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.


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.

At what cost?

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 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 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?

Be Careful What You Wish For

When you don’t have funding, I’ve discovered, you crave information about it. You look for unturned rocks, in case there is some funding opportunity that has been missed. You apply for as many opportunities as you can, trying to hone your ideas into something that has general appeal (at least, enough general appeal for the review panels at NSF or NIH). You figure the funding rate is low, but one of these has to be of interest, one of them will get funded.....the problem is when you are crunching out grants like that and all of a sudden you hit a lucky streak! I just found out that my work on genetic clines and using genetic data to track oceanography along the coast of Chile has been funded - that’s 3 major grants this year, and another one lurking in NIH’s inbox!

Suffice it to say, I’ll be looking for help. Maybe a technician, maybe another grad student. Maybe somebody to mow my lawn, since I’m not going to have as much time around the house for a few years it seems (one can wish; it is supposed to be 99° today!)...

beautiful nauplius drawing from Perez-Losada et al. 2009 BMC Evol. Biol.


As of Friday, my startup funding has been spent: $0.00 remains. Those were the salad days. I feel really good about all that my lab has accomplished in the last 5.5 years, though of course I’ve had funds trickling in from many other sources. But it is interesting to think back on that $300k and what happened to it. There are just so many things that you don’t necessarily realize about running a lab, negotiating with the bureaucracy of a university, managing students, and just so many opportunities for poor decisions in purchasing.

I have a Bio-Rad vertical gel rig that, to my knowledge, hasn’t been successfully incorporated into a research project in 5 years. That is close to $5,000 worth of a pain-in-the-neck gizmo that just doesn’t perform half as well as the vertical rigs I used in Tom Turner’s lab, combined with the shift in methodology that has put SSCP and other fragment analysis protocols way back on our back burner. But I can’t sell it on it shall sit, hopefully we can find a use at some point. It has a nice big buffer tank, perhaps I should catch some minnows and make a small aquarium out of it (with temperature control!)?

How many frantic purchases with Applied Biosystems or other companies did I make before realizing that each one of those purchases had a hidden $30-40 shipping cost (dry ice, overnight)?

What about the half-broken chair I inherited in my office? I was told that furniture purchases on my startup funding HAD to be through Chastain’s, a furniture place in downtown Athens. Nothing against that business, but the amount of time I spent bouncing on the 5-6 models available in their showroom, only to leave with a $500 chair charged against my startup, would have been better spend buying three chairs from IKEA on my own credit card. Then I could have had different colors for my changing moods as a young professor.

Most importantly, I would have loved to have had the same amount of money with so few strings attached NOW. Just the few examples of poor expenditures noted above, add those up: I could have a draft transcriptome of any species I want for that amount of money. I could have picked a small group of related species, say the freshwater mussels that we worked on, and dramatically improved our marker availability, understanding of molecular evolution, and so on for just 1/10th of that initial startup package.

But that’s how science rolls. We make mistakes. Technology changes. And we keep writing grant proposals to move on.

Back in the Saddle

Well, if I thought things were busy in my last post - nearly 2 months ago - it seems somebody has stepped on the accelerator in the meantime. My office Mac had the new system installed, so that has taken me a while to find this document again and have something to report. But in the last 2 months, we’ve been pleased to get acceptances from 11 incoming graduate students, hooray! And I’ll be working with them again in our Intro Methods and Logic class this fall, so it will be good to get to know everybody.

Also, it seems I’m becoming more permanent around here, as my collaborations have become official: the Bio-Oce proposal with Jeb Byers and Jamie Pringle is funded and starting in June, and my collaboration with Jim Porter and Andrew Park (Ecology), Erin Lipp (EHS), and Katie Sutherland (Rollins College) was also just tabbed for funding on April 1 (we think it isn’t an April Fool’s joke....)!

So, for all the high-tech wizardry I’ve proposed in the past, ultimately I’m thrilled to be funded essentially to do biogeography and community ecology. That is what got me started down the academic path in the first place, really. Stay tuned!


Funny all the ways that “submission” gets used. Seems appropriate to assume the submissive posture as I submitted an NSF proposal and a manuscript to Journal of Biogeography today. The new “news” website is almost up and will be more hacker proof (darned wiki!) which may keep me more sane (or less bald) in years to come.