Computer phages

The similarities between the computer viruses and “real” biological viruses are getting more profound all the time. There’s already a good case to be made for the fact that the Internet is a true ecological space, a virtual hothouse inhabited by rapidly mutating organisms. Just this week CNET reported on a worm that sleeps to avoid detection. That is, it has a virulent phase when it causes mischief and a quiescent phase when it lays low to avoid being seen.

This struck me as remarkably similar to the behavior of the much studied lambda phage, a virus that infests hapless E. coli bacteria. Under certain conditions (look here for a full explanation) the wily phage goes into hiding in the bacterium’s DNA, where it waits for a trigger to make it nasty again. So we have the same pattern of virulence and quiescence. Are virus authors actively copying Mother Nature? I doubt it. But a sound evolutionary idea is a sound evolutionary idea. What else can we conclude from reviewing several billion years worth of biology? This: viruses are not likely to go away anytime soon.

Fast DNA duplication

The New Scientist reports on a novel DNA duplication technique called helicase-dependent amplification, or HDA, that promises to speed up and simplify the process required to duplicate (amplify) small amounts of DNA so that you do useful stuff with it. If this works out, DNA-based technologies will start to invade our lives in more and more obvious ways. Polymerase chain reaction (PCR) is the current technique used for identifying trace amounts of DNA. PCR was worth a Nobel prize back in the day, but it’s time to turn up the heat.

Crime forensics will benefit dramatically when DNA testing becomes as easy as dusting for fingerprints. And diagnostics for viral infections will become commonplace. Doctors have always been able to culture bacteria (like strep) to see if you have the infection in question, but you can’t really culture viruses. Because of this, viruses are almost always diagnosed by elimination. But something like HDA makes it easy to “just look” and see if the virus is present. The porn industry already uses PCR to test for HIV. HDA may permit cheap diagnostics for various strains of flu and the common cold. This in turn may let us prescribe less antibiotics; you don’t need an antibiotic if I can tell you for sure that you’ve got a virus.

This all underscores one of the main reasons I’m optimistic for rapid progress in molecular biology. What we’re trying to understand, the living cell, is a already a competent information processing system. We just need to learn how to talk to it. Don’t blow up the natives and pick through their remains trying to divine their thoughts. Just walk up and ask.

Bureau de change ici

Suppose your Rodian character in the online game Star Wars Galaxies has banked a small fortune of 10 million credits. But you’re also playing an impoverished pauper of a halfling in Everquest. If only there were a way to distribute Star Wars largesse to the Everquest needy. This is exactly the problem that
IGE’s Virtual Exchange solves. Using the exchange, your halfling is in line for a tidy windfall of 136,000 platinum pieces. I can already picture Sally Struthers pleading with wealthy Wookiees to feed the homeless children in distant Ultima Online. 400 credits a day is all it takes!

It’s a good idea to join these worlds, but it’s not clear how the exchange rate is set (the site’s FAQ is still empty). It sure doesn’t look like an open market sets the rate, which can only mean that there must be a black market somewhere. Can you buy game money on eBay? Yes you can. I just found someone offering 200,000 platinum pieces for 100 honest-to-goodness British pounds. No bids, though. One million Galaxies credits can be had on eBay for around $20. Assuming these prices are reasonable, that suggests an exchange rate of around 49 credits/platinum piece, as opposed to the “official” rate of around 83 credits/plat. Those lousy Everquest border guards are robbing you blind! They’re as bad as the North Koreans!

I’m sure it won’t be long before we have serious money changing hands in a truly open market for fantasy world money. That’s the funny thing about money. If you think it’s real, it’s real.

A game called Nash

I’m reading Sylvia Nasar’s A Beautiful Mind, the biography of the schizophrenic Nobel Prize winner John Nash, and I’ve just reached a point where, as a graduate student at Princeton, he invents a little game to illustrate game theory. This game, which captivates the math department, is called Nash in honor of the creator. It later was sold commercially under the name Hex. Hex is very similar to a game called Twixt that I remember playing as a kid. The idea is to build a chain from one side of the board to the other while simultaneously preventing your opponent from doing the same.

I went searching for it on the web and found several places where you can play it in the privacy and comfort of your own browser. Here’s a good one: MazeWorks – Hex

Incidentally, John Nash is still alive despite the fact that his best-selling biography was written years ago. Here is his home page at Princeton. He doesn’t appear to be much of an HTML hack, but you can find presentations he’s given in the last few months if you poke around. And Princeton is good enough to keep his 32 page Nobelworthy thesis available for ready download. Here it is. It’s a big PDF scan of the original, complete with typos and handwritten Greek letters. We don’t need no stinking TeX.

The coming electric navy

One hundred years or so ago, Winston Churchill, in his capacity as the First Lord of the Admiralty, worked vigorously to convert the old coal-burning Royal Navy to a newer and more efficient oil-burning fleet. This turned out to be a strategically sound decision despite the fact that it entailed a new dependence on oil that the British Isles could not supply. Oil simply had too many advantages over coal to fret overmuch about the fact that it would have to be produced in and shipped from remote, difficult-to-manage locations around the world. This single fact has, by itself, largely shaped geo-politics across the last century.

Curiously, today the U.S. Navy is undergoing a Churchillian revolution of its own: ships are being converted from oil power to electric power. The change is somewhat subtle, because the electricity comes from onboard gas turbines that in turn are still powered by fossil fuels. But there are a number of advantages. You can put the gas turbine wherever you want, and you can use the enormous electrical power generated for other purposes, like vaporizing enemy ships and planes with high-power directed energy weapons. Superconducting electric motors can be put in movable pods outside the hull, thereby eliminating the awkward drive shafts that have dominated hull design and dramatically improving maneuverability.

If this sounds a lot like the move to hybrid cars from conventional gas powered cars, it is. The exact same principle is at work, which leads me to speculate that high-power directed energy weapons will be a popular accessory for the 2005 Toyota Prius.

Ambient displays

Here in Boston, we have an ambient weather display built into the skyline: the old Hancock building (not to be confused with the sleeker newer Hancock tower by I.M. Pei) has a beacon atop it that changes color with the weather. There’s even a little rhyme to help you remember how it works.

Steady blue, clear view.
Flashing blue, clouds are due.
Steady red, rain ahead.
Flashing red, snow instead

During baseball season, the flashing red signal is means the Red Sox game has been rained out. Cocktail party conversation tidbit: a few years ago, opening day was delayed because of snow, making both senses of the flashing red signal true.

If you don’t live in Boston, you can now use the Ambient Weather Beacon from Ambient Devices. It uses a slightly different semaphore to get the message across.

The Beacon … glows more red when warmer weather is forecasted, and colder blue hues if cooler temperatures are on the way. The Beacon will also subtly pulse to show the chance of rain or snow.

A quick glance is sufficient to tell you which coat to grab on your way out the door. The Economist just ran an article about Ambient that includes this quote from the company’s CEO David Rose, “There’s a fallacy that more details are better,” he says. “What you actually want is awareness first and details on demand.” Details are vastly overrated.

Car buying tips

The last time I bought a car, I thought I was pretty well-informed by reading from sites like Edmunds.com and KelleyBlueBook.com (both have the obligatory Ten Steps to Buying a New Car: here and here). I read the buying guides, collected the data, and learned all my lines before the day of the big showdown at the dealership. But that was all years ago (way back in 2000), and the web just gets richer and denser every year. These days if you want to buy a car, you shouldn’t miss CarBuyingTips.com. The guy behind the site is clearly obsessive… obsessive in a way that’s good for you. I can’t vouch for his personal happiness, but he can sure do you some good.

Inane Popular Mechanics

Many years ago, say in the 1970s, science magazines didn’t have nearly as much to report as they do these days. Popular Mechanics in particular always seemed to be hyping silly cover stories, stories that bore no relation to things that were likely or economically worthwhile, like a hotel on the moon or a personal helicopter in every garage. It’s tabloid science, but hey, it sells magazines. “Someday you will send superfast mail through transcontinental pneumatic tubes!”

These days, there’s enough fast moving science and engineering to fill a thousand magazines, but still Popular Mechanics insists on pitching things in an absurd way. Here’s an article about nuclear aircraft that is a beautiful throwback to the days of the 1958 Ford Nucleon and the family submarine:
The Return Of Nuclear-Powered Aircraft. It’s not like the story is a pack of lies, but it’s told with the breathless excitement of Tomorrowland, when after all, they’re talking about flying nuclear reactors. But the thing that really delighted me was the painting associated with the story. Look closely at the picture and you’ll see Mom, Dad, and the kids getting out of the cockpit while hazmat-suited technicians pull nuclear material out of the back. Meanwhile, two other nuclear planes are zipping merrily through the air on an apparent collision course. Are you buying this? A fully loaded 767 is a bad enough hazard without dumping in a bucket of hafnium-178 and a powerful x-ray machine.

To be fair, they themselves acknowledge this story has been here before: “Older POPULAR MECHANICS readers may recall that an atomic plane was featured as our January 1951 cover story.” I don’t think we’ve heard the last of the atomic plane. Perhaps this latest issue of Popular Mechanics will show up in a future edition of Yesterday’s Tomorrows.

Beautiful Bloglines

You may never have heard of RSS aggregators before, but someday you will, although eventually I’m sure they’ll have a sweeter name. If you’re the least bit of an information junkie, read on. Bloglines may well be the place for you to jump in and see what the fuss is all about.

I have complained in the past that I don’t care for most of the RSS aggregators I’ve tried. I like Aggie, but it’s old and it seems pretty clear that nobody’s moving it forward. I emailed Aggie author Joe Gregorio, and he confirmed this. As he put it, “The three-paned aggregators really took the wind out of our sails.” But then he went on to recommend Bloglines, which he uses. That was a good enough recommendation for me, so off I went to set up a Bloglines account. And sure enough, I like it. It’s still somewhat like a three-pane aggregator, but has the key features that I’m after. I can sort the blogs however I like, and I can mark them all as read in a single quick button click. And since it’s an online service (rather than a browser that runs only on my machine), I can view from anywhere, and I can show you my reading list. Voila:
Bloglines | Ned’s Blogs.

Nick Denton of Gawker Media has got a similar online blog aggregator experiment going on: kinja.com. It’s a simpler, more stripped-down tool, designed to bring weblogs to the masses. As it says on the site, “Kinja is not aimed at early adopters.” Read: “RSS geekboys need not apply. We don’t need your whiny noise around here.”