GeekQuest

As we near the end of the year, I wish you all have the chance to complete one long-standing quest in the coming year.

This was one of mine.



Depending on your point of view, I'm either about a month and a half late with this (since I filmed it during Neuroscience in November), or I’m one day late with this.

All downhill from here?

Last year, I was hoping to break my record for most original papers. I tied it, with three papers. This year, I broke it.

Actually, shattered might be more apt than broke. Or maybe smithereened.

I had five data-driven papers, an ethics paper, and a chapter in Open Lab 2010. Six original peer-reviewed papers, and a book chapter that was more heavily vetted than any of the papers. A couple, though, were things that had been in the pipeline for a long time – some my fault, some not. They probably should have been out earlier.

And then there was #SciFund.

That’s still pretty productive. And it was made possible by hard working students and collaborations. As I wrote before, it was great to have two papers on subjects that I never in a million years expected to be publishing on (ecological modeling and parasitology).

The downside to having a great year is that you know you’re not going to top it next year. While I don’t have the same momentum going into 2012 as I did for 2011, I have a few things lined up for next year already. There’s the symposium for the tenth International Congress for Neuroethology; the Manuscript That Will Not Die finally seems to have left my desk for the last time and is in press; and I’ve got a paper in the hands of an editor being reviewed right now.

Maybe I’m finally getting the hand of this science thing.

I find it fascinating...

Yes, there are many end of the year lists going around right now. This one at LiveScience, “Scientists List 2011's Most Fascinating Discoveries,” is one you should read, though, because... because... okay, I’m in it and I’m vain.

The paper I picked was because it was the paper that may have changed my thinking about a subject more than any other paper this year.

Symposium announcement: Nociceptors in the real world

I’m pleased to announce a symposium that I am co-organizing for next year’s International Congress of Neuroethology at the University of Maryland.

It’s titled “Nociceptors in the real world,” and my partners in crime are Ashlee Rowe (at the University of Texas in Austin) and Ewan St. John Smith (last heard in the Science podcast explaining his work on why naked mole rats don’t feel pain from acids; he’s soon moving to the U.S.).

The title is not a reference to a reality show, but is part of the rationale for holding the symposium. Because nociception is so closely related to pain, almost all the research on nociception is geared to alleviating human pain. And that means it’s almost all research on mice and rats, because those are the standard clinical models for that kind of research.

But nociception is a distinct sensory system on a par with vision, or touch, or taste. Nociception should be widespread across the animal kingdom, but we are only just starting to do research on them.

How diverse are nociceptors in what they respond to? What species have nociceptors triggered by heat? Acids? Chemicals like capsaicin, the stuff that makes chilies hot?

What is the ecological relevance of stimuli that trigger nociception in different species? For instance, trout nociceptors can be triggered by high temperatures (>40°C; Sneddon et al. 2003). But when would a trout encounter those sorts of temperatures?

I’m super excited about this symposium. It’s going to be a wonderful meeting of minds, and I hope it will help solidify the field and move it forward.

The official announcement went up today in the society’s November newsletter (PDF here). I’ll sneak in a bonus for you that isn’t in the newsletter, namely the kinds of organisms we’re planning on covering in the four main talks of the symposium.

• Cephalopods!
• Fruit flies!
• Fishes!
• Naked mole rats!

The meeting is 5-10 August 2012. Mark your calendars if you’re interested in nervous systems, animal behaviour, or evolution!

Reference

Sneddon LU, Braithwaite VA, Gentle MJ. 2003. Do fishes have nociceptors? Evidence for the evolution of a vertebrate sensory system. Proceedings of the Royal Society B: Biological Sciences 270(1520): 1115-1121. http://dx.doi.org/10.1098/rspb.2003.2349

Tuesday Crustie: Feisty

“I may be tiny... but I’m strong!”

A local sand crab (Lepidopa benedicti) resists having its picture taken.

They always seem to find the one little fold of flesh that they can get their claws into. It doesn’t hurt much when they grab you, but I often let out an “Ouch!” more from surprise than anything else.

Sand crab shrinkage?

I spent the day in my office working on two talks I have to give next month. One is for the Subtropical Biology meeting we are hosting (13 January), and one is a public talk at the South Padre Island Birding Center (28 January).

It was lovely to just have the day to think about how to do these talks. Nobody else around. No interruptions. Just a chance to think about how to explain the science in a (hopefully) engaging way.

And along the way, I solved a puzzle that lets me fix a 25 year old error in the scientific literature. Even more satisfying.

The talks I am giving are both about one of the local species of sand crabs, Lepidopa benedicti. There’s not a lot of papers on any sand crab, including this species. But there is a nice paper that describes how the little ones grow and develop, which is relevant to my talks.

Sand crabs, like many arthropods, have a larval stage. The adult sand crabs are dedicated diggers, and are rarely seen above sand, but the babies (zoea) are adrift in the waves. They spend the first few weeks of their life as plankton, up in the water. This might give them a chance to drift away, so that populations can colonize brave new beaches, where no sand crab has dug before. Because they are tiny and tasty, many crustacean larvae have spines of one sort or another to try to keep themselves out of the mouths of predators.

Then, the larvae undergo metamorphosis into a stage the looks much more like the adult (the megalopa) and they settle out into the sand.

I wanted to put all the different larval stages together on a single slide, all to the same scale, so that people could see the growth. But when I grabbed the pictures and rescaled them all to a single size, I got this:

I was confused. Why was the second stage smaller than the first one? And the third stage was still about the same size as the first. Typically, animals, you know, grow. Not shrink.

My first thought was I’d made a mistake. Rescaling things can be tricky, with lots of multiplications and divisions, especially since these all had different size scale bars (one was a bar for 1 mm, another was for 1.5 mm, and so on). (This led to some slightly goofy efforts of me holding up rulers to my computer screen to try to measure the sizes of the pictures ad scale bars from the PDF.) But no, it didn’t seem to be a math mistake on my part.

I went back to the text, and found there was something weird going on. Stuck and Truesdale had measurements of the size listed in the text, and they weren’t in line with the pictures. Even accounting for the fact that they probably didn’t draw an “average” larvae, there was no way they could be right: the most of the stages were about half the size in the pictures that the text said they should be!

Based on the measurements in the text, the sizes should be more like this:

Ahhhhh. That makes more sense.

Besides fixing this particular mistake, there are bigger lessons for making graphics. This might have been caught if:

• Images weren’t spread over several pages.
• A single scale bar wasn’t doing triple or quadruple duty on a single figure.
• All figures were using the same scale (like 1 mm), instead of switching from figure to figure (1.5, mm, 2.4 mm, 1 mm).

Now I have my slide, and I have, in a very small way, perhaps helped there be just a little less error in the world. Even though it may not be a big deal, it’s still satisfying. Like pushing that jutting book back into place on the shelf.

Reference

Stuck KC, Truesdale FM. 1986. Larval and early postlarval development of Lepidopa benedicti Schmitt, 1935 (Anomura: Albuneidae) reared in the laboratory. Journal of Crustacean Biology 6(1): 89-110. DOI: 10.2307/1547933

A gift

Today, many of you are enjoying gifts from other people. I want to talk about one my favourite natural gifts.

For me, the best gifts are the unexpected ones; the ones you didn’t have to get. A present from someone you don’t know all that well, for instance, can be very memorable.

There are many things in nature that are beautiful. But because they lack that unexpected quality, they don’t rank as my favourite natural gifts. Rainbows, for instance. Given water droplets, some light, and the laws of optics, rainbows are inevitable. You can’t not have rainbows. Any planet in the cosmos with water and light will have rainbows.

To me, one of the most astonishing gifts on our planet is this.

The sun and the moon are the same size in the sky.

The sun is huge. Its diameter is about 1,392,000 km.

The moon is small. Its diameter is about 3,474 km.

Yet the sun is so much further away than the moon that it almost exactly compensates for the difference in size. There is no reason that our star and our satellite should match up this way. Either could be a different size or different distance away. There are probably only a small number of planets in the galaxy where you would get this view from the ground.

And that makes this possible:

The best gifts are the ones you didn’t have to get. And this coincidence makes for what may be the best gift from our planet.

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


(I was lucky enough to see a total solar eclipse in Manitoba in 1979. They are beautiful in a way that photos and video cannot capture.)

What to do with a Friday afternoon?

We used to have 50 minute classes - one hour with break between classes - on Mondays, Wednesdays, and Fridays. We had 75 minutes classes on Tuesdays and Thursdays. This was similar to other universities I'd been at, even if the stop and start times were a bit weird. (Why start hour long classes at quarter to?)

A couple of years ago, our class schedule changed. 

Tuesdays and Thursdays didn't change. We continued to have classes running three times on Mondays, Wednesdays, and Friday - but just in the mornings. Monday and Wednesday afternoons changed to have 75 classes.

Friday afternoon? It got turned into one 3 hour class slot, running 1:00-4:00 pm.

I didn't like this. I liked running classes three times a week, and there went my options to run such classes in the afternoon. I also thought it would contribute to the perception that professors weren't working a full work week.

This week, we got an email from administration complaining that there are no Friday afternoon classes.

Well, duh. A three hour class on a Friday afternoon? What the heck did you think would happen?

Administration is saying they need to offer classes in this time "to meet student demand." Colour me unconvinced that there's a big demand for Friday afternoon classes. Sure, I know that if classes get put there, there will be some students who will sign up. But I wonder if they will make, or how attendance will run over the course of the semester.

I could've warned them. But nobody asks me these things.

Expedience

Grad school committees outsource a lot of their admission decisions to the GRE, although GRE scores are not precise measures of student potential.

Search committees outsource a lot of their decisions to the editorial boards of Science and Nature and Cell, although glamour mag publications are not precise measures of faculty prospects.

Tenure committees outsource a lot of their decisions to federal grant agencies and, increasingly, to external reviewers. But with funding rates so low, there is a huge amount of luck in getting an external grant.

We use these metrics not because they are precise (though we pretend they are) but because they are expedient. They let admissions committees, search committees, and tenure committees be lazy and make decisions without the hard work of reading deeply into the narrative provided by the applicants. They are convenient ways to cut stacks of applications. The let committees kick the can of responsibility down the road.

Given the numbers of files that committees are often supposed to read, it’s understandable that people want shortcuts. But don't mistake a shortcut for a precise and meaningful assessment.

Green and gold

Since I’m making suggestions for open access advocates...

Labeling different open access types as “green” and “gold” is not helpful.

I like read about scientific publishing and the issues around it, but branding the different kinds of access by colours is so completely arbitrary and random, that even even I can’t remember what the difference between “green” open access and “gold” open access is. I have to look it up every time.

When people can’t remember the terminology, the message is not likely to be persuasive.


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

Tuesday Crustie: White Christmas

We should call it, “Snowball.”

You can read the story of this remarkably coloured lobster on BBC. Al Dove made a correction on Twitter:

Albinism in lobsters is not related to melanin; that's a mammal thing. Lobster pigments are all carotenoids.

For more, see his explanation here.

Occupy Science (the journal)

Rants against scientific publishers, like this one, are always popular. But the landscape for scientific journals and publications has been slow to move. Some might argue that publishers have barely budged, though we certainly have many more open access options now than we used to.

Perhaps one reason that the scenery has been slow to change is that the targets have been too many and too varied. Maybe it’s time to try something more... precise.

An obstacle to making open access the way to publish science is that there are no open access journals that have the impact and prestige of the glamour mags: Nature, Science, and Cell.

While open access advocates often say that one of the benefits of publishing in an open access forum is that more people will read the paper, the glamour mags are effective at pushing a story out. Papers in these journals get noticed. Namnezia wrote:

Whenever we’ve published in a fancy journal, I typically start getting random emails from people who read the paper and had questions or were interested in collaborating, etc. This never happens with society journals.

And to some degree, this is to be expected. You can’t establish credibility overnight. You can't establish prestige overnight. You can’t get the entire established science journalism ecosystem to shift overnight. Some have tried to create open access journals and push them into that league (e.g., PLoS Biology). While those have been credible and commendable efforts, nothing’s come close yet. The routine of embargoes and press releases every week from a few select sources is deeply entrenched.

Few researchers with a sexy result that they think could make it into those venues will have the courage of their convictions to withhold a hot manuscript from those journals because they’re not open access.

Instead of imitating the glamour mags, why not infiltrate one?

Nature is published by Nature Publishing Group, which is part of Macmillan Publishers. Cell is published by Cell Press, which is part of Elsevier. Both of those are for-profit corporations.

Science is different. It’s a publication of a non-profit scientific society. As such, it exists to serve its members and is not concerned about making money. If enough people joined AAAS and demanded Science move to an open access model, how could the organization refuse? If enough people showed up at the annual meeting and said at every opportunity, “Make Science open access!” why couldn’t this get on to the society’s agenda?

For that matter, AAAS has a whole series of elected officer positions. People running for those positions could say, “I’ll be an advocate for making Science open access.” Might gain more votes, might not, but again, it would shift the agenda.

I’m not even saying the whole journal need to go open access. All the news and reporting and analysis and commentary that makes up a big part of the journal could stay behind a paywall. Just make the original technical articles freely available.

Science seems rife for take-over. All it would take, it seems to me, would be people joining the society and telling the officers and board of directors. The psychological effect of one of the biggest scientific journals in the world changing to open access publicly would be huge.

Now tell me why I’m wrong and this can’t work. Because it seems so simple to me that there must be something I’ve overlooked.

Additional: This article makes a point similar to mine: 

(T)he (Open Access) movement is disorganised and because of that is ineffective.

When bluebells aren’t blue: Pollinator pulling power for flowers

Why do flowers have such beautiful colours? The quick answer that you’ll probably think of is, “To attract pollinators.”

This New Zealand bluebell (Wahlenbergia albomarginata) is – despite the name – usually mostly white. There is variation in this species, though; you can see some of this in the picture at right. Most of the related species are blue, and the typical explanation for why this species is white is that the pollinators that visit the flower dislike blue.

Campbell and colleagues argue that the hypothesis of pollinator preference for colours is often not very well tested. This surprised me since, like you, I’d hear the story about flowers being brightly coloured to attract pollinators so often. They set out with a very thorough series of experiments to test the relationship of pollination to colour.

The researchers’ first step was simply to observe. No experimental manipulations of any sort; they just watched pollinators visit flowers. They found no difference in visits to flowers based on colour, though they saw a preference for size.

Then they busted out experimental manipulations. They painted the flowers. The native bees showed no preference for white or blue, speaking against the hypothesis. Flies disliked the blue, which was consistent with the original hypothesis.

But... about 90% of pollen transfer (depending on flower colour) was by bees (who didn’t mind the blue) rather than flies. And pollen export (as estimated with dyes) correlated highly with bee visitation, but not with fly visitation.

The team didn’t find any difference in moving pollen from plant to plant that was associated with the flowers’ natural colour.

Finally, they did some larger scale experiments. The results were a bit complicated. The pollinators’ choices changed, depended on how much variation in colour the pollinators got to see, and on how big the flower beds were.

When the pollinators had a natural range of colours, they still showed no preference.

When the experimenters enhanced the colours by painting some bluebells even brighter blue, the pollinators show no preference in a small plot of flowers, They finally showed a preference for a flower colour in a larger plot of flowers!

Except it was in the the wrong direction: a preference for blue, not white.

All in all, you’d expect there to be a lot more blue flowers in this species.

The authors explored some alternative hypotheses that were unrelated to pollination. One was a possibility that there was some sort of thermal advantage to differences in colour, but there were no temperature differences between the blues and whites.

Another possibility was that there was some selective pressure from herbivores, but the team found (say it with me) no differences in how much the plant-eaters were chomping on the blues and whites.

Having eliminated a lot of functional explanations related to the bluebells’ ecology, the authors suggest that the flower colour is incidental, and there's some other factor under selection that is linked to flower colour by genetic happenstance. They’re betting on proteins, anthocyanins, that are related to both colour and to temperatures stress.

Campbell and the rest are busy breeding a bright blue and a white strain for new experiments and comparisons. Watch this space.

Reference

Campbell D, Bischoff M, Lord J, Robertson A. 2011. Where have all the blue flowers gone: pollinator responses and selection on flower colour in New Zealand Wahlenbergia albomarginata. Journal of Evolutionary Biology: in press. DOI: 10.1111/j.1420-9101.2011.02430.x

Photo by Mollivan Jon on Flickr; used under a Creative Commons license.

Comments for first half of December 2011

Gerty Z checks out fabric conference posters, which I had queued up in the Better Posters blog.

I make a cameo appearance on Ed Yong’s Not Exactly Rocket Science, which covers a topic that I wrote about: teensy-tiny insects. I was busy at Ed’s blog this month, as he wrote about how London cab drivers have an enlarged hippocampus. Hey, if you want a big hippocampus, there are easier ways than becoming a cabbie. I also comment about dinosaurs.

Jarrett Byrnes made a dancing yeti crab video. He has instructions. I add more instructions.

And at Inkfish, I defend yeti crabs from the charge that they look “uncool.”

NeuroPolarBear gets a consistent answer on how many conferences a year a professor should go to. The consistency surprises me.

David Kroll leaves his research gig behind.

Speaking of work, Scicurious looks at the hours we put in at work.

Sayonara, #SciFund

And there’s the siren! The #SciFund challenge has came to an end! Here are some of my initial reactions to the experience.

Things that I didn’t expect:

Fewer people, bigger donations. I thought most donations would be small – a dollar or two – and projects would have hundreds of supporters. Instead, projects had tens of supporters contributing $10-20, and more, often much more. Consequently,  my “I make my target if everyone chips in 50 cents” pitch to my several thousand followers on Twitter and Google Plus wasn’t effective.

Traditional media still rules. The break out success story was, without a doubt, Kristina Kilgrove’s Roman DNA project. There’s no doubt that it made it because it was on the CNN website.

Cool beats practical: Given how much talk there is on how people want to see “results” and “return on investment” in traditional funding, my one post where I described how my research might have a practical pay-off to aquaculture got the least hits of anything I did to promote my project over six weeks.

Weak relationship between video views and dollars. “Duck force” got more than ten times the views of my video, but it didn’t get ten times the donations.

Front end loaded: I expected most funds to come in at the very beginning and the very end. RocketHub confirmed that this is the normal pattern. But the “bump” in the last few days was much smaller than I expected. On my project, the amount of dollars raised and time elapsed were pretty tightly correlated.

So emotional: I touched on this before here. I got way more wrapped up in this tiny little fundraising effort than most other projects.

Not much variation. Most projects raised about the same amount, regardless of their targets. $1,000 or so seems to be the sweet spot for now.

I made the right call to keep my project target small. At one point, I almost raised it, and if I had, I don’t think I would have made it. Projects that want to raise ten grand are either going to have to be brilliant or wait for the crowdfunding of science to mature.

Things that disappointed me:

Notice us! We didn’t get as much attention from science media as I expected. No coverage in the Science, Nature, The Guardian, The New York Times, Quirks and Quarks, and so on.

Whiff: Thirty-nine projects didn’t meet their targets.

Low gear: I was hoping to be one of the first projects to get past the post. I though that I would have a good shot at it, based on responses of people to whom I showed my video, and that I had one of the lowest targets.

Left undone: I had ideas for three more videos that I didn’t get to make.

Things that made me happy:

Mad skills: I learned a lot about how to make short videos. I may be doing more.

Total: Over $75,000 for science!

Hits! Ten projects met their targets.

This time, it’s personal: And one of them was mine.

If #SciFund were to go again:

I would say: Yes. Even though it’s inefficient, it’s fun. And as I noted, I’m unlikely to walk away completely empty-handed, which is usually what I get for writing big grant applications.

Stay home: I would try not to go to the biggest scientific meeting in the world for a week. I felt I lost quite a bit of momentum because of that.

More focus: Not my call, but at first we had over 200 people express interest in doing this. We ended up with 49 live projects. I wonder if even that was spreading attention too thin.

There will be much more analysis of the #SciFund challenge in the days and months to come. It was a social experiment, and we are all scientists, after all. But for now, this is...

Photo by viking_79 on Flickr; used under a Creative Commons license.

Why “Facebook for scientists” sites keep dying

Because they continually fill up with crap like this. Here’s a selection of topics listed in a “Recent activity” email I got from a science social networking site:

How can cosmic consciousness be studied?

With paradigm-shifting hypotheses in string theory and data from the LHC. And doing a lot of drugs.

Is anybody working on 'language processing in bilinguals by using ERPs like N400 or P600?' Need help in this area. Thank You.

How could someone ever find out the answer to that question if it weren’t for a social media sites?

Hello All Well I am just an amateur in this field. But i am too intrigued about the phenomenon occurring in the highly convulated object of our body....

You may be an amateur in neuroscience, but you’re an expert in letting me know which topics to avoid.

Emg????

Because multiple punctuation marks always get more attention!ll!!eleventy!111!

These are all topics in a social networking site sponsored by a general scientific society. It’s a society that’s fairly easy to join.

The alerts show one of the problems with wannabe science social networking sites. They get organized around topics, and not people. The brilliant thing about the best social sites is that they help you find people worth listening to. People talk about a lot of different things, and part of the fun is listening and finding out the variety of little quirks and interests people have.

Twitter would be nowhere near as much fun if you followed hashtags rather than users.

Who wants to be a professor?

A lot About 80% of doctoral students want to be professors, according to this post. It goes on to note that only about 20% of them do become professors. Cue statements about the mismatch between expectation and reality and arguments to reform the system.

Based on my observations, particularly on search committees, I bet a lot of those 80% of doctoral students don’t want to be professors: scholars who are engaged in both research and teaching to some degree.

What many doctoral students want to be are researchers free to study subjects that interest them. For many, teaching, particularly undergraduate teaching, is seen as a necessary evil. I’ve seen it too many times. And I’m sorry, but if you don’t want to teach undergraduates, to me, you’re saying, “I don’t want to be a professor.”

It just so happens that professors are one of the few positions that allow someone to conduct research with a some freedom to follow their own interest. So a lot of doctoral students and post-docs hold their nose and pursue professor positions, because the jobs they truly want – independent researchers – are in even shorter supply that tenure-track professor positions.

Additional: See comment by Dave K. re: correction.

Grades and learning

On our campus, there is discussion about more evaluation of teaching and learning. We recently got an email encouraging faculty to incorporate assessment of student learning and assessment of teaching improvement into our faculty evaluations. This is partly driven my accreditation agencies, who require us to create “student learning outcomes” for our department and for each individual class.

The response of many faculty: “Why do we need a separate evaluation of student learning? That’s what grades are for.”

Of course, many faculty will also bemoan that students who passed their English courses can’t write. They’ll complain that grad students whose undergrad GPA was more than 3.0 perform horribly on their preliminary oral exams.

There’s some interesting locus of control psychology going on here, I think.

External link

Measure it

Tuesday Crustie: Coping

A lovely translucent copepod (Calanus finmarchicus). Look at the length of the antennae!

Photo by Michael Bok on Flickr; used under a Creative Commons license.

A patent clerk’s pay, or, why is science so expensive?

In The Guardian, Philip Ball writes:

It is a shame there aren’t more scientific problems that can be solved with pen, paper and a patent clerk’s pay packet.

The “patent clerk’s pay” is a reference to Albert Einstein’s day job when he was young. It sounds so modest. But is it?

I went to Salary.com and looked for “patent clerk.” It didn’t offer any information for that job title, so I went with the patent-related jobs.

The American national median salaries for patent attorneys start at $80,040 for Patent attorney I (entry level, needing 0-1 years experience), and go to $207,858 for a top patent attorney. But lawyers tend to have high salaries, and Einstein was not a lawyer.

Patent agents have an average salary of $74,5000, according to this page. It notes that patent agents have a higher average salary than scientist or engineer. Salary.com gave $83,850 for Patent agent II, but listed no other job levels.

Salaries for American federal patent examiners go from $41,969 to $155,500.

Most of these wages are more than I’m making now as a mid-career, tenured professor. The low end for patent examiners is just slightly lower than my starting salary as an assistant professor was (not adjusting for inflation). Holding out the prospect of stable salaries at a patent clerk’s wages could be a step up for a lot of up and coming scientists.

The broader point here is that we forget how much scientific discovery is simply a question of work force.

We often think that the biggest expense in science is equipment and supplies and machines that go “Ping!” The biggest expense in grants I’ve reviewed and written is for salaries, mostly for students.

We often think that the limiting factors to doing science are intellectual or technological. There are many unsolved scientific problems that we know how to answer. We aren’t waiting for any conceptual breakthroughs or new technologies. We’re waiting for people. We need “hands at the bench” to put in the time to collect the data.

The instabilities of salary is a major limiting factor for science and is probably a big reason a lot of them get out of science: they don’t see a way to pay the bills. Creating permanent, stable positions for scientists would release a lot of scientific research.

Even if it was “just” the salary of a patent clerk.

Additional: xkcd on the pressure of being a patent clerk now.

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

Additional take on the Ball’s piece by John Hawks.

#SciFund: Achievement unlocked!

We. have. MADE IT!

I was sitting at home, working on just one last video to try to convince people to support my #SciFund project, when I heard the sound of an email alert. When I saw it was from RocketHub, I was excited, because I had been getting close to my target. How much closer might I get?

When I read the email, I almost had a heart attack. It was enough to push me past the finish line!

My day went from this:

To this:

(Since I was sitting at a computer, of course my first move was to tweet about it.)

The #SciFund challenge isn’t over! I still want to see if I can squeeze out one more video promoting my project. We are allowed to have donations exceed the target. If there is enough money, I will take a student with me on the expedition! And RocketHub even rewards people who fuel a project after it hits its target with the Supernova badge!

And for those who watched my promo video all the way to the end, you’ll know I have another project  I promised to reveal if I met my target:

The Beach of the Goliath Crabs!

I will be revealing the secret of this project soon!

Thank you to those who have supported this project, either financially or morally!

#SciFund: Practical Procambarus

We are getting down to the wire in the #SciFund challenge. Perhaps you have seen my project, but are not yet convinced. You may be asking, "Sure, this research on the crayfish is cool, but does it have any practical benefits?"

Here's one possibility.

Marbled crayfish reproduce asexually. One of the big mysteries about asexual reproduction is why so few species use it. In theory, asexual species should overrun sexual species by dint of numbers.

Think of a female who can have four offspring in her lifetime, on average. If this species reproduces asexually, she will have four daughters, and each of those daughters can have four daughters - sixteen grand-daughters of the original female. If this species reproduces sexually, she will probably have two sons and two daughters, and those two daughters will have four offspring - eight grand-offspring of the original female.

This imbalance in numbers would get bigger every generation, of course. This is a major cost to reproducing sexually.

This is a great scientific puzzle! It's one of many reasons why studying both a sexual and asexual species that are so closely related is so fascinating.

But I said I was going to talk about something that might be more practical.

There's plenty of crayfish aquaculture around the world. What if we found out a way to flip those farmed crayfish species from sexual reproduction to asexual reproduction? At least one other crayfish species seems to be able to flip between sexual and asexual reproduction. The potential increase in yield would be tremendous.

This would be a long-term goal. Lots of legwork would have to happen before we could even think about something like that.  There are reasons it might not work.

But we won't know until we try. That's the point of research, after all.

And that is today’s reason why you should go to RocketHub and fuel my #SciFund project!

Does Open Lab show how much career scientists suck at writing?

The much anticipated selections for Open Lab 2012 were announced earlier this week. (Yes, the buttons I made said, “Submit to Open Lab 2011,” but due to a change in publisher, 2011 is going to be skipped.)

The 51 posts are awesome displays of writing. I’m pleased that a lot of things I nominated (alpong with who knows how many other people) are in there.

The breakdown of authors is interesting to me. Around half of the contributors are professional writers, journalists, and editors. Roughly one quarter of the contributors are early career scientists: grad students and post-docs. What you might consider traditional established scientists are not well represented.

This isn’t a huge surprise. Pro writers are good at what they do, because you don’t survive otherwise. In a highly competitive selection process, it stands to reason that works by experienced wordsmiths have the edge.

Still, I see so much potential in scientists writing about their own work that I’m disappointed that they are not a little better represented. I’d like the barriers between scientists and science fans to be thinner. Are we failing at communication? We’re still too stuck in big fancy words, too torn between research and teaching and administration and service, and too tone deaf at telling good stories, I fear.

P.S.—Editor Jennifer Ouelette shares some more excellent writing that didn’t quite make it in.

#SciFund troubleshooting

You want to fuel a #SciFund project! Joy!

The RocketHub website won’t let you! Bummer!

If this happens you, contact support@rockethub.com! They are there to help!

A few people have reported problems in contributing to their favourite #SciFund project. We asked RocketHub, who told us that a few (~1%) people do run into problems.

Possible causes:

• User error in entering data. This can often be fixed just by trying again in a couple of days.
• Old browsers - Internet Explorer 6.0 and a few other very old browsers have difficulties with the contribution process.
• High-level browser security/disabled cookies - some users have browser apps or have disabled cookies, which can make it difficult to contribute.
• Invalid card - RocketHub does not accept Maestro.
• Invalid country - certain countries can’t have their cards processed, because they are deemed “high risk.”

If you have tried to fuel a project, please try again! Don’t be discouraged! Think of the joy on all those scientists’ faces when they get the email that someone has fueled their project!

Conservatives should support #SciFund

If you are a political conservative who supports science, you should be supporting the heck out of the #SciFund challenge.

Conservatives argue for small, limited government. But arguments for “small government” don’t get a lot of traction among scientists, because funding trends are going in the wrong direction.

The main sources of scientific funding in most of the world is industry and government. Industry still funds a lot of research (which makes up most of the total), but industry is reducing funding for basic research. Industry research often focuses on maximizing the next quarter profits.

Government funding is increasingly the only game in town for basic researchers. I appreciate that there are few rewards for being efficient in the current government granting system. We desperately need alternative ways to fund science.

The #SciFund challenge is the biggest, best promoted effort to find a new way to fund scientific research in a long time. You’d better believe that a lot of other researchers are watching and waiting to see what happens. If it fails, a lot of scientists are going to say, “Crowdfunding can’t work. Therefore, more government funding to science.”

I know many conservatives would rather see government involvement in research not increase. But I hope that science-minded conservatives appreciate that research isn’t free. The most effective way to reduce government involvement in funding research is to provide alternatives. Twiddle the knobs, and make the problem go away.

Conservatives are often charged with being anti-science. I’ve criticized conservative politicians (not least in one of the most popular posts ever on this blog), but I’ve always thought that was an oversimplification. Science has received a lot of bipartisan support. Step up and show people that conservatives can and do support good science.

If the #SciFund challenge succeeds, it will be something you can point as an example of innovative thinking that promotes personal freedom, and that shows people can support science without a government middleman.

If you’re a conservative who supports science, you should go to RocketHub right now and support a #SciFund project!

P.S.—And you should spread the word about #SciFund!

Tuesday Crustie: Dance

It’s another new species of crab! Er, lobster. Crobster? Lobrab?

My confusion about this is that the paper announcing the discovery of this species, Kiwa puravida, and the news articles following it, refer to this as a “yeti crab.”

But the group this species belongs to, Galatheoidea, is normally referred to as “squat lobsters.” Thanks, English, for the reminder of why we scientists ended up using Latin for species names.

The paper describing this species also has a lot of cool stuff on how this beastie is farming bacteria on its hairy claws. Cool! And even cooler is the behaviour K. puravida uses to keep their bacteria happy:



Soundtrack added by Jarrett Byrnes.

And once I saw Jarrett’s remix, I couldn’t resist getting in on the fun...

The Northern Pikes’ “Dancing in a Dance Club”:



Men WIthout Hats’ “The Safety Dance”:



More contemporary with Little Boots’ “Shake”:



And my most populare one so far, Lady Gaga’s “Just Dance”:



And, well, there’s more in this YouTube playlist. I was proud when I saw “Now trending on Science Pond: #DancingYetiCrabs” on Twitter. Shrimp on a treadmill, you’re on notice!

More coverage by Ed Yong at Nature News, the Inkfish blog, and Thoughtomics.

Reference

Thurber AR, Jones WJ, Schnabel K. 2011. Dancing for food in the deep sea: bacterial farming by a new species of yeti crab. PLoS ONE 6(11): e26243. http://dx.doi.org/10.1371%2Fjournal.pone.0026243

I was hoping for Anklylosaur...

From Fake Science:

What kind of dinosaur would you be?

Pterodactyl

You wouldn't be satisfied with being a dinosaur. You also have to be a bird. Everyone is very impressed. Now please get back on the ground and be normal.

Take the quiz on BuzzFeed.com

Science after a storm

My newest paper kind of got started because of an act of God.

Hurricanes are still considered “acts of God” in insurance policies, right?

You see, my grad student at the time, Sandra, was continuing work on spiny lobster that she had started as an undergraduate (Espinoza et al. 2006). We were gung ho to continue that work to see if we could figure out if there were behavioural differences that were related to spiny lobsters’ loss of escape neurons.

But a problem emerged. Spiny lobsters show up around South Padre Island once in a while, but they are rare. So we had gotten all our lobsters from Florida, from the Keys Marine Lab.

And Keys got smushed by Hurricane Wilma in October 2005.

And there went our supplier for spiny lobsters.

Now, we might have been able to find another supplier, but we decided to press on ahead with some crayfish experiments. We originally planned to do experiments with spiny lobsters that paralleled the crayfish experiments in this new paper. We were going to do experiments immobilizing the spiny lobsters’ antennae, blindfolding them, and so on.

But the logistic problems of getting spiny lobsters continued to plague us. We eventually abandoned those experiments.

As it happened, Sandra had a baby girl very soon after her thesis defense. She was more occupied with a child than writing up some of her thesis research. And I wasn’t quite sure what to do with these experiments. We had presented the research at conferences, and gotten reasonably good feedback. But I wasn’t sure what would be an appropriate home for the manuscript.

The paper – I suppose it was still better described as a thesis chapter at this point – sat.

Last summer, I attended the International Association of Astacology meeting in Missouri (which I blogged extensively about on the Marmorkrebs blog). During the meeting, there was considerable chat about the society’s journal, Freshwater Crayfish. I liked what the editors were trying to do: get it out more regularly, and make it more clear that it was a journal, not conference proceedings. The production values of the journal were always very good.

It dawned on me that this was probably a good home for this project. That there were some known limitations to publishing in Freshwater Crayfish – like the long time between issues – were not a big deal for this project. After all, the research had already kind of sat, waiting for me to do something, for a couple of years.

I am so pleased that it is out. Sandra is now one of the few master’s students in our departments to have two peer reviewed papers arising from her master’s degree.

And the moral of the story is: Don’t abandon hope of publishing your projects because it’s “been too long.” Patience makes many things possible.

Reference

Espinoza SY, Faulkes Z. 2011. Escaping while defenseless or blind: effects of sensory input on tailflipping in crayfish, Procambarus clarkii (Girard, 1852). Freshwater Crayfish 18(1): 13-17.
http://iz.carnegiemnh.org/crayfish/IAA/members/fc/abstracts.asp?uid=guest&pubid=287

Espinoza SY, Breen L, Varghese N, Faulkes Z. 2006. Loss of escape-related giant neurons in a spiny lobster, Panulirus argus. The Biological Bulletin 211(3): 223-231. http://www.biolbull.org/cgi/content/abstract/211/3/223

Kitten or crayfish?

We’re into the last two weeks of the #SciFund challenge! And I’m getting just a little punch drunk out here...

And so, I prove yet again that everything on the Internet eventually turns to pictures of cats.



For those who have supported me already: Thank you once again!

For everyone else: Hey, isn’t it payday today? Would you miss a couple of bucks? Even a few bucks will help me meet my target!

You should visit RocketHub and support crayfish research!

Comments for second half of November 2011

Dr. Becca starts reading CVs.

Engaging Ideas looks at bees and epigenetics.

Daniel Wolpert gets up on the big stage at TED, alas, perpetuates a neuromyth about sea squirts that I’ve debunked on this blog twice before.

Suzie Sheehy, at her blog High Heels in the Lab, discusses reasons people get out of the science business. She sees traveling to new places as a detriment; for me, it was opportunity.

Aerobics grows your brain, but does it make you smarter?

Here’s what looks to be a straightforward claim:

Increased hippocampal volume translates to improved memory function(.)

But a simple line in the Discussion section may not convey the trickiness of the analysis in the Results section.

This paper, by Erickson and company, is looking for ways to prevent or reverse cognitive decline as people age. The hippocampus is part of the brain critical to the formation of memory, something we’ve known from many unfortunate people like Henry Molaison (known in the scientific literature as HM) or Clive Wearing who have suffered damage to their hippocampi. There’s good evidence that the size of the hippocampus can be affected by experience in humans.

The experiment had two groups. One group did aerobic exercise, the other did stretching exercises. They tested people after six months of exercise, and again after a year.

People who did the aerobic exercise had an anterior hippocampus that was a couple of percentage points larger than when they started. This is pretty cool, because hippocampus size decreases with age. The authors estimate that this is the equivalent of “rolling back the clock” by one or two years. The pattern they saw with the people doing stretching exercises was more typical: their hippocampi, on average, shrank.

Hippocampus is involved in forming new memories. Aerobic exercise makes your hippocampus bigger, as shown in this paper. So the statement I quoted at the top seems to follow, not just logically, but inevitably.

But here’s my problem. In the Results, the authors write:

Both groups showed improvements in memory(.)

Wait. Both groups got better at the memory task? That’s not what I would predict if hippocampus volume relates to memory function. After all, the hippocampi of the stretching control group decreased in size. You might think, “Well, okay, maybe both groups improved, but the aerobic exercise group must have improved more than the stretching control group, right?” Wrong.

(T)he aerobic exercise group did not improve performance above that achieved by the stretching control group(.)

Wait. What? How can you claim that  bigger hippocampus volume translates into better memory, when people whose hippocampi are shrinking perform just as well at the memory task as those whose hippocampi are growing? Erickson and colleagues make this claim based on an analysis of the people in the aerobic control group only, and show that there’s a correlation between the amount of increase in the hippocampus and the improvement on the memory task.

Am I missing something blindingly obvious? I don't see how you can claim bigger hippocampus means better memory when you only analyze the test group and not the control.

This paper is very cool in what it shows about flexibility of brain size, but I am not sure what the take-home message is about whether aerobics can keep your memory sharp.

Reference

Erickson K, Voss M, Prakash R, Basak C, Szabo A, Chaddock L, Kim J, Heo S, Alves H, White S, Wojcicki T, Mailey E, Vieira V, Martin S, Pence B, Woods J, McAuley E, & Kramer A. 2011. Exercise training increases size of hippocampus and improves memory Proceedings of the National Academy of Sciences, 108 (7), 3017-3022 DOI: 10.1073/pnas.1015950108

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

Tuesday Crustie: Lurking

Not sure of the species, but I think it’s in the genus Cherax, possibly even Cherax destructor. It was taken in southern Australia.

Photo by clinton1550 on Flickr; used under a Creative Commons license.

Research programs: Pies and cupcakes

During Neuroscience, I talked to several people about doing research, and how my strategy for working at an undergrad institution differed a lot from more traditional research institutions.

When people asked, “What does your lab work on?” After the first couple of times where I tried to rattle off, “Let's see, in the last two years I’ve published on parasites, nocicieption, animal care, brain scan ethics, fighting, the pet trade, ecological modeling, colour polymorphism,” I made a list on paper because it was too hard to remember them all.

By the end, on the last leg of the flight home, I came up with a metaphor.

In most research labs, the supervisor’s research agenda is like a pie, where everyone gets a slice. Grad students and postdocs get big slices; undergraduates might only get crumbs. But there's just one pie. Sure, every piece is a little different, but each has more or less the same flavour.

I give my students cupcakes.

Each is separate. Each is smaller, so nobody can have a great big piece. But you can have a lot of different flavours.^*

Maybe one reason why so many labs are built on the pie model is that it’s less work thinking up what to do next. A lot of people think that science is about solving problems.^** But a huge part of science is about identifying problems to be solved. If you content yourself with working on a single, massive problem that will take decades, you never have to worry about scrambling for a new idea again.

But as Jose Bravo said:

People with answers always work for people with questions.

Generating a lot of questions is challenging, but it has a different set of rewards.

---

^* To use another metaphor, from Archilochus:

The fox knows many things. But the hedgehog knows one big thing.

Most research labs are run by hedgehogs: they put everything into trying to know one big thing, so big that it can sustain decades worth of research work. I suppose it’s appropriate that my lab is more fox-like, considering the number of people who mispronounce my name that way.


^** For instance, see Marie-Claire Shanahan’s wonderful post about what students identify as being a “science person” is someone for whom the problems are solved:

Many students extended definition to say that because science students are so smart they shouldn’t ever have to ask for help or further explanations. One student said in her interview that real science students “understand all concepts and go above and beyond knowledge expectations. They do not require explanation.” Another student, who didn’t see herself as a science student despite having good marks, told me that she based her assessment mostly on the fact that she asks the teacher a lot of questions to make sure she understands. “Real science students shouldn’t have to do that”, she said. This seems in some ways antithetical to science. Isn’t asking questions and pushing until you understand one of the defining characteristics of scientific scholarship? Some students went as far as to say that real science students don’t need to participate in science class because they should know the right answers already.

The #SciFund super team-up!

One of the things I love about being in the #SciFund challenge?

Teamwork.

The advantage of #SciFund is that nobody is going it alone. We have been able to share ideas and bounce ideas around between each other, and have stronger projects and more visibility than if any one of us was trying this on our own.

In that spirit, let me introduce fellow #SciFund challenger, Marisa Tellez!



P.S.—I’m stupidly happy with how this came out.

#SciFund challenge: the half-way point

Three weeks down; three weeks to go.

We’re at the halfway point in the #SciFund challenge, and my project is 51% funded. I’m on target to meet my funding goal, so I’m cautiously optimistic.

What has it all been like so far?

I’m a raging inferno of emotions here!

The moments when you see the Rockethub email coming in announcing, “Your project has been fueled!” are great big highs – the amount does not matter. It’s just knowing that someone cared enough to help, and that you’re moving towards the goal, that make each one of those emails sweet.

But when the days go by with no emails... it’s pretty damn depressing.

Even when I know that most of the action is going to happen in the first and last weeks, and I know that it’s going to be hard to maintain momentum in the middle of the campaign (that is to say, right now), that intellectual knowledge doesn’t stop me from moping a bit when a day goes without the needle on the gauge budging.

But then, I read the media coverage, and I feel like I’m back hitting the high notes. The media coverage has been supportive, and there’s been so much that I just haven’t been able to keep track of it all (but fortunately, there’s a compilation here). But it’s almost as encouraging to read something like this in Forbes as it is to see a donation:

My son and I watched the Indiana Jones-like video from scientist, Zen Faulkes, and thought, “we should ‘fuel’ this project.”

Why, yes. Yes, you should. ;)

I was also interviewed by Jennifer Welsh for her LiveScience article, which has been reprinted and reproduced on several other sites.

My project also gets an mention in the Daily Mail article on SciFund. I’m a bit... miffed, I suppose, that they are characterising all the #SciFund projects as “wacky,” when we are all bona fide scientists with serious projects.

Also, I wanted to point out a discussion that happened on Google Plus about trusting the #SciFund participants with your donations, and how you know those dollars make a difference.

The highs are higher, and the lows are lower, than I ever expected. I just cannot maintain the same detached, “We’ll see how it goes” attitude that I take with normal grant submissions. There, I submit the manuscript, but have more more contact with the thing for months. Here, there’s almost daily contact, even when it’s not necessarily donations.

P.S.—You should fuel my #SciFund project at Rockethub.com!

P.P.S.—I’m working on a few new things related to my project that I hope you will see before the end of the week!


Photo by ♥KatB Photography♥ on Flickr; used under a Creative Commons license.

Tuesday Crustie: Scene stealers

I’m featuring krill (Meganyctiphanes norvegica) today on the Tuesday Crustie for no other reason than Will the Krill and Bill the Krill (voices of Brad Pitt and Matt Damon, respectively) were two of the best things about Happy Feet Two:



Picture by The Sun and Doves on Flickr; used under a Creative Commons license.

Non-nuclear nano neurons

Living things are made out of cells. Most people with even a passing familiarity with cells knows some of the parts that they have. A membrane to keep the outside out and the inside in. Some mitochondria for energy. Some endoplasmic reticulum to make your proteins. But the part of the cell that is the most familiar, the most famous, the big mac daddy of organelles, is the home of DNA, the center, the nucleus.

But now, my friends! Prepare to be amazed! Prepare to be astonished! Prepare to enter...

The world without the nucleus.

Well, not the world, exactly, but a nervous system in which most of the neurons have no nuclei. That nervous system belongs to the animal pictured in the upper left corner: Megaphragma mymaripenne, a microscopic wasp.

The other two cells in the picture above should be familiar to anyone who took any science in school: they’re a paramecium and an amoeba - and they’re shown at the same scale as the wasp. These wasps are tiny, tiny little animals.

Alexey Polilov has counted the nuclei in these wasps, both as adults and pupae. All of them. This is not as hard as it might sound, if you’re coming in with the expectation that most invertebrates have thousands, or tens of thousands, of neurons. Just one abdominal ganglion in crayfish holds about 600 neurons. But the total number of nuclei in the adult wasp was less than 400. And this wasp is capable of some complicated behaviour, not least of which is flying. I don’t know of anyone who thinks that powered flight is a simple behaviour that can be controlled only by a simple circuit with a handful of neurons. Flying is hard.

The lack of nuclei in the adult is not because they have so few neurons throughout their life, like C. elegans (302 neurons in wild-type adult). Rather, the wasps lose nuclei during development. The younger pupae have about 7,400 nuclei in their neurons, which sounds a reasonable number for such a tiny animal. But most of the nuclei are broken apart during the metamorphosis into the adult form. I know some other cells do not have a nucleus, like human red blood cells, but wonder if the mechanisms would be similar.

How can neurons without nuclei work physiologically? Polilov doesn’t provide an hypothesis, but he notes the adult wasps live only about 5 days, which is long given the size of the wasp. I suppose it’s possible that the adult life span is short enough that the nucleus can make all the proteins the neuron needs to function for five days during the pupal stage.

Polilov suggests that the size of the neurons limits how small you can make an animal. These wasps devote proportionately more of their body to their nervous system than larger insects: about 6% for Megaphragma compared to 1% or less for a honeybee. Despite the title of this paper, Polilov only examines the one species of miniature wasp in this paper. Whether or not other miniature arthropods would show the same kind of nuclear abandonment remains to be seen.

Reference

Polilov A. 2011. The smallest insects evolve anucleate neurons. Arthropod Structure & Development: in press. DOI: 10.1016/j.asd.2011.09.001

Related posts

“Oh, what a tangled web we weave”... because of small brains?

Protester picture from here.