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By Michael White | August 23rd 2009 11:12 AM | 5 comments | Print | E-mail | Track Comments
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Welcome to Adaptive Complexity, where I write about genomics, systems biology, evolution, and the connection between science and literature,

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Craig Venter says that in a few months, his team will have created the first genuine artificial life form. As you may recall, Venter's team did the first whole genome transplant a few years back, which involved taking the genome of one species of bacteria and putting it into the genome-free cell of another closely related species. The new hybrid species was able to reboot with the new genome. According to The Times:

Artificial life will be created within four months, a controversial scientist has predicted. Craig Venter, who led a private project to sequence the human genome, told The Times that his team had cleared a critical hurdle to creating man-made organisms in a laboratory.

“Assuming we don’t make any errors, I think it should work and we should have the first synthetic species by the end of the year,” he said.


Venter's team is trying to take the next step, which is to create life from a completely synthetic genome (as opposed to using an existing genome from a bacterial cell). They've published an update on their progress in Science.

However, be careful when you read the news reports, which can be misleading: if Venter is successful, this will be the first working synthetic genome, but it's not one that has been designed from scratch. What Venter's team is doing is synthetically reproducing a genome that already exists in nature, one that we already know works coherently. It's a copy and paste operation in essence, although the technological feat, when Venter is successful, will be a major milestone.

The more challenging feat is to design a genome from scratch. I want to see someone start out at the whiteboard, make a list of all of the genes they would like their genome to have, and then go out and make a functioning genome. To do this, we need computer-aided design capabilities for biology, something like what Boeing put together for the 777. Synthesizing an existing genome is an amazing feat, but designing one from scratch is in another league altogether.



Comments

Fossil Huntress
Illuminating bit of writing on Venter. I thought they were designing a new entity entirely... a "copy and paste job" is the logical next step and an impressive one, but I thought we'd made the leap to biological creation.

Dave Deamer
Michael - I don't think we will have genome designed "from scratch" anytime soon. Before saying why not, let's first consider what is in fact possible to do from scratch. We can design nucleic acids that have never been part of biology, even making them spontaneously fold up into interesting three dimensional structures. We can also design proteins that are then synthesized by ribosomes in a cell-free system, but they probably will not be functional. We also know how many genes are required for a minimal living cell, which is in the range of 200 - 300 genes. So why not a genome from scratch? The main problem is that half of those genes are for the components of ribosomes, and there is only one way to assemble a working bacterial ribosome. The other problem is getting the genome to work as part of an integrated system with all the regulatory functions working in synch, including energy transduction and metabolism.On the other hand, the origin of life, and the first living cells were in fact assembled from scratch. If we can figure out how that happened, maybe we can design a primitive version of a genome, but we need to know a lot more before that can happen.


Even before starting from entirely synthetic nucleotides and translation systems, stitching together existing genes into a new genome using a kind of synthetic biology CAD is still not really feasible. There are still many genes with entirely unknown function and many more whose regulation, interaction with other genes and proteins, and function in different contexts is unclear. For every large technological breakthrough like this there has to be countless other relatively small experiments in genetics, biochemistry, and synthetic biology to understand how genes and genomes work before we can synthesize new ones.

adaptivecomplexity
I agree we're a long way from synthetic biology CAD, but I have a hunch (only a hunch, because I'm not an engineer) that biologists might be able to learn something from the people who model Boeing jets. 
I say that as someone who is struggling to build a useful physical model of a fairly small transcription circuit. Where modeling fits in is still an unsettled question: do you work out all of the biochemical details of a system first, and then build a model at the end (and possible not learn much)? Or can we build useful models early on in the process, before carrying out all of the parameter measurements and other biochemistry, models that can guide our choice of experiments and help us interpret the results? 

Before we can even consider designing genomes from scratch, we need to better understand how to put models to good use in biology.


Mike

adaptivecomplexity
The other problem is getting the genome to work as part of an integrated system with all the regulatory functions working in synch, including energy transduction and metabolism.On the other hand, the origin of life, and the first living cells were in fact assembled from scratch. If we can figure out how that happened, maybe we can design a primitive version of a genome, but we need to know a lot more before that can happen.

Exactly - that's the reason why I like to think of the origins of life as the ultimate systems biology problem. My guess is that, as origins of life research and systems biology make progress in understanding how complex systems self-organize and function coherently, there will be a lot of exchange of ideas between these two fields.

Venter's work illustrates a major problem in synthetic biology - our ability to synthesize large stretches of DNA has outpaced out ability to engineer biological systems. In news reporting on synthetic biology, these two issue get conflated, and you often see people equating synthesis with design.

Mike

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