'Gone'

Isabella Kirkland's picture is the subject of her talk at TedX's DeExtinction event today.

The revival of an extinct species - the Wooly mammoth - is now a real possibility, says Hendrik Poinar

Hannah Waters see narcissism in de-extinction. Stuart Pimm argues conservation of species still alive should take precedence.

"Resurrecting a Forest"

Critics have focused on the threats posed by novel life forms released into the environment, but little attention is paid to potential opportunities–to reconstruct extinct species or create customized ecological communities designed to produce ecosystem services. They may change the public perception of what is “natural” and certainly challenge the notion of evolution as a process beyond human construction.

-- from a framing statement for a meeting titled How Will Synthetic Biology and Conservation Shape the Future of Nature?, quoted by Carl Zimmer.

Endless forms

We have moved beyond a world of natural history into an era of what Richard Pell calls “postnatural history.” His new museum, the Center for PostNatural History, opened in Pittsburgh [in July 2012]. With it he endeavours to create a curiosity cabinet from the Anthropocene period - the age of man.

The only criteria for inclusion in Pell’s Wunderkammer are that the organisms have been intentionally altered by humans in a way that would be passed on through generations. Intentionality is the important bit, Pell says; after all, a museum of creatures changed by pollution, nuclear radiation or climate change would be endless.

--  from A museum of creatures re-engineered by humans

(Image: Guatemalan worry dolls constructed from cultured tissue, Oron Catts and Lonat Zurr)

The Design and Construction of “Synthetic Species”

I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr’s Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term “synthetic species” to distinguish it from “natural species”, not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment.

-- Eduardo Moreno

'A grown-up conversation about synthetic biology'

Most ethical, policy and media discussions about synthetic biology start from the assumption that these aims have already been achieved: that biology has become easy to engineer for whatever ends we choose, that the toolbox is available to any student or potential terrorist, that dangerous organisms and powerful bioweapons are easy to make, and that no effective regulation is possible. The ability of synthetic biologists to overcome serious scientific and technological challenges is taken for granted, and the economic, legal, social and political conditions for the uptake of these technologies are ignored.

Commentators instead focus on potential reckless use or misuse, overestimate the pathogenic possibilities, and worry about deep questions such as: "Do we have the right to play God?". These worries are the flip side of grand claims about synthetic biology's imminent ability to solve challenges in health, environment and energy. Utopias and dystopias seem to be the only scenarios possible.

This way of framing discussions is unhelpful.

-- Claire Marris and Nikolas Rose

More heat than light, perhaps, in the yuck factor reaction to three-person IVF. 

'The first rationally designed genome'

In the menagerie of Craig Venter’s imagination, tiny bugs will save the world. They will be custom bugs, designer bugs — bugs that only Venter can create. He will mix them up in his private laboratory from bits and pieces of DNA, and then he will release them into the air and the water, into smokestacks and oil spills, hospitals and factories and your house.

-- from Craig Venter's Bugs Might Save the World (sic)

Magnetsopirilllum magneticum

...a naturally magnetic microorganism found in ponds and lakes, which swim along the Earth's magnetic lines, aligning like a compass needle.

When they eat iron, proteins interact to produce tiny crystals of magnetite, the most magnetic of all naturally occurring minerals on Earth.

After studying how proteins inside the bacteria collect, shape and position these so-called nanomagnets, researchers copied the method and applied it outside the bacteria, in a move that has been likened to "growing" magnets.

The researchers say that enabling these nanomagnets to hold information will lead to "the hard drive of the future."

-- report

XNA

Heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

-- Synthetic Genetic Polymers Capable of Heredity and Evolution

"There is nothing Goldilocks about DNA and RNA," Holliger told Science. "There is no overwhelming functional imperative for genetic systems or biology to be based on these two nucleic acids.

-- DNA alternative created by scientists

The work heralds the era of synthetic genetics, with implications for exobiology, biotechnology, and understanding of life itself

-- Gerald Joyce

XNA analogues of nucleic acids

P.S. Good overview by Ed Yong

Life, a new manual?

Rats who build the labyrinth from which they will escape

is how Raymond Queneau described the practitioners of Oulipo, notes Ben Schott.

Oulipo derives from pataphysics, which has been defined as an approach that considers things in terms of their potentiality: what they can be instead of what they are. A foundational text is Raymond Queneau's sonnet-making 'machine', which creates a hundred thousand billion new poems from just ten originals. [1]

Oulipo imposes constraints on language in order to discover new things, and/or - as in George Perec's La Disparition -- to search for what has been lost.

The Canadian poet Christian Bök says that in writing Eunoia [2] he came to the conclusion that censorship of language is probably impossible:

Language is a very robust life form that's capable, like a weed, of finding a way to survive and thrive even under the most hostile environments.

Life itself is constrained by many things, including "the central dogma of molecular biology" which is, broadly, that DNA > RNA > protein. Scientists are now trying to reprogramme the code through the invention and synthetic evolution of new orthogonal translational components.

From the point of view of synthetic biology some old 'constraints' of life are to be broken.


Footnotes

[1] An online version here. "The work you are holding in your hands represents, itself alone, a quantity of text far greater than everything man has written since the invention of writing," says François Le Lionnais.

[2] Bök makes this Greek word the title of his book. Eunoia is, he says, "the state of mind you have to be in in order to make a friend". In Nicomachean Ethics, Aristotle uses the term to refer to the goodwill arising from spousal love. In modern English it is also used to mean "beautiful thinking" and as a medical term for sanity.

Synthia's parents

Synthetic biology is changing so rapidly that predictions seem pointless. Even that fact presents people like [Drew] Endy with a new kind of problem. “Wayne Gretzky once said, ‘I skate to where the puck is going to be.’ That’s what you do to become a great hockey player,” Endy told me. “But where do you skate when the puck is accelerating at the speed of a rocket, when the trajectory is impossible to follow? Whom do you hire and what do we ask them to do? Because what preoccupies our finest minds today will be a seventh-grade science project in five years. Or three years.

“We are surfing an exponential now, and, even for people who pay attention, surfing an exponential is a really tricky thing to do. And when the exponential you are surfing has the capacity to impact the world in such a fundamental way, in ways we have never before considered, how do you even talk about that?”

-- from A Life of its own: Where will synthetic biology lead us? by Michael Specter

SynBio and the music of chance

If our kind of mind had been confronted with the problem of designing a similar replicating molecule [to DNA] from scratch, we'd never have succeeded. We would have made one fatal mistake: our molecule would have been perfect. Given enough time, we would have figured out how to do this, nucleotides, enzymes and all, to make flawless, exact copies, but it would never have occurred to us, thinking as we do, that the thing had to be able to make errors.

The capacity to blunder slightly is the real marvel of DNA. Without this special attribute, we would still be anaerobic bacteria and there would be no music. Viewed individually, one by one, each of the mutations that have brought us along represents a random, totally spontaneous accident, but it is not an accident at all that mutations occur; the molecule of DNA was ordained from the beginning to make small mistakes.

-- so wrote Lewis Thomas more than thirty years ago in an essay titled The Wonderful Mistake.

Synthetic biologists working today believe they are not playing. Certainly, some of the language adopted in the field communicates a specific intention to rule out chance in the pursuit of value-added. Here's an example (as noted by The Synthetic Biology Project, but with emphasis added by me):

As envisioned by SynBERC, synthetic biology is perhaps best defined by some of its hallmark characteristics: predictable, off-the-shelf parts and devices with standard connections, robust biological chassis (such as yeast and E. coli) that readily accept those parts and devices, standards for assembling components into increasingly sophisticated and functional systems and open-source availability and development of parts, devices, and chassis.

If they succeed, SynBERC and others will not be creating life in the sense that Thomas had in mind. But if they create 'parts and devices' that are not completely 'robust' but, rather, turn out to be subject to mutation or other unforeseen eventualities then what?


In a different context, D. Graham Burnett quotes Nietzsche. I may be wrong to intuit a connection, but want to keep it in view:

We should leave the gods in peace … and rest content with the supposition that our own practical and theoretical skill in interpreting and arranging events has now reached its apogee. But at the same time, we must not conceive too high an opinion of this dexterity of our wisdom, since at times we are positively shocked by the wonderful harmony that emerges from our instruments—a harmony that sounds too good for us to dare claim the credit for ourselves. Indeed, now and then someone plays with us—good old chance.

Not playing

...but why stop with microbes? It will soon be possible to make entirely novel forms of plants or animals (including man). New cereal crop plants might fix their own nitrogen, eliminating the need for costly fertiliser. Or, how about custom-made insects that seek out and kill locusts or malarial mosquitoes?

-- Johnjoe Mcfadden argues that synthetic biology "provides new hope for a bright future."

The anti-GM lobby, he predicts, will howl that we should not be playing God. The last verb in that sentence, if nothing else, is surely wrong. As Craig Venter has said, "we are not playing."

Will W. Brian Arthur's mechanism of combinatorial evolution apply increasingly to biology as well as technology?

Life engineers

'Intelligent design' may be bollocks cubed; but human design of life may not be:

“We have hardly scratched the surface of what biotechnology can do,” says Drew Endy, a bioengineer at Stanford University in California. “To ask about the applications of synthetic biology today is like asking Von Neumann [the computing pioneer] in 1952 what the applications of computers would be.”

A feature of synthetic biology is the core role played by engineers such as Professor Endy. They are introducing a discipline and rigour that is missing from most of bioscience. Paul Freemont, co-director of the Centre for Synthetic Biology and Innovation at Imperial College London, says the aim over the next 20 years is to give synthetic biology the precision of electronics. “Our understanding of how living cells work isn’t as good as our understanding of electronic devices,” he says. “We want to get to the stage where we’ve got all the parts we need to build any biological machine that we want.”

-- from A new twist on life (FT).