Rambles Blog at Star Chamber

I think this is a big deal: Stanford and Venter Institute Simulate an Entire Organism With Software (NYTimes.com).

Molecular biology has been running hot and cold in the headlines department. We decoded the human genome! BUT we don’t really understand it. Systems biology will lead to dramatic new treatments for diseases! BUT the diseases that most of us have, well we still don’t understand those well enough for systems biology to make one tiny tater tot’s worth of difference. Craig Venter synthesized a living organism! BUT actually he didn’t. It was more like xeroxing with style. Which is worth something, but it’s not exactly Frankensteiny.

But things are happening faster than ever in molecular biology (which is saying a lot), and some of it feels like a real turning point in our understanding of how life works. First of all, obtaining data is getting easier and easier. New sequencing technologies can (reportedly) sequence a human genome for less than $1000. And if you can sequence a healthy human cheaply, then you can sequence aberrant tumor cells just as cheaply. And this technique is, well and truly, leading to some remarkable success stories.

And now, with Venter’s latest announcement, we are at the beginnings of simulating life. As Richard Feynman said, “What I cannot create, I do not understand.” Biology up to this point has been mostly an exercise of poking at a black box: when I do X, then Y happens. But I have no idea why Y happens. And if I do Z instead of X, I have no real insight into what might happen. Simulation opens a new world of understanding living mechanism rather than living cause and effect. Again, it won’t lead quickly to miracle cures. But it is a big deal.

As the Times article reports,

The simulation, which runs on a cluster of 128 computers, models the complete life span of the cell at the molecular level, charting the interactions of 28 categories of molecules — including DNA, RNA, proteins and small molecules known as metabolites, which are generated by cell processes.

…

“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds.”

This is as good an indication as any of how much room our computers have to improve. One tiny microbe can do what 128 computers are required to do, spewing 500 Mb along the way. To quote Feynman once again, “There’s plenty of room at the bottom.”

How big will the human population get on this planet? They’re always fiddling with the predictions, but by some estimates, we’ll top out at around 9 billion by 2050 (see this Economist video and article). More dire predictions can be found, but these seem reasonable to me, given current demographic trends.

Slowing population growth is a good thing, but there’s another factor to consider. To what extent will the aggregate needs of the human race grow even as its population begins to shrink? Geoffrey West, a physicist who studies cities, has asked an interesting question. What are the energy needs of the human animal? According to his calculations, a human being at rest runs on 90 watts. Pretty remarkable, eh? I know light bulbs that eat more than that. But then West takes it a step farther. Suppose we rolled up the energy needs of your light bulbs and your car and your house and so on, and we pinned all that on you… in other words, what are your energy needs not as an animal in a box, but as a civilized human going through a normal day? He comes up with something like 11,000 watts. That’s an energy obesity multiplier of 120! He continues.

What kind of animal requires 11,000 watts to live? And what you find is that we have created a lifestyle where we need more watts than a blue whale. We require more energy than the biggest animal that has ever existed. That is why our lifestyle is unsustainable. We can’t have seven billion blue whales on this planet.

As a person’s appetite for energy grows, the infrastructure required to feed them must expand correspondingly. Thus a population that’s getting richer and smaller can grow and shrink at the same time.

In literal terms, think about weighing everybody on the planet on one giant scale. Given enough fat people, you’ll obscure the fact that some skinny people have died. Big bellies hide many mouths. Consider this BBC article: Global weight gain more damaging than rising numbers.

So one projection has the human population peaking in 2050. What I’d like to see is a projection of when the aggregate human energy needs will peak. It will certainly be after peak population. But how much longer? Only then will the human footprint on the planet truly start to recede.

“Hey waiter! What’s this school bus doing next to my space telescope?” (Hint: not the backstroke.)

I came across this TED talk today and it looked very promising. It’s a program run by NASA to bring the solar system to your browser.

The speaker, Jon Nguyen, made some good points. First of all, NASA would like you to know that, contrary to popular belief, they are not dead. It comes as a surprise to some people that even though we are officially in the post-Shuttle era, there are still Americans living in the International Space Station. Beyond this there are dozens of robotic space probes crawling all over our curious corner of the galaxy. Freakin’ space robots! Taking awesome snapshots for their Facebook pages! What could be cooler than space robots? Why don’t people know about this?

That was the attitude of the JPL team that built Eyes on the Solar System, a sort of Google Not-Earth. As Nguyen points out, what they do is the reverse of Google Earth. You start with the earth in front of you, but instead of zooming in, you zoom out to look at other worlds. You can also look in detail at many of NASA’s space robots. At one point Nguyen said something like “everything I’m showing you, you can go to your browser and do it too.” And I’m here to tell you that it’s true. This is an impressive piece of work. Try it!

Here’s the TED talk.

And now for the answer to my question at the top of the post. If this is such a realistic simulation of outer space, then why is there a school bus next to the Hubble Space Telescope? Well, the school bus is real. It got there by following errant GPS instructions on the way back from a field trip to the St. Louis Zoo. Okay, I take it back. The school bus is part of a feature that lets you compare space robots to well-known objects. Although it seems like a waste of taxpayer money for NASA to send buses up there for that purpose…

I have a question for ye: why are olde shoppes so often prefaced with the word ye? Be they belonging to ye?

It doesn’t have anything to do with the word ye. Instead, it has to do with the mystery of the missing thorn. Thorn is actually the name of an old (sorry, olde) letter that signified the “th” sound. Thorn was a common letter in old English. Beowulf is lousy with thorns. You can’t understand a word of it, but every now and then a sentence jumps out at you.

þæt wæs god cyning! (That was a good king!)

Just as unicorns went extinct because they didn’t get on the ark in time, so too the thorns (sorry, þorns) went extinct because they didn’t get on the printing press. “It’s a fad!” they said “You’ll see. Kids today and their crazy movable type…” Now with Unicode, the thorn’s time has come round again. Watch this: þþþþþþ. Sadly, though, Unicode can do nothing for the unicorn.

At any rate, when trying to typeset English with only 26 thornless letters, some clever soul thought to replace þ with y. So “ye” is nothing more than the definite article “the.” So þere.

I came across this dandy little video on the topic while perusing a YouTube channel called MinutePhysics. I’m not sure why English spelling ended up on a physics channel, but I enjoyed it all the same.

If you’d like to watch something more in line with the physics-oriented nature of the channel, here’s a good one. Learn, in less than one minute, how Einstein went about proving that E = mc² (note: it does not involve a ka-boom). Very cool!

We have a natural grasp of the fact that we can’t see small things. Likewise things that are very large escape our notice because they exceed our field of view. We might call these aspects of the spatial domain. When I began studying engineering, I learned about this marvelous concept of a frequency domain. It’s an acknowledgment of the fact that some things happen very slowly and some happen very quickly. And just as things can hide from us because they are too small or too big, they can also hide because they are too fast or too slow.

Technology helps us on all these frontiers. High speed cameras slow down the invisible wings of a hummingbird, and time-lapse photography shows a sapling reaching sunward like a hand. And recently I’ve noticed that, as these camera technologies get better, they bring with them the cinematographic techniques of conventional cinema: zooming, tracking, and pulling focus. For time-lapse, this is a fairly straightforward process of carefully mapping out your camera’s motion across the hours. If you’re really good, you can end up with something like this.

At the other end of the frequency domain is the fast stuff. Tracking and changing focus at these speeds is more problematic. For this, you need fast, stable robotics. Here’s a wonderful “how we do it” video from a German special effects company that specializes in high-speed cinematography. They do things that you’ve never seen before. Things that simply haven’t been possible until now. Watch.

[Spotted on the IEEE Spectrum Automaton blog]

In this modern age, we’re subjected to all kinds of outrageous and essentially unchallenged assertions: the earth is four and a half billion years old, the gross domestic product of Montenegro is $4.1 billion, it takes 364 licks to get to the Tootsie Roll center of a Tootsie Pop, and so on. Most of these just wash over us. You’d go crazy trying to challenge them all. But every now and then you see some number blithely mooted and say to yourself, how could we possibly know that?

For example.

It is approximately, we are told, 2.5 million light years, give or take, from the end of your nose to the Andromeda galaxy. So: if your bathroom mirror was hanging in Andromeda, you’d have to stare at it for 5 million years before you realized you had a little hair hanging out of your nose.

Think of all the ways we measure how far away things are. Now think how none of these things could work for something so very far away. It would take way too much measuring tape. You can’t drive there and back with an odometer. You can’t bounce radar off it and wait for the reflection. You can’t use trigonometry, because you don’t know how big it is.

Measuring such remote extragalactic distances makes use of something called the cosmic distance ladder. It’s a remarkable and complex set of measurements and algorithms, but this little video from the Greenwich Royal Observatory describes it beautifully. Watch it and you’ll feel a tiny bit more in control of this otherwise bewildering world.

(thanks to the cyclist for forwarding this)

At my college reunion this weekend, the topic of Official Speak came up. Jay gave us a sonorous version of the air gate cattle call: “For those of you with small children or special needs we do ask that you come forward at this time.” The phrases we do ask and at this time are unnatural. Why do we persist in using them? What is the hidden message they convey?

There’s something soothing about codified language. It may be stilted, but it’s familiar, and it tells you where you are. Churches know this.

Our Father who art in heaven, hallowed be thy name.

The repetition is calming, mantra-like. The point is not so much to send an explicit message as to put your mind in the right state.

Please ensure your seatbelt is securely fastened and your seatback and tray table are in their full upright and locked position.

Just hearing those words calms me down. Everything is fine. The plane is landing and everything is fine.

This kind of thing reminds me of a related but more annoying phenomenon. What is the name for phrases like this?

• Don’t go there!
• It’s all good.
• How great is that?
• You had me at ____.
• It is what it is.

Are they clichés? I don’t think so, but they’re close cousins of some kind. They must have a name, but I’m too lazy to read through the whole Language Log to discover it. Sometimes the phrases come from a popular TV show. Other times it’s hard to say, but suddenly we’re all saying “You go girl!”

I hear them all the time. Some people delight in them and make a point of pushing them together like greasy dumplings on a fork. They are the comfort food of conversation: high calorie and essentially empty. Altogether they form a kind of extended vocabulary to the language, a skin that billows and blisters and eventually boils away.

Can you think of some others? And help me give them a name.

A friend of mine has been working at Twin Creeks Technologies since it was formed, and all he was able to tell me was that they were working a new angle on solar technology. So I’ve been itching to know what they were up to. For several years the Twin Creeks website was just a placeholder, devoid of meaningful information. But at the end of March this year, they finally put their cards on the table. I had expected their trick to be in the physics of the electrical generation. But instead it’s about manufacturing efficiencies, specifically, in their ability to make solar cells that are up to ten times thinner than traditional cells.

The technology is exotic, but their elevator pitch is satisfyingly straightforward. Imagine that you’re a lumberjack trying to cut thin disks of wood from the end of a log. Now let’s say you want to make a lot of very thin slices. As the slices get smaller, you will eventually be grinding up more wood with your chainsaw than you’re keeping in your finished product. How can you pop off a thin slice of wood (i.e. silicon) without throwing away a ration of sawdust?

That’s the picture. Now here’s the secret weapon (fun jargon ahead) … Proton Induced Exfoliation with the Hyperion Ion Beam. They’ve made a knife as thin as a proton, and with it they can slice the silicon neatly 20 microns at a time. Pop! Look at this page for the explanatory video, and just reflect on how insanely complex and expensive this machine must be.

Reading about this technology reminded me of Tom Murphy’s Energy Trap. The energy trap argument goes like this: It will be tempting not to invest in new energy sources as much as we should. These new technologies are expensive and risky, and old fossil power is still pretty cheap. But when old power gets expensive, we won’t have the money we need to invest in new technologies. We’ll be pedaling hard just to keep food on the table and mobs off the street. And that is the nature of a trap. You don’t realize you’re in a trap until you’re in it. And by then you’re in a trap. Or, as the addicts say, when you can stop you don’t want to, and when you want to stop, you can’t.

Which is to say, I’m really glad that there are people willing to invest the big bucks in places like Twin Creeks Technologies. And I wish them luck.

I work with a talented designer named Claudia Wey. My company is lucky enough to benefit every day from her good taste and design skills. Now you too can benefit by following her Design Snapshots blog.

Here is one of her catches: impress.js, a presentation tool. Go here and press the right arrow key to step through the presentation.

It’s a fun example of breaking out of the box of “typical” PowerPoint presentations, but too much of the spinning and vaulting gives me vertigo. The inspiration for impress.js was Prezi, and before that people like Ben Bederson have been working on zoomable UIs for years. I would guess that prezi.com is the closest thing to a true ZUI product that made it into the wild.

Here, watch this one: Meaning in Communication | Understanding Information Architecture (or lack thereof). It’s about information architecture, but the structure of its own information is jello on a roller coaster.

Is it more than a gimmick? What do you think?

I was in college when Halley’s comet came by. In the media, the comet was getting star treatment, but the comet wasn’t following the script. It made a pathetic display, fizzing at a level barely visible to the naked eye. I went to the campus observatory where a astronomy professor gave us binoculars and told us where to look. “That’s it?” said my friend when she finally found the faint greasy smudge with the famous name.

Astronomy is a funny game. It’s a cerebral activity that masquerades as a visual feast. The pictures we see from the Hubble Space Telescope set our expectation for what we will see when we peek into a telescope. But the Hubble Telescope is 350 miles above the atmosphere and it’s got an eyeball seven feet across. Nothing you see in a telescope will remotely resemble what it sees. Buy a telescope and you’ll mostly be looking at greasy smudges or bright points of light that all look more or less the same. This is why most telescopes end up in the basement.

If you can get excited by the science, then it all becomes great fun. My favorite example of astronomy as a head game is the AAVSO. That’s the American Association of Variable Star Observers based near me in Cambridge. Technology has made their job a lot easier, but these people used to stare at the same star for hours on end looking for barely noticeable changes in brightness. Train-spotting suddenly seems thrilling by comparison. But again, the science is quite interesting.

Given all this, I was pleased to see physicist Tom Murphy of the Do the Math blog addressing the issue of SUPER! MOON! DISAPPOINTMENT! The last full moon was one in which a close moon coincided with a slow news day, and so, improbably, the supermoon landed on page one, thereby leading to a sunset chorus of “That’s it?” A slightly large moon is cool, but it’s no great thrill compared to an average moon.

Hype is the enemy of satisfaction. Low expectation is the gateway to bliss.

You know what’s cool? The moon.