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.

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.

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.

Tags: teaching

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.

Tags: students, lab, life, pisaster

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/



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.

Tags: Research, publishing, funding, pisaster, RNA, expression, undergraduate, summer

In a few days, my experiment.com experiment will end. Unfunded. And that is OK. I've learned a lot from the experience, first of all that funding is extremely limited for knowledge. We are hearing from the current President's administration that funding could be even tighter in the near future, as our government perhaps is deciding that it is not so important to them. And other policy changes certainly means that all of us are more anxious about protecting our liberties and personal finances.

I also learned how uncomfortable I am with asking for money. Though some faculty gripe, I actually believe I'm well paid for my job as a researcher and instructor at the University of Georgia. And so if it is important that those next 10 RNA libraries are processed, I can fund that from my paycheck. The question then starts to split, because the reason I didn't want to do that in the first place has a lot to do with objectivity and the desire to have work validated by other scientists; otherwise there is a slippery slope of simply paying for any desired work, whether it is of true value or not.

The other side of that question involves the truth about many of us in the sciences, however. We are doing this because we are truly fascinated, and so what is the value of truth to me, personally? How far do people go in their commitment to science? Of course many of us would recognize that the grad school years are financially lean but intellectually rich, and many scientists take on great sacrifices in comfort or financial security to answer the questions they want to see answered.

What are we willing to do in this new era? Only time will tell.

So, I've entered a new era. Two of them, in fact. The first: I'm broke, as a scientist. My lab is open, we are collecting (inexpensive) data, we will keep getting papers out. But with very little room for error in budgeting. The second: I've posted my first attempt at "crowdfunding" on Experiment.com. We will see how this goes, as much as anything I'm interested here in juggling my complicated feelings about trying this avenue for supporting my research.

First, what am I asking to fund? About $3000 in additional RNA sequencing for a project in Pisaster that I think will be really of broad interest and will open up our understanding of sea star wasting disease and general responses to pathogens in marine deuterostomes. If you want more of a defense, I encourage you of course to go to the project site at Experiment.com linked above.



Why don't I pay for that myself? Darwin paid for all of his work, right? Well, yes. And I make a good salary. I find this to be a slippery slope problem: if I just admit to not being able to support my work via traditional funding mechanisms, I can pay for some things myself, but with potential costs that exceed their value to my family, and with a potential loss of objectivity that writing proposals, and getting them funded, requires.

We as scientists can't just do whatever we want, in general. We'd like to be doing what will serve our fellow humans and our planet, and to do so effectively means that I won't be plunking down my own money just to know the microbial composition of (for example) soil on a mountain bike trail versus soil that has been undisturbed. Even if it ties together my scientific skills with trail riding, it is such a marginal increase in knowledge (I think) that I recognize that to be folly.

So I am trying this platform in part to find out whether one can appeal to the public and learn about the interest in an idea. The problem of course, is that now - 2017 - everybody I know is stressed by current politics, worried about their financial futures, and already giving money to organizations like the ACLU to help protect those affected by new policies of the new POTUS. So I'm not sure that I will get this funded - and that's OK - but I'm also not sure I will heed that answer.

The other concern with paying for things myself is that it leads to questions of relative merit. If I paid for project X from my own pocket, why won't I pay for project Y? Will I pay for my friend's project, or my student's?

Now, I pay for my smartphone - which is used daily in work-related tasks. I pay for my travel to some conferences, like the Western Society of Naturalists meeting last November. That is not only tax-deductible, it is also an expense I'm willing to bear because it maintains my being part of the science community. My marine science community. So why not pay for polymerase?

I'm not saying I won't some day. There would be freedom in that, to the extent that my family is comfortable with modest expenses. But of course it also gains no traction with colleagues for whom a federal grant, however elusive, is the only currency that can unlock promotion (or perhaps respect). So it is not a good strategy to rely on.

Things are very different from Darwin's day. And his buddies probably privately mocked his barnacle collection. He knew why he was doing it, and that passion and drive is of course one reason many of us are scientists - we really just want the answers to some things. At what cost?

Tags: funding, Research, crowdfunding, money

Written by colleagues, spread by me:

In Defense of Science

We are deeply concerned by the Trump administration's move to gag
scientists working at various governmental agencies. The US government
employs scientists working on medicine, public health, agriculture,
energy, space, clean water and air, weather, the climate and many other
important areas. Their job is to produce data to inform decisions by
policymakers, businesses and individuals. We are all best served by
allowing these scientists to discuss their findings openly and without
the intrusion of politics. Any attack on their ability to do so is
an attack on our ability to make informed decisions as individuals,
as communities and as a nation.

If you are a government scientist who is blocked from discussing their
work, we will share it on your behalf, publicly or with the appropriate
recipients. You can email us at USScienceFacts@gmail.com.

Today, we learned that the EPA has had funding frozen and agency folks aren't supposed to talk about it. Rumors are that the USDA ARS is supposed to not disclose new information to the public until further notice. The National Park Service was censored on their twitter feed for posting photos suggesting that the inauguration was not very large. This, along with a number of other sweeping changes that one political party is driving to change funds allocated to the arts, humanities, and health suggest that we are indeed living in a new era.

Of course, I'm not happy about this. It does prompt reflection about what it means to be a scientist. We have had the luxury in recent decades (and beyond) of having a massive collection of scientists and agencies that work on both applied and basic research. So, the engineering necessary to get us to the moon, the work to understand how invasive species are impacting the Great Lakes - and questions about how diversity is distributed on the planet, right down to barnacle species and their evolutionary diversity. The latter is - until further notice - most certainly basic research, with a goal of knowledge for knowledge' sake. And yet it has had great benefits for our society. (Basic research, that is, though barnacle diversity has been used to identify the likely path of airplane wreckage, is involved in naval and shipping research, etc.)

It is worth exploring whether we are going to lose this luxury. Many solutions from basic science have gone on to transform health care, transportation, even quality of life. The point of these explorations is to learn about the world and how it works. This is, to put it benignly, not particularly appreciated by some political leaders. I fully suspect my own research, even that pertaining to diversity that may be sustaining our top predatory sea stars on the Pacific coast, would be mocked by our new president.

So how does one shift focus to find clear and direct application for biodiversity science? This is the challenge that many of us find our selves facing. I'm collaborating with one colleague on something I hope will be published soon that certainly is related to a health concern in the United States (more on that when it is out). I'm working on the sea star collapse caused by SSWD; arguably, the loss of predatory sea stars could dramatically change the diversity of our coasts and perhaps have impacts on shellfish productivity - we just don't know yet. My colleagues who work on ocean acidification and shifts in species ranges associated with climate change are on the fine line between basic and applied research, because if the funding agencies aren't allowed to care about climate change then the "application" goes away……

These are big, vague, questions. I don't have many answers. I had already begun to shift my focus towards more concrete questions of conservation and biodiversity loss in recent years, but even that is likely not going to be justified solely for the sake of biodiversity. I'm not arguing that we have to shift science to please our leaders; that would make it sound like some sort of authoritarian or fascist government, wouldn't it? But we do have to consider shifting science to make sure it makes some sense to our neighbors, our children, our friends and families. Government and policy changes or not, the climate impacts we are already seeing suggest that we are running out of the luxury to study things at leisure for interest alone.

So, what do you work on?