31 January 2012

Texas passes the science test

The Austin American Statesman is reporting that Texas gets a passing grade for its K-12 science standards. It’s a C, to be exact. But who’s doing the grading? The Fordham Institute, which the article describes as a conservative think tank. The American Statesman article says:

“The high school biology course is exemplary in its choice and presentation of topics, including its thorough consideration of biological evolution,” according to the report being released today.

But the evaluation also found that evolution is largely absent from middle school and elementary grades, which means that “students are not prepared to learn what they need to learn at the high school level,” said Kathleen Porter-Magee, senior director of the High Quality Standards Project at the Fordham Institute.

The report for Texas is a short, readable four pages. And while the phrase “conservative think tank” conjures bad images of other institutions, this one does not sympathize with creationism or intelligent design. Here’s a clip (my emphasis):

(T)he seventh-grade standards mention the Galapagos finches, giving the impression that the Darwinian paradigm is being presented. Unfortunately, it is not. Instead, the example of the finch Geospiza fortis apparently refers to studies by Peter and Rosemary Grant on beak size in this species, made widely known by Jonathan Weiner’s Pulitzer Prize-winning book, The Beak of the Finch. Creationists often distort these important findings to argue that Darwinian macroevolution does not occur—instead, microevolution does.

The Austin American Statesman article continues:

Steven Schafersman, president of Texas Citizens for Science and a longtime critic of the board’s conservatives, said the Fordham analysis overlooked some glaring problems with Texas' standards.

He pointed to a separate examination from the National Center for Science Education that found Texas’ standards contain “creationist jargon” and “reflect political and religious agendas, rather than good pedagogy and strong science.”

There are reports for every state, here.

Tuesday Crustie: Ode to a sand crab

With two presentations on sand crabs this month (including one over the weekend, which went very well), sand crabs have been on my brain. Another thing that’s been on my brain is this quote from Martin Palmer in a presentation to the World Wildlife Fund late last year (hat tip to Randy Olson):

We never use a word unless you can show us a poem in which it’s been used. Because if people don’t love it enough to include it in a poem, it probably means it means nothing to them.

Because I want people to care about sand crabs, I found a poem that hung on the wall of the lab in graduate school. It was written about Emerita (Emerita analoga is pictured) rather than the Lepidopa benedicti which were the main focus of my talk, but what the heck.

Ode to a sand crab

A short ode to thee, my dear friend the crab
Whose life I once thought must be rather drab.
On the whole unexciting, most boring and bland
What joy could one find living life in the sand?

I walked by the shore and saw crabs by the score
And felt in my heart a great need to know more.
So I queried the crab, without being too forward
Of her constant displacement both seaward and shoreward.

She seemed quite surprised that I should inquire
Why crabs stay where they stay, rarely lower or higher.
We looked at each other eyeball to eyestalk,
And I listened intently as she started to talk.

“If we stray to high, we’re sure to be dried
So we make quite an effort to descend with the tide.
But with the fish in the surf, we must stay out of reach,
So we go with the tide when the tide moves upbeach.”

She went on with a sigh, “Ah, the things you should know.
You people, like crabs, should just go with the flow.
The waves bring us food, the sand’s a soft bed
We spend our time eating, preparing to shed.”

I pondered the crab and the crab’s view of fun,
Hiding out from the birds, and the fish, and the sun.
No family ties, no dad and no mum
And a diet consisting of diatom scum.

The difference between us is not so profound
My head’s in the air, and your head’s in the ground.
But Nature, I think, oft tends to repeat;
We all feed and respire, find mates, and excrete.

So what if my skin is so soft and you’re hardened,
You’d think such slight differences ought to be pardoned.
Where Nature’s concerned, there aren’t any norms
A life is a life, in all of its forms.

Paul Siegel, Ph.D.
University of California, Santa Barbara

30 January 2012

Shoot the hostage

The movie Speed opens with this memorable dialog between two cops:

Harry Temple: All right, pop quiz. Airport, gunman with one hostage. He’s using her for cover; he’s almost to a plane. You’re a hundred feet away... Jack?

Jack: Shoot the hostage.

The strategy of some scientists to take down for profit publishers, notably Elsevier, keeps edging closer to shooting the hostage. Do anything that is bad for Elsevier, even if a few other researchers get harmed along the way.

The Cost of Knowledge website is gaining traction with its call to not “support” Elsevier journals. Jonathan Eisen went even further towards the “shooting the hostage” strategy. He suggested that scientists not “promote” any article in an Elsevier journal: no blogging, no tweeting, no journal club. He was convinced otherwise, as you’ll see by visiting the post. I complement Jonathan for considering other points of view.

You won’t find my name on that boycott list - yet. I’ve written before that I don’t think it’s fair to refuse to review a paper because I don’t like the journal. (Besides, if I put my name on the list but then reviewed for an Elsevier journals, who would know? Reviews are typically confidential.) I still think the best strategy is slow strangulation. Do not submit papers to those journals. Convince colleagues that there are better venues than those journals.

Shooting the hostage makes for great drama, but such a single-minded “get the bad guy by any means necessary” approach may not be desirable. There’s a reason cops don’t shoot hostages outside of action movies.

Update, 26 February 2016: The attention has turned to pre-prints following the ASAPBio meeting this month. I’m disappointed to see people trying to use the same lever of refusing to review manuscripts to try to change journal policy:

From Casey Greene.

Update, 1 July 2016: When I asked about whether this strategy does anything but harm authors, Erin McKiernan mentioned that this seems to have helped bring the matters to the former editors of Lingua. The editors of that journal famously jumped ship from their Elsevier published journal to start a new open access journal, Glossa. In this article:

UA: Had you as editors and active researchers in the field heard any complaints from your researcher-colleagues about this problem?

Dr. Tessier:
Absolutely. You reach out to people and say, “Can you review this paper for Lingua?” Increasingly people said, “Honestly, I’m not willing to review for Lingua or submit work there anymore because I don’t think it’s reasonable to support a model where the research winds up so monetized.”

Several people had mentioned to me that their universities were considering just not buying subscriptions to Elsevier journals anymore for the same reason – that it was cost prohibitive. So, we’ve lost the plot. This is no longer a viable method for research dissemination if we have to bargain as to which of the journals we’re going to be able to subscribe to.

UA: Is it normally difficult to find peer reviewers for Lingua articles?

Dr. Tessier:
It’s hard to convince people to review because it’s unpaid work and that’s always been the case. When trying to find reviewers I usually have to ask twice as many people as I need. I need three reviewers so I send out at least six asks. I don’t know how common that is across journals.

People who exclusively said, “I can’t review for you [because of the pricing model],” has only happened in the last year. I think it’s happened probably four times.

But there is no rule that says scientists can only voice displeasure about journal policies when they are making decisions about reviewing or not. Maybe the same consciousness raising can occur without delaying reviews and messing with authors.

Related posts

Pressuring journals you dislike

The Zen of Presentations, Part 48: Funny or die?

To hear a lot of people talk, you’d think telling a joke was as deadly as juggling a chainsaw.

Presenters are often told, “Don’t try to be funny.” This is bizarre to me, given that humour is one of the most often cited features of a good presentation. The thinking seems to be that failed humour is a dangerous thing to a speaker. What is at risk when you use humour? People might not laugh.

There’s two responses to that. First, people not laughing is not dangerous. It might deflate your ego a bit. But it’s not as though if a joke lands wrong, it could take your hand clean off!

And if you hadn’t told the joke? People definitely will not laugh. You have the same outcome with or without the joke.

Second, just because people do not laugh out loud at your joke does not necessarily mean they are not enjoying themselves. Sometimes they may just smile. Their smiles may not be big grins. Not everyone in the room may smile. It can be difficult to pick up those cues that people are enjoying the humour, particularly if you’re in a big room, or a dark room, and so on. Even if you’re not getting the audible laughs, you can still have a room full of people who are much more pleased with your presentation than if you didn’t make the effort.

If you tell a joke and it doesn’t work, and you panic, that is not a problem that comes from telling a joke. That is a problem that comes from poor preparation. Lack of preparation can make a talk brittle, and a presenter unable to cope with even slight deviations from plan.

If you’re not comfortable with humour in the sense of telling jokes, think of humour as used in the phrase “good humoured.” Even if you don’t deliberately say funny things, you could at least smile.

Related posts

The Zen of Presentations, Part 5: Legalized insanity
The Zen of Presentations, Part 37: What makes a good speaker?
The Zen of Presentations, Part 38: What you say vs. what they remember

External links

Live notetaking from the “Science humour” session at Science Online 2012 by Perrin Ireland.

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

Hat tip to Christie Wilcox (here and here).

27 January 2012

Replace “old” with “rich”

At some point during Science Online 12, Maggie Koerth-Baker (in middle of picture) asked,

Do you think the public communication conflicts have to do with older scientists vs. younger scientists?

Ah yes, the old joke: “Science progresses one funeral at a time.”

Let’s play a game. Think about some aspect of the way science is conducted know that you think needs reform: valuing outreach to the community (as in Maggie’s question above), promoting open access, not paying so much attention to journal impact factor. I bet that for each of those, someone who has written:

“Things will change as the new generation of scientists comes in.”

Try this: any time you see a statement about the culture of science where someone invokes age, replace “age” with “money.” When you hear people talk about “senior scientists,” replace it with “funded scientists.” * To be even more precise, “institutions with funded scientists.”

Institutions value money, and they value it in a way that is amplified and greater than the way individuals in that institution value money. Some institutions have gotten good at extracting money from research. The greater the money prospects, the more stultified and problematic the reward system becomes.

I’ve certainly seen a shift at my own institution. When I interviewed here, I was told by one administrator, “It’s not publish or perish here.” That was just at the start of a push to get more research here. As we have grown our research program, events were held to recognize people who publish in tier one journals and bring in more than a million dollars in grant money. I’m starting to hear things like, “We need to start paying attention to the impact factor of journals where people publish.”

Even when I hear administrators talk about “getting kids excited about science,” sometimes it feels like there’s a subtext of, “so they will be tuition paying students at our university in a few years.”

When you talk about how to changing academic and scientific culture, you’re talking about how to break the allure of money at the institutional level, rather than dealing with individual people who are recalcitrant.

With funding flat for the foreseeable future, it may be that the scientific reward scheme will change if the prospects for money become less predictable. Unfortunately, I think it more likely that there will be a greater push to adopt a dubious reward system that focuses on getting money, creating more prejudices against public science communication rather than less.

* Obviously, age and funding are correlated. In the United States, the average age of getting a research grant has been going up. I think it’s now somewhere in the 40s in many federal agencies.

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

26 January 2012

Once more into the cave

ResearchBlogging.orgCaves. There’s a whole series of things that tends to happen in creatures that become cave-dwellers. Over and over and over again, animals that live exclusively in caves tend to be blind compared to their closest living relatives.

This makes cave species great for studying evolution, because each cave is a “natural experiment.” Mexican cave fish are a particularly cool case, because we have in the same species both cave dwellers, which are blind, and surface fish, which are not. And they can interbreed.

This new paper looks purely at the genetics of these cave fishes, trying to figure out just how many times they have invaded caves and lost developed the “cave” phenotype. This new paper by Bradic and colleagues is an extensive crunching of gene samples, and concludes that while there were two ancestral populations, those ancestral populations in turn invaded caves several times: a total of five introductions to caves, all told.

Furthermore, although these animals can interbreed in the lab, this seems to be unlikely in nature. Their results indicate low gene flow between the surface population and the cave populations. Still, while low, it’s not zero, suggesting that there is a genuine fitness advantage to the blind cave-dwelling form.


Bradic M, Beerli P, Garcia-de Leon FJ, Esquivel-Bobadilla S, Borowsky RL. 2012. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC Evolutionary Biology 12: 9. DOI: 10.1186/1471-2148-12-9

Photo by Joachim S. Müller on Flickr; used under a Creative Commons license.


Turning light and going blind: A tale of caves and genes

25 January 2012

Males have bigger brains than females, if those males are sticklebacks from Iceland

This supershort paper contains an interesting fact: there is a population of male stickleback fish out there with big brains. The males fish that have brains 23% larger than the females of approximately equal size.

ResearchBlogging.orgThis is a bit of an unfair characterization. The paper does talk a little bit about how the look for differences in brain size according to the local eco-type that they found the fish and: mud or lava. the nails from allow the environments have bigger brains than those from muddy environments, but there is no such difference in the females.

This is an interesting difference, because so few animals have differences in brain size mispronounced between males and females. Kotrschal and colleagues say that this is the biggest difference in overall brain size in males and females to date.

What are we to make of this one interesting fact? The team speculates that this might be because the males make complicated nests, and compete for females through courtship displays. But it seems that there are many other animals that have similar differences in behavior without the differences in overall brain size. Maybe the real question is not why male brains are so big, but why are female brains in this fish so small? The authors speculate that this might be because the females are investing energy in egg production. Again, it doesn’t really answer why it should be so specifically strong in this particular population of this particular fish when all sorts of females invest energy in making eggs.

While the fact that this paper presents is interesting, a fact in isolation is mainly a curiosity, to borrow a phrase from psychologist Ernst Hilgard. I would’ve liked to have seen this fact presented slightly longer paper with a few more experiments and a little more context. There will surely be some interesting follow-up studies to do.


Kotrschal A, Räsänen K, Kristjánsson B, Senn M, Kolm N. 2012. Extreme sexual brain size dimorphism in sticklebacks: a consequence of the cognitive challenges of sex and parenting? PLoS ONE 7(1): e30055. DOI: 10.1371/journal.pone.0030055

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

24 January 2012

Tuesday Crustie: Fresh ink

Keeping with last week’s hydrothermal vent crustaceans...

ResearchBlogging.orgThis is another hydrothermal vent shrimp, Alvinocaris komaii. The tattoo belongs to one of the authors who formally described it for science, Kevin Zelnio of Deep Sea News. It was completed last week at the Science Online 2012 conference, by Dogstar Tattoo.

This shrimp lives near hydrothermal vents just north of New Zealand, where they normally are found on beds of mussels. They are probably generalist feeders.

One of the recurring questions with hydrothermal vent animals is that given that the vents are so separated, how do the animals living at them disperse from vent to vent? The paper alludes that that when it discusses the relationships between the shrimps in this genus. The geographic locations of the species don’t seem to make well with the relationships, which would be consistent with animals that have to disperse widely and live in short-lived habitats.

It’s interesting to compare this artistic rendition to the formal figure from the paper:


Zelnio K, Hourdez S. 2009. A new species of Alvinocaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vents at the Lau Basin, Southwest Pacific, and a key to the species of Alvinocarididae. Proceedings of the Biological Society of Washington 122(1): 52-71. DOI: 10.2988/07-28.1

23 January 2012

The disembodied tail

When things are bad, and I mean really bad, horribly you-are-in-the-jaws-of-death bad, sometimes you have to let go of something.

Like a tail.

This leopard gecko (Eublepharis macularius) can, when hassled, have its tail fall off. Losing a limb (autotomy) is not a particularly unusual trick for this species. Lots of animals can drop legs and tails if necessary. But this one is noteworthy because if it does so, the tail doesn’t just come off, but it will continue to twist and writhe for up to several minutes after the tail has been separated from the rest of the body.

We’re not just talking about simple twitching here. We’re not talking about something regular, like a horror-show heart that beats after removal from the body. Higham and Russell show that that the tail is doing at least two things. One is a slow, rhythmic swinging, and occasionally, much faster contortions that made the tail flip or jump around. The flips tend to fade out faster than the slower swinging, though.

When we think about vertebrates movements, we normally think that the brain is involved somehow. But here, the tail has been completely severed from the brain, so how are these movements generated and controlled?

Taking the information from the muscle recordings they made from the tail, Higham and Russell think that the slower rhythm is generated by neurons left in the spinal cord of the tail. We’ve known for a long time, probably since the 1970s, that the spinal cord in vertebrates holds a lot of the neural circuitry needed to generate basic locomotor motions.

Higham and Russell argue that the gecko’s tail the faster movements are more interesting. They think that these flips are not controlled by a set of neurons in the spinal cord that out a rhythm. They marshal a few pieces of evidence for their hypothesis. First, they note that the flips only occur for a couple of minutes after the tail’s been removed, whereas the slow movements continue for up to half an hour. Second, the flips are extremely variable compared to the slow movements, even after you take into account the fact that they’re shorter. Third, when a flip occurs, the muscles along the tail are active simultaneously, compared to the slow movements, where the muscles along the tail are activated one after another.

They don’t know yet what the mechanism of these fast flips might be. Higham and Russell note that working on the neural basis of this behaviour has an advantage: you can do neurophysiological experiments on the spinal cord without having to kill the animal. I’m sure that the gecko appreciates this, but I still bet it will miss that beautiful tale it used to have. They never grow back as nice as the original one.


Higham T, Russell A. 2012. Time-varying motor control of autotomized leopard gecko tails: multiple inputs and behavioral modulation The Journal of Experimental Biology 215(3): 435-441. DOI: 10.1242/jeb.054460

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


20 January 2012

Logo study: Texas Academy of Science (rejected version)

Last year, the Texas Academy of Science announced they were interested in a new logo. I could see why when you looked at their previous logo. It looks a bit complicated and a bit dated to me.

I submitted one, which was not selected, but I wanted to show it off anyway.

The original announcing the competition suggested that people might want to consider incorporating the “pillars” of teaching, research, and service in the logo. It also recommended that simple designs were often effective.

As a general state society, you’re sort of limited in what you can do, because you need something that conveys the geographic location. Fortunately, Texas has an advantage there. Its border cuts a distinctive shape. It’s the Lone Star state. It’s virtually synonymous with the old west.

Normally, I don’t sketch much on paper when designing, but this an exception. I decided to make the state outline the point of the design.

I toyed a lot with trying to work the curves of the southern border into something like a molecule, or something else related to science. In the top sketch, you can see I tried to play with the idea of bringing in math by putting in some right angle symbols. Along the southern border, you can see some dots that I think were meant as half a DNA molecule.

One idea that was too high concept, but that I played with for a long time before abandoning, was to work in the shape of an orbiting spacecraft, in reference to Texas’s important role in the great NASA missions.

You can see in the lower sketches the other idea that I pursued, though, which was to work the shape of the “T” into the state border. My original plans were to use a typeface that was a more traditional “Old West” slab serif, but they didn’t fit the shape as I wanted.

I wanted something that was a simplified version of the Texas map, rather than realistic one that showed every little jag. I wanted lines of varying thickness for a bit of visual interest, and ended up with brush strokes, which I made by traced over a state map in CorelDRAW.

Since I had the brush strokes for the map set, I played with my options for the text. I set the letters in place, then scrolled through almost every text font I had installed on my computer looking for a good fit to the space. And I found one that was not what I had in mind, but was a better fit than what I had in mind.

I loved how the center lines in the letter forms lined up with the strokes I had made for the state borders. The horizontal bar in the “A” also was pretty much bang on the northern border, strengthening the closure of the brush strokes.

I also liked this design because it would hold up well at any size, from a small black and white logo on a letterhead, to a big colourful conference banner. I liked the state colours in the logo (right).

I’m very proud of this design. The only thing that I do see as a problem is that it doesn’t contain any elements that say, ”science.” But many logos have no connection to the thing they represent, so I didn’t worry to much. How does the Nike swoosh say “shoes,” or the Pepsi ball say “cola”?

Apparently, the logo contest was crowdsourced to 99 Designs (see the designs here). I missed the announcement, which I guess was made after my submission. This is the society’s new logo.

The society website comes with this explanation:

The three colored sections represent the focal areas of the Academy: Research, Education & Service. The color green represents our early foundations in the biological sciences and our attention to research impacting the environments of Texas. The color yellow serves to encourage wisdom, enlightenment and mental stimulation. The color grey indicates our long-standing history as an institution and the stability of our practical approach to mentorship and training of the next generation of Texas scientists.

To me, explaining a logo is like explaining a joke. If you have to do it, you’re missing the point of the exercise. You should just get it.

I also worry a bit about how well this will reproduce at small sizes, and in black and white. I do think it is an significantly more contemporary looking logo over the old one. I like that the designer spelled out the society’s name, which I think I toyed with for mine, but abandoned, because I went for simplicity.

Logo love external links

Todd Klein’s logo studies
Tony Jay’s blog

19 January 2012

Föreign länguaje

I’ve been watching some of the highest rated episodes of the original Mission: Impossible television series. I was watching part 2 of “The Bunker.” This episode is set in an unspecified foreign country, where a rocket scientist is being held hostage.

Everyone in this foreign, presumably non-English speaking, country speaks English with an eastern European accent to show that they are not in the United States. It’s much easier than teaching actors to speak a foreign language and sub-titling everything.

What language are they supposed to be speaking? I didn’t pick it up on this ignition button...

But a few minutes later, when they showed this, I noticed that the signs were not exactly convincing...

I thought, “Wait... did ‘Master control’ just become ‘Master kontröl’?”

And as the episode progressed, I spotted more “foreign” signage that looked a lot like misspelled English with surplus diacritics.

By the time we were near the end of the show, I was laughing out loud at this:

There’s more umlauts in this episode than in a heavy metal festival! (Though, come to think of it, “Füel Mix Dänjer” wouldn’t be a half bad name for a heavy metal band...)

18 January 2012

Delivering postcards with supercars: big neurons and information transfer

In the world of neurons, bigger may not be better, but it is usually faster – which is almost as good.

The wider an axon, the faster a signal travels along it. You can see this readily by playing around with a computer simulations. This is the traditional explanation for why the largest, fattest neurons are almost always found in escape circuits. Escape systems push neurons to the limit of what is physically possible to shave off every possible microsecond in the response time, because every single one could make the difference between life and death.

But when you get away from these largest neurons, what explains the differences in the axon diameter? Can everything be explained just by the need for speed?

ResearchBlogging.orgPerge and colleagues look at the issue of axon size (which, for reasons unclear, they call “caliber”) across lots of different structures. For the most part, they use mammalian brains. They didn’t include motor neurons, because the problems motor neurons are largely forced by the distance to a muscle. They are more interested in the differences in sizes within tracts contained within the central nervous system, where all the neurons are more or less starting and stopping in the same place.

Their hypothesis is that the differences in axon size within a brain are related not to speed so much as to the ability of a neuron to convey information. The smallest axons convey information at the lowest rates, according to their discussion. Big axons can transfer information at higher rates, they argue, because there is less “jitter” in their timing. Plus, a big neuron can send a signal to many more cells downstream than a small one.

The problem, though, is that big neurons are expensive. Smaller neurons, with lower rates of spiking, convey information less rapidly, but do so more efficiently. It’s like using a Bugatti Veyron to deliver a postcard: it’s fast, but it’s an absurd extravagance. To reduce the time signals spend traveling along the axon, the authors argue that brains typically try to minimize the distance the signal has to travel instead of increasing the size of the axon.

I was also interested to see a little aside about the amount of mitochondria in neurons. Neurons are famously energy hungry cells. They noted that nonspiking neurons have fewer mitochondria than myelinated spiking neurons, and unmyelinated spiking neurons typically have the highest fractions of mitochondria.

They don’t provide any of their own original recordings of spiking rates here. The new data are all anatomical, based on electron microscope sections. Their data serves, almost incidentally, as a nice little review of neuronal diversity.

I always find papers discussing “information” to be a bit tricky, and this one is no exception. But it’s a useful paper to get you thinking about “how neurons work.”


Perge JA, Niven JE, Mugnaini E, Balasubramanian V, Sterling P. 2012. Why do axons differ in caliber? The Journal of Neuroscience 32(2): 626-638. DOI: 10.1523/​JNEUROSCI.4254-11.2012

Sculture photo by nicoleversetwo on Flickr; used under a Creative Commons license.

Veyron photo by Philipp Lücke on Flickr; used under a Creative Commons license.

17 January 2012

Tuesday Crustie: Hot or not?

This shrimp is a new species that is mentioned in a new paper on a new hydrothermal vent community by Connelly and colleagues.

The Daily Mail recently ran this story on this discovery with the headline:

So how on Earth do you cook THIS? The shrimp that lives in water four times hotter than boiling point

Time for a classic facepalm.

I can see how this headline got cobbled together, but still... sigh. No. No, no, no, and again, no. These are not invulnerable super shrimp.

Time to become... a TRUTH VIGILANTE! Quick! To the Truthmobile!

ResearchBlogging.orgThe original paper the news story is based on makes no claim that the shrimp can tolerate super-hot temperatures. But it helpfully shows the change in water temperature as you descend into the sea in Figure 2. By the time you get to below 1000 m, the water temperature is only a couple of degrees above freezing. And these vents are almost 5,000 m down. It’s freakin’ cold down there – except where there are hot vents.

It’s like having a campfire in the winter.

According to the logic of this article, the person who took this picture should have been burned alive. Fires are hot! And the middle of the fire is hot and will burn you.

But step back a little ways, and you can be very cold. You have to find the sweet spot where the warmth from the fire is just counteracting the surrounding cold. (The optimal spot for your hot dogs and marshmallows is rather closer.)

The exact same thing happens at these hydrothermal vents. You have superhot water emerging from the vents, but it’s surrounded by very cold water under very high pressure. The shrimp have to do a constant dance to find just the right distance, darting in and out near the turbulent high temperature plumes to avoid getting cooked.

Oddly, the Daily Mail article gives the shrimp a name, Rimicaris hybisae, which is nowhere to be found in the scientific article in Nature Communications. I hope they have the paper describing this species accepted, because otherwise, these reports might end up jeopardizing the name.


Connelly D, Copley J, Murton B, Stansfield K, Tyler P, German C, Van Dover C, Amon D, Furlong M, Grindlay N, Hayman N, Hühnerbach V, Judge M, Le Bas T, McPhail S, Meier A, Nakamura K, Nye V, Pebody M, Pedersen R, Plouviez S, Sands C, Searle R, Stevenson P, Taws S, Wilcox S. 2012. Hydrothermal vent fields and chemosynthetic biota on the world's deepest seafloor spreading centre. Nature Communications 3: 620. DOI: 10.1038/ncomms1636

Classic facepalm by Alex E. Proimos on Flickr; campfire photo by mismisimos on Flickr; used under a Creative Commons license.

16 January 2012

How expensive is that glamour mag?

The New York Times has a an article on scientific publishing that relates to several of my posts in the last month. In December, I wrote about making Science magazine a target for open access. The New York Times, as luck would have it, quotes the publisher on exactly this issue:

“I would love for it to be free,” said Alan Leshner, executive publisher of the journal Science, but “we have to cover the costs.” Those costs hover around $40 million a year to produce his nonprofit flagship journal, with its more than 25 editors and writers, sales and production staff members, and offices in North America, Europe and Asia, not to mention print and distribution expenses.

To some degree, I addressed this here. People may not be reading Science for the science in their field, but are reading it for the news, analysis, and opinion, job ads, and other things bundled in with the original peer-reviewed research.

Then there’s the question of allocation of resources. How much of that cost revolves around the actual scientific articles, and how much of it revolves around other things? How much of that costs involves printing paper copies of Science, which is perhaps a luxury good these days that could be cut? How much of the cost involves keeping staff writers and flying them them to conferences to keep abreast of the latest developments? How much involves writing press releases and managing embargoes? Are offices on three continents still necessary? And so on down the list.

I have a lot of questions about alternate kinds of finance. Could submission of publication fees from authors subsidize part of those costs?

Leshner continues:

Dr. Leshner, the publisher of Science, agrees that things are moving. “Will the model of science magazines be the same 10 years from now? I highly doubt it,” he said. “I believe in evolution.

“When a better system comes into being that has quality and trustability, it will happen. That’s how science progresses, by doing scientific experiments. We should be doing that with scientific publishing as well.”

All of this makes me think my post in December may have been on the right track. I still would like to see Science become the first science glamour mag to make all its scientific articles open access.

Related links

Occupy Science (the journal)
ESA still not supporting open access
Open access without anger

Comments for first half of January 2012

I make a cameo appearance at Neurotic Physiology, in which SciCurious discusses GeekQuests.

Gerty Z asks when it’s okay to turn down interviews.

Dr. Micro O checks in on the number of conferences a freshly minted assistant professor should attend.

Deevybee argues scientists shouldn’t do any work for Elsevier. This idea has been floated before, and I have problems with it.

Dr. Becca wants your teaching tips.

Deep Sea News asks a question I can get behind: “What crab is the fightiest?

Katie Ph.D. looks a policy to require grad students to publish their research to get a degree.

Dan at Archaeopop has one of the ever-popular rips on scientific publishers.

Dead again: Failing in games and classes

Video games aren’t fair.

When classes aren’t on, such as over Christmas, things calm down enough that I can play a few games. And I was reminded that when playing video games, you can’t win. Well, you can win, but you’re going to die a lot along the way. You’re going to restart the game many, many times.

Hm. I should be able to drop down behind that suck there, without alerting him and… Whoops, they’re shooting at me! Where do I go!? And… I’m dead. And the Joker’s laughing at me as they take away my body. Ugh, this is humiliating.

When you play many video games, it is impossible to succeed in a lot of tasks on the first go. You walk into a room, press a button to open the door,and suddenly you have monsters released from hidden candles in every section of the room completely surrounding you, and you're dead before you have a chance to react.

Or, as they used to say in the school ground, “Bang! You’re dead.”

Only after you have been in that room, made the mistake – usually multiple times – are you able to figure out a strategy for how to deal with monsters suddenly appearing out of every orifice, and leave the room alive.

And then there are fighting games where the entire point of the game is to get beat up. But as you’re getting beat up, you’re learning the patterns and the tells of your opponent so that you can anticipate which punch is going to be thrown next.

It is impossible to play most games all the way through without dying. Repeatedly. But it’s okay. Because you know you can easily retry what you just failed, and you get better as a result.

I know from my own experience that there are a lot of concepts and ideas that I really didn’t get in class. It was only through continually working with them that I really started to get a hold of them. Now, I think that a lot of learning consists of getting used to an idea. In other words, I kept retrying and kept replaying and kept redoing until I got it.

In teaching classes, it seems that we often expect the students to do the equivalent of playing through a very long, complicated game without dying. And the students expect situations where they will be able to do that: get through on the first try with no mistakes.

This may be particularly true of university students in the sciences. They might expect to be able to take a class and get through without ever falling off the moving platform into the toxic waters below (to use a game metaphor). They usually gotten to where they are because academics have been pretty easy for them. They may never have really had to struggle with classes. Some will encounter that, “This is really hard, and I’m failing! I’ve never failed before!” for the first time in their lives in university.

How often do we give students a chance to learn like they learn in a video game? Where they can keep trying until they get it?

I suspect that there are ways to build this into the structure of classes. Indeed, I think that there should be situations where we tell our students up front, “You will not succeed at this the first time. But the first time is not going to be the only time.” Below, Ryan Dancey talks about setting players up to fail in tabletop gaming. Just replace “GM” with “teacher” or “instructor”:

The delicate balancing act I am required to perform as GM is to make them pay the cost for their mistakes without letting random bad luck doom them (or allow them to know that random bad luck was altered by GM fiat). ...

When I was a younger player I often took the attitude that the players should be free to be as foolish as they wanted. Now however I feel it’s my responsibility to play the metagame back at the players directly. I flat out told them that they could not win this fight. That, combined with the obvious damage I was doing to the party, was enough to trigger the “correct” response – getting the hell out of there.

That payoff? Maybe it will be a little something like this:

The reward is in the story: the players are going to self-generate a fantastic epic tale that will be so much more meaningful because they have to work for it as opposed to just having victory handed to them.

By having students fail, maybe a few times, before succeeding might make them feel like heroes when they do succeed.

External link

How to tell if you suck at last year’s games.

“Run away!” When gamers can’t beat the monster.

13 January 2012

Open access without anger

Open access has been the subject of much talk this week due to the Research Works Act (text here) and requests for information on scientific publishing.

And I’m getting alienated by a lot of the discussion.

First, a lot of the open access discussion seems fueled by a righteous anger about many scientific publishers being profitable private businesses. I’ve tried to get upset over that, and I just can’t. I’m in favour of businesses making a profit. Nor does it upset me that they make money from funds that come from taxpayer dollars. Plenty of businesses get government business and taxpayer money. There are lots of taxpayer funded things that are not generally free to anyone who wants them because they paid taxes. There are still toll roads. Public universities don’t take every student, and they don’t get free classes.

Scientific publishers add value to papers. There’s far more involved in making a good journal than digitizing a paper. There’s website design, server upgrades, copy editing, RSS feeds, assigning DOIs, making sure abstracts get to PubMed. I don’t pretend to know everything that goes on, but I do fear what would happen if scientists bought into “make a PDF and stick it on the web.” I see what happens when scientists self-publish every time I go to a conference. And it ain’t always pretty.

That said, while I am not angry at publishers for running successful businesses, said publishers are annoying me mightily with their refusal to innovate, exemplified by their support of the Research Works Act. While I support your right to earn a profit, publishers, you don’t have a right to do it by trying to get legislation passed that protect your current business plan.

And publishers, when you’re pissing off someone who is kind of on your side...

For instance, would it kill you to sell me an article for $1 instead of about $30? Open access has changed what people think they should pay. You’re not going to be any more successful at hanging on to that model than the music industry was when they tried to keep people buying pieces of plastic to get music.

The emergence of open access has not dented submissions or the profits of Reed Elsevier. The publishers have the opportunity to invest, to experiment, and to provide valuable new services for their readers. “Open access” does not equal “non profit.”

Second, almost all of the arguments for open access have used out the “taxpayer” argument. The most prominent example was a prominent New York Times editorial this week by Michael Eisen. I’ve mentioned that I don’t like the argument (here and here). I think it means a lot to a small number of people, but it doesn’t resonant with me, or, I think, a lot of other academics.

When I keep hearing about, “taxpayers support research,” I keep  thinking, “not all of it.” Yeah, I have a chip on my shoulder about this. I’ve published and paid for a lot of stuff out of my pocket. Most of my colleagues in my department don’t have external grants (though not for lack of trying). And sure, you can can say that’s because of the kind of institution we are at (between the lines: you are not cutting edge researchers and you can’t compete), but the percentage of grants funded at NIH looks to hit historic lows, and NSF is taking measures to reduce the number of full applications they are reviewing.

The trend is for less taxpayer supported research, not more, for the foreseeable future. And as the number of people who are not funded by taxpayers goes up, they are much more likely to be looking for publication venues where they will not be paying publication fees out of pocket. I’ve already seen one person arguing that any journal that has a publication fee is not open access (here, down in the comments).

There is a better argument for open access that has not been made nearly enough: the importance of sharing.

I support open access because sharing is part of my ethos as a scientist. I want people to read my stuff. There’s a reason all my blogs have Creative Commons licenses. Because ideas that spread, win, as Seth Godin says.

People get that sharing is good. People understand and respect the generous impulses behind sharing. Sharing is one of the most simple and basic lessons we teach kids to help them get along with other people. Sharing time and effort is how you get Wikipedia and YouTube and social media.

People understand that science is a public endeavor. Results need to be available to people who want to check them.

Appealing to people’s willingness to share could be a much more powerful argument for open access than appealing to their sense of outrage over payments that many of them will never make. Complaining about value for tax dollars feels kind of small in comparison to, “We just want everyone to be able to read the stuff we do. Because it’s awesome.”

Scientists want to share what they have to share. That’s why we should promote open access and why the Research Works Act not try to stop it.

12 January 2012

My favourite spaceship

A while ago, I shared a little video about my GeekQuest to see the original Enterprise model. But I have a confession to make. The Enterprise isn’t my favourite spaceship.

Regular readers might know my massive love for Doctor Who, and think, “Ah!, I’ll bet it’s the TARDIS.” Nope.

It’s the Eagles from Space: 1999.

The reason is simple. The Eagles looked real to me: practical, achievable machines. The Eagles looked like a reasonably logical progression from the real spaceships of the day; you could see design elements from the Apollo lunar excursion modules. They were clearly meant to run on liquid fuel, rather than some imaginary power source. I particularly loved the small steering rockets on the sides of the landing pads, which would be necessary to adjust the position of a spaceship in airless space. (Sadly, the Eagles were usually filmed swooping through space like airplanes. More realistic depictions of maneuvering would have to wait for Babylon 5.)

My quest to see the Enterprise, the restoration of the Eagle, and the excitement over the discovery of a Serenity model makes me a bit sad for the nearly complete transition of special effects from model making to computer generated imagery. With computer images, there’s no actual object that a fan can ever go see. That makes me just a bit sad.

Shame such a great design was stuck in a usually sub par show.

Additional: The Bad Astronomer, Phil Plait, has a great article on why Victor Bergman from Space: 1999 is his favourite depiction of a scientist on television.


Restoring the original 44" Eagle 1 studio SFX model
The 44" Eagle 1 studio model today

11 January 2012

Through the Sandglass guest post

Through the Sandglass is a blog authored by Michael Welland. He also authored what may be the definitive book on sand, simply titled Sand: The Never-Ending Story.

I have a guest post there today, talking about some of my recent work on the local sand crab. Check it out!

10 January 2012

Making Watson a winner

A recurring point I make here is that while everyone love a breakthrough and wants “transformative research,” the reality is that most science is slow, small, increments.

So I’m pleased that someone who built the team that built the Jeopardy! winning computer Watson said this (emphasis added):

(T)he scientists would have to reject an ego-driven perspective and embrace the distributed intelligence that the project demanded. Some were still looking for that silver bullet that they might find all by themselves. But that represented the antithesis of how we would ultimately succeed. We learned to depend on a philosophy that embraced multiple tracks, each contributing relatively small increments to the success of the project. ...

In the end, the hero was the team, not any individual member or algorithm. Eventually, everyone came to appreciate that. Well into the throes of the project, one researcher commented, “Compared to the way we work now, it’s like we were standing still before.”
Hat tip to Flowing Data.

Tuesday Crustie: Duck

An odd looking shrimp by the name of Leander plumosus. A quick look through science databases reveals nothing about it, except its name in geographic species checklists. What could the function of that large front end be? There’s at least a master’s thesis in that for some student.

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

09 January 2012

ESA still not supporting open access

The Ecological Society of America drew attention to itself last week for a statement regarding open access for scientific publication. Jonathan Eisen covered it here.

I posted the link to Eisen’s post this on ESA’s Facebook page, and today, there was this comment from ESA on Facebook:

ESA’s recent letter in response to OSTP’s Request for Information has generated discussion in the social media realm. This is perhaps a good example of the inherent conflict between the interests of those who believe research publications should make their content freely available to all and the reality that there are significant costs associated with publishing scholarly research journals. This topic will continue to be one with which the scientific community must grapple and one that will continue to evolve.

My response was that they seemed to be confusing “access” with “profit.” PLoS ONE has proved that open access journals can be profitable. Other publishers (Brill; see here) have recognized this.

If journals are worried about losing their subscriptions, I suggest this: Keep the technical articles free and print other, original content that people will pay for.

For instance, let’s go back the the journal Science, which I suggested would be a good target to convert open access. Only a small fraction of the original technical articles in Science are going to be relevant to any particular reader. As it stands, a subscriber to Science is getting a lot of non-targeted articles that are irrelevant to them.

What Science has been really good at is providing news and commentary. That is much more widely relevant to a broader spectrum of readers. I think if all the technical articles were still free, people would probably still be willing to pay money for all the other original writing. The conference reports, the policy analysis, and so on. That original work by professional writers is something that people realize should not be free. At least, the arguments for making it free are different than the usual ones used to justify open access, that is that publicly funded scientists are doing all of the intellectual work.

But oddly, the tendency for general journals has been to do the exact opposite. Journals have tended to make a few of their comments freely available, while locking down all the original science.

ResearchBlogging.orgSo, ESA, if you want people to stay members of your society, to give them reasons to do so besides original journal articles. I doubt it’s the main reason that most people join scientific societies. In fact, ESA, you yourself have surveyed why people joined your society.

The number one reason given in a membership survey for joining ESA was, “Supporting the field of ecology.” For young members, under the age of 35, “opportunities to present or publish my work” was third in the list but that’s difficult to interpret because it includes presenting at conferences and not just the journals. Regardless, it’s not just for the journals you publish.

When they asked lapsed members what might make them rejoin the society, the three main reasons were for information and career development. These were things that require more than just original journal articles. For example, the first item on the list was, “Help me stay abreast of developments in my field.” Sure, that is something that is partly about original research, but good original analysis and news reporting would also seem to be valuable to members. Why not give it to them?


ESA. 2012. ESA membership survey, February 2011 summary of results Bulletin of the Ecological Society of America 93(1): 13-23. DOI: 10.1890/0012-9623-93.1.13

Hidden potential, and the concept of syngeny

ResearchBlogging.orgThere’s much excitement about a new paper in Science that shows how ants have hidden potential. In short, there are a few species of ants that can produce “supersoldiers”. Other ant species, however, can also make supersoliders when they are experimentally give the right dose of hormone.

Crudely, it looks like the ants’ ancestors had the ability by changing the hormone levels, but the pathway that was sensitive to the hormone remained. When species started to evolve differences in hormone levels again, the supersoldier body type “re-emerged” after a long period of suppression.

Ed Yong covers it here and here. One of the authors talks about it on Quirks & Quarks.

I wanted to talk not about the paper so much as a concept it illustrates that I don’t think has gotten enough attention in the evolutionary biology literature.

Homology is a critical concept in evolutionary biology. A generally used definition is a feature that two different species share because they inherited it from a common ancestor. But homology can be tricky, because a “feature” or “trait” isn’t a single thing. Features have different levels of organization: genes, cells, tissues, organs, and so on. And each level can evolve long a different path than the others.

Plus, the concept of homology was first proposed first by Richard Owen, who rejected the idea of evolution by natural selection. And it was widely used before we had learned a lot about the subtleties of genetics.

For instance, we’ve learned that just because you have a gene doesn’t mean it’s expressed. Much like the supersoldier ants, you can imagine a scenario where a gene (or gene network, etc.) is present in an ancestral species, but not expressed. The species diversifies, and diversified, leaving many daughter species with the unexpressed genes. Then, independently, several of the daughters of the original ancestor start expressing the genes, and the trait pops up in distantly related species.

From the point of view of the phylogeny, that feature doesn’t look homologous, even though there is evolutionary continuity at the genetic level from a common ancestor.

Butler and Saidel recognized this scenario some time ago. They coined the term “syngeny” to describe a feature arising from genes that are present, but rarely expressed. I heard Butler discuss this at a J.B. Johnston Club meeting, citing a particular fish brain structure that appears only in a few, not closely related, species. The idea was great.

What the ant story brings that they didn’t have at the time was the ability to bring their feature back through an experimental manipulation. It’s likely that many cases of syngeny are not going to be as easy to show in the lab as in the ants.

Rajakumar and colleagues, the authors on the ant paper, call what they’re seeing parallel evolution, but syngeny might be a better description.


Butler A & Saidel W. 2000. Defining sameness: historical, biological, and generative homology BioEssays 22(9): 846-853. DOI: 10.1002/1521-1878(200009)22:93.0.CO;2-R

Rajakumar R, San Mauro D, Dijkstra MB, Huang MH, Wheeler DE, Hiou-Tim F, Khila A, Cournoyea M, Abouheif E. 2012. Ancestral developmental potential facilitates parallel evolution in ants. Science 335(6064): 79-82. http://dx.doi.org/10.1126/science.1211451

Picture by SouthernAnts on Flickr; used under a Creative Commons license.