Sat, 30 May 2026 10:31:29 -0700WeeblySat, 30 May 2026 12:50:33 GMThttps://www.coxevolab.org/the-itinerant-naturalist/why-study-reptiles-and-amphibiansI often define myself as a scientist by kinds of questions I ask, so I normally say that I am an integrative evolutionary biologist or physiologist. But another way that you can characterize a scientist is by the type of organisms that they study, and by that criterion, I am definitely a herpetologist. The overwhelming majority of my publications (>95%) are on reptiles or amphibians, and most grad and undergrad students in my lab have studied reptiles and amphibians. So why do I study reptiles and amphibians?
 
            Unlike other vertebrate groups, studying reptiles and amphibians requires a bit of justification. If you study birds, mammals, or “fishes”, usually there is the potential for something that can be applied to humans or one of our food sources, either in the context of agriculture or wildlife and fisheries biology. Reptiles and amphibians are only rarely an important food source, and none have really been domesticated and cultured in captivity like some birds, mammals, and fishes. Hence, the justification for studying reptiles and amphibians usually requires justifying on the basis of basic scientific knowledge that can be gained by studying them. I think that there are at least five reasons for why reptiles and amphibians can make good study systems in organismal biology.
           
One of the reasons that reptiles and amphibians are a good model system is that you can handle most of them safely. Amphibians and reptiles have very few zoonoses, and washing your hands after handling them is usually sufficient to protect against getting sick. As long as you are gentle, most reptiles and amphibians can also be handled without danger to the animal itself (although this can be complicated with some amphibians, and best practices is to have wet hands and/or a barrier like gloves). Most non-venomous squamates (snakes and lizards) can’t really hurt you if they bite you besides drawing a little blood, with the obvious exceptions of the big ones (e.g., pythons, iguanas, monitor lizards). Almost all turtles are capable of delivering a painful bite, and the big ones can do some real damage (such as removing digits), but they are not that flexible and so can generally be handled safely by holding onto the rear margin of the carapace (upper shell) between the two hind legs. Crocodilians are an exception- there is no way to safely handle any species without substantial training. Where I grew up in the Midwest, there were no venomous snakes, and so I grew up catching toads and turtles and snakes. The reason that at child could catch these animals (and grow fascinated with them) is also what makes them great study systems- they can be easy to catch safely, sometimes in large numbers.
 
Another reason for the appeal of reptiles and amphibians as study systems is that they are a vertebrate that can be extremely abundant. Because they are ectothermic and are often small bodied, they can be packed more densely into a landscape than even comparably sized birds or mammals, which must divert most of their energy input into endothermy. In the eastern US, red-backed salamanders (Plethodon cinereus) can be at extremely high densities- I have found over fifty individuals in a half hour of searching, and this was a random site that I was visiting for the first time. In the Midwest, snakes can be present in extremely high numbers- a single afternoon can yield dozens of garter snakes in wet prairies in Iowa or hundreds of ringnecked snakes in Kansas. Anyone who has spent time in the desert southwest has surely noted the abundance of many different species of lizards even in a resource-depauperate aridland. Scientists, particularly those that work in nature with wildlife, are often in a struggle to increase sample size and statistical robustness of results, and reptiles and amphibians are often the best way to get a high sample size for a terrestrial vertebrate.
 
Beyond permitting high sample size, the fact that all reptiles and amphibians (with a few facultative exceptions) are ectotherms means that they represent a very unique style of terrestrial life, compared to birds and mammals. All mammals and birds are limited in the body size and shape that they can evolve based upon the constraint of being endothermic. Surface area to volume relationships means that there is a limit on how small you can be and maintain a body temperature higher than that of the environment. These same constraints also prevent the evolution of body forms with a high surface area to volume ratio, such as very elongate or flattened forms. Hence, within reptiles and amphibians, we have snakes and caecilians and legless lizards, as well as flattened horned toad and softshell turtles. The smallest terrestrial vertebrates are reptiles and amphibians of multiple different lineages. Hence, if you want to understand nearly half of the diversity of tetrapods (tetrapods are basically all terrestrial vertebrates, or all vertebrates excluding “fishes”), studying reptiles and amphibians is the only way to do it.
 
Reptiles and amphibians are also good study systems because they are very sensitive to the environment, and can be bellwethers of environmental disturbance. All reptiles and amphibians are ectotherms, so they are often sensitive to or responsive to environmental shifts in temperature. Many species are habitat specialists, and cannot persist outside of their specialized habitats. Reptiles and amphibians are sensitive to wildlife disease, from two different chytrid diseases that have caused enormous crashes in the biodiversity of salamanders and anurans, to snake fungal disease that is negatively impacting populations of snakes in the US, particularly the eastern US. Moreover, because many are small-bodied and feed upon tiny invertebrates, they can connect parts of the food web that would be otherwise separated. In fact, loss of amphibian communities has been linked to the collapse of other vertebrate taxa, emphasizing their important but environmentally sensitive role in the ecosystem.
 
Finally, studying reptiles and amphibians is useful and interesting because we know so little about them. New species of squamates and amphibians are described at a pace that far outstrips descriptions of new mammals and birds. Some groups like amphisbaenians, scolecophidian snakes, and caecilians, among others, are still quite poorly known, with new families of caecilians discovered in the past couple of decades. One reason that we are discovering many new species is that many are quite cryptic and live in places where they are unlikely to encounter humans, such as the canopy of trees or underground. Because of that, we are also constantly learning new information on the ecology and behavior of reptiles and amphibians. As an example, only a few years ago, researchers discovered that not only do caecilians have post-birth parental care, but the offspring beg to be fed, and the mothers release cloacal milk in response to the begging of their offspring. This observation challenges our notions of when and where elaborate parental care evolved on the tree of life.
 
There are many other reasons to study reptiles and amphibians (e.g,, public health issues around venomous snakes, studying the evolution of toxins and venom). But I wanted to at least give a sampling of why it might be not only interesting, but important, to study these creatures. Reptiles and amphibians are fascinating and cool, and for all of the reasons that they are so appealing to some people, they can make great study systems in integrative and comparative biology.
]]>Sun, 10 May 2026 19:38:48 GMThttps://www.coxevolab.org/the-itinerant-naturalist/grants-dont-matterThe admittedly provocative title of this post is definitely wrong. Grants matter because they can pay people that work on the grant, and grants provide funds to conduct research. Grants matter for a lot of institutions because they often include “overhead” or “F and A” or “Indirect” funds that essentially pay for the maintenance costs of conducting research at universities. But where I think grants don’t matter, or at least don’t matter as much as they are currently weighted, is in evaluating research quality and productivity.
 
            The only thing that makes what we do science, rather than an expensive hobby, is that the results get shared via scientific publications. Of course, results can also be shared in grey literature like reports, or via database acquisitions, but these are not universally available and so are not the focus of my argument. Hence, the only research that matters for the broader scientific enterprise is research that gets shared with the broader community in scientific publications
 
            My basic argument is that grants are only mediators of research productivity and quality, and are not themselves a type of research product. Grants are frequently important for evaluation of scientists, and at research-intensive institutions, are the most important factors for tenure and promotion. However, the grants only matter for the progression of science if they result in publications. It does not matter how much money you bring in if that money does not result in published research.
 
            Because obtaining grants is so competitive, they can be a signal of research prominence or quality. But grants alone are an imperfect signal for two reasons. First, not all grant funds are equal. Some research funding is more like a contract, rather than the funding of a research program. For example, scientists can be funded for monitoring work that may well be important for informing agency decisions, but is not hypothesis driven and is less likely to result in publications. In my experience, this work is less likely to push science forward, although it can contribute to other important societal outcomes. But for evaluating research quality and productivity, receiving the grant is not a good signal, although the resulting publications would be a good signal. Second, some grants fund specific research programs (e.g., regular NIH and NSF grants), and this work is more likely to be hypothesis driven and advance the scientific enterprise. However, the work has to be published to actually matter, and so we should use the resulting scientific publications to evaluate productivity, rather than simply receiving the grant.
 
            ​There are other reasons to conduct research than advancing knowledge in your field. As mentioned before, monitoring research can be important for a number of reasons. Research can be a crucial part of teaching in labs and field courses, even if the goal is not publications. But then I would argue that this research (and the funding that supports it) is best evaluated as broader impacts or part of teaching, not as a way to evaluate research productivity.
 
            I understand why institutions value the acquisition of external funding for evaluations like tenure and promotion. Requiring all faculty to generate some income for the university in the form of F and A is a great way for the university to recoup salary and startup of faculty. But as an individual faculty member, whether some gets funding or not does not really matter to me for evaluating research productivity. Of course, getting funding might be a good measure of how they support the graduate program, or training of undergraduates, but that is a different type of evaluation. Indeed, research productivity is only one of several evaluation categories to consider for hiring or promotion. However, for evaluating research productivity, I pay attention to the quantity and quality of scientific publications, which is the only real direct evidence of how the research of an individual faculty has influenced their field and contributed to the corpus of human knowledge. ]]>Sun, 03 May 2026 15:35:57 GMThttps://www.coxevolab.org/the-itinerant-naturalist/why-should-you-go-to-scientific-conferencesConferences are expensive and time-consuming. You usually have to travel to get to the conference location, and preparing your talk or poster can take up time that could be used for more tangible tasks like writing papers or grant proposals. So why should you go to conferences? I think it is a good idea to go to conferences because none of us does science in a vacuum, and our work is embedded within the broader context of work done by the community of scientists in our field. Publications are usually published months to years after the research has been completed. Conferences are the best opportunity to take the pulse of the field and see what your colleagues are working on right now. They are also a way to make connections in the field with future colleagues that will be reviewing your grants and papers and might even be future collaborators. Finally, going to conferences is a great way to break out of a mental rut and feel inspired by cool science.
 
            One thing that I don’t do a great deal of during conferences is attend talks. Some of this comes from my upbringing- my family went to church three times a week, which was quite the challenge for a kid who struggled to pay attention. I have developed a bit of an allergy to a full day of sitting and listening to people speak. My ability to sit still and focus has improved a bit as I have moved into middle age, but I still won’t attend more than a couple dozen talks at most. However, I don’t think attending talks is the best or only way to get caught up with colleagues. In fact, I think the best way is to focus on meeting with colleagues that you see once a year, during poster sessions or coffee breaks. This is where you really get to learn what your colleagues have been up to for the past year.
 
            All of the above is not to say that you shouldn’t attend talks- I am definitely inspired every year by cool talks. For me, finding sessions with lots of relevant and exciting talks is the best way to balance socializing and attending talks. I rarely switch sessions, and I try to avoid going to any talks where I am a coauthor (after all, I already know what we did and what we found). Instead, I go to (some) plenaries, best student presentation sessions, and symposia where all the talks are of interest. If I go to a few of those per conference, I almost always see a talk that gets me amped about collaborations or new techniques or exciting new paradigms.
 
            The notion that a conference is all about making and reinforcing connections within the broader community may seem challenging if you are introverted and new to the field. I think one instinct that some folks have is that they want to meet the most famous or influential people at the conference. But keep in mind that those people are often very senior, and meet way too many people for them to remember every brief interaction. Also, those superstars in the field may well be retired or in the twilight of their career if you meet them when you are a grad student. By all means meet the superstars if you have an opportunity, but I have found that the most important and lasting connections are the people closer to my career stage. Some of the postdocs and early-career faculty that I met as a grad student are now the big and senior names in the field, and grad students and postdocs closer to my career stage are now my colleagues and peers that review my work.
 
            At the conference that I attend regularly, I have slowly built up the number of people that I know, so that I am often in conversation with colleagues. I am fairly shy about meeting new people, and it is hard for me to approach someone that I don’t know. For me, being introduced to folks through better connected colleagues was a more comfortable way to start making connections.  If you are new to attending scientific conferences, it is okay to be by yourself or to primarily interact with other members of your lab or people in your program. But be open to meeting new people, and try to put yourself into situations where that will be possible. The more people you can meet and make connections with, the more the conferences will start to feel like a fun reunion rather than an intimidating professional event. ]]>Sun, 26 Apr 2026 14:00:32 GMThttps://www.coxevolab.org/the-itinerant-naturalist/it-is-okay-and-expected-to-ask-for-letters-of-recommendationIf you are an empathetic and caring person, you might feel bad about asking for letters of recommendation from current and former mentors as you apply for postdocs or permanent jobs. I don’t like to impose on other people, and I remember that there was a lot of activation energy before I would ask for a letter of recommendation earlier in my career. At this point in my career, I write dozens of letters of recommendation each year, and I have done so for at least a decade. With all this experience, I don’t think anyone should feel bad requesting a letter of recommendation.
 
            This post is oriented primarily towards graduate students and postdocs. I don’t think that undergraduates should feel bad about asking for letters of recommendation, but whether a given professor can write an informed letter will depend a lot on the specific circumstances such as class size and performance. However, you are well within your rights, and also well within standard practice in the sciences, to request a letter of recommendation from any of your grad advisors, or anyone that serves on your graduate committee, or any senior collaborator.
 
            Writing letters of recommendation for my trainees is part of my job. One of the things that I am paid to do is to train and mentor graduate students and postdocs, and writing letters of recommendation is part of that job. If you have a mentor who is reluctant to write a letter of recommendation, or tries to discourage you from applying for an opportunity because they would have to write a letter, they are in the wrong. Of course, there are caveats- if someone can’t write you a positive letter because you were a jerk or did not do your job, that is on you. Another caveat would be that you might not want a student to apply for something for a valid reason that has nothing to do with a letter of rec (i.e., the opportunity is not the best move, etc.). But simply not wanting to write a letter because doing so requires work is not acceptable.
 
            It may feel like you are responsible for a lot of work if you are applying for 40 tenure track jobs and most of those need a letter from your advisor. But besides being their job, it is not that much additional work to customize a letter for each opportunity. At this point, I have written letters of recommendation for each of my students, and updating and customizing is not a major effort.
 
            Besides being my job, I also don’t mind writing letters of recommendation because I want my mentees to end up in great positions. It is fun to write about the great work done by my junior colleagues, and I like explaining to search committees just why I think my colleague would be an excellent choice. Of course, I would not be in my current position without my mentors writing me letters of recommendation. So don’t hesitate to ask for letters of recommendation, and be enthusiastic about providing letters of recommendation for your trainees when your time comes. ]]>Sat, 04 Apr 2026 13:38:59 GMThttps://www.coxevolab.org/the-itinerant-naturalist/working-with-difficult-or-bad-mentorsDuring a career in science, you may be put in the position to work with difficult people. This can run the gamut from people with tricky personalities to abusive or toxic personalities. This can be difficult enough if they are just coworkers, but sometimes these difficult people will be your boss.

            Obviously, toxic or difficult personalities are not limited to academia or science. I worked for seven years for Radioshack (remember Radioshack?). This was an ideal job for me in high-school and college, and I made great money (for a part-time job) selling cellphones and TVs and computers. I had six managers during that time, and they ranged from the best and most influential mentor I have had in my life, to downright verbally abusive. On the positive side, I had a manager at Radioshack who assigned readings to broaden my horizons (Malcolm X’s autobiography!) and challenged me to do better in my college classes. I also had a manager who showed up drunk and stumbling, and was frequently verbally abusive (he was eventually fired). I had another manager who was a creep, not towards me, but he said many things that made me uncomfortable. I had another manager who was as dumb as a bag of hammers. So when I started graduate school, I was looking forward to having mentors that were experts, and who I could respect.
 
            I also have experience with mentors in science who were bad people. I am going to be vague about career stage for privacy reasons, but I had one mentor who was just a terrible person. Their transgressions included abusing research animals, sexually harassing students, verbally abusing and belittling everyone in the lab, and sleeping around in a department where their spouse also worked. I reported all of the awful behavior to the department chair and other faculty, and absolutely nothing was done about it. I have a decent capacity for suffering, so I just gritted my teeth and tried to leave the lab as quickly as possible.
 
            A substantial minority of the people that I know in the sciences have worked with a bad person, and almost everyone has worked with a difficult person. Sometimes even good people treat people poorly during period of stress (like being a pre-tenure faculty member, or high-stakes field or lab work). I think for decent people who may not be aware that they are having a bad impact on trainees, setting boundaries and explaining the bad impact of their behavior can help reduce any issues. However, for bad people, this may not work.
 
            There are steps that you can take if your mentor is irredeemably bad. First, you can just try to power through, like I did for a while. This may not be a good choice depending on your personality, if you have a long time to completion, or if the abusive behavior is really bad. I am not sure that it was the best choice for me, but it is what I did.
 
            Second, you can try to get help resolving the situation from sympathetic allies that are in a position of power. My experience is that this works best if you can actually remove yourself from the orbit of the toxic mentor (e.g., complete a chapter of a dissertation in another lab), as the toxic person is unlikely to respond to criticism from someone else. They might ease off just enough to let you finish and be done.
 
            Third, you can try to seek help from someone higher up the chain (e.g., if your undergraduate advisor is being abusive, you can reach out to the department chair). I think whether or not this works has a lot to do with the institutional culture around such things. Institutions are usually most interested in protecting themselves, and in my experience prefer to suppress reports of bad behavior, rather than solve them. I also think that the presence of a toxic personality in an academic unit might well be a signal that the unit does not care about reducing abusive behavior. My personal experience was that my reports of illegal and unethical behavior were ignored. But this happened back in the mists of time in the early 2000s, and I do think that awareness of bad behavior by mentors has increased, and tolerance for abuse has decreased. I also think that if something illegal is happening, and you have evidence/documentation, the institution may be forced to act. Whether or not you formally report bad behavior depends a lot on the specifics of your circumstances.
 
            Finally, you can always leave an abusive mentoring situation. This is what I did when I could, and I think it is often the best choice. After all, why choose to continue to work with someone who is being a jerk? I think many people, including myself, fall for the sunk cost fallacy when making these decisions. If you are two years into a five-year dissertation, it may feel like you wasted two years if you leave the lab. But those two years are gone, and suffering through another three years can have profound impacts on your mental health. Also, those two years are not wasted, even if you switch fields, because you have likely completed classes and learned research techniques that you can bring to a new position. Also, in the grand scheme of your life, two or three or even five years is not that long, and my perspective is that life is too short to be miserable for very long.
 
            However, you may well encounter difficulties leaving a toxic situation. Often the personality traits that make someone abusive also makes them want to sabotage your ability to leave. In my case, my toxic advisor tried to make me stick around longer, and I informed them that I was leaving at a certain point, regardless of completion. You might also be threatened with career sabotage. All I can tell you is that reports that a trainee is terrible are met with a lot of suspicion, and at least in my corner of integrative biology, nobody has such centralized power that they can scuttle careers at will. My only advice to you is that you deserve to be treated well, and if you have decided that leaving is the best course of action, then you should feel empowered to do so.
 
            Nobody deserves to be treated poorly or abused. And I think that the preponderance of mentors in our field are humane and decent people, even if all of us stumble sometimes in our mentorship of junior scientists. So if you are in a bad situation, reach out to people that you trust, and consider leaving if it is possible for you. You will be amazed at how life improves without a malevolent force in your life. And choosing to stick around in an abusive situation can have far-reaching negative impacts. All of us should take the lessons learned from all mentors, even the evil ones, and incorporate them into our mentorship to make sure that we treat our mentees in an ethical way.  
]]>Sun, 22 Mar 2026 18:00:07 GMThttps://www.coxevolab.org/the-itinerant-naturalist/why-is-multicausality-uncommon-in-ecology-and-evolutionary-biology I kind of enjoy the raging debates that you often see in the literature in the broad fields of ecology and evolution. These debates can be useful, because folks feel strongly about the points that they are making, and so often marshal all of their resources and rhetorical skills to advance their position. Although I definitely see the benefits of these debates, I often feel that many of them boil down to one person saying that Factor A is the only important thing for explaining some pattern, and the other side is saying the same thing about Factor B. But this makes me wonder why organismal biologists would think that most patterns are driven by a single causal factor, when I think the universe is multivariate and multicausal.
             In my own little corner of organismal biology, I have noticed this pattern in studies of the evolution of viviparity in snakes and lizards. We don’t need to get into the weeds on this, but the dominant hypotheses for the evolution of viviparity is that viviparous species can regulate temperature of the eggs, while oviparous species cannot (squamates usually have eggs in burrows that are not attended). Hence, selection would favor egg retention, with an endpoint of viviparity. The evidence for this pattern is biogeographical- at high latitudes and elevations, which are cold, a high proportion of species are viviparous. The fly in the ointment is that myself and other scientists think that it is possible that other biophysical variables are important. In fact, most squamates species are found close to the equator, so species at high elevations in the tropics constitute a big chunk of viviparous squamates. After all, oxygen availability decreases with elevation, as does water vapor pressure, and of course both of these variables are correlated with temperature and with each other. Because these are so intercorrelated, isolating the effect of one variably is difficult statistically. However, most papers have stuck with temperature being the only variable that matters, frequently not even considering other variables. Why wouldn’t other variables matter as well? I think it is because some people must think that only one variable could matter, when it seems more plausible to me that whatever drives the evolution of viviparity must be multicausal.
             There are many other great examples, such as whether scaling exponents are 0.75 or 0.67 for the metabolic relationship with body size, because the scaling exponent indicates whether volumetric scaling or the fractal nature of nutrient delivery networks drives metabolic scaling. Yet it seems obvious to me that both factors can be important.
             ​So why do we have dogmatic arguments about which factor drives X, without a whole lot of nuance or room for other factors? I am not really sure, but there are several possibilities. Making the case that it is a single, simple factor behind some broad pattern may be appealing to our psychology. Writing papers with a single driver may be more appealing to high-impact journals. And I think it is natural, if you put it out there in your papers that Factor A is most important, that you defend that conclusion.
             But I don’t think that is the best way to do science. We should be happy to prove ourselves wrong. A paper is not a static statement of truth. It is a data-based document with our best explanation at the time, which is going to be limited by the tools and information available to us when we wrote the paper. And more generally, I think our literature would be better if we moved beyond simplistic discussions of whether factor A or B matter, and take a more holistic approach that acknowledges the potential of multicausality driving biological patterns.
             I should note that there are many counterexamples that do acknowledge complexity and multicausality, and I think most work in most fields is not dogmatic about a single causal driver of patterns. It is also probably true that those examples are harder to remember because they are not beset with drama and conflict. However, I think that this is a pervasive pattern in our literature, even if it is not in the majority.
             What do I think should happen in my ideal world? Well, I wish journals, particularly higher impact journals, would not be so biased towards “clean” stories. I think The American Naturalist is a good example of a journal that publishes impactful work, but also tends to acknowledge complexity and potential for multicausality. I think it would be better if (for example), it would not be seen as invalidating or a threat to previous work to acknowledge that things may be a bit more complicated than we originally thought. And I hope that scientists grow more comfortable with thinking about how many biological patterns may be caused by multiple drivers. ]]>Sun, 15 Mar 2026 17:17:54 GMThttps://www.coxevolab.org/the-itinerant-naturalist/you-can-pick-your-job-or-your-location-but-it-is-hard-to-do-both
It is no secret that the academic job market is highly competitive. I am at a large, research intensive university in south Florida, and even very specific positions attract dozens of applicants. Besides being highly competitive, academic positions are often very specific. While really large and prestigious institutions might put out a general call (that is still quite specific relative to the diversity of fields in biology) for an ecologist or an evolutionary biologist, most jobs are more specific: a microbial ecologist, or a plant ecologist, or evolutionary biologist who studies invertebrates. The combination of a highly competitive job market and the uncertain and specific positions that open in a particular university means that even highly competitive applicants can pick either the type of they want, or the location where they want to live, but only rarely both.
            I should hit the pause button here and explain that I don’t put a value judgement on prioritizing either the type of job you want or where you want to live. All of this depends on the specifics of your situation and how you want to live your life.  I am just trying to be descriptive, not prescriptive. I am also not defending the way that things are, but I don’t think that anything is likely to change any time soon.
            I think as soon as you acknowledge and understand this tradeoff, then it makes the strategy for applying for jobs much more straightforward. If you can only be happy in the Bay area in northern California, you will need to be open to academic positions beyond the tenure track, and probably non-academic positions as well. On the other hand, if your primary goal is to be a tenure-track faculty member, you should apply broadly, irrespective of the location of the position, which will maximize your chances of getting the kind of job you want.
            By the way, I think this sort of logic applies to any type of specialized job. If you want a job in a zoo, or you want to work for the National Park Service, you also are unlikely to be able to have a great degree of control over the location of your job. Of course, there are many jobs (nurse, doctor, lawyer, accountant) that can be relatively easy to transfer between locations (at least relative to jobs in academia).
            As with many things, there is a sort of middle ground. I think you can perhaps focus on a particular region, or try to avoid a region, and still be successful, particularly if you have a competitive application. For example, while I grew up in the corn belt of the Midwest in Iowa, I don’t particularly like cold weather. So while I applied to jobs across the US, I focused on jobs in the southern third of the country. Some regions (e.g., the West Coast, the Northeast, the Midwest, the Southeast) have a ton of schools, and you would be more likely to be successful in focusing on those areas than on a single city or state.
            Finally, I think it is a good idea to try and be open minded (if possible given your circumstances) about where you would be willing to live. Way back in 2014 when I was first on the job market, I got interviews at many places (rural Kansas, rural Illinois, rural Pennsylvania, Jackson, Mississippi) that would not have been at the top of my list of places that I wanted to live. However, in each case, I met amazing people doing good work in those schools, and I was usually surprised by how much I liked the town and the area. So if there is a chance you might be willing to live somewhere that is not your top choice, go ahead and apply, and you might be surprised at how much you end up liking the institution and the area. ]]>Sat, 07 Mar 2026 20:51:02 GMThttps://www.coxevolab.org/the-itinerant-naturalist/what-is-the-most-stressful-part-of-an-academic-career-in-scienceThere is no doubt that academia is stressful for many folks. And while not all scientists are in academia, almost all will have academic training at the undergraduate, M.S., or PhD. level. So what is driving the stress in academia? Well, there are many candidate factors- high to unrealistic expectations, a competitive culture, lots of critical external evaluations, and uncertainty. I think anxiety is an important factor for many people in what kind of jobs they want and whether they want to stick with science.
 
            One thing that I wanted to mention is that I don’t know that academia is more stressful than other careers that are highly competitive and involve years of training. I would have to imagine that vet med school, or med school, or law school, are just as stressful or more stressful than grad school in the sciences, at least for most folks. I suspect that competition, and the accompanying uncertainty, is probably always going to be a generator of stress.
 
            My own experience with stress in academia might be a bit atypical, because I rarely feel much in the way of stress, and I struggle to be aware of when I might feel stressed. I don’t think I am consciously suppressing anything, but I just don’t seem to notice that I am stressed out unless something makes it obvious. As an example, I am pretty sure that I was at my most stressed out when I was a postdoc, particularly during the final year or two when I was on the job market. I recall feeling busy, but not particularly stressed. However, during this period, I would sleepwalk regularly, enough so that it was a joke between my wife and I. I had not sleepwalked as an adult before, and have not since. I have to imagine it was stress, driven by busyness and uncertainty at this transitional period in my life.
 
            I was curious about how typical it was to feel high stress at the postdoc stage, so I asked about a dozen of my friends in science. These folks have positions ranging from working for the federal government to professors at liberal arts colleges. This is of course not a random sample, but it is a bit of a sampling of when mid-career folks like me have felt the most stress.
 
            Almost everyone I talked to (10/12) felt the most stressed out at the end of the PhD and during their next position, whether it was as a postdoc, adjunct lecturer, assistant professor, or other professional position. The two folks who were not most stressed during this period felt the most stress either as a pre- or post-tenure faculty.
 
            The most straightforward interpretation of this pattern is probably that uncertainty and contingency are major generators of stress and anxiety. While I was having some success getting interviews and offers during my “big” year for applying for a permanent faculty position, there was also a massive amount of uncertainty. The offers kind of dribbled in, and I had to turn down okay offers before I had a better offer a couple of times, which was a gamble that I was pretty nervous to take. In addition, while my wife is not an academic, there was some uncertainty around whether she would have a job when we moved. And I also think just not knowing where you will be for the next substantial chunk of time can be stressful.
 
            ​Beyond contingency, I think the other major factor is if the job/school/advisor is a bad fit, or if you end up working for toxic person. At least a quarter of the people who I spoke with had a difficult boss during their most stressful period. Clearly, being required to work with someone who you don’t click with, or someone who is a jerk, would spark anxiety, particularly if they control your paycheck and your future.
 
            ​I don’t know that any of the above will necessarily help anybody who is in a stressful period. I think in most careers there will be times of high stress. If you have an anxious personality, I suppose it might be good to be prepared for the stressful times, and it most likely will be during the end of the PhD and beginning of the postdoc. I have a bunch of friends who saw mental health professionals and took anti-anxiety meds to make it through the difficult times, and I think that could be a great way to be prepared for the tough times. If the stress is due to something you can change (e.g., a toxic mentor), then it might be in your best interests to pivot to a different lab or project. But mainly I just wanted to convey that almost everyone experiences these periods of high stress during an academic job, and the experience of myself and my network is that these periods do not last forever, and you can often come out the other side more resilient and hopefully empathetic with others who are having a tough time. ]]>Wed, 24 Dec 2025 17:11:47 GMThttps://www.coxevolab.org/the-itinerant-naturalist/everyone-is-someones-first-choicePart of being a scientist is applying for things- grants, fellowships, jobs, and others. And of course, much of the time you are rejected after applying. However, sometimes you do get a grant, or a job, and at least part of the time, you might know that you were not the first choice. So what does it mean if you are a second choice, and what should you do about it, if anything?
            I have personal experience with being the second choice. I happen to know that I was the second choice for the postdoc position that I eventually got. I was also the second choice for my current position. How I know does not particularly matter, but there is often evidence of being the second choice in the timing of an offer. In both of my cases of being a second choice, I was informed by my prospective employers that I was the second choice, so I could not salve my ego with the balm of ambiguity.
            What does it mean that you are the second choice? I think the only thing it means is that the prospective advisor, or search committee, or department, decided to offer the position to someone else first. You won’t ever really know why this happens, but having seen this from the other side, it is usually contingent and has nothing to do with candidate quality. The other candidate might just fit the job ad or position a little better, even if the department (or postdoc advisor) really liked you. You might actually be the first choice, but the department choice was vetoed by the chair or dean. Even if you were not the first choice of the department or dean, you were some of the faculty’s first choice, guaranteed. And even if it is just one person making a decision (like a potential postdoc advisor), they are making their first and second choices with imperfect information. Speaking again from the other side of the decision-making, I have often reflected on how a department’s second choice turned out to be perfect for what we needed, and probably worked out better than our first choice.
            So what should you do about it if you find out you are the second choice? I think the only thing you need to do is not give that fact any weight at all. You were someone’s favorite (at least if a department or committee is making the decision), and nobody remembers who is first or second after a few months anyhow. My postdoc advisor ended up being a friend and long-time collaborator, despite being his second choice. I have loved my time at FIU, made friends with good colleagues, and earned tenure at FIU despite being second choice. It would be a real tragedy if something ultimately trivial like being a second choice poisoned what was otherwise a good opportunity. 
]]>Sun, 07 Dec 2025 18:19:48 GMThttps://www.coxevolab.org/the-itinerant-naturalist/the-dangers-of-abstraction-in-biology​I worry about abstraction in biology. When I refer to abstraction, I am generally referring to anytime we somehow transform, or abstract data in some fashion so that we are interpreting a transformed version of the data, and not the original data. What might be an example of this? I always think of molecular phylogenetics. The actual data used in molecular phylogenetics are individual sequences of DNA. There is then a layer of abstraction in aligning those DNA sequences to infer homology, then yet another layer of abstraction when those alignments are fed into an algorithm to infer a phylogeny.
            Of course, abstraction is inevitable. In the example of molecular phylogenetics, abstraction has occurred before we actually get to the DNA sequences. If we imagine that those sequences are generated by Sanger sequencing, then what is actually read by a sequencer is length of a sequence and reflectance of a labelled nucleotide in a capillary, which is then abstracted by a program into a linear DNA sequence. But I would argue that in this case, we can assume a nearly one to one correspondence between the actual DNA sequence and our abstracted linear sequence in a text file. I think where we need to be concerned is when we have reasons to think that the relationship between the actual data and the abstracted data is diverging from that one to one relationship.
            So why do we need to be concerned about abstraction? I think because it can generate problems that are non-identifiable. Using the same example of molecular phylogenetics, the step of alignment and assuming homology might not be appropriate because of pseudogenes or errors in alignment (particularly for very large datasets). There are many issues that can occur with the next step of reconstructing phylogenies, either problems like long-branch attraction that occur due to data problems, or because the method of reconstruction is inappropriate or incorrectly implemented. Of course, the phylogeny is rarely the last step of the process, as the phylogeny can then be used to map the evolution of traits, or trace the biogeography of a group, or to understand historical demography. For example, if we actually want to know how many times a trait has evolved convergently, we then need to use hierarchically abstracted data to make the actual biological inference that we are actually interested in. If our abstraction has created misleading patterns in the data at any stage, this could lead to making inaccurate inferences.
            I have been using the example of molecular phylogenetics and phylogenetic comparative biology, but that is only because these are fields where I have a lot of practical experience with data and methods. I can come up with similar issues with abstractions with species distribution modelling, visual models, and biophysical modelling, and of course there are many others.
            What should we do about abstraction? Well, I don’t think the solution is to avoid all abstraction altogether. I think that as scientists, we are already pretty comfortable with uncertainty, and in historical fields like phylogenetics and phylogenetic comparative biology, making inferences based upon heavily abstracted data is unavoidable. I do think that one thing that we can and should do is to both acknowledge the uncertainty that results from abstraction, and resist the urge to write papers more forcefully than is merited by our data and methods. I know that in order to get higher impact papers, making a forceful case for a single narrative is often the best bet for acceptance and impact. But we should also be precise in the confidence of inferences. From a pragmatic perspective, if we are making abstractions (e.g., inferring species distributions or physiology based upon remote sensing data) that can be groundtruthed with actual data, we should do so, either in the same studies, or encourage studies that do so. Additionally, even for historical data that cannot be groundtruthed, we should try to conduct robust and severe tests of hypotheses (sensu Platt and Deborah Mayo) with different types of data and analyses (e.g., integrating fossil data into biogeographic studies based on molecular phylogenetics). I think that the best work already employs these practices, but there is great scope for wider adoption of these methods. ]]>