01 July 2015

The rules ain’t always all that: lessons from Battlebots

Over the weekend, I was watching remote controlled robots bash each other into scrap metal. As one does. And an interesting situation arose in one fight:


The team running a robot called Complete Control sent their robot out with a gift-wrapped present. The other robot, Ghost Raptor, runs into it in the first few seconds, rips open the box... and there’s a net inside. It completely messes up the spinning attack arm of Ghost Raptor, and that was pretty much it for the match.

Except... everyone is going, “Whaaaa...? How is that legal?”

The Complete Control team gets quizzed fast about this net. They say they checked the rules about entanglement, “It’s not in there any more.”

Now, to me, things seemed pretty clear cut at this point. Award the win to Complete Control. They followed the rules. The rest of the teams had gotten rules, because the announcers had made some comments about the weight limits for the machines (250 pounds, if I remember right).

But no! After a commercial break, the host explained:

Given the fact that Battlebots has historically always banned the use of entanglement devices, the fight has been nullified. They have agreed to a rematch.

I found this interesting, because it’s a great example of the tension between explicit rules and community standards, which is something that is a very live and real tension in science. A lot of people want standards, want explicit rules. I find this to be particularly true of early stage students: they crave structure, so they can know if they’re doing things “right.”

The Complete Control team, however, show one of the problems with this. The team was apparently known for pushing the limits of what was allowed. As Teresa Neilsen Hayden wrote:

Over-specific rules are an invitation to people who get off on gaming the system.

In this case, “It’s known in the community” won out. Somewhat to my surprise.

The downside to the community standards approach is that it sure seems uninviting to newcomers and outsiders. There was a great example on Twitter the other day when Rachel French complained about the format of an NSF proposal. Prof-Like Substance spoke up to say, “It doesn’t really mean that,” leading to Rachel and Karen James annoyed by “super-sekrit NSF in-crowd culture” (as Karen put it). And understandably annoyed, in my view. I wouldn’t have guessed that.

“Community standards” and “community practices” at loggerheads all the time in science. How authorship is assigned and interpreted is a big one. (“We know who did what on that 1,000 author paper.”)

There has to be a balance, but with so many issues floating around these days about how science is seen by many as unwelcoming, I would like to see our scientific communities push more towards creating explicit rules than “the people in the know, know that.”

30 June 2015

Tuesday Crustie: Yeti another one

It’s kind of cool to think that when I started this blog, nobody had heard of yeti crabs. We got the first in 2006, the second in 2011, and now we’ve got a third! Meet Kiwa tyleri!


What’s cool about this creature is that it is a polar creature. Like the first two yeti crab species, this one also lives near hot spots, hydrothermal vents.

Related posts

Off the “to do” list
Tuesday Crustie: Dance

Reference

Thatje S, Marsh L, Roterman CN, Mavrogordato MN, Linse K. 2015 Adaptations to hydrothermal vent life in Kiwa tyleri, a new species of yeti crab from the East Scotia Ridge, Antarctica. PLOS ONE 10(6): e0127621. http://dx.doi.org/10.1371/journal.pone.0127621

29 June 2015

Crayfish feel the heat but not the burn (of chemicals)

Having a couple of papers accepted in the last few days (hooray!) reminded me that I haven’t told the story behind the most recent paper I co-authored, which came out a couple of months back.

This paper, co-authored with Sakshi Puri, was a long time coming. It’s a little hard to believe that our first crustacean nociception paper was released five years ago. When that paper came out, a lot of stuff done that just came out in the new paper was already done.

Here, for instance, is some video we shot testing one of our stimuli. The description of this in the paper ended up being written in typical academese:

One author (Z.F.) ate representative slices of the peppers, similar to those fed to the subjects, to confirm that there were noticeable differences in pungency, and the habanero slices were unpleasantly pungent.

But here’s what really happened:


Very early on in the process of working on this project, Sakshi and I were pretty confident that we were going to have two papers. We had plans to to behavioural and physiological experiments testing the responses of crayfish to acids and bases, and to chemical stimuli like capsaicin (the stuff that makes chilies hot).

Our first plan was that the first paper would be just the behaviour, and the second paper would be all the physiological recordings or neural activity.

Well, that plan didn’t survive contact with the enemy (a.k.a. reviewer #2). Journals kept rejecting our manuscripts that had only behavioural experiments. We decided that instead of dividing the experiments up by technique, into “behaviour” and “physiology” papers, we would divide them up by the stimuli, into “pH, with both behaviour and physiology” and “chemical stimuli, with both behaviour and physiology” papers. As soon as we did that, our first paper got accepted.

The experiments for capsaicin and isothiocyanate were locked down even before the first paper came out. You can see them in the poster at right, done for a conference just a few months after Puri and Faulkes (2010) came out.

What held up this new paper was experiments for high and low temperature.

We wanted to test high temperature, but it took us a while to figure out how to do it. We were concerned about the animals. We’re not in the business of torturing crayfish here. We wanted to give the animal a way of getting away from the stimulus if it wanted to.

Inspired by Dan Tracey’s paper on fly nociception (Tracey et al. 2003), we tried using a soldering iron as a noxious high temperature stimulus. Our original idea was to let the crayfish grab the tip of the soldering iron, and measure how long it was before it would let go. This turned out not to be practical, because crayfish don’t like grabbing hard things. But in our preliminary tests, it was clear that just touching the claw got a reaction from them when it was hot, much more so than when it was room temperature.

We have a plot of the behaviour in the paper, but the video is so clear:


A positive result was a first for this project. I’m always telling people that one of the advantages of working with crayfish are that “They’re cheap as dirt, and tough as nails.” Crayfish had been oblivious to everything else we’d thrown at them, and this was the first thing that bothered them. We were very curious as to whether a positive result  would make this paper have an easier ride than our first paper, which kept saying, “Nope, nothing here, either.”

While we continued the work, we presented this work at the 2011 Neuroscience meeting. Sakshi wrote about here experience here. I met lots of online people for first time, including Scicurious, Doc Becca, KatieSci, Namnezia, and too many more to mention at Doc Becca’s BANTER party.)

The feedback on the poster was good, but a key moment was when I saw another poster by Brenner and Gereau (whose work was later published in PLOS ONE, in 2012). They had come up with a simple way to test for low temperature nociception: use dry ice. Brilliant!

And the moral of this part of the story is: Don’t skip the poster sessions at conferences!

After the conference, we ran the behavioural tests for low temperatures.

We’re now around the start of 2012 with this project. And this is where we kind of got stuck, which was my fault. From the experience with our first paper, we were pretty sure this wouldn’t got anywhere without the physiology. But we couldn’t get enough physiology experiments in the can.

Unfortunately, moving from stimulating the antennae (which we’d used for acids and bases and chemicals) to the claws had created a problem. It turned out that recording from the nerve in the claw is trickier than the antennae. Trying to get what we considered the bare minimum number of recordings of the neuron turned out to be hard enough that we ultimately abandoned it. The Neruroscience poster is one of a couple of posters where we presented neural activity from the claw. The claw stuff just didn’t make it into the final paper.

We also had to change the stimulus when we tried to record action potentials. We couldn’t stick a soldering iron tip in water, but the tissue needed to be a saline solution. Plus, the soldering iron introduced electrical noise, making it impossible to see action potentials. We would have liked to have used the same stimulus, but it wasn’t possible.

We decided to move back to the antennae, because we knew we could get good neural recordings from those (we’d published a lot of them in the 2010 paper). If I remember right, I starting doing the physiological recordings there first, before doing the behavioural experiments. I knew that reviewers would savage the paper if I had behavioural and physiological data from two different parts of the crayfish. Fortunately, the antennae experiments were clear – the crayfish acted differently to hot and control – although not as interesting to watch as the claw experiments.

And Sakshi completed her bachelor’s degree along the way and got a job.

And I had a crazy few months of writing, and writing, and writing some more on projects that had deadlines. The papers from the parasite symposium I did with Kelly Weinersmith, a commissioned comment piece in Neuron, and writing and editing a crayfish book that will finally see the light of day next month, I hope.

So after many, many reminders from my co-author that we needed to get this out, submissions, rejections, workshopping it in journal club, resubmission, and final revisions, I was so pleased that this paper finally found a home.

To promote it on social media, I created some memes. These were fun to make. I think you’ll need to click this one to enlarge to read it:


I did one for hot, so I needed another for cold:


I’ll probably go to hell for this next meme, but I couldn’t resist:


The pre-print went up in March, and was the #2 more read article that month! This pleases me. I was hoping we’d top that, once the paper moves from “early edition” to the final volume.


Alas, “number one with a bullet” eluded us. But in May, we were still in the top ten!


I will admit that I thought we might get a little more media attention on this paper. “Does it hurt crustaceans when you boil them alive in the pot?” is such a common question, and this paper addresses that issue more directly than anything published before.

But there is little more satisfying than seeing a long project completed and published.

Related posts

Crustacean nociception: the embargo lifts
Crustacean nociception: Origins, part 1
Crustacean nociception: Origins, part 2
Crustacean nociception: The worry
Top ten again for crayfish nociception!

External links

Variations on a theme: crayfish nociception

References

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. http://dx.doi.org/10.1371/journal.pone.0010244

Puri S, Faulkes Z. 2015. Can crayfish take the heat? Procambarus clarkii show nociceptive behaviour to high temperature stimuli, but not low temperature or chemical stimuli. Biology Open 4(4): 441-448. http://dx.doi.org/10.1242/bio.20149654

Brenner DS, Golden JP, Gereau RWIV. 2012. A novel behavioral assay for measuring cold sensation in mice. PLOS ONE 7: e39765. http://dx.doi.org/10.1371/journal.pone.0039765

Tracey WD, Jr., Wilson RI, Laurent G, Benzer S (2003) painless, a Drosophila gene essential for nociception. Cell 113:261-273. http://dx.doi.org/10.1016/S0092-8674(03)00272-1

25 June 2015

Leader of the pack: fleshing out Velociraptor behaviour in Jurassic World


“Do we know Velociraptors were pack hunters, or did the filmmakers just make that up?”

That question came up on the Nature “Backchat” podcast during discussion of Jurassic World. None of participants had a good answer, so here’s mine.

The first thing you have to understand is that the Velociraptor in Jurassic Park / Jurassic World is not the Velociraptor that actually lived. It’s Deinonychus in disguise.

It’s a shame that Velociraptor has stolen the thunder from Deinonychus. It’s hard to underestimate how important Deinonychus was to our current conception of dinosaurs. When Ostrom (1969) published his description of Deinonychus, people were still showing sauropods in the swamps and lakes. Dinosaurs were sluggish lizards.

The description of Deinonychus blew those ideas of dinosaurs out of the water. The claw on the legs was the feature that led Ostrom to suggest that Deinonychus must have been an agile, active hunter. The claw only made sense as a slashing appendage.

The frontispiece of the description is this reconstruction by Bob Bakker (who would go on to be a major proponent of “hot blooded” dinosaurs):


Badass, right?

And not at all far from what you see in Jurassic World! The main difference is that Ostrom estimated Deinonychus stood about one meter high, and was maybe three meters from nose to tail. It’s a lot smaller than the Jurassic World beasts.

Here’s where the idea of theropods as pack hunters all started, on page 144 of Ostrom’s monograph:

(A)t least three and perhaps four or five individuals are represented among the Deinonychus remains collected from just a small area at the Yale site. These remains were associated with fragments of only one other species — a moderate-sized ornithopod that weighed perhaps five or six times as much as Deinonychus. The multiple remains of the latter suggest that Deinonychus may have been gregarious and hunted in packs.

(Ornithopods, incidentally, are big herbivores like Iguanadon.)


 So Jurassic Park did not just pull the idea of pack hunting dinosaurs out of nowhere. It was a serious suggestion made by a proper scientist in the scientific literature.

For some reason, when Michael Crichton wrote the book Jurassic Park, he took that idea of Deinonychus as pack hunters and applied it to velociraptors. I’m guessing that the reason he did this was so he could call them “raptors,” which people knew as birds of prey. Crichton was very big on emphasizing the relationships between birds and dinosaurs. It comes up over and over again in the book, and was carried through to the movie. (When I rewatched Jurassic Park in the last month in preparation for Jurassic World, the “just like birds” didactic dialogue felt the most dated.)

Crichton’s decision was weird, though, because velociraptors were, um, way less badass than Deinonychus:


Velociraptors were pretty small. (Dan Telfer does a hysterical riff about this in his stand-up routine, “The best dinosaur.”)

When Steven Spielberg made Jurassic Park, he thought even Deinonychus was too small and made his theropods bigger than any that had been found at the time. He was vindicated, however: the same year, a Jurassic Park-sized dinosaur called Utahraptor was described (Britt et al. 1993).

A year later, Ostrom gave a talk where he described Deinonychus as “the ultimate killing machine,” which suggests he was still on board with the portrayal of theropods in Jurassic Park.

How has the pack hunting hypothesis held up since 1969? Maybe not that great. Roach and Brinkman (2007) reevaluated the pack hunting idea:

(W)e conclude that this hypothesis is both unparsimonious and unlikely for these taxa(.)

Sigh. There you go again, science, wrecking childhood dreams! Years from now, we’ll get adults saying, “What do you mean, raptors weren’t pack hunters?!” with the same indignation that we’ve seen over the loss of Pluto or Brontosaurus as names. (Though we might have gotten bronto back!)

The portrayal of pack hunting meat eating dinosaurs is so entrenched now that we’ll probably get movies showing us feathered theropods before we get solitary ones.

Update: Anthony Martin pointed out that there has been some more evidence on theropod group behaviour. A 2008 paper by Li and colleagues found six sets of footprints of Deinonychus-like animals, running in parallel and closely spaced, apparently made simultaneously.


They interpreted this as evidence for group behaviour. For instance, that they are parallel suggests that these weren’t just six animals walking along in the same direction because of some physical feature in the landscape. Then, the tracks might go in the same direction, but overlap when one animal walked behind another.

Of course, this doesn’t prove pack hunting. The fossil you’d want to find would be one big animal buried with a few theropods with their claws embedding in the prey’s body. Maybe that fossil exists, still waiting for someone to dig it up...

References

Britt B, Chure D, Stadtman K, Madsen J, Scheetz R, Burge D. 2001. New osteological data and the affinities of Utahraptor from the Cedar Mountain Fm. (Early Cretaceous) of Utah. Journal of Vertebrate Paleontology 21: 1-117. DOI: 10.1080/02724634.2001.10010852

Li R, Lockley M, Makovicky P, Matsukawa M, Norell M, Harris J, Liu M. 2008. Behavioral and faunal implications of Early Cretaceous deinonychosaur trackways from China. Naturwissenschaften 95(3): 185-191. DOI: http://dx.doi.org/10.1007/s00114-007-0310-7

Ostrom JH. 1969. Osteology of Deinonychus antirrhopus, an unusual theropod from the lower Cretaceous of Montana. Bulletin of the Peabody Museum of Natural History 30:1–165.
http://peabody.yale.edu/sites/default/files/documents/scientific-publications/ypmB30_1969.pdf

Ostrom JH. 1994. Deinonychus, the ultimate killing machine. In: Rosenberg GD, Wolberg DW, editors. eds. Dino Fest: proceedings of a conference for the general public, March 24, 1994. Knoxville, TN University of Tennessee, Department of Geological Sciences. pp. 127137. (The Paleontological Society, Special Publication 7.).

Roach BT, Brinkman DL. 2007. A reevaluation of cooperative pack hunting and gregariousness in Deinonychus antirrhopus and other nonavian theropod dinosaurs. Bulletin of the Peabody Museum of Natural History 48(1):103-138. DOI: http://dx.doi.org/10.3374/0079-032X(2007)48[103:AROCPH]2.0.CO;2

23 June 2015

Tuesday Crustie: Blue legs

This week, another brand new crayfish species to be given a name!


It’s Cherax gherardii. Im pleased that it’s second, specific name is given in tribute to the late crayfish biologist, Francesca Gherardi. I had to good fortune to meet Francesca at one of her last conferences, the Society for Integrative and Comparative Biology in 2013.

It was sometimes called the “rainbow crayfish” and “blue moon crayfish” in the pet trade – although these names are also used to designate other species in the same genus. The authors recommend “blue-legged crayfish” as a common name.

This is at least the sixth crayfish species in twelve years that was found and sold widely in the pet trade before being introduced to the scientific literature.

To give you an idea of how little we know about it, you can’t find its native habitat (the Ajamaru River and adjoining lakes) on Google Maps. Luckily, there’s a map in the paper, and boy, its range is small.

Reference

Patoka J, Bláha M, Kouba A. 2015. Cherax (Astaconephrops) gherardii, a new crayfish (Decapoda: Parastacidae) from West Papua, Indonesia. Zootaxa 3964(5): 526-536. http://dx.doi.org/10.11646/zootaxa.3964.5.2

External links

Remembering Francesca Gherardi

22 June 2015

What does an institution brag about?

There are times it feels like my university is focusing on all the wrong things.

I may be a grumpy prof, but I’m still a prof. I wondered if it was just my confirmation bias. Is there more coverage of stuff that annoys me, or do I just remember the stuff that annoys me?

I decided to do a little survey. I went to my university’s news site. It had the last four months of press releases up. I went though each one, and categorized the press releases into a few categories. (Click to enlarge.)


It’s understandable that the most common press release was to promote upcoming events. Plays, exhibitions, public lectures, and the like.

I was pleasantly surprised to see student success coming up in second place. Showcasing our students is one of the most important things an institution should do. The plugging and cheering for the other members of the university community – faculty, staff, administration, alumni – was surprisingly even in representation.

Some of the things that I thought was getting more attention than they deserved (those who know me can probably guess) weren’t anywhere near as high on the list as I expected them to be. I probably was indulging in a little confirmation bias, but I’d almost like to do a breakdown of other venues, like tweets and media coverage, before I completely chalk my annoyance at news coverage up to my grumpiness.

This time frame (February to June) included the end of the school year, a time when there are lots of “end of the year” awards. I wonder if the distribution of news would be different in the fall semester.

18 June 2015

“I didn’t get into med school. Should I do a master’s?”

Biology is the most popular undergraduate major in the United States, and I think the major reason for that is that an awful lot of people want to be physicians. And they’ve been told a biology degree is the best route to get to med school.

Even in an institution like mine, which has had great success in getting people into med school (which the university trumpets often) has a good percentage of pre-med students that are not accepted into medical school.

And let me tell you, the dream dies hard.

Because people tend to privilege childhood dreams, a lot of students will not let go of the idea of getting into medical school. One of my colleagues, seeing a student with a dangerously low GPA, asked the student getting advised, “What do you plan to do?”

“I’m going to med school.”

“With that GPA, you’re not going to get your bachelor’s degree!”

Consequently, in my role as grad program coordinator, I talk to quite a few students who didn’t get into med school, and who say they want to do a master’s degree in biology as a way to get into med school.

I caution on that plan of attack, for several reasons.

1. A MS in biology is primarily intended and designed to be a stepping stone into a Ph.D. in academia or a research-related job, not an M.D. in the health professions.

2. Because of (1), faculty have little experience mentoring students to be successful into getting into medical school. They are academics, not health professionals, and they are not connected to the profession you want to enter. They don't know what makes for successful med students.

3. Many biology graduate programs have very little human biology in the curriculum, less so than an undergrad program might have. So there is not a lot of the material that pre-meds are most interested in.

4. Because of (1 + 2 +3), pre-med students who are trying to get into med school who try master's program are often unhappy and quit the program before completing a degree.

But!

Some students have completed a master’s and successfully transitioned into med school that way. The problem is that I don’t know what percent of students that works for. I’ll bet it’s low. Unfortunately, pre-med students, who are often working on the sort of “Believe in yourself!” ethic in middling anime series, they will believe they’re the one that can beat the odds.

One of the other pieces of advice for those students is: always check with the people who run the program you want to join. If you want to join a medical school, as the medical school if a master’s degree will help get you into medical school. They will have a much better sense of the patterns and decision process than a grad program coordinator will.

It’s not as useful to ask the master’s program coordinator. The grad program coordinator has a potential conflict of interest. A grad program coordinator usually wants to bring in more applicants and more students into the program. Departments are evaluated on things like headcount and credit hours generated. Pre-med students are often reasonably sharp academically, notwithstanding not being let into med school. There can be a tendency to for a program coordinator to say, “Come on in, the water’s fine” even if it’s not the best move for the student because the program can benefit from a warm body.

Finally, I asked this question on Twitter (click link to see some of the responses):

Would you tell a student with BS in hand who didn’t get into med school to do an MS as a back door into med school?

The overall response so far has been mostly, “No,” with several people adding, “It depends on why they didn’t get into med school.” But certainly the overall advice seems to be that pre-meds who didn’t get in have better options than doing a master’s to further their career.