Tuesday, February 28, 2006


The U's site licence with Nature appears to be on the fritz at the moment, so discussion of the article mentioned in the previous post will have to wait until I can get a copy of it. Apologies.

Treatment for drug addiction?

Well, that's interesting:

Some habits are hard to break. Others become addictions. The latter group could be a figment of the past thanks to a new universal addiction-blocking substance developed by an international research effort led by the University of Saskatchewan.

The team created a peptide, a short chain of amino acids, from PTEN, a natural enzyme that acts on the ventral tegmental area, the reward center of the brain, where most drugs take effect. The peptide blocks the natural rewards that an addict experiences from an increase in serotonin—a neurotransmitter associated with learning, sleep and mood—when taking his or her substance of choice. The regulation of serotonin then modulates the levels of dopamine, a neurotransmitter active in the brain’s pleasure system...

...The study published in the March issue of Nature Medicine found that rats given large doses of both nicotine and THC, the active ingredient in marijuana, for eight days straight would show no signs of addiction or withdrawal when treated with the peptide after their course of the illicit substance ran out...

...The chemicals that wash over a human brain while under the influence of a drug are more complex than those that are active in a rat brain, and the peptide only blocks out serotonin receptors right now. Also, it’s more difficult to inject the peptide directly into a human brain.

(emphasis mine)

Okay, this really looks like a textbook example of popular media jumping the gun, which is something I wouldn't expect from Seed. Let's look at this:

1. A lab has demonstrated a method of pharmacologically manipulating a rat brain in a fashion that seems to block addiction (and it's not clear how at all, from this article, but I'll get into that later). This is actually pretty common in the literature. For instance: I, a lowly undergrad, am currently helping run an experiment in which we are currently using our third manipulation intended to prevent development of addiction. Now, I admit that there's a difference between prenting development, expression, and blocking addictive behaviors--but it's not clear from this which they're doing.

2. The phrasing of the article implies that the modified form of PTEN is taken at the end of a drug course week: "rats given large doses of both nicotine and THC, the active ingredient in marijuana, for eight days straight would show no signs of addiction or withdrawal when treated with the peptide after their course of the illicit substance ran out," although explaining that "the peptide blocks the natural rewards that an addict experiences from an increase in serotonin—a neurotransmitter associated with learning, sleep and mood—when taking his or her substance of choice" makes it sound like it would have to be taken concurrently with drug.

Now, obviously, taking a drug while you're taking cocaine specifically designed to prevent the cocaine from having effects has obvious drawbacks as a prevention paradigm. But it makes a bit more sense, from their explanation, to believe it may need to be administered within a day or two of the last drug use. You see, there's some evidence starting to build for a model of a two-step (at the level of simplification to absurdity) circuit for drug addiction, involving the Ventral Tegmental Area and the Nucleus Accumbens. The basic idea of this model (which is by no means noncontroversial) is that the VTA seems to undergo short-term changes in response to addictive drugs--lasting on the order of a day or two after last drug administration. These changes seem to induce long-term changes in the NAc, which seems to be a long-term site where addiction is maintained. Now, obviously, there's a whole lot more going on than this, but the gist of it is that I would strongly suspect that pharmacological interventions in the VTA needed to be performed within a matter of days after last drug use to have any meaningful impact on addiction. But I'll check out the article, and find out if I'm wrong (seriously, the standard "I'm an undergrad" caveat applies throughout here).

3. At present, the drug has to be injected directly into the brain. I really think that's all that needs to be said. But I can throw in a bit more: there are two possible reasons this may need to be done, and either or both may apply:

  • It can't cross the blood-brain barrier. There are a couple of ways this may be overcome. One is that it's often viable to come up with a less polar version of a drug with basic chemical modifications, that can still be bioactive at the brain's pH. I have no idea how easy this approach is, however, and suspect it can be a bit of a long shot. The other option is my household's favorite: it's also possible to circumvent the BBB via nasal administration. Yes, snorting medications is the way of the future. Unfortunately, I haven't heard of any medications taking this novel approach yet; this may be because it's still relatively new information, or perhaps just because of the obvious difficulties in standardizing doses plus the social stigma. Still, we have high hopes.

  • There is difficulty getting drug to the site of action in appropriate quantities. This is also a definite possibility, and one I have no idea how to approach. They're dealing with a modified enzyme here (which seems a bit odd, and I suspect the article might've gotten that wrong, since the only PTEN I'm aware of is a tumor suppressor gene), and it has to have more sites of activity than just the VTA. So it's quite possible that if you systemically administer enough of the drug to assure activity at the VTA, you could have all sorts of systems going haywire. So in this case, you'd have to administer directly to the VTA to limit the range of effect.

Now, I would like to make clear that I'm not trying to show any disrespect to the work of Dr.s Zhang and Quirion here, I'm just trying to demonstrate how easily a popular science article can take an interesting--but not world-changing--publication and hype the results far beyond what they seem to actually imply. I'll try to find time to look at the journal article later today, and let you know what I think about it itself and what I was wrong about.

Monday, February 27, 2006

Lab Meeting Fun

A nice little quote from our lab meeting this morning:

Patrick--the grad student I'm working with--was talking about the project we've been working on, and said something along the lines of, "If we're right about this, it'll be--well, not quite the Holy Grail. What's the step below that?"

The rest of the lab: "Um..."

Patrick: "You know, not King Tut's tomb, for instance, but some random other thing in Egypt."

Mark (our Professor): "The crown of Hatshepsut?"

Patrick: "Sure, why not."

Sunday, February 26, 2006

In the streets

BBC: Animal lab supporters go on march:

Students, academic staff and members of the public gathered near the lab site, being built under strict security.

Anti-vivisection activists, who believe animal testing "belongs in the past", want to stop the centre opening.

Supporters of the centre argue it is essential for research into treatments for human medical conditions.

Physiology professor John Stein said: "Imagine yourself with a drowsy, whimpering three-year-old with meningitis.

"Fifty years ago, that child would have died. Now, due to the discovery and isolation of penicillin in this university, we can stop that child dying."

That's exactly the argument to make. It's pretty hard to imagine a person in the western world today who doesn't know a single person that would be dead right now were it not for products that were produced by or were tested on animals. And that's the level at which we need to maintain this argument: this isn't a convenience issue, or a comfortability issue; this is a fundamental quality and quantity of life issue. And it should be addressed as such.

Also? As someone who works in a lab and conducts tests with animals, it warms the cockles of my heart to see people marching in support of what I do. Thanks, Pro-Test.

Friday, February 24, 2006

Oh. My. God.

Wow. Thanks to Pharyngula, I've now learned about the stupidest law ever.

I'm going to go shoot myself now.

In the face.

Friday Random 10

Sorry I've been missing all week... I think weeks in the lab are just gonna be like that, given the complete lack of free time.


1. Delerium - Resurrection
2. Ayria - Infiltrating My Way Through The System
3. Meat Beat Manifesto - Dynamite Fresh
4. Coil - The First Five Minutes After Death
5. Coil - Penetralia
6. The Shamen - Space Time
7. Tom Waits - Town With No Cheer
8. Clawfinger - Shine On You Crazy Diamond
9. Underworld - Sola System
10. Louis Armstrong - I Can't Give You Anything But Love

And in other news:
BBC: License rejected for world's first medicine produced by a GM animal.

Tuesday, February 21, 2006

My own $0.02 on this whole UAE/ports thing...

On the one hand, leave it to the right to jump all over the racist card on this game. The Arabic race-baiting I've seen over the last few days is rather getting under my skin.

But on a purely cynical note, I have to point out that this issue is tailor-made for the Dems. Simple party line:

1. Acknowledge that yes, it is incredibly racist the way everyone jumps all over this because it's the UAE--the idea that Arabs should not be allowed equal footing with anyone else in this regard.

2. Also acknowledge that perhaps, if the administration took national security the least bit seriously, it wouldn't be outsourcing it in the first place, much less outsourcing it to entities wholly-owned by foreign nations. Because that's still stretching it.

Monday, February 20, 2006

Sunday Night I Wanna Go To Bed And My Computer Does, Too Linkblogging


Postgenomic aggregates posts from life science blogs and then does useful and interesting things with that data.

It looks interesting; I think it'll be much more so once I start to figure it out (or, perhaps, once THEY start to figure out and tell their audience).

Developing Intelligence explains Ronald Rensink's experiments on sensation awareness vs. conscious perception. Or something.

The Ambien's TOTALLY starting to kick in now.

Totally for my own selfish purposes, some new Neuron articles that are right up my alley:
A New Peptide Input to Learning and Addiction

Orexin A in the VTA Is Critical for the Induction of Synaptic Plasticity and Behavioral Sensitization to Cocaine

Transient and Selective Overexpression of Dopamine D2 Receptors in the Striatum Causes Persistent Abnormalities in Prefrontal Cortex Functioning

LiveScience: Why Men Report More Sex Partners than Women

And other than to say that the NBA All-Star weekend was the best relaxation I've had since school started, that's all she wrote.

Good nite.

Sunday, February 19, 2006

Randy Olson: How to Communicate Science

So Randy Olson, director of Flock of Dodos (warning: loud, potentially annoying), was recently given a guest post by Carl Zimmer so he could present some suggestions on how to present science to the nonscientific public more effectively.

Some have responded well. Several, shall we say, responded a tad more negatively. A common complaint seems to be that they're interpreting Olson's suggestions as being tips on how to dumb down science for laypeople, which they take great humbrage in.

Some of my own thoughts:
--I don't think he's saying we should dumb down science.
--That doesn't mean you don't--pretty much as a rule--HAVE TO dumb down science for laypeople.

I understand. In science--and among intellectual pursuits in general--there's a bit of a stigma against the idea of dumbing things down. But you know what? I'm of the opinion that even in scientific journals, things are too rarely presented in a fashion that's accessible to scientists outside of small subsets of a discipline. I can follow most articles on drug addiction at this point--my current area of expertise--but not necessarilly all, and outside of that I'm often hosed. I admit I'm an undergrad, but I'm a senior who's been studying this for a year and (I hope) a pretty smart guy. I freely admit I'll be able to understand more of this once I'm working on my doctoral, but come on: journal articles should NOT only be accessible to PhD.s working in the field. This is my humble opinion.

But more importantly, when we're presenting information to laypeople, we're not presenting it to fellow scientists. And this is key: he's talking about how to present scientific knowledge to people who aren't even interested in science. To win the battles he's talking about, you have to be able to communicate effectively with people who are already biased against scientists, or at the very least with an English major (no offense to English majors; I was one once, I swear!).

I don't think he's telling us how to present info to college classes; and he's not telling us what each and every scientist should do. He's pointing out what tools we should use to communicate science through the media to the public. And although I don't agree with him 100%, I do think he's generally pointing in the right direction. Look at suggestions like "Quality Control" and "Modernization": these aren't suggestions as to how Professors should be presenting things (although a few I've had could learn from that); these are pointing out that to persuade people about science, we need to present information in a format people will be willing to experience, and present it to them in a style that people will WANT to experience. He's right: some cutting-edge school should have a "Science Electronic Media" program. How to present real science in an engaging format on the web, that will make home browsers that don't have extant interest in science want to come by. How to make television programs that will make non-geeks want to watch them all the time, and learn from them.

Dr. Free-Ride disparagingly presents this quote:

6) Understanding - intellectuals are handicapped as mass communicators. I had this line in my film, but took it out because it sounded too insulting. But its true. Mass audiences do not follow people who think, they follow people who act. Intellectuals are trained to think, not act. Its one of their charming traits, but it's also a handicap. Try taking an acting class and you'll get to know about this intimately. And it's not that you necessarily need to do something about this right now, it's just that you need to start developing some awareness of it.

Okay, first off. When he says, "they follow people who act," he doesn't mean we need Heath Ledger to be presenting science to the public. And maintaining otherwise is either actively deceptive or simply utterly missing the point. He's using act in the sense of "do," and anyone who's taken an acting class knows this: you can't think on stage. You can't just sit still and talk at your audience. Even on broadway, the audience will get bored in a minute if that's all that's going on. Audiences are there to WATCH things. And that's a key point he's getting at: sciencists are scientists because they find science intrinsically interesting. But when you're dealing with someone who's not a scientist, it is not an unsafe presumption that they may--perhaps--find it less interesting than you. Give them a reason to find it interesting, give them some entertainment value, and then they can grow to realize that the science itself is of intrinsic interest.

Dr. Freeride goes on to say:

It may be enough for an actor to get the audience to feel something. However, the scientist usually aims to get the audience to think. Successful scientific communication doesn't just dump a bunch of facts at the audience's feet. Rather, it leads the audience through a thought process -- what could these facts mean, what are the most consistent ways to fit them together, and how are these conclusions more reasonable than the alternatives? Just as artists, novelists, and yes, even the makers of your better films and television programs make the audience do some work, so should scientists and populizers of science. Audience participation (at least in the sense of an audience actively engaging the message rather than having it poured into their skulls) is not an unreasonable thing to ask.

And oddly enough, I think that's exactly what Orton's getting at.

How many scientists got where they are today because they thought dinosaurs were kickass when they were ten years old? A lot, I'd wager. But just because I've already made the leap from Tyrannosaurus Rex to psychomotor models of incentive salience, doesn't mean I assume that anyone I'm talking to is ready to make it in a single step.

Friday, February 17, 2006

Update on Global Warming, or, Crap! We're Screwed!

According to a paper in this week's issue of Science, Greenland's glaciers are flowing melting much faster than predicted by any current global warming models. This is rather bad, for a couple reasons:

1. It indicates that global warming is having a bigger impact faster than anyone had guessed.
2. Apparently, current climate models do not take glacial flow into account. This seems to show us that glacial flow will have a serious impact on sea levels, which worsens the overall outlook.

Combined with the reported today at the annual meeting of AAAS that in the CO2 and methane-rich atmosphere of around 100 million years ago, ocean temperatures in at least one region where 20 degrees Fahrenheit warmer than they are now, potentially as hot as 107 degF--which is also much hotter than expected by current models--I'm almost ready to grow my beard and hair out so I can carry my placard down the street and warn people about the apocalypse.

Let's just get one thing straight: much like evolution, global climate change is pretty much a fact at this point. Like the best science, hypotheses and theories have been put forward and confirmed through experimentation and observation. All that matters at this point is doing what we can to minimize its effects. And maybe, just a little, cut down on our current carbon usage to try not to exacerbate the symptoms. This is quickly turning into a problem that we won't have the option to leave to our children: because we're going to have to deal with it ourselves.

I'd have to admit I'm tempted, too...

Thanks to Neurodudes for pointing out this amazing article from MIT's Technology Review. What's so awesome about it, you ask? Here you go:

Bill Newsome, a neuroscientist at Stanford University in Palo Alto, CA, has spent the last twenty years studying how neurons encode information and how they use it to make decisions about the world. In the 1990s, he and collaborators were able to change the way a monkey responded to its environment by sending electric jolts to certain parts of its brain. The findings gave neuroscientists enormous insight into the inner workings of the brain.

But Newsome is obsessed with a lingering question: How does consciousness arise from brain function? He feels the best way to answer that question is by implanting an electrode into his own brain -- and seeing how the electric current changes his perception of the world.

Now THAT's awesome. Go read the rest.

A Role for Prions in Inheritance?

The most recent issue of Seed (I think) has an article online by Dr. Alain Bussard, titled The Prion Anomaly.

The thesis of this piece is that as we learn more about prions, we are starting to realize that they have endogenous activities. Furthermore, since prions are resistant to degradation, they are heritable and thus can transfer heritable information from one generation to the next. This leads to him predicting an imminent paradigm shift as the evolutionary synthesis is forced to account for the role of prions in inheritance. Or, as he puts it:

More recently, prions were found to have a role in another sacred domain of biology: the transfer of hereditary information in a non-Mendellian fashion from parents to offspring. It was in yeast that researchers first found evidence that prions could alter the expression of enzymes from one cell to another. Far from being pathologic, this form of protein-based information flow was an adaptive mechanism, conferring evolutionary advantages onto recipients. And recently, Susan Lindquist at the Whitehead Institute in Cambridge, MA (who has been working on prions with her group since 1993) has found a notable example: a molecular chaperone, the prion Hsp90, that strengthens the hereditary evolution of drug resistance in diverse fungi. But it is the evidence that prions play an important role in the formation and maintenance of long-term memory—discovered by Eric Kandel at Columbia University in New York—that seems to me of greatest importance.

Scientific revolutions concern the replacement of an old paradigm by a new, incommensurable one. However, the conflict of paradigms often does not end with the death of the old one. Rather, the new theory is incorporated into the older framework so as to make it more universal. Physicists have become quite used to this and have been quick to adapt their common views to new theories. But I wonder if we are not, today, in a new epistemological situation in which two apparently incompatible paradigms can exist simultaneously: in this case, the classical (molecular biology) paradigm and the prion paradigm. After all, is it not the case in physics that Albert Einstein attempted for 40 years to reconcile the relativity and quantum paradigms, with no success?

Now, I think this is an incredibly cool idea if only because I like to see people stir things up. Furthermore, as Dr. Bussard is a Professor at the Department of Cellular Immunology at the Pasteur Institute, it seems probably that he knows more than me. Nonetheless, I think he's jumping the gun a bit.

First off, here's the article about prions in yeast (Nature: subscription required) that I think he's referring to, Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. And here's the article I assume he's referring to about Hsp90 (Science: subscription required), Hsp90 Potentiates the Rapid Evolution of New Traits: Drug Resistance in Diverse Fungi. I'm really just linking to these so you can make up your own mind.

Next, I should point out I'm way out of my area of expertise here. But nonetheless: this is not the first epigenetic phenomena we've encountered. As an example off the top of my head, cellular organelles (such as the endoplasmic reticulum or the mitochondria, to use two contrasting examples) must be reproduced independently during cell division. In the case of the mitochondria, it has its own genetic information that must be duplicated. In the case of the ER, it's required for protein synthesis; if the daughter cells had no ER, how would they build a new one? So although inheritable prions that play a role in heritability is an intensely interesting idea, it's not quite as novel as he makes it sound.

Also, Hsp90 is not a prion. It's a molecular chaperone, albeit one that they claim in the article from the Lindquist lab is acting in a prion-like fashion. But exactly what that fashion is, is far from clear.

And although I find the work by Eric Kandel (who's certainly not the Nobel Prize winner I would choose to mess around with) suggesting prion involvement in formation of long-term memory fascinating, it doesn't yet seem at the point that we know where this is going for sure. But, I must admit I'm less familiar with it than I could be.

But ultimately, my argument is this. Referring to the current paradigm as the "classical (molecular biology) paradigm," sort of makes my point for me. The current paradigm already has room in it for protein, and I see no reason why it can't make more. One demonstration of yeast prions, another of a heat shock protein, and an involvement of prions in memory does not convince me that in five years we'll be in the middle of a revolution demonstrating the ubiquitous involvement of prions in all things inherited. It's possible that this could occur, but it seems to me that we're just continuing to find out that things are a little more complicated than we might have thought a decade ago. Which I firmly place in the category of "science as usual."

EDIT: No sooner do I get this up than I discover Seed has just posted a much more interesting article about prions, including a potential role in early neuronal differentiation. Nothing revolutionary (aside from continuing evidence that prions have an endogenous role in animals), but interesting nonetheless.

The Richard Cohen Bandwagon

Everybody else is already talking about this Richard Cohen column for The Washington Post. Aye, I verily expect the blogosphere to soon split in half and erupt in civil war over the topic. Much like last week.

Now, more thoughtful people than I are going to be dissecting this poor man to pieces for his crimes against lower mathematics. So here's my two cents: being completely unfamiliar with Mr. Cohen's ouevre, has he really managed to be an opinion columnist for an extended period of time without having any grasp of basic algebra or even percentages? I mean, doesn't that sort of limit what kinds of topics you can talk about? Or does he not let his lack of comprehension hold him back from going on at length about topics--like, say, the economy--where a basic ability to read a graph in a useful fashion (which is certainly algebra) is fairly necessary?

And is this indicative of the general state of journalism? That's got me sort of curious. Because I'm fully aware of the stereotype of English-major-who-just-wants-to-avoid-math, but I've never been sure it really existed because I don't see it much in the real world. But it could possibly explain a lot of bad reporting out there, if it turned out that journalism was some sort of refuge for those who are bad at math but still want to inflict their opinions on the rest of the populace.

Wednesday, February 15, 2006

How To Teach Science: Linkblogging

Time Magazine: Looking for a Lab-Coat Idol:

A teacher must feel confident in the subject to veer from the rote learning that turns so many students off. At Frick Middle School in Oakland, Calif., science teacher Caleb Cheung turned seventh-graders into inquisitive crime-scene investigators when he introduced a unit last fall on cells and microscopes. Students arrived in class to find an empty birdcage and a ransom note--someone had apparently kidnapped Cheung's pet doves, Herbert and Angel. For the next six weeks, the young detectives analyzed fingerprints, interviewed witnesses and compared hair and fabric samples under microscopes to find the perpetrator.

(Via Aetiology)

Zygote Games: Where Fun Begins!

BONE WARS: The Game of Ruthless Paleontology

Out in the field, fossil hunters must survive natural disasters and attempts by other players to steal and destroy dinosaur bones.

Back at the museum, the conflict continues when the scientists carry their battle to the newspapers and scientific journals as they race to achieve scientific immortality!

(Via the next link)

Carl Zimmer: Movie Night

I talked about how my own experience as a science writer certainly meshed with some of Olson's own experiences. I can remember getting into discussions with biologists five or six years ago about the rise of intelligent design, and they would just give me blank stares. When I explained what was happening beyond their lab, most of them seemed to assume that I could only be talking about ten or eleven people very far away. Once intelligent design began popping up in newspapers and magazines and education standards, the biologists did perk up and take notice. But their responses were not quite up to the challenge. I recounted how a bunch of representatives from a lot of scientific societies gathered for a meeting on challenges to evolution and came away a clarion call to action: each society would post a statement in support of evolution on their society's web site. Other biologists didn't even think it was their place to get involved. If not them, I wondered, who?

WorldChanging: Biology Direct:

The growing acceptance of the "open access" scientific publishing model has made possible further experiments in the world of academic literatures. Open access publication makes scientific work available at no cost, in order to further the spread of knowledge and ideas among communities -- such as scientists in the developing world -- often locked out of cutting-edge science due to limited resources. The non-profit Public Library of Science (PLoS) journals are perhaps the best-known open access effort, but now BioMed Central -- which had sought to combine open access with commercial publication -- has embarked on an arguably even more radical experiment. Biology Direct, a newly-launched series of biology journals, combines the open access model with a new, and very open, system of peer review (PDF): the reviews are published alongside the articles, with no anonymity -- and no rejection, even if the reviews are uniformly negative. (The author may choose to pull his or her article in such a case, of course.)

Tuesday, February 14, 2006

Quirks & Quarks on Brains Both Bat & Human

I'm an unabashed fan of the CBC show Quirks and Quarks, although I often don't have the time to set aside to listen to it each week. But when I have a particularly long night ahead of me at the lab, I'll often find an interesting recent episode to listen to while I'm cleaning up. Tonight I discovered that I'd somehow missed this great episode over break.

The pieces:

--Dr. Kathleen Martin Ginis of McMaster University explains how exercise impacts body image in both men & women.

--Dr. Jack Rink, also of McMaster University, talks about giant apes.

--Dr. Scott Pitnick of Syracuse University talks about the inverse relationship in the size of bat brains and bat testicles.

--And finally, Dr. Brenda Milner talks about her groundbreaking research demonstrating the existence of separate neural pathways for motor learning and conscious memory.

Every single one is awesome. You should definitely check it out if you have time.

Maybe I'd remember my reading better if I read it backwards...

New Scientist: Play it again, brain, but in reverse:

While the rats ran and then paused after reaching the food, the neurobiologists directly measured the animals’ brain cell activity using carefully placed electrodes. They focused on the hippocampus, a region of the brain believed to handle learning and memory.

The recordings revealed that, as the rats ran along each track, the cells in their hippocampus would fire in a particular sequence. But when the animals stopped for food at end of the new track, the same cells would also fire in the opposite order. This reverse-replay did not occur as often when they rested on either end of the familiar track.

The researchers suggest that the reverse signalling etches information into the brains of the rats as part of the learning process.

Sunday, February 12, 2006

Happy Birthday...

We here at Neurophile would like to wish a Happy 197th Birthday to Mr. Charles Darwin:

Charles Darwin could totally take you.

We would also, in the spirit of celebration, like to present you with a chapter from his best known work, On the origin of species by means of natural selection, from Chapter VI, pp. 186-190 of the 1st Edition. This selection is a well-known one, on one of our favorite sensory organs: the eye.


He who believes in separate and innumerable acts of creation will say, that in these cases it has pleased the Creator to cause a being of one type to take the place of one of another type; but this seems to me only restating the fact in dignified language. He who believes in the struggle for existence and in the principle of natural selection, will acknowledge that every organic being is constantly endeavouring to increase in numbers; and that if any one being vary ever so little, either in habits or structure, and thus gain an advantage over some other inhabitant of the country, it will seize on the place of that inhabitant, however different it may be from its own place. Hence it will cause him no surprise that there should be geese and frigate-birds with webbed feet, either living on the dry land or most rarely alighting on the water; that there should be long-toed corncrakes living in meadows instead of in swamps; that there should be woodpeckers where not a tree grows; that there should be diving thrushes, and petrels with the habits of auks.

Organs of extreme perfection and complication.—To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated; but I may remark that several facts make me suspect that any sensitive nerve may be rendered sensitive to light, and likewise to those coarser vibrations of the air which produce sound.

In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition. Amongst existing Vertebrata, we find but a small amount of gradation in the structure of the eye, and from fossil species we can learn nothing on this head. In this great class we should probably have to descend far beneath the lowest known fossiliferous stratum to discover the earlier stages, by which the eye has been perfected.

In the Articulata we can commence a series with an optic nerve merely coated with pigment, and without any other mechanism; and from this low stage, numerous gradations of structure, branching off in two fundamentally different lines, can be shown to exist, until we reach a moderately high stage of perfection. In certain crustaceans, for instance, there is a double cornea, the inner one divided into facets, within each of which there is a lens-shaped swelling. In other crustaceans the transparent cones which are coated by pigment, and which properly act only by excluding lateral pencils of light, are convex at their upper ends and must act by convergence; and at their lower ends there seems to be an imperfect vitreous substance. With these facts, here far too briefly and imperfectly given, which show that there is much graduated diversity in the eyes of living crustaceans, and bearing in mind how small the number of living animals is in proportion to those which have become extinct, I can see no very great difficulty (not more than in the case of many other structures) in believing that natural selection has converted the simple apparatus of an optic nerve merely coated with pigment and invested by transparent membrane, into an optical instrument as perfect as is possessed by any member of the great Articulate class.

He who will go thus far, if he find on finishing this treatise that large bodies of facts, otherwise inexplicable, can be explained by the theory of descent, ought not to hesitate to go further, and to admit that a structure even as perfect as the eye of an eagle might be formed by natural selection, although in this case he does not know any of the transitional grades. His reason ought to conquer his imagination; though I have felt the difficulty far too keenly to be surprised at any degree of hesitation in extending the principle of natural selection to such startling lengths.

It is scarcely possible to avoid comparing the eye to a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we naturally infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrument, we ought in imagination to take a thick layer of transparent tissue, with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. Further we must suppose that there is a power always intently watching each slight accidental alteration in the transparent layers; and carefully selecting each alteration which, under varied circumstances, may in any way, or in any degree, tend to produce a distincter image. We must suppose each new state of the instrument to be multiplied by the million; and each to be preserved till a better be produced, and then the old ones to be destroyed. In living bodies, variation will cause the slight alterations, generation will multiply them almost infinitely, and natural selection will pick out with unerring skill each improvement. Let this process go on for millions on millions of years; and during each year on millions of individuals of many kinds; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction. Or again, if we look to an organ common to all the members of a large class, for in this latter case the organ must have been first formed at an extremely remote period, since which all the many members of the class have been developed; and in order to discover the early transitional grades through which the organ has passed, we should have to look to very ancient ancestral forms, long since become extinct.

Saturday, February 11, 2006

Tom Bethell vs. People Who Know What They're Talking About Redux

So you remember this post? So you may have wondered--as I did--how one could argue that there's no AIDS epidemic in Africa. So Aetiology has tackled that very question, and it turns out that the answer is simple:

If you're just willing to make stuff up to support your argument while ignoring the real world, you can once again prove whatever you feel like proving. She also points out that Mr. Bethell once sat on the Board of Directors of the Group for the Scientific Reappraisal of the HIV-AIDS Hypothesis. Yes, that's right, he's an HIV-denier. Who is being strongly promoted by the right, being featured on the front page of Fox News' science section. Sort of makes it hard not to suspect where their sympathies lie, isn't it?

Cognitive Dissonance, Vagina-Style

I'm not sure which part of this article is weirder for me:

--That The Vagina Monologues still manages to be controversial in this day and age. I acknowledge that I consciously realize that there are many people in this country who are uncomfortable with frank discussions of sex, not to mention everything else that gets discussed in the show. But to describe such a thing as somehow being inherently anti-Catholic? Especially in the context of a university, especially one as big as Notre Dame? Besides, if The Vagina Monologues is the negative of Catholicism, does that mean these people want us to associate Roman Catholicism with violence against women or something? Or just that the Church is anti-Vagina? I'm not just being hyperbolic and demagogic, I'm seriously curious here. It's just sort of surreal to me.

--That someone can write an AP article on such a topic, and even explicitly mention that the show is generally performed around Valentine's Day and not even mention the context of V Day seems pretty sloppy. Either Mr. Coyne didn't bother to do his research AT ALL, there's a strong bias at work here, or both. Could, I suppose, answer some questions from the first bizarreness.

Who knows?

Friday, February 10, 2006

Random Thought of the Day (Profitable)

So I'm grabbing some glorious caffeine at the corner store, and it occurs to me: how is it that no one has released an energy drink called Gibb's Free Energy? I mean, come on: your brand, your logo, and your marketing are all pretty much taken care of in advance, so all that's really left is to run some taste tests and sit back and collect profit. I'll take London, you take New York, and then we'll hit the Cayman Islands once a year to visit our MONEY.

Friday Random 10

You can tell when I've left my computer on for a few days, because loading up my entire TV collection and then randomizing it makes my computer wanna kill.

1. Cargo Cult - Rain
2. Hide - Flame
3. Birmingham 6 - One of These Days (Unashamed)
4. Safri Duo - Baya Baya (Spanish Fly Mix)
5. Funkstar Deluxe vs. Laid Back - White Horse
6. Laibach - Das Spiel Ist Aus
7. Front Line Assembly - Deception
8. Scooter - Hysteria
9. NWH - Granny Says Kick Yo Black Ass
10. Pigface - Closer to Heaven (Muzz McCoy Remix)

Thursday, February 09, 2006


Posting's been way too sparse this week. Sorry.

My first wave of midterms is all next week, so I've been rushing to actually get caught up so I'll be able to study this weekend and first half of next week.

Soon... mad posting. Maybe.

In the meanwhile? Scientists Find 'Lost World' in Indonesia:

Describing a "Lost World" — apparently never visited by humans — members of the team said Tuesday they also saw large mammals that have been hunted to near-extinction elsewhere and discovered dozens of exotic new species of frogs, butterflies and palms.

"We've only scratched the surface," said Bruce Beehler, a co-leader of the monthlong trip to the Foja Mountains, an area in the eastern province of Papua with roughly 2 million acres of pristine tropical forest.

Tuesday, February 07, 2006

How to go to Grad School

For someone who's destined to be worrying about much of this in the immediate future (and for the following decade), I must thank Inside Higher Ed for the piece, What They Don't Teach You In Grad School.

(Thanks also to Evolgen)

Sunday, February 05, 2006

REALLY random musing

I think just walking up to someone and being able to say off the top of my head that I'm working with alpha-amino-3-hydroxy-5-methylsoxazole-4-propionic acid or N-methyl-D-aspartate glutamate receptors would be pretty cool.

Random musings on experimental design

These thoughts are inspired by going over this article from Peter W Kalivas' lab (Neuropsychopharmacology, sub. appears to not be required) in preparation for my lab meeting tomorrow. However, this should not be considered a critique of the article or the persons involved--it may not, in fact, apply to this paper at all--they just happened to be the people who inspired these ruminations. This post gets prefaced by pointing out that I have not studied experimental design or the philosophy underlying said in any big fashion, and that my approach to both is probably fairly simple at best. Nevertheless...

As I understand it, the predominant paradigm in modern science is Popper's idea of falsifiability. There are two key aspects of this idea for this discussion (very simply put):

1. A scientific theory is defined as being one which is potentially falsifiable. That is to say, a theory is scientific if it can potentially be proven wrong in a reasonable fashion. Therefore, a model can be accepted by the scientific community to the extent of A: its explanatory power and B: its potential for falsification.

2. The ideal method--under this paradigm--with which to test a hypothesis is to prepare an experiment designed to prove a hypopthesis false. Thus, if you fail to falsify your hypothesis when testing it at its theoretical breaking point, you have more rigorously demonstrated that it has a high probability of truth (note that this does not make the hypothesis true: just that it is more likely to be true than if it was successfully falsified, or even if it had been tested under less rigorous circumstances).

Now, I cannot speak for non-neuroscience disciplines, because my knowledge of how they are studied in the modern era is relatively limited. But it seems from my experience of studying neuroscience and reading neuroscience papers that this approach, although not abandoned, is weak to a certain extent. Instead, the common phrase one hears is "one should put one's best foot forward." And although there is a strong fixation on making sure one does not try to muddy the waters by putting forward data which might be bad, there is also a strong emphasis on making sure one gets usable, publishable results.

I can think of a few reasons underlying this. For instance, one problem is that we're dealing with one of the most complex aspects of biological systems, which are inherently more complex than nonbiological systems (or so I would argue). Thus, an experimental design intended to falsify a hypothesis could easily succeed in falsification for the wrong reasons--for example, an attempt to make an experiment more rigorous by examining a structure a further step removed from the activity you're studying could result in falsification because a slightly alternate pathway is involved, or because the understanding of the connections between these two structures is just slightly flawed, or because a drug one is experimenting with is processed differently in one region than another. And, you begin to see, you quickly end up with results that falsify a hypothesis: but which hypothesis?

Another problem is the publish-or-perish model currently dominating the field, both in terms of funding, and in terms of careers. A successful falsification of a hypothesis that doesn't dominate a field is inherently less sexy than putting forward evidence supporting such a hypothesis. Anyone, after all, could come up with something wrong and demonstrate that it's wrong. The trick is coming up with something that's right. Similarly, the model leads to a rush to publication, which means you want to have the best data demonstrating the viability of a hypothesis as quickly as possible.

There's a lot more involved than this. And one should not take this as a claim that neuroscience, or biological science, or even science is inherently flawed and can't potentially be used as a tool for discovering knowledge about the universe. I wouldn't be here right now, and I wouldn't be writing this right now, if it was the case. It's as much an interesting piece of gristle that I'm chewing on right now as anything else.



Sorry blogspot's been down so much lately, thus preventing you from reading posts and me from writing them. I'd do something about it, but... ah... I can't. C'est la vie.

Friday, February 03, 2006


#1. Carl Zimmer continues to try to convince me to study neurally-acting parasites in grad school:

The wasp slips her stinger through the roach's exoskeleton and directly into its brain. She apparently use ssensors along the sides of the stinger to guide it through the brain, a bit like a surgeon snaking his way to an appendix with a laparoscope. She continues to probe the roach's brain until she reaches one particular spot that appears to control the escape reflex. She injects a second venom that influences these neurons in such a way that the escape reflex disappears.

From the outside, the effect is surreal. The wasp does not paralyze the cockroach. In fact, the roach is able to lift up its front legs again and walk. But now it cannot move of its own accord. The wasp takes hold of one of the roach's antennae and leads it--in the words of Israeli scientists who study Ampulex--like a dog on a leash.

Seriously, what more do you need to know?

#2. Dave Munger tells us about the measured differences in implicit and explicit racial biases. Check it out.

#3. Cutting-edge research in perception from the University of Chicago:

Scholars have long debated whether our native language affects how we perceive reality — and whether speakers of different languages might therefore see the world differently. The idea that language affects perception is controversial, and results have conflicted. A paper published this month in the Proceedings of the National Academy of Sciences supports the idea — but with a twist. The paper suggests that language affects perception in the right half of the visual field, but much less, if at all, in the left half.

Science For The Masses

I would like to give a hearty recommendation to read Chris Mooney's new Seed column, and I supposed I pretty much just did.

It relates to his book, The Republican War on Science, and is an attempt to answer the question: well, yeah, but what can we do about it? An attempt to answer what scientists and everyday citizens can do to reverse the antiscientific trends in power in this country. And that's a good question, and an important one.

Unfortunately, after three pages, it seems like his main answer is still, "scientists should hire PR firms." Admittedly, this is a bit reductionist, since he does make a very good point about the empirical nature of modern cognitive linguistics. And, to a certain extent, he's definitely right, and that's something that should happen. But that doesn't help me. There isn't much of an answer in there as to what I myself could do.

So I'm hoping to work on a list of what scientists can do to save science. If you can think of anything, let me know.

Thursday, February 02, 2006

Last SotU post. I promise.

Thanks again to Washington Monthly for pointing out this choice quote:

"I believe in a relatively quick period of time, within my lifetime, we'll be able to reduce if not end dependence on Middle Eastern oil by this new technology" of converting corn, wood, grasses and other products into ethanol, he said.

Mr. Drum points to it being a bouncing ball of responses to the issue. He's a bit more forgiving than I; I'm skeptical enough to suspect that the President is saying one thing while his handlers say another.

Also? On the scale in which we're concerned about global warming, at the very least--and also the scale on which we're worried about oil supplies--he really seems to be saying that we'll be able to reduce or end dependence on Middle Eastern oil at around the time we have no choice in the matter. A tip of the hat to Captain Obvious.

Manduca sexta nervous system, part five.

Manduca sexta nervous system, part five.
Originally uploaded by Mal Cubed.

Today's a Thursday, so you probably won't be seeing me again today.

As a special present for being such good guests, you get a picture of an abdominal ganglion from Manduca sexta, the sphinx moth. Although it was a caterpillar at the time.

Are the President's pants... On Fire?

Thanks to Knight Ridder's Kevin J. Hall:

WASHINGTON - One day after President Bush vowed to reduce America's dependence on Middle East oil by cutting imports from there 75 percent by 2025, his energy secretary and national economic adviser said Wednesday that the president didn't mean it literally.

What the president meant, they said in a conference call with reporters, was that alternative fuels could displace an amount of oil imports equivalent to most of what America is expected to import from the Middle East in 2025.

But America still would import oil from the Middle East, because that's where the greatest oil supplies are.

But you're saying to yourself, "Hey! He seemed pretty specific about that, didn't he? I can't recall exactly how that went..." To which I respond, it went a little like this:

We must also change how we power our automobiles. We will increase our research in better batteries for hybrid and electric cars, and in pollution-free cars that run on hydrogen. We'll also fund additional research in cutting-edge methods of producing ethanol, not just from corn, but from wood chips and stalks, or switch grass. Our goal is to make this new kind of ethanol practical and competitive within six years. (Applause.)

Breakthroughs on this and other new technologies will help us reach another great goal: to replace more than 75 percent of our oil imports from the Middle East by 2025. (Applause.) By applying the talent and technology of America, this country can dramatically improve our environment, move beyond a petroleum-based economy, and make our dependence on Middle Eastern oil a thing of the past. (Applause.)

And yet, when asked about it by reporters:

"This was purely an example," Energy Secretary Samuel Bodman said.

Hrrmmm... I'm starting to sense a familiar pattern of deception coming from the White House... but it's not quite gregarious enough yet. It needs something that isn't quite a lie, something that's just a sort of half-truth that they can claim they're being criticized about when they're criticized about the lie...

Through the first 11 months of 2005, the United States imported nearly 2.2 million barrels per day of oil from the Middle East nations of Saudi Arabia, Kuwait and Iraq. That's less than 20 percent of the total U.S. daily imports of 10.062 million barrels.

That'll do.

So, to recap:
A: The President announced in the SOTU the intent to replace more than 75% of our imports on oil from the Middle East by 2025.

B: The Middle East is responsible for less than 20% of our imported oil. Since we import ~60% of our oil, off-the-cuff math implies that we import 12% of our total oil consumed from the Middle East.

C: And yet, apparently he was lying--let's call a spade a spade, shan't we? And further off-the-cuff math tells us that if he's only referring to reducing our oil consumption by that much, he boldly intends to cut down our oil consumption by ~9% over the next 20 years. Although I will admit I would be impressed if he could even manage to keep it even over the next two.

D: Yes, I realize we're treading on a bit thin ice here in reference to our forte, with three consecutive posts about the SotU. Sorry, but I'm a politics junkie--and I'll officially claim that this matters since it indicates how far he intends to take his initiatives on research funding. Which is apparently not very.

(via Washington Monthly)

Wednesday, February 01, 2006

Further thoughts on the SotU...

So two of the big domestic policy announcements last nite were a dedication to research for alternative fuels, and some proposals to increase funding for scientific research.

A series of responses:

A: This isn't the first time he's proposed alternative fuel funding, is it? I'm pretty sure I recall an SotU from, oh, a few years back where he dedicated himself to promoting hydrogen fuel cell cars... haven't seen a lot of work on that, have we? And as has been pointed out elsewhere (too lazy to look up the link), he's mentioned reducing depending on foreign oil in every State of the Union to date, with no headway.

B: I understand the importance of funding research into alternative fuels, and in fact applaud it. But there's a lot of stuff already out there. Couldn't we get a bit of funding for implementation? Greater encouraging of hybrid electric cars, tax credits for home solar panels, that sort of stuff could go a long way. Not that any of that is in the spoken interests of the oil companies and power companies he's beholden to...

C: If Bush is seriously trying to reshape himself as the Science President, I would have to hope it goes better than his attempts to become the Education President, the Balanced Budget President, the Wartime President, or even the No-Dependency-on-Foreign-Oil President. As a research scientist, I'm sort of worried at his decision to help out our field. Based on administrative incompetence to date, I fear he could run us into the ground.


Yahoo: Women Sue Wal-Mart Over Contraception:

BOSTON - Backed by abortion rights groups, three Massachusetts women sued Wal-Mart on Wednesday, accusing the retail giant of violating a state regulation by failing to stock emergency contraception pills in its pharmacies...

...The plaintiffs argued that state policy requires pharmacies to provide all "commonly prescribed medicines."

It's stupid to have to do it this way, but if it's the only way to make sure people can get access to emergency contraception, then it has to be done.

Remember: the groups that are opposing the morning-after pill are by and large the same people opposed to ANY contraception at all. This is not an issue on which a single inch of ground should be given.

You have GOT to be kidding me.

I am having a hard time not using strong words right now.

Apparently, during the State of the Union address last nite, our President spent awhile advocating increased funding of research, and then announced his intent to ban a common research technique for studying human genetic diseases:

A hopeful society has institutions of science and medicine that do not cut ethical corners, and that recognize the matchless value of every life. Tonight I ask you to pass legislation to prohibit the most egregious abuses of medical research: human cloning in all its forms, creating or implanting embryos for experiments, creating human-animal hybrids, and buying, selling, or patenting human embryos. Human life is a gift from our Creator -- and that gift should never be discarded, devalued or put up for sale.

As Dr. Myers appropriately points out, human chimeras are an important tool used to study a number of human diseases. He uses the notable example of Down's Syndrome, but this is a technique that potentially applies to any number--possibly the majority--of diseases that are genetic in origin. Consider Huntington's, Parkinson's, or even sickle cell anemia (I should preface my ignorance here as to the actual utility of chimeric models for these specific diseases, they're examples culled from the top of my head).

A common problem in animal models of disease is that since animals aren't human, we have to manipulate the system in such a fashion as to produce a disease that has the same end result. Consider MPTP, for example, commonly used to create animal models of Parkinsonism. Yes, it helps us look for treatments for advanced cases of Parkinson's. But it's not very useful as a preventative approach, and is useless for searching for genetic therapeutic techniques. Wouldn't it be nice to be able to give a mouse a slip of human DNA that meant it literally had the same problem?

I understand that there are common ethical questions with animal testing. But this is not the argument he seems to be making: he's arguing that there is something inherently sancrosanct about humans that makes it inherently immoral to insert a human gene into an animal. I don't even think he's arguing that, though: I'm not sure he has that level of understanding of the issue. Regardless, this is a present to the religious right and a punitive attack on anyone who's lineage carries a potential genetic disease. Which is to say, all of humanity.

I would also like to point out that I'm giving President Bush the benefit of the doubt here, and desperately hope that by banning "human cloning," he doesn't mean banning the culturing of human tissues (such as skin cultures for burn victims), PCR (a cloning technique utilized ubiquitously, a reasonable example at present being its use in examining DNA from crime scenes), gene therapy, or a host of other common applications. But again, I must say I lack confidence in his ability (or even that of any of his advisors) to actually have any knowledge of these distinctions; or that all of these tasks fall under the heading of "human cloning."

I do assume, however, that he intends to ban cloning human embryos for creation of stem cell lines. Oh, wait, he already did.

Totally time to let the computer take a nap, so I leave you with these final two links:

The Scientist: Is This Life?

Seed: Seeing Things

Everyone else has done it, why can't we?

Well worth reading: Michael Berube's presentation on academic freedom.


Is it just me or is this potentially revolutionary?

Researchers from the Mayo Clinic, Toronto, and Baltimore report today that infant heart transplant patients can fight off infections despite having a T-cell count comparable to full-blown AIDS patients.

Let me rephrase that: in these patients, who are receiving treatments that demolish their ability to produce T cells, an alternate--and unknown--immune pathway seems to be acting. But I'll let the abstract say it:

For cardiac transplantation in infants, T cells are depleted and the thymus is removed. These manipulations should cause profound defects in the T cell compartment. To test this concept, 20 subjects who underwent cardiac transplantation in infancy and healthy age-matched subjects were studied. The number of T cells in the blood was nearly normal in all subjects 1–10 years after surgery. However, newly generated T cells were undetectable in 10 recipients and 10-fold less than controls in 10, suggesting absence of thymic function. TCRbeta chain diversity, measured by a novel technique, was ~100-fold lower than controls. T cell function, deduced from levels of human herpesvirus 7 and response to hepatitis B immunization, were notably impaired. Yet cardiac transplant recipients were generally free of opportunistic infections. Our findings demonstrate a novel approach to measuring lymphocyte diversity and suggest that understanding how these subjects resist infection could yield important insights into immune fitness.

Now, I am not an immunologist, so this could just be one of those scenarios where I'm being overly impressed by something from another discipline. But doesn't this just sound interesting? I mean, all we really know is that we have patients who can resist infections that they should be physically incapable of resisting. If we can figure out what's acting to replace the missing T cells, there's a pretty widespread potential of immune disorders that are potentially treatable here.

(via EurekAlert)

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