Life with a synthetic genome

If you haven’t already seen this plastered all over the news, Craig Venter’s team has created the first replicating cell using a completely synthetic genome.

The video of the press conference while a bit dry, is definitely worth watching

I haven’t read the paper yet, so this is a quick summary based on the conference and on reports elsewhere.

First to clear things up, this is not a completely synthetic life-form. Only the DNA of the life was synthesized outside of a cell and then assembled and inserted into a host cell (of another species.) The DNA was made of known sequences with a few added “watermarks” as Venter says. Even so, this is a remarkable accomplishment and if nothing else demonstrates that there is no special “vital force” in DNA that causes life.

What’s even more exciting about this is the technological breakthroughs the team had to make and the insights into what is necessary for life. For instance the number of genes that were “disposable” in an already minimalistic genome, the ability to grow the synthetic genome in a yeast cell, extracting it from there and then transplanting it into the host cell.

The “watermarks” are an interesting feature too. As I’ve gathered from the video, they’ve added the names of the scientists involved as well as 3 quotations in the genome. These messages are themselves encoded (as a kind of puzzle, I suppose.) Also, to make sure this added code doesn’t form proteins, another layer of encoding is used to insert stop codons. As Venter says, “a code within a code within a code.”

The funny thing though is that this code won’t last long if they continue to grow the bacterium naturally. Since the code by design has to be in non-coding “junk” DNA, it’s not going to be conserved evolutionarily. Point mutations will accumulate over time and since the organism has been designed to have a short life span, the code is bound to be garbled quite soon, maybe even before someone has time to break it. 🙂

I should have another post once I’ve grokked the paper and read some more of the commentary online.

Going google-eyed over AI

It all started with this blog post by John Battelle which mentioned Larry Page talking about AI at an AAAS conference.

Who wouldn’t be interested? Harish and I watched the short clip on ZDnet and we were both a bit taken aback by what Page was saying. (You can get a video of the complete speech on this page.)

If you look at your DNA its just about 600 MB compressed, which is smaller than any operating system. Your Linux, windows, any operating system. That includes booting up your brain, right … by definition. So your algorithms are probably not that complicated, its probably about the overall computation.

I spotted the obvious flaw there that genome size is directly related to complexity of the system. Now any biologist worth her salt will tell you that this is simply not true. Gone are the days when we believed that knowing the complete genetic code of an organism will tell us everything we need to know about that organism. Far from it, the questions raised by sequencing genomes are far more than ones it answers!

But what does this all have to do with artificial intelligence or AI? Well apparently, a lot of people are buying Larry Page’s argument! Now believe what you will about the complexity or simplicity of AI. I’m no expert in the field. But to use the supposed “simplicity” of the DNA “program” to prove your point about AI is plain wrong.

I spent some time explaining to Harish the biology behind my thinking and he converted his understanding into a blog post with a clever title. He also went around posting comments in the blogosphere talking about why Page’s logic was flawed and pointed back to his post. Except for a couple of people, most didn’t understand the point Harish was trying to make with all the biology in his post, so let me try it this one time.

Page’s argument as I understand it is:

  1. Human DNA is simple to understand.
  2. Human DNA programs for the human brain.
  3. The human brain makes human beings intelligent.
  4. Therefore, AI is simple

All cut and dried. What’s wrong? Well, a couple of things. I could debate about how simple or not simple human DNA is, but lets assume it is simple. We’d still be stuck at step 2. DNA does NOT “program” in any sense the human body or brain. Using the metaphor of a “program” is quite wrong and it is this precisely that which leads most people to make mistakes in assuming what DNA can or can’t do.

My point is that the sequence of DNA in a genome is an incomplete description of a living system. Therefore it is not a good way to estimate how easy or hard it would be to build an AI system.

I do not know enough about AIs, nor the current state of research in that field to be able to debate how close or far away we are from building one. But I do know enough biology to tell you that using DNA to argue that AI is around the corner is wrong.