He sat down at his desk. He had angled his computer screen away from the window so that when necessary he could focus on it, but now he sat in his chair and gazed out across the atrium. He was near the end of his year-long stay at NSF, and the workload, while never receding, was simply becoming less and less important to him. Piles of articles and hard-copy jackets lay in stacks on every horizontal surface, arranged in Franks complex through-put system. He had a lot of work to do. Instead he looked out the window.
The colourful mobile filling the upper half of the atrium was a painfully simple thing, basic shapes in primary colours, very like an infants scribble. Franks many activities included rock climbing, and often he had occupied his mind by imagining the moves he would need to make to climb the mobile. There were some hard sections, but it would make for a fun route.
Past the mobile, he could see into one hundred and eight other rooms (he had counted). In them people typed at screens, talked in couples or on the phone, read, or sat in seminar rooms around paper-strewn tables, looking at slide-shows, or talking. Mostly talking. If the interior of the National Science Foundation were all you had to go on, you would have to conclude that doing science consisted mostly of sitting around in rooms talking.
This was not even close to true, and it was one of the reasons Frank was bored. The real action of science took place in laboratories, and anywhere else experiments were being conducted. What happened here was different, a kind of meta-science, one might say, which coordinated scientific activities, or connected them to other human action, or funded them. Something like that; he was having trouble characterizing it, actually.
The smell of Annas Starbucks latte wafted in from her office next door, and he could hear her on the phone already. She too did a lot of talking on the phone. I dont know, I have no idea what the other sample sizes are like No, not statistically insignificant, that would mean the numbers were smaller than the margin of error. What youre talking about is just statistically meaningless. Sure, ask him, good idea.
Meanwhile Aleesha, her assistant, was on her phone as well, patiently explaining something in her rich DC contralto. Unravelling some misunderstanding. It was an obvious if seldom-acknowledged fact that much of NSFs daily business was accomplished by a cadre of African-American women from the local area, women who often seemed decidedly unconvinced of the earth-shattering importance that their mostly Caucasian employers attributed to the work. Aleesha, for instance, displayed the most sceptical politeness Frank had ever seen; he often tried to emulate it, but without, he feared, much success.
Anna appeared in the doorway, tapping on the doorjamb as she always did, to pretend that his space was an office. Frank, I forwarded that jacket to you, the one about an algorithm.
Lets see if it arrived. He hit CHECK MAIL, and up came a new one from aquibler@nsf.gov. He loved that address. Its here, Ill take a look at it.
Thanks. She turned, then stopped. Hey listen, when are you due to go back to UCSD?
End of July or end of August.
Well, Ill be sorry to see you go. I know its nice out there, but wed love it if youd consider putting in a second year, or even think about staying permanently, if you like it. Of course you must have a lot of irons in the fire.
Yes, Frank said noncomittally. Staying longer than his one-year stint was completely out of the question. Thats nice of you to ask. Ive enjoyed it, but I should probably get back home. Ill think about it, though.
Thanks. It would be good to have you here.
Much of the work at NSF was done by visiting scientists, who came on leave from their home institutions to run NSF programmes in their area of expertise for periods of a year or two. The grant proposals came pouring in by the thousand, and programme directors like Frank read them, sorted them, convened panels of outside experts, and ran the meetings in which these experts rated batches of proposals in particular fields. This was a major manifestation of the peer review process, a process Frank thoroughly approved of in principle. But a year of it was enough.
Anna had been watching him, and now she said, I suppose it is a bit of a rat race.
Well, no more than anywhere else. In fact if I were home itd probably be worse.
They laughed.
And you have your journal work too.
Thats right. Frank waved at the piles of typescripts: three stacks for Review of Bioinformatics, two for The Journal of Sociobiology. Always behind. Luckily the other editors are better at keeping up.
Anna nodded. Editing a journal was a privilege and an honour, even though usually unpaid indeed, one often had to continue to subscribe to a journal just to get copies of what one had edited. It was another of sciences many non-compensated activities, part of its extensive economy of social credit.
Okay, Anna said. I just wanted to see if we could tempt you. Thats how we do it, you know. When visitors come through who are particularly good, we try to hold on to them.
Yes, of course. Frank nodded uncomfortably, touched despite himself; he valued her opinion. He rolled his chair towards his screen as if to get to work, and she turned and left.
He clicked to the jacket Anna had forwarded. Immediately he recognized one of the investigators names.
Hey Anna? he called out.
Yes? She reappeared in the doorway.
I know one of the guys on this jacket. The PI is a guy from Caltech, but the real work is by one of his students.
Yes? This was a typical situation, a younger scientist using the prestige of his or her advisor to advance a project.
Well, I know the student. I was the outside member on his dissertation committee, a few years ago.
That wouldnt be enough to be a conflict.
Frank nodded as he read on. But hes also been working on a temporary contract at Torrey Pines Generique, which is a company in San Diego that I helped start.
Ah. Do you still have any financial stake in it?
No. Well, my stocks are in a blind trust for the year Im here, so I cant be positive, but I dont think so.
But youre not on the board, or a consultant?
No no. And it looks like his contract there was due to be over about now anyway.
Thats fine, then. Go for it.
No part of the scientific community could afford to be too picky about conflicts of interest. If they were, theyd never find anyone free to peer-review anything; hyper-specialization made every field so small that within them, everyone seemed to know everyone. Because of that, so long as there were no current financial or institutional ties with a person, it was considered okay to proceed to evaluate their work in the various peer-review systems.
But Frank had wanted to make sure. Yann Pierzinski had been a very sharp young bio-mathematician he was one of those doctoral students whom one watched with the near certainty that one would hear from them again later in their career. Now here he was, with something Frank was particularly interested in. Franks curiosity was piqued.
Okay, he said now to Anna. Ill put in the hopper. He closed the file and turned as if to check out something else.
Okay, he said now to Anna. Ill put in the hopper. He closed the file and turned as if to check out something else.
After Anna was gone, he pulled the jacket back up. Mathematical and Algorithmic Analysis of Palindromic Codons as Predictors of a Genes Protein Expression. A proposal to fund continuing work on an algorithm for predicting which proteins any given gene would express.
Very interesting. This was an assault on one of the fundamental mysteries, an unknown step in biology that presented a considerable blockage to any robust biotechnology. The three billion base pairs of the human genome encoded along their way some hundred thousand genes; and most of these genes contained instructions for the assembly of one or more proteins, the basic building-blocks of organic chemistry and life itself. But which genes expressed which proteins, and how exactly they did it, and why certain genes would create more than one protein, or different proteins in different circumstances all these matters were very poorly understood, or completely mysterious. This ignorance made much of biotechnology an endless and very expensive matter of trial-and-error. A key to any part of the mystery could be very valuable.
Frank scrolled down the pages of the application with practised speed. Yann Pierzinski, PhD bio-maths, Caltech. Still doing post-doc work with his thesis advisor there, a man Frank had come to consider a bit of a credit hog, if not worse. It was interesting, then, that Pierzinski had gone down to Torrey Pines to work on a temporary contract, for a bioinformatics researcher whom Frank didnt know. Perhaps that had been a bid to escape the advisor. But now he was back.
Frank dug into the substantive part of the proposal. The algorithm set was one Pierzinski had been working on even back in his dissertation. Chemical mechanics of protein creation as a sort of natural algorithm, in effect. Frank considered the idea, operation by operation. This was his real expertise; this was what had interested him from childhood, when the puzzles solved had been simple ciphers. He had always loved this work, and now perhaps more than ever, offering as it did a complete escape from consciousness of himself. Why he might want to make that escape remained moot; howsoever it might be, when he came back he felt refreshed, as if finally he had been in a good place.
He also liked to see patterns emerge from the apparent randomness of the world. This was why he had recently taken such an interest in sociobiology; he had hoped there might be algorithms to be found there which would crack the code of human behaviour. So far that quest had not been very satisfactory, mostly because so little in human behaviour was susceptible to a controlled experiment, so no theory could even be tested. That was a shame. He badly wanted some clarification in that realm.
At the level of the four chemicals of the genome, however in the long dance of cytosine, adenine, guanine and thymine much more seemed to be amenable to mathematical explanation and experiment, with results that could be conveyed to other scientists, and put to use. One could test Pierzinskis ideas, in other words, and find out if they worked.
He came out of this trance of thought hungry, and with a full bladder. He felt quite sure there was some real potential in the work. And that was giving him some ideas.
He got up stiffly, went to the bathroom, came back. It was mid-afternoon already. If he left soon he would be able to hack through the traffic to his apartment, eat quickly, then go out to Great Falls. By then the days blanching heat would have started to subside, and the rivers gorge walls would be nearly empty of climbers. He could climb until well past sunset, and do some more thinking about this algorithm, out where he thought best these days, on the hard old schist walls of the only place in the Washington DC area where a scrap of nature had survived.
TWO In the Hyperpower
Mathematics sometimes seems like a universe of its own. But it comes to us as part of the brains engagement with the world, and appears to be part of the world, its structure or recipe.
Over historical time humanity has explored further and further into the various realms of mathematics, in a cumulative and collective process, an ongoing conversation between the species and reality. The discovery of the calculus. The invention of formal arithmetic and symbolic logic, both mathematicizing the instinctive strategies of human reason, making them as distinct and solid as geometric proofs. The attempt to make the entire system contained and self-consistent. The invention of set theory, and the finessing of the various paradoxes engendered by considering sets as members of themselves. The discovery of the incompletability of all systems. The step-by-step mechanics of programming new calculating machines. All this resulted in an amalgam of maths and logic, the symbols and methods drawn from both realms, combining in the often long and complicated operations that we call algorithms.
In the time of the development of the algorithm, we also made discoveries in the real world: the double helix within our cells. DNA. Within half a century the whole genome was read, base pair by base pair. Three billion base pairs, parts of which are called genes, and serve as instruction packets for protein creation.
But despite the fully explicated genome, the details of its expression and growth are still very mysterious. Spiralling pairs of cytosine, guanine, adenosine, and thymine: we know these are instructions for growth, for the development of life, all coded in sequences of paired elements. We know the elements; we see the organisms. The code between them remains to be learned.
Mathematics continues to develop under the momentum of its own internal logic, seemingly independent of everything else. But several times in the past, purely mathematical developments have later proved to be powerfully descriptive of operations in nature that were either unknown or unexplainable at the time the math was being developed. This is a strange fact, calling into question all that we think we know about the relationship between maths and reality, the mind and the cosmos.
Perhaps no explanation of this mysterious adherence of nature to mathematics of great subtlety will ever be forthcoming. Meanwhile, the operations called algorithms become ever more convoluted and interesting to those devising them. Are they making portraits, recipes, magic spells? Does reality use algorithms, do genes use algorithms? The mathematicians cant say, and many of them dont seem to care. They like the work, whatever it is.
Leo Mulhouse kissed his wife Roxanne and left their bedroom. In the living room the light was halfway between night and dawn. He went out onto their balcony: screeching gulls, the rumble of the surf against the cliff below. The vast grey plate of the Pacific Ocean.
Leo had married into this spectacular house, so to speak; Roxanne had inherited it from her mother. Its view from the edge of the sea cliff in Leucadia, California, was something Leo loved, but the little grass yard below the second-storey porch was only about fifteen feet wide, and beyond it was an open gulf of air and the grey foaming ocean, eighty feet below. And not that stable a cliff. He wished that the house had been placed a little farther back on its lot.
Back inside, fill his travel coffee cup, down to the car. Down Europa, past the Pannikin, hang a right and head to work.