Mediocrity

Let me warn you, readers, that the following is a rant brought on by a meeting with my advisor, and that I’m well aware that I’m probably repeating what other scientists have been saying for years. Still, let me say it.

The scramble for limited resources (both funding and places in prestigious journals, not to mention tenure-track jobs), while encouraging innovation, also discourages thorough comparative studies, cataloguing of natural history, and replication.

In Heliconius butterflies, for example, there’s a glut of work on finding the genes involved in speciation, especially those that control wing colour pattern and mating preferences for said patterns. It’s increasingly hard (according to my advisor) to convince reviewers—whether for grants or for publications—that simply looking at the same genes in yet another Heliconius species is novel enough to warrant money/a place in a prestigious journal.

And yet, these studies are exactly what we need. It would be fantastic to have a suite of speciation genes identified in every Heliconius species; the comparisons we could make would be useful and perhaps more generalizable than just a handful of studies on a small fraction of the genus’ members. Think of how we could test hypotheses about speciation with such a dataset! We could look for a snowball effect with a sample size of more than three! We could figure out how often the same genes are involved in different speciation events, and how often hybridization promotes or prevents speciation! Yet amassing that much data would take up several PhDs’ worth of effort, and once a minimum threshold of species is reached, the research program ceases to be novel, and therefore becomes non-competitive. It’s also work that requires too much effort for a side project (assuming you ever want to graduate) or to hand off to an undergraduate minion. So it doesn’t get done.

Oh, and if you want to try replicating some else’s study, the way the scientific method allegedly works? Definitely not novel. This is also a problem. (Seriously, read this paper if you have access to it. Every scientist should read it.) Or if you want to pursue as a side project some outstanding question on your study organism’s behaviour in the wild? That’s extremely labour-intensive, and not likely to get you a “good” publication. But these sorts of studies can lead to important innovations.* Not always, maybe not even often, but eventually.

If I had my way, I’d try churning out as many of these uninteresting/redundant studies as possible. I don’t particularly want to be a brilliant scientist, just a competent though mediocre** one. But given the current PhD to academic job opening ratio, mediocrity doesn’t cut it.

*In fact, we argue in a similar vein when governments try to divert resources from basic research to applied (I’m looking at you, Harper Government): we can’t predict what basic research program will eventually lead to important innovations.

**Sometimes this word does not have a negative connotation!

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It has come to pass

Your intrepid blogger is going to be studying Heliconius butterflies for her PhD.  And she promises to actually write blog posts once in a while.

She’ll also usually use the first person. Usually.

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How to be a field assistant

My colleague at the blog Curious Interactions has a great post up about how to supervise field assistants.

I’ve been a field tech for several conservation biology/ecology-focused projects in remote and muddy places over the past two years, and I’ll be conducting research of my own in the tropics in the years to come. So here are some thoughts on the other end of the equation – how to be a responsible and successful field assistant.

Field work, especially when it takes place in remote and rugged areas, is challenging: it’s physically rigourous, it’s a test of emotional endurance, it demands compromise and flexibility, it forces you into close proximity with people you’ve never met, the hours are overlong and unpredictable, communication with family and friends is often sporadic, the monetary compensation always sucks, there are risks of illness and injury, and often the local culture and language is completely different from that of one’s home country.

There are also, obviously, rewards: spectacular landscapes, unique wildlife, living in places few people ever get to see, meeting likeminded people, and participating in interesting and possibly useful research. If that list seems sparse to you, you’re probably not a biologist.

Here are what I think are the most important things to keep in mind as a field assistant. If anyone has advice to add, feel free to chime in in the comments.

1. Sometimes you will be miserable, even during a “good” field season. Here are some coping strategies for day-to-day morale lapses.

Remind yourself that the field season will come to an end – count down if it helps. Basically, contact your inner child: Tell yourself you’re an adventurer/explorer. If you study birds, remember that they’re really dinosaurs! Make a game of collecting data, or do something goofy to take your mind off of things (for example, I once decided to pick a bouquet of flowers for our dinner table in the field, and it cheered me up disproportionately!). Take a short sanity break if you need to.

Just don’t get sucked into the game of fantasizing about what sort of foods you’ll eat as soon as you get home. This never helps morale.

If there are more serious problems, do what you need to to take care of yourself, and report them to a supervisor if at all possible.

2. You don’t have to be the toughest one there.

Everyone at your field site, including yourself, is there because they like challenging themselves physically and perhaps psychologically. You don’t have to prove this to anyone, and don’t let anyone make you feel like you have to. So if you can get access to some luxury like a hot shower, or if you feel like pampering yourself somehow, do it. Likewise, don’t look down on other people who take these opportunities. Does someone feel like putting on makeup once in a while? Has someone complained to you that they’re sick of being covered in mud? That’s fine; it doesn’t make them a wimp.

3. Be meticulous.

You’re probably working for a graduate student or postdoc who feels, rightly or wrongly, like his or her entire future career is riding on the data you collect. Do the absolute best you can to collect data accurately. Don’t be afraid to suggest improvements to the protocol to your supervisor. Most importantly, if you can’t remember or don’t understand how to do something, ASK. Don’t make stuff up. And if you realize you’ve done something wrong, admit it.

4. Before you go, ask lots of questions.

Contact your supervisor and/or previous years’ field assistants to find out things like what you should bring, what sort of internet/phone access you’ll have, how often you’ll have time off, how secure your field site is, etc. Also, I’ve never had a really bad experience in the field, but keep in mind that bad experiences do happen, and previous field assistants might be able to warn you off. For example, a recent survey of people who worked at anthropological field sites shows that incidents of sexual harassment are far from unheard of.

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An update on your intrepid blogger’s whereabouts

Southern Louisiana. For the next three-plus months. I’m a field tech for a project that’s studying the long term effects of oil spills on seaside sparrows and marsh rice rats.

So far (I’ve been here a week), I’m more or less high on all the zany wildlife that are commonplace here: pelicans, egrets, herons, ibises, armadillos, dolphins, anoles, tree frogs, anhingas…Expect lots of gushing and many exclamation points in upcoming posts.

Here, have a bird picture (it’s a savannah sparrow):

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Seafloor Explorer

Ever wanted to be a marine biologist? Now, from the comfort of your own home, you can!

Seafloor Explorer is a citizen science project that asks participants to identify substrates and creatures in pictures of the ocean’s floor. The pictures—millions of them in the database—are all taken along the northeastern coast of the U. S. by HabCam, an underwater vehicle created by a collaborative team that includes the Woods Hole Oceanographic Institution and local fishers and engineers. It’s quite simple to do: a tutorial teaches you how to classify the substrate as sand, shell, gravel, cobble, or boulder. Then you mark any fish, crustaceans, seastars, and scallops in the image and note whether there are any other creatures present. There are many unexpected delights to be found, like this – a pair of eels over a gravel bed (with some scallops and a crab; click to enlarge):

All images in this post courtesy the HabCam group, a collaboration between the Woods Hole Oceanographic Institution, commercial fishers, and independent scientists.

Or this image, showing a squid in the lower right and anemones in the upper right:

The data from Seafloor Explorer will allow scientists to study habitat and species distribution and abundance. Even more exciting, though, is the chance that we’ll see something we’ve never seen before. Already (the site was launched Sept. 13th), members may have identified a new species! Tentatively called the “convict worm“, it appears to live in sandy tubes and has a white body with narrow black bands.

If you’re more keen on actual stars than seastars, there’s also the Galaxy Zoo project, which asks for help classifying images of distant galaxies.

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Citizen science, both high- and low-tech

Two news stories that have warmed my heart in the past couple of weeks both involve non-scientists making important scientific discoveries. If you follow any biology blogs, you’ve probably heard about the new species of lacewing that was discovered on Flickr (here’s the paper describing it). Semachrysa jade was photographed by Gueg Hock Ping in Malaysia, and when entomologist Shaun Winterton saw the photo on Flickr, realized it was an undescribed species. Guek captured a specimen—necessary to confirm that the species was new—the following year. Along with Steve Brooks, another entomologist, they published the description in the open-access journal Zookeys. Interestingly, they found a second specimen of S. jade, already in a museum collection—one of perhaps millions of specimens that no one has yet realized represent new taxa.

The second story is a bit more old fashioned but exciting for a Mary Anning fan like me. The Keating family, while walking their dog, stumbled across a spectacular fossil on a rocky Nova Scotia beach. The beast is a juvenile sail-backed mammal-like reptile (maybe something like Dimetrodon) from the Carboniferous period (i.e. pre-dinosaurs). While this discovery is more low-tech than the lacewing from Flickr, what they both have in common is (1) someone with a keen eye getting out in nature and (2) the layperson connecting with scientists who can properly identify and document their find. In one case, a scientist reached out to the photographer, while in the other the family sought out experts when they found the fossil. Anyone could make the next cool biology headline.

So, in the words of Ms. Frizzle, get out there and explore!

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The well-fueled field biologist: recipes inspired by my life as a field technician

Manu* Libre

• some amount of Ron Cartavio
• some other amount of room-temperature (haha, “room”, I mean ambient jungle temperature) Coke
• slice of lime
• candles

Mix the rum and Coke to taste. Light the candles and/or turn on your headlamp. Wait for moths and other nocturnal insects to swarm around the lights. If you’re lucky you’ll spot a Peruvian giant cockroach! Eventually a moth will land in your drink. Make sure you rescue it ; it’ll probably dry off and fly into a candle later (the moth, not the drink). The moth’s wing scales will leave a nice powdery residue on the surface of your drink. Enjoy.

Really Dirty Martini

• gin (or vodka if you’re one of those types)
• olives
• empty plastic bottles (pop bottles will do)

Transfer gin and olives to plastic bottles so you don’t have to worry about broken glass while you hike them to your field site. After a few days in the field, during which you don’t bother to wash out your coffee/tea/hot cocoa mug, pour yourself some gin and add a few olives and maybe some olive juice. Enjoy the taste of grime and coffee residue combined with the ultimate in classy cocktails.

The Best Way to Eat Peanut Butter

• jar(s) of peanut butter—whatever kind you like
• spoon

Eat the peanut butter right out of the jar with the spoon. Duh.

Oatmeal: Breakfast of Field Techs

• bowlful of rolled oats. Remember, real men don’t eat “quick oats”.
• boiled water
• cinnamon
• brown sugar or honey
• raisins
• any other flavour-containing edible thing you can possibly find, such as peanut butter, hot sauce, haupia (coconut pudding) powder, walnuts, fish sauce, cheese, soy sauce…

Dump any rat turds or dead bugs out of your bowl. Add oatmeal. Pour boiled water over oatmeal until everything looks soggy enough. Add other ingredients. Repeat every single morning for the entire field season. See how long it takes before you put hot sauce on it, and how long before you would rather just not eat at all.

*Weird coincidence: Manu was the name of the park in Peru where I took my first bird job…and it’s also the Hawaiian word for bird!

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Formatting citations and its discontents

Today’s adventure in pedantry is brought to you by a certain biological journal that shall remain nameless to which I’m preparing to submit a manuscript. The author guidelines for this journal are detailed, and clearly have been given much thought. Yet there are multiple aspects of the bibliography formatting requirements that are simply idiotic. In some cases they waste space; in others they are simply visually unappealing or distracting. Bibliographies are hugely important parts of a scientific publication because they link claims made by the present paper to previous findings or hypotheses in the literature. They should be designed to make information retrieval, i.e. finding the item you’re looking for in the list and getting the details you need from it to retrieve the cited paper, easy. Furthermore, there are ease-of-reading considerations when formatting in-line citations, as well as ease-of-typesetting and printing. Bibliographies should be useful and they might as well look decent too. Here are my thoughts (supported only by my own brain and not the result of any sort of controlled research) on how this should be accomplished. (I do not address the issue of numbered versus alphabetical (author-year) citations, as I think there are good uses for both. I’ll be talking only about author-year formats throughout.)

Perhaps you think this matter is unimportant, because software exists that formats your bibliographies for you—you don’t have to spend time changing font styles or indenting meticulously. Perhaps use BiBTeX to generate your bibliographies. Good for you! So do I! But alas, there are yet some prehistoric publications that refuse to accept LaTeX submissions. And sometimes your advisor wants you to submit your manuscript to them.

Aha, you say, but I also have EndNote/Mendeley/whatever the kids are using these days to put bibliographic information into their Word documents. To you I say, at least have some consideration for your readers! Do you want them to read a paper that looks ugly? Don’t you ever wince when you read a paper from that one journal with the painful typesetting where it takes you forever to find that thing you’re looking for in the works cited list?

Consider: There is absolutely no reason to put a comma between the author’s last name and the publication year in your in-line citations (e.g. “Lennon & McCartney, 1966”). It is a waste of space that does nothing to ease the reader’s understanding. If anything, this makes lists of in-line citations more difficult to read: compare “Lennon & McCartney, 1966; Jagger & Richards, 1966; Wilson et al., 1966” to “Lennon & McCartney 1966; Jagger & Richards 1966; Wilson et al. 1966”.

Nor is there a reason to insist that citations of papers with three authors list all the authors the first time you cite them but “Firstauthor et al.” subsequently. Mind you, I’ve only ever seen one journal insist on this policy. (Bonus points if you know which journal.)

As for the actual bibliography, simplicity should be paramount. There is really no need to put the author’s names and/or the year in bold, or the journal’s name in italics. Really the only italicization should be of scientific names. All this extra formatting is distracting. A simple indent to draw the eye to where different entries start is enough.

The list of authors’ names should also be as easy to read as possible. My preferred format is sans periods and with commas only to separate authors, thus: Lennon J, McCartney P, Harrison G, Starr R. Adding periods after the authors’ initials is mildly visually distracting. Worse still is putting commas between the last name and initial as well as between authors—e.g. Lennon, J, McCartney, P, Harrison, G, Starr, R. Worst of all is listing the first author in Lastname, Initial format but subsequent authors as Initial Lastname—e.g. Lennon, J, P McCartney, G Harrison, R Starr. As to whether to separate the last two authors in a list with “and” (or &), I have no preference, but (and this is the case in the journal to which I’m planning to submit) it seems logically inconsistent to insist on listing all three authors (with an “&”) in in-line citations but not putting “&” in the list of references.

Finally, can we please stop italicizing “et al.”? Everyone uses this phrase. It’s not really foreign. I can see italicizing more obscure Latin terms like sensu latissimo, but et al. shows up in literally every scientific publication.

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DIY underwater webcam

One of the fun parts about field research (and much lab work too) is making equipment for really obscure purposes on a tight budget. My pond enclosures, for example, are made of window screen sewn together with fishing line. This year the DIY component of my experiment had slightly wider applications and could potentially be a fun thing to do if you have a fish tank or a favourite local watershed that you want to film.

I originally decided to film the stickleback mate choice trials so that I could figure out how long to run them for. Last year, I had no fish spawn in the first 30 minutes, but more than expected spawn after 24 hours (including way more inter-species mating than there should have been). I decided to try four-hour trials but hoped that I could eventually cut it to two hours if most spawning took place before then. Since I didn’t want to disturb the fish during the trial, filming seemed like the best option. Filming the trials would also potentially give me more data—I could record not only whether spawning took place but when, and how many times the female checked out the nest before deciding to spawn. So I needed to figure out a cheap way to waterproof a webcam and anchor it next to a nest.

My supervisor found this tutorial. It’s a pretty neat camera housing design, really cheap, and surprisingly easy to do—I used a Swiss army knife for virtually every step. I bought the cheapest webcams I could find, and used some old body lotion containers. I cut a window in each of these and covered it with a piece of an old CD case. The trickiest part was rewiring the webcam – I had to make a hole in the housing for the cable to go through, then cut the cable, thread it through the hole, and reattach all the wires. To keep the lens from fogging up, I put some silica gel inside the housing to absorb moisture. I glued everything up with aquarium silicone (which woudn’t leach harmful chemicals into the pond). Since the housing was full of air, it was positively buoyant, so I attached them to dive weights to keep them on the bottom of the pond. The cameras were connected via a bunch of boosted USB cables (actually the most expensive part of the project!) to a laptop on shore.

The results were mixed. The cameras worked as well as could be expected (they were, after all, dirt cheap). But positioning the camera so that it faced the nest was extremely difficult. I tied a piece of fishing line to the housing so that I could move it around without pulling on the cable (which would dislodge the silicone and cause a leak), but this often ended up slipping off the camera—so I had to pull it up by the cable anyways. Fortunately, the first few times they leaked I was able to dry everything out and reuse them. Eventually, however, the cameras just died. Possibly next time I should try drying them out in a jar of rice instead of just air-drying. (“Next time”, yeah right.) I also probably could have come up with a better way to attach the weight and fishing line, but I decided not to worry about it. The positioning problem made it clear that I wasn’t going to get much data from the videos, so I changed my goal to just trying to get some decent video I could show in a presentation. (Research is all about redefining goals, a.k.a. lowering your expectations.)

I did get some statisfactory footage. Here’s a benthic male nesting in the open (ish). I ended up not using this trial because the female wasn’t actually ready to spawn, and, as you can see, the male’s nest is actually in sparse vegetation that I had overlooked when I put him in the enclosure. It shows some of the nesting behaviour well, though. The male is in bright nuptial colouration—blue body and iris with a bright red throat—and he pokes around at the nest and occasionally deposits spiggin. At about the 1:50 mark, he also swims through the nest, which is pretty adorable. (Oh, and there’s a backswimmer kicking around in there too.)

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Pond withdrawal

The minor blog hiatus of the past two weeks was due to my defending my Master’s thesis. Take that, science!

This past week, I officially ended my habitat choice experiment (explained here). Yes, I continued this experiment virtually up to the day of my defence; don’t ask—like all experiments, it did not go smoothly. Anyways, I removed all the remaining fish—which will be used by other grad students for their own projects—from my ponds, took out the enclosures, washed them, and packed them away for some future scientist’s use. It was a little sad. But it was impressive to see how well those enclosures held up after more than a year exposed to the elements. What was even more impressive was how they became part of the pond environment: there were plants and algae, especially Najas flexilis, growing up through the mesh, so that the bottom edges of the enclosures were almost sewn into the pond bottom. The enclosures were also crawling with tiny tree frogs, as well as a legion of baby water scorpions, so I had a lot of fun just picking creatures off the enclosures as I pulled them out of the water.

The frogs are funny creatures: being tree frogs, they’re mostly terrestrial (okay, arboreal), and so not actually all that keen on being in the pond once they’ve metamorphosed from their tadpole form. They don’t swim very well at all—as soon as they stop actively propelling themselves, they float upright (it seems as if their heads are more positively buoyant than the rest of their bodies). And when they’re in open water they make a beeline for the nearest shoreline-like objects. This resulted in many frogs trying to climb up my legs.

Here’s a gratuitous frog picture. This little dude was sitting on top of a pole that was propping up one side of the enclosures. I thought this spot looked too hot and dry for a frog, but it seemed perfectly happy there—this funny hunkered-down pose, with legs tucked underneath the body like a sleeping cat’s, is their favoured posture.

So I guess my “Pond county almanac” is coming to an end. I have a couple of follow-up posts lined up, but I’ll no longer be at the ponds on a regular basis. This is a weird feeling, especially since it feels like summer’s only just started—as I’ve mentioned before, we’ve had unseasonably cold and wet weather this year. I think this has translated into fewer insects emerging from the ponds, although there are other variables that could explain the pattern I’ve seen. Here’s a picture of a section of enclosure from roughly this time last year: it’s covered with insect exuviae. When I took them down, there were about half as many exuviae as there were last year.

And finally, what the hell, here’s another frog picture. They’re so darn cute.

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