Spit and adenosine triphosphate

How is it you can drink saliva all day long and never run out of the stuff?

Sorry to put the image of spit-drinking in your mind, but you’re doing it right now, am I right? And the more you think about it, the more you do it. Before today is over, you’ll have swallowed more than one vice-president of the stuff. Here’s how I figure it: a healthy human (that’s you) consumes something like a liter of spit per day. That would fill up a typical pitcher, and John Nance Garner, who was vice president under Franklin Roosevelt, once remarked that his job was “not worth a pitcher of warm spit.” So the vice-president, as a unit of saliva volume, is therefore less than your daily output. This reminds me of the names of champagne bottle sizes. The larger sizes are named after rulers of Israel and Babylon. So a double magnum, or three liters of champagne, is known as a Jeroboam (the first king of northern Israel). By extension we might measure salivary volume in terms various legislative occupations. How much is a Speaker of spit? Or a House Minority Whip of spit?

But I digress.

My point is that your body is a collection of remarkably dynamic processes that give the illusion of stasis. And the thing that got me started on this line of thought was this sentence:

In order to provide energy to sustain our lives, every day, each one us produces a quantity of ATP by this mechanism that is approximately equal to our body weights.

Yikes! That’s an astonishing amount of flux for one single molecule. Do you want to see how (most of) this ATP is made? Look at this.

The quote and the image come to us courtesy of the Mitochondrial Biology Unit at Cambridge University. We’ve known for a long time where the ATP was being synthesized. But now we know the shape of all the insane molecules that do that work. The ATP mill you’re looking at here isn’t something exotic. Your body has enough of them to pump out a pound of ATP every ten minutes or so, one molecule at a time. And that is a spitload of ATP.

Molecular biology cinema

Hey, so I totally scooped the New York Times with my post last week about animation and molecular biology. Only two days ago they came out with this article: Molecular Animation – Where Cinema and Biology Meet. I’m sure they were peeved about my piece, and they probably rushed theirs into production as a result, but it’s a nice article.

It’s accompanied by this video, which I would embed here, but it appears they don’t permit that.

Cell Size and Scale

In a Zoomable User Interface (ZUI), you can move up and down the scale of a spatial dimension easily. This feels very natural when you’re zooming through something that you have some physical intuition about, like a picture of the inauguration, or a map of the planet. It can be very disorienting when you’re zooming through an abstract space.

Here’s an especially nice example of where it can work well: Cell Size and Scale.

It’s always eye-opening to see how tiny cells are, and then to see how tiny (most) bacteria are relative to eukaryotic cells. Consider: you couldn’t cram one of your chromosomes into an empty E. coli shell if you used a spatula and two shoehorns. I don’t know if I’m more impressed with my size or E. coli’s minuteness.

Evolution and geology

I just finished reading Sean Carroll’s book The Making of the Fittest. Subtitled “DNA and the Ultimate Forensic Record of Evolution”, it’s the follow-on book to Endless Forms Most Beautiful. In this book Carroll devotes several chapters to demonstrating how, against our natural intuition, there really is enough time (given a few hundred million years) for DNA to mutate bit by bit and still make amazing new structures like eyeballs, wings, and that pink dangly thing that hangs at the back of your mouth.

Carroll also points out that while almost everything is in flux, genetically speaking, there are some stretches of DNA so crucial to life that they never change. Which is to say, they can’t change because any variation would be fatal. Here, for example, is a six amino acid stretch that has been found in every single living thing: KNMITG. It’s an immortal sequence, unvarying across more than a billion years.

The last chapter deals with the controversies associated with teaching evolutionary theory in public schools. This is well-traveled ground, but it got me thinking about how much the opponents of evolution focus on man, monkeys, and biology class. But shouldn’t they be attacking geology too? Some of them do, insisting, for example, that the Grand Canyon formed during Noah’s flood. But it seems that a serious and consistent creationist ought to stick those little “this is only a theory” labels in every science book on the shelf. The astronomy book, the geology book, the physics book, they should all be thrown out the window along with The Origin of Species. Why is poor old Darwin always taking the heat?

Funny gene names

Do you suppose, if your house was knocked over by Hurricane Fifi, that you might feel more slighted than if the same damage had been done by a storm with a more muscular name? Generals have long understood the value of giving their military operations intimidating names like Rolling Thunder and Urgent Fury. If you have a rare disease, it can be a source of perverse comfort to know that it is named after a pair of stern and bespectacled Old World doctors like Creutzfeldt and Jakob or Kugelberger and Welander.

But geneticists and molecular biologists have a couple of strikes against them when it comes to naming genes. First of all, they tend to name genes for what happens when the gene doesn’t work, which ends up making a critical functionality sound like a problem. Thus eyeless helps make eyes. The other problem is that it never occurred to them that the silly inside-joke names they gave to their fruitfly genes would have such straightforward parallels in humans. As it says in the NY Times article ‘Sonic Hedgehog’ Sounded Funny, at First:

It’s a cute name when you have stupid flies and you call it a ‘turnip.’ … When it’s linked to development in humans, it’s not so cute any more.

I came across a link to the Times article because of an entertaining blog post from the bioinformaticist Nick Saunders: What’s in a (gene) name? . You never know when a name is going to matter.

The year of the personal genome

Want to buy a slightly used genome?

Back in 2000, Craig Venter and Francis Collins (and Bill Clinton) announced the completion of “the” human genome. Not to take anything away from that achievement, but genomes are just as varied as humans. Whose genome was the human genome? Or to come at it from another direction: if they popped that first draft genome into a baby printer, who would it come out looking like? The Celera version would probably look an awful lot like Craig Venter, because he just couldn’t stop himself from secretly “volunteering” his own DNA to the project.

More recently, Venter gave up any pretense of secrecy and published the most thorough human genome to date: both sets of 23 chromosomes for… Craig Venter. And not only that, it’s published on PLoS Biology, so you can go inspect every nucleotide. Or you can just print out this poster for your room. Think of it as a pin-up for the bio-geek set (I see London, I see France, I see someone’s 16 base pair non-genic heterozygous indel).

So old Craig gets to see all of his genes. Do you want to see yours? If so, you’re in luck, because, as noted in Technology Review, several new companies have set up to service your genomic needs. While you can’t get the royal (i.e. accurate and thorough) treatment that Venter and James Watson get, you can do pretty well.

23andMe, DeCodeMe, and Navigenics all will take something like $1000 from you and send you a bunch of genomic data. As many have observed, the exact value of the data is a sketchy. You may learn some things that will do little more than make you anxious.

Even so, I suspect these services will be a commercial success. There is a desire to know what cards you’ve been dealt that somehow trumps any rational medical value. When it really comes down to it, knowing about your personal DNA is almost more of an aesthetic experience than anything else. So it makes sense that there’s a company that can turn your DNA into art. That may be the most reasonable thing to do with your genes, at least for now. Hang them in your living room.

The best proof I’ve seen that biology is going mainstream is this ad for a PCR machine. Check out the insanely high production values on this video that’s peddling a piece of lab equipment for the white coat crowd. Amazing.

Cellular pornography

We live in some kind of golden age of microscopy. In the old days, people relied on stains that made cells look like this.


Useful, but not too pretty. It kills the cells too, but more to the point, no matter how useful it is, a picture like this is never going to land you on the cover of Science or secure your next grant. Not anymore. Why? Because the bar has gone way way up. This is what cellular imaging looks like now.


Va-va-va-voom! It’s like some kind of crazy Post-Impressionist fruit bowl on black velvet. That picture has my vote in the 2008 presidential election.

If you want to see some racy, juicy-looking cellular images, look at the winners of the latest Olympus BioScapes Digital Imaging Competition. The honorable mentions are just as good. Look, for example, at this brainbow image and keep in mind that individual brain cells have been genetically induced to color themselves distinctly. Not only are they able to live in this state, you simply couldn’t get this kind of cell-by-cell contrast with the old heavy-handed staining approach. As a result, you can draw maps of the interconnections of individual brain cells.

I know the colors are all pumped up with computer graphics, but still, look at those pictures. I am simultaneously impressed with the image-making capability and the thing being imaged. Leeuwenhoek would be proud.