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IEET > Security > SciTech > Life > Innovation > Fellows > Jamais Cascio

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Give My Creation… Life!


Jamais Cascio
Jamais Cascio
Open the Future

Posted: May 24, 2010

The Venter Institute announcement that it had successfully crafted the first self-replicating synthetic organism caused quite a stir, even among people who are otherwise pretty jaded about emerging tech.  It’s useful to understand exactly what is—and what isn’t—going on here.

Where we are:

Synthetic genome copied from natural genome and transplanted into existing cell structure.

This is a moderately big deal, but only that; it’s a stepping-stone to a real big deal down the road. What the Venter Institute has done is synthesize a genome that reproduces the genome of an existing organism, then insert that genome into the body of an existing cell, replacing its own DNA. That cell was then able to self-replicate, indicating that the synthetic DNA copy was sufficiently complete.

“Synthetic” here doesn’t mean artificial, by the way. The DNA of the synthetic genome comprises the same base pairs and nucleotides as a natural genome, but was synthesized in the lab rather than replicated from an earlier cell. The best analogy I can think of is if, rather than copying the MP3 of your favorite song, you pulled together a really sophisticated music creation application and reproduced the song yourself, exact in every detail. It’s the same, but a synthetic version.

If that sounds like a lot of work to get something that is essentially the same as the natural/original version, you’re right. But this step was never the real goal—it’s just preparation. The real goal is to create an entirely novel life form, comprising both entirely new DNA and an entirely new cell. That’s still to come.

Where we aren’t:

Transgenic synthetic genome (natural genome copy with genetic code from other kinds of organisms).

The synthetic genome created by the Venter Institute is a streamlined version of the original Mycoplasma mycoides bacteria, containing enough of the original code to replicate and function as M. mycoides. Adding transgenic features—that is, genetic material copied from non-M. mycoides species—should be fairly straightforward, as it’s essentially doing standard bioengineering.

In principle, this should actually be somewhat safer than current transgenic biotech, as they’ll have much more precise control over the engineered genomes.

Novogenic synthetic genome (entirely constructed novel genome).

The ultimate goal would be to create an entirely new bacterial species by creating genes that do new things, or by combining diverse known DNA sequences to create a functional, replicating bacteria that doesn’t mimic any existing species. This will be hard, but clearly not impossible.

The bonus goal:

De novo creation of cell structure.

The cell in which the synthetic DNA is housed already existed, but with different DNA (it was the cell of a related species of Mycoplasma). One likely future step will be to create an entirely synthetic cell by throwing together the right set of proteins in just the right way. Like the latest breakthrough, that will undoubtedly start out by simply reproducing an existing cell structure. Ultimately, they’ll want to create cellular bodies that have novel features, such as (conjecture here) additional mitochondria for added power.

Where we go:

So what does this all mean?

The idea is to turn bacteria into microscopic machines, carrying out designated tasks in massively-parallel operations. Given the extreme range of things that bacteria can do in nature, the extent to which bacterial machines might be used is pretty staggering, particularly concerning environmental response. This would be a perfect platform for methanotrophic remediation of melting permafrost, for example; the Venter folks are already talking about building synthetic bacteria to do carbon capture. Biofuels are also high on the agenda.

The big concern about synthetic biology is the potential for the creation of hazardous materials—aggressive, infectious bacteria, for example. We should also consider, at the same time, its biomedical potential. Are there ways of delivering drugs via synthetic bacteria?

One advantage of the big splash this relatively modest development has made is that it opens up the possibility of laying out the parameters of what ethical, responsible management of this technology would look like before have to confront its fully-developed form.

Should we require a “shut-off” gene in any novogenic organism, one that kills the cell if certain conditions are (or aren’t) met? A reproduction-limiting set of genes that only permits replication in the presence of a rare chemical? Public registration of all novogenic genomes?

One suggestion that we know is possible, because a variation appeared in the Venter announcement: all synthetic genomes should be signed. According to Wired:

“They rebuilt a natural sequence and they put in some poetry,” said University of California at San Francisco synthetic biologist Chris Voigt. “They recreated some quotes in the genome sequence as watermarks.”

What Voigt refers to as a “watermark” should instead be thought of as a “DNA signature.” We should require that all synthetic genomes include something like this, unique sequences following a designated pattern, identifying the organization behind the genome, the lab responsible, the date, and any other useful bits of information. Multiple copies should appear throughout the synthetic genome, so it doesn’t get mutated away.

That way, if something unexpected happens, we know whom to talk to.


Jamais Cascio is a Senior Fellow of the IEET, and a professional futurist. He writes the popular blog Open the Future.
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COMMENTS


The promise of this science is worth the risks involved. We can hope for required shut off switches in this exciting new field, but let’s face facts, if you intend to do harm, you don’t care what the rules are. So the next question is ... how long before Iran or North Korea start working on this?





Although this is astounding work, it looks like once again the techology is moving faster than the ethics.  Until the scientific community comes to a conclusion on how to deal with the ramaifcations of this work, it should stay in the virutal world of computer simulations.  It should never be allowed to be created in the real world until how to handle improper or malicious uses of this technology are ironed out.





Quote : ” It’s useful to understand exactly what is:and what isn’t:going on here.”

Well that’s cleared that up now I’m more confused than I was previously! Here’s the Sciencedaily version from May 20th..

“The research team, led by Craig Venter of the J. Craig Venter Institute, has already chemically synthesized a bacterial genome, and it has transplanted the genome of one bacterium to another. Now, the scientists have put both methods together, to create what they call a “synthetic cell,” although only its genome is synthetic.”

“In the Science study, the researchers synthesized the genome of the bacterium M. mycoides and added DNA sequences that “watermark” the genome to distinguish it from a natural one.”

“Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.”

“The scientists then transplanted the synthetic M. mycoides genome into another type of bacteria, Mycoplasm capricolum. The new genome “booted up” the recipient cells. Although fourteen genes were deleted or disrupted in the transplant bacteria, they still looked like normal M. mycoides bacteria and produced only M. mycoides proteins, the authors report.”

>> http://www.sciencedaily.com/releases/2010/05/100520131435.htm

This sounds more like good ole tape splicing than MP3 manipulation??


Re. Watermarks and errors

“But once this synthetic genome was inserted:the would-be host cell failed “and we did not know why,” Gibson says. By cross-checking the entire genome gene by gene, they found the fatal flaw after three months of work: a single missing base in the dnaA gene, which is required for life. “Accuracy is essential,” Venter said. “There are parts of the genome where it cannot tolerate even a single error.”

“Venter and his colleagues also included four “watermarks” in the code to distinguish the synthetic microbe:dubbed Mycoplasma mycoides JCVI-syn1.0:from natural organisms, including 46 names of scientific contributors to the synthetic genome, an email address and a web site based on a code derived from the four letters of the bases and 64 combinations of the four letters, or triplets, possible in the genetic code. “When you put English text into [the code], it generates very frequent stop codons in the genetic code and won’t produce big proteins,” said JCVI microbiologist Hamilton Smith, a Nobel Laureate in medicine. “It’s designed to be biologically neutral.”

“Gibson adds: “If one is able to translate the watermark sequences, they will be able to send us an email and prove that they decoded the sequences.”

“The man-made genetic code also includes three quotes: “To live, to err, to fall, to triumph, and to recreate life out of life” from James Joyce; “see things not as they are but as they might be” from Robert Oppenheimer via the Ethical Culture School in New York City; and “what I cannot build, I cannot understand” from physicist Richard Feynmann. “

This is from the link within the Arthur Caplan post from ScientificAmerican >> http://www.scientificamerican.com/article.cfm?id=synthetic-genome-cell

Now that’s what I call a watermark!





How can one control these organisms?

We believe we know how things work but we truly do not understand

Our problems are self created and looking to solve a sympton will not stop the problem

it just makes it easier for us to live with.





CalTech biologist and Nobel laureate David Baltimore said that Venter has “overplayed the importance” of his results, which represent “a technical tour de force” rather than a scientific breakthrough. Venter “has not created life, only mimicked it,” Baltimore said.

Boston University bioengineer James Collins called Venter’s work: “an important advance in our ability to re-engineer organisms, not make new life from scratch. Frankly, scientists don’t know enough about biology to create life. Although the Human Genome Project has expanded the parts list for cells, there is no instruction manual for putting them together to produce a living cell. It is like trying to assemble an operational jumbo jet from its parts list:impossible. Although some of us in synthetic biology have delusions of grandeur, our goals are much more modest.”





Hi all. In the light of the recent breakthrough at the Craig Venter Institute http://www.telegraph.co.uk/science/science-news/7762711/Synthetic-life-Dr-Craig-Venter-seeking-monopoly-claims-gene-pioneer.html many Christians I know claim that these synthetic life creations indeed proves the possibility of ID and spells trouble for the Evolution theory.
Although I am very sceptical about this claim, I need to formulate a response, as I am not really as scientifically inclined as many other atheists. Are there any of you bright young scientists that could explain their claim and also state how one can disprove it. I am sure it cant be that difficult.

Thanks
Thanks all for some interesting responses! I am still a bit baffled about this but surely seeing it in a bit of a different light





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