2016

Diversity

In the absence of a strong statement from the UGA President regarding the recent election, and more importantly the implications for bigotry in our society, I just have to say something on this blog - my tiny forum.

(was that a comma splice?)

I hope it is evident from the fact that of my 9 graduate students to date, 7 have been women; that when you look at the undergraduate researchers in my lab, and including the 2 women in the lab now (one starts in January) there have been 18 that have made substantial contribution to the lab's mission and 14 of those are women (and 3 people of color); that when you look at the postdocs in the lab we have had only two white males out of 5…. well, a lab that studies diversity as its index of interest has done OK in terms of having a diverse group of researchers.

I hope it is evident that we interact with folks from all faiths, all races, colors, creeds. I hope it is evident that a study of diversity on this planet, whether it be of barnacles, seastars, fishes, or folk music, requires that we be open to what that diversity means.

It shouldn't be necessary, but I want to be clear: everybody is welcome to learn what we have to pass along in the Wares Lab.

Healing through Natural History

I just got back from the 2016 Western Society of Naturalists meeting in Monterey. It was obviously a meeting upset by our post-election fears over funding, bigotry, the environment…. but a good time for us to come together (sometimes cry a little) and celebrate the more-important-than-ever work that we have as ecologists. It can make one doubtful, knowing that your "president elect" is somebody who would almost certainly mock your work.

What was really inspiring was seeing all that the people in this group of strong, brave ecologists create. Knowledge, beauty, and even buttons :) Jackie Sones, the WSN Naturalist of the Year, is not only a brilliant biologist but also someone who shares what she sees on a near daily basis, and reminded us that we need to proudly claim the title "Natural Historian" or "Naturalist". Below, I proudly show my Ed Ricketts button, she had a whole series!

So, I'm back to work. And, maybe, a little more "woke up" than I was before. The fight moves forward - in politics, in the intertidal, and in between.

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Family Time

A little over a year ago, I wrote about how hard it is to keep up with life as well as everything we are challenged to do at work. I'm adding to this a bit today; it is hard for all of us. It is doubly hard for those of us raising kids, and I'm going to add - raising a kid with autism. For some it is hard to identify the boundaries of autism, or people have pretty severe preconceptions of what that means. A really inclusive term I've learned lately is "neurodiversity", which really helps us understand all of the interactions we end up having all day, with all sorts of people. But in particular, it reminds us that some folks are exceptionally talented in some elements of cognitive and/or social thought, and others have a mixture of differences in how they perceive sensory or other stimuli. That - to be vague, because otherwise it is personal business - is my son.

I think we take it for granted that faculty, especially junior faculty who are getting themselves known, will travel to give talks at lots of different universities, do fantastic amounts of outreach, as well as establishing top-notch research programs. But those of us considering the efforts of our junior colleagues need to be aware of the toll that going and giving talks has on family life, not to mention requests from our funding agencies to spend a week out of town to serve on funding panels! This work is necessary, and certainly service for our community of science. But, as with most invitations to give a talk at another school, I see that as an unnecessary burden to put on my family. I'm not going to shirk my support of the community, I pretty much never say no to an ad hoc proposal review, and I do plenty of manuscript editing and reviewing as well.

Travel, however, is something we should all be considering carefully in an age in which information can be shared so readily. I fully recognize that nothing yet replaces putting a bunch of colleagues in a room to discuss ongoing collaboration, to meet over shared interests, to consider the merits of a new idea or proposal. But we should find recognizable modes of service and sharing in our community that don't require so much travel, so much time away from home. There are certainly some junior faculty out there whom I've gotten to know their research because of social media; there are others who are great at other forms of sci-comm.

When you can, save the big trips for fun with your family and friends. You'll value that more some day.

Implicit Bias - When we teach?

Look at your syllabus and the papers/books you are having students read. Now look at the composition of your students - is there a mismatch?

For me, a few years ago, I (finally) noticed this. Our grad population has been majority women as long as I've been at UGA, sometimes overwhelmingly so (certainly my own lab has been). So I started trying to be sure that when I'm representing science to them as an instructor, our students see how science output is generated by a diverse population of scientists - right now, just focusing on gender.

It can be tricky. I’ve had easy success in my climate change classes, where I readily know of work by folks like Jenn Sunday, Morgan Kelly, Sinead Collins, Gretchen Hoffman, Christina Richards, so many researchers representing tremendous diversity of background, gender, and so on. The challenges come when putting together a new class, or on-the-fly changes. When I wanted to follow G. E. Hutchinson’s Santa Rosalia paper in the ECOL 8000 class later this semester with a series of other readings/exercises on diversity and function, the first papers that came to mind simply happened to all be by men. So, I have sat down to address this and I am still fine-tuning what papers and people fill the same roles while representing diversity better in science. Now Karina Acevedo-Whitehouse, Randall Hughes, and Jane Lubchenco are certainly in the mix.

This process has its hiccups. In my coalescent theory grad class, it is easy at first to think of Kingman, Wakeley, Hudson, Tajima, Turelli, and so on. I saw that the readings so far were heavily white men (not heavy white men!). So in a week when we needed a paper to look at how summary statistics and site frequency spectra are used in applied ways, I thought - who do I know that is a talented population geneticist working on interesting data sets? The first younger name that came to mind was Melissa Wilson-Sayres, and I quickly (being in a rush with standard faculty/home life) found a good paper analyzing diversity on the Y chromosome. Was it the perfect paper for our needs? No. It is good but has some confusing details that I didn’t intend to hit the students with (yet). But it will lead to a good discussion.

And maybe this is the interesting part as a teacher, as a mentor, in representing diversity. We are often going to our easiest, most readily-available, resources that we know fit the job. We are overwhelmed, or sometimes actually feeling lazy. And to do better - representing those needs while representing diversity - means we need to add reading to our already tall reading pile! In this case, I maybe should have looked through this and a few other of Melissa’s papers, as well as those by folks like Rebekah Rogers or Lacey Knowles (whose papers I know well enough, but I didn’t want to get into the structured coalescent yet, the realm of phylogeography). 

These are of course just a few quick examples of ways to pay attention to lazy bias in our academic world. How many of the invited speakers you have hosted have been women? (In my case it is less than half, but if you include a couple of invitations that had to be turned down, my list doesn't reject a null hypothesis of equality 😀 ) Who is being invited for your symposium or panel? Who is being invited to be an editor or a reviewer? And of course, who is being hired? These are questions being generated and answered by the new Diversify EEB list, initiated by Gina Baucom - one of the Ph.Ds from UGA Genetics.

Now, I better get ready to go teach - today is graduate class in coalescent theory (80% women) and ECOL 3400, professional aspects for undergrads to consider as biologists. And one of the things they will certainly be considering is their place in this world of science, and how to make it better.

Sharing

Some of you know my lab space is unusual. We have a sofa in the lab, along with crepe paper streamers and dangling jellyfish and fish over our map/planning table. There is usually a dog in the lab. There might be beer somewhere nearby.

Much of our work is on computer, so there is lots of space for computer work, scope work, jars for tissue handling and specimen curation. It doesn't look like a "genetics" lab beyond the row of pipettors and a couple of centrifuges, a few beat-up thermal cyclers. It is a place where biology happens, for sure.

One of the most important things to me about a lab is that it is a place where we interact. That's why some of the shelving came down a few years ago, so we could see each other and talk more effectively. So we could get drawn into each others' problems, and victories. So we could make each other better biologists, better scientists.

A great example of this has been the increased presence of Bud Freeman in the lab. Really, its our lab now. Some days we talk seastars; some days we talk bass. Some days we talk about whatever the students want to talk about, or we geek out about iPhone technology and new apps. But the shared space makes us better scientists, lets us ask questions and take things a little bit more slowly, give everybody time to think about a problem. I appreciate that immensely.

Below is a rare photo of Bud and I, not in the field, not in the lab, astoundingly both wearing jackets and shirts with buttons. We were at the State Botanical Gardens to celebrate the retirement of Jim Porter, a great night to be thinking about great colleagues.

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Detritus

I came across this short piece I wrote a couple years back - maybe you'll enjoy.

At this point in time, almost anybody with a Facebook account and an interest in the sea has been introduced to the crowds and chorus lines, even desk workers, cast in cement and placed in the tropical waters off Cancún. These statues were created by Jason deCaires Taylor specifically for their transient appearance of life underwater - that is, human life underwater - while creating a more permanent home for the community of marine invertebrates that foul hard substrata (underwatersculpture.com). Calcareous beasts, corals, tubeworms, tunicates, sponges, all create a mesh of real life on top of the visual; mobile invertebrates scan through the matrix for food and shelter, and with time the original features are being obscured. At some point, we can imagine that only the arrangement of these structures will be perceived as somehow non-random, the original features masked by a husk of life. If our current culture loses the coordinates of these installations, and they are later rediscovered, will we have left clues that we were once there despite the ways in which other phyla have bent the original message?

Efforts like these suggest our collective desire to achieve art at large scales, as with landscape architecture and massive installation art, and to imaginatively consider how our interaction with the natural world can be a process, not simply an intervention. One question worth considering is whether we have asked the ocean, and its fauna, which of our creations it prefers? Osborne Reef is effectively one of these exercises where we dig a hole only to fill it in; in this case two million tires were lashed to the sea floor near Fort Lauderdale in the hopes that sea life would colonize the structure and provide a boost to local biodiversity and tourism. Unfortunately, while tires at the water surface on floating docks are appreciated by the ‘fouling community’ of tunicates, bryozoans, and hydroids, the project was a distinct failure and is now being used as an exercise for military dive crews to go clean up the unfouled (but unsightly) tires. It is often not easy to know how marine life will respond to our presence. Ecologists famously study the recruitment (larvae settling and surviving at a location) of marine life with what can be afforded at Home Depot. PVC pipes, Saf-T-Walk, plexiglass plates, mesh bags filled with rocks, dish scrubbers, bricks covered with zip-ties; all of these and more have been used in the quest for the appropriate rugosity or ‘feel’ that animals or algae will appreciate, the ability to find the device again once it is fouled (they are usually bolted or staked to the substrate), and something of little value so it is not picked up by curious clam diggers or tourists.

Sometimes, of course, it is less important what component of our modern life has been submerged in the water than that it is voted on by the beasts that live there. Gregariousness is the tendency of marine animals to settle, as nearly passive larvae, near their relatives (preferably the same species). They sense the residue of brethren in the water, as if asparagus eaters preferred each other among humans, and are attracted to settle somewhere that has seemed to be a good choice for those who chose before. Generally, once these organisms choose a home, that is where they will remain for the rest of their life, and the success of their offspring will also in part depend on this choice. The general strategy of marine invertebrates is to produce offspring far in excess of the number that would replace the adult generation: for every thousand or ten thousand offspring released, perhaps one is successful in finding a home that is suitable for releasing another thousand or ten thousand offspring.

The action of settlement, sometimes in pulses of familial larvae, sometimes entrained by the chemical clouds leading to gregariousness, means that limited resources for recruitment often cannot fully represent all the life that is out there. Thus a truism in the field of biogeography, the study of how organisms are distributed: as more area is assayed, more species will be found. They are often non-randomly clumped around the tires ringing floating docks that are tied there to protect boats, themselves harboring barnacles and limpets until their season in dry dock and a fresh coat of paint. If you search all the tires, you will start to recover a distribution of species that better reflects the pool that is out there (though not the corals hoped for at Osborne Reef!): a few species that are quite common, and then a few specimens of things that are quite rare, a plotted curve that defines distributions of cell types in organs, languages in society, and genetic variants (alleles) within the species of fish that come by to nibble away at the organisms that have settled on the dock, close to slicks of diesel fuel but often safe from being exposed to the air as the tide goes in and out.

Really, whenever there is an edge between land and water, humans seem to have an urge to put what they no longer want into the water, and leave it there. Chad Pregracke is a man who has made his life’s calling into that of steward of the Mississippi River. The number of things that he and his crew have recovered and recycled is unbelievable, including a tractor that by that time had trees growing through it and encrusted by zebra mussels along the muddy insertion points. Many local and regional organizations do these kinds of river clean-up events as well. Sometimes what gets into the river is because of storms and flooding, washing our remains into the storm sewers and rivers, and ultimately out to sea where the chemicals we ingest change the genders of fish and invertebrates; where the plastic we toss, so much every day, forms translucent islands the size of states in the middle of our oceans. Sometimes the sofas, vehicles, refrigerators, engines, oil filters, condoms, hair clips, shoes and shopping carts are submerged below the waves or the river so that nothing more complicated must be done, or so something more criminal is hidden. Or, maybe it was just fun - these items are living out a scenario that nobody ever expected. What our detritus adds to the environment is structure, like a submerged stump or brush or a gravel bed might naturally provide heterogeneity in the water. Fishermen know that diversity thrives on edges (and that is where they are most likely to lose their line), and so even as we create unsightly banks of 20th century remains, we can ask how these things – positively as shapes, negatively through the chemicals they may leach – influence the pattern of biodiversity.

Dusty Kemp, a marine biologist at the University of Alabama at Birmingham, told me that in doing survey work on a new cruise ship channel off of Key West the number of things found just beyond the piers and plazas was unbelievable. Bicycles, car parts, and cutlery, as Bjørk might sing, all of them shiny at first and eventually succumbing to the oxidative process of the sea and of becoming a home for animals that must partially burrow in, that change the chemistry near the surface, that are digesting and egesting and eventually replacing the original form, as with fossilized wood. Our trash is home, our trash is food – for something. Shipwrecks, popularized as new habitat for the coral reef community, can temporarily devastate the same community as local concentrations of iron and pollutants goes up, firing up the algal and microbial communities and changing the food web as long as the resource is available.

So what happens when we intentionally place art into the ocean, as with the sculptures, or into the rivers or bays? These events can be treated as minor biogeographic events, where the organisms are distributing themselves across our art to create something more palatable to divers and biologists. But there is an ecology going on there as well. Wim van Egmond (micropolitan.org) is a Dutch photomicrographer - that is, he makes his living and his life taking pictures of the miniscule in their drops of water. At some point he recognized, as many aquatic ecologists do, that the distribution of organisms is not uniform in the fluid. This is known as the paradox of the plankton, in some circles. That is, since we assume as big terrestrial organisms that an ocean or lake is just a big well-mixed homogeneous bathtub, it is difficult to envision how so many diverse organisms partition this space and find unique sets of resources on which to thrive without competition eliminating all but the most generalist consumer. However, in any fluid medium there will be adiabatic packets of fluid that contain slightly different environments and mix at a rate slower than we would expect when we are used to cooking and stirring with a wooden spoon. Wim recognized that terrestrial interjections into these fluids also present non-homogeneous substrata for colonization. Putting artwork into the canals of Amsterdam, he discovered that different types of freshwater inverts and algae would colonize particular types of paintings, with greater (and in his words, more interesting) diversity colonizing “good” art than starving-artist-back-of-sofa art, covered in nematodes. This may be the medium: oils and pastels versus acrylics. Or it may be a component of the biological world recognizing the quality at some higher level of what we are inserting into their world.

Van Egmond indicates that this is more than the typical dictum of the microbial biologist: “everything is everywhere, and the environment selects”, meaning that small organisms have a cosmopolitan distribution in the global sense, but are found in varying densities depending on the microhabitat being evaluated. His work in microbial art climatological research depends on careful observation and identification of microscopic organisms after immersion. His project so far has suggested that organisms such as desmids and chrysophytes, two types of algae, are associated with some of the highest quality art. Even with these simple organisms, there may be distinction between masterpieces, and those works that are “aesthetically pleasing…[but] may lack a meaningful content.” Other algae, such as Pediastrum, are observed to “blossom [only] on trivial works of art.”

At times the type of organism attracted to a piece could be indicative of the intent of the art: amoebas with “fluid forms and contemplative works”, copepods on “tense, mediocre works”, nematodes on art with too many colors, and ostracods with “solid and robust works of art” (even an indicator of investment value!). The research, importantly, has controls on its own results. Wim indicates that when radiolarians are found on a piece, it is a “sure sign that the submerged artwork has drifted too far, and you are now situated in the middle of the ocean. Flush the artwork thoroughly and start all over.” With bacterial colonies representing the nadir in artistic merit, it may yet be necessary for modern DNA sequencing technologies to properly sort the association of these microbes from their preferred (and designed) habitats.

Our every creation ultimately interacts with the natural world. A disproportionate amount of what we have made and consumed is now defining either the subterranean microhabitats of landfills or is crossing the boundary into the aqueous through rivers, lakes, and oceans. Here lies an opportunity not only to study the biological impact of excess, but the aesthetic impact. Users on Facebook can 'Like' pages like those showing the images of Jason deCaires Taylor all they want, but until we ask the remainder of the biota, maybe we don't really understand the varied appeal of what we do. The appeal of design is a democratic process, and the designer has to consider her constituency carefully.

Tired of the BSC

In a recent blog post, Jerry Coyne argues that recent evidence that there are 4, not 1, giraffe species, is insufficient. This argument is predicated on the almighty Biological Species Concept - that if they aren't reproductively isolated, they aren't species. I'm getting tired of this purity test. To me, reproductive isolation is sufficient but not necessary. There are ample cases of reproductive isolation (to varying degrees) within species, among populations - whether it is Drosophila, Mimulus, or Pisaster. An incredible suite of dynamics affects populations and the fitness of outbreeding can be determined by far more than the on/off switch of Dobzhansky-Muller interactions. Perhaps if "species" were not our holy grail for quantifying diversity and naming it, we would recognize that reproductive isolation is not a species-level trait. Sometimes it affects populations within an ecologically and phenotypically distinct unit that is worth recognition as a "species" because it likely has a distinct function on this planet. Sometimes, clearly distinct species are not reproductively isolated - and this is the argument being made by Coyne. How can we call the 4 new Giraffa species "species" if we don't attempt to cross them?

Again, this sort of purity test avoids the rationale for why we name things. We name things because they are evolutionarily and/or ecologically distinct, with different distributions, functions, or histories on a landscape. The point of cataloguing species is not to satisfy evolutionary biologists - it is to understand how this planet works.

More to the point, naming species and drawing a boundary around them ignores the importance of ecological and evolutionary diversity within those entities. Do I think the two lineages of Notochthamalus scabrosus are separate species? Probably not. But who cares? They interact with the world in different ways, and it is important we know they exist and where they are.

Reproductive isolation is one of several traits that may be used as a criterion for distinguishing our biota. To throw away the other criteria, suggesting they are less important or less useful, biases and slows our ability to really understand what makes this planet tick, and that is far more important to me since this diversity is disappearing so quickly.

Back in the Saddle

First day of the Fall 2016 semester is upon us! I'm not able to teach my "evolutionary responses to climate change" class as it didn't attract enough students, that's a bummer. Instead I'll be teaching a grad workshop on coalescent theory, and teaching part of the Intro grads class for Ecology. Seems like enough to do!

I'm still wrapping up loose ends from the summer of teaching and research at FHL. Two projects have emerged, one where we will be doing some RNAseq on individuals from an experiment on Pisaster, one where I am resequencing a cline to see if it is stable. The lab is now one grad (Karen), one undergrad (Katelyn), one comrade (Bud), I know we have enough to do and time to write proposals too.

Friday Friday

OK, so this has to do with the final push of getting the class ready for Friday Harbor. Morgan and I only netted 6 students this year - so I don't know what that means for the long-term scope of this class. But still, a lot of quality time to be given to the 6 students, a lot of lectures, pulling reagents and equipment lists together, figuring out logistics and tides and vehicles and housing and field guides and ….

But it is Friday. Yesterday I pulled together a manuscript for a colleague for whom English is a second language; it will be submitted before I go. Today I finished a grant proposal draft that isn't due for a while, but my colleague and I are both going to be away most of the summer so we are kicking that around. Edits on another manuscript earlier this week. Meetings with teachers at school.

But it is Friday. So much still to do.

But it is Friday. The building is so quiet.

It is Friday.

I might not get more done today.

Friday Harbor

Done teaching for the spring. Whew.

For the first time, however, I'm actually teaching in the summer. I've done a Maymester course with Jim Hamrick for OTS, but generally I use the summer for research, travel, R&R, writing proposals. This year I'm delighted to be an instructor at Friday Harbor marine lab, one of the most amazing places in the world to be a biologist and interact with other amazing biologists.

One of the few downsides, however, is that to do research there - the exact projects we have proposed - means getting our act together ahead of time, knowing exactly what we need and when we need it. A lot of equipment and supplies are already at FHL, but that doesn't mean they are laying dormant waiting for us. Cooperating with the whole crew at Friday Harbor is, of course, part of the experience of getting research done close to the field (unless you are lucky enough to live there!).

So, this month is a good time for me to be in the lab. All the undergrads are gone, and as it turns out after 20 years I'm pretty good at rocking out a PCR here, a gel there, organizing equipment and supplies, and thinking of how amazing it will be when I'm there.IMG_7510

Publishing Prowess

Delighted to have a paper out today in PeerJ describing my work with Lauren Schiebelhut where we show that the apparently overdominant diversity at an elongation factor locus in Pisaster ochraceus is, somehow, miraculously, associated with sea star wasting disease.

I'm super pleased with the paper - I'd had a hunch about this for years - but also pleased with the collaboration. Getting the chance to work with Lauren, who is at UC Merced, happened opportunistically because she is also studying diversity in Pisaster. But the way Lauren threw herself into the project on my behalf was really nice, and in the end we found a surprising result that we - and everybody else - will still have to scratch our heads on "how?".

In fact, the fortuitous sharing involved in bringing a project like this together - samples were also kindly provided by Morgan Eisenlord, a student in Drew Harvell's lab, along with specimens collected by PISCO and by folks working with Mike Hart at Simon Fraser - is one of several reasons I went with PeerJ over a better-known, dare I say "prestigious" journal.

I've had three papers now, along with several other pre-prints, published at PeerJ. The experience has always been great: super professional and friendly, inexpensive, quick, effective. My paper on mitochondrial diversity in Agaricia corals was intended as a minor contribution, yet has been downloaded over 300 times already. These alt-metrics give us a better sense of how our work is actually being utilized. It has only been cited once so far (it is only 18 months old) but as I said, I assumed it would be of minor impact, and if nothing else it led me to a great interaction with Josh Drew through his student.

But this Pisaster paper I actually do think could have a greater impact. I even pondered if it was good enough for a "big" prestige journal. What stopped me? I'm tired of the ego-stroke of these big journals, in exchange for huge dollars going into publisher pockets, my science being hidden behind a paywall for students and scientists who are at institutions that do not subscribe, and no guarantee that this work gets any better exposure. The peer review works the same at PeerJ, only they actually tell me they are sorry when it takes more than a few weeks. The reviews are published alongside the manuscript so you can learn some of the process by which the paper is improved. I believe that publishing is changing, and if I cling to the old way I cannot contribute to that change.

I've been very happy with my PeerJ publications so far. This paper is probably my most interesting test. As a pre-print, it had already been downloaded nearly 100 times - that suggests that the work is of interest to people. It is free for you to read, or for a young person in a distant country to read if they have internet access. The science is just as good as in any other journal, but it is immediately accessible and I believe that I'm not contributing to this name game that scientists play: without reading each others' papers, they gain a general sense of not just the TYPE of science, but the quality of that science, by simply scanning a CV. We all know that isn't true, but it is a shorthand, a means of quickly pondering what somebody has done.

Instead, I'm asking you to read my work. In ten years, I hope that a huge number of my papers are in PeerJ, and you won't know if the work is interesting unless you actually read it.

More on Wiki

I've professed my love for wikis as a tool for organizing knowledge before! I've used so many flavors over the years, including PmWiki, a wiki platform based in Python (had terrible problems with access control, my inexperience…), and MediaWiki (which is the software that runs Wikipedia, but requires some pretty tricky MySQL installations). Around the lab, research, and in teaching, I use the OS X flavor of wiki, because it requires the least amount of knowledge of mark-up language and so some of my colleagues have actually contributed (much moreso than in instances when we were using MediaWiki, for sure).

Last year as I prepared to teach my molecular ecology course for grads, I was contacted by the WikiEdu foundation and asked if there were assignments using Wikipedia that could be incorporated into my class. I actually knew exactly what we could do: prior to this month, somehow despite all that was already on Wikipedia, there were no entries for two key, basic models used heavily in population genetics: the Infinite Sites Model and the Stepwise Mutation Model. Students in my class wrote these entries as one of their major assignments for the course, and I'm very pleased with the resulting contribution.

These entries will almost certainly be edited and updated, I hope you take a look and consider making your own contributions and additions. The goal isn't permanence, but an entry into understanding both these models (I'm pushing very hard on making sure the class understands and ponders assumptions, as molecular ecology is an inference-heavy field) as well as epistemology - how we know what we know. It changes ones opinion of the science literature, of books, of Wikipedia entries, of newspaper articles, whatever, if you have actually contributed to this knowledge.

The WikiEdu folks were extremely helpful; I deviated pretty heavily from their plan for the lessons, but not because their lesson plan wasn't a good one. And, in fact, there is a lot that could have been done better with this exercise. I'm sure the students thought it might be a bit of overkill on the time involved for what in a typical class might have been a 2-3 page paper that gets red-penned and returned, a grade recorded. I get that; I'm no perfect instructor.

But I really appreciate the thought and consideration that went into these entries. Having your work made public is kind of scary; it continues to be for me even though I've been doing this for 15-20 years. A paper coming out is an opportunity to share what you know, and often results in being told something you didn't know (and perhaps should have known). Nevertheless, if we don't share what we learn, share what we know, it is very difficult to build and grow scientifically.

Lecturing

I'm almost halfway through teaching "molecular ecology" to 10 PhD and MS students and a handful of postdocs. Today we are grappling with the history, and more importantly the contemporary view, of phylogeography - a method to understand how time and space and the earth sciences interact with time and demography and evolution.

I feel almost guilty that, with high hopes as the course began, I have settled into a weekly pattern: Tuesdays we tend to open class with a little "molecular ecology moment of zen" to re-wrap everybody's minds around the topic at hand, usually a short exposition of a paper that has just been published (today it was this cool one on spider phylogeny), and then I lecture.

(Thursdays are for practical exercises and discussion of a paper or concept, led by a student and often heavily facilitated by me)

The lecture part though - I'm supposed to be embarrassed by this these days. We are told from all directions that our students need to be engaged frequently, that blocks of talking longer than 10 minutes are hard for them to stay focused on, that practical experience trumps even the best presentation of a topic. And I'm not skeptical of these claims. It makes sense, practice and the experience of turning data over with mind and hands is hard to replace. In my class, the students are required to do most of this outside of the classroom - analysis of data and computational work. This is in part because we don't have much time, and my experience (teaching for 2 weeks with Jim Hamrick in Costa Rica, as well as leading an evolution lab course for 5-6 years) is that when computational work is involved, a good 25% of the time an instructor spends teaching the method in the classroom is acting as IT, fixing permissions and login issues, reminding the students which button to push, and when.

That … is not my job. Part of the learning of analysis is figuring out how to make it happen on your own computer, with the quirks of your own data, with the ability to absorb the output of each step. So I avoid bringing this into the classroom, when I only have 75 minutes twice a week to work with the students. That I feel can be safely left to them to explore. So I also engage, I ask questions, we work through things on the board (my style with a wipe-erase board could be improved I"m sure).

But mostly, on Tuesdays, I lecture.

And I feel guilty about this, but maybe I shouldn't. A contributed op-ed to the New York Times last year valiantly defended the lecture, and claimed it as still relevant to the humanities. One of several points made that resonate with me is that I, having 20 years experience working in this facet of the sciences, have experience that not only can be shared but can be harnessed to distill what is most important for students to consider. Our class has a textbook (maybe that was a bad idea), and reading the relevant chapter yesterday made me frustrated for all that it didn't convey. Each week, my 75 minutes at the pulpit is my opportunity to shine a light on what I think is most important about our topic (remember, it is "molecular ecology" - the use of genetic or other biochemical markers to help illuminate ecological processes like demography, dispersal, isolation and interaction).

It's my chance to shape how these students will think about the field in the future. There isn't a set encyclopedic entry for the field that will guide them in that way (wow, does that entry merit some update/addition…). Perhaps that makes a course like this very different from introductory biology, where active learning is perhaps far more appropriate. When we go to graduate school, whether we realize it or not you are being inculcated in particular philosophies and approaches to science, with a goal of exploring what we don't yet know. When I chose between University of Connecticut, Duke, and George Washington University (probably my top 3 choices at the time, though really it was UConn and Duke far at the top), I didn't realize that one of those choices would have dramatically changed me as a scientist. One of those schools had a fundamental, philosophically different approach to molecular systematics than the other two (those I was going to work with at GWU were cladists who didn't like modern statistical/likelihood approaches to phylogeny; I learned from some of the greatest minds in the advancing field at Duke).

So, today I had a chance to dismiss the treatment their textbook gave to nested clade analysis (as an example). To push them to understand the contributions of coalescent theory, for all the complexity it appears to add it is truly an elegant mathematical approach to exploring the history of population genetic diversity. And I took that opportunity, and take it each week. I talk to them. I tell them what I think. I help them see my reasons.

I don't know if I'm a good lecturer. But I lecture. I'll admit it.

Rejuvenation

I have been posting sporadically in part because twitter now takes up a lot of my bandwidth, but also because of some glitches involved in the transfer of this site from using an older version of RapidWeaver. As with any software, sometimes there are issues that need attention, but I have to say - I get complements on this site (its OK if you don't agree) and in large part I credit RapidWeaver for making it easy. So, I changed the little c-in-a-circle date down at the bottom of the screen to 2016 and we are ready to move forward!

What's new? Let's see, everything. From a postdoc and 2 finishing grad students a few months ago, to a 1st-year grad, two freshmen, a sophomore, two seniors - a lot of new things happening in the lab, and a lot of new people involved. At some point I will catch up with more photos of people, I assure you.

What else? I have resigned as graduate coordinator. It is a very meaningful and important position to me, and I just couldn't bring the energy that it deserved anymore. I will serve up until the day I get on a plane to teach at Friday Harbor this summer….

KellyWaresFHL

… where I will be teaching with Morgan Kelly as well as (hopefully) trying out some small experiments to move further with the work shown here. Let me know what you think about that….the idea is that variation at a single locus in the Pisaster ochraceus genome may be linked to some important function that seems to limit the effects of the virus that causes seastar wasting disease. I will keep you updated as this paper moves through peer review.

As much as anything, just trying to keep all the balls juggled in the air successfully. This website is one of them, and glad to have things fully functional again. Ciao!

Student Season

The new season of recruitment is already upon us! It seems strange, this new ILS program - we have just taken a new student in, many of us, and now it is time to start talking with applicants in Ecology and ILS. Today’s Graduate Student Symposium in the Odum School is a chance for the recruits to see all the amazing science that the grads are doing, if there is anything I’ve seen in 20 years of being in science its that good students do more to recruit good students than anything.

The lab is kicking, even without much money - as of this week, there are projects on bass, darters, other minnows, freshwater mussels, barnacles, copepods, and viruses all moving along at the same time. It means I am easily confused when I run into one of the students: what are you working on again???

But, really, this is what we do - it is easy to get an ego about the science, but the most important thing I do is train the next generation(s) of scientists, people who are fluent and able to understand, whether they are generating data or interpreting it for policy or for the public. A lot of fun people to work with, I’m lucky.