Wednesday, June 27, 2007

Then why do casinos make money?

This Nature article fits perfectly with my current neurology kick. Everybody's heard of Pavlovian experiments, where an animal is trained to produce a physiological response to a normally unrelated stimulus by repetition. In Pavlov's case, he simply rang a bell and fed steak, and over time was able to induce salivation by ringing the bell only.

That's all well and good, but this paper asks what happens when ringing the bell is only assigned a probability of bringing steak. They showed four of ten shapes to monkeys, and then allowed to look at either a green or red target. Each shape carried a probability with it of a reward being given for a red or green choice. They were then able to train the monkeys to select red or green based on the most likely outcome, given the shapes presented.

The paper focuses heavily on the neurons in the parietal lobe involved in probabilistic reasoning. That's where the statistics get a little too dense for me, but I find the concept interesting; they were able to demonstrate the region of the brain associated with logic based on probabilities, rather than proven results.

Friday, June 22, 2007

Real-life lab conversations.

Me: See, Lisa? That's how you build a good relationship with your PI.
Lisa: What, by making fart jokes?


Thursday, June 21, 2007

Considering replacing my bench with a cot.

Sorry for the lack of posting; it's been a long week in the lab. Today, I set my record at four gels in one day. Something tells me I'll have doubled that record by April. Since I don't have anything intelligent to say, and I'll be gone to Toronto for the weekend, here's a funny comic I found on Pharyngula for the meantime.

Wednesday, June 20, 2007

Holy Frig, Newton!

Not only was Isaac Newton a belligerent jerk, he was also a religious nut. Back then, I guess, they were all a little religious, but this goes beyond the Liebnizian belief that God created calculus, et cetera. Trying to match the dimensions of the temple with the stars? I always thought Newton was a pioneer of purely empirical, non-religious science. I guess not.

Monday, June 18, 2007

More on the origins of life.

Yesterday, I read a fantastic article in Scientific American about the chemical origins of life. It started off with a review of the RNA world hypothesis, which essentially postulates that life began by the chance formation of a catalytic RNA molecule which had the ability to self-replicate. At this point, however, it has become obvious that the odds of that happening are so extraordinarily astronomical that it's almost certain that something else came first. Even in the famous Stanley Miller experiment, there were only amino acids formed; no sugars or bases. In addition, ribose has proved nearly impossible to synthesize under the prebiotic chemical conditions.

This all led to the metabolism-first hypothesis, the main subject of the article. It's a lot more general than the RNA-first hypothesis, and requires much smaller molecules. What it boils down to is an energetically downhill redox reaction of a mineral fuelling an uphill organic reaction, say A to B. A is eventually regenerated by a stepwise series of exergonic reactions; in other words, a rudimentary cycle. The hypothesis then says that chemical and physical interference with the reactions would cause them to find alternative routes to get back to A, forming more complex networks, and the opportunity to form catalysts. The author goes as far as saying that nucleotides originated as some form of catalyst or energy-producing reaction (after all, ATP is a pretty universal energy-storing compound). The jump to RNA would be made by the chance polymerization of nucleotides, something far far more likely than a de novo formation. And now we've got to the RNA world.

The argument that the article seems to have the most trouble dealing with is how this system of reactions stores information. The author suggests that the chemicals themselves store it in a "compositional genome," which is replicated by the diffusion of chemicals from one physical compartment to another. This theory leaves open the possibility of something like a chemical founder effect - a drastic change in concentration occurs, and a new network is formed. This would in turn allow for the selection of some chemical systems that are better able to grow in concentration than others, and there you have it: evolution. It's a pretty good theory, but it seems a little lacking because it doesn't specify the barriers that would separate these systems, since they would only travel by passive diffusion. How would a new cycle "pinch off" from an old one?

At any rate, it's clear that something that can clearly be defined as life occured before RNA. This sounds like a pretty damn good idea, but it needs a little more data and a little more theory. I'm too lazy right now to look up the actual papers. Maybe if I'm feeling particularly bored I'll read some and post about them.

Sunday, June 17, 2007

Och aye, the McCat is slain.

On Friday, I took that test of all tests, that exhalted exam, that furious final, the rite of passage for millions of let's-go-to-med-school-because-I-don't-want-to-do-research science students around the globe, the MCAT. To be honest, it really wasn't that bad, including the studying. I suppose I can say that now, looking back, after a solid weekend of pretty much nothing but Guitar Hero, fast food, and beer.

I know I "symbolized [my] signature by clicking 'Yes' to the non-disclosure agreement," but there was a random question about oximes (yes, oximes, of all chemicals), and I ----in' NAILED it. Synthesized by hydroxylamine hydrochloride? Yuh-huh.

Sorry. I had to get that out.

However, today I had a scary few hours when I realized that I never clicked "save" during the written portion. I just let time run out. Today, however, my saviour Meg let me know that it automatically saves my answer when I move to the next section. Looks like Andy's movin' up from a J to a K. Ohhh baby.

Anyway, I just read an awesome Scientific American article about the origins of life, and how the RNA world hypothesis probably isn't right. Too tired to post about it right now, but it'll come tomorrow.

Tuesday, June 12, 2007


This man is brilliant. His talk makes me want to switch into neuroscience - and believe me, I loves me my bugs. It also just gets me all excited about the future.

Can you tell I'm addicted to the TED talks?

Sure beats my chicken-dance interpretation of bacterial glucose transport.

Interpretive dance is always something I've made fun of. It still is. This one's an interpretation of symbiosis by two Cirque-du-Soleil-style dancers with the great-grandmothers of all wedgies. It's pretty mesmerizing for the first few minutes, but come on. I'm all for the appreciation of biology as a beautiful thing, but this is a little over the top; on the other hand, I think it would be hilarious if someone got Christopher Hitchens and Richard Dawkins to do it.

Monday, June 11, 2007

The NEW design

I ran into Areiyu today. We talked about the Blog and how we both hated the layout and colors.
I decided to take a little initiative and select a more appropriate "template". I like this new template better although I was temped by others. I think the colors match the feel of summer.


Aaron, was that you? The blog . . . she's so different. What's 565? I kind of liked the microarray background. But this one's cool. The colour scheme fits with the whole microbiology thing. I think.

Saturday, June 9, 2007

Post (Post) post post

Thinking of the name of this blog, I found this site with some hilarious oddities in species taxonomy. I recommend giving it a full read, but here are some species name highlights:

- Bison (Bison) bison bison
- Scrotum humanum
- Lainodon orueetxebarriai
- Mozartella beethoveni
- Colon rectum
- Ia io


Thursday, June 7, 2007

I think it's the lead paint.

I had a brief conversation today in total darkness with a couple newly-acquainted summer students at Lyman Duff while developing a film. We discussed the overall quirkiness that the professors in our department share.

The biochemistry department at McIntyre is full of straight-and-narrow hardcore scientists, the sort you'd find on CBC soundbytes with embroidered lab coats and interestingly-coloured solutions in the background. In microbiology and immunology, however, they're all a bunch of kooks. Many are totally bonkers. But they're good kooks, the sort you laugh about nostalgically ten years after graduating, which I already foresee myself doing. I think I like having the crazy profs more; it gives the department character. Take, for example, these now-famous quotations, both from the same virology professor:

"Prions are elusive pathogens. It was once thought that they originated in some sort of primitive cow. Sounds a little like my ex-wife."

"The truth is, almost all influenza virions are harmless. You could probably snort a handful of bird shit like crack and not get sick [uproarious laughter from class]. Then again, knowing some of the dealers in Montreal, that's probably what you're getting [scattered, awkward laughter from class]. What, none of you has bought crack recently? [half-uproarious, half-awkward laughter from class] I find that hard to believe."

Other quirks involve a somewhat scary ability to kill tens of mice in a matter of minutes, the look of constantly having to pee, a ridiculously soft and sleep-inducing manner of speech, and a general lack of variety in fashion choice.

Anyway, a short list of nicknames for a few profs in the department, based mainly on their quirks, that have been suggested mainly by Aaron and me, but also others:

- Bebop Scatter (also known as Bebop Scat, and Bebop Scatdaddy)
- ppGpp
- Laser
- Bainesy (not really a quirk - it's his name)

UPDATE - We made a couple more:

- Silk
- C9

Wednesday, June 6, 2007

Membrane pores aren't irreducibly complex.

Check out this somewhat odd-seeming PNAS paper (don't worry, it's open access) about diffusion across pores. Using two macroscopic models, one real and one virtual, they showed that a concentration gradient can be maintained across a membrane with leaky pores in it without the need for gating, antiporting, charges, or anything. All that's needed is a physically asymmetric pore - wider at one end.

When I first read the paper, I thought it was so obvious that I wondered why the research even had to be done in the first place. But then, I realized that it's not so intuitive; it seems to go against a lot of what we're taught about diffusion equilibria. Simply changing the geometry of the pore shifts the equilibrium to one side, without even the need for bigger particles to block one end of the pore. The reason it's relevant, the researchers suggest, is that it shows the potential for an extremely rudimentary metabolism at the very beginnings of life. It's possible to maintain a particle gradient of, say, sugars and ions, across a membrane without any of the fancy multimeric gated two-way channels that we advanced eukaryotes sport. An early ion pore could easily have evolved from a protein that already bound that ion and underwent a mutation that bound it to the membrane.

Tuesday, June 5, 2007

Instead of studying . . .

While doing a practice MCAT this weekend, I had to read a Verbal Reasoning passage about the origin of retirement communities during the 60s and 70s. For the most part, it wasn't interesting, but it made a fascinating point early on. It pointed out that until relatively recently, old age and death were not really associated with each other. During the French Revolution, for instance, only about 10% of mortalities occured in people over sixty. About a quarter of all deaths were infants. Thus, as late as the mid-nineteenth century, at the beginnings of modern medicine, no one's mental picture of death included old people, which at least to me, is quite a thought.

Ordinarily, I'd start pontificating at this point, but I have to study.

Monday, June 4, 2007

"I pledge allegiance to the Christian flag . . ."

1. Last night I watched Jesus Camp, a 2006 documentary following several Missouri children at a radical Evangelical Christian's summer camp in North Dakota. It's disturbing and worrisome on several accounts:

- The organizer of the camp openly admits to using the same tactics for brainwashing (though she rejects the term "brainwashing") children as the Jihadists in the Middle East.
- The children are mostly homeschooled, and taught falsities such as creationism.
- Everyone believes that the President was sent from God (notably, they pray to a cardboard cutout of George W. Bush).
- Everyone believes that the end of days is near.

But these were not the most haunting aspects of the film. Two of the most prominent characters are Levi and Rachael, twelve and nine years old, respectively. They have both been fully brainwashed into all the above beliefs; however, they're quite different in one central respect. When Rachael speaks, it's very obviously rehearsed. It sounds like a child of equivalent age acting in an elementary school theatre production. The language seems above her level, like it's something she memorized from a book. The thing is, she's not acting. At least she doesn't thinks so. There's a vacancy in her eyes that gives you the uncomfortable feeling that subconsciously, she's questioning everything she says.

Levi, on the other hand, delivers a much more convincing sermon (literally - he's asked to preach to the other kids). But when he talks, he's unequivocal. Although it seems just a little rehearsed, there's no doubting his sincerity.

So which situation is worse? What the parents did to Rachael is tantamount to torture, and what they've done to Levi is tantamount to murder. Rachael's right to freedom of thought is dying a slow death, but Levi's has long since perished. Is it worse to have removed the capacity for rationality long before it had the chance to develop, such as in Levi's case, or to severely cripple the faculty, leaving the child a moral vegetable with a glimmer of doubt? I suppose it's all in Jesus' greater plan.

Monday morning video.

Another neat CGI video of a biological process. We originally saw it, once again, in our Mic-Phys class. In this episode, we switch to the prokaryotic flagellum. It's not as cool as the first one, but I still lurves me my biographics.

Admittedly, the video was posted by some Coke-Can Creationist (or maybe Koke Kan Kreationist?) as "Evolution's Nightmare & Demise." Whatever. Like, everyone knows it's just a specialized type II secretion system. Jesus - I mean, uh . . . Darwin?

Sunday, June 3, 2007

Game Theory: Application - Toilet Seat Politics

Toilet Seat Politics refers to the annoyance that most women encounter:
"The toilet seat was left up and now I have to put it down because I can't pee standing up. Those BASTARDS!".

In the defence of men, I feel women should at least understand why some like it that way.
I would argue that men like the seat up because it is more convenient to stand, as we are quick in there anyway.
Although I like it down, I remember that I live with a female/(society with females), and that I should put the seat down. BUT AT WHAT COST!

This article relates this societal problem to game theory and claims that
Putting the seat back up in inefficient!

In this paper, we show conclusively that the social norm of leaving the toilet
seat down after use decreases welfare and by doing that we hope to convince the
reader that social norms are not always welfare enhancing. Hence, there is a
case for scientifically examining social norms and educating the masses about
the fallacy of following social norms blindly.

I was first introduced to game theory in Economics. To learn more see: Nash Equilibrium.

Lime 'n' Dust underwent a name change

The new name of this blog is Cheesobacillus furiosus. We at Cheesobacillus furiosus feel that it better reflects our view of the scientific world today. And our intense love for Cheetos, Cheesies, and all other forms of artificially-flavoured neon-orange rod-shaped cheese-like snacks.

It all started from our abuse of Latin species names in our Mic-Phys class. Two species names appeared on the screen: Pyrococcus furiosus and Congregibacter litoralis. Aaron's initial dirty joke, that started it all, was that it would be funny to stick a "C" in front of "litoralis" (oh come on, it's funny). Then I observed that Clitoralis furiosus would be quite possibly the funniest possible bacterial species name. However, it would be too offensive to be the title of this blog.

So about six months later, Aaron commented on the rather bacilloid shape of cheesies. We decided Cheesobacillus would be an appropriate name. In keeping with our love for C. furiosus, we compromised by making Cheesobacillus the genus name to replace Clitoralis; hence, Cheesobacillus furiosus is born.

Saturday, June 2, 2007

This one goes out to all those OHRIers out there.

I've never even played Dungeons and Dragons, but this is hilarious. Props to Pharyngula for posting it.

all this time, I thought my lanky fingers were a disfigurement

You know what they say about men with long 4th fingers...
HUGE - Math skills ???
In the spirit of the notion that big hands, feet, nose, whatever = big penis,
an interesting study correlates the size of the 4th finger in males to aptitude at math.

"Boys with the longest ring fingers relative to their index fingers tend to excel in math, according to a new study. In girls, shorter ring fingers predict better verbal skills. The link, according to the researchers, is that testosterone levels in the womb influence both finger length and brain development."

So ladies, if we assme that large hands = larger 4th finger (still to be proven): if relative finger length is percieved as an indicator of 'sexual aptitude', but also correlates to mathematics, then shouldn't you be "integrating some natural logs" (Stern A. M "Mathematical Jokes" Residence Conversations. 2005)?
Hold that thought, I'm having a nose bleed, battle star galactia style.

Friday, June 1, 2007

Better than the Discovery Channel

This video is amazing. In short, a young buffalo strays too close to a pack of lions, the lions attack the young buffalo, then a crocodile gets involved, and the rest of the buffalo herd returns to fend off the lions. Watch the whole thing; it's great. I found it on The Voltage Gate, another great blog from ScienceBlogs.

I, for one, welcome our moth overlords

Man, Darpa kicks ass. Turns out that within the next few years we'll be flying robo-moths over enemy camps. I think this officially trumps the sharks with lasers attached to their foreheads. If you go beyond the military applications, this technology could be used everywhere. Imagine the research you could do if you could grow mice to behave exactly as you wish, without intefering with, say, the immune system.

The ethical issues will be enormous though. In medical science, I've always been part of the "them or us" camp, and I think for the most part, I'd remain resolutely there even if we made remote-controlled mice. If anything, it would reduce pain and suffering by cutting down on the need for risky anaesthesia or missed injections, if you could grow some sort of internal iv bag, with a remote-controlled release. It would also eliminate mistakes in euthanasia, if there could be some immediate, painless way of killing the mice using internal machinery. It's all just speculation, but this technology will be immensely valuable.

Surface Computing

This, is probably the coolest thing I've seen in a while.
Jeff Han, research scientist for NYU's Courant Institute of Mathematical Sciences, demonstrates his intuitive, "interface-free," touch-driven computer screen, which can be manipulated intuitively with the fingertips, and responds to varying levels of pressure.

I originally saw his segment on "TED talks" and subsequently, Microsoft has designed the follow up application for the technology.

It reminds me of that Tom Cruise movie, set in the future, with the 3 aliens who can predict the future, and they are like time cops or, pre-crimes or...
Oh that's right, it was MISSION IMPOSSIBLE, anyway, I guess it reminds me of that.
(In actual fact, the movie was : Minority Report)