31 May 2011

Texas intelligent design bill is dead

Bill Zedler’s bill to protect university professors doing intelligent design research went nowhere, according to the National Center for Science Education.

Update, 15 April 2013: If at first you don't succeed, try, try again.

Tuesday Crustie: Treadmill superstar

This species has been the subject of renewed interest since the release of a report last week criticizing the National Science Foundation, as shrimp research was something of a poster child for “questionable” projects.


What species is the shrimp in the video? According to the abstract, it’s probably Litopenaeus vannamei (formerly Penaeus vannamei), a Pacific shrimp.

If you’ve seen one of the shrimp on a treadmill videos, you know this animal is not always clear. This particular one is, I suspect, very young, which is why it is transparent. It’s been well fed, which you can tell from the fact that you can see its entire digestive system running through its body.

Photo from here.

30 May 2011

How my ethics of brain scanning paper was overtaken by events

ResearchBlogging.orgI know my most recent paper is probably going take some flak as being naïve.

This is the price you pay for trying to expand your horizons. An invert neuro guy writing an ethics paper? About brain scans? In humans? With spies? The potential to look foolish is huge.

But since I’ve gone and done it anyway, let me tell you how it all came about.

This paper started about three years when I ran into my colleague Cynthia Jones at lunch at the student union. I actually hadn’t seen her for a while. She looked rather different than when I’d last seen her, and she thought I didn’t recognize her (this had been happening to her a lot), but I was just feeling particularly grumpy then. She had just launched an ethics center.* Over my sandwich and chips, she started telling me about this ethics conference that she was organizing about the intelligence community. Less formally, this is the spy community.

I mentioned my interest in brain scans and the possibilities for extracting information. After all, I’d already given a Brain Awareness Week talk about it in 2006. (Indeed, if you listen to the talk from five years ago, you’ll hear some very similar phrases to those in the paper.) Cynthia invited me to give a presentation at the conference.

The conference took place in November 2008, which I wrote about here.

It was always the plan collect papers from the conference in theme issues of Global Virtue Ethics Review, which has its editorial office at my university. For various reasons, the editorial process was... lengthy. I submitted the manuscript over a year ago.

Because of that lead time, my manuscript was overtaken by events.

In a lot of cases, that time from submission to publication actually wouldn’t matter very much. But because the research on brain imaging is so abundant and moving so fast, I knew this paper would have a “use by” date. Indeed, on the first page, I wrote:

(T)his review is only a single snapshot of a rapidly moving target.

But even I didn’t expect some findings coming out that would be so relevant, and, had I known then what I know now, would have substantially dampened the tone of my article.

Many people think that brain scans are being oversold, and that a lot of distinctly dodgy stuff is being pushed out there about what brain scans are able to do. My paper seems fairly optimistic in comparison about the future potential of brain scans to detect covert information.

I’m feeling rather less optimistic these days. In particular, a paper by Ganis and colleagues (2011) showed that there are some dead simple countermeasures that will make the detection of deception way more difficult than I thought.

You can also see similar limitations in this interview with Jesse Rissman (my emphasis).

We could tell quite reliably whether people thought each face was familiar or new, but we couldn’t tell the true status of the memory. When we tried to distinguish faces the person had seen from those he hadn’t, we were correct less than 60 percent of the time. ... The idea that our brain contains a veridical record of our experiences is, I think, fanciful.

This runs counter to some research I cite in my paper that suggested it might be possible to distinguish true from false memories. (In fact, that was the finding by Slotnick and Schacter in 2004 that first got me tracking brain imaging research at more than a casual level.)

If I were to rewrite the paper now, many of the arguments would stay the same, but the tone of the paper would be much more pessimistic about how soon or even how likely it is that we could move out of the pure research stage on the detection of deception.

Still, another new paper that just hit (Shirer et al. 2011) pushes me back to thinking this might truly be a viable enterprise. (I just found the reference as I’m writing this, so can’t comment in detail on it yet.)

Nevertheless, there is still a lot that I’m very happy about in my new paper. For instance, I like a bit where I argue that fMRI is already acting as a “mind reader,” from a certain point of view. Since then, I’ve drawn the distinction between “mind reading” (determining a subjective mental state) and “telepathy” (determining someone’s stream of conscious verbal thought), a distinction I wish I could have got into the paper.

While I may be able to make some excuses for scientific naïvite on lead time and new research, I know I am still taking a risk on the ethics side. I hope that the discussion there is reasonably sophisticated, but I am now ready to take any lumps thrown my way regardless.

Additional:  The same day my article went online, Nature reported that the American Department of Homeland Security has been testing devices to detect people’s intent to carry out a “disruptive act.” This swings me towards the cynical again, as even at my most optimistic, I would not be field testing something like this yet.

References

Faulkes Z. 2011. Can brain imaging replace interrogation and torture? Global Virtue Ethics Review 6(2): 55-78. http://www.spaef.com/article.php?id=1266

Ganis G, Rosenfeld JP, Meixner J, Kievit RA, Schendan HE. 2011. Lying in the scanner: Covert countermeasures disrupt deception detection by functional magnetic resonance imaging. NeuroImage 55(1): 312-319. DOI: 10.1016/j.neuroimage.2010.11.025

Rissman J, Greely HT, Wagner AD. 2010. Detecting individual memories through the neural decoding of memory states and past experience. Proceedings of the National Academy of Sciences USA 107: 9849-9854. DOI: 10.1073/pnas.1001028107

Shirer W, Ryali S, Rykhlevskaia E, Menon V, Greicius M. 2011. Decoding subject-driven cognitive states with whole-brain connectivity patterns. Cerebral Cortex: In press. DOI: 10.1093/cercor/bhr099

Slotnick S, Schacter D. 2004. A sensory signature that distinguishes true from false memories. Nature Neuroscience 7(6): 664-672. DOI: 10.1038/nn1252

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

* It’s officially a “collaborative,” because apparently “center” has some special administrative meaning.

27 May 2011

Texas State Board of Education looking for a new chair

The Texas State Board of Education will need a new chair, according to the Dallas News. The current one, Gail Lowe, wasn’t approved by the Texas senate. This appears to be continuing fallout from the last few years of the Board’s K-12 education standards, which attracted national attention for their unabashed conservative nature and the often unusual processes used to pass them.

Lowe was less vocal than previous chair (and sound bite master) Don McLeroy, but was solidly voting along the same lines on issues before the Board.

Sexy eyes? Estrogen in the visual system

ResearchBlogging.orgNeurotransmitters get all the glory as the most interesting molecules in the nervous system. They are responsible for the fast signalling between two neurons; things that are all over in a few milliseconds.

But the nervous system is awash in chemicals, which influence neurons in many ways. Hormones, for instance, influence behaviour by acting on nervous systems.

It’s a little unusual, though, to think of brains making their own hormones. Oh, sure, the pituitary gland sits right next to brains in mammals, but it’s still generally considered an endocrine gland rather than neural tissue.

I was therefore intrigued by a new paper showing that the visual cortex in mice makes estrogen, which is a classic sex hormone, and responds to it. The evidence is quite straightforward for some of the story. Jeong and colleagues used fluorescent labels for messenger RNA for the chemical to show that neurons make it (left column in figure), and another fluorescent label for the messenger RNA of estrogen receptors to show that the neurons were able to detect it (middle and right columns).

The production of the estrogen doesn’t seem to be dependent on, or affected by, by visual experience. Mice raised in the dark had the same density of estrogen-producing neurons in three different areas of the visual cortex. Similarly, there was no change in that density when mice were given different degrees of visual stimulation after being placed temporarily in the dark.

What is this brain-produced estrogen doing to vision? Not clear yet, but there seem to be analogs in other brain regions. Estrogen affects auditory cortex in mice, and can alter the physiology of neurons in the hippocampus. The effects may be subtle, and might not have noticeable perceptual consequences for the mice.

Reference

Jeong J, Tremere L, Burrows K, Majewska A, Pinaud R. 2011. The mouse primary visual cortex is a site of production and sensitivity to estrogens. PLoS ONE 6(5): e20400. DOI: 10.1371/journal.pone.0020400

26 May 2011

My latest cameo

I make an appearance at the start of the 18 May edition of Dr. Karl’s weekly call in show on Triple J. Sort of.

In the previous week’s show (12 May), a caller asked if insects had pain receptors. Karl said he expected that they did, but he didn’t know any peer-reviewed papers on the subject.

As soon as I heard that on my iPod, I hopped on to Twitter and sent Karl the link to this paper:

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

Karl was kind enough to mention this at the start of the show. Another crisis averted!

Here’s a direct link to the mp3 of the “answer” podcast; my thing is literally the first. The “question” show is here.

Before you attack science, could you at least learn to use Google?

Here we go again.

It is a long established trick of politicians in opposition to mock research funding as a waste. The latest in this depressingly regular sideshow comes from Tom Coburn, who is weirdly aided by ABC news, labelling his criticisms as “exclusive.”

And yeah, it’s kind of personal for me. Because their first example is... crustacean research. And it’s even kind of related to locomotion, which is what I did my Ph.D. on.

You've probably heard of shrimp on the barbie, but what about shrimp on a treadmill?

The National Science Foundation has, and it spent $500,000 of taxpayer money researching it. It’s not entirely clear what this research hoped to establish, but it’s one of a number of projects cited in a scathing new report from Sen. Tom Coburn, a Republican from Oklahoma, exclusively obtained by ABC News.

“Not entirely clear”? Your interns have let you down, ABC, so let me Google that for you! Shrimp on a treadmill is a full-blown internet meme thanks to a variety of musical remixes of the researcher video.



There were at least 60 of these a few years back; who knows how many there are now.

But what about the science? Is the reason for the research buried behind a paywall in an obscure journal somewhere?

No. In fact, because of the popularity of the shrimp music videos, the research was covered all over the place: in The Telegraph, MSNBC, and Live Science, to name just a few.

The researchers were on the Today Show talking about this, for crying out loud! Do you know how many crustacean researchers get to be on nationally televised morning shows? Not many. These two may be it. (I’m jealous; I would love to have that kind of opportunity.)

Or, for that matter, did anyone think of looking at the NSF’s award page to find what the researchers wanted to accomplish? Because a little search of “shrimp performance” plus the popular press clippings led me straight to this abstract that says exactly what the researchers wanted to achieve.

It is expected that these studies will show that, at least among crustaceans, the immune response itself may make it more difficult for an organism to respond to hypoxic environments or to engage in significant physical activity. While engaged in this research, which addresses questions related to the health of ecologically and economically important species, these investigators will continue to teach, train and publish with students from four primarily undergraduate institutions in the US.

The researchers want to study how sick shrimp are able to move around and do stuff.

So what? We want healthy shrimp so we can eat them. The shrimp fishery is a multi-million dollar industry in the United States alone. This research clearly has implications for the management and health of that fishery, and therefore, the jobs of all those who catch shrimp and prepare shrimp.

The abstract also points out that this research didn’t just pay for the shrimp and the treadmill; it supported undergraduates from four different universities to get them involved in research. It wouldn’t surprise me if a large chunk of that money was to employ students.

This is the second time in recent memory that crustacean research specifically has been selected as a target. Former presidential candidate John McCain made fun of lobster research. It’s weird that they keep picking on research that is easily related to things like fisheries; the NSF funds things that are way more esoteric.

Are you just bitter, ABC, because NBC beat you to the story?

Are you just bitter, Republicans, because the shrimp on a treadmill videos get more YouTube hits than yours do?

Additional, 27 May: The Science policy blog has an analysis of the report.

But the report, The National Science Foundation: Under the Microscope, is itself filled with errors and questionable analyses, say science lobbyists.

More additional, 27 May: More scientists defending their research.

Still more additional, 31 May: We have lost.

A quick in-class critical thinking demo

In one of my recent classes, I wanted to start off with a quick exercise to get people thinking about hypothesis testing and critical thinking. I used a demo that are used to hawk balance and power bracelets and “applied kinesiology.”

In brief, you have someone stand on one foot with both arms extended sideways. You press down on one arm, and they tend to fall over. Then, you give them a gizmo of some sort (I used a rubber band), and repeat the test, and people find they don’t fall over anywhere near as easily. A video is below; another quite good one is here.


The trick is a very slight difference in the direction you press. To make them fall off, you press slightly outward from their body; to keep them balanced, you press every so slightly towards their body.

I did this in class, having seen the video but never having done this before. I went through four or five different volunteers, and was able to get the effect every time.

Nobody believed that my rubber band was the cause of the difference. When I asked people for ideas as to what was going on, several of them could be easily tested on the spot. One person suggested I had placed my hands in different locations in the two tests. I got a new volunteer, placed my hands very precisely in the same spot, and was able to tip or not tip them at will.

One suggested a placebo effect. Problem: None of the people I gave the rubber band to believed the rubber band was the cause, which made it hard to argue that it was a placebo.

We also talked a bit about the mechanisms that some bracelet makers propose for how their bracelets are supposed to improve balance. Some invoked things like “natural energy fields” or “life energy,” which was a great lead in to talk about how living things differ from non-living things. Do living things have some sort of energy that non-living things don’t?

Eventually, one person near the very front of the class figured out what I was doing. I think that with a little practice, though, it would be very difficult to detect.

In summary, this is easy to do, requires nothing but a student volunteer, and is a great jumping off point for all kinds of discussions about hypothesis testing, evidence, mechanisms, and lots more.

That you get to push people around is just a bonus.

25 May 2011

More for those that have the most?

A little more evidence that institutions are not interested in a level playing field.

Larry Faulkner, the former president of UT-Austin... wants more funding for the great universities.

Not all universities. The great ones.

That’s from a report on a panel discussion about research universities in Texas in The Texas Tribune.

Not only are people saying that the institutions with the most money should get even more money, they also want the most promising talent pool funneled into them too:

Rex Tillerson, the chairman and chief executive of Exxon Mobil... argued that there was a need to “differentiate” in terms of placement of students in universities — i.e., to make sure that the best students go to well-funded, top universities, as opposed to trying to help everyone equally.

... He added: “If we want to take advantage of our great research universities, we cannot burden them with remedial education.”

A reason that teaching is seen as a “burden” is because there are not enough professors. Open up tenure-track positions. Many hands make light work. (I understand this is not a popular option for universities right now, because there is a push to cut instead of invest.)

Ray Bowen, the chairman of the National Science Board and the former president of Texas A&M, said that Texas faced a “unique problem,” because many of our brightest students go out of state as a result of the state’s lack of research universities.

I’d be interested to see the data supporting that statement. I doubt the vast majority of high school students are looking around going, “I dunno, that department didn’t have enough Nature papers over the last five years...”

It is always interesting to watch those with power and money argue that they need even more power and more money.

Related posts
Inclining the playing field
Balkanizing small universities
To have and have not. Mostly not.

24 May 2011

Tuesday Crustie: Work of a master


Apparently someone attacked its weak spot... for massive damage!

Although many crustaceans are beautiful, it’s rare to find them as subjects of art, particularly paintings by the masters. This particular rendition by Van Gogh of a brachyuran crab is fairly anatomically accurate. It’s unfortunate he immortalized the crab in such an uncompromising position.

You can see the framed versions of these works in photographs here and here.

23 May 2011

Third 3 Quarks Daily blogging contest

3 Quarks Daily is once again accepting nominations for their regular science blogging contest. A thousand dollars (presumably American ones) for the winning entry!

Nominations close 31 May.

Catching a fly with a dragonfly eye

Dragonflies are visual predators, able to catch other flying insects in mid-air, mid-flight, as the video below shows.



They don’t miss very often. Dragonflies hit what they aim at.

What makes this visually guided, in flight navigation even more remarkable is that you and I might look at a typical dragonfly environment and see something like this (and yes, there is a dragonfly in there):


A dragonfly looking at the view might see something more like this:


This is about one sixtieth the resolution of the original. Dragonfly eyes are probably even lower resolution than that.

ResearchBlogging.orgTo catch prey as they do, dragonflies have a series of neurons in their brains that are highly tuned to specific properties in their visual field. A lot of progress has been made studying these cells with very abstract, precisely controlled visual stimuli in the lab. But the real world that the dragonfly has to navigate is one of booming, buzzing confusion. How do these neurons compute in such messy real world settings?

Wiederman and O’Carroll examined this with a visual neuron given the descriptive but uninspiring name of Centrifugal Small Target Motion Detector 1 (CSTMD1). Using 360° pictures of a woodland and a parking garage (‽), they placed a small black square that was predicted to drive the visual neuron bonkers. There were also some natural “distractors” in the image, and Wiederman and O’Carroll were able to photoshop those out to see the difference in response.

These sorts of results are probably best appreciated in relatively raw form (slightly modified version part of their Figure 2; click to enlarge). There's a lot going on here, but I’ll walk you through it.


At the top is the picture they used. There are three “targets” expected to make CSTMD1 fire at high frequency, indicated by the three vertical lines. The first on the left is a set of leaves, the middle one is a tree stump, and the right one is the “perfect” stimulus added by the experimenters to the scene.

The three boxes with red and black tick marks show when the CSTMD1 neuron is firing an action potential. Each row is one pass of the photograph. Each animal was tested multiple times, and each animal’s data is grouped together by alternating colours. All the recordings from one animal are in black, the recordings from the second animal are grouped together in red, and the recordings from a third animal are back in black again.

The lines on top of the boxes show the averaged firing rates of the neuron.

The CSTMD1 has a little spontaneous activity, but you can definitely see the responses on the neuron as the visual field passes over the targets. Keep in mind that the CSTMD1 neuron in an interneuron in the brain, not a simply sensory cell in the eye. It is receiving and integrating input from many photoreceptors in the eyes, which is why the response to the targets is wider than the targets themselves.

These data show that this neuron is able to filter out a substantial amount of visual “noise” from the environment.

The second box is interesting, because it shows the response to the tree stump is enhanced when the “perfect” target that the experimenters added is taken out of the picture. The reason for this seems to be that the left CSTMD1 neuron gets inhibited by the right CSTMD1 neuron. Again, because these neurons integrate information over a wide field, the presence of a strong target on the left side can dampen the response to a stimulus on the right side.

The authors don’t have an explanation, though, for why the response to the tree stump gets smaller when the leaves are retouched out of the photo (third box). There are obviously some other influences on this neuron that haven’t been documented yet, and Wiederman and O’Carroll suggest this is a good reason to keep making computer models of these circuits to track all these influences.

This paper is a nice demonstration of how neuroethological research can slowly move from completely artificial lab settings back into the things that we want to know about: behaviour in a natural setting. We’re not there with dragonflies yet, but we’re getting closer. The next step would be to present dragonflies with naturalistic video instead of just still pictures, especially videos with moving prey items flitting about. Or better yet, take the recording rigs outside and do some science in the sun.

Related posts

Neurons in the wild
For new brain cells, go to the wild

Reference

Wiederman S, O'Carroll D. 2011. Discrimination of features in natural scenes by a dragonfly neuron. The Journal of Neuroscience 31(19): 7141-7144. DOI: 10.1523/JNEUROSCI.0970-11.2011

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

18 May 2011

The Zen of Presentations, Part 41: Consistency

I spend a fair amount of time reviewing students’ PowerPoint presentations. The thing I probably spend the most time fixing is not their science, but their friggin’ lists of bullet points.*

I often see bulleted lists like this:

  • Readers distracted by content of a page when looking at its layout.
  • Lorem Ipsum Looks Like Readable English.
  • Now default for desktop publisher and web page editors

Two points have sentence casing; one has headline casing. Two have periods; one does not. For a list of short points, it doesn’t matter if you put a period at the end of each point or not. But could you at least do it consistently?

To make matters worse, people often end up changing typefaces without realizing it. And point size. And sometimes colours. Longer pieces of text will be ragged right on one slide and justified on the next.

Consistency becomes harder as you add more slides. I often see a series of slides with the title containing some abbreviation of “continued”. But sometimes it will be “Con’t”, sometimes “cont”, then “Con’t.”, followed by “(con't)”. I think I have seen every permutation of four letters and punctuation marks that it is possible to make.

Maintaining consistency becomes downright treacherous when you are creating presentations with several pieces of software. For instance, you might use Verdana as a typeface throughout your PowerPoint slides... but then forget that your Excel chart has the axes labelled in Arial.

Does anyone notice? For scientific or technical presentations, the answer is almost certainly, “Yes.” The audience is going to be filled with people whose livelihood depends on obsessing over details.

You want your audience to believe that you are someone who cares about details. Being consistent in your typography and slide design shows you are paying attention.

Pick a style and stay with it!

* I try to tell them to get rid of all those damn lists that everyone hates, but they’re all too scared. Wusses.

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

17 May 2011

Tuesday Crustie: But did it wear loud shirts?

ResearchBlogging.orgNext month, The Crustacean Society will be holding its summer meeting in Hawaii. While nobody would be surprised by the number of crustaceans in the waters around Hawaii, there is something surprising about the islands’ crustaceans.

There are no land crabs.

This is surprising, because land crabs are common on other Pacific islands. Is Hawaii just too young for crabs to have invaded the island and evolve into a terrestrial form?

Hawaii is young geologically, but it’s not that young. There are no land crabs on the island now – but there used to be.


The picture above shows a new species found on Hawaii, Geograpsus severnsi. (Scale bar is 1 cm.) I use the term “new” only in the sense of “new to science.” These are actually fossil remains, dating back to before human colonization of Hawaii a few thousand years ago. The fossils are found inland at quite high elevations, indicating that this was primarily a terrestrial species.

Based on the fossils, Geograpsus severnsi appears to have been an offshoot of Geograpsis grayi, which still survives and is found across much of the western Pacific. Geograpsus severnsi seems to have been abundant on Hawaii before humans arrived, but promptly took a nose dive into oblivion once humans arrived on the scene. Coincidence? While humans may not be directly to blame for the crab going extinct by hunting them to extinction, those early settlers may have brought in rats, dogs, or pigs that could have contributed to the end of this species.

Reference

Paulay G, Starmer J. 2011. Evolution, insular restriction, and extinction of Oceanic land crabs, exemplified by the loss of an endemic Geograpsus in the Hawaiian islands. PLoS ONE 6(5): e19916. DOI: 10.1371/journal.pone.0019916

16 May 2011

Who might be reviewing Texas science supplements?

The Texas Freedom Network is reporting on the list of reviewers of supplemental biology materials for Texas K-12 science classes. A PDF of the list of nominees is here.

Some people are educators, both at the university and K-12 level, several of whom have expertise in biology. Other nominees, to my untrained eye, seem... odd. We have as suggested reviewers people whose affiliations are Dell, retired (no indication of experience), and “Law offices of Albert Wai-Kit Chan,” and “Accudata Systems.”

The Texas Freedom Network, who watches these things more closely than I, pegs three of them as creationists.

If you want to peek at supplemental material that has generated the most discussion, Mother Jones shows a picture from the proposed supplemental material from International Databases. So does Care 2. Even putting aside the content issues, the presentation looks amateurish.

And finally, we have another case of where all of this maneuvers are making the state of Texas look bad – even when it isn’t deserved!

Bill Allen at The Huffington Post repeats this untruth about Texas:

After all, this is the State where that political board proposed, among other things: (snip)

6. To mandate that teachers give the religious-based, factually-bereft fiction of creationism equal footing with evolution, the basic organizing principle of all modern biology.

That is false, if Allen is referring to what has been happening in the last four years. There was never any mandate to put creationism into the Texas K-12 science standards. Indeed, Don McLeroy (former chair of the Board) was said:

McLeroy insists he doesn’t have any desire to have creationism taught in classrooms. “It’s a religious philosophy,” he says. “It doesn’t belong in schools. Same with intelligent design. Evolution is the scientific consensus, so we’ll teach that.”

Yes, the Board of Education weakened the standards on evolution in ways sympathetic to creationism and intelligent design. The creationists on the State Board of Education were quite adept in their dealings with the science standards.

The point is that Texas is perceived as a place where the teaching of creationism has been officially approved by the state. This is not a good perception for a state that wants to attract high tech business. And I fear that eventually, some poor teacher is going to think it’s okay to teach creationism, and is going to get sued.

Supertouch

The superhero Daredevil had few powers. His fighting abilities and roof-running were the result of Matt Murdock’s athleticism and a technological ingenuity (DD’s self-made billy club). His true superpowers were his hyper-keen senses (click to enlarge):


The irony, of course, was that the bad guys never knew they were getting taken down by a blind man.

ResearchBlogging.orgDaredevil’s story follows the belief that if you lose one sense, the others become more sensitive to compensate. This belief is old and common, and in a way, shows that we must have had some inkling about brain plasticity much more than 20 years ago.

If this is so, how does that compensation happen? Is it just a case that those brain centers used for vision automatically repurpose themselves for other sensory modes? Or could it be something more mundane? Blind people are better at some sensory tasks because they practice, practice, practice.

To test this, Wong and colleagues examined the ability of three groups of individuals to detect changes by touch: sighted people, people who were blind, and people who were blind and read Braille.

Of course, this is a simplification, because the blind participants were a very mixed group. Some had been blind since birth, while others had been born with normal vision. Not everyone was equally proficient with Braille.

The test they used was to determine the position of a slotted rod (right). All three groups performed this touch test using their fingertips, and with their lips. (I’m assuming that’s what’s shown in the lower right... though I have never personally seen lips quite that shape.) Using the lips provided a way to test if any differences in touch sensitivity of the Braille readers were due to an increase in touch sensitivity across the board, or if any improvements were found only in the fingertips.

The myth of blind people having sharper senses? Plausible.

There is not an overall enhancement of touch across the board. Blind people did better on the touch task for the fingers, but not with the lips. Further, the more proficient the blind person was with Braille, the better they performed on the task. The results pointed to practice being an important factor – maybe the most important factor – in this increased sensitivity.

Because this paper is in The Journal of Neuroscience, you might expect it to present some data on how the brains of these groups differ. I expected to see some fMRI scans or something similar. To my surprise, there are no brains or neurons or spikes in the methods or results of this paper. It’s straight psychophysics. Next paper, maybe?


This paper is good news for everyone who wants to be a hero. It says that you don’t need to lose your sight to an accidental mysterious toxic waste spill to improve all your other senses. You need dedicated practice. And that’s something that anyone can do.

Reference

Wong M, Gnanakumaran V, Goldreich D. 2011. Tactile spatial acuity enhancement in blindness: evidence for experience-dependent mechanisms. The Journal of Neuroscience 31(19): 7028-7037. DOI: 10.1523/​JNEUROSCI.6461-10.2011

15 May 2011

Comments for first half of May 2011

Dr. Micro O looks at the concept of academic pedigrees.

Michelle at C6-H12-O6 does a nice job explaining how mosquitoes withstand the heat of the blood they drink.

14 May 2011

More on proposed Texas intelligent design supplements

The Christian Post has an article that is very similar to this one that appeared in The International Business Times. There is one new piece of information worth repeating:

Regardless, (Josh) Rosenau believes that Sample’s materials will not be accepted by the board based on technical grounds.

“Not even getting to the issue that is creationist, it doesn’t cover all the new standards as it is supposed to, it has typos, it has basic errors of fact,” shared the director, according to Atheists At Large. “It is hard to imagine it going anywhere.”

13 May 2011

Where the science happens

Earlier this week, Jacquelyn Gill on Twitter said she wanted to see lab and fields sites. Let’s start with a field site:


Here is one of the places I go to collect sand crabs (Lepidopa benedicti) on South Padre Island, Texas (see Nasir & Faulkes 2011). This is some ways north on the beach, away from the main town center. You can see some of the high-rise hotels in the distance.

This particular day is not a happy collecting day: the amount of shells on the beach makes digging for the beasties a pain, pain, pain.The cloud cover is welcome, though. As you might imagine, south Texas sunshine while shoveling ten meter transects on the beach is, um, rather warm (euphemism for “sweating like a pig”). More papers from this site are forthcoming, I hope!

Sorry, Jacquelyn, but you’re not getting a picture of my lab until after the end of semester / start of summer clean up. Here’s an old one, with a crayfish condo under construction (I talked about this on another blog; see also Jimenez & Faulkes 2010; she’s the first author of that paper).




References

Jimenez SA, Faulkes Z. 2010. Establishment and care of a laboratory colony of parthenogenetic marbled crayfish, Marmorkrebs. Invertebrate Rearing 1(1): 10-18.
http://inverts.info/content/establishment-and-care-laboratory-colony-parthenogenetic-marbled-crayfish-marmorkrebs

Nasir U, Faulkes Z. 2011. Color polymorphism of sand crabs, Lepidopa benedicti (Decapoda, Albuneidae). Journal of Crustacean Biology 31(2): 240-245. DOI: 10.1651/10-3356.1

11 May 2011

Antsy

I have a symposium proposal that has been under review for a couple of weeks.

The editor of journal that has a paper of mine in press said they were hoping to have the next issue up by Easter. No issue in sight yet.

I have three co-authored manuscripts that have been in the hands of editors and under review for one month, two months, and five months, respectively.

I would kind of like to see something happen on at least one of those sometime soon.

10 May 2011

Tuesday Crustie: Massive damage!

How could I miss a crustacean meme?


In 2006, Sony announced a game that was based “battles which actually took place in feudal Japan.”

And the very next words were: “So here’s this giant enemy crab.”

09 May 2011

More on publisher of proposed Texas teaching supplements with intelligent design

Maybe the superficiality of this story in The International Business Times could be because it’s not a story about business. It’s a story about proposed supplemental materials that have intelligent design materials (which I wrote about here). The story does have some new information: the publisher is all of one person.

One submission has come from a company called International Databases, LLC. It's a one-man operation run by Stephen Sample, who says he has a degree in evolutionary biology and taught at the high school and junior college levels for 15 years.

I wish there was more reportage here. He “says” he has a degree in evolutionary biology. How advanced is the degree? Couldn’t someone check? It makes a difference if this is someone with a bachelor’s degree in biology versus someone with a doctorate. Few undergraduate programs are specifically for evolutionary biology at the level; most are “biology.”

Those sections say the “null hypothesis” is that there had to be some intelligent agency behind the appearance of living things. It is up to the scientists proposing a naturalistic explanation to prove their case.

Sample seems to be confused with the concepts of a null hypothesis with burden of proof. A null hypothesis is used in a specific experiment, which the origin of life is not.

As for “burden of proof,” the normal rule is that the burden of proof is on the person making the more extravagant claim. Following Sir William of Occam’s principle that the explanation with fewer entities is the more conservative one, the burden of proof would fall on someone who claims the origin of life is due to natural forces plus an unspecified intelligent agent (two entities), not the person invoking natural forces (one entity):

Ordinarily teaching from a religious perspective is forbidden in public school science classes. The principle was decided on in the Kitzmiller v. Dover, in 2005, when a judge ruled that teaching the theory of "intelligent design" was actually a form of religious instruction and therefore not allowed in public schools.

Not quite. The legal judgements against teaching religious points of view in science classes goes way back before Kitzmiller v. Dover. American Supreme Court cases go back to 1968. The National Center for Science Education has an excellent round-up of such cases.

Sample says the "null hypothesis" is such because the old experiments that attempted to produce "building blocks" of amino acids failed to do so.

The facts here have been mangled by someone, although it’s not clear if Sample or the reporter is doing the mangling. It seems to be a reference to the so-called “Miller-Urey experiments,” which succeeded in making amino acids.

Sample says it isn't stealth creationism - he says the intelligent agency might just as well be aliens.

Every intelligent design advocate that I have seen follows, “It could be aliens,” with, “Although I personally think it’s God” when pressed. There are vast reams of writing about intelligent design being compatible with certain theistic religions, particularly Christianity. There are no serious discussions in the intelligent design community that I have read that seriously discuss extraterrestrial intelligence. This is probably because the “aliens did it” hypothesis doesn’t solve the origin of life, but moves it off of Earth.

But he emphasizes that he wants students to learn to think critically, and that unlike the physical sciences, there aren’t any experiments you can do to demonstrate evolutionary theory.

If I’m generous, Sample might mean that there is no single experiment that can “prove” evolutionary theory, which is true. But science deals in evidence, not proof. And there are large numbers of experiments that have demonstrated evolutionary theory. You wouldn’t recreate all-female lineages of lizards in the lab without deep evolutionary thinking, to give just one recent example.

Additional: Sample is also silent on what experiments one could do to demonstrate intelligent design.

Is your research future predicted by your supervisor’s research past?

ResearchBlogging.orgAt the end of last week, I published a bit of a rant. After I had cooled a bit, I wondered if the response of my gut would survive scrutiny by my head.

The NeuroTree website says:

Big families stay big. Children of researchers with many offspring tend to have many offspring of their own.

This suggests a “pedigree” effect that many would see as positive (more students means more success). They don’t give the data supporting that claim, though.

I went looking for research on the effect of “pedigree.”

Goodwin and Sauer have a paper that sort of addresses the issue, although (1) it’s about economists, and; (2) they rated the prestige of the institution where a person got their doctorate, not the specific mentor (I suppose “lab” doesn’t have much meaning in business school). They find economists who received a degree from a “top 20” doctoral program gain a significant advantage in research productivity.

In contrast, a slightly newer paper by Long and colleagues (looking at management professors in business schools this time) found no effect of where someone got their doctorate, which seems to be evidence against “pedigree” being a useful predictor. Much more important to productivity was the quality of the institution where the faculty member was ultimately employed.

Williamson and Cable, again studying management faculty, found a positive correlation of productivity of doctoral supervisor with early career productivity. The more productive your boss, the more productive you are. Because it looked at the supervisor, not the program or institution, it seemed to be the closest to what I was looking for.

But the trail dried up for me when I went looking for similar data in the biological sciences. I’m sure there are papers out there, but I couldn’t find them very easily. If anyone knows any, I’d love references.

Evidence suggests that “pedigree” is an predictor of success. I was wrong.

I stand by my dislike of the term, however, with all the negative connotations that it has. “Pedigree” implies your past defines you. I prefer the term “heritage,” which recognizes that you are shaped and influence by your past, but are not necessarily defined by it.

References

Long RG, Bowers WP, Barnett T, White MC. 1998. Research productivity of graduates in management: Effects of academic origin and academic affiliation. The Academy of Management Journal 41(6): 704-714.

Goodwin TH, Sauer RD. 1995. Life cycle productivity in academic research: Evidence from cumulative publication histories of academic economists. Southern Economic Journal 61(3): 728-743.

Williamson I, Cable D. 2003. Predicting early career research productivity: the case of management faculty Journal of Organizational Behavior 24 (1): 25-44. DOI: 10.1002/job.178

06 May 2011

Academic pedigrees

Academia is a meritocracy, where the only thing that matters is your own output, hard work, and skills. Ideally.

I hate being reminded of how far away from the ideal the reality is. The term “academic pedigree” is one of those reminders.

I understand the interest in looking for connections between academics. I’ve written about my own a few times, most recently here. What I dislike is that this is seen as some sort of meaningful yardstick for judging a person’s suitability for jobs, particularly tenure-track jobs. Indeed, I’ve read at least one post somewhere saying that pedigree was the most important factor.

Do people not think that discussing job candidates and grad students and post-docs using the same terminology as livestock and show dogs is not just a little demeaning?

“Pedigree” also has connotations with aristocracies. And one of the bad things about aristocracies is that they often set things up to keep all the power to themselves. Aristocracies often want preserve the status quo and making sure the playing field never becomes level. Because when it’s all about breeding, well, there’s nothing one can do about that, now, is there?

How would the discussion change if every time someone talked about “academic pedigree,” it was replaced with “well connected in the old boys’ club”? Let’s make it explicit that this discussions of pedigree are discussions about power relationships, and not merit.

Related posts

Inclining the playing field
Balkanizing small universities
To have and have not. Mostly not.

External links

Reason No. 52 not to go to grad school
Science professor - see the comments

Hat tip to Dr. Micro O.

Dog pedigree by ronmichael on Flickr; cow pedigree by dan mogford on Flickr; both used under a Creative Commons licence.

05 May 2011

Personal statements and “I-don’t-know-what-is-it-but-I-like-it”

Imagine you were going to listen to a bunch of new songs. Could you tell me which songs you would like before you heard them?

You could probably make some good guesses, in broad strokes. “I like jazz, but I’m not very into country.”

But it starts to get very unpredictable at the level of individual songs? Even for my favourite artists, for songs I know well, I couldn’t tell why this song works for me so much better than that one.

There isn’t a formula to predict what songs are going to be global worldwide hits, and which ones are going to find an audience of maybe a few thousand. The small audience may love their song as passionately as the large audience loves the global hit. But the only way to tell which is which is to put it out there to the masses.

I realized today that personal statements, which we use so much for things like grad school applications, are like that for me. I can often pinpoint why I don’t like something retroactively, but I can’t easily articulate the common features in ones that I like.


This is frustrating for me as a teacher and grad program coordinator. I teach biological writing to my undergraduates, and I always have them do personal statements. It’s always the students’ favourite assignment. They find it useful. I try to help students who want to apply to grad school.


It’s as difficult to explain to people what will make a successful personal statement as it is to explain to them what will make a hit pop song. The things I can explain to people are very general – like saying, “Accordion songs are not likely to be huge hits.”

Of course, for students, it may be a revelation that they may have to put away the accordion if they want to reach a large audience. But I wonder how much more can be conveyed on the subject.

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

04 May 2011

The Zen of Presentations, Part 40: Lighting a fire under speakers

Ignite! talks rock.

We have a seminar class in my department, which all our majors must take. Normally, this class meets an hour a week, and every student gives one 15 minute talk, with 5-10 minutes for questions.

The problem is, each presentation becomes very high stakes, with no opportunity to try again. If you screw up once, you’re done. I wanted to give everyone a second crack at giving a talk, so I decided to have everyone do two talks: a 12-15 minute one, and an Ignite! talk.

The Ignite! format: You have five minutes flat. 20 slides, auto-timed for 15 second each. Then you sit down and shut up. Somewhere I saw the Ignite! motto was something like, “Enlighten us, but make it snappy.”

Across the board, my students’ Ignite! talks were head and shoulders above their long talks.

When I said this on the last day of class, I say a lot of heads nodding in agreement. So it wasn’t just me; many people thought these talks were better.

There were many differences between the long and Ignite! talks. For the long talks, I banned PowerPoint and I picked the topic (these were both intended to push students out of their comfort zone). But I don’t think those were why the Ignite! talks were better.

They were better because of the energy everyone brought to their talks.

Faced with 15 second per slide, people had to know their story, had to concentrate, and absolutely no dawdling! That meant every speaker had to crank it up, and it was so much more fun to watch overall.

And even if it wasn’t great, you knew you wouldn’t be stuck listening to a crummy talk for more than a few minutes.

Not only am I sold on the value of doing these for my students, I would love to see more academic conferences try Ignite! sessions. You can get a surprising amount of information out there in five minutes if you plan it right. It could leave a lot more time for the things that people like the most, which are the meetings in the hallways and over coffee.

If you haven’t done one, try it! The format lives up to its name.

External links

Presentation Zen: The Ignite presentation method
Speaking about Presenting: The fastest Way to create an Ignite presentation (several students told me this was very useful to them)

03 May 2011

Tuesday Crustie: Know that I glory in this nose of mine

ResearchBlogging.orgI was pleased that people liked last week’s description of a new squat lobster and its whimsical name, Uroptychus pinocchio. Today, let me introduce its cousin, another  species new to science with an equally choice nom de science:


Like its relatives, Uroptychus naso and Uroptychus pinocchio, this new species lives in the western Pacific. These three are distributed from Japan in the north down to Australia in the south. Something interesting happens as you travel along this way on the various islands: the species of plants and animals that you find seem to change suddenly as you go south. This transition point is now called Wallace’s line, after the naturalist and co-discoverer of natural selection, Alfred Wallace, who noted this.

But do you get similar effects in ocean species? These squat lobsters do line up in a way that is reminiscent of Wallace’s line: the new species are at the north and south end of the range. Even the better known U. naso, which is more widely distributed, has some populations that appear to be rather isolated from the main lineage.

These squat lobsters are live several hundred metres down. The geologic history of the ocean bottom in creating the shelf zones they inhabit may be as important for the distribution of some of these species as the geological history of the islands are for the distribution of these terrestrial species.

The name of this second new species? Like U. naso and U. pinnochio, this species’ name celebrates its prominent rostrum.
 
Uroptychus cyrano, after the famed French poet and swordsman.



Reference

Poore GCB, Andreakis N. 2011. Morphological, molecular and biogeographic evidence support two new species in the Uroptychus naso complex (Crustacea: Decapoda: Chirostylidae)  Molecular Phylogenetics and Evolution: In press. DOI: 10.1016/j.ympev.2011.03.032

02 May 2011

Carnivals for May 2011

Encephalon #86 is hosted at Forensic Pscyhologist. By the way, this carnival needs hosts for the next couple of months! Check out here if you want to contribute.

The carnival of Evolution #35 is hosted by Lab Rat.

Circus of the Spineless #62 is now available at Squid a Day.

Want us to teach more?

Ronald Trowbridge, writing in the Texas Tribune, thinks public universities in Texas should be teaching more and doing less research.

Our universities have shifted priorities to research first, students second. “The ultimate source of this cultural shift,” writes Harry Lewis, a former dean at Harvard University, “is the replacement of education by research as the university’s principal function.”

But Trowbridge doesn’t examine the reason for that shift. I suggest that this shift may have occurred because there is money to be had through research. Successful research programs are a revenue source. If Texas politicians and taxpayers want more teaching, they should be willing to pony up the cash that will replace the money that will be lost as less research is done.

Trowbridge also bemoans the number of adjuncts and graduate students teaching introductory classes. I agree; I’d love to see more tenured and tenure-track faculty teaching such classes. Again, who’s willing to pony up the cash for those more permanent positions?

Trowbridge argues that professors teaching two classes a semester is normal, when this is only true at the two major institutions in the state. He also apparently doesn’t consider working with research students “teaching,” when it is arguably some of the most important teaching at a university.

I’m for transparency and accountability, but “accountability” is not a license to allow you to demand the outcomes you’d like.

01 May 2011

Comments for second half of April 2011

Cephalove talks about why octopuses are “honorary vertebrates” in European animal care regulations.

Christie, I’m so disappointed.

Prof in Training wonders about authorship credit for students. Much discussion ensues. Hey! A lot more people should read my letter in Science about this.

Prof-like Substance wanted people to promote their blogs.

At The Meandering Scholar, BrooksPhD asks what people do for their scientific societies. And why don’t people do more?