Category: Research

Well, that only took 20 years!

It's about time
There are those rare, but wonderful, moments when you realize that the tool you’ve always wanted (but didn’t actually realize that you desired) was right there in front of you.

I just had one.

I’ve used LaTeX for preparing my scientific documents for nigh on two decades now. For all its oddities and annoying little bits, it’s the standard for technical writing in computer science as well as numerous other areas in math and science, and it allows you to make and manage complex documents that stay consistent and look really nice.

Through most, if not all of that time, I’ve used various weird hacks to leave notes for myself in the document where I wouldn’t miss them. A paragraph in bold face, for example, reminding me to double check a formula, or go get the right reference for a certain idea. They’ve worked, but none of the mechanisms have been optimal. They’ve often been more missable than something like that should be, and they’ve frequently broken the flow of the document, making it harder to check for things like page counts and widows.

Working with Tyler on IM tonight on a paper he, Brian, and I are trying going to finish by Sunday, Tyler was musing about how it would be nice to be able to put notes like that in the margins in red.

And the lightbulb went off.

Of course! LaTeX can do that, and I’m pretty sure it can do it easily! (At least the margin part – I didn’t really care about the red either way.) Sure enough a 10 second search on Google confirmed that the command existed and was trivial. \marginpar{ ... }

Duh.

Now those little notes are set out in the margins, not affecting the flow of the document, and quite unmissable. Now a quick scan of the document will immediately verify that we’ve removed (and hopefully addressed) all of them before we submit the final copy. Now they really work.

Simple, clean, and effective.

And it only took me twenty years to figure out.

Damn.

Thanks to Tyler for sparking the idea, and to all the crazy nuts that have poured their sweat into TeX, LaTeX, and the various related tools (I really like TeXShop for the Mac!) over the years.

Tags: editing, LaTeX, typesetting

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This isn’t science fiction anymore

The stupid selfportrait by dhammza
What price are we collectively willing to pay for fewer cavities?

A week or two ago I caught a cool interview with Jessica Sachs on the 24 Oct issue of the SciAm Science Talk podcast, and chose to subscribe to her blog as a result.

She just posted a piece that is a great example of both how totally cool and utterly creepy modern molecular biology can be. The short version is that Jeff Hillman has done some pretty amazing (and potentially scary) engineering on Streptococcus mutans (the micro-organism in your mouth responsible for much of your tooth decay) in an effort to reduce our problems with cavities. He’s done this by:

  • Identifying a variety of Strep. mutans that tends to crowd out other varieties.
  • Knock out the gene that produces the acid that eats away at your teeth.
  • Splice in new genes that produce alcohol instead. It turns out that the acid was crucial to the bug’s waste disposal process, and without it it died. The alcohol can serve a similar function, without being damaging your enamel. And, yes, the amounts of alcohol are so tiny as to have no inebriating effect.

In theory, then, he can introduce this newly engineering bug into your mouth, and it will crowd out the bad Strep. mutans currently beavering away at your beautiful teeth, leaving you with a mouthful of (presumably benign) alcohol producing critters and fewer cavities as a result.

Hillman’s had trouble getting permission to run human trials, though, in part because the FDA is concerned about his bug “escaping” into the wild and having unexpected consequences. They’ve required that he create a way to essentially put the genie back in the bottle if need be, so he’s engineered a version that doesn’t produce a key enzyme it needs, so users will have to swish daily with a solution containing the enzyme to maintain their population of tooth-friendly bugs. His first approval allowed him to work with two people with dentures, but he’s just gotten permission to work with people with real teeth, although “the volunteers will be isolated in a biohazard ward for the study’s one-week duration”.

This all sounds a lot like a Michael Crichton novel, and I’m sure there are those who are dismayed by the FDA’s caution regarding what sounds like a potentially revolutionary win for human dental health. Their concerns definitely aren’t irrational, however, as Hillman’s essentially proposing releasing a deliberately invasive species into the complex ecosystem of human mouths all across the planet. Unfortunately our track record with deliberate introductions ain’t real hot (rabbits in Australia anyone?), and these genies have typically been impossible to re-bottle.

From a commercial perspective, for example, it would clearly be easier to sell the treatment if they removed the need to swish daily, although there’s no doubt good money to be made in selling the swishing stuff, and re-selling the treatment to people that missed their swish and need to start over. Without that safeguard, however, then this can (and presumably will) spread pretty quickly through the human population before we will have any clear idea of the long term implications of replacing a long-standing resident in our mouths.

It’ll be interesting to see how this plays out, and I suspect that the true long-term impact (for good or for ill) won’t be known even in my lifetime. In the meantime, careful who you kiss – you never know what kind of heavily engineered super-critter might be living in their mouth.

Thanks to dhammza for the cool photo.

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