Welcome to the Genomics Forum blog

Based at The University of Edinburgh, the ESRC Genomics Policy and Research Forum is part of the ESRC Genomics Network and pioneers new ways to promote and communicate social research on the contemporary life sciences.

Tuesday, 31 January 2012

Beginning with M


A while ago I blogged about thinking of genomics in terms of things beginning with "M". Memory was in there...so was machine...so was "mastery". The above link is to a lecture given at Edinburgh University by Professors Siddharthan Chandran and Charles ffrench-Constant on Tuesday 9 November 2010.

These guys have just hit the news in a big way. Using the same kind of adult pluriopotent stem cells that gave us Dolly the Sheep - (that was breast tissue used to create a whole clone...breast...Dolly...Dolly Parton...breast...get it? Scientists are such BOYS!!!) - but, HUMAN adult pluripotent stem cells derived from human skin...and they've made human brain cells. Yup. Brain cells.

The medical potential of regenerating healthy brain tissue is literally mind blowing...many of the most devastating brain disorders from stroke injury to motor neurone disease and multiple sclerosis are based on damage to particular cell locations or cell types. This technology could be targeted to address these problems with only the most minor surgery. The same is of course true of every other organ, muscle...

Now...they haven't made a brain, Dr Frankenstein...yet...But we do have to add an M to our list. "Miracle." Honest.

Check out the lecture above.

Meanwhile, on the "memory" front, news from Australia that it took 24 million generations for something the size of a mouse (which was the size of the common ancestors of all today's mammals before the dinosaurs pegged out) to evolve into something the size of an elephant...once the dinos were out of the way. This is being published in the Proceedings of the National Academy in the US...and when there's a link available I'll paste it.


And mastery...or destiny, anyway...research in Glasgow describing the epigenetic poverty trap. Apparently the level of methylation of DNA in poor people means that poverty really does kill you, your children and your children's children.

Put all this together - all these things beginning with M - and what do you get? No. I'm really asking.

Peter Arnott is Resident Playwright at the Traverse Theatre Edinburgh, Peter will be hosting a number of public engagements as he explores ideas and seeks inspiration for a genomics related play.

Tuesday, 24 January 2012

The Fact of Totality

In the play I'm going to write, which is going to be called "The Fly Room", the characters are the inhabitants of a total library. Like in the legendary Library of Alexandria (of which this is a 19th Century German engraving of an imagining thereof), all the wisdom of the ages, including all the genetic information, is stored in one place, curated and researched by a genetically dedicated team, whose universe this library is.

Years ago, something happened. A power outrage...a war...they don't know. What they do know is that they have had no contact with the outside world for hundreds of years, and that, in the disruption, the total information the library held was scrambled...not destroyed, but differentially encoded. Now, at last, they've found the code...and are beginning to re-assemble and reinterpret the material of their world. The ideational underpinning of this sci fi scenario comes from my own experience of texts...and libraries. I was writer in residence at the National Library of Scotland before coming here...

As to texts, if 1859's Origin of Species was the Ur-text of evolutionary thought, then Erwin Schrodinger's "What is Life?" from 1944 was the founding text of what one might call the genomic view of life. The great quantum physicist applied what he had come to understand about matter to the special form of matter that "lives"...and his text was a direct inspiration to the generation of physicists turned biologists...Crick, Gamow, Szilard, Urey etc etc etc...who took his intuitions about the mechanism of inheritance and turned it to evidence and then an industry in the seventies and eighties...an industry that pulled clumsily, expensively and not always happily together to accomplish biology's equivalent to the Apollo missions to the Moon : the sequencing of the total human genome.

That text...the genome...is now itself a foundation and a map for a dizzying array of ideas and explorations, and, most crucially, mechanisms...life has in FACT as well as idea, become a machine. But the logic of all this still comes down the question Schrodinger asked in his introduction :

How can events in space and time which take place within a living organism be accounted for?

Accounted for, that is, within the materialist viewpoint of physics and chemistry, rather than a teleology - divine or otherwise. From the point of view of the physicist, what is strange about "life" is how orderly it is. Life is an island of anti-entropy. James Lovelock noticed the same thing...it's the basis of his Gaia hypothesis, where all life on earth needs must be considered as a single self regulating entity...jut like the individual organisms that make it up.

Now, I'm agnostic on Gaia. This is partly because I'm instinctively attracted to arguments that start by treating the familiar as anomalous. Hence I'm loath to dismiss it as easily as most right thinking materialists have.

(My theatrical master, Bertolt Brecht, said that the playwright must always treat what his or her society sees as self-evident as surprising!)

It's also because I have yet to come across the argument that would convince me that it is any more weird to regard life-in-total as "impelled by the survival imperative" than it is to regard individual cows, fruitflys or mushrooms as "impelled" to live and survive and reproduce...and self regulate. Genomics has demonstrated self-regulation, switching...choices being made by molecules in four dimensions at every level of natural selection from genes to populations...and at every stage in embryonic development into adulthood and beyond. So why is that impossible for "life" in the world? All of it? Real question.

Anyway, my librarians exist to be tortured by the certainty that they have access to all the information any conceivable civilisation could ever need...but that none of it is reliable. They only have their own inherited flaws and capabilities to go on and to judge with. What they are hoping to discover first is who has put them here and why. For they know that a library cannot, surely, have arisen by chance...I mean...if you found a watch lying by the roadside, could you not deduce a watchmaker?

Oh...there is a fab cartoon set about Schrodinger's famous dead-and-alive cat at: http://abstrusegoose.com/secret-archives/in-a-parallel-world

Peter Arnott is Resident Playwright at the Traverse Theatre Edinburgh, Peter will be hosting a number of public engagements as he explores ideas and seeks inspiration for a genomics related play.

Wednesday, 18 January 2012

purposeful dreaming

To continue the thought from the last post a little, it may be that what was hyped as the revolution was actually a sideshow. Just as it was the technologies arising from the EFFORT of the Apollo moon shots rather than the moon shots themselves that ended up changing the world (principally through developments in computing, semi conductors etc etc) it may be that it is the ethos and methods that went into the effort to sequence the human genome rather than the headline sequencing itself that is the real change.

Thomas Kuhn's definition of "paradigm shift" is centred on changes to the daily practice of science, rather than its ideology or "meaning".

Horizon, the BBC's flagship science show had a huge impact on me in the 70s, partly because I'm the right age for the properly childish excitement of the moonshots and Viking and Voyager and all that...to have hit me between the eyes growing up.

Take a look at this recent episode, if you missed it the other night. The excitement has become complicated by unease.


In the show, the rendering of genetic material and the proteins to which genes code...that is, the making of machines out of living material...is surveyed by Adam Rutherford, who, like me, is a bit staggered and disoriented...by putting silk-making genes from spiders into goats in Utah...and then getting silk from the milk...(seriously!)...by feeding sugar to yeast and getting diesel...(no, really) in California. And in a community centre based bio-tech lab with open source access for all...and six year olds transferring luminous genes from jellyfish into E Coli...all at the touch of a mouse...(oh, and the mouse with its brain wired to a light source so that it gets dopamine hits by pushing a button...I couldn't watch that at all)

The shift is in what people DO...every day...what we think about what they do comes after, and not nearly fast enough to keep up.

The hardest shift in my work is to go from research (which feels like work) to purposeful day-dreaming...which is how you actually get to create things, but makes you feel guilty. (or me, anyway)...and maybe a bit of my, and Adam Rutherford's discomfort at what is happening in synthetic biology all the way from the mega-corporations buying up rainforest so they can feed sugar cane to microbes and get a substitute for petrol to the folks in their garages building lego monsters out of biobricks is that it feels like all this has passed me by...and I was looking out for it...

Out of control? World gone wrong? I'm too old? There are times I wake up a Tory.

Thursday, 12 January 2012

Brother, Can You Paradigm?

I asked very early in the residency about whether or not this thing called "genomics" represented what’s called a paradigm shift. This is the confirmation of a scientific idea or principle that fundamentally alters both the general frame of ideas and the daily practices of science and was coined by Thomas Kuhn in his "Structure of Scientific Revolutions" in 1962.

I still don’t know the answer, but maybe it wasn’t quite the right question. There’s lots of work going on using the genomic understanding of evolution, and of development in utero, of personalised genetic diagnosis, of the making of nanomachines for targeted drug delivery, for the synthesising of micro and macro organisms for the purposes of research. Despite out straitened times, there’s still a lot of money around. There’s a lot of thinking about the economic potential of all this, and the potential impact on our ideas about identity, humanity…life itself.

Does this constitute a paradigm shift? Are we really asking different questions or arriving at different answers? Or are ideas lagging behind the day to day lab practice which certainly has shifted...is there anything, ideationally speaking, new?

(If the Higgs Boson turns not to be anywhere at any voltage, THAT's a shift...that's a rending of garments and a gnashing of textbooks)

As I head away from researching primary sources and towards scripting the first performed sharing of some ideas specific to the play that I’ve started to write, it is general ideas, worlds, that I am starting to imagine. A play is, in one way of thinking, a place. The theatre space in the imagined here and now is an arena, a world where personality and principle can fight it out. It is a place with rules…and it is those rules that I’m thinking about at two very different orders of scale.

First…that my life, our lives, a paramecium’s life, a dog’s life….rather than being actually existing things that share an abstract quality called life, are in fact all distinct abstract expressions of an actually existing thing…a thing that is called life.That matter itself, let alone living matter, is best metaphor-ed as “an island of localised order”…and is a temporary anomaly soon to be corrected…”in an ocean of entropy” - and if James Lovelock isn’t onto something with his Gaia hypothesis, I wish he was.

In terms of daily practice…that The Fly Room, the experimental space where the evolution of fruit flies has been messed around with by biology students since TH Morgan more than a hundred years ago, is where we live every day. That our daily practice of life is taking place in an experimental environment where we have no control and no guarantees of ever understanding what's going on and who or what the test is all about.

This is the world view my play will describe and that its characters will inhabit, and I’ll be reading and thinking about it and sharing it every so often…as I go looking around in it, testing it on their behalf.

And is that a paradigm? Is the world of a play a sort of paradigm? Where only certain actions can take place and are comprehended in specific ways…and if a character escapes from the world the playwright makes, does that break the play and make it unwatchable?

Or is that the shift we’ve been waiting for? Is that what makes it a hit?

Peter Arnott is Resident Playwright at the Traverse Theatre Edinburgh, Peter will be hosting a number of public engagements as he explores ideas and seeks inspiration for a genomics related play.