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.
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?
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.
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 eBay....here 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.
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!