Friday, February 26, 2010

Article: Can A Biologist Fix A Radio?

J. & T.,

You might enjoy this short article by a microbiologist on the difficulties involved in making scientific progress in understanding complex phenomena like apoptosis--or a radio. It's quite readable, takes maybe ten minutes to finish.

Can A Biologist Fix A Radio?

[snip] How would we begin? First, we would secure funds to obtain a large supply of identical functioning radios in order to dissect and compare them to the one that is broken. We would eventually find how to open the radios and will find objects of various shape, color, and size (Fig. 2, see color insert). We would describe and classify them into families according to their appearance. We would describe a family of square metal objects, a family of round brightly colored objects with two legs, round-shaped objects with three legs and so on. Because the objects would vary in color, we will investigate whether changing the colors affects the radio's performance. Although changing the colors would have only attenuating effects (the music is still playing but a trained ear of some people can discern some distortion), this approach will produce many publications and result in a lively debate.

A more successful approach will be to remove components one at a time or to use a variation of the method, in which a radio is shot at a close range with metal particles. In the latter case, radios that malfunction (have a "phenotype") are selected to identify the component whose damage causes the phenotype. Although removing some components will have only an attenuating effect, a lucky postdoc will accidentally find a wire whose deficiency will stop the music completely. The jubilant fellow will name the wire Serendipitously Recovered Component (SRC) and then find that SRC is required because it is the only link between a long extendable object and the rest of the radio. The object will be appropriately named the Most Important Component (MIC) of the radio. A series of studies will definitively establish that MIC should be made of metal and the longer the object is the better, which would provide an evolutionary explanation for the finding that the object is extendable. [snip]


"When people are married, instead of trying to get rid of each other, reflect that you have made your choice, and strive to honour and keep it." --Brigham Young

If you're so evil, eat this kitten!

Thursday, February 18, 2010

Theory and practice


You might find this article interesting. It's on commercializing a research tool for static analysis of software, and the surprising differences between academic requirements and commercial requirements. The article took me around a half-hour, and the whole thing was worth reading.


This is the research context. We now describe the commercial context. Our rough view of the technical challenges of commercialization was that given that the tool would regularly handle "large amounts" of "real" code, we needed only a pretty box; the rest was a business issue. This view was naïve. While we include many examples of unexpected obstacles here, they devolve mainly from consequences of two main dynamics:

First, in the research lab a few people check a few code bases; in reality many check many. The problems that show up when thousands of programmers use a tool to check hundreds (or even thousands) of code bases do not show up when you and your co-authors check only a few. The result of summing many independent random variables? A Gaussian distribution, most of it not on the points you saw and adapted to in the lab. Furthermore, Gaussian distributions have tails. As the number of samples grows, so, too, does the absolute number of points several standard deviations from the mean. The unusual starts to occur with increasing frequency.

For code, these features include problematic idioms, the types of false positives encountered, the distance of a dialect from a language standard, and the way the build works. For developers, variations appear in raw ability, knowledge, the amount they care about bugs, false positives, and the types of both. A given company won't deviate in all these features but, given the number of features to choose from, often includes at least one weird oddity. Weird is not good. Tools want expected. Expected you can tune a tool to handle; surprise interacts badly with tuning assumptions.

Second, in the lab the user's values, knowledge, and incentives are those of the tool builder, since the user and the builder are the same person. Deployment leads to severe fission; users often have little understanding of the tool and little interest in helping develop it (for reasons ranging from simple skepticism to perverse reward incentives) and typically label any error message they find confusing as false. A tool that works well under these constraints looks very different from one tool builders design for themselves.

"When people are married, instead of trying to get rid of each other, reflect that you have made your choice, and strive to honour and keep it." --Brigham Young

If you're so evil, eat this kitten!

Tuesday, February 2, 2010

The Parable of Bob and the Bill

[letter excerpts]

Posit: Day-old bread is better than nothing. Posit: Nothing is better than chocolate. Conclusion: Day-old bread is better than chocolate.

Once there was a man named Bob who attended a charity auction. The auctioneer explained that this was a pay-as-you-bid auction, like poker: you pay as you bid, and if you lose you don't get your money back. "That's dumb," thought Bob, "but I guess if it's for charity…" Then the auctioneer unveiled the item up for bid—a twenty-dollar bill. Bob, who considered himself a very rational person, looked around the room at the other thirty-odd people and thought, "If I bid and lose, I lose everything. If I win, I get twenty dollars. I have a one in thirty chance of winning twenty dollars, so the bid is worth $(1/30 * 20) = 67 cents to me." He immediately bid a quarter, hoping to make a profit, and put his quarter out in front of him.

Another bidder bid fifty cents, and someone else bid seventy-five cents. "Going once," said the auctioneer. Bob frowned in thought. "Odd. There's only three of us bidding. That raises my expected value to $6.67, so I can afford to bid a dollar rationally." The other bidders, after some hesitation, matched his bid and soon the price was at $5. Bob shook his head, "Let's end this," and bid $6.67. Further bidding would be irrational. Bob would pocket the $20, and they could all go home.

The third bidder immediately bid $10. "Oops," said Bob, now seeing the flaw in his reasoning. "No matter what the odds are, the payoff for winning is $20, not $6.67, so of course other people will bid above $6.67. My profit is the difference between my winning bid and $20, not between my winning bid and $6.67." So he bid $15, hoping for a 33% profit on his investment. Bidder #2 bid $17, and bidder #3 bid $18. Grumbling, Bob bid $19.99. Bidder #3 sat down abruptly. Bidder #2 hesitated again, then bid $21.

Bob couldn't believe it. "Who would bid $21 for a $20 bill?" he said to himself. Then with a sudden sick shock he got it. "No," he said, "bidder #2 already bid $17. If he loses, he lost $17. If he wins at $21, he lost only $1. Clearly it is rational to bid again to reduce his losses." And with the same sick certainty, Bob knew the same logic applied to himself. Bob bid: $25. Response: $28. "Again," thought Bob, "I have the choice between losing everything, only it's $25 instead of $19.99 this time, or paying $4 for a 50% chance at winning the $20. 50% of $20 is $10, and $4 is less than $10 so clearly the only rational action is to invest another $4." Bob bid $29, hopelessly, while the rest of the audience watched in fascination. This could have gone on for quite a long time but Bob's wife hit him with her purse and told him to stop being a nit. Bidder #2 won at $30. The auctioneer thanked them all, gave $20 to bidder #2, and put their combined bids ($18 + $29 + $30 = $77) in the charity cashbox. Everyone applauded and Bob went to lie down.

Last story for today: my dad went to med school in Louisiana when I was one or two years old. Some of my earliest memories are of Louisiana and Tulane University—going for stroller rides with my mom, playing in the pool, etc. I'm not sure but I think I might even remember the flood that buried the streets in over a foot of water. (Then again, I might be getting it mixed up with the floods from my mission, which I definitely remember, including what it did to our basement rooms: it was like an indoor swimming pool, which is bad news for missionaries. Or an indoor baptismal font, which is good news I suppose.) In particular I remember a large room, which must have been at Tulane, and one wall of the room was covered with transparent glass cubes or jars, stacked one on top of the other. In each jar was yellow liquid, and in the liquid floated a dead baby. I remember two babies in particular. One had a big corkscrew of a belly button that seemed several inches long and reminded me of a screw. The other baby had two heads. I thought that was quite interesting. I don't remember if this was before or after I saw the two-headed snake at the Santa Ana zoo, which was interesting because it was alive, but I think the baby was even more interesting because it was human and had arms and legs and stuff, which snakes do not. Anyway, I don't remember feeling scared at all but I wasn't sure why the liquid was yellow and I think I drew the obvious conclusion for a two-year-old at that—especially a two-year-old familiar with swimming pools and babies—and perhaps that did disturb me a little.

"When people are married, instead of trying to get rid of each other, reflect that you have made your choice, and strive to honour and keep it." --Brigham Young

If you're so evil, eat this kitten!