Molecular biology animations

dna-replication.jpg
A few years ago, PBS ran a series called, simply, DNA. It included some of the spiciest, most inspiring animations of biological molecules in action that I’d ever seen. I longed to linger over them and savor them, but they came and went so fast in the show, and until this evening I had no idea who did the work. Over at information aesthetics I came across the 2006 infographics winners from Science magazine. One of these winners was Drew Berry of the Walter and Eliza Hall Institute in Melbourne, Australia. He’s the guy who made the beautiful animations.

Armed with this information, I was able to track down the mother lode in short order. Here is a page pointing to the QuickTime videos that gave me the shivers. May I particularly recommend the insane fruitbat circus otherwise known as DNA replication. If a Divine and Perfect Intellect is responsible the design of this unlikely contraption, somebody’s got a lotta ‘splainin’ to do.

Finally, here is an interview with Drew Berry about how he got the gig for the DNA TV series.

Cruel 2 B Kind: the friendly assassin

The game Assassin, as Wikipedia helpfully puts it, is a “live-action role playing game” where every player is trying to kill other players until only one remains. Unlike a card game or the round-the-table Werewolf game popular at Foo Camp, Assassin can span many days and include dozens of people. That means it collides with Real Life in fairly obvious ways. You can, for example, be killed on the way to class. But what does it mean to be killed? In one game you might be done in with a squirt gun, in another it might be a rubber band. But a new version of the game, as I learned at Collision Detection, involves killing with kindness.

Cruel 2 B Kind is a version of Assassin designed to get around one of the inconveniences of the game: freaking out bystanders with disturbing and apparently dangerous attack and evasion dramatics. Intead of murdering someone with a squirt gun, you do it with a targeted compliment. Thus, a badly-aimed volley will only brighten a bystander’s day rather than dampening their shirt or soiling their pants.

This all sounds clever to me, but I knew exactly where to go for the straight dope. At great expense, we have retained the services of Assassin Expert JMike and asked him for his opinion on the matter. When it comes to Assassin, JMike knows whereof he speaks. Over the past 15 years he has played and managed dozens of Assassin games great and small. Here’s what he had to say.

The “random act of kindness” shtick is a little sappy. Granted,
assassin-style games have always had a problem: how to arrange a game that
is played out in the real life urban jungle? People who design these kind
of games — well some of them anyway — fantasize about being able to set up
stake-outs, open-clandestine meetings, elaborate hits, etc. out in public,
but obviously you have this problem that the more realistic the setup, the
more likely it will be confused for the real thing (with dire consequences).
So the realism wing of the gaming world takes the action into controlled or
semi-controlled environments: college campuses, convention hotels, private
rural land, and they accept the necessary compromises: complex relationships
with the authorities and/or slightly watered-down action (paintball, boffer
weapons, very simplified role playing dynamics, etc.). This other wing of
the gaming world seems to be evolving recently, where they use VERY watered
down action in order to be able to play out in the real world. I’d say that
the recent movement of live performance art — I forget the name of the
phenomenon, but where you get like 200 people to meet and go up and down the
escalators in some iconic hotel lobby in town — is very closely related to
this wing of the gaming world. Anyway, I think modern technology is going
to be a big advance to this wing of the gaming world, in that you’ll be able
to do more complicated things where you get the thrill of the chase and
even, in a way, the thrill of the kill, without having to do things that
look dangerous or threatening to non-players.

SO I guess my take on it is that this is kind of a confluence of the old
school live-action role playing gaming scene with the
whatever-its-name-is-performance-art scene and more power to it. I hope and
expect to see some pretty good and funny things come out of it. Random act
of kindness warfare is a little bit of a sappy start though :)

So there you have it. One of my favorite things in life is knowing just who to ask when a certain topic comes up. You’d be surprised how often JMike is that person.

Voice recognition works now

I recently bought NaturallySpeaking, a program that does voice-to-text speech recognition. It’s owned by Nuance now, but the Dragon Systems technology has been bought and sold multiple times since work started on it in the 1980s. The latest versions (I bought Preferred version 9) have been getting consistently good reviews and I have a lot of text to enter, so I decided to take the plunge.

Sure enough, this software is almost disturbingly good. I picked up a book on alchemy that happened to be on my desk and read the following:

Standing between science and art, philosophy and religion, the mysterious practice of alchemy has long been cloaked in a veil of mystery. To this day, scholars are unsure of the precise origins of this esoteric craft, the forerunner of modern chemistry, which reached its peak in the Renaissance.

It didn’t make a single mistake in that passage.

As part of the training process for using the software they have you read one of several passages. I chose John F. Kennedy’s inaugural address. I was sorely tempted to read it in a funny John F. Kennedy voice, but the downside was obvious: I would have been obligated to speak in a funny John F. Kennedy voice every time I wanted to dictate something, and my fellow Americans, that is something that this administration cannot condone and will not support.

Some observations after using NaturallySpeaking for a few days: Even when dictation is 99.9% correct, you really want it to be 100% correct. I was also surprised to see just how much time I spend in editing, formatting, and fiddling with text, which is to say stuff that voice commands are not so good at. Voice is now good for laying down text in big blocks, but not so good at spatial fiddling. Even when you’re sitting next to a human who understands your words perfectly, it takes a lot of work for them to understand your intent. If you’re telling them how to use a GUI, you quickly end up in tech support hell, saying things like: “Double click on that. Not there… over there, just above that red thing. No, to the left! Farther left! Oh crap, you just launched Visual Studio. Here, give me the mouse.”

Another funny thing is that since the contextual understanding is so good these days, the errors that you do get are harder to spot in a quick proofing pass. In a world of clever machines, be grateful for obvious miss steaks. Ha ha. Just kitten.

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!