Thursday, July 19, 2007

If only she weren't considered a materials engineer . . .

I was conscripted by the head of the honours program in my department to help organize a guest lecture in October. My top choice was Robert Shapiro, the author of the origins-of-life paper I mentioned a few weeks ago. As it turns out, he's already coming to Montreal from New York the week before the date of my lecture, which is half-unfortunate. It means I still get to see him lecture, which should be great, but it means I'm not the one to bring him here. My next choice was going to be Angela Belcher from MIT, whom Scientific American named 2006's Researcher of the Year.

Her research is incredible. She has built a battery out of phages. She has phages that encode semiconductors, and ones that can form liquid crystals. She figures some day, we'll be able to construct complex circuits by encoding them with DNA sequences. Just grow your own computer.

This is the 2006 Science paper in which they constructed a lithium ion battery out of phages coated in cobalt oxide and gold. They expressed metal-binding glutamate-rich peptides fused to the major coat protein of M13, a helical phage, then simply soaked it in a metal solution. M13 can form long crystals, which when coated in metal, act as nanowires. Using the right substrate, it also spontaneously forms two-dimensional structured arrays. Craziness, I say. Craziness.

Unfortunately, I was vetoed, and we won't be trying to bring her in to Montreal(after all, it really isn't that close to Microbiology and Immunology).

Thursday, July 12, 2007

Special guest contribution: What's the worst thing to mix with beer?

At my workplace there is a weekly tradition called "Friday beers". Basically, after work on Fridays, the company provides beer and wine to those who want it. Most people want it. It's a great way to get to meet other people in the company, even though some of them are a bit odd.

One person at my company has an interesting party trick: he can drink anything mixed with beer, no matter how disgusting, without hesitation. Milk and beer? Check. Orange juice and beer? Yup. Coffee and beer? Yes, that too. This led into a discussion of what the most vile beer-liquid combination would be if we weren't limited by the kitchen's poor selection. (You might ask what this has to do with science, but don't worry, there's some chemistry at the end for those who are into that.)

Lots of suggestions were made. Ketchup and beer. Ground beef and beer (even though the case for ground beef being a liquid is arguably weak). Pølsevann and beer. (Pølsevann is the Norwegian term for hot dog water.) But one suggestion sent a shudder down all of our spines: Coffee-Mate and beer.

For those who are unfamiliar with the product, Coffee-Mate is a coffee creamer: a powder you put in your coffee if you want it to be creamy. And taste horrible. You might ask, why don't people just use regular cream? I don't have an answer for you. All I know is Coffee-Mate has, inexplicably, been selling strong for 46 years.

The worst thing about Coffee-Mate, apart from the taste, is that it contains no natural ingredients. The only ingredient that has anything to do with cream is sodium caseinate. The connection? Casein is a protein found in cow's milk. It also contains dipotassium phosphate, which is a pesticide for fungal diseases as well as a fertilizer. The remainder of the ingredients are mostly corn syrup solids (yum) and various chemicals that make it look somewhat white-ish and ensure it doesn't clump. There's also a few artificial flavours in it that are supposed to make it taste like cream. They don't do a very good job, though.

There's $20 in it for the first person to post a YouTube video of him/herself drinking a beer with half a can of Coffee-Mate mixed in it.

Wednesday, July 11, 2007

Also make sure the cat can't eat the toast.

Aaron and I had a discussion about perpetual motion machines the other day. Of course, I am entirely convinced that it's impossible. There can't be a 100% efficient transfer of energy; the second law of thermodynamics says so. Aaron remained at least a tiny bit agnostic, thinking that maybe, just maybe, the second law isn't really a law after all. At any rate, this guy certainly didn't quite get it yet.

It reminds me of the Mythbusters episode with free energy machines. It's incredible how much time and energy (pun intended) some people put into finding a counterexample to something completely accepted by every scientist since, well, a long time ago. One guy had this gigantic Ferris Wheel-sized contraption in his backyard. What did it do? Turn very, very slowly. I think most of the supposed perpetual motion machines move using magnets, which some people seem to think are exempt from the whole delta-S thing. Since all those kooks are barking up the wrong tree, here's my plan to build a perpetual motion machine:

Step 1: Buy a cat.

Step 2: Buy a loaf of (preferably sliced) bread.

Step 3: Toast a slice of bread.

Step 4: Butter one side of toasted side.

Step 5: Fasten toast to cat's back using string or otherwise secure mechanism, with unbuttered side making contact with cat.

Step 6: Cover kitchen floor in KY.

Step 7: Drop cat-toast from a one-meter height onto lubricated kitchen floor.

At this point, the fifth law of thermodynamics, which simultaneously states that cats land on their feet and toast lands buttered side down, takes effect. So what happens? Well, naturally, the cat-toast never finds equilibrium, and constantly flops around on the lubricated surface for all eternity. As controls, one could drop a cat without toast, toast without a cat, a cat with unbuttered toast.

An alternative experiment could involve strapping one cat to another cat, and dropping it. But cat squirming could interfere. Also, I suppose one could also just butter both sides of the toast. But then that wouldn't involve cats, so, like, what's the point?

Thursday, July 5, 2007

This post looks like it sucks. Therefore, it sucks.

Today I was reminded of a segment on Daily Planet (oh shut up, science snobs) about how visual perception changes taste. For instance, from a large sample of people, they found that a brownie served on a napkin was opined to taste worse than an identical one served on a plate with a fork. That was mildly interesting, but the craziest demonstration involved yogurt. They sat someone down, and told her that they wanted to determine which of the two strawberry yogurts presented in front of her had a more authentic strawberry flavour. They blindfolded her, but before allowing her to taste them, they switched the yogurt for vanilla yogurt mixed with a small amount of chocolate sauce. Lo and behold, she had a very strong opinion about how authentic the strawberry flavour was, and made detailed comments about the subtleties of the flavour. And there was absolutely no strawberry flavour there! They repeated the experiment with several people, and everyone tasted strawberry. It's interesting how one sense can so strongly influence another. Maybe it's why people still find their spouses attractive as they age.

Speaking of visual media with the word "planet" in the title, if anyone's thinking of buying me a five-month-early birthday present, may I suggest Planet Earth, one of these David Attenborough mega-eco-documentaries. It would be fun to rent out an OMNIMAX(apparently now called IMAX Dome to watch it, but I'd settle for my apartment. Or maybe we could screen it at the department as a fundraiser, or substitute it for yet another boring HIV talk.

Monday, July 2, 2007

What happened to the cat with dry skin? Purrrrritus.

I've often wondered why we scratch itches. If you think about it from an objective point of view, it doesn't make any sense to scratch. If anything, it only irritates the skin more. So why does it feel good? Thankfully, the back page of Scientific American, bringer of useless yet fascinating information, had a short article explaining it. Turns out that the "pruritus" (note quotation marks for fancy Latin name for itching) neurons are separate from "pain" and "rubbing" (note quotation marks for non-fancy non-Latin names for pain and rubbing) neurons. Because of a local inhibitory effect, these neurons trump the pruritus sensors, temporarily relieving the itching sensation. The itching arises in the first place from things like dryness and chemical irritation.

Maybe it could work the other way. We could be treating soreness and pain with poison ivy, or something, if the pruritus sensory neurons can also inhibit the pain ones.

Also, "pruritus" is an incredibly tough word to pronounce. It's like "rural," but harder. I can only imagine trying to say it in French; I think I'd need some Halls afterwards.

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)

Thursday, May 31, 2007

How it all started.

My cloning worked. Looks like sacrificing all those mice to the cloning Gods worked after all.

While waiting for said cloning to work, I found this very interesting Nature article about our innate mathematical ability. It essentially shows that our nonsymbolic arithmetical capabilities (i.e. manipulation of, say, dots) precedes and even dominates over our symbolic capabilities (manipulation of actual "numbers"). They showed that preschoolers with no training in arithmetic were able to complete addition and comparison tasks better than chance, and that their performance in nonsymbolic tasks followed a similar pattern to adults. They concluded, or at least suggested, that once we learn arithmetic, we form a mapping of the arithmetical symbols (i.e. numbers and operators) onto real visual arrays of objects. In other words, we don't do math in our heads; we move dots around.

I've always been interested in the roots of math. It's become such an important part of our culture and education that we sometimes forget what it really is. As was said in an excellent and famous book about the origins of math, math originated from our ancestors' realization that three dots and three oranges and three mountains and three days are really just manifestations of the same abstract concept: three. So perhaps we evolved some sort of number recognition software. When you think about it, it's a pretty impressive trait. Dots, oranges, mountains, and days aren't remotely related, and yet we, as well as other higher animals, have the ability to recognize the link. And then to think of all the wonderful discoveries about our view of the universe have been made because of this link. It's astounding.

Tuesday, May 29, 2007

Why does he have such big teeth?

So naturally, the one positive clone among the 200 I screened had the insert in the wrong orientation. Now I'm stuck screening 400 more tomorrow.

Anyway, Check this out: they recreated Pac Man's skeleton. Yup. I guess they didn't use fossils. Although maybe this will start a trend: video game anthropology. You could trace the evolution of Italian plumbers, optimal rotational speeds of talking blue hedgehogs, and make life-size panoramas of space wars. I'd totally see that exhibit.

Sharks with Frickin' Laser Beams on their Heads

As a fan of Austin Powers and DARPA, I was delighted to see the very first step towards Dr. Evil's dream of LASER-SHARKS, not to be confused with the hilarious SNL skit : "Laser Cats".
What this will mean for the future? More JAWS movies.

Human = Bacon?

One can always count of the extreme innovation of Japan.
A robot capable of identifying cheeses, meats and hors d'oeuvres will recommend wines to go with them. However, there is one problem: It thinks we are delicious.

Monday, May 28, 2007

Even this blog entry is false.

Seed Magazine, the greatest magazine on Earth, has a short summary article about the work of John Ioannidis, most specifically his article in PLoS Medicine entitled "Why Most Published Research Findings are False" . I haven't read the whole article yet, since it's quite long and involved, but it implies some interesting ideas; essentially, that almost all research is actually false because of bias on the part of the researchers, a scientific culture that demands publication, and most importantly, abuse or ignorance of statistics. Since I haven't read the whole thing, it's hard to analyze, but I like the part about misinterpreting p-values. The 0.05 p-value is the gold standard of statistical significance. But Ioannidis proposes a new measurement of significance that more directly measures the probability that the findings are true. The new measure, PPV, is similar to p-value in that it depends on alpha and beta (the probability of type I and II error, respectively), but also the probability before the study that the relationship exists, as well as the bias from the researcher in the form of selective reporting and distortion of data.

It's an interesting report, but it's hard not to ask the question of whether or not it is true itself, given its own findings. It seems a little Godelian to me; it's like saying "this statement is almost certainly false." Maybe he stumbled upon a new proof of incompleteness, or at least a real-world application!

Sunday, May 27, 2007

They should contact Dreamworks

Man, I love this video. I'm not sure why it was made, other than to look cool, but it sure gives me the tingly feeling. I'm impressed by how authentic it is, like the ribosome assembly on the mRNA: first the 40S binds, then it scans to the start codon, then the 60S binds. Or the lipid raft at the cell surface. Everything is so damn well put-together. They should make another one of a viral infection like poliovirus, showing it hijacking all the translation machinery until the cell is just a bag of virions.

Friday, May 25, 2007


Want to be the ultimate exhibitionist? Frame your DNA. These guys are awesome. You send them a cheek swab, they prep it and, I guess, either digest it or PCR some variable tandem repeats, run it on a gel (or, as they call it, a "gel"), and take a photo with a geldoc (or, as they call it, a "special camera"). Here's the artistic part. They open Photoshop, click Image--->Adjustments--->Hue/Saturation. Then they move the little scale bar. Next, they give a creative name for the colour, such as "firesky." The final step is convincing people to pay 450 dollars for it. I must say, they do a good job with the whole "yah dude, science is like, art in its, like, most, uh, basic form . . . dude" schtick. Maybe I can hire them as marketing consultants for my science restaurant.

That, or I could make polyacrylamide sculptures such as these. Note the avant-garde (read: corny) titles. Photos courtesy Karen Yam.

Forgotten Controls

Overreaction Coupling

Thursday, May 24, 2007

Visa-14 Dating?

It seems I've inadvertently created quite the procrastination tool. I should probably be studying for the MCAT right now, but whatever. It's only, you know, my future.

Apparently the Brits are trying to be all environmental now, with the Labour proposing this absolutely wacky idea for carbon rationing to cut down on pollution. I don't know the first thing about British politics, but this really doesn't make any sense. It seems more like a Jack Layton-style let's-say-ridiculous-things-to-sound-innovative initiative, except without the rather offensive moustache. The logistics and cost of this project would be absurd. Imagine trying, from scratch, to set up the entire Visa network; they would have to use something along those lines in order to keep it secure. This thing has fiasco written all over it. If I were President of the World (or at least Prime Minister of the UK), I'd start with a carbon tax. There's virtually no infrastructure to set up, and it's easily subject to modification.

Did you hear? Jesus was a shark. Or at least Mary was a shark. Or sharks gave rise to humans. Or something. Somehow I get the feeling the creationists are going to try to spin this as proof of the immaculate conception. The argument would go like this:

Creationist: "Sharks are capable of parthenogenesis. Therefore, Jesus was conceived without a mortal father."
Rational Person: "How do you make that conclusion?"
C: "Well, you see, the Bible says Mary was impregnated despite being a virgin. And sharks are a present-day example of that possibility."
RP: "So..."
C: "So the Bible said so. Ergo, it's true. Asshole."

And so on. I'm sure R-Dawk would have a better version, but it's the best I could think of. And has "asshole" in it.

Wednesday, May 23, 2007

Inaugural Post

As creator of the blog, I'm giving myself first post. Sorry Aaron. I got the idea from some folks at the Ottawa Health Research Institute, who run a science blog called Bayblab, and essentially post interesting news articles and stories. Then I started my addiction to ScienceBlogs, an offshoot of Seed Magazine. There are some amazing blogs there. I especially recommend "The Daily Transcript," written by a post-doc from an RNA lab like mine; "Good Math, Bad Math," written by a (gasp!) sane mathematician; and, if you really like atheism and all that jazz, "Pharyngula." So I guess these blogs sort of inspired me to convince Aaron to do this. Right, Aaron? You're inspired, right? . . . Aaron?

I'm not entirely - or even partially - sure what we're going to talk about. I guess I just want to have somewhere to put all the crazy ideas we come up with (like " reverse suspenders" - stay tuned), or to share news stories or articles we find. That, and I finally want something to put in the "website" slot on Facebook.

Anyway, Karen from my lab sent me this article about chefs who do pseudo-scientific experiments to make wacky dishes served on things like pillows. I say good on them; if people are really willing to pay fifty dollars to inhale the vapours of a spoonful of icing sugar heated over a flaming cornish hen doused in huckleberry liqueur, then let them. The idea of experimenting with our sense of taste is interesting, though. We're at a point where, if we're not already there, we could figure out exactly what molecules or functional groups taste good and in what context. It can't take that much screening. Then we could design super-tasty molecules. Maybe even undigestable ones that go right through you, and therefore contain no calories. I'm sure it would cost a ton of money to develop, but I bet Coca-Cola or someone would totally shell out the clams.

The Star article (Starticle?) also brings me to my life-long (well, at least one-point-five-year long) dream of opening a restaurant or bar (or perhaps, restobar) where all dishes are served on scientific ware. Think about it. Beverages served in beakers. Shots out of 25 ml Erlenmeyers. Pipette chopsticks. Scalpel knives and fork-ceps. It can't fail. Right? Right? . . . Aaron?

Well that's enough for tonight. I have to bone up on osteoclasts (hiyo!). Well, not really - I just wanted to make that joke.