After seeing PZs comments on Stuart Pivar’s new version of his book, titled “Lifecode: From egg to embryo by self-organization”, I thought I would try taking a look. I’ve long thought that much of the stuff that I’ve read in biology is missing something when it comes to math. Looking at things, it often seems like there are mathematical ideas that might have important applications, but due to the fact that biology programs rarely (if ever) require students to study any advanced math, they don’t recognize the way that math could help them. So, hearing about Pivar’s book, which claims to propose a theory of structural development based on the math describing structural distortions of an expanding figure in a constrained space – well, naturally, I was interested.
So I wrote to the publisher of his book, to see if I could get a review copy. I wanted to try writing a review from the perspective of a mathematician. To my immense surprise, a courier arrived at my door two hours later with a copy of the book! It’s a lucky thing I was working from home that day! So I started reading it monday afternoon. I didn’t have a lot of time to read this week, so I didn’t finish the main text until thursday, despite the fact that it’s really quite short.
I got hit by a mutant meme; I don’t remember who tagged me. I’m not terribly into these
meme things, but I don’t pass up excuses to post recipes. So below the fold are four recipes that I’ve created: seared duck breast with ancho chile sauce; saffron fish stew; smoked salmon hash; and
spicy collard greens.
I just finally got my copy of Mandelbrot’s book on fractals. In his discussion of curve fractals (that is, fractals formed from an unbroken line, isomorphic to the interval (0,1)), he describes them in terms of shorelines rather than borders. I’ve got to admit
that his metaphor is better than mine, and I’ll adopt it for this post.
In my last post, I discussed the idea of how a border (or, better, a shoreline) has
a kind of fractal structure. It’s jagged, and the jags themselves have jagged edges, and *those* jags have jagged edges, and so on. Today, I’m going to show a bit of how to
generate curve fractals with that kind of structure.
One application of graph theory that’s particularly interesting to me
is called Ramsey theory. It’s particularly interesting as someone who
debunks a lot of creationist nonsense, because Ramsey theory is in
direct opposition to some of the basic ideas used by bozos to
purportedly refute evolution. What Ramsey theory studies is when some
kind of ordered structure *must* appear, even in a pathologically
chaotic process. Ramsey theory is focused largely on *structures* that
exhibit particular properties, and those structures are usually
represented as graphs.
Today, I’m going to talk a bit about two closely related problems in graph theory: the maximal clique detection problem, and the maximal common subgraph problem. The two problems are interesting both on their own as easy-to-understand but hard-to-compute problems; and also because they have so many applications. In particular, the two are used extensively
in bioinformatics and pharmacology for the analysis of complex molecular structure.
The WSJ is, in general, an excellent paper with really high quality coverage of economic
issues. But their editorials page has long been a haven for some of the most idiotic
reactionary conservative nonsense this side of Fox News. But this latest piece takes the
cake. They claim that this figure is an accurately derived Laffer curve describing the relationship
between tax rates and tax revenues for different countries; and that the US has the highest corporate tax
rates in the world.
1. **Marillion, “If My Heart Were a Ball It Would Roll Downhill”**: Very neat track from
one of my favorite neo-progressive bands. Catchy, but with lots of layers.
2. **Mandelbrot Set, “Constellation of Rings”**: math-geek postrock. What’s not to love?
3. **The Police, ;Every Breath You Take”**: I’ve always been a fan of the Police. But
what I like most about this song is how often it’s been used by clueless people. I’ve
heard this at multiple weddings, where the couple thought it was a beautiful romantic
song. If you listen to it, it’s anything but romantic. It’s actually a rather evil
little song about a stalker: “Every breath you take, every vow you break,
every smile you fake, I’ll be watching you… Oh can’t you see, you belong to me?”
How can anyone miss that?
4. **Naftule’s Dream, “Speed Klez”**: John Zorn-influenced klezmer mixed with
a bit of thrash. Insane, but very very cool. Thrash with a trombone line!
5. **Jonathan Coulton, “Todd the T1000″**: Sci-fi geek pop. It’s a catchy little pop
song about trading in your old robot for a new one which turns out to be a
psychopath.
6. **Hamster Theater, “Reddy”**: A short track from a great band. Hamster Theater
is a sort-of spin-off from Thought Plague. It’s a bit more traditional than
what you’d hear from TP; still very dissonant, sometimes atonal, but more often
closer to traditional tonality and song structure. This track is a short instrumental
featuring an accordion solo.
7. **Transatlantic, “Mystery Train”**: great little song. It’s a track by one of
those so-called supergroups; Transatlantic is a side-project formed by members of
Marillion (bassist Pete Travawas), Dream Theater (drummer Mike Portnoy), Spock’s Beard (singer Neil Morse), and the Flower Kings (guitarist Royne Stolt). In general, these
supergroups have a sort of shaky sound. These guys are *great* together; it sounds
like they’ve been playing together for years: they’re sharp, there’s a great interplay
between the different instruments, it’s all incredibly precise. I’ve heard that the
music was written in advance mainly by Morse, but even with polished music pre-written,
it’s got a great sound, and you can here the distinctive musical voices of each of the
musicians.
8. **Godspeed You! Black Emperor, “Antennas To Heaven”**: It’s Godspeed – which means
that it’s brilliant post-rock. This starts off with a very rough recording of a very
old-timey folkey tune, and uses it as a springboard into a very typical God-speed
texture.
9. **The Flower Kings, “Devil’s Playground”**: more neo-progressive stuff. This is an
incredibly long piece (25 minutes), very typical of Roine Stolt’s writing. It’s not
the sort of way-out-there kind of thing that you’d hear from, say, King Crimson; it’s
very structured, very melodic, but put together more in the structure of a symphony
(theme, development, restatement) than the typical ABACAB structure of a rock song.
10. **Porcupine Tree, “Sleep Together”**: a brilliant song by yet another neo-prog
band. Very odd… a strange electronic pulse drives the entire song; but it starts
off as a very quiet song with this electronic pulse giving it a tense feel. Then
the percussion comes in, and shifts your sense of the rhythm… And then it gets
to the chorus, which is big and loud, and features a full string section. Strange,
but wonderful.
Part of what makes fractals so fascinating is that in addition to being beautiful, they also describe real things – they’re genuinely useful and important for helping us to describe and understand the world around us. A great example of this is maps and measurement.
Suppose you want to measure the length of the border between Portugal and Spain. How long is it? You’d think that that’s a straightforward question, wouldn’t you?
It’s not. Spain and Portugal have a natural border, defined by geography. And in Portuguese books, the length of that border has been measured as more than 20% longer than it has in Spanish books. This difference has nothing to do with border conflicts or disagreements about where the border lies. The difference comes from the structure of the border, and way that it gets measured.
Natural structures don’t measure the way that we might like them to. Imagine that you walked the border between Portugal and Spain using a pair of chained flags like they use to mark the down in football – so you’d be measuring the border on 10 yard line segments. You’ll get one measure of the length of the border, we’ll call it Lyards
Now, imagine that you did the same thing, but instead of using 10 yard segments, you used 10 foot segments – that is, segments 1/3 the length. You won’t get the same length; you’ll get a different length, Lfeet.
Then do it again, but with a rope 10 inches long. You’ll get a *third* length, Linches.
Linches will be greater than Lfeet, which will be greater that Lyards.
The problem is that the border isn’t smooth, it isn’t a differentiable curve. As you move to progressively smaller scales, the border features progressively smaller features. At a 10 mile scale, you’ll be looking at features like valleys, rivers, cliffs, etc, and defining the precise border in terms of those. But when you go to the ten-yard scale, you’ll find that the valleys divide into foothills, and the border line should wind between hills. Get down to the ten-foot scale, and you’ll start noticing boulders, jags in the lines, twists in the river. Go down to the 10-inch scale, and you’ll start noticing rocks, jagged shapes. By this point, rivers will have ceased to appear as lines, but they’ll be wide bands, and if you want to find the middle, you’ll need to look at the shapes of the banks, which are irregular and jagged down to the millimeter scale. The diagram above shows a simple example of what I mean – it starts with a real clip taken from a map of the border, and then shows two possible zooms of that showing more detail at smaller scales.
The border is fractal. If you try to measure its dimension, topologically, it’s one-dimension – the line of the border. But if you look at its dimension metrically, and compute its Hausdorff dimension, you’ll find that it’s not 2, but it’s a lot more than 1.
Shapes like this really are fractal. To give you an idea – which of the two photos below is real, and which is generated using a fractal equation?
This is a short one, but after mentioning this morning how woo-meisters constantly invoke
fractals to justify their gibberish, I was reading an article at the 2% company about Allison DuBois, the supposed psychic who the TV show “Medium” is based on. And that
led me to a perfect example of how supposed fractals are used to justify some of the
most ridiculous woo you can imagine.
The most well-known of the fractals is the infamous Mandelbrot set. It’s one of the first things that was really studied as a fractal. It was discovered by Benoit Mandelbrot during his early study of fractals in the context of the complex dynamics of quadratic polynomials the 1980s, and studied in greater detail by Douady and Hubbard in the early to mid-80s.
It’s a beautiful example of what makes fractals so attractive to us: it’s got an extremely simple definition; an incredibly complex structure; and it’s a rich source of amazing, beautiful images. It’s also been glommed onto by an amazing number of woo-meisters, who babble on about how it represents “fractal energies” – “fractal” has become a woo-term almost as prevalent as “quantum”, and every woo-site that babbles about fractals invariably uses an image of the Mandelbrot set. It’s also become a magnet for artists – the beauty of its structure, coming from a simple bit of math captures the interest of quite a lot of folks. Two musical examples are Jonathon Coulton and the post-rock band “Mandelbrot Set”. (If you like post-rock, I definitely recommend checking out MS; and a player for brilliant Mandelbrot set song is embedded below.)
So what is the Mandelbrot set?
Take the set of functions
where for each , is a complex constant. That gives an infinite set of simple functions over the complex numbers. For each possible complex number , you look at the recurrence relation generated by repeatedly applying , starting with :
If doesn’t diverge (escape) towards infinity as gets larger, then the complex number is a member of the Mandelbrot set. That’s it – that simple definition – repeatedly apply for complex numbers – produces the astonishing complexity of the Mandelbrot set.
If we use that definition of the Mandelbrot set, and draw the members of the set in black, we get an image like the one above. That’s nice, but it’s probably not what you expected. We’re all used to the beautiful colored bands and auras around that basic pointy black blob. Those colored regions are not really part of the set.
The way we get the colored bands is by considering *how long* it takes for the points to start to diverge. Each color band is an escape interval – that is, some measure of how many iterations it takes for the repeated application of to diverge. Images like the ones to the right and below are generated using various variants of escape-interval colorings.
My personal favorite rendering of the Mandelbrot set is an image called the Buddhabrot. In the Buddhabrot, what you do is look at values of which *aren’t* in the mandebrot set. For each point before it escapes, plot a point. That gives you the escape path for the value . If you take a large number of escape paths for randomly selected values of , and you plot them so that the brightness of a pixel is determined by the number of escape paths that cross that pixel, you get the Budddhabrot. It’s fascinating because it reveals the structure in a particularly amazing way. If you look at a simple unzoomed image of the madelbrot set, what you see is a spiky black blob; the actually complexity of the structure isn’t obvious until you spend some time looking at it. The Buddhabrot is more obvious – you can see the astonishing complexity much more easily.