	TOTAL:	118
	Poeciliid	42
	Stickleback	30
	Centrarchid	6
	Cichild	5
	Salmonid	5
	Other	30
Reptiles	TOTAL:	8
	Lizards	6
	Turtles	1
	Snakes	1
Amphibians	TOTAL:	3
	Salamanders	2
	Frogs	1
Insects		6
Plants		3
Isopods		3
Mammals		2
Arachnids		1
Birds		1
Gastropods		6

The really striking thing here is how taxonomically biased this is. The single genus Gasterosteus has five times as many studies citing L&D than all studies of insects, which collectively are of course at least as diverse as stickleback, and possibly even as important from a practical standpoint.

            Why is this widely-applied method being effectively ignored by the vast majority of researchers? I think the answer is pretty simple: because the original paper was applying their method to study fish evolution, fish evolutionary biologists were more likely to read it. Worryingly, this suggests that when we publish a new method, we might reach the largest audience if we omit application of the method to any one taxon (or, if we apply it to many diverse taxa). Equally worringly, it suggests to me that because of our inherent taxonomic biases we are missing the boat on many important ideas and methods.

            The other hypothesis of course is that parallel evolution may be an exceptionally hot topic among fish biologists, especially stickleback- and Poeciliid-researchers. Bandwagons happen. We tried really hard in our Annual Review manuscript to branch out and cite studies involving something other than stickleback. That’s hard both because this is the system we are collectively most familiar with, and because this is such a great parallel-evolution system that many of the leading studies on the topic use this organism.

            There’s not an easy solution to this, other than to check our biases at the door: when writing, and when reading, ask yourself how diverse your citations (or paper choices) are. Try to step out of your comfort zone, read something about an organism you know nothing about, at least once a week if not more often. You’ll learn a lot of biology in the process, and maybe get some new ideas that help you step out of your taxonomic box.

A cross-post

In my capacity as (soon-to-be) Editor-In-Chief of The American Naturalist, I am also occasionally going to be posting on the AmNat Editor's Desk blog. Here, I'm just drawing attention to two new posts I put on that site.

1) As incoming EIC I wanted to articulate some aspects of AmNat's values and policies for our Associate Editors. They received a version of this by email. But I realized some of the points may be more broadly applicable, and useful to prospective authors as well. So, I also posted this as an open letter for anyone to read. You can read the full text here.  Contents include some thoughts about:
- What the heck does AmNat publish (or not publish)?
- How fast should decisions be?
- When to decline without review?
- When to "decline without prejudice", and what exactly does that mean?
- When to send a revision back out to review, or not?
- The importance of value-added comments by Associate Editors' decision letters
- Special Features in The American Naturalist
- Progress in diversifying the AE board, thanks to Judie Bronstein and to be continued.

2) This fall I had an extended conversation with Tim Parker from Whitman College, who is Co-organizer of the “Tools for Transparency in Ecology and Evolution” group. In this blog post I provide a summary of the TTEE standards and what AmNat will or will not do, to meet them.

While we are on the topic of this journal, here's an item of historical interest: a screen shot of the announcement in the 1960's when page charges were first instituted, to avoid having the journal go bankrupt and disappear.




Enjoy!

-Dan Bolnick

What have you done for me lately?

Nearly every context for evaluation in academia (or, really, anything) focuses on recent progress. What grants have your received in the last five years? What papers have you published in the last five years? How many students have you supervised in the past five years? I understand the logic behind this approach and I am not necessarily criticizing it overall. After all, why should a formerly influential faculty member get to keep hanging onto funding and space for decades after they became “dead wood” in the department.

However, a few years ago, I encountered a pretty weird version of this “what have you done lately” approach to evaluation. I was an external member of a committee seeking to hire a professor. During the meetings to evaluate candidates, one other member of the committee used, as a key criterion, the trajectory of citations in Google Scholar to judge whether a person was “declining in influence”. I found this criterion really weird as a person with few citations in recent years could rank higher than a person with tons of citations in the same year. (Of course, other valid reasons exist to not weight citations highly in evaluations in general.)

And then I looked at my own Google Scholar profile. Lo and behold, I was “declining in influence.” OK, fine, whatever: my happiness does not depend on the trajectory of my citations.

Now, a few year’s later, however, it looks like this.

Now that I am on the upswing again, I am more convinced than ever of the uselessness of the trajectory of citations for evaluation. Here are two key reasons:

1. As citations always lag publications, the period of my declining influence was – presumably – precisely the time I was publishing papers that would prove to be increasingly influential.

2. Any career is likely to involve ups and downs in year-to-year citation rates, which clearly do not reflect any real trend in “influence.”

In short, while I agree that old less-than-active folks shouldn’t continue to take funds and space from more up-and-comers, citation trajectories is NOT a way to make such assessments.

Dawn Phillip - an exceptional collaborator and person

Dr Dawn A.T. Phillip

1965-2017

Andrew Hendry: One of my great regrets as a scientist is that I never got to know Dawn Phillip very well. She was of immense help to my students and postdocs in Trinidad, far above and beyond just common courtesy. Inspired by this regret, I asked my students – who knew her far better than I – to provide their testimonials of appreciation. Before that, however, Anne Magurran – Dawn’s PhD supervisor, friend, and frequently collaborator – provides her own thoughts.

Anne Magurran: Dawn Phillip’s sudden death last month means that we have lost a talented biologist, inspirational teacher, role model and friend.

Dawn during her PhD field work. Photo by Anne Magurran

Dawn did her bachelor and masters’ degrees at the University of the West Indies (UWI) in her native Trinidad and Tobago, before joining me in Scotland for her doctoral research.  She graduated with a PhD from the University of St Andrews in 1998 with a thesis entitled ‘Biodiversity of Freshwater Fishes of Trinidad and Tobago, West Indies’. After her PhD, Dawn secured a faculty position in Life Sciences at UWI. She had been promoted just a short time before her death and was delighted to be rising through the academic ranks.

Dawn was an extremely knowledgeable and insightful ecologist. Like her PhD external examiner Rosemary Lowe-McConnell, Dawn made important contributions to neotropical fish biology. Particularly notable is her Zootaxa (1) paper - the authoritative overview of the status and ecology of freshwater fish in Trinidad and Tobago and essential reading for the many researchers drawn to the rivers of Trinidad’s Northern Range. This paper, as well as the guide to freshwater fishes (2) that resulted from her PhD research, and indeed all of her research output, was under-pinned  by meticulous field work, exceptional commitment to her research and a deep appreciation of the ecology of organisms in their natural environment. I think it is fair to say that I learnt as much from her as she did from me.

Dawn always made me feel welcome in Trinidad and I valued her friendship and the chance to catch up whenever I visited. We continued to collaborate and had been working on a paper and exchanging emails about it the day before her death. She was upbeat and looking forward to future projects and challenges. It is hard to take in the fact that she is no longer with us. I will miss her.

1. Phillip DAT, et al. (2013) Annotated list and key to the stream fishes of Trinidad & Tobago. Zootaxa 3711:1-64.

2. Phillip DAT & Ramnarine IW (2001) An illustrated guide to the freshwater fishes of Trinidad and Tobago (University of the West Indies, St Augustine, Trinidad & Tobago).

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My own cherished copy of Dawn's guide book. Photo by Andrew Hendry.

And now some testimonials, remembrances, and reflections from my students and postdocs.

Jonathas Periera: “Sorry to upset your Saturday. I have to inform you that Dawn died in her sleep sometime last night. We will update you as more info becomes available. Sincerely yours, Mark Phillip.” This was how I learned Dawn has passed away in October 28. Although I knew she had some sort of health issues, this message in whatsapp was a shock. It still is. I had just been with her in Trinidad, where I stayed five months doing field work. Dawn saved my ass many times and greatly contributed to the (at least partial) success of my field trip. Always smiling (even 4am in the morning!!), I feel Dawn is perhaps the best representation of a true “Trini” to: always in good vibes, no matter what. Dying over her sleep was perhaps the best way death could find to take her life. My most sincere condolences to her family, friends, and the University of the West Indies.

Felipe Perez-Jvostov: As everybody else starting a PhD, I spent the first several months trying to understand my study system: who has done what, where have they done it, what did they find. Confusion was commonplace – at least until my first field season in Trinidad when start getting first hand experience. During that trip I met Dawn Phillip. Dawn came to our research station to meet the research crew. She had worked with guppies, Rivulus, and many other fishes that have been so intensively studied in Trinidad, and she was always interested in what people were up to, and how she could help. Her personality made it so easy to get along with her – an air of familiarity that made you feel comfortable. In my many subsequent trips, I would often chat with Dawn about my projects (or more often the problems with them). She would always have a warm advice, and calm me down with a smile. I was very sad to know of her passing. The research community has lost a wonderful colleague, and those who knew her personally have lost a dear friend that was always available to help – you just needed to ask. At least for me, I will always remember that first time I met Dawn, and how she would not say no to a « beastly cold Carib ». 

Gregor Rolshausen: Dawn was an indispensable and very helpful colleague of mine in Trinidad. She was an expert on tropical fish communities, and introduced me to some of the most fascinating ecosystems I have seen. A dedicated scientist and teacher at Western Indies University, Dawn also had a passion for organizing field excursions and connecting her students to international research projects. But above all, I remember Dawn as a truly warm-hearted friend with a great laugh. It is very sad to say goodbye this way.

Kiyoko Gotanda: Dawn was a wonderful scientist and generous with her knowledge. Her research has been an inspiration for my own work in Trinidad. She is a co-author of a guide to freshwater fishes of Trinidad of which I had a black and white copy. Dawn shared her colour plates with me, and the guide was invaluable in helping me with identify the different species of fish I was sampling. My first field season in Trinidad, I had wanted to explore some of the oily and non-oily sites in the southern part of Trinidad. I had no experience working in that part of Trinidad. Dawn provided maps, information, and one of her graduate students to assist me in my sampling of these sites. Without her generosity and willingness to collaborate, I would likely have never even found the sites! I am grateful that I had the opportunity to work and interact with Dawn, and she will be greatly missed.

Lea Blondel: I met Dawn in 2016 during my third visit to Trinidad. We had already exchanged emails before that, because I needed a local supervisor and because she helped a few other students from my lab before. I immediately connected with her thanks to her kind, generous and outgoing personality. Even if we didn’t interact much when I was in Montreal, she always showed great interest to my project when we met in Trinidad. The memory I will keep with me is the day we spent together at her house this past March, talking about exciting ideas and eating roti. The day was really warm so we got some rest under the porch of her house, before driving along the east coast of Trinidad where she shared some of her favorite places with me. It was a really special day and I feel lucky to have had the opportunity to know the great person and the great researcher she was.

Dawn during field work just last year. Photo by Lea Blondel.

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I hope others who have benefited from Dawn’s kindness and help will add comments to this post.

Phases of the RET experience

(NOTE: The following post was written by Tania Tasneem, a middle school science teacher in Texas.  Tania worked in Dan Bolnick's lab for three summers. In 2006 she was supported as an REU student (Research Experience for Undergraduates), paid by a REU supplement to an NSF grant. Shortly after, she graduated and began teaching middle school. In 2013 she returned as an RET (Research Experience for Teachers) to do both field work in British Columbia, and lab work in Austin.  Her salary came from the fantastic 'Research Experience for Teachers' (RET) program that NSF funds as supplements to new or existing grants, in this case  a collaborative grant between Dan Bolnick, Andrew Hendry, and Katie Peichel. Tania returned in 2014 for an additional summer's RET, this time exclusively doing lab work in Austin identifying fish stomach contents and parasites from the samples she helped collect in 2013. As a result of this work, Tania is a co-author on a Nature Ecology & Evolution paper, and on another manuscript in preparation.  Since 2013, the Bolnick lab has hired 7 RETs to participate in research, usually in pairs, or paired with an undergraduate studying to become a K-12 STEM teacher. Most of these teachers have ended up as co-authors on one or more published articles. The following essay conveys the RET's perspective on this experience.  I have posted this without editing, to clearly convey both the pros and cons of the RET experience in the hopes that this information can improve other researcher-teacher interactions.- Dan Bolnick, Nov 8, 2017)

The author, Tania Tasneem, as an REU student in summer 2006 in British Columbia

I recently went to a training for seasoned teachers on how to best support new teachers during their first year. Figure 1 shows the progression of a first year teacher’s attitude toward teaching and was projected at the end of the day long training to remind us of all of the emotions a first year teacher encounters.  As the first semester of my 11^th year comes to an end, I can assure you that this data holds true to most teachers every single school year. The figure also mirrors some of the emotions I encountered during my first field/lab experience in the Bolnick lab as an REU during the summer of 2006 and again as an RET summer of 2013 and 2014.

For each of these emotions, I have tried to reflect on my mindset/paradigm shifts as an REU (in my early 20s and a novice teacher) and as an RET (in my early 30s with 8-9 years of teaching experience) about joining the project, doing field work, my lab experience during the summer, and the impact on my teaching practices. I’ve tried to give a brief explanation of what that phase is like as a teacher and how it is related to the field/lab experience in the summer from the perspective of a novice teacher (REU experience) and a veteran teacher (RET experience).

Anticipation Phase (Before going into the field)

The anticipation stage begins during the student teaching portion of pre-service preparation. My first field experience was the summer before I started my student teaching semester so I can definitely relate to feelings of excitement and anxiousness as I became closer to the start of a school year with a mentor and being in the classroom every day. New teachers, myself included entered with a tremendous commitment to making a difference and a somewhat idealistic view of how to accomplish these goals. Seasoned teachers on the other hand are more anxious about new district and campus initiatives, administrative/teacher turnover and impacts for their campus, what their new student needs will be for the upcoming school year. This feeling of excitement carried me through the first week of field work and carries me through the first weeks of school every year. 

Survival Phase (In the field)

During the survival phase, teachers (new and seasoned) are overwhelmed, bombarded with a variety of problems and situations they had not anticipated, and trying to keep their heads above water. New teachers are learning a lot at a very rapid pace and consumed with the day-to-day realities and routines of teaching. There is little time to stop and reflect on their experiences. It is not uncommon for new teachers to spend up to seventy hours a week on schoolwork. While seasoned teachers can manage these realities a little bit better, most seasoned teachers have a similar work load or work as mentors to help new teachers survive this phase. There is little time to stop and reflect on their experiences. It is not uncommon for new teachers to spend up to seventy hours a week on schoolwork.

Particularly overwhelming is the constant need to develop curriculum. Veteran teachers routinely reuse excellent lessons and units from the past. New teachers, still uncertain of what will really work, must develop their lessons for the first time. Even depending on unfamiliar prepared curriculum such as textbooks, is enormously time consuming.

Disillusionment Phase (Field season almost over)

This is the “I’ve made a terrible mistake, what was I thinking?!?!?!” phase. After six to eight weeks of nonstop work and stress, new teachers enter the disillusionment phase. The intensity and length of the phase varies among new teachers. The extensive time commitment, the realization that things are probably not going as smoothly as they want, and low morale contribute to this period of disenchantment. New teachers and veteran teachers alike question both their commitment, competence, and career choices during this phase.

 

Rejuvenation Phase (field work is over, to the lab)

The rejuvenation phase is characterized by a slow rise in the new teacher’s attitude toward teaching. Having a break makes a tremendous difference for new and veteran teachers alike. It allows them to resume a more normal lifestyle, with plenty of rest, food, exercise, and time for family and friends. This vacation is an opportunity for teachers to organize materials and plan curriculum. It is a time for them to sort through materials that have accumulated and prepare new ones. This breath of fresh air gives teachers a broader perspective with renewed hope.

During this phase we are ready to put past problems behind us, have a better understanding of the system, an acceptance of the realities of teaching, and a sense of accomplishment. Through their experiences in the first half of the year, teachers gain new coping strategies and skills to prevent, reduce, or manage many problems they are likely to encounter during the second half of the year. Many feel a great sense of relief that they have made it through the first half of the year. During this phase, teachers have the time to focus on curriculum development, long-term planning, and teaching strategies.

Reflection Phase (End of the summer lab/field season and on to the new school year)

The reflection phase is a particularly invigorating time for teachers. Reflecting back over the year, allows us to highlight events that were successful and those that were not. We think about the various changes that we plan to make the following year in management, curriculum, and teaching strategies. The end is almost in sight, and we have almost made it; but more importantly, a vision emerges as to what our next year will look like, which brings a new phase of anticipation.

Tania Tasneem as an RET in summer 2013