Ideas, models, and design

Discussions of the relative merits of intelligent design and natural selection fill endless web pages, but it strikes me that these discussions consistently overlook the nature of design itself. Intelligent design happens all the time; we may disagree on whether God or pasta-themed deities design, but we can at least agree that humans do it.

But what is design? Or, put another way, if God is doing intelligent design, then what exactly is he doing?

What a designer does is rapidly iterate through a bunch of ideas, testing them against his experience, rejecting some and keeping others for further tuning. The precursor ideas for this process come from variations on pre-existing designs. In other words, design is a process of selection with descent and variation.

If God is a designer, then maybe he’s doing it right now with lions, lemurs, begonias, and bloggers through the subtle but decidedly unmiraculous process of natural selection. You don’t have to damage science to imagine Galapagos finch beaks as God’s thoughts unfolding. Of course, that’s a matter of taste and scarcely debatable. It doesn’t prove anything and it doesn’t “mean” anything, but it is one way to frame the problem so we can just move on.

Design is predicated on an experiential model of reality. The intelligent design that humans do differs from the “design” that happens in natural selection primarily by the rate at which generational culling happens. Humans have the benefit of rapidly simulating how a design will perform without needing to build it first. Increasingly we will give this skill to our synthetic descendants. Here’s a beautiful example of how modeling operates at the boundary of action and thought.

The Cornell Computational Synthesis Lab: Robotics Self Modeling

Be sure and watch the video of the damaged robot struggling to walk. Depending on your outlook, it’s either very disturbing or spine-tinglingly beautiful. Either way, I promise you it’s a bona fide glimpse of the future.

Visualizing biological experiments

Video blogs are getting more and more interesting. This one, My JoVE, isn’t really a blog so much as a repository of valuable information for biologists, but it aspires to become a kind of video journal. JoVE stands for Journal of Visualized Experiments, and they’re trying to attack two big problems in biological research: “low transparency and reproducibility of biological experiments, … and time-consuming learning of experimental techniques.” Here’s their answer to the question: why a video-based scientific journal?

As every practicing biology researcher knows, it takes days, weeks or sometimes months and years to learn and apply new experimental techniques. It is especially difficult to reproduce newly published studies describing the most advanced state-of-the-art techniques. Thus, a major part of the Ph.D. and post-doctoral training in life sciences is devoted to learning laboratory techniques and procedures.

They are addressing two needs specific to the biology community, but they are picking up another one along the way: educating non-biologists and interested amateurs. You can find lots of experimental protocols online (see OpenWetWare), but these suffer from a few shortcomings: they use unfamiliar vocabulary, unavailable equipment, and they are often written in the stilted science-report prose that is beaten into all student scientists.

But like the how-to videos at, these videos are delightfully conversational, and anybody can look at the shape of an Erlenmeyer flask without having to know the specific term for it. I am unlikely to buy an electron microscope any time soon, but I like to know what it looks like to drive one. I will certainly admit that watching someone use micro-forceps to invert the cuticle on a fruit fly larva and fish out the central nervous system is very far from knowing how to do it yourself. Still, it’s amazing how much those summer camp arts-and-crafts skills pay off in the lab.
(Spotted on the Sciencebase Science Blog)

For the love of chemical synthesis

Now this is why I read blogs: Paul Docherty is head-over-heels in love with chemical synthesis and wants to tell you all about it. And I want him to tell me about it. His blog, is crackling with enthusiasm and filled with lovely diagrams and little stories that report on the latest news in the world of organic chemical synthesis. This is exactly what you don’t get in a typical chemistry class. Can you imagine how many chemists we’d have if high school teachers were half as thrilled as this?

Here’s a sampling from today’s post, Modern Aldol Methods for the Total Synthesis of Polyketides.

With all this focus on polyketide/macrolide synthesis, I thought I’d highlight an interesting review in this week’s Angewandte; a genuine masterclass in the aldol reaction.

There’s nothing pretentious about it. It’s all sinewy facts knotted together with excitement, punctuated by little self-effacing asides like “I was quite taken with this transformation, but it obviously shows that I need to brush up on my diazo chemistry…” Somehow I feel as though I’m learning something terribly useful, even though I don’t understand a word of it.

I’ve always loved technical jargon as used by someone joyfully immersed in it, whether it’s 19th century sailing terminology or dental jargon. Bring on your ipsilateral translation of the condyle, your girt lines and masting falls! Money pays the bills, but it’s Kocienski–Julia olefination that makes the world go around.

Pop Sci blogging fun

Popular Science magazine also hosts a blog, and it’s got a bunch of fun stuff on it. I had always thought of the old school Popular Science as a pretty silly magazine, mostly about hyped up quasi-science fluff. But it’s gotten a lot better over the last few years, and their blog is so entertaining that it definitely drives me to purchase the actual paper magazine more often.

They’ve been a real tear with their last few entries. I don’t know if they’re getting any work done on the magazine, because somebody’s doing an awful lot of web surfing. Here are a few choice items from the past week:

Watch a racing motorcycle crash and burst into flame. The rider is okay, and there is an interesting discussion of why this kind of thing never happens with cars, but did with this motorcycle. Goodbye, Moto

Watch a crane trying to lift a truck out of a river and back onto a bridge. As it happens, the truck pulls the crane down into the river. The Breakdown: Crane Overboard!

Every physics teacher who teaches the concept of resonance needs to show this in their class. A Boeing Chinook helicopter has two rotors, and if they start exciting vibration modes of the fuselage when it’s sitting on the ground, bad things can happen. If the word “resonance” doesn’t sound so bad, take a look at this video: Shake, Shake Chinook.

And don’t miss the African watering hole cam. It’s a live video feed with sound, and there’s something very appealing about listening to crickets on another continent.

How to use as a podcast

I don’t know if you buy into the Web 2.0 meme, but I do. There’s an amazing amount of good stuff to keep up with these days. It’s getting ever easier to create, package, route, re-package, re-route, and consume information. Mashups, those unanticipated combinations of multiple websites, were a good indication that things were getting interesting. Sticking apartment prices on a map is a nice, practical example of a mashup, but on beyond that, things get really weird. My current favorite nominee for unanticipatable Web 2.0 mash-hack was on display over at Jon Udell’s blog at InfoWorld. In this post, Jon is actually talking about the nature of video demonstrations, but his example is a lovely hack by Pascal van Hecke that involves turning into a podcasting tool.

So let’s review what’s being done here: an embedded Revver video is showing you how to combine a Greasemonkey script on Firefox with some special commands so that you can funnel random MP3s into a unified virtual podcast that your iPod can automatically scoop up and pour into your waiting ears. That’s not a mashup. That’s alchemy.

This stuff is pretty far out there if you’re not hip-deep in kool-aid, but I am and I find this example amazing for the virtuosic cross-pollination of information tools it displays. It looks gratuitous, but it’s actually very useful. Authoring at this level (composing? recombining?) is the skill that will be rewarded in the next decade. You have to start telling yourself: All data is free. All services are free. Now what?

Hidden dialogue and “Touching the Void”

Recently I watched the movie Touching the Void the story of two British climbers who have a really wretched experience climbing a mountain in the Andes. A friend of mine, who is a climber, had told me that this was the climbing movie that gets climbing right. This statement intrigued me, because climbing is a technical skill and it’s easy to screw up the movie about a technical topic.

If you are directing a movie in which much of the dialogue is built on a complex understanding between skilled professionals, you have a real problem. You have to find a way to explain to your audience what’s going on without damaging the scene. You see different approaches to solving this problem. Sometimes, a naive character is introduced so that one of the professionals can explain the technical details. More often, though, the director simply chooses to have two skilled professionals address each other using explicit elementary language that would never occur in real life.

This kind of thing often shows up in movies about pilots. Consider: you are a pilot, and your plane is about to crash into a mountain. What do you say? On the one hand, anyone dealing with a plummeting airplane is, at some level, scared. On the other hand, pilots are trained to deal with terrifying situations. They have years of experience all built around the idea of emotionless, concentrated problem-solving right to the bitter end. No matter how much a director wants it said, a pilot will NEVER EVER look at another pilot and say “I’m so scared.”

It’s the same with climbers. So much goes unsaid. In real life you get “Hmmph” instead of “Hey Joe, don’t drop that rope, okay? ‘Cause if you do I’m going to drop 3000 feet onto those pointed rocks down there.” How can a director communicate what’s not being said? In “Touching the Void” the director approaches the movie almost entirely as a documentary. You see nearly silent actors on the mountain against a narration by the original real-life protagonists. It’s a powerful combination. It surfaces the hidden dialogue and also solves the second problem of movies about technical topics. If you let the geeks make movies about geeks, they will put the correct technical details into a movie devoid of any emotional spark. Making a movie like this is a balancing act, but sure enough, “Touching the Void” gets it right.

What is the illuminating but hidden dialogue that follows you around throughout the day? Maybe something like this: “Hey Joe, if you knew you were taking the last of the coffee, then why didn’t you make more for the rest of us? Now I have to throw you over a 3000 foot cliff onto those pointed rocks down there. Asshole.”

Helium collaborative writing

Twice a year, I help run a MATLAB programming contest in which contestants try to write the fastest code to solve a math puzzle, using a resource any work done by previously submitted entries. In other words, you’re welcome to steal from those who came before you. It’s a free intellectual property open source barbecue. It works surprisingly well and results in seriously optimized code. So the first question I get when I explain it to people is this: can’t we apply this technique to some useful real world problem? But here’s the thing: the programming contest has a great advantage in its unambiguous figure of merit. If you can make the code run faster, that’s all I need to know, and I only need a clock to figure that out.

Suppose you wanted to make a similar contest to write a great poem. You’re immediately faced with a big problem: There’s no automatic poem analyzer. Who gets to judge whether or not your poem is better than the current leader’s? The Wikipedia approach comes close to programming contest idea here, in that lots of people are busy making improvements (or changes at any rate) to the same “code” or Wikipedia entry. But you can’t make a running report of the “goodness” of the article over time. It may get longer, but is it getting better? That’s a matter of opinion.

Into this space comes an interesting startup called Helium. They solve the problem of quantitative evaluation by letting members vote. So the same topic (say “How to find the best mortgage rate”) may have multiple articles, but only one of them will be voted number one. The lowest rated article for the mortgage question was this: “go to and write down How can I get the best rate on a mortgage? you will get the best rate.” Good advice, but wouldn’t it be cool if the top rated result was this very page?

I think there’s still an optimal mix of Wikipedia and Helium that doesn’t exist yet, but we’re getting closer. (Helium spotted on Techcrunch)

Chess PHP pictures

My friend Steve is not only an image processing wizard with a book title under his belt, he’s also a chess player. He is modest about his mad chess skillz, but he has done something unquestionably useful for the chess community in creating a nifty chess diagram widget. Written in PHP, it lets you use a standard chess notation to draw images of games easily. For instance, if you write


you get a picture like this:

Venturing farther afield, Steve’s little chess board also lets you indulge in fanciful tactical positions. For instance, can Black be expected to win this game?

Or how about this one: a cautious Black has just castled on his king side, and White has retorted with some ugly, aggressive posturing of his pawns. Now, Black to mate in 4. Do you see it?

Believe it or not, this example is from a real match, the famous Bush-Cheney-Rumsfeld vs. Kerry match (2004). Also known as the Guantanamo opening (or, less frequently, the “Hanging Chad”), Black narrowly escapes disaster by buying assorted hardware from the Supreme Court. The debt thereby incurred was simply levied on the audience. Brilliant!

Finally, if you are a fan of M.C. Escher, you’ll enjoy reading about Steve’s chess problem epiphany:
Unexpected chess problem at my office.

Don’t forget to vote!

The word “virtual” is meaningless

When I was at Foo Camp last summer, I heard Philip Rosedale, the founder of the 3-D virtual world Second Life, describe how this community has not only virtual newspapers to serve its citizens, but paper versions too. They were handing out free copies copies. I picked up a tabloid that advertised stores and tourist traps that existed only in the electronic ether.

Moving in the other direction, which is to say a real reporter in a virtual world, Reuters recently announced that it will be assigning a regular correspondent to a Second Life beat.

“As strange as it might seem, it’s not that different from being a reporter in the real world,” Adam Pasick, the Reuters correspondent who will serve as the virtual bureau’s first chief, said in a Reuters report. “Once you get used to it, it becomes very much like the job I have been doing for years.”

So my question is: is it silly to put real person on a virtual newsbeat?

This leads to the question: what does the word virtual mean, anyway? And the answer is: nothing. Wherever you see the word “virtual,” strike it out and you’ll have a more compact phrase that means the same thing. Virtual newspapers are newspapers. Virtual neighborhoods are neighborhoods. Virtual economies are economies. A lot of money changes hands in Second Life, and the taxing authorities are starting to notice.

It’s always been troublesome to define a word like “virtual” because it describes something that both is and isn’t real. But increasingly it simply means “what you said, only on a computer.” I was curious to see what dictionaries are saying about the word these days. Sure enough, the dictionary entry has a long digression on this very topic.

Here’s my interpretation of the word virtual. It means “I’ve just removed from X something formerly considered an irreducible quality of X, and yet its X-ness is intact.” It is a linguistic onion peeler. You thought it was necessary to print a newspaper on paper, so you called my paperless newspaper “virtual”. But somehow its paperness remains intact. That which remains is nessful. That which was virtualized away is nessless.