A reasoned rant: the case for hypotheses

Yeah, this is one of those essays that starts by quoting Darwin

About thirty years ago there was much talk that geologists ought only to observe and not theorize; and I well remember someone saying that at this rate a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view to be of any service.

The hypothesis is the pivot point around which science turns.

This is one reason why “No one has ever collected this data before” is, by itself, a weak rationale for a dissertation.  It is impossible to fund your research by promising only to collect cool data. It is the hypotheses that make the data cool, or, at the very least, show why its cool.

So what is an hypothesis?  It is a series of assumptions, tied together by logic, that generates novel predictions. Collectively, it is an explanation that answers a scientific question.  Let’s break that down.

Why we do science: it’s not all about the applications

Senator John Pastore: “Is there anything connected with the hopes of this accelerator that in any way involves the security of the country?”

Physicist Robert Rathburn Wilson: “No sir, I don’t believe so.”

Pastore: “Nothing at all?”

Wilson: “Nothing at all.”

Pastore: “It has no value in that respect?”

Wilson: “It has only to do with the respect with which we regard one another, the dignity of man, our love of culture. It has to do with: Are we good painters, good sculptors, great poets? I mean all the things we really venerate in our country and are patriotic about. It has nothing to do directly with defending our country except to make it worth defending.”

As we busy ourselves writing grants and justifying our existence, it’s good to take a step back.

hat tip to Boing Boing

Why we do science: quantum mechanics remixed

These guys give me hope.

On writing better–Kurt Vonnegut

One could do far worse than to model your writing after Kurt Vonnegut. His mythic stories are simply constructed, easy to read, and stay with you long after you’ve shelved the book (or, better yet, given it away).

In his book of essays Palm Sunday, Vonnegut provides some tips on how to write elegantly, simply, and memorably.

Below the fold, I interpret the master’s advice for the beginning science writer.

Brown Food Web Friday–millipede ecstasy

I spend much of my scientific life crawling around in the forest litter, studying the microbes, the microbivores, and their predators that teem in this fantastic world beneath our feet. One of my favorite litter critters is the millipede. What’s not to like? They carry around in their guts a poorly explored plethora of microbial symbionts that help them digest old dead leaves. It’s hard to see a millipede and not think of a commuter train that runs on biofuels with the help of its passengers.

The other reason to love millipedes is that, because they are slow moving litter fermentation tanks, millipedes are sitting ducks (at the risk of mixing our taxonomic metaphors). If there were to be any new generations of millipedes, the ones that were somehow defended would have to leave more offspring. In fact, National Academy member Tom Eisner has done a bang-up job discovering the many ways (from spines, to crunchy exoskeletons, to cyanide and other poisons) that millipedes have evolved to make sure this train stays on the track.

And where nature produces toxins, there are always intelligent-ish animals waiting to get high…

On the Five Stages of Proposal Writing

I’m preparing to dust off a proposal that was rejected six months ago. It’s a resubmission to the National Science Foundation. In such cases the word submission is particularly apt. When NSF is funding less than 10% of the proposals it receives, one is pretty much resigned to one or more rewrites before you have a chance at funding. And since you often have only one or two chances a year to submit a proposal for 3-5 years of work, well, one doesn’t have to be a whiz on the quantitative side to see proposal writing as a lovely lesson in the brevity of all things mortal.

But I digress.

While dwelling on such things existential it was great to come across FemaleScienceProfessor‘s take on the the process of writing a grant proposal. What emerges is the notion that successful grants have to be in some way transformative, that their writing is not linear but aggregative, that much of it has to do with juggling budgets and filling out forms, and that, when it’s all over (after months of nurturing the baby that you then unceremoniously kick out of the nest), well….I’ll let her do the honors…

And then.. someone in the grants office pushes a button and the proposal is gone. I get an automated email. I am relieved, but there is also a melancholy feeling of emptiness at the departure of the proposal out of my intellectual grasp. What will I do next? I contemplate cleaning my office, but I don’t actually do it.

FSP is a worthwhile blog. Check it out.

See also:

10 steps toward better grant writing

5 ways of dealing with that rejected manuscript

Another GTDA haiku

GTDA Poll: What book inspired you to choose science?

The things that motivate our life’s path are often only clear in retrospect. But on occasion there are those singular moments that light a fire. For me, an amazing number of those moments come with my nose buried in a book–in a coffee house, on a beach, in an airport. Something crystallizes.

I remember clearly my freshman winter at Nebraska, picking up John Steinbeck’s The Log from the Sea of Cortez.The book is an account of an expedition to map the organisms that live in the bays and beaches of along the Baja peninsula. The characters are Steinbeck, his colleague the marine biologist Ed Ricketts,  a crew of sardine fisherman, and the variety of critters they collect along the way.

I read Log over Xmas break while hunkered down in my basement room. I fell in love with Steinbeck, whose lucid prose revealed a person with deep regard for the human race. But I also fell in love with idea of field biology: the romance of exploration and the drudgery of wading through the muck. The solitude of peering into a tidepool–miles from any other human soul–and the comraderie of the team, plowing through burlap bags of specimens while drinking cheap beer. I didn’t just want to become a biologist, after reading Log. I desperately wanted to become a biologist.

That book, and the idea it planted, helped get me through that first year of college–the huge classes with the (mostly) bored professors. And as the years passed, and I got my shot, it was with considerable delight  that I found Steinbeck had pretty much nailed it.

So, dear readers, dish. What book helped point you down the path you are on?

One project: one project log

Lab scientists are all over the concept of keeping a laboratory notebook. This is your one-stop summary of a given project, from near-conception through publication. We field biologists, not trained at the lab bench (which tends to be conveniently flat and relatively protected from rainstorms, mud, and leeches) often find ourselves compiling the notes and assorted detritus associated with a given project in computer folders, desk drawers, and refrigerators.

Which is not to say that, at the very least, a logbook, or diary, isn’t extraordinarily useful when you find yourself juggling a variety of projects.

My protocol is to open a new file, named “_Log_projectname” in Word or (now) Omni Outliner–any program that allows you to timestamp a given entry.  The “_” at the beginning of the name is an old trick to make sure this file sits at the top of the folder, along with the manuscript files, figures, data files, etc.

Then, whenever you do something substantive on that project, you make a dated entry describing what you did. My rule of thumb?  If you open up the manuscript, work on a figure, add new data, or perform some analysis, that deserves an entry.

As an added bonus, at the end of that entry,  type out a few of the next steps you foresee in turning that project into published manuscript.

Once you have this habit down–opening up, and adding to, a “_Log” file for every project–you can confidently set it aside for a short time to work on something else. When you return, just read the “_Log” file from beginning to end to get yourself back up to speed.

Just don’t wait too long…

The grad school challenge: balancing diversity and depth

Last spring, Carlos Martinez del Rio visited our program. After one discussion, I asked (as I am wont to do) if he had any advice for beginning graduate students. I recall at the time many of the faculty nodding, and some of the students looking at Carlos, looking at each other, looking at Carlos again, then looking down at their notes, slowly transcribing.

I might be mistaken, but I could have sworn I heard the muted buzz of molars grinding.

His remarks, and my commentary, below.

The residue of design

As a scientist, you know you’ve made it when Boing Boing covers your stuff. I recently collaborated with a team of scientists (Steve Yanoviak, Robert Dudley, and George Poinar) on a manuscript coming out in The American Naturalist. It’s about a nematode whose life cycle has it spending time in the guts of birds and ants, and that has a pretty unique way of doing it. Here’s the, um, straight poop.

Worker ants of the species Cephalotes atratus, like many ants of the treetops, have a hankering for bird poop (lots of nitrogen and salts in a piece of bird poop). Some bird poop, however, is infected with the eggs of our nematode parasite. Now most adult worker ants can’t take solid food; they feed it, instead to their brood back in the nest. However, when infected poop is fed to the brood of Cephalotes atratus ants by their older sisters, the nematodes cause the brood to grow up with bright red (dare we say, berry-like?) gasters. In the paper we build a plausible hypothesis that birds mistake the red gasters (now full of nematode eggs) for fruit, harvest them, pass them as feces, the feces are harvested by Cephalotes workers who bring them back to the nest, and the cycle continues (one key bit of evidence–it’s easy to pluck off an infected gaster and much, much harder to remove the gaster of a healthy ant).

There is no evidence this is a voluntary arrangement–we see no advantage to the ants of harboring these nematodes. Rather, this seems to be another case of a parasite, once inside its host and with its hands on the wiring and machinery, tweaking the host to do its bidding (my endocrinologically inclined pal points out that the nematodes and ants share a host of neurochemicals, so replace “hands” above with “hormones”). The nematodes even make infected ants raise their gasters vertically, making the egg-filled butt-berries infinitely pluckable.

Long before there were neurobiologists, apparently, there were parasites paving the way.

Below the fold, the real story of how this sordid story of manipulation came about.