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.