Friday, March 31, 2006

"It's like a religion, only they actually know it's not real." - Alan

Alan's right. I can't believe I've never heard of before:

Aristasia is a largely imaginary all-female society existing primarily in England, but with adherents in other parts of the world, notably the United States. Also known as the Feminine Empire, it's partly a "micronation," partly a role-playing game related to separatist feminism...

...The word Aristasia refers to two different things:

* Aristasia Pura is a fictional world in which men do not exist. Instead, there are two feminine sexes, blonde and brunette (with hair colour being a secondary sex characteristic).
* Aristasia-in-Telluria is an attempt to create Aristasia in "Telluria" (the real world); that is, an all-feminine counter-culture in response to the perceived death of mainstream Tellurian (Earth) culture.

Damn... is that hot or what?

Wednesday, March 29, 2006

Computer Imminent Reboot Tabs Closing Link Dump

You want it, you need it: DANGER! DANGER!

Crooked Timber: Chris Mooney Seminar

Gene Expression: George W. Bush, Randian superman?

Rockstars' Ramblings: Jack Chick Remixed

The Loom: Mad Cow Memories

News Blaster Nature Archive: Prion proteins may store memories

Eric R. Kandel - Nobel Lecture

Cosmic Variance: Unsolicited advice, 1: How to get into graduate school & Unsolicited advice, Part Deux: Choosing a grad school

I am now less vexed.

Thanks to the endless march of scientific innovation:

A DEVICE that can pick up on people's emotions is being developed to help people with autism relate to those around them. It will alert its autistic user if the person they are talking to starts showing signs of getting bored or annoyed...

The "emotional social intelligence prosthetic" device, which El Kaliouby is constructing along with MIT colleagues Rosalind Picard and Alea Teeters, consists of a camera small enough to be pinned to the side of a pair of glasses, connected to a hand-held computer running image recognition software plus software that can read the emotions these images show. If the wearer seems to be failing to engage his or her listener, the software makes the hand-held computer vibrate.

In 2004 El Kaliouby demonstrated that her software, developed with Peter Robinson at the University of Cambridge, could detect whether someone is agreeing, disagreeing, concentrating, thinking, unsure or interested, just from a few seconds of video footage. Previous computer programs have only detected the six more basic emotional states of happiness, sadness, anger, fear, surprise and disgust. El Kaliouby's complex states are more useful because they come up more frequently in conversation, but are also harder to detect, because they are conveyed in a sequence of movements rather than a single expression.

I'm waiting for this to become an OTC prosthetic a few years down the line... I have a few friends that this would make a great present for.

Although I'm sure a number of people are desperate to give one to me.

(thanks to Boing Boing)

This vexes me. I am vexed.

Thanks to the MN Daily, I got up this morning to discover the existence of House Bill HF2798: "English pronunciation policy required as a condition of instructing students at public postsecondary institutions."

Ultimately, the bill requires Minnesota state colleges and universities (I'm interpreting this as "those funded by the state," because at some point I lost all ability to usefully interpret statutes) to "adopt a clear, understandable written policy" that must at least fulfill the following requirements:

(b) Before employing or assigning an individual to instruct undergraduate students, the chair of the department in which the individual would be employed or assigned must conduct an oral interview with the individual and document that the individual speaks English clearly and with good pronunciation.
(c) If a student notifies in writing the chair of the department and the dean of students of the public postsecondary institution the student is attending that the student believes that an individual employed or assigned to instruct a class in which the student is enrolled, does not speak English clearly and with good pronunciation the postsecondary institution, upon request of the student, must reimburse the student for all tuition and fees paid for the class and permit the student to withdraw from the class without financial or academic penalty.
(d) When the dean of students of any public postsecondary institution receives notices under paragraph (c), from students equal in number to ten percent of those enrolled in a class on the tenth academic day, the individual must be reassigned to a nonteaching position and may not be permitted to instruct students until a hearing before a panel is held and determines that the individual can speak English clearly and with good pronunciation.

Now, at this point, I really wish I had a lawyer handy (by which I mean, I wasn't too lazy to call my friend who's in law school), because the statute doesn't seem to have any sort of actionable penalty. I assume, however, that this sort of bill is just attached to budgeting regulations in some fashion.

But anyways, this seems to me like a horrible idea. So horrible, in fact, that I've even called my state senator and my state representative and told them so.

Why does this seem like a bad idea?

First off, let's address the fashions in which might incline me towards it. I can understand the frustration students sometimes feel. At Macalester, I encountered a few professors whose command of English was less than perfect. However, I only had one I can recall at the moment whose command seemed poor enough to me to interfere with my ability to learn from them. And she was a foreign language teacher, a category where I think that English pronunciation is less important. But that's neither here nor there: Macalester is a college that emphasizes itself on the international experience--both in students and the faculty--and more importantly, will not be affected by this law.

So what about the U of M? Well, I realize that anecdote is not the singular form of data, but I haven't really had any problems with professors at the U. I've had a number of problems with TAs, and I do think that the U needs to develop a better policy for dealing with that area, but I would never suggest that a law like this be implemented in that regard.

But why does this really frustrate me?

First off: regardless of what the author of the bill may claim, there is definitely not an epidemic of public university instructors whose command of English is so poor as to prevent students from learning. I would argue that if such were the case, I probably would've interacted with at least one in the last four years. At the very least, perhaps a legislator from a district that actually contains a public college or university might have put such a bill forward. I've had a few whose English was certainly less than perfect, but none so bad as to require legislation.

And that's another reason this bothers me: even if this were (or is) a serious problem, I'm inherently uncomfortable with the government legislating who can and can't teach a class. If the legislature really needs to deal with this, adopt a nonbinding resolution. Let the schools deal with this in their own fashion: it's in their own best interest to provide the best experience possible to students. Do we really want colleges to be so afraid of the least common denominator that they must only hire professors who can be understood by the least attentive 10% of the class? Do we really want professors who speak English as a second language to be constantly paranoid that at any time, a few students might decide to complain about their English skills and thus force the professor out of a teaching position?

That's the other big problem with this bill for me: it seems rife for abuse. If this bill is passed into law, any student failing a class taught by a foreign-born professor can just complain that they can't understand it and get a free pass out of the class, plus a full refund of their full tuition and fees for the class. At any time.

American schools are dealing with enough problems getting top-tier grad students, postdocs, and professors from abroad due to the insanity of the nation's current approach to immigration; it seems like the only purpose this bill can serve is to make schools actively afraid to hire them in the first place.

Maybe I'm making a mountain out of a molehill: I've got no idea how much support this bill might have at the legislature. But I'm very uncomfortable to see xenophobic-leaning bills like this being introduced in the first place.

Tuesday, March 28, 2006

Tanning Addictive? I bet not.

Um, okay, uh, this is pretty weird.

I'm technically at work right now, so I can't really go into it, so follow the link. Maybe later I'll have time to track down the article and look at it (NOTE: this is a joke), but in the meanwhile I think I'll probably stick with my gut instinct, as reported above.

Modelling Clay The Universe

Thanks to Bitwise comes a Seed article I can't believe I haven't seen posted all over the entire internet in the last 24 hours:

Prime Numbers Get Hitched

Why, do you ask, would I expect this to be linked to everywhere from here to high heaven? Well, I can show you quite easily:

There is an important sequence of numbers called "the moments of the Riemann zeta function." Although we know abstractly how to define it, mathematicians have had great difficulty explicitly calculating the numbers in the sequence. We have known since the 1920s that the first two numbers are 1 and 2, but it wasn't until a few years ago that mathematicians conjectured that the third number in the sequence may be 42—a figure greatly significant to those well-versed in The Hitchhiker's Guide to the Galaxy.

It would also prove to be significant in confirming the connection between primes and quantum physics. Using the connection, Keating and Snaith not only explained why the answer to life, the universe and the third moment of the Riemann zeta function should be 42, but also provided a formula to predict all the numbers in the sequence. Prior to this breakthrough, the evidence for a connection between quantum physics and the primes was based solely on interesting statistical comparisons. But mathematicians are very suspicious of statistics. We like things to be exact. Keating and Snaith had used physics to make a very precise prediction that left no room for the power of statistics to see patterns where there are none.
(emphasis mine)

So there you go. I'm off to class in a bit, I expect discussion of this to be peppered all over the internet when I get back.

Otherwise, you will have failed me, the internet. Or at least, not lived down to my expectations.


Um. Dude. LiveScience: New City-sized Iceberg Created Near Antarctica:

The iceberg is about 8 miles wide and 15 miles long. It broke free of the Fimbul Ice Shelf, a large glacial ice sheet along the northwestern section of Queen Maud Land, in the eastern Weddell Sea near Antarctica...

Last year, a larger wandering iceberg named B-15A rammed into the continent and single-handedly ripped two other new city-sized icebergs free.

Maybe this means something about global warming, I dunno. It's just that this is the sort of scale I don't really think about things floating around on the ocean in.

Other than when thinking about plate tectonics, I guess.

Ocean's Thirteen

If there is a God, then he has abandoned his creation.

Monday, March 27, 2006

Paper Problems

One of the more annoying types of papers is what I like to refer to as the "What The Heck Were They Thinking" (WTHWTT) paper. These papers will have bizarre protocols, an odd selection of what types of controls they will utilize, where they apply said controls, and make far-reaching claims based on their data.

The most annoying parts are:
A: They still get published in prestigious journals.
B: You finish reading the paper and realize that as frustrating as the paper is, they're probably still right.

Tonight's example--a paper I am reading in class this week--will not be named, because that would be rude. I am still a lowly undergrad, and I must freely admit that these people DO have a better idea of what they're doing than I do. Nonetheless, I must confess to being irritated by a few aspects of their approach. I'm at the point where I've read enouugh papers on drug addiction that I know what the protocols look like. Also, this paper involves a technique that my lab does a lot of, although I am forced to admit that I have never performed these experiments myself.

First off, they utilize two control groups: an untreated group and a sham group (a group which undergoes the same treatment the experimental group does, with saline replacing the drug in question). That's fine: especially since the procedure involves a survival surgery, it's sensible--and applaudable, since it's not always done--to make sure that the surgery itself is not responsible for any of the changes they monitor. However, although the untreated group is used as a control for all of their experiments, the sham group is only used in a few randomly selected experiments. This is the reverse of how it's usually done: one usually compares the exprimental group directly to a sham group, and then utilizes an untreated group for a few key experiments (if at all) to demonstrate a lack of difference between the sham group and an untreated group. I'm forced to conclude that I missed out on the great saline shortage of the late 90s.

Even though they've previously demonstrated a difference in response when utilizing an electrical stimulation vs. application of an agonist for the receptor in question, they only utilize electrical stimulation in this experiment and interpret their results assuming that agonist application would result in the same data, except where they don't. They claim that further confirmation of these presumptions is impossible with their current protocol--with no more detailed explanation, even though this claim makes no sense--and then confirm it using agonist application for one of the half dozen or so experiments they perform. Furthermore, if their protocol prevents them from getting the data that's actually important to their hypothesis, they should either use a different protocol or restrict their claims about results to what they've actually demonstrated. That's why papers have a "discussion" section in which you "discuss" potential extrapolations of your results and future avenues of research.

Almost all of their data is from brain slices in baths containing a few ingredients (only added to the experimental groups) that I haven't seen added in similar papers, and I'm pretty sure we don't use our selves. It's really quite possible that I'm just not as up on how this is done as I think I am, or that it was just done differently at the time than it is now. However, they only do one experiment where they compare the result of these ingredients when added to the baths for untreated slices, and they never perform an experiment where they show results without the ingredients in the bath. Again, in their defense, if they're right and I'm wrong it would in fact throw off the data.

They use one of their experimental groups first for experimental data, and then claim it as a control for their previous experimental data. It's possible this is thoroughly acceptable, but it feels like a bit of a no-no.

But their worst offense is going to be difficult to explain. The first experiment performed demonstrates that their primary experimental group and the untreated group are different in the magnitude of the basic response being studied. What does this mean, in your human english?

It means that statistic analysis indicates that the two groups are intrinsically different in terms of this response. It means that when you look at the data from these two groups--measure the magnitude of a response--you can safely say that you're actually dealing with two groups in terms of this response, that the differences are not due to chance. Now further experiments performed are based on--comparing how the two different groups respond to an inhibition of the response, or to an enhancement of the response. That's pretty safe, since the differences between the groups in those experiments are--shall we say--"more different" than the two groups are without modulation.

But then they perform an experiment in which the slices are sorted into groups based on the basic magnitude of their responses, which they then compare. And I'm forced to go: huh? Didn't they just demonstrate that these two groups are not, in fact, directly comparable in this respect? And to top it off, half of the groups have responses of magnitude 1.5-2.5 times greater than the highest magnitude achieved in the initial experiment, with no claim that the protocol was somehow different or even any acknowledgement that this might seem odd.

So, yeah: it's been a frustrating night.

By the way, I should make my presumed caveats clear at this point:

  • I'm not claiming the researchers are incompetent. I assume, in fact, that they are much more competent than myself--although perhaps not very good writers. It's possible that I'm just being overly paranoid about their approach, and these are all acceptable approaches I just haven't encountered or just don't understand. I do, in fact, intend to bring up my questions in class tomorrow and attempt to find out what I'm missing.

  • What they're doing is very very hard. I happen to have it on good authority that the type of experiment performed is one of the hardest to be found in neuroscience. I've been told that even people who have been great at it for years will suddenly hit dry patches where they can't get any data out of it for a month. I can understand the urge to cut some corners.

  • I have some fair amount of confidence in their data. I know that much of this has been confirmed by later research. Much of the rest, seems to be consistent with other results I've seen in similar areas. I just think it comes across as more than a bit sloppy, leaving a fair number of loose ends to be tied up.

Friday, March 24, 2006

Friday Random Ten: Sick of Data Edition

I've spent all day staring at this laptop, plugging data from my last couple experiments into our spreadsheets, and I'm really sick of fiddling with it. I'm reminded of a conversation I had with my friend Phil a few weeks ago: if anything's going to kill the traditional pen-and-paper, non-spiral-bound-journal approach to lab notebooks, it's the simple fact that scientists in a variety of disciplines regularly have to process things in such a fashion as to make the data far too large to fit in such a notebook. And even if it could fit in a reasonable fashion, it would still be meaningless outside of its computerized context.

But anyways, enough of that: this is R & R time. So today's Friday Random Ten, now with free comments.

Note: Links are mostly to the eMusic page, with the exception of a few things I didn't get from eMusic. Does this count as some sort of shilling: am I no longer to be trusted? Probably, at least in relation to conversations about pay-for-download music sites. Fortunately, it doesn't come up too often around these parts.

1. Bebel Gilberto - Mais Felis (Monoaural Remix), off of Tanto Tempo Remixes

I still remember the first time I heard about the existence of an album by the daughter of Joao Gilberto--the founder of bossa nova--and Astrud Gilberto--singer of the "the Girl From Ipanema"--and that it was also a bossa nova remix album? It's not often that you claim that the world gives you great high concept. But it did right there, and I've been a fan ever since.

2. Deathboy - Antimatter, off of Digital Deviant

Okay, the backstory here is a bit weird. So when I was in college, one of my best friends was Deathboy. Not these guys, but just this random guy who went by Deathboy. Yeah, we made fun of him a bunch. But so anyways, one day my friend Ryan tells me about this band he saw in London, named Deathboy. I laughed a bunch, and made a mental note to check it out, as I was still DJing goth & industrial at Macalester at the time. Didn't get around to it until much later, which I rather regret. They're very solid, and heavily promote themselves with free downloads. Of this I heartily approve. Anyways, this is off of Digital Deviant, a free album Scott Deathboy put up a few months back which I immediately fell in love with. The weird thing is, I think he later said he'd accidentally put up a version that had accidentally had the pitch modulated up. I'm afraid to listen to the corrected version.

3. Ella Fitzgerald - Ella (With Taft Jordan), off of Ella Fitzgerald: With Friends, 1936-1950

I think they say that if you're tired of Ella, you're tired of life. Or something like that, maybe.

4. Mylene Pires - Eleanor Rigby, off of Mylene

More of the electronica-influenced downtempo Brazilian love. Other than to point out that this is a cover, which gives me even more reason to love it, there's little left to say.

5. The Gits - Absynthe, off of Frenching the Bully

The debut album from the short-lived, notorious Seattle punk band. A man was convicted of Mia's murder back in 2004; we toasted that day.

6. Atmosphere - The Arrival, off of You Can't Imagine How Much Fun We're Having

I'm from Minneapolis. I don't think I'm allowed to not like Atmosphere--not that there's any danger of that. If the Prince fan club ever find out about my true feelings, tho... then I'm in a world of trouble.

7. Spahn Ranch - Dubnosis, off of Beat Noir

There's something perfect about Beat Noir, you can find a bit of it on Architecture as well. Unlike what attracts me to many bands, I find very little of what I like about Spahn Ranch elsewhere. Oh, well, the Goth/Industrial/Dub/Fusion/pop sound is clearly an acquired taste.

8. Johnny Cash - Cry! Cry! Cry!, off of The Complete Sun Singles, vol. 1

I'm not going to insult you by pretending you don't already know everything you need to about the Man in Black.

9. Immortal Technique - Bin Laden Remix (Street), off of Bin Laden Remixes

I know absolutely nothing about Immortal Technique, other than that the few tracks of there's I've heard are good-but-not-great rap, with an impressively self-aware approach to the politics in their lyrics.

10. Death Ride 69 - Needle, off of Screaming Down the Gravity Well

Some great industrial rock, balancing the power rock approach with the electronics for the dance floor very well. Great vocals. I think these guys came into my life from one of the Diva X Machina comps.

Wednesday, March 22, 2006

Congratulations to the NIH

First step down: evolgen reports that the Specter-Harken amendment to increase the NIH budget. This is important: the NIH budget, which is responsible for a lot of basic biomedical research, hasn't increased in something like four years. Even for inflation. This is only the first step, there are several more to go. But it's worthy of note, especially since both of my Senators voted for it--rather pleasantly surprising, as Norm Coleman is stepping out of his adopted role as administration puppet.

Tidings of Joy!

today announced a permanent cease-fire as of 24 March.

One would almost hope they intended to blow up something rather impressive tomorrow, albeit with no casualties.

On a similarly off-topic but otherwise unrelated note, That one's really hard to celebrate in your own neighborhood, isn't it?

Tuesday, March 21, 2006

Quickly, before my Human Physiology textbook finds me hiding

1. Respectful Insolence shows us that the AP has a newfound respect for logical fallacies. That's awesome. Let me know if there's anything I can do to make this a new trend: I can't wait for them to start calling anyone on the Naturalistic Fallacy! I'll weep with joy!

2. Pharyngula brings us the greatest "scientific" figure EVER. I'm having a hard time not giving into the urge to replace my icon with the lower half. Someone reassure me that it's a bad idea.

Monday, March 20, 2006


Science Creative Quarterly: SIZE MATTERS: THE IMPENDING DEATH OF THE Y CHROMOSOME (via evolgen)

TimesOnline: Yes, genes can be selfish

For the thirtieth anniversary of The Selfish Gene, Stephen Pinker on Richard Dawkins. (via Science and Reason)

Sunday, March 19, 2006

The decision's been made.

That does it. We decided today that we're just gonna have to pack up and move to Oregon. Then, by the time we have our Ph.D.s, we'll be in the only state whose economy is still viable.

Friday, March 17, 2006

Some quick linkblogging

Developing Intelligence gives us some insight into the distinction between perception and imagery...

Anyone who would ever like to understand but doesn't needs to read this article from the Science Creative Quarterly...

I knew that tongue piercings could lead to strange side effects... but then I saw the beginning of this press release on EurekAlert... and for a few brief blissful moments I believed that tongue piercings could induce growth of a second tongue. It was TOTALLY METAL!

And thanks to Bitwise... Artnatomy, a flash site that shows you how the muscles of the face correspond to various facial expressions. It's awesome.

And one final note: the first in-man monoclonal antibody trial has gone horribly awry: Derek Lowe has the details. Our thoughts are with the subjects of the trial.

Thursday, March 16, 2006

Intro to Neuroscience, Part 1: EC Gradients

Alright, I've been meaning to get around to this post since I started this blog. So I'm very enthused to finally present you with our opening lecture on : Electrochemical Gradients of Cells.

So let's break this down to the basics. I assume that everyone reading this knows what a cell is. If not, we can start a remedial biology course in the comments thread. I will freely admit, however, that the idea of an "" may be a bit more confusing to the neuro-illiterate.

First off, an electrochemical gradient is, for purposes of our discussion, a special type of concentration gradient. This means that we have a membrane, and we have different stuff on each side of it. In terms of a concentration gradient, this could really mean anything. We could have a gallon of distilled water on one side of the membrane, and a gallon of water saturated with food coloring on the other side of the membrane. Now if we were to punch some microscopic holes into this membrane, sized such that the imaginary food coloring could cross it, can you guess what would happen?

That's right, it would across the membrane. If you need some help visualizing, I recommend the first image at that link.

So that's a basic chemical gradient: a chemical that is forced to be more concentrated on one side of a membrane (or in a membrane-enclosed compartment) than the other. Now, the important thing to remember about this gradient is sort of confusing: to thorougly anthropomorphize things, the chemical "wants" to equalize the gradient on its own, so the energy to promote diffusion is provided by the gradient itself. This is gonna be important in the next chapter, which will come at some point in the near or distant future.

Now things are somewhat more complicated in neurons (and, indeed, in cells in general): the concentration gradient consists of , and thus you also have to deal with an as well. Exactly how this works is one of the things that often kills people first being introduced to neuroscience, so I'm going to explain this as simply as I can.

The key idea here is that a cell--specifically, in this instance, a neuron--has certain established concentration gradients with respect to certain ions. Because of a difference in the distribution of these ions across the membrane, there is an electrical potential established across the membrane: the interior of the cell is more negative than the exterior of the cell. Since a potential is a comparative value (that is to say, one can't define it in absolute terms but only in reference to something else), the outside of the cell is defined as having a potential of 0 mV, and the potential of the inside of the cell is defined in reference to that value.

Following are some values of the important ion concentrations for an average mammalian neuron. It is important to realize that there can be some wide variation between different neurons, between different compartments of a single neuron, etc. These are just to give you a general idea of what you're looking at here, and are cribbed from my copy of Neuroscience, 3rd ed., by Purves et al (2004):

Potassium (K+): 140 mM (intracellular); 5 mM (extracellular)
Sodium (Na+): 5-15 mM (intracellular); 145 mM (extracellular)
Chloride (Cl-): 4-30 mM (intracellular); 110 mM (extracellular)
Calcium (Ca++): 0.1 nM (intracellular); 1-2 mM (extracellular)

Neurons generally have a resting potential in the range of -40 to -90 mV. This can be calculated based on the ionic concentrations utilizing the , a variant on the . I will torture neither you nor myself by attempting to go more into that now, so I think we can agree to just leave it at that.

Now, looking over that list of concentration gradients, I can imagine you might have a few questions. I'll see if I can guess a few:

  • Why is the inside of the cell negative, when it has about as much positive stuff inside as outside, and a bunch of negative stuff outside as well?

  • How does the cell keep a bunch of those two positive ions on the outside of the cell (calcium and sodium) while keeping a bunch of another one (potassium) inside the cell?

  • Why does all this matter to the cell, anyway?

Unfortunately, the answer to all of these is: it's complicated. But I'll do what I can to simplify things.

The simplest answer to the first question is that the most of the stuff inside a cell is negative, especially the DNA. So the potassium inside of the cell mostly serves to balance out the negative charge that lies therein. Also, there's the fact that the potential difference is not very large, in the grand scheme of things, and mostly exists at the membrane itself.

The answer to the last is that neurons communicate in an electric fashion, via action potentials. The electrochemical gradient is essential to enabling the action potentials to occur.

The middle question is where things start to get interesting. Let's start by pointing out that the cell membrane is selectively permeable. In our example of diffusion to explain concentration gradients above, we poked a bunch of imaginary holes in a membrane that would only allow food coloring to pass through. A cell membrane has a bunch of similar holes in it. These are called . A given ion channel is generally permeable to only one ion, or a class of ions. So it will only allow certain ions to pass through, while excluding others.

But where it gets really interesting is when we start discussing how the cell establishes these ion gradients. It's certainly possible to imagine a cell that just spends all of its time kicking sodium and calcium out of the cell, while bringing potassium in. And there is a lot of that going on, by activities such as the , for example. But that's not the most important thing going on.

Let's start by imagining a pair of compartments, one of which is full of sodium and one of which is full of potassium. This is a viable model of the electrochemical gradient because these are the two main ions participating in action potentials, and the main ions responsible for the electric potential at rest. Although calcium and chloride ions do effect the EC gradient, they take part in more specialized circumstances. It is also important to mention that in the diagrams that follow, the amounts of ion displayed are fairly arbitrary, and should not be seen as representing any value in actual cells in any serious fashion. These compartments are separated by a membrane:

Now, as you can imagine, since the ions in question "want" to diffuse, there's a driving force for both of these ions to go to the other compartment. But so long as they're separated by a membrane, they can't. Now imagine that we were to place two potassium "leak" channels in this membrane, which would allow two-way transfer of potassium ions:

As you can imagine, we would quickly get to the point where potassium was starting to travel over to the other compartment:

But notice something: now that we have more potassium ions in the other compartment, that compartment has started to develop a positive charge. This causes the potassium compartment to develop a negative potential. This is because the positive charges in the one compartment are starting to repel each other. The sodium ions are still trapped in their compartment, so they are forced to stay put. Potassium ions, on the other hand, can travel back to their starting compartment, since these ion channels are two-way:

Note that at this point, the amount of potassium flowing back into the cell is smaller than the amount flowing out. This is because at this point, the concentration gradient is still the primary driving force for net flow of potassium. Although the electrical gradient is reducing the outward flow, it is not the dominant force. Eventually, though, the power of the two gradients equalizes into a :

I should point out that I just realized that my drawing is a bad example because in a real cell there is still much more potassium in the cell than out. But that aside, the key point here is that at this point there is still potassium driven out of the cell by diffusion, and driven back into the cell by charge repulsion. Thus, the net driving force on potassium is zero. The net driving force on sodium, on the other hand, is much greater. But since sodium cannot travel through the potassium leak channels, it is stuck outside of the cell, hammering on the gates.

What happens when the cell opens the door and invites sodium in? The action potential--but that's a story for another day.

Any questions, clarifications? Feel free to post a comment below. I want to make sure I got this right, and I want to make sure you guys understand, because this is the foundation for some of the stuff I'd like to actually dig into later.

Wednesday, March 15, 2006

What the heck is going on?

Hwang Woo-Suk: Stem Cells
Rusi Taleyarkhan: Sonofusion (possibly)
And now... Ian Wilmut: Dolly?

Admittedly, this new case seems to be a bit smaller in scale than the others. Hwang Woo-Suk blatantly lied about results and doctored data; the evidence is starting to suggest that Taleyarkhan did as well. In comparison, Wilmut just seems to have taken credit for the work of others in his lab (a trait archetypally common amongst Professors heading up labs, although I've seen no evidence thus far that it is actually common)... but at least the work was actually done.

But what's going on? These are three of the biggest publications of the last decade, and they're all being tinged with fraud and misconduct. Of course, it's easier to publish something important if you're going to rig your data. But the questions for me still stand: where are we going wrong? Or are we going right?

Let's break down the possibilities from my perspective:

1. This level of fraud and misconduct has always been occasionally occurring and eventually publicized, and I'm just young enough and inattentive enough that I didn't hear about previous generations.

2. This level of fraud and misconduct has always been occurring, but we're finally good enough at detecting it that it's coming to light.

3. In some fashion, the system is breaking down and starting to allow fraud and fraudulent claims of authorship to slip through.

As above, so below: is this sort of fraud being duplicated in lower-tier research, or is it mostly restricted to the race for big, top-tier achievements?

Finally, it's also worthy of note that Nature has some egg on their face, after they've been gloating about Science allowing the first two to slip through. Admittedly, publishing an article where someone falsely takes credit for someone else's work is not in the same league as publishing a dishonest article, but it's still a sign that the system needs some sort of fixing.

Two Things

1. is in fact terribly awesome. It has immediately earned official placement on the list of quite awesome things that I will never get any use out of, but will nonetheless geek out in glee over the fact that I live in the same universe as it.

2. A few requests for updates:
A. A hybrid map, preferably with some sort of slider for the amount of hybridicity. The elevation map already mostly includes this, but it would be sort of nice to have a bit more control over it.
B. Higher resolution. Yeah, yeah, I know, not gonna happen. But I want to see the head on Mars in its context, in all its glory. So there.
C. While you're giving me a hybrid mode, include in it so I can see the canals in all their glory too.

Then I will be a very happy camper indeed.

Tuesday, March 14, 2006

Don't go to Laurentian University...

...if you intend to work with animals:

The problems began for students on Wed., Nov. 9 when LU administration changed all the locks to the research facility where the behavioural neuroscience program operates, preventing them from accessing any of their animals...

..."Institutions meeting guidelines are given a Good Animal Practice Certificate," said De la Riva. "Institutions failing to comply with CCAC guidelines have this withdrawn and are also likely to lose funding. In 2004 LU's ACC was disbanded following a CCAC visit which placed their Good Animal Practice Certificate on probation. The university put an interim committee in place and eventually appointed a new one. It was this new committee which rejected or would not renew the animal use protocols without significant changes."

The conflict has reached fever pitch, with the students employing legal representation in order to gain access to the facility or gain compensation.

"I am, sort of, a member of the ACC, however I am excluded from participating in the discussions concerning the neuroscience research group's protocols because they deem me to be in conflict of interest," said graduate student Debra Meades. "They refused to let ongoing projects continue while all the details were ironed out. Obviously they do not care about research."

LU administration is unmoved by the students' plight. De la Riva highlighted their position in a press statement.

"Laurentian University is under no obligation to have an animal research facility," he said. "However, as long as it operates one, it will be administered in accordance with CCAC guidelines, as required by the relevant granting councils."

The students are currently pursuing an injunction to have the facility reopened.

You can find all the details at the link above, and some good discussion at Adventures in Ethics and Science.

Music as Interpersonal Test

Cognitive Daily gives us an excellent post on Peter Rentfrow and Samuel Gosling's research into music's utility as a predictor of personality traits. Way awesome.

Brain Awareness Week: Highlight Reel 1

Seeing as how it's and all, it seems sensible to give you a few highlights of brain-related news, discussions, and lectures that have been placed on the web over the last few days.

Thanks to , we have a short piece on using nanofibers as a scaffolding to assist in the repair of damaged neurons:

A team of neuroscientists at the Massachusetts Institute of Technology and their colleagues at Hong Kong University purposefully wounded 53 newly born hamster pups. They cut a relatively deep gash--1.5 millimeters deep and two millimeters wide--through the optic tract in the brains of the young rodents. The wounds of 10 of the pups were then treated with 10 microliters of a solution composed of 99 percent water and 1 percent of a special ionic peptide. These short amino acids are capable of creating a molecular scaffold that can bridge such gaps.

Within 24 hours, the gash in the treated pups had begun to close (shown by the green area in the picture above, depicting regrowth), and by 30 days had completely closed. "We had never seen that before in any animals," says neuroscientist Rutledge Ellis-Behnke of M.I.T., who led the research. By placing a biological tracer in the hamsters' eyes the researchers also discovered that the neurons had actually grown back and reconnected through the center of the cut instead of routing around the wound--another first. None of the control animals showed any healing whatsoever.

The scientists then inflicted a similar wound on some adult hamsters to see if such connections could actually regenerate vision. By injecting 30 microliters of the solution, the scientists again healed the gaps in 30 days. And in subsequent behavioral tests, the animals had regained the ability to turn their eyes and heads toward a sunflower seed in their peripheral vision, though their turning response was slower than normal.

The Eide Neurolearning Blog impresses us with the important lesson that allowing students to make predictions is a valuable part of learning.

Gene Expression gives us a link to the NYT article The Twists and Turns of History, and of DNA, and blows our minds with a brief suggestion of gene-culture coevolution.

Via EurekAlert, we learn learn that UCI researchers have discovered a novel memory disorder: near perfect recall.

That's all I've got for now: if you've got more to offer, let us know.

Brain Awareness Week Part 1: Your host & brains

First off, I would like to apologize to our regular customers for not getting this post up yesterday, as was my initial plan. I opened Spring Break by driving to Chicago and back this weekend, which sort of wiped me out even more than I intended to, leaving me just barely re-achieving the phenomenon of human consciousness by last night.

So I thought I would open this week's posts celebrating by giving a bit of a short introduction and explanation for my own interest in and obsession with brains.

I would like to point to some half-remembered memory, a definitive childhood moment. Or even a definitive adolescent moment, where I started to appreciate the brain in all its glory, and became obsessed with its proper functioning, its wiring, laying in bed at night while dreaming of neurons firing. But to the best of my recollection, there isn't one.

As I mentioned in my profile, my degree in Neuroscience is actually a second Bachelor's, with my first being a BA in Religious Studies from Macalester College in Saint Paul. I generally don't talk about that, because there's a level in which I'm a bit embarassed. I was never a student who knew exactly where he wanted to go in life, what he wanted to do. There was a certain level on which I wanted to eventually become a writer, but I had a certain appreciation for some idea that I'd have to deal with the real world before I'd experienced enough to have something to write about. I never really thought about it much more than that, which was my fatal error.

My approach to my education at Macalester was that of a ten-year-old in a candy shop: I wanted one of everything. I had no interest in focusing in on any one topic, I just wanted to take classes on whatever random topics came up that happened to interest me. I never really thought about what I would do with my education: I was going to school because I was a smart kid, and it was the thing that smart kids who wanted to have a future did when they graduated. They get into good schools and go onto great things. There were points at which I realized I hadn't really figured out what reaction occurred as A -> B, but I just sort of figured that I'd figure out the arrow in my own course. And I suppose, after a fashion, I did.

The point being that I got a major in religious studies because of all the things I was interested in, it was the easiest major that I had the most abstract interest in learning about, and left me with the most time to take other classes that I was also interested in learning about. In terms of what I would do with it, I pretty much convinced myself that most things I would enjoy doing would really only care that you had a piece of paper from a secondary institution, not what it said on it.

That didn't work out so well, as I'm sure you can imagine. So two years out, I'm working a crap temp job at the local home mortgage monolith. I've already come to realize that I have no interest in this becoming a life path whatsoever, and need to do something different. I'd recently applied to go to the local tech school to get into their sound engineering program, on the theory that it sounded interesting and would be a viable career that I'd enjoy and actually make a living off of. And then sitting at work today, I had a series of revelations. It was honestly the closest I think I'll ever have to a religious experience.

Revelation #1: I have a brain. I should use it.
I wouldn't argue that there's a dearth of smart people in the world, but it nonetheless seems the case that the world can use every one of them that it can. And there's not point in being furious about the world's problems if you're not doing anything to fix it. So revelation #1 can be best phrased, a human is personally responsible for using the tools at their disposal to determine how they can best better the world around them.

Revelation #2: Science was no longer intimidating.
I had been intensely interested in science as a kid--along with everything else. At some point, it became somewhat initimidating--I think--and I convinced myself that I should stick with the humanities. I think taking Calc. 2 in my junior year of high school may have had a part in this. But for whatever reason, science had always seemed too threatening at a college level for me to want to try it at Macalester. But by this point, that had worn off. I was dating a bio major at Mac. One of my best friends was a neuroscience major at Mac, another was a bio major working on her Master's in Plant Bio. So I realized that on a certain level--not to sound condescending or anything--that if my friends could manage this, I could too.

Revelation #3: Decisions can be required solely to overcome inertia.
This is the part that, in memory, is almost reminiscent of Paul on the road to Damascus. My problem at Macalester--as I'd said--had been a lack of desire to actually focus on any one topic. I realized that when I'd come to Macalester, I'd reached a crossroads I'd never really passed. One that I was still waiting at. I had considered going back to school before this point, but had never been willing to commit to any one topic as the one I would study for the rest of my life. It just wasn't in my blood, I told myself. And at this point, my fundamental realization was that sometimes a decision has to be made simply for the sake of making the decision. Why did I choose Neuroscience? I didn't, yet--I chose Bio. Because it interested me at that point as much as many other things, and I had to choose something. I was clearly influenced by my aforementioned friends in this regard. If I did it again now, who knows? I may have decided to become an engineer and build solar panels for the third world, for all I know. If I'd waited another six months, that seems like a very realistic possibility.

I ultimately ended up adopting neuroscience after realizing that I'd have to basically do the bio program from scratch, so why not just add on another year and get something even cooler? But I don't want this to seem like a long-winded anecdote about how I'm studying neuroscience for purely arbitrary reasons and don't really care about it that much.

Although it may be a bit late for that.

So why is Jonathan Michael Ehrich, BA & imminent BS, studying neuroscience? Why does he care about brains? Why is he obsessed with brains?

There are a lot of reasons. Here's a few:

--I'm interested in mind. One of my big interests in cognitive psychology, because I'm fundamentally interested in how the mind works. But I'm of the opinion that I can't really understand how the mind works on a useful level until I know the hardware through & through.

--I'm interested in questions about materialism and mechanism. The brain is a collection of parts, wired together, that seems to synergistically generate consciousness. Just think about that for a moment. Although it may be fundamentally unknowable, I will nonetheless posit the claim that a rat or a cat has no sense of self, no ability to reflect on its existence, no ability to think about things. And these are mammals that have most of the same parts we do, just smaller. At some point, we reached a perfect size and a perfect development, and suddenly reached cognition. Did it just flip on like a switch? No, probably not. But it's just such a bizarre idea, this historical accident, that it makes me want to understand how it functions in every gory detail.

--Those questions have, for now, led me to study drug addiction. Because it's this weird state where a human can take something that just totally messes up the system--but in an incredibly specific way. Mark Thomas, my Professor, is interested in drug addiction because it's this bizarrely gross-yet-very-specific manipulation that can tell us a lot about learning. And that intrigues me as well, but I'm more interested in it as an intersection of fundamental pharmacological functions of brain with higher-order, cognitive functions of brain.

Just think about it, your brain and your mind. Our minds generally feel like our own, like the one thing we can usually argue we have some useful control over. But do we? We feel that our desires, our wants, are our own. We may want things that aren't good for us, but at least we can appreciate this and make decisions from this stand point. But can we? The idea that you can add a drug to this balanced system of desire, motivation, and reward that throws the whole thing out of whack, making you want the drug more than you care about food or the fundamentals of life... it just fascinates me. And I want to know how that works.

Alright, I think that's enough of my deep dark secrets for now. More later on, throughout the rest of Brain Awareness Week!

Friday, March 10, 2006

Link Dump

Sorry, guests coming over at the last minute so I need to take care of all my tabs so I can shut down my computer. Enjoy!

My Life Has Been Forever Changed

Seed: Microscopy And The Art of Sudoku:

One day, while wrapping his brain around a Sudoku grid, Elser realized that the tension set up in the puzzle was the same as what he had been trying to solve with his algorithm to render images from diffraction microscopy.

In order to analyze the light waves created during diffraction microscopy, scientists must know the amplitude of the waves and the phase angles at which the light was collected. If these two separate conditions are not met, the image will come back as "noise," according to Elser.

"What will happen in all cases—except when you have a correct phase—is that these waves will combine and they will give you something that you know right away can't be this object," said Elser.

But diffraction microscopy is not the only function that has two sets of independent constraints. Sudoku puzzles are arranged so that the digits 1 through 9 must appear nine times throughout a nine-by-nine grid. The second constraint is that all nine digits must be used within each of the six three-by-three blocks.

It seems sort of sad and pathetic that I can sit here, reading the article and nodding intellectually at the microscopy problem he's dealing with, when I suddenly sit up and shout "Holy Crap! AND it can solve sudoku?!?!?"

Sigh. We are composed of our obsessions.

Wednesday, March 08, 2006

Also off topic

I just spent the last hour figuring out how to finally set the blog up for actual trackback.

See how much I love you? This much!

See how much I love studying for my animal dissection midterm? This little!

Off Topic

No, I have no idea why I randomly switch between first person singular and the royal we when writing blog posts. Maybe someday I'll finally get around to fixing that... but which do I choose?

Attack on the Holocaust History Project?

It's been said best rather succinctly: Only Nazis burn books.

So who burns businesses that sell books about the Holocaust?

Thanks to Orac, it's come to my attention that there was an act of arson committed upon the warehouse complex housing . It's not at all implausible to presume that THHP was the intended victim. This doesn't seem to have been picked up by the news wires yet--a yahoo news search for "arson THHP" turned up nothing, and "arson holocaust" didn't help either--so we've been encouraged to spread the news by blog, in the hopes that someone will pick up on it.

Although the library was not contained at the location in question, it's still something of a setback. As mentioned in Orac's post, the private business of Harry Mazal--the director of THHP--was located there. Needless to say, our hearts and hopes are with the people of the Holocaust History Project, because they're people doing work that needs to be done.

For more info, see the links above or read the press release.

A little Linkblogging

Ugh... I've got such a headache. I think I'd spend the day on the couch pretending I'll be productive at any moment if it weren't for the review session for Friday's Cell Bio midterm...

Anyways, the HD's still messed up but I was able to recover most of the data. I'll try to get it in for the manufacturer's warranty by the end of this week, and hopefully be back up to normal posting rates during Spring Break next week. We shall see...

First off, The Scientist"s Glenn McGee gives us the rundown on the NIH budget cuts--the first in 30 years. I am reminded of my response to Bush framing himself as the "Science President" in the SotU:

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.

Secondly, I thought I'd point out that next week is Brain Awareness Week. I'm gonna try and put together some special treats for you guys (yes, BRAIN COOKIES!), and I'll keep an eye out for extra goodies from the rest of blogistan.

Actually, that all is it for now. I know, I'm boring this week. We'll get you some more action soon.

Sunday, March 05, 2006

Procrastination, Inc.

I really need to get back to the homework, but thanks to Washington Monthly I have discovered what could turn into my new favorite website. I'll check it out later and let you know how it goes.

Saturday, March 04, 2006

Friday Random Ten: A Day Late & A Dollar Short

Fortunately for my desperate need to write contentless silly posts, my laptop serves as a suitable replacement for my lack of a hard drive with music on it at present:

1. DPGC feat. Snoop Dogg, Nate Dogg, Kurupt, Daz Dillinger - Sunshine
2. DJ Cheb i Sabbah - Durga Puja (remixed by TJ Rehmi)
3. DJ? Acucrack - Damage Control
4. Lard - I Am Your Clock
5. Wyclef Jean - Generation X
6. Batidos - Agua
7. Turbonegro - Turbonegro Must Be Destroyed
8. Junkie XL feat. Dave Gahan - Reload
9. Jello Biafra & Mojo Nixon - Hamlet Chicken Plant Disaster
10. Jah Wobble - Swallow in the World

Friday, March 03, 2006

Computer Issues

The data hard drive on my desktop died last night. This will probably lead to some lighter posting over the next few days to few weeks, for the obvious reasons.

Wednesday, March 01, 2006

I'm calling you out, AdWords!

One short post on my opposition to animal-rights activists, and I've got links to animal-rights activists on the top of my blog all week long. Consarn it. And I've probably just made it worse by writing this.

Is Peak Oil upon us?

Thanks to WorldChanging (still, by the way, my favorite blog), a link to today's essay from The Oil Drum titled "Why peak oil is probably about now". Which is really all that it says it is.

Since the immediacy of peak oil is--at best--a controversial proposition, anyone who knows of a comprehensive and sensible rebuttal to such claims can feel free to throw a link my way so I can throw it out. If such rebuttals are lacking, however, those with piles of cash money lying around may wish to look at another WorldChanging post from today, Investing in Alternate Energy.

I'll take up Friday Cat Blogging...

When I can get my cat to do this:

Russian clown Yuri Kuklachev has a troupe of cats who do handstands, crawl along high wires and balance on balls and he says the secret to training them is realizing that you can't force cats to do anything.


Wednesday Morning Pre-Class Linkblogging Fun!

Thanks for all to EurekAlert!.

Elders' stereotypes predict hearing decline:

To measure age stereotypes, participants were asked, "When you think of an old person, what are the first five words or phrases that come to mind?" The responses were judged on how negative or positive they were and how internal or external they were. Stereotypes rated negative included "senile" and "feeble," whereas stereotypes rated positive included "wise" and "active." External stereotypes included visual images such as grey hair, wrinkles and stooped posture. The study adjusted for initial levels of hearing, as well as several other variables that are known to affect hearing including age, education, gender, race, depression, chronic conditions and smoking history.

Older persons with more negative and external age stereotypes performed worse on hearing measures at the end of the three-year study. According to Levy, "Hearing loss is the third most common chronic condition among persons age 65 years and older and can lead to increased social isolation, self-denigration, loneliness and depression."

The evolution of right- and left-handedness

A study from the April issue of Current Anthropology explores the evolution of handedness, one of few firm behavioral boundaries separating humans from other animals. As researchers find new cultural behaviors among chimpanzees and other primates, language is the only other characteristic accepted to be unique to humans, and both language and handedness appear to relate to the separation of functions between the two halves of the human brain, also known as lateralization...

..."We studied two groups, one a modern group of Canadians, for whom we could document hand preference and physical activity histories, as well as the breadth of the part of the humerus that makes up the elbow joint," explain the authors. "We then applied the same measurement to a group of medieval English villagers known to us only through their skeletons. This allowed us to demonstrate the usefulness of this trait to determine changes in hand preference in populations separated in time by over a thousand years."

Delayed-release stimulant used to treat ADHD may be less subject to abuse

Playing the Part of the Fool, Getting In On the Fun

First things first: FrontPage magazine is conducting an online poll to determine the worst Professor in America. I insist, on basic moral grounds, that that award goes to no lesser luminary than the esteemed Michael Berube. Professor Berube was cheated of his previous demolishment of the vote by an erasure of the vote as of Monday afternoon. We must regain momentum, and fight again! Show David Horowitz the face of the man you fear, and the name that belongs to that afeared face is Michael Berube! If you have any care for democracy at all, especially incarnate in the form of online web polls, you must act! Vote now! Vote early! Vote often! Vote using computers belonging to a number of dead Chicagoans! Noam Chomsky must be conquered!!!

No offense to Professor Chomsky intended. He seems like a very nice man.

And in side news, I've managed to do a cursory look over the Nature Medicine article discussed earlier today, and I really don't have anything new to say about it. It's of a fair amount of interest to people who focus their addiction research on the VTA, a moderate amount of interest to those of us who focus on other areas (in my case, the Nucleus Accumbens), and of little interest outside that. Further publication, with more detailed data and methods, will probably help increase that amount of interest immensely.

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