Simulating life

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

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.”

The population is shrinking! The population is growing!

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.

NASA’s Eyes on the Solar System

“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…