Rambles Blog at Star Chamber

I’m a big fan of Bloglines, the free online newsfeed aggregator. I keep talking about how aggregators are a big deal, and as time passes I believe this more and more. And aggregators are a natural fit for an online service like Bloglines (as opposed to a downloadable client like FeedDemon), because they can benefit from a sort of “super-aggregation” across all Bloglines users. I get good recommendations on new blogs to subscribe to, and of course I can use the exact same setup at home and at work. Here’s my current personal newsfeed list.

Here’s an example of why aggregators are so damned useful. I wanted to follow the Tour de France, but I’m not a huge cycling fan; I was just hopping on the Lance Armstrong bandwagon. So I wanted to have a quick and easy way to check the cycling headlines every day. I found the page I wanted on the BBC’s site: BBC Sport | Other Sports | Cycling | UK Edition. From my Bloglines account, I subscribed to the RSS feed for this page, and voila! I had a simple but effective headline news about exactly the story I was interested in. No need to scan through the sports pages. And now that Lance has picked up trophy number six, I can unsubscribe and stop paying attention to cycling news.

It turns out that Jon Udell also likes Bloglines. Check out his comments here.

Nick Currie, a.k.a. Momus, is a musician who lives in Japan and keeps a clever blog called Click Opera. I came across his excellent entry on Japanese-ness recently: Superlegitimacy. He makes a number of sharp observations about the differences between East and West, beginning with his reverie about the strange behavior of his train conductor.

At each station he made an immaculate white-gloved gesture — a series of florid manual curlicues more like the gestures of an orchestral conductor than a train driver. He pointed at the TV screens in his console showing the doors, then pulled the train away with both gloved hands on his accelerator lever, uttering as if by compulsion his ecstatic falling cry: ‘Kkkkyyyyyoooooooo!’

Did the conductor have Tourette’s, or a mild form of autism? No. He was Japanese. He was at peace and at home. He was superlegitimate. When you feel superlegitimate, it’s hard to go wrong.

Here’s an article by Ben Hammersley about the fantasy game money exchange I talked about last week: A virtual fortune: “A unique market has grown up whereby high-level achievers in online role-playing games can trade their virtual world characters for cash.”

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.

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.