May 2009 Archives

Wouldn't it be great if reading your computer screen were just like reading a Kindle, which is just like reading a piece of paper? Think of the reduced eye fatigue. No more late nights lit only by the glow of the monitor. You'd have to turn the light on to be able to read your screen. (Seems almost anachronistic, doesn't it? But that's technology--two steps forward--whoops, that second step wasn't so good--one step back--wait, one step forward?)

But for now, ambient-light screens are just so much science fantasy. We'll be screen-bathing in front of our LCDs for years to come. Right?

Maybe not. Folks at MIT have been working on ambient-light screens that run on orders of magnitude less power than a traditional backlit screen. Their article "Bioinspired Electrochemically Tunable Block Copolymer Full Color Pixels" is a pretty full meal, but here's the quick snack version, as near as I can figure:

They made a new kind of pixel, whose color can be changed ("tuned") by firing an electrical charge into it. It doesn't generate any of its own light, so its color range is only as good as the ambient light it can reflect. If it's exposed to full-spectrum white light, it can be any color of the rainbow. Which wavelength (=color) it reflects depends on the actual physical structure of the pixel.

This sounds weird, right? Why should the structure of an object determine its color? Cubes, spheres, and plates are all equally capable of being vivid red or yucky green.

That is true on a macroscopic level, true for objects that you can see and handle. But on a microscopic level, the shape, size, and structure of an object are integral to its color. That's because visible colors are just wavelengths of light, between 380 and 750 nanometers in length. So a nanometer-scale object can get all up in a color's business, and have an actual physical altercation with blue, if it's feeling feisty.

The new pixels created by Walish et al. are just that tiny. They're a type of object called a 1D photonic crystal, which consists of lots of very thin layers. When the layers are closer together, they reflect shorter wavelengths (read: blue) and when they are further apart, they reflect longer wavelengths (read: red). Fine. The truly amazing part is that these guys figured out is how to spread a gel (that's the "block copolymer") between these thin crystal layers, like a multi-decker jelly sandwich using a miraculous kind of jelly than expands and contracts when you jolt it with varying voltages. (And if there's anything scientists are really good at, it's got to include jolting systems with varying voltages!)

As far as I can tell by wading through this study, which is by the way the first article in Advanced Materials that I have ever read, they made a single pixel. One. And they can change its color from red to green over the course of a few seconds. Normally you watch movies at 29.97 frames per second. So, it's kind of a far cry from a TV screen.

So why the big honking deal? Why do I even know about this, and why did I feel compelled to wade through the article at all? The answer, as always, is that there's a cephalopod involved.

One of the most wonderful aspects of being known far and wide (read: to friends and family) as a cephalopodiatrist is that I no longer have to read the news. Oh, no. It comes to me. And you know which cephalopod has been in the news lately? Cuttlefish. And TV screens.

To put it kindly, the media are doing some pretty advanced yoga to be able to stretch that far. Here's the connection, as worded by Walish et al:

Fish such as the blue damselfish, neon tetra, and paradise whiptail all employ 1D photonic crystals in which the lamellar spacing is controlled through chemical secretion by the sympathetic nervous system. Color change in the squid Lolliguncula brevis is also thought to be controlled by secretion of a chemical trigger causing changes in the thickness of the high refractive index protein platelets within the iridophore resulting in a change in reflected color.

Despite the fact that this mechanism (electrical signals changing the spacing in a layered crystal) is known to be employed by fish and thought to be employed by squid, the only picture of an animal in the paper is, in fact, of a squid (Figure 1a). I guess cephalopods are just that much more photogenic than fish. Sorry, vertebrates!

Anyway, the cephalopods horned their way into the paper in the form of the lovely brief squid (really, that's its common name!). So where do the cuttlefish come in? Televisions.com reported:

"Cuttlefish change their color by secreting different chemicals to change the spacing between membranes," explains MIT-professor Edwin Thomas. "We have created an artificial electrical system to control the spacing between layers."

Who's to say what happened in the interview--maybe the interviewer had never heard of squid, only cuttlefish, so Prof. Thomas tried to put it in terms the poor guy would understand. We'll never know.

In any case, I now feel obligated to explain that cuttlefish (and squid, and octopuses) use a lot more than just 1D photonic crystals (which are called iridophores when they're living in cephalopod skin, by the way) to change colors. In fact, the more prominent cephalopod color-changing mechanism is the chromatophore system.

This is where cuttlefish really shine (only, not really, because "shining" would be a better description of the iridescent structural colors produced by iridophores, and . . . shut up, self!) Anyway, cuttlefish have the highest DPI of any cephalopod. That is to say: they have more chromatophores per square inch of their skin than any squid or octopus. How many? We're talking up to 500 chromatophores per square millimeter. That's over five hundred DPI*.

And each chromatophore is considerably more complicated than just a "dot." A chromatophore is a tiny elastic sac of pigment surrounded by muscle fibers, like spokes on a wheel. When the muscles are relaxed, the chromatophore is just a small dark pinprick at the center of the "wheel." When the muscles contract, they pull on all sides of the naturally elastic chromatophore, and the sac has no choice but to expand, becoming a spot of color on the skin--black, brown, red, or yellow, depending on the color of the pigment filling the sac. (Cephalopods seem to have partitioned their chromatophore pigments to take care of the warm colors, while the iridophore structures produce cool colors.)

How does the octopus, squid, or cuttlefish contract the chromatophore muscles? The same way you or I contract muscles: by sending a nervous signal, a natural jolt of electricity. You may remember that's how the iridophores are controlled, too. This means that each of the animal's millions of chromatophores and iridophores is under direct nervous control. That's the secret. That's why cephalopods are the color-change masters of the world. Chameleons? Forget them. They actually change their colors through chemical diffusion, a painfully slow process in comparison with electrical signals zipping down the nerves of a squid or cuttlefish. Chameleons take multiple seconds to change colors. Cephalopods can flash multiple complex patterns across their entire bodies in the space of a second.

If you are feeling jealous of the cuttlefish's incredible resolution and frame rate, I cannot help you. Not yet. There are no dynamically changing cephalopod-inspired clothes that I am aware of. (Materials scientists? Can you get on that please?) But if you can be content with static designs, there are some really wonderful wearable cephalopods. I have a list! And I finally figured out how to move it over to my blog! So, check it out, over there on the left under "pages": Ceph Gear.



* I have just learned that dpi is a 1D measurement, so, literally dots per inch, not per inch squared. I was always a little fuzzy on that. Now I know! Thanks, live-in tech support!

Tangential note: As far as we know, cephalopods are color-blind. Isn't that crazy? The evidence for color-blindness is both mechanistic and behavioral. We can't find any mechanism whereby they could distinguish colors, since they have only one visual pigment. And we can trick them behaviorally by placing them on patterns with different colors of exactly matched intensity (so the only way to tell them apart is by wavelength, just like those red-green bubble tests). And the cephalopods can't color-match. But . . . it's still so hard to believe.

In Which I Make Liberal Use of Blockquotes

Mark C. Taylor recently(ish) wrote an Op-Ed in the NY Times titled "End the University as We Know It," claiming that American graduate education creates "a product for which there is no market and develops skills for which there is diminishing demand, all at a rapidly rising cost." Awesome! But never fear--Taylor has six suggestions for thoroughly restructuring the university, to benefit not only grad students but all of society.

Before getting there, he explains that the model of academic research is all about division of labor, leading to endless specialization: "research and publication become more and more about less and less." Graduate students are trained in this ever-narrowing scholarship, forming the core of the university's teaching and research force. But all good things must come to an end, and, on an unrelated note, all students eventually graduate. (Or quit. A not unpopular option!) Newly minted PhDs are then treated to the pleasure of finding that the only jobs they're qualified for are already taken by their (better-qualified) advisors.

So, what the heck, grad school? Why is this situation not remedied? Basically, says Taylor, because the entrenched academics like it that way:

[An] obstacle to change is that colleges and universities are self-regulating or, in academic parlance, governed by peer review. While trustees and administrations theoretically have some oversight responsibility, in practice, departments operate independently. To complicate matters further, once a faculty member has been granted tenure he is functionally autonomous. Many academics who cry out for the regulation of financial markets vehemently oppose it in their own departments.

Hmm! That sounded kind of familiar. Here's another academic writing about academia, Stephen Quake in "Letting Scientists Off the Leash". He's grinding a different axe, but the sentiment is surprisingly similar:

It strikes me as one of the ironies of modern life that professorial faculty members, who by and large lean to the left politically, accept such a brutal free-market approach to their livelihood. If they can't raise grants to support their research every year, they won't get paid. So not only do they have to worry about publish or perish, it's also funding or famine, in the very real sense that without a grant there might not be food on the family dinner table!

I couldn't have responded with more appropriate snark than Aurelie Thiele offered in a review: "Quake's post doesn't enhance the image of academics, unless whiny is the new cool."

Of course, Quake and Taylor are opining on the granting system and the modern university, respectively, which are distinct (though related) topics. They're also coming from different fields. Taylor is the chair of the religion department at Columbia, while Quake is a professor of bioengineering at Stanford.

In my very limited experience, humanities grad students tend to be woefully underpaid in comparison to the sciences (not that grad school in any field is a particularly lucrative profession) and to have virtually no non-academic career options. While science grads are often ill-informed about non-academic career options, they're definitely out there: plenty of science PhDs holds jobs in government, non-profit, and for-profit sectors. (Quake himself is, in addition to a professor, an investigator at the Howard Hughes Medical Institute.) All this is to say: it might make sense for a humanities academic to be more concerned about the plight of graduate students.

Meanwhile, science is a lot more expensive than humanities, and the need and competition for grants is correspondingly fiercer. So this might explain Quake's (over-dramatic) attention to the granting situation.

Getting back to Taylor's piece, let's take a look at his six-fold path towards an enlightened university model:

1. Restructure the curriculum, beginning with graduate programs and proceeding as quickly as possible to undergraduate programs. The division-of-labor model of separate departments is obsolete and must be replaced with a curriculum structured like a web or complex adaptive network. Responsible teaching and scholarship must become cross-disciplinary and cross-cultural.

As a recent grad from my program put it, "Interdisciplinary studies are great, but c'mon, welcome to 10 years ago." At least in the sciences I know, we're fairly well inundated with interdisciplinary classes, organizations, workshops, degrees, etc. But not every class can be interdisciplinary, either. If you want to learn calculus, there's no way around taking a plain old calculus class.

2. Abolish permanent departments, even for undergraduate education, and create problem-focused programs. These constantly evolving programs would have sunset clauses, and every seven years each one should be evaluated and either abolished, continued or significantly changed. It is possible to imagine a broad range of topics around which such zones of inquiry could be organized: Mind, Body, Law, Information, Networks, Language, Space, Time, Media, Money, Life and Water.

Okay, this is . . . a little spacey. I'm all for considering unusual, unexpected solutions to problems, but I'm considering this one, and . . . no. Again with the calculus: maybe you could offer calculus in the Space zone of inquiry, as a precursor to learning Physics, and then Astrophysics. And then when you abolish the Space zone, you can start offering calculus in the Water zone . . . but really, why not just keep a nice Math department where you can offer calculus year after year?

3. Increase collaboration among institutions. All institutions do not need to do all things and technology makes it possible for schools to form partnerships to share students and faculty. Institutions will be able to expand while contracting. Let one college have a strong department in French, for example, and the other a strong department in German; through teleconferencing and the Internet both subjects can be taught at both places with half the staff. With these tools, I have already team-taught semester-long seminars in real time at the Universities of Helsinki and Melbourne.

This is a pretty cool idea. We've got a new local thingy that's trying to get all courses offered at all local institutions cross-listed and opened to all local students, regardless of student affiliation. When the institutions are in close physical proximity, this is great, but I'm not sure remote classes are quite there yet, as far as providing the same level of intellectual engagement. (Incidentally, the idea of specializing educational institutions reminds me of the idea of specializing news organizations.)

4. Transform the traditional dissertation. In the arts and humanities, where looming cutbacks will be most devastating, there is no longer a market for books modeled on the medieval dissertation, with more footnotes than text. . . For many years, I have taught undergraduate courses in which students do not write traditional papers but develop analytic treatments in formats from hypertext and Web sites to films and video games. Graduate students should likewise be encouraged to produce "theses" in alternative formats.

As a student who has been producing school assignments in "alternative formats" since grade school*, I'm theoretically delighted by this suggestion. But I really don't think this will cut it in the sciences.

5. Expand the range of professional options for graduate students. Most graduate students will never hold the kind of job for which they are being trained. It is, therefore, necessary to help them prepare for work in fields other than higher education. The exposure to new approaches and different cultures and the consideration of real-life issues will prepare students for jobs at businesses and nonprofit organizations. Moreover, the knowledge and skills they will cultivate in the new universities will enable them to adapt to a constantly changing world.

All I can say is: Yes, oh yes!

6. Impose mandatory retirement and abolish tenure. Initially intended to protect academic freedom, tenure has resulted in institutions with little turnover and professors impervious to change. After all, once tenure has been granted, there is no leverage to encourage a professor to continue to develop professionally or to require him or her to assume responsibilities like administration and student advising. Tenure should be replaced with seven-year contracts, which, like the programs in which faculty teach, can be terminated or renewed. This policy would enable colleges and universities to reward researchers, scholars and teachers who continue to evolve and remain productive while also making room for young people with new ideas and skills.

Ah, the tenure debate! I'm not sure where I stand on this anymore. My initial reaction to the tenure system is impatience and disappointment--but I've heard some decent arguments for its continued relevance and importance. I keep thinking: why can't academic jobs be like other normal jobs? The impression I have of normal jobs (which is just an impression, since I have, um, never had one) is that most people live neither in constant fear of losing their job nor in smug satisfaction that it can never be taken away from them. I guess part of the big difference is that an academic department is a network of peers, not a hierarchy of bosses and subordinates. And when your peers are the ones evaluating you and deciding your job security, everything is just a bit trickier.

I'll have to think more about tenure, and give it a post of its own later . . . any thoughts to contribute?


* When we studied Greece in elementary school, I wrote a series of letters from various Greek soldiers, reporting home to their friends and families about the Trojan war. But these were not ordinary letters. Oh, no. I wrote them on tiny pieces of paper, packaged them in tiny envelopes with tiny addresses and stamps, put all of them into a tiny mailbag that I cut and sewed out of scrap fabric, and then put this tiny mailbag on the arm of an OCTOPUS POSTMAN that I cut out of CARDBOARD. Yes. I managed to work an octopus into an assignment about Ancient Greece. Hi, I'm a dork! And apparently have been since I was ten!

Alas, poor James, so he believed,
But then they dragged the net too deep.
He knew swim bladders do expand,
But, unaware how much they can,
Eager James leaned o'er the trawl--
Crustaceans, jellies, fish, and all.
Dear Jim died when a fish exploded--
He didn't think rattails were loaded.

* A direct quote from a Deep Sea Biology lecture . . .

Back in January, I had to go out on a boat. This happens sometimes in my line of work, so you might think that I'm used to it. And I am, for it is surprisingly easy to get used to any unhealthy relationship.

I love boats! Every time I climb on board I hear Ratty, from The Wind in the Willows, exuberantly claiming that "there is nothing--absolutely nothing--half so much worth doing as simply messing about in boats." Fresh wind in the hair! Rainbows in the salt spray! It's incredible!

Boats, meanwhile, hate me. Boats want me to be as sick as possible. They want to wring as much pleasure as they can out of my whole boating experience. But I will not be daunted! I am determined to continue loving boats, and so every time I am invited on board I say yes! Defiantly I toss back my meclizine, chew the ginger, munch on Triscuits, and dare the boat: do your worst.

Generally speaking, it does.

It's an arms race: me finding new ways to stave off seasickness, and boats finding creative new combinations of yaw, pitch, and roll. Back in January, I thought I might have finally won. I took a tablet of prescription-strength meclizine hours before the boat left, and popped a chewable Bonine every two hours on the boat. I ate lots and lots of crackers, and I felt fine. I felt great! I could have stayed on that boat all day! Come to think of it, I did.

After that, I didn't have occasion to get on a boat again until last Tuesday night. I remembered to bring all my anti-seasickness weapons to work, and I remembered to take the meclizine a couple of hours before we hit the water. But other than that one quick swallow, I wasn't thinking about seasickness at all. Instead, I was caught up in the packing list, the float plan, the science to be done.

(This is my problem, you see. Selective memory. Unchecked optimism. It does not matter how vomitiously ill I have been on a boat trip, that sickness remains but the faintest of clouds on the horizon of an otherwise idyllic boating memory. So by the time another boating opportunity presents itself, all I can think is: Yes please! I love boats! . . . But I digress.)

Hah, just kidding, we've left the parenthetical only to plunge into another digression. Let's meet that meclizine I keep talking about:

It's an antihistamine (blocks allergic reactions, like Benadryl) and an anticholinergic (blocks the neurotransmitter acetylcholine). I got a prescription for it back when I was going on a boat for a month and asked a doctor for something to help me with my nausea. (Incidentally, this turned out to be pretty foolish, because after the first night I got my sea legs and was just dandy fine for the whole month.) According to the copious labels covering the little orange plastic vial, it may cause DROWSINESS and BLURRED VISION (the latter illustrated with a charming pair of noses).

What is awesome though, and I didn't realize until much later, is that apparently Bonine is made out of meclizine, and in fact it has more meclizine per tablet than my prescription. Does that make any sense? No. It is dumb. Even dumber is that I keep taking the prescription stuff, feeling like it should have more of an effect than an OTC drug, although there is less drug in it. Hi, I'm a scientist! I'm clever!

So, why does an antihistamine/anticholinergic think it can do anything about seasickness? And why did it perform so spectacularly well in January and so appallingly badly last Tuesday (as you will read about)?

Before answering those questions, I'm going to take a step back and try to understand seasickness itself. My thoughts (as you may have noticed!) are somewhat chaotic, so I have attempted to impose order by organizing the rest of this post in three parts: I. Seasickness, II. Drugs, and III. How Tuesday Night Was The Worst Thing Ever, The End.

I. SEASICKNESS

As I was educating myself on this subject, I stumbled across a 1926 article from Time Magazine. According to the doctor quoted in this article,

There are five theories for [seasickness'] causation: 1) the labyrinthine (the ear contains two tiny sacs, the utricle and the saccule, and three semicircular canals, all of which aid in special orientation); 2) "muscle sense" disturbance (the muscle nerves localize in space the position of the limbs, head, eyes and other parts of the body); 3) eyestrain (the patient gets dizzy looking at the ever-changing sea); 4) peripheral vagus-nerve irritation (the insides get shaken up by the complicated motion of the boat and by the minute, incessant vibration of the engines); and 5) psychic stimuli (the patient sees others kharouping and vomiting over the rail and gets sick).

Let's take a moment to lament the fact that "kharoup" might not have seen print since 1926. What a great word.

Okay, let's look at those theories. Dr. Desnoes kindly states theories 3, 4 and, 5 in layman's terms that make some intuitive sense. For theories 1 and 2, however, he takes care to define "inner ear" and "muscle sense" but makes no mention of how motion would affect them negatively. Presumably they are "disturbed" in some way.

In the intervening decades, medical science hasn't come a whole lot closer to a definitive explanation for motion sickness.

The explanation you most commonly hear these days is a combination of Dr. Desnoes' theories 1 and 3. Your brain gets one message from the inner ear and a different message from the eyes, and this makes it confused. This makes sense, whether you're looking at the boat (which is moving along with you, so it looks like you're still) or the water (the waves that you're looking at are not the ones underneath you, so you're not moving in sync with them) or even the horizon--although this latter option is an oft-touted method for staving off sickness.

But why should conflicting messages from the inner ear and the eyes make you nauseous? In the immortal words of Eddie Izzard,

Throwing up is controlled by three little bones in the inner ear. They're called Shadrach, Meshach and Abednego. And they control hearing and vomiting. Don't know why they go together. God went, "Inner ear, you shall have hearing and vomiting as well. Yes, that'll be fun."

I don't know why they do it! Do you? Does anyone?

In fact, there's a researcher out there who thinks this whole "conflict theory" (inner ear vs. eyes) is total bunk. "Stoffregen has branded the conflict theory with the highest-order insult a scientist can muster: unfalsifiable," reads the article in Scientific American. This guy Stoffregen has a new theory: postural instability. This is sort of like a combination of Dr. Desnoes's theories 2 and 4. Basically, your body is getting shaken around on an unstable platform, you have a hard time keeping your balance, and that makes you sick. An interesting theory, and one that's gaining some support.

But he's got nothing to offer to those of us still hungering for a mechanistic explanation. Even if it is postural instability that causes motion sickness--again, why with the vomiting?

So, we don't really know why you get seasick. But here, have some nasty medicine!

II. DRUGS

An endlesss variety of related drugs are used to treat nausea and vertigo. Here are some of the most common (brand names in parentheses): meclizine (Bonine, Antivert), scopolamine (Transderm-Scop, usually a patch, Maldemar), dimenhydrinate (Dramamine), promethazine (Pentazene, Phenergan), and cyclizine (Bonine for kids).

They are all both antihistamines and anticholinergics, and the reason they work against nausea is, well . . .  "The precise mechanism of action in inhibiting the symptoms of motion sickness is not well understood." Honestly, this shouldn't be surprising. Since we don't know the mechanism behind seasickness, how could we possibly know the mechanism behind the drugs that work against it? It's pure trial and error. Come to think of it, the situation is not unlike psychiatric medication.

However, I'm pleased to report that there are plenty of studies about the practical effectiveness of various treatments. And not just the drugs, either.

Various behavioral modifications can be effective treatments too. Eating constantly works well for me (when I can keep it down), and others swear by it. Where on the boat do you stand? Where in the world do you look? Stoffregen might suggest that if we all just walk around straddling the deck, we'd be fine!

As usual, attitude is often the best drug. If you're afraid you'll get seasick, you probably will. If you're determined you won't, you'll likely stay healthy. But no matter how fervently I believe in mind over matter, it just won't work for me. Case study: Tuesday night.

III. HOW TUESDAY NIGHT WAS THE WORST THING EVER, THE END

(No, it's not quite the end. I know, I know, have I ever been so verbose? If you are still reading, thanks! You're a trooper! I promise to be done soon!)

Tuesday night: I took meclizine. I got on the boat with a fellow grad student, our advisor, and an intrepid captain. I ate about a quarter of a box of Triscuits. We arrived at our first station, did some science. I took careful notes. We embarked on a very bumpy ride to our second station. The boat stopped, in the sense that the motor was turned off, but kept going, in the sense that we were being juggled by some of the more unperiodic, unpredictable waves I've ever felt. I looked up, noted the beginnings of mutiny from within, and announced, "Sorry guys, I'm not going to be much help."

I tried, I really did, to keep taking notes. With intense focus, I wrapped my hand around the pen, and labored to scribe each letter and number. My fingers were tingling as though asleep, so I began to work my hands vigorously, trying to bring them back to life. Instead, the tingling spread. I noticed it in my arms, legs, and torso. Have you ever felt pins-and-needles in your torso? It's novel. Also, freaky.

While Fellow Grad and Advisor engaged in Science, I engaged the captain in a conversation about the tingling phenomenon, and discovered that I was suffering neurological symptoms in my speech as well. That is to say: I was slurring like a drunk. Fabulous.

My fine motor control was pretty much gone, so I gave up the notebook and concentrated on keeping myself alive. It was freezing cold, so I pulled on my gloves and scarf, although sometimes I would get the sweats and have to open my jacket and pull the scarf away from my neck so I could feel like I was getting enough air. It's worth recording that I was practically hyperventilating at this point. The captain suggested that I breath more slowly. I told her that I couldn't.

What an interesting set of symptoms, you are saying, yes, yes, but what about the nausea? I was nauseous, but I didn't come close to throwing up until near the very end of the Science, and it wasn't until we were almost back home that I managed a really good kharoup. After that, recovery proceeded quickly to basic usefulness, but exhaustion and mild nausea clung to me persistently through the next day.

Wow, you are saying now, thanks for sharing! I didn't need to hear that story at all! Okay, true, but here is the interesting medical information: meclizine, like many another antivertigo drug, acts to prevent you from throwing up. (By blocking acetylcholine, apparently. Who knows why that works?) But it has no effect on the other symptoms of seasickness, like exhaustion and dizziness,and it doesn't even alleviate your nausea, it just keeps you from vomiting. Which would probably make you feel better. Thanks for nothing, meclizine!

But it's even better than that--blocking acetylcholine can have some delightful side effects of its own. Blurred vizion and dizziness are, of course, well advertised on the packaging, but I feel pretty comfortable blaming my slurred speech and tingling on the meclizine, too. I'm lucky I didn't get any hallucinations.

We did catch squid that night, didn't we?


* The title of this entry came from a friend of mine who used to be a naval engineer. If I understand correctly, part of her job was to calculate a seasickness index for every area of the ships she worked on--"vomitiously ill" being an unacceptable level of seasickness. Or something.