Friday, October 25, 2013

Genomics pioneer Craig Venter warns about biohacker boo-boos


Image: J. Craig VenterIn his latest book, genetic guru J. Craig Venter envisions a brave new world where DNA can be teleported between planets and where custom-made bacteria producedrugs, food and biofuel — but he also worries that do-it-yourself biohackers could spoil that vision.

"One of the concerns that I address in my book is this new emergence of do-it-at-home biology," Venter told NBC News. "One important part of scientific training is that scientists learn the boundaries, the safety issues, how to properly deal with and dispose of chemicals and reagents.

"While it's great at one level that there's excitement and people wanting to do experiments at home, playing with things without the proper knowledge set and the proper training, I think, legitimately raises concerns for an increased chance of unintended consequences," he said.

As Venter points out in his book, "Life at the Speed of Light," he's not the only one worried about biohacker boo-boos. Almost three years ago, a presidential commission on bioethicsraised concerns about the risk of "low-probability, high-impact events" such as the creation of a doomsday virus. Bioterror is one aspect of the issue, but Venter says he's also concerned about bio-error — "the fallout that could occur as the result of DNA manipulation by a non-scientifically trained biohacker or 'biopunk.'"

Some have called for more regulation of synthetic biology and home biotech. Venter, however, says overregulation can be as harmful as laxness. It's possible to add built-in safeguards — such as biological kill switches, suicide genes or molecular brakes and seatbelts — to make sure genetically engineered microbes don't escape from the lab. And law-enforcement agencies like the FBI are finding it more advantageous to work with the do-it-yourselfers than to work against them.

The last thing Venter wants to do is kill off the curiosity. "We need to find a way to channel that great level of curiosity into places where people can get proper training, and at the same time exercise their curiosity in a healthy fashion," he told NBC News. "Every university lab and serious research lab has that training. That's where I'd start. I don't think we need a new system for it."

What is life?
In Venter's mind, public ignorance about biotech is a bigger problem than biotech's risks. "It's very hard to have a conversation when over 50 percent of people don't know that tomatoes have DNA in them," he said. "They don't realize that every plant, animal, insect on the planet only exists because it has DNA software. The scaremongers and the worriers, that tells me that we need to greatly improve science education so we can at least start to have an intelligent conversation."


Reading Venter's latest volume provides a good antidote for biotech ignorance: The book was spawned by a talk he gave last year in Dublin, as a follow-up to Nobel-winning physicist Erwin Schrödinger's famous lecture series titled "What Is Life?"
"Life at the Speed of Light" tells the story of biology from the 16th century to the current revolution in genetics, framed as a quest to understand how life is defined.
Venter has had a key role in that quest — as one of the leaders in the race to decode the human genome, as an adventurer seeking to catalog the ocean's microbes, and as the head of a team thatcreated the first synthetic genome in 2010.

Now his main focus is to "rewrite the software" for life, and enlist genetically engineered organisms to manufacture synthetic insulin, vaccines and other kinds of medicines; produce food and fuel for humanity; to clean up toxic waste sites and soak up atmospheric carbon dioxide.

DNA to beam up
One of the tools that Venter and his colleagues are developing for the task is a "biological teleporter," or digital-biological converter. Synthetic Genomics Inc., one of Venter's ventures, has already built a prototype with backing from the Defense Advanced Research Projects Agency. The converter is designed to turn huge strings of digital code into synthetic molecules of DNA.  


"We can rebuild the Martians in a P4 spacesuit lab — that is, a maximum-containment laboratory — instead of risking them splashing down in the ocean or crash-landing in the Amazon," Venter writes. He suggests that the same technique could be used to reconstruct the life forms of aliens beaming their own information from distant planets. That's assuming, of course, that E.T. is broadcasting the proper code on the proper channel.Future versions of such a device could read the code of an organism robotically at a remote site — say, beneath the surface of Mars — and beam the data back to a lab for reconstruction.

And if life's code could be sent at the speed of light from Mars or Gliese 581, couldn't it be sent from Earth to the stars as well?

"In the past decade, since my own genome was sequenced, my software has been broadcast in the form of electromagnetic waves, carrying my genetic information far beyond Earth, as they ripple out into space," Venter says in the book. "Borne upon those waves, my life now moves at the speed of light. Whether there is any life form out there capable of making sense of the instructions in my genome is yet another startling thought that spins out of that little question posed by Schrödinger half a century or more ago." 

Wednesday, October 23, 2013

The brocading revolution

by 
Ryan Bethencourt 

"What is biocoding? For those of you who have been following the biotechnology industry, you’ll have heard of the rapid advances in genome sequencing. Our ability to read the language of life has advanced dramatically, but only recently have we been able to start writing the language of life at scale.

The first large-scale biocoding success was in 2010, when Craig Venter (one of my scientific heroes) wrote up the genome of an entirely synthetic organism, booted it up and created de novo life. Venter’s new book, Life at the Speed of Light, discusses the creation of the first synthetic life form. In his book and in video interviews, Venter talks about the importance of ensuring the accuracy of the DNA code they designed. One small deletion of a base (one of the four letters that make up the biological equivalent of 1s and 0s) resulted in a reading frame shift that left them with gibberish genomes, a mistake they were able to find and correct. One of the most amusing parts of Venter’s work was that they were able to encode sequences in the DNA to represent each letter of the English alphabet. Their watermark included the names of their collaborators, famous quotes, an explanation of the coding system used, and a URL for those who crack the code written in the DNA. Welcome to the future — and let me know if you crack the code!

Biocoding is just the beginning of the rise of the true biohackers. This is a community of several thousand people, with skill sets ranging from self-taught software hackers to biology postdocs who are impatient with the structure of traditional lab work. Biohackers want to tinker; do fun science; and, in the process, accelerate the pace of biotech innovation. There are plenty of differences between writing computer code and writing code in the building blocks of life, but the important thing is that it can be done and is being done now by citizen scientists working both from shared biohacker labs (like Biocurious, Genspace, and Counter Culture Labs) and at home (for example, Cathal Garvey, who works out of a spare bedroom in his mother’s home). Drew Endy’s short video about Engineering Biology gives a great overview of what we can accomplish when we start programming the genetic code. One of his projects is genetically encoded data storage — but it’s not just about replacing dry silicon with wet carbon; it’s about what can happen when you can do computing in an environment where you couldn’t possibly place silicon: inside a living cell.

Biotech is the wet nanotech we’ve been waiting for. It’s a little less logical and a lot buggier than we’d like, but we now have the tools to write DNA, insert this code into a cell, reboot the cell and make those cells produce custom-designed proteins and substances, and engineer biology. The potential for synthetic biology and biotechnology is vast. The biocoding era will be as transformative as the computer era, and we all have an opportunity to create the future together.

Biocoder is a new O’Reilly quarterly newsletter chronicling the rise of DIY bio, synthetic bio, biohackers, Grinders, and the new innovations being developed at the edges of the biotech industry. Check out Biocoder and download it for free."


The biocoding revolution | SynBioFromLeukipposInstitute | Scoop.it

http://oreil.ly/16tARi5

Wednesday, March 20, 2013