Updating

Finally some time to catch my breath at the end of the semester. All the grades are in, I'm setting up a PCR (!), interviewed a prospective student yesterday. Updating the website a little bit so it looks better when I link it to collaborator's pages (and maybe so the prospective student will choose to come to UGA!). And of course following the news.

It can be hard to keep focused with such social and political turmoil around us. I'm trying to keep my focus on my family, our health, and keeping our home functional with some minor renovations over the break. And here in the office/lab, the little bit of Sanger sequencing I'm trying to finish before I leave for a short holiday is to pad the data for a paper I hope to have out to collaborators in January.

Academy Member and founding member of the UGA Genetics Department, Wyatt Anderson, once pointed out that what we should look for in our colleagues is having "a habit of writing". We are scientists, but the science isn't real until it is communicated. The better we can do at having a habit of writing, the more effortless it becomes. Not that there isn't a tremendous amount of headache and woodcrafting to make it all come together, not to mention the diligence of editors and reviewers to make it better. But I find that references, ideas, context, flow from me so much better than they once did. When I was a grad student, a postdoc, I felt like each paragraph was a monument to my ideas mixed with the great work that came before me. Now I realize that the paragraphs aren't about me or my ideas - they are the context that helps other readers, new to the field as well as experienced, figure out why I thought this had to be done, why I worry that there is more to do or to be done differently, and why this information might be useful.

My favorite paper on technical writing, by Gopen and Swan, establishes the need to meet 'reader expectations'. What things are the readers worrying about after each sentence? What keeps them on track? What gets my message across most effectively, and simply?

I can't claim I do that all the time, but I'm better at it for sure. I've tried to convey this to my students, undergrad and grad alike - and I'm always happy when one of them brings their own gifts to the writing and helps me become better through our interaction as well.

A bit of a long ramble, but I'm glad to have so many ways to spread the word of what I think is useful to track in science. This silly blog, my twitter, my publications, my teaching. Even when this job beats me down, it brings me a lot of joy at the same time.

Radio Silence

Hello all, it has been a CRAZY semester. Sorry I haven't posted here much. Coming up for air now that it is Thanksgiving break just to say I hope all are doing well, and I'll update more as the semester closes out.

Teaching

It has been a busy summer. Doesn't feel like I had much time away from the office. I'm currently inundated with teaching duties - it isn't going badly, but it is taking all the energy I have to keep it from going badly. The goal of this course is a survey of why we study organismal biology, for students who are not majoring in biology. So we just spent the past few weeks learning about how organisms are intimately and physiologically tied to their environment (and introduced the problem of climate change as an opportunity to test this idea with surveys to compare with historical distributions and forecasts for the coming decades). Next up is the whole of biodiversity itself.

I was also able to finally publish Katelyn's paper in PeerJ. It came out really nicely thanks to the help of one kind peer reviewer in particular; I think I was emphasizing some of the wrong points in the first version of the manuscript and now it really makes it clear that the EF1A mutants (those carrying one copy of the mutant allele) are physiologically distinct beasts. Should be a lot of interesting work to be done following that up!

Otherwise, like you all, I'm overwhelmed. Too much to do, anxiety about doing it well, anxiety for how so many are being affected by terrible weather and yes, terrible politics. What a year.

Ups, Downs.

I'm back from my travels to Friday Harbor Laboratories - my zoologist "home base" since 1996, though only my 6th stay at the labs. The original intent of the trip was a micro-sabbatical (UGA does not have real sabbaticals, unless you find external funding for it) to write, prepare for teaching in the fall, and put my feet amidst the Fucus and Balanus again at low tide, in a habitat I know less well than I'd like but better than almost any other.

My plans were interrupted. First, by good news - my work on Pisaster is recommended for NSF funding along with colleagues Mike Dawson, Lauren Schiebelhut, Ian Hewson, and Pete Raimondi. Fantastic news that required some scrambling to address a few issues before anything could be finalized, and of course made trickier by me not being at my office. So, good news for sure and you'll hear more about that in the coming few years.

Then, the very next day (still in my first week at the labs), terrible news. One of the most incredible undergraduate students I've yet interacted with, Katelyn Chandler, passed away unexpectedly. She was only 20. I worked with her first as a teacher in my "Monsters" class, and then for 3 semesters in the lab where she learned how to do qPCR, genotyping sea stars, and eventually her Honors thesis on differential expression among EF1A genotypes of Pisaster. She was incredibly intelligent, engaging, diligent, and creative, and will be very much missed by all of us in the Wares lab.

Below is a photo I took of her presenting the poster she made with almost no help (in terms of design, content, and so on), discussing science that she had done much of the creative and intellectual work on.

Katelyn will receive a posthumous degree from the University of Georgia; in only 2 years at UGA she had already amassed tremendous number of credits, had completed her Honors thesis, had coauthored a scientific publication, and had touched the lives of very many.

IMG_0834

Field and Stream of Consciousness

Good morning y'all. What a busy time summer is! Tomorrow I will head out to Skidaway Institute of Oceanography, one of the USG marine labs, to collect some Chthamalus for a project one of my undergraduates (Katie Skoczen) has started. I can't quit you, barnacles! And of course a nice little chance to drop by the beach before Memorial Day weekend too. After that, a short writing retreat and research prep trip to Friday Harbor Laboratories, my touchstone for my entire basis as a marine zoologist. Really looking forward to that!

I mention all this fun and hurry because we ARE all so busy. At some point it just feels good, maybe necessary, to call something "done". So I'm happy to also point to a new PeerJ PrePrint from the lab, work that my other fantastic undergraduate Katelyn Chandler has contributed to.

https://peerj.com/preprints/2990/

Fig3

Shown is Figure 3 from this manuscript. We think we are homing in on a story to tell about Pisaster and tolerance to Sea Star Wasting Disease! What this figure shows is changes in expression: individuals carrying the ins mutation on the left in each panel, individuals without on the right. All 3 panels tell the same story: the ins heterozygotes have dramatically lower expression of HUNDREDS of loci than homozygotes do. The first panel is all data; the second panel excludes one individual because it appears to be a funny recombinant (Katelyn's project for this Fall semester); and the third panel is focused on the elongation factor 1-alpha gene. You'll have to read the paper to know why all of this is so interesting!

As with some of my other papers, I have doubts about putting this paper at a "non-impact" journal like PeerJ, one that is focused through peer review on the correct analysis and interpretation rather than whether the story is sexy. Of course I think this story is sexy! But it has already been rejected without review from 2 journals, which reminds me (A) big data is not a big deal in an era of big data, and (B) all of the ego stroking of science often flows through a small handful of gatekeepers and reviewers. They may not be wrong, but lets remember they don't represent the ultimate impact of the science.

That, and the fact that I have very little funding to splurge on many of the more expensive OA journals (did you know Nature Communications costs $5200? Does that seem like those funds could be better used for science in an era of thin funding??? and yet that isn't Nature, it is another journal generated for the hunger of so many scientists needing to publish their work), and that I feel I can get this story out even if name recognition of the cover of the journal isn't as big for some of my colleagues, is why I continue to go with the good publishing experience at PeerJ.