The Basepoint


It's a colored brain. Image by Zeynep Saygin.

It’s a colored brain. Image by Zeynep Saygin, courtesy of MIT’s Koch Institute.

When I see an art+science event announced, I brace for disappointment. Usually I go anyways because I’m curious to see the failure mode. Which will it be?

1. Art loosely inspired by science (Heisenberg’s uncertainty principle and Einstein’s relativity and everything is chaos man).
2. Science *as* art (a colorized photo of a cancer cell, a video of a chemical reaction).
3. Art as an illustration of science (a drawing of a cell or a nucleus, a rendition of a particle collision).
4. Science as a means of production for art (I took data from cosmic rays and ran them through five algorithmic filters to make this soundtrack, or EEG traces to color a print).

3 and 4 are inoffensive, but don’t warrant special treatment. They are just sharing best practices and tools. MIT’s Koch Center displays images which might be tarred as 1, but their press talks about the connection between science and engineering, not science and art.

Anyway, it was a great relief when this morning’s panel at swissnex began with the choreographer Gilles Jobin laying out an axis:

illustration                          coherence                               inspiration

In coherence, there is some part of the art piece which directly corresponds to a scientific concept. Like in a good metaphor, a part of one thing is precisely aligned with a part of another, but neither whole is subordinate.

Jobin came to San Francisco by way of CERN, home of the Large Hadron Collider, the most intricate engineering project ever. (Sorry iPhone.) He spent three months as a resident artist, talking with particle physicists and engaging in his own movement research. I think the dance he subsequently produced does occupy that middle ground.

A dance produced by an artist-in-residence at CERN. Movement premised on atomic dynamics. Can you see that residue?

Jobin is primarily concerned with the generation of movement, and took from the physics a few conditions (or algorithms or formal exercises) to set his dancers. For example:

-Positively charged particles repel, and deflect before collision. (In fact, all physical forces act ‘at a distance’; direct contact is an illusion of the macroscopic.)
-Molecules are constantly vibrating
-Magnetic fields cause atoms to align

A long residency gives time for subtlety, to get beyond the pat explanations which scientists tend to give the public. Take the magnetization of iron. In a chunk of metal, every atom spins in some direction (the direction of a spin is the axis of rotation, think of the earth). The usual story is that turning on a magnetic field whips all the atomic spins into alignment, pointing uniformly, say, to the right.

– – – – –

– – – – –

But the field actually induces a preference, a mere statistical tendency for the atom to wobble in one way.

– / – / –
– \ – – \

The idea of a tendency getting turned on and then amped up over time is more physically correct and more kinetically interesting.

Jobin was also surprised to learn that physicsts think about kinds of symmetries. He had previously thought of symmetry as a binary idea; a thing is symmetric or not. (Mathematicians classify symmetries too; eg: there are exactly 17 kinds of symmetry possible in repeating planar patterns like Turkish tiles or Navajo blankets. I’ve been meaning to do a sweet html5 illustration of this, we’ll see if future Josh gets his ish together.)

In 2012, installation artist Julius von Bismarck was the (first) artist in residence at CERN. As part of his duties, he hosted a few interventions with the locals. First, he had a “coffee in the dark” discussion, where in a pitch-black room physicists talked about how they imagine the shapes of the things they study. Ten dimensional symmetry groups, subatomic particles, etc. He also taught an art-school-in-30m class, where after a brief discussion of form and style the participants had to make a piece which he then subjected to a scathing critique (“cheesy, naive…”). A taste of his own harsh training. Jobin, for his part, decided to infiltrate the library extremely slowly. For 3 hrs dancers were glacially rolling across the floors and slowly sliding along the bookcases. Hardly anyone noticed.

Physicists can be rather disinterested in people. The universe is made of particles moving according to certain laws; earth is an incidental mote in the cosmos. Showing a photograph of the CMS detector at CERN, a physicist said “to get an idea of the size of the 14,000 ton detector, look how small the human being working on it appears.” The concern with the invisible and impalpable, with the long time, is different from that of the choreographer; no feelings! (Also, no aesthetics…have you ever seen a slide from a physics preso?) For Julius, who lives in the incestuous Berlin art world, inhabiting a place where human concerns were secondary was just like whoa.

It seems to me like the primary benefit of interdisciplinary interaction is those moments where you realize that other people pay attention to different parts of the world, sort of like the benefit of travel. By spending time with people whose givens and goals are different than yours, your mind opens up. The point of studying abroad is not to take the language you learn or contacts you make and start some international business or translation service. I have yet to write any math poems, but spending years in close quarters with a poet did change me.

Lately, I’ve been doing some dancing and hanging out with dancers. Different modes of interpersonal communication, different things to look for, that click-click-click feeling of accessing a new dimension of being. (I mean dimension literally. Separating the motion of the core from the hips and the shoulders adds a degree of freedom. The phase space of the human skeleton is about 200-dimensional.) Will that affect my mathematics directly (maybe working on algorithmic dance, like Cunningham choreo, or moduli problems of jointed rigid bodies)? Possibly, but that feels like the minor effect. It’s just improving my life, and I can’t help but think that the place in the of the mind where ideas are born is becoming more fertile. It’s sort of like meditation: the benefits of regular meditation for a host of physiological, emotional, and mental indicators are well-documented, but it’s not like you need to work on something about or inspired by meditation.

The cool thing about the CERN artist residency is that they are investing in the growth of the artist as a person, and trusting that it will lead to better art. The US Fullbright programs are similar in spirit; it seems like they deliberately avoid asking you to execute the ostensible project.

Next step: who is going to fund three months for a scientist to visit Jobin’s studio? Have you seen the way those people move?

Coda: Another piece of Julius von Bismarck that I’m kind of in love with is called Punishment, in which the artist whips nature.


Bowman v. Monsanto Co.

Last week, the supreme court ruled that “a farmer who buys patented seeds may [not] reproduce them through planting and harvesting without the patent holder’s permission.”

Soybean plants making replica seed. (Photo courtesy

Soy plants with their beans/seeds (Photo courtesy

The patented seeds in question are Roundup Ready soybeans, a strain engineered by Monsanto to be resistant to a broad-spectrum herbicide called glyphosate, also developed by Monsanto. At first, I thought this was a case about genetically modified crops–patents, GM, corporate litigation, big agra, and rivers of herbicide go together, right? And the gene for glyphosate resistance had been inserted into soybeans by infecting them with a DNA-altering bacterium. I’ve been learning a bit about the science of genetic modification, which should probably be called technology given how ubiquitous it is (Harvard scientists make GM mice whose neurons fluoresce in a 20-color brainbow.) So I got all excited to talk about the history of genetically-modified plants, and the maybe-genius maybe-disastrous uses scientists, in universities and multinationals, have in the pipeline.

But this is really a case about patenting seeds, cells, and plants, which has been going on at least since the Plant Patent Act of 1930. That law does what it says (which is rare among laws, cf No Child Left Behind) and explicitly allows for the patenting of plant varieties. Clarified in 1954 to include seeds, mutants, and hybrids, the law has been used to patent more than 20,000 distinct species of plant. Most recently, plant patent #23,600 was awarded to a British woman named Brenda Bowyer for (conventionally) breeding a variety of helichrysum she christened “Ember Glow,” after the way its red bulbs orange with age. The delicious and now popular Honeycrisp apple was the result of three decades of iterated crossing by hand-pollination and careful selection at the University of Minnesota; the plant was patented in 1998, and for the next 20 years, the U of M charged $1.30 per seedling. In 2008, the US patent expired, and now anyone can sell the seedlings/branchings royalty free. Apple breeding is a pretty well-functioning part of the plant-patent world, and is responsible for the disturbing turnover of apple varieties since I was a kid (those Piñata apples have been showing up a lot lately–patented in 2000).

It turns out, though, that none of the famous GM crop patents, including the Monsanto patent on glyphosate-resistant soybeans, are actually plant patents. No, those are just ordinary (utility) patents which happen to be on plants. This subtlety, plant patent vs patent on plants, is pretty typical legalese, and as as all my lawyer and would-be lawyer friends well know (congrats on finishing xL), the whole case can ride on such distinctions. If Monsanto’s patent had been a plant patent, the farmer would have been a clear victor and the case would never have made it out of district court.

So who is the farmer here, what did he do, and why is it, in the unanimous opinion of our supreme court, obviously illegal?

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Mould broth filtrate

…for convenience, and to avoid the repetition of the rather cumbersome phrase “Mould broth filtrate,” the name “penicillin” will be used.

When Alexander Fleming noticed that a colony of mold had contaminated his tray of staphylococcus bacteria, and that the bacteria near the mold had begun to die (or lyse), he did some science. He grew the mold in five kinds of sugar broth (including lactose+glucose=milk+honey), then poured a bit of each broth on a tray containing the bad -coccuses (strepto, pneumo, gono, staphylo) and watched them retreat. He tried filtering out the mold, boiling the mixture, and then diluting it 600-fold, and still it killed bacteria. Injects huge quantities of filtered moldy broth in mice and then rabbits–seems nontoxic. Upgrades to putting drops into some bold man’s eye every hour for a day–no problem. The mold-water kills bacteria and is safe for humans. Time to write the paper and tell everyone.


But what to call the elixer? As he later writes in the intro, the phrase “mould broth filtrate” is rather cumbersome, not to mention seriously gross. As drug companies know, a sexy name is key to convince people to put something in their bodies (compare “botox” to “botulinum toxin”). But “mold” is also too general, as a half-dozen other molds he tested had no anti-biotic effects (asparagus soup is good for you, aspergillus fumigatus soup, not so much). He knew the name he picked would become famous, and as any political spinster or derridaian graduate student can tell you, the choice of name matters a great deal.

There were a few ways he could have selected a name.

1. Named after a person

It would be presumptuous to call it the “Fleming solution,” so he would presumably pick someone vaguely related, perhaps a teacher or already-famous person. Consider the Poisson spot, named for its greatest skeptic, or any other instance of Stigler’s law. Some ecologist named a blind precambrian arthropod “krygmachela kierkegaardi” after her favorite philosopher.

2. Named after a function

“Bacteria-killing mold” or “staph-lysing mold” or some latin equivalent. Compare “anteater.”

3. Named after an attribute

“Yellow-sporal solution.” Compare “three-toed sloth.”

4. Named after the first place you saw it

Strange in a lab, popular with diseases and lifeforms. “West nile virus” or “brazil nut.”

5. Named with an arbitrary combination of sounds.

“Quark” or “bandersnatch” or “prozac.”

Fleming decided to go with “penicillin” for the “mold broth filtrate,” derived from the name of the mold itself. Of course the Petri surprise had given itself no name, but by growing other molds known to inhabit laboratory air and comparing their appearance and lethality to his new dish, he determined that it was at least closely related to penicillium rubrum. Where did this nice latin root come from? Penicillus means paintbrush (type 3).


A light micrograph of penicillium spores.

I think that a big merit of using latin names in science is that they become free-floating signifiers. Proper names work this way too, and are popular in math–my last paper was on Khovanov homology. If you don’t know the language/person involved, then it’s just a collection of sounds whose meaning can evolve over time as your understanding of the object changes. Such is not the case for Penicillin Binding Protein.

After Fleming discovered that this mold could kill (some) bacteria while leaving human cells unharmed, people wondered just how it worked. Lots of science and about 40 years later, it became clear that penicillin disabled a bacterial protein, which was immediately named “penicillin binding protein”. But that’s totally unfair to the protein. It did its job, which turns out to be linking chains in the cell wall, long before penicillin came around. The fact that penicillin could distract the protein, leaving weak cell walls which would break like a burst like a levee under stress, is hardly a definitive feature of the protein itself. And now when these bacteria are studied with absolutely no penicillin around, a key enzyme is named after its number one enemy.

It’s like calling Lou Gherig the “amyotrophic lateral sclerosis binding man” or your brain “stroke-bait.” Just rude.

I think that’s why acronyms are so popular in the biology literature, why all the papers talk about PBP instead of penicillin binding protein. By dropping any pretense at description, “PBP” attempts to specify without prejudice about form or function or meaning. Unfortunately, this can make reading biology (and corporate reports) a pretty surreal experience, when PBP coactivates PPARy in the ARC complex.

Objectively and ahistorically yours,


Grandpa’s genes

3 gen Batson men

Are you genetically related to your grandfather?

I know I am. I’m male, so my Y-chromosome came from my dad (left). And he’s male too, so his Y-chromosome came from his dad (right).

But I’m getting worried about my sister. I know she got an X from dad, which was grandma’s to start. There were 22 other chromosomes in the lucky spermatozoon which fertilized the egg which became her first cell. Each of those were picked at random–a 50% chance it came from grandma and a 50% chance it came from grandpa. Could they all have come from grandma? Could she have missed all 22 chances at inheriting grandpa’s genes? It’s not super likely–the probability is 1/2^{22}, or about one in four million.

But there are ~160 million women in America–could it be that 40 of them are unrelated to their biological grandfather?

I thought so, until I remembered chromosomal crossover–the dance where your genes do-si-do. Before the climactic moment of meiosis, when all of my dad’s chromosome pairs lined up, then got yanked into two bunches (one of which begat my sister), before that, both sets of grandparental chromosomes were hanging out together. On occasion, they would swap pieces (when called to do so by recombinase proteins).

Hoping to preserve the idea that there might be these 40 pseudo-granddaughters wandering around, I checked out just how often. According to a genetical study of a few hundred icelandic families, between generations there is a one percent chance of a crossover in each stretch of a million DNA base pairs. There are about 3 billion base pairs in the genome, so this makes a no-crossover generation pretty unlikely; one in a trillion zone. So maybe this has happened to an ant, but never to a human.

Takeaway: for better or worse, you are related to your relatives.