Happy anniversary, L5R!

You may know me as Doctor Zen, but there was a time when I was known online as the Crab Clan Scholar.

This weekend was tinged with a little sadness for me, because it celebrates the twentieth anniversary of something pretty important in my life: the card game Legend of the Five Rings – or L5R, as fans know it. There was a big twentieth birthday party at GenCon over the weekend, and I was disappointed that I couldn’t go.

I was not there when the game debuted in demo form in summer of 1995, but I started playing in December of that year. And I got in deep. That there was an entire faction of the game called the Crab Clan helped a lot. I was a die hard Crab player, and took to tagging my sig as “Crab Clan Scholar” in my posts on Usenet. (Yeah, I’m old.)

I was intensely involved in L5R for well over a decade, first as a player, then eventually as a part of the Rules Team and freelance writer. I can’t even begin to summarize how much stuff I did with L5R. I can’t begin to tell you how important it has been to my life. This game is, as co-creator Ryan Dancy put it, welded to my DNA.

I haven’t played in a while, and I miss that badly.

But in the spirit of celebration, I wanted to draw attention to a couple of projects that chronicle the game’s early days.

I make a cameo appearance in the book 40 Years of GenCon. This book has a few pages about key events in L5R history when L5R was but a wee game of two and three years old (GenCon 1997 and 1998, to be precise).

The Legend of the Five Rings Gold Edition Encyclopedia is mostly a list of cards from that particular arc of the game. but I had the supreme pleasure of writing an introduction. The book opens with an 8 page section called, “L5R: Its founding and history,” which is one of my favourite things I’ve ever written. I got to interview a lot of people who were involved in the creation of the game, and tell the story of the creative process of making something as big and complex as a trading card game.

I had so much fun writing it, I turned in something that was substantially longer than what I had been asked to write. Now, I always try to be a professional, and write to requested length. I made sure that the extra stuff could be cleanly severed if they wanted to keep the length to what was originally planned, since I’d done it purely “on spec.” But I guess they liked it, because they kept it in.

For anyone who wants to see how L5R started twenty years ago, the intro to that book is the thing to read.

It is a wonderful thing to see something you love be a success. I couldn’t be happier than Legend of the Five Rings has been in pretty much continuous production for two decades.

Come hell or high water, I’ll make it to the twenty-fifth anniversary party, damn it.

Utz! BANZAI!!!

External links

Legend of the Five Rings Gold Edition Encyclopedia
40 Years of GenCon

Picture by AEG head honcho John Zinser on his Facebook page.

Comments for second half of July 2015

Dr. Becca talks about how to get yourself noticed as a scientist, in a good way.

Richard Poynder has a piece looking at one scientific publisher’s policies on embargoes, which concludes with a sour analysis of the effect of the open access movement: pretty much none, he reckons.

Small Pond Science looks at that “Facebook for scientists” site, ResearchGate. Funny how showing that people read your papers makes you pay attention.

Connections in my scientific career

If you’ve never seen the television series Connections by James Burke, you are missing out. Whereas most histories of science emphasize a “march of progress,” Burke’s series emphasized contingencies: you couldn’t have this if there hadn’t been that, and how those this and that were related were not obvious or predictable. In episode 9, “Countdown,” for instance, Burke connects the divorce of Henry VIII to the invention of television.

I got thinking about this with the publication of my most recent paper, which was nexus point between a couple of different research projects. I’ve joked with people that I have “science ADD,” but there are relationships between my projects. They just might not be obvious to people who are not me.

As an undergraduate, I worked on a project about walking by octopuses. This got me interested in locomotion, and I looked for a related project for graduate school. This led me to do a doctoral project on sand crab digging.

Sand crabs dig with their legs, so this led me into looking at the leg motor neurons of crustaceans. I’d found a discrepancy between the description of leg motor neurons in spiny lobsters and everything else that had been looked at. I wrote a post-doctoral fellowship proposal to study that, and got it. I went to work with David Macmillan in Australia for a post-doc.

David’s students had some projects on crayfish escape responses going on while I was there. Meanwhile, spiny lobsters were hard to get and hard to work with, I moved to working with slipper lobsters. I remember standing in David’s office, chatting about trying to get as much use out of the slipper lobsters as possible (they weren’t super cheap), and saying something like, “We’ll do some sections of the abdominal nerve cord, just to look at the giant interneurons and see that they’re there.”

Except they weren’t there.

Discovering that some species were missing a major set of very well-studied neurons was a completely unplanned observation.

That led me to working on the escape response in crustaceans. Because I was seeing substantial differences between species, I thought I needed to see how those neurons developed; take an “evo devo” approach to the problem.

I got very interested in marbled crayfish as a developmental model for the escape neurons from chatting Steffen Harzsch at the Neuroethology congress. I got some marbled crayfish for my lab, fully intending to start working them up as an experimental model. I started the Marmorkrebs.org website.

While I was thing about things to post on the Marmorkrebs blog, it became obvious that there were quite a few Marmorkrebs in the pet trade in the U.S.. Those crayfish were a potential problem if they got loose. This led me to doing research on the pet trade, and about the same time started doing species distribution models. All of this led me to be co-author on a forthcoming book on crayfish (out next week!).

I was also looking for a way to get the relatives of marbled crayfish in my lab. That led me to participate in the #SciFund Challenge, which became a scientific experiment in its own right.

Meanwhile, I was still plugging away on the escape response. I’d studied slipper lobsters, spiny lobsters, and had moved on to shrimp. While I was looking at the backfills of the shrimp, I saw things moving in the nervous system. And those moving things were parasites.

Finding parasites in the nervous system of shrimp was another completely unplanned observation. And before you know it, I’m helping Kelly Weinersmith co-organize a whole symposium on the subject at an international conference.

And the sand crabs? I still liked those guys, and recognized that we knew almost zero about most species. So with the incentive of finding a field project for an undergraduate student, I started collecting very basic natural history data for the ecology of the local sand crab species.

So you see, it all makes perfect sense. (Well, most of it does: there are a few papers that don’t fit neatly into that narrative.) But you are not likely to recognize the “this happened because of that” connections by skimming the titles of the papers.

The moral of the story? One is that it’s absolutely worth doing exploratory experiments and keeping your eyes open. I’ve had two findings (interneurons missing in slipper lobsters, parasites in shrimp) that came about not because there were hypothesis driven experiments, but that I got by happenstance, and those opened up whole new lines of research and resulted in multiple papers for me.

What a strange trip it’s been.

Tuesday Crustie: Hasta be Shasta

Not this kind of Shasta...

This kind of Shasta:

Chris Lukhaup posted this on his Facebook page earlier today, describing it as the rarest crayfish in North America. It’s the Shasta crayfish, Pacifastacus fortis. This is a critically endangered species. It’s got a tiny range of only a few square kilometers. It’s been under pressure from introduced cousin, the signal crayfish (P. leniusculus) and damns (Light et al. 1995). It needs really pristine water. It’s not doing well, but I hope that with people like Chris making the effort to show how beautiful these animals are in their natural habitat, we can make things better for this beastie.

Reference

Light T, Erman DC, Myrick C, Clarke J. 1995. Decline of the Shasta crayfish (Pacifastacus fortis Faxon) of Northeastern California. Conservation Biology 9: 1567-1577. http://dx.doi.org/10.1046/j.1523-1739.1995.09061567.x

This calls for a celebration

This is the remains of my treat to myself after a paper I co-authored was published in spring.

Back in February, when I went back to Canada for the first time in years for a training workshop, I picked up a stash of Canadian chocolate bars at the airport. Extra large sizes when possible. There are a lot of these things that are just about impossible to get in the U.S., so these are precious things to me. I didn’t want to just snarf through them. No, these are something to savour. I wanted to keep them for special occasions. I decided that I would only eat one what a new paper was published. Not just accepted – published, with the final thing out there in the world available for people to read.

This is the aftermath of the celebration of the publication of my new paper in PeerJ this week:

I think I have enough to celebrate the publication of four more papers, and I’m already trying to decide which I’ll have when my next paper comes out. But I’ll probably be saving the Crispy Crunch for last.

What do you do to celebrate success in your lab?

Shrimp FFMN FAC: social media exclusive!

Yesterday, I talked about the shrimp neurons that I think are the most beautiful thing I’ve imaged in science (right). It’s in my new paper in PeerJ.

But PeerJ didn’t get everything I did in this project. Not even for this particular stain that I like so much.

The nerve filled in this image has axons that project both forward and backwards. Most of the neurons’ cell bodies are forward from the fill. This anterior ganglion is more interesting scientifically, because it has the key motor giant neurons with their weird structure. It’s also hard to show all all the neurons’s cell bodies, because several of them are almost right on top of each other.

Consequently, I have a lot of images of the anterior ganglion in the paper; it takes up a bunch of space in Figure 2. I also created a “cheap confocal” movie that combines several images at different depths of field, and that went in as supplementary information.

The posterior ganglion... didn’t get that much love in the paper.

In crayfish, there might be two or three neurons on the left and right sides in that posterior ganglion (4-6 cells total), and these are grouped together in the FAC cluster. In white shrimp, only one cell body on the left and one cell body on the right get stained (2 total). The structure of those shrimp FAC cells is not terribly complicated, either. I didn’t think that scientifically, it was necessary to show the shrimp FAC neurons in the same level of detail in the paper as the other clusters of neurons in the anterior ganglion.

But before I reached that decision, I took a lot of pictures. And I had made another little movie to show the three dimensional structure of the FAC motor neurons within the ganglion.

And here it is!

I did make a few other “drive through the ganglia” movies, but they aren’t quite as nice as the ones I got from this one spectacular stain.

Related posts

The most beautiful thing I’ve made in science

Reference

Faulkes Z. 2015. Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus). PeerJ 3: e1112. http://dx.doi.org/10.7717/peerj.1112

The most beautiful thing I’ve made in science

Truly, this is the social media age. I learned my latest paper had been published when the journal tweeted the article.

This paper contains probably the most beautiful thing I’ve made in my scientific career:

These are shrimp fast flexor motor neurons stained with a technique called backfilling or sometimes axonal filling. This technique can show you a lot. You can do colour coding, as shown here (cells filled from the left are yellow, those from the right are blue).

Backfilling has one problem: it’s unpredictable. To figure out what neurons are connected to the nerve you’re filling, you have to build up a composite picture from a lot of fills.

That’s why this image is so beautiful to me. It’s not just one fill, but two – left and right sides – and it is complete. Every neuron filled, so they are all there in one image. The only thing I could have wished for was to have the axons filling darker so they would be more visible. It’s no accident that this preparation appears in two figures and a movie in the supplemental information in the new paper: you can see a lot.

Here’s an animated image of the anterior ganglion, that runs from ventral (where the cell bodies are) to dorsal:

The sad thing is that I’ve waited about eight years to share this image with you. Ieee. Here’s why.

Based on work in my last post-doc, I’d published a paper on the fast flexor neurons of slipper lobsters (Faulkes 2004). Slipper lobsters didn’t have some of the giant neurons used for escape that had been so well described in crayfish. This lead me to looking for other variations in this set of neurons.

I knew from decades old research that shrimp motor neurons in the escape circuit differed from crayfish in a few ways. One neuron, the motor giant (MoG) had fused axons. Some of the escape neurons were myelinated, which is unusual for an invertebrate. (I stunned one neurobiologist when I mentioned this in a conference talk.)

Nobody had re-examined these shrimp motor neurons with newer techniques, even simple ones, so I went looking to see if there was anything different than crayfish, and to confirm that those anatomical features in the old papers were correct. This is often derided as a “fishing expedition” in grant reviews: you cast your line and see what you get. But the thing about fishing expeditions is that sometimes, you catch some fish. I caught some fish (so to speak).

Here’s a graphic summary of some of the differences between the white shrimp I studied, the old research on prawns, and the best studied species, the Louisiana red swamp crayfish:

The biggest surprise was the massive MoG cell bodies in the white shrimp, which were completely unlike those in crayfish or other shrimp that had been looked at.

That’s where I got stuck.

I looked at those huge MoG cell bodies and thought, “Those look like a bunch of little cell bodies fused together.” When I went to the International Congress of Neuroethology in summer of 2007 and the Society for Integrative and Comparative Biology meeting in early 2008, most people I showed my pictures to either volunteered that idea without me suggesting that idea, or agreed that the idea of neuronal fusion was plausible.

I tried a lot of different ways to show that the MoGs were fused cells. And I kept not getting anything definitive. I knew that the paper would be so much cooler if I could show that the cell bodies were fused. I kept playing that game of, “If I was the reviewer, would I be satisfied?” And the answer was always, “I would want to see evidence of cell body fusion.”

Meanwhile, all this stuff about the escape circuit that was rattling around in my mind turned into a review article (Faulkes 2008). It included a coy mention that I had more to publish on this subject, citing my SICB conference abstract:

Additionally, the MoG cell bodies have an unusual appearance in the dendrobranchiate shrimp species Litopenaeus setiferus [Faulkes, 2007], suggesting that there is yet more diversity in the escape circuit to be described in the non-reptantian decapods.

I think at this point, I had the fast flexors, and went back and did a few more fills on the extensor side to see if I was seeing similar patterns (fewer neurons than other species).

But I still couldn’t get evidence on whether the MoG cell bodies were fused or not. I kept telling myself, “I’ll just wait and see if a student wants to pick up the project to finish off.”

Meanwhile, I picked up other projects, not the least of which was figuring out that weird things I saw in the nerve cord while looking at shrimp motor neurons were, in fact, larval tapeworms (Carreon et al. 2011, Carreon and Faulkes 2014).

Sometime earlier this year, I just realized, “Zen... it’s been a long time. No student has picked up this project. You should try to find a home for this instead of waiting for even more years to get that one last bit of evidence.”

So during spring break this year, I reached that breaking point where I decided, “I want to submit this.” A flurry of work ensued, and I pushed the “submit” button on the afternoon of last weekday of the break.

One of the benefits of waiting on a project for eight years is that entirely new publishing options open up for you: in this case, PeerJ.

PeerJ didn’t exist when I’d started this project. I’d bought a PeerJ membership very early on, because I was very interested in the journal’s ideas, but hadn’t been able to take advantage of it before now. (And that was not for lack of trying! Anyone who suggests it’s easy to publish in open access journals is wrong.) That PeerJ doesn’t review for “significance” made it a logical place to submit, because my own gut instinct said that any journal that reviewed for “significance” would want evidence showing whether or not the MoGs were fused. Just like I did.

Submitting to PeerJ was smooth, yet still challenging. The submission process for the figures and tables in particular is quite different from many other biological journals, so I messed things up in quite dumb ways. Sorry, reviewers and Fabiana (editor of the article).

Once the manuscript was accepted, I was very impressed by how fast I got page proofs to check. It’s one of, if not they, quickest turnarounds I’ve had. It’s nice that something in the creation of this paper was fast.

Of course, I still want to know if those neurons are fused. If anyone reading this has some ideas as to how to test it, I’d love to provide them with the shrimp you’d need!

References

Carreon N, Faulkes Z, Fredensborg BL. 2011. Polypocephalus sp. infects the nervous system and increases activity of commercially harvested white shrimp (Litopenaeus setiferus). Journal of Parasitology 97(5): 755-759. http://dx.doi.org/10.1645/GE-2749.1

Carreon N, Faulkes Z. 2014. Position of larval tapeworms, Polypocephalus sp., in the ganglia of shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 54(2): 143-148. http://dx.doi.org/10.1093/icb/icu043

Faulkes Z. 2004. Loss of escape responses and giant neurons in the tailflipping circuits of slipper lobsters, Ibacus spp. (Decapoda, Palinura, Scyllaridae). Arthropod Structure & Development 33(2): 113-123. http://dx.doi.org/10.1016/j.asd.2003.12.003

Faulkes Z. 2007. Motor neurons involved in escape responses in white shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 47(Supplement 1): e178. http://dx.doi.org/10.1093/icb/icm105

Faulkes Z. 2008. Turning loss into opportunity: The key deletion of an escape circuit in decapod crustaceans. Brain, Behavior and Evolution 72(4): 251-261. http://dx.doi.org/10.1159/000171488

Faulkes Z. 2015. Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus). PeerJ 3: e1112. http://dx.doi.org/10.7717/peerj.1112

Tuesday Crustie: Classy and glassy

The transparency of shrimp can be both a blessing and a curse when doing experiments. You can see what you’re doing, but sometimes they are so lightly built that it’s difficult to work with them.

I picked this picture today not just because it’s a lovely colourful image, but because the species shown, Litopenaeus vannamei, is a close relative of a shrimp species studied in my new paper at PeerJ! I’m working on a “behind the scenes” post for tomorrow.

Photo by Santi DeFerrol on Flickr; used under a Creative Commons license.

Comments for first half of July, 2015

Katie looks at the thorny issue of data ownership.

Nice post from Duffy Ma about the grand challenges in biology.

Anticipation

Not too many journals do this: list papers that are “forthcoming” without page proofs or accepted manuscripts.

It’s nice to see acknowledgment of one of my new papers coming out someplace besides my own website.

External links

Knowledge and Management of Aquatic Ecosystems

Tuesday Crustie: Before the Internet, there was the Weekly World News

From the Weekly World News, 17 September 2002. You must click to enlarge to fully appreciate the photo...

I’m surprised that nobody has taken this as evidence of immortal lobsters. I do want to use the “lobster facts” call out the next time I talk about crustacean nociception:

They have no cerebral cortex – which means they feel no pain.

Hat tip to Neil Gaiman.

Glorifying overworking: another self-inflicted crisis in Science Careers

Here we go again.

I like to work hard and be productive. But I’m stunned by this article by Eleftherios Diamandis in a careers website:

I worked 16 to 17 hours a day, not just to make progress on the technology but also to publish our results in high-impact journals. How did I manage it? My wife—also a Ph.D. scientist—worked far less than I did; she took on the bulk of the domestic responsibilities. Our children spent many Saturdays and some Sundays playing in the company lobby. We made lunch in the break room microwave.

Let’s count all the ways this one paragraph is terrible, in the order they appear.

First, sixteen hour work days are crazy. That statement should come with a warning: “Do not attempt.” Maybe some people could do this for short bursts, and maybe a rare few people could do this for extended periods, but this is not how most people are going to turn out their best work.

Second, there’s the glorification of “high impact journals” as the path to career advancement. You mean the paywalled ones where retractions correlate more strongly with their Impact Factor than their citations?

Third, and probably worst, the “woman gives up career so man can have his.” As Alice Gorman pointed out:

She ‘worked far less’ sounds a hell of a lot like ‘worked far more’ to me.

I understand that this is the decision some couples make. People have their private discussions and make hard decisions about how to live. This may have been the right choice for these particular two people. But again... to blithely drift past this as, “This is what I did to get ahead” suggests that Diamandis thinks this is easy, and normal, and acceptable. It’s hard, and exceptional, and crappy.

Fourth, kids playing in the lobby and eating out of the microwave doesn’t sound good for your general health and well-being, even if you were working normal hours, which is not the case.

When I look at Diamandis’s website, it’s clear that this work load was not a one time thing that he did to get the position he describes in the article. He co-authored thirty papers last year alone (twenty data-driven and ten reviews). I’m concerned that this guy, in a leadership position, is making a people around him do the same things that he did, whether they want to or not.

And where do we find this? On the Science Careers website! Again! I say again, because you may recall, Science Career got stung just last month for Alice Huang suggested a women faced with a man continually looking down her shirt “you put up with it, with good humor if you can.”

I am wondering if the Science Career website has the same editor as last month. Because if so, there’s a bad pattern emerging. And it needs to stop.

Last time, the “Ask Alice” column was taken down within the day. I am willing to bet that a similar fate will happen here. Article removed, another nonpology from both the Science Careers editorial board and the author, who just don’t see what all the fuss is about.

Major hat tip for Oliver Robinson, who brought this to my attention with this bottom line summary:

Errr... message from this Science piece seems to be: success = poor work-life balance + wife to do domestic duties.

Additional: Rajini Rao notes that I didn’t hit every piece of awfulness in the article, which is true. (There was so much in just that one paragraph!)

You left out the part about walking in front of dept chair to get noticed. Which is just silly.

Yeah. That’s some preening right there. And there’s no way of telling if this did him any good, or was pure superstition.

More additional: My head is reeling at reading that Diamandis lists himself as co-author on 702 papers, and that list ends at 2013.

Related to this culture of “work and nothing but,” I’d like to point to this article about post-doc salaries in the United States (my emphasis):

This is about how, as the reaction of US postdoc shows, no one in this country actually believes in labor law anymore. No one believes that they can be protected from overwork, that pay should be proportional to hours worked as well as talent. No one even believes in the benefits their employer gives them. I have yet to meet a single person at my workplace who takes our (generous) 20 day vacation allowance. And trust me, it’s not just because they love their work. I’ve spent enough time with Americans to know how they are socialized to view vacation as a professional liability.

Still more additional: Terry McGlynn nails it:

The dudes running the system, who got in charge by exploiting their spouses, can’t be allowed to impose their values on our generation.

And even if the Diamandis’s wife did not feel she was exploited, there is no doubt that there are many women who were. And it’s not okay for people to set that expectation, even incidentally by example.

Update, 15 July 2015: Diamandis has responded, briefly and in a slightly cryptic way (not clear if that’s his email or the editing at fault):

Eleftherios P. Diamandis, head of clinical biochemistry at a hospital of the University of Toronto, said via email that he had seen the criticisms. “It is a free world; all opinions respected,” he wrote.

I’m not sure if that means that we are supposed to respect his opinion, or whether he respects other people’s criticisms of him. If the latter, it would be nice if he addressed the criticisms instead of shrugging them off.

He added, “If I stayed home, would my wife be sexist?”

To which I say:

That’s not what happened.

What might have happened and how his wife might have been viewed does not change what actually happened. A woman was asked to take over all the housework again. It’s not as a though this is a rare thing. It’s common. As I wrote above, this may have been the right choice for this couple, but in a context and culture where women disproportionately give up their career options for domestic duty, this sends a bad signal of unfairness.

So, as Dave Mellert answered, if a man’s wife took up the professional overload, and the man stayed at home to do all the housework, the woman wouldn’t be sexist. She might be bigoted or prejudiced or many other unfortunate things, but she isn’t part of a larger continuing pattern.

Hat tip to Karen James - who Inside Higher Education should have referenced when they quoted her tweet. Same with Jacquelyn Gill. Talk about making someone’s contribution invisible.

Update: Scott Jaschik has indicated that the Inside Higher Education article will link the tweets from Karen and Jacquelyn.

Update, 16 July 2015: Times Higher Education covers the criticisms of this, and several other articles, that have appeared in Science or Science Careers. It includes several new comments from Science’s editor-in-chief, Marcia McNutt. Most relevant to this piece is McNutt’s argument:

Dr. McNutt went further to point out that the journal’s first person accounts are being mistaken as advice columns, and says that such future accounts will be paired with alternative commentary or perspective.

That’s a weak claim. Let’s look at the text on the Science Careers homepage (my emphasis):

Clinician-scientist Eleftherios P. Diamandis says that making sure you are noticed can give you the edge over your silent competition.

Similarly, there’s this line in the opening paragraph:

But a well-planned, long-range effort to ensure your visibility among those who have hiring responsibilities can be the deciding factor.

The repeated use of “you” turns this article into an advice column, not a biography. If this article was intended to be merely descriptive and not proscriptive, it’s been poorly written and edited.

Another update, also 16 July 2015: Retraction Watch is reporting on the Diamandis article and the letter criticizing Science for its multiple missteps. Down at the end, updated today, it notes that Jim Austin is no longer the Science Careers editor. He was the individual who, in response to a cover of trans women that didn’t show their faces, called moral indignation “boring.”

Related posts

Breaking brand: Science magazine’s latest self-inflicted crisis

External links

Getting noticed is half the battle
Laboratory of Dr. Eleftherios P. Diamandis
Diamandis’s faculty webpage

Grand challenges for biology

Meghan Duffy, writing at Dynamic Ecology, has a nice post about “grand challenges” in biology. The first time I heard this particularly phrase was at a Society for Integrative and Comparative Biology meeting, where the National Science Foundation was soliciting ideas about what the “grand challenges” in biology are. In other words, this is grant speak.

I have some misgivings about this approach, of asking scientists what they big problems are. I think it’s too likely to be blinkered and limited: like asking city dwellers at the end of the nineteenth century what problems they needed to solve. They’d probably have been adamant about needed more and better horses for transportation.

The NSF has five grand challenges for biology, and so does Meghan. There is some overlap in these lists, but they aren’t quite identical.

• Predicting individual organisms’ characteristics from their DNA sequence (NSF) / Linking phenotype to genotype (MD)
• Understanding biodiversity (NSF and MD)
• Understanding the brain (NSF and MD)
• Interactions of the Earth, its climate and its biosphere (NSF)
• Sustainable agriculture (MD)
• Synthesizing life-like systems (NSF)
• Origins of life (MD)

To me, “grand challenge” has a few desirable features. It should be something that many people in the discipline are actively working on. That is, it’s a question many scientists are engaged and committed to answering. There are some reasonably clear ideas for what constitutes success.

For those reasons, a couple of the proposed grand challenges leave me cold.

“Understanding the brain” is, to me, is not a challenge for biology. Neuroscience is its own discipline now. The descriptions of “the brain” – singular – make it clear that people are talking about the human brain, and not the brains of the millions of other animal species.

Worse, the NSF document talks about the “emergent properties” of the brain, which is code for “consciousness.” I don’t think we have even a clue as to what an answer to that question might look like.

“Origins of life” is an unanswered question, yes, and an important one. For a grand challenge, it doesn’t feel like one that a large proportion of people in biology are actively grappling with. There’s a lot of speculation, but I don’t see this as something that people think they have a clear path to make headway on it.

“Synthesizing life-like systems” is a weird way of renaming a technology – synthetic biology – as a challenge. I’m not so much interested in life-like systems as I am in actual living systems studied with techniques to (say) make synthetic DNA.

When the J. Craig Venter Institute announced they had created a cell that ran from artificial DNA, Venter said one of the questions they wanted to answer is, “What’s the minimal genome?” What is the smallest amount of instructions that you can have that will allow a cell to be alive? That’s a fascinating question, but unless / until a lot more labs start pursuing it besides the J. Craig Venter Institute, I don’t think it qualifies as a
grand challenge.

“Understanding biodiversity” is something that I can get behind, although I’d like it even more if it was a bit more focused. Something like, “How many species are there?” We don’t know that. It would be nice to see basic taxonomy put more in the forefront, because that stuff needs more attention. And just cataloguing all the species is a grand challenge.

External links

How many species are there?

Top ten for three months running!

Just realized that the recent crustacean nociception paper I co-authored is in the top ten most read articles for the third month running in Biology Open! It was #2 for April, #6 for May, and #6 again for June.

Thank you to all who have taken an interest and read this!

Tuesday Crustie: Release the Kraken!

John Wyndham is actually a favourite author of mine. I’ve read his novel The Kraken Wakes. But I never visualized it quite like this artist behind this Italian edition...

Hat tip to Pulp Librarian and Paul Cornell.

I don’t think early retirement is for me

I heard a scientist talking about wanting to retire at 55, and it’s been bothering me ever since.

First, I’m kind of amazed that anyone in academia would have the financial savvy to have enough cash to retire early. I sure wouldn't feel financially secure retiring early.


Second, it got to me because couldn’t quite wrap my head around the lost research opportunities. As I mentioned a while ago, I’m scheduled to be promoted to full professor this fall. And that has been bringing me some anxiety. Full professor means you’re no longer early career, or mid-career – even given academia’s generous definitions of those terms, which mean you can be “early career” in your 40s. Cue jokes about graybeards and deadwood.

I’ve got a paper coming out that has been sitting on my hard drive for a while. It’s a reminder to me of how hard it can be to get stuff completed, and that I’ve got a lot of questions I want to know the answers to. And it’s not likely that other labs are going to pick up those questions. Which means if I don’t answer them before the clock goes ding on my career, I’ll never know the answers.

Related posts

Nowhere to go from here

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. There’s a video here (embedding seems to be disabled, sorry).

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.”

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

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

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. 127–137. (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