30 November 2010

Tuesday Crustie: Does whatever a spider can


A spider crab (Leptomithrax gaimardii) from Australia.

Picture by Saspotato on Flickr. Used under a Creative Commons license.

29 November 2010

Guest Blog post at Scientific American

The decade the clones came” is the title of a new post I wrote for Scientific American’s Guest Blog. I’m pretty happy with how it turned out, so please check it out.

Writing a blog has one little disadvantage: it’s all in bits and pieces. When I was asked if I wanted to contribute to the guest blog, it occurred to me that this was a chance to pull a story about marbled crayfish together. That the first mention of Marmorkrebs on the CRUST-L list was about ten years ago was also a nice coincidence, and made me think that a cohesive retrospective would be worthwhile.

I’d like to thank Bora Zivkovic for the opportunity to pull the piece. Though I say it as a contributor now, Bora has done an fantastic job of getting top notch material for the Guest Blog. If you haven’t been reading it lately, you’re missing out on some good stuff. I’m proud to be part of it!

Only a few hours left to nominate posts for Open Lab 2010

Just another little reminder that there is still time to nominate writing for the fifth annual blogging anthology:





You can nominate posts from 1 December 2009 until 30 November 2010.

For instance...

Maybe you enjoyed the story of male lizards mistaken for females. It even got a retweet from Ed Yong! Ed also liked the deathstalker story and my discussion (okay, rant) on paper myopia in academics.

How about this competitor in the NESCent evolution blogging competition about pigging out? Or how fish react to reflections?

Or just a bad attempt to imitate the inimitable Sacha Baron Cohen?

My most popular post over the last year, though, by a wide margin, was my discussion of why snakes have slit pupils instead of round ones. It got almost twice as many visits as the next contender on cockroach mind control. I think this post’s popularity has more to do with this being one of those questions that people think about, can’t think of a good rationale, and hop on to Google to find an answer more than my sparkling prose.


Although maybe the prose sparkles just a teensy bit.

Tracking Crayfish Zero: The threat of pet crayfish

(Last week, my latest paper snuck out without me noticing. As with the last paper I co-authored this year, I wanted to tell you about the backstory that doesn't fit into the actual paper.)

“Patient Zero.”

That’s the typical name given for the first person to be found carrying a new infectious disease. The point of origin. The last time you heard the term a lot in the media was during the SARS outbreak some years ago.

That was very much the idea that was behind my newest paper.

When I started working with Marmorkrebs back in 2007, there were already people in North America who had them as pets. This struck me as odd, given that they had first been found in Europe. I got very curious. Who would have brought them overseas? And when?

I created the Marmorkrebs.org website late in 2007 (first version shown at right). During 2008, I put up a “Mail me!” link asking Marmorkrebs pet owners to contact me soon after, because I thought that might give me an idea of how long they’d been in North America.

I can’t remember the point at which I thought, “I should do this in an organized way.” Fortunately, I had the presence of mind to realize that I was going to have to do something I had never done before:

I was going to have to get IRB approval.

Because I work with invertebrates, I had never had to go through a university approval process for an experiment before. I was a little nervous, because this wasn’t just an animal experiment, but humans. And even an online survey needed an okay from the Institutional Review Board (IRB). That was an interesting. I had to undergo a little online ethics training course. There were sections of text that I needed to add to the survey, telling people about the risks of completing an online survey.

It seemed a bit odd at first. Risks? From an online survey? From what? Carpel tunnel syndrome?

Once the survey was up and running, a slow but steady stream of people started filling it in. There were enough data to send my student Steph off to the American Ecological Society meeting with a poster about it and her crayfish fighting work.


I let the survey run for about a year, though 2009 – not because that was a nice round number, but because a deadline was coming up for the journal I wanted to submit a manuscript to! I wanted to include the animal care data from the survey. With half the survey data going into the animal care paper, I took a while to figure out what to do with the rest of the data I’d collected. I wasn’t sure if I should pool it together with some other information (like the fighting research it had been paired with at the ecology meeting), or just try to get it out on its own.

It was very important for me to publish this paper in an open access journal. This paper was entirely possible because of the generosity of the people taking a few minutes to complete my survey, and I wanted them to be able to read the papers and think, “I helped with that.” I was familiar with the journal Aquatic Invasions because they had published some papers by Charlie and Gretchen Lambert, who I’d co-authored a tunicate survey with, and this journal has also published a Marmorkrebs paper last year.

When the papers were published, I emailed everyone I could, and was pleased that some of them responded that they were glad to hear about the crayfish research.

The other thing that I found interesting about this process was how it was made possible by online tools. I built the survey in Survey Monkey and plotted locations in Google Maps and Indie Mapper (which was just transitioning from a free beta version to a subscription service as I was preparing this paper). In fact, here’s the Google Map I created:


View Marmorkrebs pets in a larger map

While some journals are starting to get rid of supplemental materials, there’s no reason I can’t make and host my own.

And because a pre-print was available online and open access, this paper has already been cited by another paper - one that was officially published in the same issue of the same journal, in fact!

While I’m pleased with this short paper in many ways, I’m disappointed that I failed in one thing that I set out to do.

I wasn’t able to track down North America’s “Crayfish Zero.”

I just hope it didn’t escape.

Reference

Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450. http://dx.doi.org/10.3391/ai.2010.5.4.16

P.S.—Yes, I know the top picture is Prisoner Zero, not patient zero, but I don’t care.

26 November 2010

Countdown for Open Lab 2010

If you haven’t hugged a science blogger lately, you could at least nominate someone for...





You can nominate posts from December of 2009 until the end of this month.

Maybe something like whether octopuses feel pain like mammals. Or the origins of bone. Or maybe dingo detours tugs at you. Or a letter to someone who dislike blogs altogether?

25 November 2010

Synthpop symphonies

For me, this has been the best music geek week in a long time.

First.

I’m not into nostalgia. I don’t listen to music for the memories. I mean, I can tell you my memories about The Human League. How my present to myself after graduating high school was listening to their new album Hysteria for the first time, for instance. But that’s not important. The Human League has always been about the future (they were even called The Future in one early incarnation), never the past.

I am happy that that The Human League is still releasing music more than 30 years after their first strange experimental electronic recordings. It’s been a long, long wait between every album, but every one has invariably worked its way into my head in a way that not many other artists manage.

It’s not too long until their next album, Credo. And their first single, released Monday, is a wonderful tribute to nightlife.



What’s better than a brand new hero? An old hero who hasn’t lost it.

I know, I know, I’ve said it before, but it’s worth saying again.

But I love brand new heroes, too.

Second.

The Human League has many descendants, but one of the truest is probably Parralox. I have just now downloaded Metropolis, their third album, today. Like The Human League, Parralox are all about the future – although it’s sometimes a future imagined in the early twentieth century. Even the title of the new album brings to mind Fritz Lang’s silent film classic of the same name. Their lyrics often draw on classic science fiction ideas, and the minimalist art direction also brings to mind the optimism of art deco. Type nerds will even pick out these elements in their logo (set in Futura).

In both bands, I love the female voices against warm synth sounds, and the smart words with infectious melodies.



Until Little Boots announces when her second album is coming out, Credo and Metropolis will be stuck on my iPod for a long time.

24 November 2010

Defeating the deathstalker: How bats snack on scorpions

“Do not be distracted by the pincers when it is the tail that can kill you.” - The Tao of Shinsei

The thing that most people know about scorpions is that they sting. For humans, those stings range from painful to deadly. For a smaller animal, you would expect scorpion stings to be even more deadly and even more to be avoided. But for some bats, scorpions are meals.

Hemprich’s long eared desert bat (Otonycteris hemprichii) doesn’t just make the occasional meal of a scorpion. At some points of the year, scorpions make up make up most of what they’re eating.


ResearchBlogging.orgThis post was chosen as an Editor's Selection for ResearchBlogging.orgWe know bats can pick flying insects out of the air through echolocation (thanks to the work of my intellectual great-grandfather, Donald Griffin). Scorpions – thankfully! – do not fly. But bats’ world of sound is probably as rich and as detailed to them as the world of light is to us. It’s been estimated that bats can resolve spatial features of less than a millimeter with echolocation. One hypothesis is that the bats are able to feed on scorpions by disabling the stinger with precision strikes.

Holderied and colleagues looked at how the long eared desert bat is able to make a meal of scorpions, using a combination of lab and field studies. They gave the bats several choices of their potential dinners, including Leiurus quinquestriatus, which they call the yellow scorpion.

Other people call it the deathstalker.

If something was called a “deathstalker” in a movie, it would have glowing red freakin’ eyes. It would move in bullet time. And it would only carry a sword, because guns are just too noisy and inefficient. Something that you just know is going to be nasty.

And yes, this species is on the high end of the scorpion sting danger scale.

How do the desert bats catch these scorpions?

They listen for their footsteps, swoop down, and grab them, oblivious to the stings.

The bats do echolocate, like many other bats, but their echolocation calls are much quieter than those that are also using echolocation to forage for insects on the fly. There was no evidence that the bats were using these calls to glean. If the scorpion was silent and unmoving (say, a recently deceased scorpion), the bats missed it every time. The bats are using passive gleaning to hunt, rather than active. In some ways, this strategy is very similar to how barn owls hunt.

Once a bat get within range of the scorpions, they would start biting. The scorpions would try defending themselves with their stingers, but to no avail (emphasis added):

We filmed scorpions stinging bats several times sometimes on head and face, once even under an eyelid. Bats made no attempts to disable or avoid the stinger. The successful bat tore the freshly killed scorpion off the string and flew to a feeding roost to consume it. Scorpions were eaten head first, in the majority of cases including stinger and poison gland.

Even the deathstalker had no effect on the bats. When they presented bats with a choice between two species, the bats picked the more venomous species 49% of the time – about as close to a predicted random value as you’re ever likely to get in science.

The authors don’t really have a handy explanation for the scorpions’ impotence in the face of bat predators. They speculate that the stings may not be able to pierce the bat’s skin or that the bats have at least partial immunity to the scorpion venom. That the bats seem to be so indifferent to the venom, even going so far as to routinely eat it, makes me favour the latter hypothesis. At the last International Congress for Neuroethology, Ashley Rowe gave a poster just two spots down from mine talked about how grasshopper mice have developed mechanisms for resisting scorpion venom. Some of this work has been published, but isn’t cited in this paper.

Bats are the deathstalker’s stalker.

Reference

Holderied M, Korine C, & Moritz T. 2010. Hemprich’s long-eared bat (Otonycteris hemprichii) as a predator of scorpions: whispering echolocation, passive gleaning and prey selection. Journal of Comparative Physiology A. DOI: 10.1007/s00359-010-0608-3

Rowe A, Rowe M. 2008. Physiological resistance of grasshopper mice (Onychomys spp.) to Arizona bark scorpion (Centruroides exilicauda) venom Toxicon 52(5): 597-605. DOI: 10.1016/j.toxicon.2008.07.004

Bat picture by Charlotte Roemer on Wikipedia. Scorpion picture by Furryscaly on Flickr. Both used under a Creative Commons license.

23 November 2010

Tuesday Crustie: 47th

This edition of Tuesday Crustie falls on the anniversary of Doctor Who. And at least once, a crustacean has been the monster! Fear... the Macra!




The only reason these clips from The Macra Terror still survive is because they were censored in New Zealand because they were too scary. But many pictures still exist, and have been compiled into a photonovel. Audio from the story also exists, and has been released as an audio book (available on iTunes).

And because Russell T Davies is such a fanboy, he actually brought them back decades later...



22 November 2010

Don’t let the door hit you as you go or as you come back in

The Texas Tribune has an interview with Don McLeroy on his last meeting as a member of the Texas State Board of Education. As he almost always, he talks about the place of evolution in the Texas science standards.

After hanging up, McLeroy sent an e-mail saying he had thought more about what he wanted to say about his time in the limelight. He wrote that to understand the events of the past two years, “you need to know that for our opponents, nothing makes sense except in the light of evolution.”

“The great story coming out of Texas is that their spell has been broken,” he added. “We have ended the dogmatic teaching of evolution, and we have restored the founders’ idea of a Creator.”

I’ll leave it to a historian to discuss the views of American founders’ on God and Christianity. My cursory impression is that they were... complex.

"I mean, golly, I love this stuff. You haven't seen the last of Don McLeroy,” he says, noting that while he’ll watch to see what happens during this legislative session’s redistricting process, he’ll likely run for his old spot on the board in two years.

But Mr. McLeroy, how could we miss you if you won’t go away?

The deal is rotten

Warning: This post contains strong language.

One of the official bloggers for the recent Neuroscience meeting was Pascal Wallisch, who blogs here. Over at Tideliar’s post conference examination of the SfN “offical” blogs, he posted this comment:

Upon seeing my posts, some senior people in my department have already strongly advised me to “stop fucking around” and “cut the shit” and focus on “the only thing that counts (papers)” instead. They were unambiguous about that.

I cannot begin to describe how much this anecdote upsets me. It’s an unwelcome reminder that I am a participant in a corrupt system.

Yes, corrupt. I can’t think of a better description of a system that not only allows, but seems to encourage this sort of utter disdain for everything but the narrowest of research goals. It’s the same myopia that seems to infect Scott Kern.

I bet the argument is not “nothing matters but papers,” but probably a more complex chain: papers matters because they get grants, and grants matter because universities are making hiring and tenure decisions based on grant and potential for grants.

I’m also willing to bet that this argument gets made a whole lot more in biomedical fields. The National Institutes of Health (NIH) don’t require any plans for broader impacts (unlike the National Science Foundation), probably on the basis that the benefits of medicine is seen as so self-explanatory. And NIH is, from my understanding, more likely to pay entire salaries than other agencies.

So good bye to education to our students (except our grad students and postdocs, because they’re the labour force, and damn it, they have to learn how to run the machine) or anyone else who will never be on a federal grant review panel. Screw them.

And thus is created the image of academia and science of being completely self-interested, hell bent only on preserving their own vested interests, and perceived as fat cat millionaires. And thus does public trust and interest erode, and politicians who vow to take on elites and intellectuals get voted into office and wreck science budgets and evidence-based policy.

While conversations about outreach projects like Rock Stars of Science and Science Cheerleaders go on, at least they are trying to do something. At least they have some a sense that there is a world out there beyond the “Submit now” buttons on journal websites.

Additional: Jerry Coyne's reflections on joining the blogosphere and passing four million views (ack!) is relevant to this discussion. I’ve added some emphasis:

I thought that my job was to dispense professorial wisdom to eager and untutored recipients, hungry to learn about evolution. Oy, was I wrong! I had no idea that among the readers would be many scientists and professional evolutionists, many of whom know a lot more than I do about topics I cover. And not only that, but philosophers, musicians, literature addicts, and even a Nobel laureate or two. I can hardly make a post in which I don’t learn more than I teach. And I don’t think I’ve ever written a single post in which I didn’t say something wrong. I appreciate the corrections, but it is humbling.





Photo by futureatlas.com on Flickr, used under a Creative Commons license.

18 November 2010

Come work with us

My department has two, count ‘em, two tenure-track assistant professor positions up for grabs. One is for someone who does virology, the other, fungal biology. Please help spread the word among your colleagues who do research in these areas.

NESCent evo-blogging update

Check out the first compilation of entries in the NESCent travel award to attend the Science Online 2011 conference. Tickets to that conference sold out in 45 minutes this year, so expect this year’s entries to be extra competitive!

Those clicking will see that I have a horse in this race: my post on the evolution of the pig out is here.

Are big brains better for long trips in bats?

Previously, on NeuroDojo...

(M)igration causes brain size to reduce, rather than the other way around.

ResearchBlogging.orgThe quote might be a bit misleading, though, because that was in reference to bird migration. All manner of animals migrate, and it is possible that birds face pressure other creatures don’t.

A good first place to look for a comparison would be bats. Because despite being separate by several hundred millions years of evolution, bats have one very obvious similarity to birds: they fly. And, like birds, they migrate, though their migration tends to be shorter than birds. So you would expect some of the same patterns of brain size to happen in bats as in birds.

McGuire and Ratcliffe decided to take this a step further, not only looking at overall brain size, but the size of the hippocampus. The hippocampus is deeply involved in learning about your position in space, and it has been shown repeatedly in many species that those with heavier demands on their spatial memory (say, from having a larger home range tend to have a larger hippocampus). You might expect migrating bats to have a larger hippocampus than those that don’t.

One of the recurring problems with trying to figure out these sorts of questions, though, is what data you use. Generally, you can’t go out and get new brains, and do detailed measurements of how much each bat species migrates. You have to go back into published reports on migration.

There are biases both ways: people might not realize a species migrates (bats being nocturnal). And for those bats that don’t migrate, it might not get explicitly mentioned, because it’s “normal” for bats, which means you get no information. And within one species, some individuals will migrate and others won’t. Still, they ended up with a list of over 300 bats species for which they had some brain and behaviour data.

Migrating bats indeed had smaller overall brain sizes for their size – just like the birds. This supports the idea that brains are expensive, and so is flying, and the combination of the two is incredibly difficult to fit into the energy budget.

I’d be interested to see if there were differences in the brains of migrating and non-migrating invertebrates, like butterflies. They tend to have smaller nervous systems relative to their body size than vertebrates, so would they also have the same energetic costs to shave off neurons here and there? Or vertebrates that migrate without flying?

More surprising was that the hippocampus showed no difference between the migrating and non-migrating bats. McGuire and Ratcliffe suggest there are just too many confounding factors for any signal to rise above the noise. What we need are some bat neuroethologists (and I know you’re out there) to do some studies on how bats use the hippocampus in a controlled lab setting.

Reference

McGuire L., & Ratcliffe J. 2010. Light enough to travel: migratory bats have smaller brains, but not larger hippocampi, than sedentary species. Biology Letters: In press. DOI: 10.1098/rsbl.2010.0744

Photo (Myotis myotis) by Jan Svetlík on Flickr; used under a Creative Commons license.

17 November 2010

Defending the liberal arts education

Genome Biology published an open letter to the president of the State University of New York At Albany, George M. Philip. Mr. Philip (not Dr. Philip, apparently, somewhat unusual for someone in academia) decided to cut five departments in his university: French, Italian, Classics, Russian and Theater Arts.

The letter, by Gregory Petsko of Brandeis, hits with the full force of a body blow. It’s an astonishing piece of rhetoric. It takes apart Mr. Philip’s decision at the seams, then rips out the stuffing.

I wanted to echo the central theme. At many different levels, universities are often being encouraged now to throw their weight behind science and engineering. It’s critical that they continue to support all the disciplines.

I wrote before about how valuable the undergraduate classes in acting were to me as a graduate student and beyond.

Although I’m not taking formal classes now, the crafts of typography and design are heavily influencing one of my favourite projects, the Better Posters blog: my quest to make conference hallways more beautiful and more effective.

I currently have my neurobiology course in a learning community with a philosophy of mind course, on the idea that the two approaches are mutually enriching.

Universities, and particularly faculty, are supposed to be collegial. It’s not collegial to devalue the scholarship of other disciplines, or to think that one is somehow easier or less valuable than others. Universities are supposed to be places that value scholarship and knowledge of all sorts.

16 November 2010

Library newsletter

I somehow managed to get myself featured in our university library newsletter. Just so you know.

Tuesday Crustie: Fresh


Aeglids are little known crustaceans. They’re anomurans, which makes their closest relatives squat lobsters, hermit crabs, sand crabs, and the like. Unlike all their anomuran kin, however, they are a freshwater lineage living in South America.

Picture from here,  where this interesting little guy (species unknown) is given the unfortunate moniker of cockroach crayfish.

15 November 2010

Texas house bill 104

I just learned of a bill that has been pre-filed by Fred Brown that would, if passed, completely restructure the Texas higher education system.

Texas universities are currently under the domain of the Texas Higher Education Coordinating Board. The bill would abolish this and put universities under the control of the Texas State Board of Education.

Yes, that State Board of Education. The divided, bickering State Board of Education that routinely ignores the advice of its experts, and that has weakened science standards, particularly in regards to evolution, and that has members to have expressed open contempt for university professors.

I found a brief news report here.

Under Brown’s House Bill 104, the State Board of Education would provide oversight of the newly formed entity, a potential move that could raise some eyebrows. Despite harsh criticism directed at the board in recent years, Brown is confident the 15-member body will serve well.

“They are smart people,” he said. “They have to have a passion for what they do or else they wouldn’t run for office in first place.”

Maybe. But passion is not the same as competence.

Fred Brown’s legislative history is here. This blog notes:

This legislation does not seem to have support within the education community, and it is unclear if it will gain any traction among lawmakers since the financial savings are likely to be small.

Another blog is more pithy:

Yeah, we think not so much.

Fuuuuuuuuuuuuuuuuuuuuuu....

More as I learn it.

Neither me nor thee: the fish in the mirror

If you want to get a Siamese fighting fish (Betta splendans) like this, show it another fish...


...or its own reflection.

ResearchBlogging.orgThis post was chosen as an Editor's Selection for ResearchBlogging.orgFamously, very few animals understand reflections as representing themselves. There are veritable reams of papers written about the “mirror test” and how much it suggests about animal self-awareness, and therefore, animal consciousness.

Whether you agree with great apes or dolphins showing self-recognition in the mirror test, pretty much everyone agrees that fishes do not. The example of the betta doing a threat display to a mirror goes back in the scientific literature over 75 years.

Desjardins and Fernald looked at this question in an African cichlid, Astatotilapia burtoni, rather than a betta. I suspect that the reason for using this particular fish is that they know a little more about the cichlid’s genetics than the betta’s.

The experiment is dead simple. Take fish, put them in two adjacent tanks with a divider, and pull back the divider to reveal an empty tank, a mirror, or another animal. After 20 minutes of video recording the behaviour, the fish are sacrificed. Blood samples are taken to measure hormone levels (as things like testosterone are associated with aggression), and brain tissue is analyzed for gene expression.

The gene expression in the brain is different depending on whether the fish sees a reflection or another animal.

That caught me, and the authors, flat-footed. Are all those decades of observations made by who know how many fish owners wrong? What is going on?

The genes they examined were c-fos and egr-1, both of which can be “switched on” rapidly. c-fos is more interesting to me, because lots of c-fos is thought to be correlated of neurons generating lots of action potentials. The pattern was the same in three of the four brain regions they examined: both genes were expressed way more if the animal saw a mirror than of the fish saw another fish or a control. In the fourth area, both reflection and foe caused higher levels of gene expression than an empty tank.

The authors found no difference in behaviour or hormone levels depending on whether fish saw a mirror or another animal. This is good, because it replicates the older results: there is no behavioural difference between mirror and opponent.

But the gene expression indicates that something different is going on in these two circumstances. It’s not at all clear what that might be yet. Desjardins and Fernald suggest the mirror might be inducing more “fear” than an opponent. This word has a little more cognitive baggage than I would like, personally, but they provide some supporting references that suggest egr-1 is induced during stress responses.

The follow-up experiments that I would want to do would be to use a video system to start messing with the reflection. Delay the image, so that the movement of the reflection doesn’t perfectly track the fish. Flip the image horizontally or vertically. Stickleback have been shown to respond to video images many times (e.g., Rowland 1995). If these fish have better visual discrimination than stickleback, maybe HDTV will work: earlier this year, Pronk and colleagues showed octopuses would respond to HD TV images. I think these would work.

While I am a great believer in the power of a behavioural analysis, this paper points out that there may be more subtle things going on in the brain. One doesn’t necessarily mirror the other.



Reference

Desjardins J, Fernald R. 2010. What do fish make of mirror images? Biology Letters 6(6): 744-747. DOI: 10.1098/rsbl.2010.0247

Bradbury J. 2005. Social Opportunity Produces Brain Changes in Fish PLoS Biology 3(11) DOI: 10.1371/journal.pbio.0030390

Pronk R, Wilson D, & Harcourt R (2010). Video playback demonstrates episodic personality in the gloomy octopus Journal of Experimental Biology, 213 (7), 1035-1041 DOI: 10.1242/jeb.040675

Rowland W (1995). Video playback experiments on stickleback mate choice: female motivation and attentiveness to male colour cues Animal Behaviour, 49 (6), 1559-1567 DOI: 10.1016/0003-3472(95)90077-2

Betta picture by calwhiz on Flickr; used under a Creative Commons license. Astatotilapia burtoni picture from Bradbury.

Comments for first half of November 2010

Pondering Blather has that always popular topic, “Advice for people applying for tenure track jobs.”

Southern Fried Science asks if the Society for Integrative and Comparative Biology did the right thing in moving its annual conference out of Louisiana.

Arthopoda blog is selling stuff.

Retraction Watch asks when people should lose their doctoral degrees. And by lose, I don’t mean “misplace between the couch cushions,” I mean “have it forcibly taken away by the awarding university.”

Code for Life asked bloggers how long it took to write a science blog post.

13 November 2010

No, they haven’t – but not for lack of trying

I don’t know whether to blame the interviewer, Mitch Potter, or the interviewee, history professor Jill Lepore. In the middle of a fairly interesting article on the American constitution, the Texas science standards suddenly appear (emphasis added).

Lepore links worship of the Constitution to other flashpoints in broader, ongoing tensions between the U.S. division of church and state. She points to Texas, where conservative-dominated school boards have successfully implanted the teaching of creationism in the study of science.

Look, I’ve been as critical of the Texas State Board of Education as anyone about their treatment of evolution in the science standards. But they have not “implanted the teaching of creationism” into the standards.

When you say that there is creationism in the Texas school system, all those conservative State Board of Education members are going to ask you to point out where the word “creationism” is in the standards.

And they’ll have you cold and you’ll look dumb. Because it isn’t there.

They weakened the wording about evolution, yes. That the reason they did so was because many of the State Board of Education members are creationists seems indisputable.

But being vague about one thing is not the same as implanting something else.

Right, back to grading...

12 November 2010

The toughest scientists

The Guardian put out a photo gallery of the hardest of hard core scientists. You know, the ones who experiment on themselves and put themselves in harm’s way for the sake of science.

Sadly, this list is incomplete.

For no list of tough scientists can be complete without the man they call... Doctor Popsicle.



Hat tip to Ewan for the Guardian list.

Additional: I didn’t realize that the photo gallery was separate from another article asking to compile a list of the “hardest” 100 scientists. You can see discussions on Twitter (and yes, I nominated Dr. Geisbrech, a.k.a. Dr. Popsicle, to be on the list!)

Grad school drama, continued

The story about the grad student who was awarded a doctorate after failing requirements has been making the rounds on Twitter. I got some interesting comments there, particularly on the nature of anxiety, with two people pointing out that not seeking help for anxiety is common, as it often develops late.

With a little more thought, here’s what I would like to have seen. I would have tried to get everyone – the student and the graduate faculty of math – to figure out what a reasonable accommodation would be, and have everyone sign off on that. Then, the student does whatever everyone agreed to. Or not.

Everything is above board, everyone has agreed, and nobody is making a unilateral decision.

I’m less certain about the decision of the university to suspend a professor objecting to all this. But it certainly doesn’t look good from a distance.

11 November 2010

Expanding retraction

ResearchBlogging.orgShould a scientific paper be retracted because it is mistaken?

We’re not talking here about misconduct, or deliberate fraud. We’re talking about a result that is, for whatever reason, wrong: a false positive or a miss, or an overly enthusiastic interpretation, or a good old honest mistake.

At the Retraction Watch blog, Tom DeCoursey argues that papers that are wrong should be retracted from the scientific record. His main argument is that people waste a lot of time trying to reproduce results that later papers have been unable to confirm.

This may be a rather different view of retraction than has typically existed. My impression is that previously, retraction occurred primarily when there was scientific misconduct: fabricated data, or an editor doing an end run around the peer review process. In the medical literature, retracting could also occur in case of an error that might kill people from mistreatment (“lethal error”; Horton 1995).

I get the impression that papers are getting retraction for a much wider range of reasons than ever before, for reasons that have nothing to do with the quality of the science (e.g., authorship squabbles; embargo violations; pressure from bloggers).

I went looking for whether anyone has conducted research on the reasons for retraction. A quick search turned up work by Snodgrass and Pfeifer (1982). Of the papers they looked at, 94% of the retractions they studied had a reason given, but they don’t break down those reasons into any categories.

Six percent of retractions were not explained at all. I’ve seen papers much more recently with no reason given, so the practice hasn’t stopped.

If we widen the use of retractions, all sort of questions are raised. What level of evidence, of failure to replicate, should be enough to warrant a retraction? One of my own recent papers was an extended attempt to replicate another experiment, without success. But it would be presumptuous of me to demand the original paper be retracted.

In the case of honest mistakes, how should a retracted paper factor into promotion, tenure, or funding decisions? And how should journals seek to notify readers? Remove the paper from the record, which is how retraction was supposed to work? Label it as retracted?

Another take on this from Biochem Belle.

Additional: An abstract describes a study (which I don’t think has been published yet) that ranks reasons for retraction: Misconduct makes up 15% (data fabrication, 5%; data falsification 4%; plagiarism, 16%); “mistakes” make up a larger component of about 29% (honest research errors; 28%, non-replicable findings, 11%). Then you have issues that are harder to categorize: redundant publication, 17%; disputed authorship/data ownership, 5%; inaccurate/ misleading reporting, 4% (not sure what that could be); and the kicker, no stated reason at 9%.

Reference

Horton R. 1995. Revising the research record The Lancet 346(8990): 1610-1611. DOI: 10.1016/S0140-6736(95)91935-X

Snodgrass GL, Pfeifer MP. 1982. The characteristics of medical retraction notices Bull Med Libr Assoc 80(4): 328-334.

10 November 2010

Exam anxiety + academic standards = drama!

A math graduate student doesn’t complete all his required classes. Instead, an undergrad class is allowed to substitute for a doctoral class.

The student fails the comprehensive examinations. Twice.

After failing the exams twice, the student then claims to have exam anxiety, and asks for accommodations for this disability. The University of Manitoba decides to award the student a doctorate in mathematics.

Oh wait, we haven’t even gotten to the drama yet.

Astonishingly, an assistant professor (that is, someone without who probably does not have tenure, the major mechanism in place to protect instructors from being punished for speaking their minds), Gábor Lukács, goes to court, asking that his university not award this student a doctorate.

The University of Manitoba suspended Dr. Lukács without pay for three months for insubordination.

I’m sorry, but University of Manitoba? You are in the wrong on this one, at least on the issue of the initial request for accommodation. Someone should ask for accommodation before the fact, not after it - twice. That’s the transparent thing to so. Accommodation should be limited by what is reasonable, and not be a permit to do whatever the requester wants.

The facts of the case were reported by The Current radio show, Macleans, and the National Post.

It’s nothing personal, it’s just that my brain is bigger than yours


Now you may be thinking that lemurs are all just the same. You know, cute and cuddly adorableness. But let me tell you, you would be mistaken.


Look at Maurice here. Very efficient, smart enough to be recognizing true greatness in his kingly king when he sees such magnificence presented in front of his eyeballs.


But now we have Mort. Mort is, shall we say, easily swayed by shiny objects. I blame the extreme difference in the seasons where... Mort? Mort! Do not be touching the feet of the king!

ResearchBlogging.orgAs I was saying, there are many reasons to have a small brain. For one, it can be very efficient to have a small brain. Trust me. This big brain of mine? Exhausting. It is no wonder I have to be eating so much to keep up my smarty-pants.

It is also to your advantage to have a small brain when one glorious day is much like the next glorious day. I mean really, you don’t need to be exercising your gray matter much if the problems you solved yesterday are the same problems your going to solve tomorrow. Especially if you can just send Maurice to look after them.

And I know this because van Worden and crew measured the brains of many lemurs. Okay, there were lorises too, but really, how interesting are those? Bug eaters. Do you really want to be known for saying to your friend, “Oh look, you have a grub stuck in your teeth”? No. No you do not. They had this idea to test whether the changing seasons would make lemurs (and stupid lorises) have small brains, because it was expensive to keep them going in the down seasons when there’s little food, or have big brains, because the lemurs (and stupid lorises) need to have the smarty-pants to figure out what to do when the weather changes.

After they do all their fancy crunching of the numbers, they tell me that the places with the biggest changes in seasons are the places where the lemurs (and stupid lorises) have the smallest brains. And I said, “Well, that explains it. Mort is from Bekopaka, and you know what they say about Bekopaka? If you don’t like the weather, wait five minutes!”

This royal joke was lost upon them.

So the finding is that if you want to have a big brain like myself, you need a constant supply of food, not one that goes and comes like the weather fairy friend. Maurice! I’ll be taking that refill on my plate now.

Reference

van Woerden J, van Schaik C, & Isler K. 2010. Effects of seasonality on brain size evolution: evidence from strepsirrhine primates. The American Naturalist 176(6): 758-767. DOI: 10.1086/657045

09 November 2010

Tuesday Crustie: En masse


Red crabs (Gecarcoidea natalis) making their famous annual migration. Read more on ABC Science.

08 November 2010

Breach of etiquette

The role of anonymity in the scientific process continues to interest me. Last week, Nature reported about emails lobbing accusations of scientific misconduct by stem cell researchers.

The point that these are anonymous is brought up several times, always negatively.

Critics argue that Stem Cell Watch is not following scientific etiquette, which says that concerns should be addressed directly and openly to the authors of a paper. (Doug Melton, co-director of the Harvard Stem Cell Institute in Cambridge, Massachusetts) says he received a message, addressed only to him, from the group earlier this year. The e-mail accused another stem-cell researcher of misconduct, but because it was anonymous, Melton simply deleted it.

Enmphasis added to the next one:

“We appreciate any opportunity to respond to critique or concerns raised about our work,” (Johan Ericson and Thomas Perlmann at the Karolinska Institute) said in a written statement. “However, we regret that these serious accusations were made anonymously, as we strongly believe in the concept of an open and transparent communication about suspected errors in published data.”

I wonder if Ericson and Perlmann insisted on signed peer review. Probably not, as most of the “top” journals still use anonymous peer review. Like, oh, maybe... Nature?

“We wouldn’t encourage anonymous accusations, least of all those broadcast indiscriminately,” says Philip Campbell, Nature’s editor-in-chief.

I can’t wait for these people to discover The Third Reviewer website. They will be shocked and possibly appalled.

Or, for that matter, I can’t wait for these people to realize that there are hundreds of science bloggers out there, writing about stem cells... and many of them aren’t using their real names! (Yes, I know most of those are pseudonymous rather than anonymous. Where that falls on the continuum of anonymous to transparent is complicated.)

It seems to me that there’s an interesting double standard on anonymity here. People reject anonymity, except when they’ve come to expect it. Or it’s convenient to them personally.

05 November 2010

We rallied ‘round our nerd

“Nerdy” Christie Wilcox has won the scholarship competition (which I described here) for her Observations of a Nerd blog - against an astonishingly resilient cosmetics blog.

Congratulations, Christie!

The new Texas State Board of Education

Texas Freedom Network and It’s Okay To Be Smart have post-election analyses of the Texas State Board of Education, my seemingly endless source of blogging fodder. Executive summary: Cautious optimism.

Science cheerleaders

This is going to be a tough post to write. Nobody likes admitting, “I’m a close-minded bigot.”

But I think that’s how I’ve been about cheerleading.

I despise everything cheerleading represents. I hate how it’s about looking a certain way. I hate its reinforcement of conformity. I hate the encouragement of macho bullshit that makes up so much of sport. I hate the crass sexism of women on the sidelines. I hate the sexualization surrounding cheerleading, with all the creepy “barely legal” overtones. And I hate how much it reminds me and represents the harsh social stratification, and in some cases ostracism, that occurs in schools.

Cheerleading makes me gag.

Yeah. I have issues.

So this article and the video below leave me feeling utterly conflicted.



I’ve written about the need to have science “fans” in the ways that sports has “fans.” We scientists need evangelists, and I don’t doubt for one second that these women are wonderful evangelists.

My head and heart get the video, and what Randy Olson writes about them, like this:

There are A LOT of professional cheerleaders who are seriously interested in science and other STEM stuff. And when you watch this little video we made you see the women aren’t just vaguely connected with science careers — they are the real deal.

In each of the interviews the women also told their personal stories of discrimination, harassment and even abuse for being cheerleaders. We didn’t want to drag this first video down with the heaviness of their stories. But we will, eventually, make use of that material. They have fascinating stories which are not the least bit predictable.

Even though the whole concept of cheerleading still makes my guts churn.

Call me a bigot on this one. I probably deserve it. I’ll try to be better about it in the future.

04 November 2010

The silent, the hidden, and the lawless


I love this list of how things might be “supernatural” at Cosmic Vicariance:

Rather that declare once and for all what the best definition of “supernatural” is, we can try to distinguish between at least three possibilities:
  1. The silent: things that have absolutely no effect on anything that happens in the world.
  2. The hidden: things that affect the world only indirectly, without being immediately observable themselves.
  3. The lawless: things that affect the world in ways that are observable (directly or otherwise), but not subject to the regularities of natural law.

A problem that I see is the difficulty of distinguishing “the lawless” from the rare and / or the complex.

For us to determine if there are underlying regularities, we often need a large number of observations. But there are some events we just cannot conjure up on a whim, and these rare events may be important.

And causal chains can be so complicated that we can’t necessarily parse them out in law-like terminology.

03 November 2010

Why a lie about sharks beats the truth about naked mole rats

ResearchBlogging.org“Sharks don’t get cancer.”

Many people have heard this, and many people believe it, even if they wouldn’t go so far as to buy a cancer treatment from shark materials. Even the BBC fell for this myth. You can find refutations from Nerdy Christie Wilcox, with some additional info from Why Sharks Matter.

I don’t want to rehash the debunking of the myth here. Instead, I want to talk about why people aren’t rushing out to buy naked mole rats.

For animal behaviour researchers, the naked mole rat (Heterocephalus glaber) is yesterday’s news. There was a lot of interest in the social behaviour of naked mole rats in the 1980s when it was discovered that they had some behaviours surprisingly similar to bees and ants.

But it turns out that this species is remarkable in many other ways, not least of which is its apparent immunity to cancer. New Scientist recently had a story about the interesting research being done on naked mole rats.

Nearly all mice have cancerous cells lurking in their bodies by the time they die but cancer has never been seen in a naked mole rat. “Every time one of our animals die, we try to figure out what they die of,” Buffenstein says. “We haven’t seen a tumour, we haven’t seen lesions, we haven’t seen signs of lymphoma. We know they don’t get age-related cancer.”

(“Buffenstein” is Rochelle Buffenstein, who does physiology up the road from us at the University of Texas Health Science Center in San Antonio.)

For that matter, crustacean cancers are also rare (Vogt 2008). (Somewhat ironic, considering that “cancer” can also refer to crabs.) And in discussion with one of my friends whose done real honest to goodness cancer research, I seem to recall her saying that several other groups of mammals rarely got cancer.

Why has the shark myth taken hold of public consciousness when real examples have not?

I think it’s purely magical thinking.

One kind of magical thinking is that things have an “essence”. It might be good or bad, but importantly, that essence can spread. People want to touch an object if they are told it belonged to a famous musician or leader, but will not want to touch it if they are told it belonged to a serial killer.

It’s the same kind of logic that led people to hunt tigers and rhinos for aphrodisiacs. It’s the exact same reasoning that led people to gruesome beliefs like one where you could gain powers using body parts from people with albinism. Or that you would gain your enemy’s strength by eating their heart.

A shark is a powerful. Large. Fearsome.

A naked mole rat is ugly. Small. Comical.

We want to think that sharks can beat cancer. It seems absurd that a naked mole rat could defeat something that causes so much grief in humans. But the real absurdity is how far astray we can be led by magical thinking.

References

Seluanov A, Hine C, Azpurua J, Feigenson M, Bozzella M, Mao Z, Catania K, Gorbunova V. 2009. Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proceedings of the National Academy of Sciences 106(46): 19352-19357. DOI: 10.1073/pnas.0905252106

Liang S, Mele J, Wu Y, Buffenstein R, Hornsby P. 2010. Resistance to experimental tumorigenesis in cells of a long-lived mammal, the naked mole-rat (Heterocephalus glaber). Aging Cell 9(4): 626-635. DOI: 10.1111/j.1474-9726.2010.00588.x

Jarvis J. 1981. Eusociality in a mammal: cooperative breeding in naked mole-rat colonies. Science 212(4494): 571-573. DOI: 10.1126/science.7209555

Vogt G. 2008. How to minimize formation and growth of tumours: Potential benefits of decapod crustaceans for cancer research. International Journal of Cancer 123(12): 2727-2734. DOI: 10.1002/ijc.23947

Picture by Smithsonian's National Zoo on Flickr. Used under a Creative Commons license.

02 November 2010

Carnivals for November 2010

The Carnival of Evolution #39 is up at Byte-Sized Biology.

Carnival of the Blue #42 is up at The Beacon.

Meanwhile, Circus of the Spineless celebrates its 59th edition at Cephalopodcast with a sweet redesign of their logo...

Tuesday Crustie: At ease!


I liked last week’s soldier crab picture so much, I couldn’t resist having a second look at one of these guys.

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

01 November 2010

B.A.N.T.E.R.

I am not going to the mega-massive Society for Neuroscience meeting this year. (No, not because I’m wondering about their blogger choices.)

But if I was, I would probably be planning to be here:


You can read more about this event here.

Fingers in the pie

Previously, I wrote about some of the laws that the Texas legislature passed that affect universities. This got me wondering if other states pass more or fewer laws concerning universities than Texas does. The administrative creep seems high to me. But again, I don’t have much to compare it to.

A few examples.
  • Texas requires all students to take two classes in Texas history as part of their core.
  • Texas decided that since accreditation agencies required a minimum of 120 credit hours to get a bachelor’s degree, that most degree plans shouldn’t go even one credit hour above that minimum.
  • The “six drop” law that prevents students from dropping more than six classes in their undergraduate career. 
  • And, as mentioned Monday, requiring us to put up a syllabus for each class a few months before the class starts. And our CVs.

There’s a joke that makes the rounds that state universities have moved from being state supported, to state funded, to state tolerated, to state located. I think there’s one more step that could be taken: state regulated.

University education and critical thinking skills are sort of like alcohol, tobacco, and firearms – you better keep that stuff contained, because it can be dangerous in the wrong hands.

Additional: Here’s an article in the Austin American-Statesman describing more stuff that Texas wants to do to universities.

Comments for second half of October 2010

Biochem Belle, over at There & (Hopefully) Back Again, asks about people’s experiences blogging under their own name versus blogging under a pseudonym. I find it interesting that the vast majority of bloggers in the comment thread are blogging under an assumed name.

Outdoor Science asks for advice on blogging basics.

Andrea Kuszewski, writing at The Rogue Neuron, thinks scientists used to be more creative.

I run a poster blog, so you know I can’t resist a thread about posters at Tales of the Genomic Repairman.

ScienceLine recycles a neuromarketing press release that I talked about here.

Gerty Z tells a spooky tale of the tenure track job application stack! It grew.. and grew! Until it threatened to consume everything in its wake!