Nice article on the limitations of the new field of Synthetic Biology
March 16, 2013 12:35 AM   Subscribe

Current state of Gene hacking leaves much to be desired but there's hope for a pull back from the rush to applications to a more basic science approach.
posted by aleph (13 comments total) 7 users marked this as a favorite

 
"The hype is a thing that's hurt the field,"

LOL

Finally an actually good article in mainstream journalism talking about the real story of synthetic biology, the massive piles of bullshit everyone with half a brain and a basic knowledge of what an agar plate is could tell you was bullshit, but no one listens to people who know what they're talking about anymore. Synthetic biology does actually have some really neat potential in both the short and long term, and there are people who are not idiots working in it, but they are a solid minority of people who describe themselves as synthetic biologists. Gene switches working reliably would indeed have a lot of power to do really neat things in both genetics and genetic engineering but fodder for Singularian liberation theology they are not.

Also hey, here is a neat self link that links to a damn paper
posted by Blasdelb at 1:02 AM on March 16, 2013 [4 favorites]


Also the current state of Gene Hackman leaves much to be desired
posted by XMLicious at 1:37 AM on March 16, 2013 [4 favorites]


s/gene hacking/3d printers/g and the article is still true.
posted by DU at 4:46 AM on March 16, 2013


With Cantor's encouragement, Collins and Gardner leapt into a new, wet world. Neither was versed in the field, and the idea of reading Molecular Biology of the Cell left Collins cold. He couldn't get past the first page; too much detail.

Ladies and gentlemen, MacArthur Genius Jim Collins.
posted by mr_roboto at 5:32 AM on March 16, 2013 [3 favorites]


from the rush to application

Would that be rush to patent application? I kid, but I do kind of wonder how much of the slow down of progress might be laid at the feet of patents and royalties in this field.
posted by Toekneesan at 5:41 AM on March 16, 2013


> Neither was versed in the field, and the idea of reading Molecular Biology of the Cell left Collins cold. He couldn't get past the first page; too much detail.

Ladies and gentlemen, MacArthur Genius Jim Collins.


... and then three years later they were published in Nature.

It's really a pretty cool story: they approached a new field that seemed ripe for experiment, picked a particular tiny problem that a mentor told them was worth working on, jumped into trying to solve it, asked experts what they were doing wrong when things didn't work, and after (presumably) a great deal of effort over three years ended up making a new contribution to the field. Science!

Speaking of embarrassing pull-quotes, how about:

The almost irrational complexity of life has been one of the biggest surprises to synthetic biologists, says Tim Lu ....

It's almost like life emerged through random processes rather than by the design of a rational creator, almost.
posted by jhc at 6:47 AM on March 16, 2013 [3 favorites]


Also the current state of Gene Hackman leaves much to be desired

I dunno. This line is a thing of beauty:

“Our officers got a call from a homeless male who said he’s just been beat up by Gene Hackman,” Sgt. Andrea Dobyns told Albuquerque ABC affiliate KOAT-TV.

He is like the flip side of Bill Murray.
posted by ricochet biscuit at 6:55 AM on March 16, 2013


Speaking of embarrassing pull-quotes

Frankly, I think the whole thing reads kind of like a hit piece on Collins. This, for instance: "For Collins, though, the definition is simple. It's 'genetic engineering on steroids.'" I doubt Collins really defines synthetic biology as "genetic engineering on steroids", and to quote him saying so makes him seem like a bit of an idiot.

That said, a hit piece on synthetic biology appeals to my own prejudices.
posted by mr_roboto at 7:34 AM on March 16, 2013


"It's sort of like using a jacked-up, loaded system to answer a question that's been out there for a while, a really fundamental one," Bashor said. "How do you get more complicated signaling networks? ... There's a feedback between discovery science and synthetic science that I think more people are starting to appreciate now."

You could almost say it's some sort of selection, like that found in nature.
posted by benzenedream at 8:27 AM on March 16, 2013


You could almost say it's some sort of selection, like that found in nature.

This gets to a core criticism of synthetic biology. For over 20 years, engineers interested in designing biological systems have been using directed evolution; basically, creating diversity and applying selective pressure in the lab to force a microbial population (or a gene, or a limited set of genes) to evolve towards an engineering goal. This is a very effective technique! Then the synthetic biologists came in, with little understanding of biological complexity, claiming that they could treat biosystems like microprocessor circuits, pluggin in modular building blocks. Biological systems did not evolve modularly, however, and synthetic biologists are quickly realizing that evolution-like selection techniques are the best approach to engineering metabolic pathways and complex signaling pathways. This seems a little like reinventing the wheel to many of us.
posted by mr_roboto at 8:42 AM on March 16, 2013 [2 favorites]


Then the synthetic biologists came in, with little understanding of biological complexity, claiming that they could treat biosystems like microprocessor circuits, pluggin in modular building blocks.

My belief in this statement is why I do not work for iGEM.

Sincere question: Where is the line drawn between protein engineering and synthetic biology?
posted by maryr at 9:07 AM on March 16, 2013


"Sincere question: Where is the line drawn between protein engineering and synthetic biology?"

One of them actually works, the other is filled with characters like these.
posted by Blasdelb at 9:50 AM on March 16, 2013 [1 favorite]


Some organisms did evolve to be genetically modular, though. Making genetically-recombinant bacteria by getting them to accept a plasmid (small circular piece of DNA, for those playing along at home) with your gene of interest spliced into it is totally old hat these days and works great. It takes advantage of horizontal gene transfer capabilities that are very much evolved traits in bacteria.

I don't dispute your basic point, mind you. Genomes are complicated-ass molecular machines and they often react poorly to hamfisted attempts to muck about with them. Weirdly though, there are at least some cases of genetic modularity that we can and do exploit in the lab to great effect.
posted by Scientist at 10:16 AM on March 16, 2013


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