Author: gulley

Freely transmitted neglected tropical diseases

The Public Library of Science has the laudable goal of making the world’s scientific and medical literature a freely available public resource. In the current sclerotic journal system, the flow of money greatly impedes the flow of information, and important scientific results are locked away behind expensive subscriptions. If you’re inside the privileged White Coat Curtain, you can find what you need. If not, good luck to you.

Another way that money skews medical publications is that editors consider diseases of the rich much more interesting than diseases of the poor. It’s surprisingly hard to fund and publish research about chronic infectious diseases of tropics. That’s not surprising given how markets work, but with the Internet we can do better now. Consider the case of the latest PLoS journal: Public Library of Science to launch new, open access journal on neglected tropical diseases.

Neglected Tropical Diseases (www.plosntds.org) will focus on the overlooked diseases that strike millions of people every year in poor countries, including elephantiasis, river blindness, leprosy, hookworm, schistosomiasis, and African sleeping sickness. The journal, supported by a $1.1 million grant from the Bill & Melinda Gates Foundation, will begin accepting submissions in 2007.

I can’t help but wonder if they will ever become so successful that they have to change their name to something like PLoS Reasonably Well-Known Tropical Diseases (not unlike questions on the Star Chamber RAQ list). Then again, if Al Gore is right about global warming, it might become PLoS Diseases We All Get Now That The Entire Planet Is a Hellish Fireball. It’s no joke that the tropics are coming your way, and they’re bringing their friends with them.

eBay Second Offer scam?

I was bidding for some software on eBay this weekend (new, unopened, never registered). I had the winning bid for a long time and just as the auction ended I was outbid and lost the auction. Fair enough… that’s life on eBay. Sniping happens all the time. What made the story more interesting is that soon after I was informed that I lost, I got a “Second Chance Offer”. According to the offer, “the high bidder was either unable to complete the transaction or the seller has a duplicate item for sale.” Something about this struck me as odd, but since I had already done my comparison shopping and convinced myself that my offer was a good value, I went ahead made the purchase.

But the experience got me thinking about the Second Chance system. You’re officially forbidden to bid for your own items (known as shill bidding), but I suspect a lot of people do it anyway. But I had always assumed that at least the seller would have wasted their time with a shill bid. For example, say you run a week-long auction and end up winning your own item. Now, oops! you’ve got to start another auction with the same item. So at least there is some real cost to the seller, besides the risk of getting caught. But the Second Chance policy lets you run a very efficient shill-bidding process. Your sock-puppet shill makes a very high bid to draw out the highest prices people will pay. Your sock puppet wins the auction, but of course is unable to pay (sock puppet insolvency is rife). Now you double back to offer the item to the next highest bidder who has been completely exposed at their high water bid. No need to re-offer the item, and you squeeze optimum value out of your market. That’s got to be a pretty tempting hack for your average seller. Anybody heard of this kind of thing?

As a coda to this story, I googled around for “eBay Second Chance scam” and learned of an entirely different hazard associated with this transaction. After a legitimate sale has closed, a third party thug claiming to be the seller can contact a losing bidder. The losing bidder happily sends money, and the phisherman departs with his cash. In the meantime, the actual seller is completely unware this is happening. So beware of phishy addresses if you get a Second Chance offer.

Hearing about this scam made me nervous, but the details of my sale checked out. Then again, I haven’t received my goods yet, so you never know…

Visualizing flights; visualizing Google

I’ve spoken to several people who really liked the airplane flight visualizations that I linked to here and here. The patterns are so beautiful that they are practically aching to be put into the hands of an artist. That artist is among us, and his name is Aaron Koblin. Via peterme I found out about his work. You must go look at his take on the FAA planes-in-flight data for March 20, 2005. The raw data is inspiring enough, but Koblin makes it look like the U.S. is juggling 19,000 brightly colored balls, or scintillating with pyrotechnic tracers, or in the pièce de résistance, spawning molten globules of amoeboid protoplasm. Sorry for the overwrought prose, but this stuff is really good.

Until very recently, data patterns like this were being interpreted either strictly by engineers or, in the best cases, an engineer who happened to have a good sense of design. Now the pros are starting to arrive. When has this happened before? I was wondering what the pre-computer analogy would be to an artist taking on a technical topic with technical tools. Was there a time when photography was just transitioning to art, before which it was considered only the domain of 19th century gadgeteers? And I suppose architecture has always been on this cusp.

In passing, I wanted to link to an eerily similar animation of Google search activity that I found via A Day of Google” href=”http://radar.oreilly.com/archives/2006/09/a_day_of_google.html”>O’Reilly Radar site. This an animation of where searches are originating all over the world for one 24 hour period. One take-away observations: planes sleep more than Google searches do. Lots of people are staying up too late banging away on their computers.

Speaking of which, where did the time go? Good night!

Foo camper puzzler

I’ve been slow to sort through my Foo Camp notes, partly because it was such an overwhelming experience, and partly because so many of the people from Foo Camp are famous and prolific A-list bloggers. What can I possibly add to the story that they have already blogged about in such detail? Well, of course they have their stories and I have mine. And if you don’t keep up with A-list bloggers that went to Foo Camp, then just maybe you’ll hear about it here first.

The place to start is the name: Foo Camp. The “Foo” part is a kind of quasi-joke that stands for “Friends of O’Reilly” in a winking sort of way. But the “Camp” part is not a joke. We really did show up in Sebastopol, California and camp in the grassy area behind the O’Reilly Media headquarters. Just imagine pitching a tent in a business park and you’ll get the basic idea. Here is what it looked like. And, in the spirit of an un-conference, we really did throw together an improvised conference schedule on Friday night. And we really did drink at the proverbial Foo Bar. I’m sorry, I meant to say the literal Foo Bar.

Without getting too much more into it now, I will say that absolutely everyone there was smart and interesting. It was intimidating to meet so many fascinating and accomplished people, but it was positively alarming to come home and read more about their accomplishment online. I camped next to D. Richard Hipp, an open source developer from North Carolina. When I was poking around his web site after I got back, I came across this lovely puzzler page. I hope it wastes a lot of your time, because it sure burned up a lot of mine.

SculptorHouse: place as art

olu.jpg
You’ve heard of landscape architecture. Now get ready for the architected landscape. My brother-in-law Craig Pleasants is an artist who has worked on sculptures at an architectural scale. With years of experience to draw on, he’s now turning the idea of architectural sculpture into a business opportunity with a site called sculptorhouse.com. The picture shown here is actually one of Craig’s first architectural projects: the house he lived in for many years. Eight sided, eccentric, and endearing, it became known in our family as the OLU, for Octagonal Living Unit. Now with Craig’s help you can have an OLU of your very own. Contact him at the sculptorhouse.com site and he will create something beautiful on your property.


Incidentally, Craig has also done some writing and illustration. One of my favorite stories of his is the ethnohistoriographical deconstruction of the Three Little Pigs story. I won’t give away the surprising conclusion, but I will say that the first little pig deconstructs a straw house, and the second little pig deconstructs a… well, just be sure and read all the sidenotes.

Segway dealerships

segway-dealer.jpg
I’m just back from a week’s vacation at Lake Winnipesaukee in New Hampshire. Between vacation and Foo Camp, it’s been a hectic couple of weeks, but things should be getting back to normal now. I mention the vacation because, at a stop for dinner on the way up, I happened to notice this dealership sign: Segway of Northern New England. It was like a sign from the future that didn’t quite happen. A few years in the future from a few years ago (i.e. now) we were all going to be zooming around on Segways. Weren’t we? Weren’t we?

One critique that seems to stick to the Segway is that, at some basic human level, it’s just weird to see someone standing still and moving at the same time. The Segway-ist can’t help looking comical. It reminded me of the difference between motorcycle cops and bicycle cops. Psychologically there’s just no comparison: the bicycle cop is approachable. He’s your friend. He’s on your side. You want to talk to him. You want him to catch the bad guy. But the motorcycle cop moves without moving. He is remote and menacing, an enforcer from another domain. You might even be tempted to help his frightened prey escape. Which all leads to the question: what about the cop on a Segway? Intimidator, friend, or buffoon?

The Segway of Northern New England showroom really exists of course, but then New Hampshire is Dean Kamen’s back yard. I don’t imagine there are too many other dealerships around the country. I wonder what kind of business it does.

Cheap DNA sequencing

abi3730.jpg
This is a picture of one DNA sequencing machine: the Applied Biosystems 3730xl DNA Analyzer. It costs a few hundred thousand dollars and it’s starting to show its age, but it’s still the sweetest thing on the market if you want to sequence DNA accurately and fast. Here’s another DNA sequencing machine: RNA polymerase. It’s been around for a few billion years, and you’ve got trillions of them in your body right now, most of them sequencing DNA faster than the fridge-sized 3730xl. If not, you’d be real dead.

One of the reasons I’m optimistic about our ability to understand what’s happening inside the cell is that a cell is already a sophisticated information processing engine. If we can learn how to listen to it as it’s working, we won’t need to blast it to bits and paste its little smithereens back together in a kind of glorified biotech forensics lab. The violence of the language we use is telling. Polymerase chain reactions? Shotgun sequencing? Please. Why don’t we just ask that busy little RNA polymerase to tell us what it’s doing?

Of course that’s easy for me to say, but it turns out that’s exactly what Steve Block is doing in his Stanford lab. By stringing DNA between two tiny polystyrene beads, he can effectively listen to the sound of transcription and infer the sequence. The title of his paper drives home the fact that you can’t get much smaller than this: Single-Molecule, Motion-Based DNA Sequencing Using RNA Polymerase. If you don’t have a subscription to Science (which I don’t) you can read about papers like this in places like Alex Palazzo’s Daily Transcript and then you can go directly to the publishing lab for the paper (PDF).

Misspelled aquaria

This morning, as we were planning to go to the Boston Aquarium, I checked the website, as you do, to verify the Sunday hours. No point in showing up only to discover that it’s closed on Sunday or undergoing massive renovations or some such thing. As I began typing the letters “boston aq” into the Google Toolbar, the following word completions were helpfully suggested to me.

boston aquarium 1330 results
boston aqarium 1140 results
boston aqaurium 856 results
boston aqurium 682 results
boston aquariam 626 results
boston aquirium 64 results
boston aqustics 14 results

I’m not terribly surprised that the word aquarium is so easily misspelled, but I am amazed that the correct spelling accounted for only 28% of the overall result count, not to mention the fact that it very nearly came in second. This is fascinating data, and it illustrates that Google is in possession of the finest set ever made of data on spelling in English. What could schools do with this? For one thing, we’ll be able to watch trends over time. Are we getting better or worse at spelling? It also seems that by correlating a list of frequently used words against frequently misspelled words, we could at least make our spelling tests more practical. Screw up a word like flagellar and nobody gives a damn, but if you write erotic instead of erratic, it might get you in some hot water. Nobody likes an erotic spellor, or mabe they dont realy care much any more, sinse Google can fix it all.

Google will always know what you mean, even if nobody else does, for Google knows what is in your heart.

Incidentally, Boston Acoustics is the name of a speaker company. And yes, Google will indeed suggest that perhaps by aqustics you meant acoustics.