Comments on a cultural reality between past and future.

This blog describes Metatime in the Posthuman experience, drawn from Sir Isaac Newton's secret work on the future end of times, a tract in which he described Histories of Things to Come. His hidden papers on the occult were auctioned to two private buyers in 1936 at Sotheby's, but were not available for public research until the 1990s.

Tuesday, July 16, 2013

The Powerful Promises of Synthetic Life

Synbiosafe DVD cover (2009) © Markus Schmidt and Camillo Meinhart. Image Source: Synbiosafe.

More breathless excitement: MSN reports that scientists are on track to build a synthetic yeast life form by 2017 (via Machines Like Us):
British scientists are taking part in a global effort to build the first synthetic life form whose cell structure resembles that of plants, animals and humans.

The researchers have been given almost STG1 million ($A1.67 million) in government funding to help them construct one of the organism's 16 chromosomes.

They are part of an international consortium committed to creating an artificial version of yeast by 2017.

It will be the first time scientists have built the whole genome, or genetic code blueprint, of a "eukaryotic" organism whose DNA is stored within a nucleus.

All animals and plants fall into this category. Bacteria and blue-green algae are examples of more primitive organisms that lack nuclei.

Three years ago a team led by American geneticist Craig Venter created a synthetic bacterium genome from scratch in what was described as a landmark achievement.

The new project takes the creation of artificial life to the next level by making the jump to a eukaryotic organism.

Professor Paul Freemont, a leading member of the team from the Centre for Synthetic Biology and Innovation at Imperial College London, said: "It's a massive leap forward. Yeast is a eukaryote - it's a much more complicated cell. These are chromosomes that mimic the chromosomes in our own cells."

But he made it very clear this was not a first step towards attempting to build Frankenstein-like human life in a lab.
The Imperial College site for the Centre for Synthetic Biology and Innovation notes:
Synthetic Biology is the engineering of biology. It is an exciting new area of research combining science and engineering to design and build new biological functions and systems, and to understand existing biological life through its rational re-design.
Is there any cause for larger moral concern, or concern about weaponized synthetic biology? Scientific American mulled these questions over vaguely in a 2010 article. While the writer,

Excerpt from Adventures in Synthetic Biology (2007). Image Source: MIT/Nature via h+ magazine.

In 2007, Wired reported on a bit of MIT publicity outreach, published through Nature, which was designed to make synthetic biology more friendly and accessible to the public, and especially to children interested in studying science: "MIT’s Synthetic Biology Working Group partnered with cartoonist Chuck Wadey, to create a comic book, Adventures in Synthetic Biology, to showcase the principles of the field." You can see the whole comic, starring Bacteria Buddy, Device Dude, and System Sally, here.

In 2007-2008, a project, Synbiosafe, won 236,000 euros to explore the ethical and safety issues associated with synthetic biology. The grant came from an EU program, New and Emerging Science and Technology (NEST). The Synbiosafe project was coordinated by Austrian scientist Dr. Markus Schmidt. Just his affiliation - with the Organisation for Internal Dialogue and Conflict Management (IDC) - should clarify where researchers think synthetic biology could go.

Schmidt's personal site notes that he works
in the area of technology assessment of novel bio-, nano- and  converging technologies (such as synthetic biology); [he] explores the interface between science, society and art; and [he] engages in documentary film production and art-science exhibitions. Schmidt is founder of Biofaction and co-founder of IDC.
IDC's project list shows the spheres which synthetic biology touches: environmental pollution; a sustainable energy policy for Africa; promoting biodiversity conservation in Cambodia; improved agricultural portfolios in Europe and Asia; biosafety and genetically modified crops in South Africa.

That's comforting: "Survival of the fittest – the constant battle for resources, the dynamic equilibrium between growth & decline, survival & adaption - is as valid at a human scale as at a microscopic scale." Yeast Pixels 1.0 art installation by pavillon 35/ Silvia Hüttner. Image Source: Pavillon 35.

Biofaction's work tends to concern the 'softer' impacts of synthetic biology, such as an exhibition this summer on how artists understand this technology, or this artistic collective, Pavillon 35 [sic: this is German for 'pavilion']. You can see Pavillon 35's bioart projects here. They have also launched a video game, Synmod, which teaches synthetic biology through science gamification. You can download the Synmod app here.

It looks like the limitations on the burgeoning merger of biology and engineering may not come from ethical considerations, but simply from patents. Like many aspects of today's exploding Tech Revolution, property rights exert a drag and pull effect. They slow things down. That might be a good thing, in some cases, because deeper thinking about what is going on during the tech boom can be thin on the ground in places.

Nevertheless, patents also worryingly corner the market for big players. The question that comes up behind all our new, shiny tech, again and again, is energy, and who controls it. In this case, biofuels are a central focus of this research. The promise of biofuels awakes competition and power grabs just as ruthless as any in the petroleum or nuclear industries. From The Council for Responsible Genetics:
[I]n 2007 the J. Craig Venter Institute applied for a frighteningly broad patent of its "minimal bacterial genome" called Mycoplasma laboratorium. This organism was an attempt to create life with the minimum number of genes by cutting out as many DNA sequences as possible without removing its ability to reproduce or survive. U.S. patent numbers US2007 0264688 and US2007 0269862 describes creation of the first-ever, entirely synthetic living organism-a novel bacterium whose entire genetic information is constructed from synthesized DNA (but whose genome is a near-replica of a naturally occurring genome).

This patent claims exclusive monopoly on the genes in the minimal bacterial genome, the entire organism made from these genes, a digital version of the organism's genome, any version of that organism that could make fuels such as ethanol or hydrogen, any method of producing those fuels that uses the organism, the process of testing a gene's function by inserting other genes into the synthetic organism, and a set of non-essential genes. These patents are not restricted to any specific cell type-it currently applies to prokaryotes and eukaryotes - or size of a synthetic genome.

While these patents have yet to be granted, the claim shows the extent to which some synthetic biologists are testing the limits in the battle to control the fundamental building blocks of life and actual living organisms. While it is likely this specific patent application's scope will be limited to cover only bacterial cells, such a patent would still grant Venter and company an exclusive license to create synthetic fuel-producing bacteria and the tools to create such organisms. Conveniently, Venter's company, Synthetic Genomics, has contracts with both Exxon Mobile and BP to produce "next-generation" biofuels from synthetic cells (or at least genetically engineered cells that contain synthetic DNA sequences).

Amyris Biotechnologies is a synthetic biology company that used genetically engineered yeasts that contain synthetic DNA to break down sugarcane to produce isoprenoids-which are then being converted to biofuels, industrial chemicals, among other products. Patent US 7,659,097, granted to Amyris in February 2010, covers the production of many different isoprenoids created though a number of different microbes. Amyris already has deals with major oil and chemical companies to turn Brazilian sugarcane into high-value commodities. Again, Amyris' "biosynthetic pathways" are near-copies of metabolic pathways found in nature with some "tweaking" of the DNA pathways to allow the yeast to do some things that traditional genetic engineering could not accomplish.

The novel challenge created by the emerging field of synthetic biology is that not only can natural or synthesized DNA be patented, but the processes used to synthesize DNA and create synthetic organisms can also be patented. Furthermore, the living organisms created with synthetic DNA are covered in these patents, as are the products they are engineered to produce. ...
What must be done
While it is clear to us that current court rulings would likely support the patenting of synthetic genomes as developed by Venter's lab and other researchers, Congress should prevent the patenting of DNA sequences that simply copy naturally occurring DNA. To do otherwise would in effect allow another way to patent natural occurring organisms and their DNA-just make synthetic copies of them. That is in no one's interest but the patent holders'.   
See the videos below the jump which promote and debate various synthetic biology concepts. There is also a Youtube playlist of 2011 talks delivered at the Royal Academy of Engineering here; the first video in that playlist is below the jump.

Synthetic Biology promo for Synbiosafe project DVD. Video Source: Youtube.

A historical perspective: What is Life? Public talk by Craig Venter at Trinity College Dublin (12 July 2012). Video Source: Youtube.

Caption for the above video: "One of the landmark events of 20th century science was celebrated and reinterpreted for the 21st century in Trinity College Dublin on 12 July 2012 as part of the Science in the City programme of ESOF2012. Dr Craig Venter, one of the leaders of the Human Genome Project in the 1990s and a pioneer of synthetic biology delivered a lecture entitled, 'What is Life? A 21st century perspective' recreating the Irish event that inspired the discovery of the structure of DNA.

In February, 1943 one of the most distinguished scientists of the 20th Century, Erwin Schrödinger, delivered a seminal lecture, entitled 'What is Life?', under the auspices of the Dublin Institute for Advanced Studies, in Trinity College Dublin. The lecture presented far-sighted ideas on how hereditary information could be encoded in a chemical structure (aperiodic crystal) in living cells. Schrödinger's book (1944) of the same title is considered to be a scientific classic. The book was cited by Crick and Watson as one of the inspirations which ultimately led them to unravel the structure of DNA in 1953, a breakthrough which won them the Nobel prize."

"The first symposium in an international collaboration between the six national science and engineering academies from the UK, USA and China." Royal Academy conference (13 May 2011) on synthetic biology. Video Source: Youtube.

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