Old school DNA purification

I often muse about the difference between the biology world and the software world. They’re ramming into each other more and more these days, and sometimes the result is more like a car accident than a gentle merger. Bioinformatics and systems biology are two rapidly growing fields where you are as likely to find a physics refugee bootstrapping a new career in biology as a biologist learning a few programming tricks in perl. The physicists and the biologists often betray their doubts about each other (as well as their own insecurities) to amusing effect.

One thing I know about software that works really well, though (you can see which side I come from), is how quickly well-written software tools can lower the barriers of entry to others that follow. For instance, I don’t need to write graphics primitives or web search engines, because someone else has written them for me. Even so, some people grumble… years ago a friend of mine complained that search engines were killing the joy he took in his skilled code hunting techniques using ancient tools like Gopher and Archie. I admire people who can chip their own flint spearpoints, but how nostalgic do you really want to be for a society of hunter-gatherers?

Given all this, I was entertained by this post on the Daily Transcript, a blog by cell biology postdoc Alex Palazzo. In a post about a product called Systems Biology Plasmid DNA Purification, he rips into those Johnny-Come-Lately’s who don’t know their protein assay from a hole in the ground. As he tartly puts it: “Now even a clueless Physicist can purify DNA without thinking about how this stuff actually works!” Ouch! Much better, though, was the comment posted by one of the blog’s readers.

Everyone is ripping on kits these days to prove how “old-school” they are. Look, you’re no Jacob Monod just because you make your own alkaline lysis buffers. You’re not a good scientist because you can isolate more DNA per cell than the other guy. You’re a good scientist because you can answer important questions quickly and definitively.

Well said. All those biology guys are just idiots who don’t get it.

Ooooh, I wish I hadn’t said that.

Meta-popularity list

Witness the hive mind in action at popurls.com. It’s the next logical step after popularity aggregation websites like digg.com, furl.net, and del.icio.us: take all of the popularity aggregation websites and aggregate them into a one giant meta-popularity conglomeration. Obviously we’re not out of meta’s yet… one can imagine this process continuing for a few more generations. What I worry about, though, is what happens when we have a meta-meta-meta-meta-popularity list that’s been winnowed down to one single URL so irresistably popular that it amounts to an informational black hole. There’s a chance that everyone on the planet could click on it at exactly the same moment, thereby imploding the metaverse and taking down this sector of space-time. It makes me shudder to think that the apocalyptic singularity may result from a bad video of teenagers lip-synching to an old Backstreet Boys song.

Potential catastrophes aside, popurls.com is a pretty entertaining place to graze. It feels to me like a slice through the Great Brain. Or maybe an MRI snapshot of the hive at work.

Gasoline heat map

How much are you paying for gas? The people at GasBuddy.com will tell you, and they’ll also tell you where to find the cheapest gas in your area. They’ve got a good social network/web application thing going where people around the US regularly report what gas costs near them. So, for instance, here are the prices in Watertown, Massachusetts. They’ve also got historical trend charting available, which turns up some intertesting stuff. I compared Boston to New Orleans for the past year, and I was amazed to see that Boston prices jumped 60 cents in less than a week after Katrina last August, while at the same time gas prices in Louisiana were constant. But it turns out this was more of a legal mandate than anything else… Atlanta and Houston both had the same post-hurricane spike as Boston.

The pièce de resistance for the site, however, is the gas temperature map. Here you can see in one place, county-by-county, what the average price is for a gallon of gas anywhere in the country. It’s very entertaining to make up theories to account for the disparities. California is always most expensive because of its more demanding (and expensive) refining requirements. But what explains the difference between Wisconsin and Minnesota?

Muybridge animations

muybridge.jpg
When a horse is running, is there ever at point at which all four feet are off the ground? That was the question that vexed Leland Stanford, the California governor, robber baron, and eponymous university benefactor. Today high quality photography and video makes it difficult to believe that this could actually be a controversial question. But in 1872, Stanford retained the magnificently named Eadweard Muybridge to determine the definitive answer. Muybridge’s photographic work anticipated the movie; by using multiple cameras he was the first to capture a sequence of images that show exactly how a horse gallops. Muybridge was like a 19th century version of MIT’s “Doc” Edgerton who used strobe photography to stop time as, for example, a bullet exploded through an apple.

Using multiple still cameras to suggest motion has come back in vogue lately, most notably with the so-called “bullet time” effect seen in The Matrix. This effect, known more generally as time slicing, extends the Muybridge idea: the camera seems to move infinitely fast, viewing the subject from multiple directions at the same instant. The technique can also be used for less purely cinematic purposes. Here’s a nifty timeslice video of a cheetah running through an African encampment.

Seeing all this stop motion photography made me think of fun little video I saw over at Google: The Art of Motion by Russell Wyner. It has several Matrix-like homage shots. And finally, when it comes to goofing on the Matrix, you can’t top the magical ping pong video. Turn the volume up and watch it all the way through.

And for the record, galloping horses do have all four feet off the ground at one time or another.

Paperback book notifications

Ben Hammersley has shut down the Lazyweb, but the key insight that it embodied still endures:

…if you wait long enough, someone will implement that wacky idea you had… (or already has!) Alternatively, that if your blog has enough readers, a reader will know and provide the answer to a question you are too lazy to research yourself.

I make no claims to a vast readership, but I am certainly lazy. So when I imagine a web service that must exist somewhere, I ask clever people like you where to find it. The service I’m thinking of this week is paperback release schedules. I love books, but I don’t often buy hardback books. I don’t like them. They are less pleasing than paperbacks in several dimensions: bigger, heavier, harder to handle, more expensive, harder to flip through (if it has those silly ragged pages), and you’re always having to worry with that stupid paper cover thing that wants to fall off. But since they are more profitable, publishers are clearly motivated to sell them exclusively for as long as possible, and so I’m often in the position of seeing a new hardback book for which I want to buy the paperback edition. I want a web service that lets me register my interest in, say, Philip Ball’s new biography The Devil’s Doctor: Paracelsus and the World of Renaissance Magic and Science, and then emails me when the paperback edition gets released. Does such a service exist? It seems like it should, but my Google scrying glass was cloudy and my searches came to naught.

On a related note, since I consume a good many books by audio these days, I want a similar service that will notify me when a given book is released in audio form (unabridged editions only, naturally).

No business model is the new business model

After much shopping around for online to-do lists that I like, I have settled on one called tasktoy. It’s not very flashy, and it’s not very professional looking, but it works well, and it has a few features that I absolutely must have. The most important is that I can post new items to it using a URL rather than having to go to a special web page and click on a special button. Clicking on buttons is so 2004.

The site’s creator is Toby Segaran, a Boston-based New Zealander who made tasktoy not as a business opportunity, but merely because it scratched an itch for him. And since he found it useful (here comes the fun paradigm-shifting part) he thought, “Say, while I’m at it, why not make this available to everybody in the entire world?”

One reason being cited for all the recent proliferation of hot young Web 2.0 companies is that the cost of launching a business has plummeted since Bubble 1.0. Some cheap hardware, a handful of open source software, and a good idea can take you pretty far these days. But if making a company is dirt cheap, then so is not making a company. I read some recent musings by Toby Segaran in his blog, and the following passage hit me on the head like a figurative heavy thing:

A number of people have emailed and asked me how I’m making money from tasktoy and lazybase. Others have said, somewhat critically, in blog postings and forum comments that they just “don’t see the business model” for such applications. The truth is that I don’t make any money from these applications. They were never intended to be a business. I wrote them because I wanted them, it was an opportunity to learn something new, and like most people I love creating things.

I determined that for less than I spend on coffee, I could put them online and share them with everyone.
… There is no business, and there is no business model. Think of something that you would do anyway and imagine being sent thank-you notes from all over the world just for doing it, and you’ll see why there doesn’t have to be.

I added those italics, because that’s the part that really knocked me on the head. For less than he spends on coffee, he can run a service that adds significant ongoing value to my life and the lives of hundreds of others. Tasktoy is a service I would pay for. At any other time in the history of mankind, it’s a service that would absolutely demand payment or subsidy. This kind of new age gifting is bound to have a significant economic impact over time. Software gets more interesting every day.

Stump the Semiotician

I just got back from a vacation in northern California, and while I was strolling down Telegraph Avenue in Berkeley, I happened across this sign at the Mediterranean Cafe.

I haven’t seen a sign like this in a long time, but I suspect partial nudity is a bigger problem in Berkeley than in most of the places I frequent. Seeing this sign reminded me of another sign outside the playground just around the corner from my house. I often go there with my kids.

These signs have similar syntactical construction. What about their semantics? If we believe both signs follow the condition-consequence model, then the following is clear: Unless you bring two or more dogs to my park, you may not play golf. Or maybe you can play golf if there are dogs on the premises somewhere. On the other hand, if each is merely a list of negatives, then it follows that patrons of the Mediterranean Cafe should expect neither a shirt, nor shoes, nor service of any kind. How they stay in business is anybody’s guess, but presumably they have no objection to partial nudity, since they dispense no clothes.

Do you find semantic sharpshooting entertaining or intensely irritating? Know any weirdly ambiguous signs? I want to hear about them.

Animal-like robots

We’re definitely entering a new realm with robotics. Before robotic motion was always painfully awkward and stilted, not something you would ever mistake for the smooth motion of an animal. But these days you can find plenty of examples of remarkably fluid “un-robotic” behavior. Things will progress very rapidly from here. The YouTube video below shows human-controlled robots. They’re being driven by remote control, but they’re still a treat to watch.

This next example is a video of a robotic eel, and it truly has to be seen to be believed. Again, it’s radio-controlled, but still, LOOK AT THAT FELLER SWIM! Straight out of a Bond movie.

Tattoos Sacred and Profane

You may have heard about Engrish.com, the site that tracks amusing abuses of the English language in Japan (“Let’s happy and feel the lucky!”). But what about the view from the other side? Are Americans abusing Asian languages by any chance? Yes they are, and whereas Japanese have a knack for zany T-shirts and signs, Americans prefer to make their mistakes in the form of permanent tattoos. Tian Tang, an engineering student who lives in Arizona now but was born in China, has a site called Hanzi Smatter that is dedicated to airing the kinds of mistranslations, mistransliterations, and textual nonsense that pass for Chinese in American pop culture. Recently he’s been getting some high-profile press:

Cool Tat, Too Bad It’s Gibberish – New York Times
Indelibly lost in translation – Los Angeles Times

The whole concept of what people look for in a tattoo, and what constitutes magical writing, has fascinated me for some time, so I collected my thoughts in the somewhat longer ramble below.

Continue reading “Tattoos Sacred and Profane”

Chimpanzees in context

Jane Goodall and her team are still at it, observing chimpanzees in Gombe Stream National Park in Tanzania, but now they, like every other primate on the face of the earth, are also blogging. What’s interesting, even beyond the bit about the chimps, is the fact that the blog appears (primarily) in Google Earth rather on a web page. This allows you to see exactly where Emily saw Fifi’s eighth child Flirt. In a more general sense, it answers the question “Okay, I know chimpanzees come from Africa, but where in Africa? It’s a big place, after all.” Seeing the Gombe preserve set among the mountains of along the shores of Lake Tanganyika and then reading about camp life provides more tangible context than the maps in National Geographic ever did. Plus it’s got news you can use: if you visit, put your shoes in the “large cage where we hang the laundry… because if you leave those things outside unprotected, you will almost certainly lose them to a crafty baboon or chimp.”