Tuesday, February 21, 2006

The realities of lab work

As I start to do more labwork, I'm gaining an appreciation for two things:

- The often-peddled view of "breakthrough" experiments obscures the fact that the majority of time needed to do experimental work is spent just making all the stuff you need for the experiment you really want to do. Doing the "final"/"breakthrough" experiment itself is often one of the quickest bits.
- A lot of experimental molecular biology is based on exceedingly unlikely events and making it up on volume.

Let's take the second bit first. An analogy, inspired somewhat by personal experience: suppose you have your windows open on a warm summer night and a bat flies in and starts flapping around in circles in your living room. You'd like to catch the bat and toss it back out on its ear, so to speak. One [admittedly batty, haha] scheme would be to reason as follows: a bat is sort of like a mouse with wings. Now, what catches mice ? Cats, that's what. Are there any cats on hand ? Yes, there are. So, how about tossing a cat into the air and hoping that it catches the bat ? [Assume, for pedagogical purposes, that the cat available to you is sufficiently composed to recognize the most important aspect of the situation, viz. that there is a mouse to be caught, and ignores such trivialities as the fact that it's being tossed into the air.]

Now, the chances of the cat catching the bat on any single toss are miniscule. However, if you toss the cat, say, a million times, the chances that the bat is caught start to rise into the realm of not-totally-improbable. And that's how a lot of experimental procedures in molecular biology work: you throw together a bunch of things that might snap together in the right way maybe once in a million times, but if you do this with bajillions of cells [and you can easily get a million cells in a milliliter of cell culture], the chances are good that you'll get a few instances where things snap together correctly.

Ok, so you get lucky occasionally, but given that lots of lab work consists of mixing colourless liquids together to make more colourless liquids and you can't really look inside cells to see what's going on at the molecular level [recent cool developments notwithstanding], how do you figure out when the desired event has taken place ? This is where the high art [and science, I suppose] of genetic selections comes in. A lot of genetic selections are predicated on arranging things such that if the right thing happened, the critter lives; if the wrong thing happened, the critter dies [or vice versa; both types of selections are used].

For example, a commonly used selection is antibiotic resistance: take cells that are normally vulnerable to an antibiotic like ampicillin, perform your experimental procedure on them and then looks for cells that have acquired resistance to ampicillin. If the right thing happened, a small fraction of the cells will have acquired a gene that makes them resistant to ampicillin and will grow on an ampicillin-containing medium whereas the rest of the cells that you used for your experiment will die. Genes like the ampicillin resistance gene are referred to as "markers", because they mark the cells that you want.

A concrete example of all this: one of the ways to insert foreign DNA into a yeast cell is to use a mechanism called homologous recombination. Pretend the yeast genome consists of actual text, like:

"Tonight I ask you to pass legislation to prohibit creating human-animal hybrids because I think they're the work of the devil"

If you now introduce a piece of DNA whose beginning and end are the same as some stretch of genomic DNA into the yeast cell, like:

"creating human-animal hybrids like me and other members of my administration because"

then, a few times in a million, there's a bit of "cut and paste" so the yeast genome becomes:

"Tonight I ask you to pass legislation to prohibit creating human-animal hybrids like me and other members of my administration because I think they're the work of the devil"


This sort of swapping is called homologous recombination. It's a rare event -- the new piece of DNA needs to "find" a stretch of genomic DNA that matches at the right spots and, even for something as simple as yeast, the genome is over 13 million letters long so there's lots of ground to cover; the cell is a pretty crowded place; the right protein machinery needs to be around to make the swap happen etc. And, of course, you have to get the details of the experimental procedure [mostly] right.

Even though it happens so rarely, homologous recombination is one of the main ways used to modify the yeast genome. The selection that's often used to find the cells in which it happened is to use cells that can't make an amino acid that they need [and so they won't grow on medium without that amino acid] and, together with the new DNA, introduce a gene that allows them to make that amino acid. Cells that have successfully recombined the new DNA into their genome then acquire the ability to grow on medium lacking that essential amino acid, which ends up looking like this -- the white spots are colonies of yeast cells that are able to grow successfully.

Of course, there's now another complication: the number of easily usable marker genes is fairly small, certainly less than 10 for yeast. If you use up one marker gene each time you modify a cell, this means that you're limited to less than 10 successive modifications. So if you want to make lots of changes, you have to figure out a way to recycle your marker genes. Doing so often requires that you have what's called a "counterselectable" marker -- if you grow cells in one way, only cells that contain the marker survive; if you grow them in a different way, only cells that don't have that marker survive. So the entire procedure requires that you first do your experiment such that only cells in which the right thing happens acquire the marker and survive and you then take the survivors from the first step and grow them under different conditions so that only the ones that have now lost the marker stay alive.

Each such iteration takes, say, 1-2 weeks if you're good at it, have all the necessary raw materials [like the pieces of new DNA] readily available, and don't run into any trouble [which is, unfortunately, not a sufficiently rare event ...]. So, to make, say 10 changes in the genomic DNA of a yeast cell, you're talking 3-6 months until you have the yeast cells that you want to actually experiment on.
If, along the way, you've had to construct the new pieces of DNA yourself, a process that's pretty much the equivalent of self-flagellation, it'll probably take twice as long. Throw in a fudge factor of "I've never done this before, so I'll make lots of mistakes along the way" and you're up to about a year.

Now you can finally start doing things like checking how these cells respond to being poked with the molecular equivalent of a sharp stick. And, of course, if you're unlucky, they won't do anything interesting at all, so you've just spent a year of your life on mind-numbing work and constructed something that's about as exciting to watch as this. Congratulations !

All this is just a long-winded way of saying: this whole lab work thing is definitely 99% perspiration, 1% inspiration.

Throwing stones from the inside

After recently reading "Off-Center", which presents some pretty persuasive evidence that the Republican party has managed to mostly stamp out dissent within its ranks and is heading hard-right to kookville at full speed, it's nice to see that there are still some Republicans who aren't afraid to tell it like it is [together with, of course, the obligatory administration shill ...]. The description of Bush [attributed to Bartlett's book] as a man not at all inclined towards thoughtful analysis resonates with me all the more because I just finished "The Survivor: Bill Clinton in the White House", which portrays Clinton as the diametric opposite: so interested in considering all the angles that he was sometimes paralyzed.

It's hard to imagine a worse match than this man, a personification of the adage "For every complex problem, there is a solution that is simple, neat and wrong" , with a world that's as complicated as ours.

Friday, February 17, 2006

Cheney, truly a minion of Hell

Only a creature of dark aspect would be able to strike such fear in the hearts of men that they apologize for getting shot by him and are concerned about his well-being.

I mean, damn. That's a serious Dark Jedi mind trick.

[An alternative theory is that Whittington's statements are a consequence of the affection and love that Cheney inspires in all who meet him, but we all know that would just be crazy talk.]

Wednesday, February 15, 2006

Numbers, useless

From a story about the man who was unwise enough to be around a Dick Cheney packin' heat:

Dr. David Blanchard, the emergency room chief, estimated that Mr. Whittington had more than 5 but "probably less than 150 to 200" pellets lodged in his body.

That really rules out only 1-5 pellets, but leaves the door open for, say, 20000 pellets because of the artful "probably" dodge in the second half of the estimate. Translation: "I have no clue, but since you insist on me giving you numbers, here they are. Satisfied ?". Kind of like Musharraf's recent take on the likelihood of terrorist fatalities.

[Not that I'm generally in favor of people getting shot but this whole thing still has me chuckling. It would have been even funnier if Cheney had been the one with the indeterminate number of pellets inside him.]

Friday, February 10, 2006

What I tell you four times is true

Hmm. I've been tagged with the "4 things" meme, the blog version of a chain letter. At least it comes without the "If you don't pass it on, a friend of yours will be gored by a rampaging boar when he least expects it" threats that usually accompany such things.

Four jobs I've had:
1. Gardener, in a cemetery. Very laid-back patrons.
2. Programmer in a high-energy physics group. FORTRAN, I hardly knew ye ... thank god.
3. Footsoldier for the now-mired-in-bureaucracy, Not-Really-Very-Evil Empire. Nothing like some TPS reports, with accompanying cover sheet of course, for slowing down the inexorable rise of evil.
4. Stacker and general monkey boy in a college library. This allows me to scoff at the admonitions in a library not to re-shelf books myself because I know the secret code of Dewey.

Four movies I can watch over and over:
1. "Enter the Dragon"
2. "Crouching Tiger, Hidden Dragon"
3. "Princess Mononoke"
4. ... actually, I can watch [bits of] lots of movies multiple times, regardless of how good/bad they are, something that utterly baffles Christina.

Four places I've lived:
1. Wernau, Germany
2. Accra, Ghana
3. Philadelphia, PA
4. Seattle, WA

Four TV shows I like:
1. Arrested Development
2. Curb your Enthusiasm
3. House
4. Six Feet Under

Four places I've vacationed:
1. Namotu, Fiji
2. Itacare, Brazil
3. Sayulita, Mexico
4. Matapalo, Costa Rica

Four of my favorite dishes:
1. Haribo gummy bears [trust me, I can make a meal of them]
2. Sauerkraut and Spaetzle
3. Fried plantains and jerk chicken
4. Real German pretzels, with salami

Four sites I visit daily:
1. Superbike Planet
2. Surfermag.com
3. Arts and Letters Daily
4. NY Times

Four places I'd rather be right now:
1. Just about any MotoGP racetrack, on a dry, warm, sunny day, riding a motorcycle I don't have to worry about crashing
2. Sitting on a longboard in warm, non-sharky water, with very few other people out and consistent, glassy waves that are gentle enough that even I can surf them and no reef or rocks to worry about on the frequent occasions that I wipe out
3. At the Amazon website, with no spending limit
4. Seattle

Four bloggers I'm tagging:
1. Christina
2. Brandon Watson
3. John Miller
4. Lawrence David

Four books/series I like:
(arbitrarily restricted to fiction)
1. Anything by Iain M. Banks
2. Anything by Neil Gaiman
3. Richard Morgan's Takeshi Kovacs series
4. Ursula le Guin's Earthsea series

Four games I can (and do) play over and over again:
1. Scrabble
... and that's about it. Not much of a game player.

There. All of me, in 4-sized chunks.

Wednesday, February 08, 2006

Graphic violence

For some reason, I think this headline would be funny if it weren't so tragic:

"Bush Urges World Leaders to Halt Violence Over Cartoons"

Friday, February 03, 2006

A month's worth of reading

Well, the next semester is almost upon us -- classes start on the 7th and with that my responsibilities as TA begin [actually, they've already begun; we've already written the first problem set]. The last few weeks have been mostly marked by reading. To wit, I have devoured the following:

- "Birds Without Wings": Another Louis de Bernieres tragicomedy, more tragic than comedic. Not quite as entertaining as the triad that begins with "The War of Don Emmanuel's Nether Parts" but definitely larger in scope.
- "Dreams from My Father": This didn't do much for me, I must admit.
- "The Great Influenza": A well-written, if sometimes rather repetitive, account of the 1918 flu. What makes this more than just a long-winded version of "Lots of people died from the flu" is the account the book gives of all the social and cultural factors that influenced the course of the flu: the First World War, the recent emergence of science-based medicine, the state of [biological] science in general, Wilson's decision to devote all American resources single-mindedly to the war etc. The book even has an interesting thesis that indirectly pins World War II on the 1918 flu.
- "Anansi Boys": More gods-walking-among-us fare from Neil Gaiman, this time based on Ananse, a character I heard/read lots of stories about growing up in Ghana. An easier read than "American Gods", I thought.
- "Woken Furies": A good conclusion [maybe ?] to Morgan's Takeshi Kovacs novels. Less predicated on Takeshi being faster/smarter/stronger than everybody else and much more "internal", so to speak.
- "Market Forces": Capitalism taken to the extreme, plus legalized road rage. Entertaining, but the ending left me a bit flat.
- "The Algebraist": More Iain Banks goodness, with the usual Banks ending -- the story is [ostensibly] over, but you can sense that a new interesting tale is being born and so you wonder what happened to the characters next.
- "The Republican War on Science": The title pretty much says it all and the book makes a convincing case for it [on the off chance that anybody is seriously still in denial about the issue].
- "Lamb: The Gospel According to Biff, Christ's Childhood Pal": Very funny satirical account of the first thirty years of Jesus' life. Kind of like "The Satanic Verses" [or recent cartoons], minus the accompanying fatwa and insanity.
- "Fluke": Another comedy by the author of "Lamb", but not quite as funny.
- "Off Center: The Republican Revolution and the Erosion of American Democracy": Viewed in a disinterested way, a very interesting handbook of how one party has managed to ignore the pressure to remain close to the center and instead moved extremely far to one end of the spectrum, without having an overwhelming majority anywhere. From a less detached perspective [eg you think the leaders of said party are bunch of scumbuckets], well, it's just plain scary and somewhat disheartening.
- "Superman: Red Son": What if Superman's rocket had landed in the Soviet Union instead of the middle of America ?
- "Marvel 1602": The X-men set in, well, 1602, period costumes and all. Nicely done.
- "Batman: The Dark Knight Strikes Again": A 60-year old Batman once again comes back and cleans house, putting the hurt on Superman [who just isn't very bright, despite being "super" in all other respects -- if he'd stayed on Krypton, would he have been considered a bit slow ?]

... and several hundred pages worth of scientific papers as I try to nail down my thesis project.

Somehow, I suspect I'll be doing less pleasure reading for the forseeable future.

Wednesday, February 01, 2006

The jesters speak truth

Here. There's more I want to say about the State of the Union speech and the smarmy f!ck who gave it but let's not even go there.