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.

Thursday, 22 December 2011

This Is The Way The World Ends...not with a bang, but repeatedly passed through a ferret

H5N1 is a strain of bird flu. Scientists in Wisconsin and Rotterdam have just proved its future transmissability between mammals by repeatedly infecting a chain of unfortunate ferrets, and the virus has evolved along the way, like viruses do. This hellish material now exists in a new strain that is airborne and can pass from mammal to mammal.

This research is of course essential. One of these days a virus is going to make the species jump that was made in the past by Measles (from cows), Scarlet fever (horses), HIV (chimps) ...and will one day become a threat to human health. And we need to know if and how that's going to happen. Hence the research.

But none of them, according to the US National Science Advisory Board for BioSecurity (NSABB) have got anything on this baby. NSABB chair Paul Keim said in November "I can't think of another pathogenic organism that is as scary as this one. I don't think anthrax is scary at all compared to this."

In 1918 and 19, a form of bird flu killed 100 million people...with a death rate of 2%...that is, for every 100 people who were infected, 2 died. This one, apparently, comes in at 60%.

Sixty. Six Nothing. So...do the wee bit of math...with the same spread as last time, that's three billion people...now factor in an increased human population and air travel...and...

AAAAAAGGGGHHHHH! Stop breathing! Everybody! Immediately!

The reason this has been in the news in the last couple of days is that the NSABB has asked Science and Nature to redact...censor...the publication of these results. They think that we're going to get some fundamentalists buying themselves some chickens and some ferrets and start making this stuff in a garage somewhere. There is a lot more horror from the scientific community about the censorship than there is about the apocalyptic potential of terrorists getting hold of this stuff. Research and prophylaxis will be hampered, they say, unless the the flow of information gets everywhere it needs to get.

And making a weaponised version of this stuff is going to be TOUGH...you can't just pop it in the post. It was a long time ago that the idea of how to make an atom bomb occurred to Leo Szillard. And no one's put one in a suitcase yet.

(He was crossing a road in London in 1933. He blanked out when he put one foot on the road...and when he found himself standing on the other side of Southampton Row, he knew that it would work. But it took a lot of time and money to turn his epiphany into a mushroom cloud over Hiroshima...after which he reinvented himself as a biologist and sci-fi novelist.)

Besides, and this is the real point, something is going to get us one day. Bound to. Nature works like that. Viruses evolve very very fast...and they're always looking for new places to live. HIV doesn't want to kill people...you don't want to blow your new house up...but it takes a while to adjust to each other. We'll be naturally immune in a thousand years or so...and we'll both be happy. In the meantime, however...

Remember Jared Diamond's "Guns Germs and Steel"? It was Measles that conquered America. John Wayne only had a bit part. The Europeans had immunity. And the Native Americans didn't...the rest was just mopping up.
And one day sooner or later evolution of some kind or other, cosmic, climactic or biological is going to give us a right good kicking. Asteroids, climate change, viruses are all waiting in the queue for the apocalypse.




(This is all ending up in the play I'm going to write, by the way. It's a science fiction play, and no good science fiction can miss the trick of wiping out humanity some way or other.)

I think I've just found the way it's going to be. But it won't be terrorists who do it. Nah. Who needs blokes with beards and fixed opinions on homosexuality? As Mark Honigsbaum wrote in yesterday's Guardian, when it comes to terror, nature is the man for the job.

http://www.guardian.co.uk/commentisfree/2011/dec/21/bird-flu-bioterrorist-h5n1?INTCMP=SRCH


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, 13 December 2011

Rare



This is an illustration of the Drake Equation, which is a mathematical model that has been used since the 1960s (when CETI was set up) to calculate the number of intelligent life forms "out there" who might have something they wanted to say to us. Even a brief hello...or maybe something in exchange for the transmissions of the X Factor we're currently beaming into eternity. Like a death ray if there's any justice.

The first three numbers, entirely unfeasibly at the time of its first formulation, are creeping up and up and up. As measured by gravitational wobbling and periodic dimming of stars, the number of planets found is now in the hundreds, and those within the "ecoshell" as pushing half a dozen...probably. Even the fourth number, given all the water and vulcanicity which seems to be around in our solar system, is at least theoretically not zero...probably.

So what's keeping them? When will ET do his duty by us? And save us from ourselves?

Well, the more I read in the converging disciplines of developmental biology, chemistry, paleontology, climatology...and genomics, the bigger the conceptual gap between fl and fi, the fourth and fifth terms of the equation, seems to be. And the more apparent it is that we have to look to ourselves a bit sharpish for salvation.

Andrew Knoll, in his magnificent, every five pages mind-boggling ""Life on a Young Planet" , summarises it like this: "While the story of evolution undoubtedly includes human beings, it is not about us...life's history is a gripping saga of cyanobacterial survival, a cautionary tale of trilobitic fall, or the inspirational story of yeasts finding sustenance in rotting fruit...Whatever the merits of viewing earth as our world, we could not persist without the bacteria and algae, as well as the plants and animals"

The number of things that had to go right, and keep going right, for life not only to exist but for life to exist with the right chemistry for getting on for 4 billion years, with water having arrived here at just the right time, for the temperature to have ranged so narrowly, for the right abundance of oxygen and calcium to coincide for the formation of skeletons (a prerequisite for diversity of form and function), leaves a yawning, maybe more or less unbridgeable gap between there being life and there being complex, multi-cellular life...leave alone all the stuff that's happened since the Cambrian explosion gave rise to plants and animals...including mass extinctions and climate change that has fortuitously coincided with mutations in wheat grass to let us discover agriculture which is the sine qua non...etc etc etc...and I didn't even get to beating Hitler, which was helpful

Man made global warming is the least of it. Take a look at this graphic.

The present day is at the right hand end. As you can see, it's pretty damn cold at the minute...earth has usually been much, much hotter than it is now. It is, nicely for us, a bit parky.

And before Nigel Lawson gets all excited and says "Well there we are then...fire up my Hummer immediately", just because climate change is natural doesn't mean it's good for us. Our civilisation has emerged in a period of warming at the tail end of a glaciation period (whose end we are accelerating) and the climate owes us diddly squat.

God may be dead, but his shadow falls over us whenever we imagine that we are "meant" to be here. Meant by whom? Ourselves, of course, is the only possible answer to that question, which means that, as as ever, we are, like all forms of life ever, on a cusp between altruism and individuality as a survival strategy. We have to decide who "we" are.

The language of evolution has been hijacked ever since Darwin to justify the rich in doing whatever they feel like doing and paying no tax in the meantime. Progress and natural selection have been culturally identified with psychopathic behaviour in the marketplace and on the battlefield. Just like Divine Providence once upon a time.

The fact, however, is that the tension between cooperation and competition as alternatives WITHIN taxonomic groups is as universal as DNA itself...more so. I am finding it possible now to conceive of all our political conflicts within this view of life, and to read in the graph of climate change a political imperative to identify the values that will alone protect us from the next set of depredations of the rich, for which, honest to God, the latest unequal division of economic pain is only a minor rehearsal. If people like Murdoch are still in charge when the whip comes down, then the survivors are not going to be nice liberal folk like you and me...they're going to be unpleasant beyond the dreams of Al Quaida. There's an unnatural selection coming, and we really don't want those people making the rules.

I observe too, tangentially, that just as it was possible for Dante Alighieri to write a poem that encompassed the universe in 1309, for the first time since, that holistic view is possible again. And it's called human science. As above so below...uncertainty at every scale - convergence and homogony and happenstantial selection are everywhere you look. It is breathtaking and beautiful to be alive right now.

Science awaits its Dante. And climate change its Karl Marx. I don't imagine that's a job description I could fill...I'm just writing an undivine comedy about genetically engineered librarians. But to finish my blogs before the hols, I did want to attempt a brief panegyric.

We live on rare earth
At exactly the right time
We should act like it.

There. Stick that Boson up your accelerator and detect it.

Happy Holidays.
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.

Thursday, 1 December 2011

11 Small Songs About Everything

1

At the heart of
Lived and illusory experience
Is the feeling that there’s somebody watching

That we’re apart from the things we are a part of
That there are always two of each of us.

2

Our ancestors became objects of worship
So very early on,
Because it is unsettling that the dead
Those who are absent from the world
Stay present in our minds

I suspect that our being incomplete and double,
Has, Ab-originally speaking.
Something to do with feeling
that if, after we’re dead
We exist - Why not now?

3

The future tense
The ability to imagine consequences
To make plans, have ideas, write them down
And imagine alternative future versions of ourselves
(if we sow or eat the harvest)
Is a subset of this initial, unnerving intuition
And finding death when we discovered life

There are two of me in the future depending
on me right now

4

In compensation for the experience
of memory and anticipation,
We evolved or we invented
(it hardly matters which)
Our sense of self, a continuous being
With a name
Who was, and is now, and ever shall be.

Perhaps that’s what happened when
Eve bit the apple.
Perhaps that was the Fall


5

Our conversations with God
Have always been ways to talk
About the future with ourselves.

(The future briefly replaced God, even,
As an object of hope and worship
And as a repository for justification
But has been found to be equally untenable.)


6

While atheists are fond of saying,
(Leaning forward with a pipe and a pint)
"God has proved himself
An unnecessary hypothesis,"
Some of us, even atheists
Are not comfortable
With the future going the same way.

To live without God and Hope too
Makes us mean and instrumental
Narrow and unpleasant to be with


7

Reality isn’t good for us
But then
We’ve always known that

We’re still looking for something, anything, in reality
To console us for dying

In the molecules of our sameness
Of memory and inheritance,
Can we find in genomic longevity
A substitute for immortality?
In molecular homogony, for belonging?
Can we find in the changes and contingencies
Of amino acids our identity?
And ways to be happy about what happens next?
Can we pray to the way things really are?
Can we learn
How not to need God
And how not to be him as well?

8

There is the comfort
That our questions now
Across the wastes of time and political economy
Are the same ones we’ve been asking
Since we got ourselves kicked out of the garden.

Our answers too are all the same
Negotiations of the same dualities
Lostnessess and wishes,
And all of these have been useful.

We’ve made beauty from them
As well as thefts and murders.

9

Our deeper realities than the real
Called Brahma and quanta and the like
Are better means than they are ends.

Lovely things have been done with them
Our condemned and privileged, evolved or invented
loneliness and love

And terrible, terrible things.


10

We are adapted to watch ourselves experiencing
The unlikeliness of being real.

Like all adaptations to reality
The only end is failure
while reality goes on.

11

The measure of everything is everything
The rest is songs and silence.



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.

Thursday, 24 November 2011

In Search of the Great Money River - Bacteria that Cheat and Biologists that Patent

Following on from the philosophical ramblings in previous posts, I think I'm ready for a case study of living in two worlds at once. The source of the story I'm going to attempt to reconstruct is James Watson's racy and readable account of the making of the DNA business from inception to corporation (DNA : The Secret of Life Random House 2003). The immediate inspiration, however, is watching my colleagues here at the Forum, talented brainboxes to a man and woman, spending most of their time filling out funding applications. Whatever we think our jobs might be, our real occupation is seeking for the Great Money River.

(Hence the above illustration of John Manning Speke and his splendid beard "discovering" the place where the chaps in the background have been living for quite some time.)

"The Great Money River" fiction fans may recognize as the single most instructive image of capitalism ever devised...from God Bless You Mr Rosewater by Kurt Vonnegut Jr, who passed on to sit on the right hand of the Almighty not too long ago.

I quote:

" forget about hard work and the merit system and honesty and all that crap, and get to where the river is. Go where the rich and the powerful are and learn their ways. They can be flattered and they can be scared. Please them enormously or scare them enormously, and one moonless night they will put their fingers to their lips, warning you not to make a sound. And they will lead you through the dark to the widest, deepest river of wealth ever known to man. You'll be shown your place on the riverbank, and handed a bucket all your own. "

Well, for a while there the Human Genome Project was a ladder down the bases to the Great Money River...allaying anxieties and promising immortality to the rich. There's a book I'm reading published at the height of the genomic hype in the 1990s (BEFORE the thing was sequenced/published/drafted, significantly) called The DNA Mystique by Dorothy Nelkin and M. Susan Lindee where they quote entertainingly from the claims of universality and truth which were the marketing hallmark of the enterprise.

The scientists themselves, unless they're chasing money, tend to eschew what some call "astrological genetics" - where there are held to be, for example, genes "for":

"obesity, criminality, shyness, directional ability, intelligence, political preferences, violence, celebrity, pleasure seeking, sinning, saving and being a couch potato....Genetic essentialism reduces the self to a molecular entity, equating human beings with their genes"

Nelkin and Lindee go on to say that "DNA in popular culture functions as a secular equivalent of the soul. Independent of the body, the genome is immortal. Fundamental to identity, DNA explains individual differences, moral order and human fate"

That was the pitch...that was the temptation. And it ignored the fact that most of the genome isn't "genes" at all - but junk. It turned out later on that the junk - repeats, introns - was fascinating in its own right. As a structure, as a moleculer, the human genome is a biography of all of our "species" encounters with viruses, and with evolutionary paths not chosen...and some of it, in terms of the spaces between genes (and hence how they work together in different organs, different stages of life) is essential to how the genes...the exons...work

...none of this was (or is) of much interest to the rich...who want power and cures...and hence offers no route-map to the money river. So why I'm following it above all God knows...

Handing over to Watson, remembering the early days of the project from which he was edged out: "Why should we sequence the entire genome - why bother with the junk? There is actually a quick and dirty way to secure a snapshot of all the coding genes in the genome using reverse transcriptase technology" - that is, working back from the messenger RNA to the coding sections of DNA - "Purify a sample of messenger RNA from the brain...using reverse transcription you can create DNA copies (called cDNAs) of these genes...and the cDNA's can be sequenced."

Not just sequenced (cloned) but OWNED...patented...liscenced.

And that's exactly what happened...and would have kept happening had not the publicly funded scientists not just started publishing them in open internet sources...

(Gawd bless the public sector...sod you Michael Gove)

This meant that the new science od "Genomics" was already divided into two...one half (the sexy bit) was capable of being monetized, while the other remained "merely" a description of how things are and what it all means.

Which is, I think, a local manifestation of the dichotomy, or split personality, of all knowledge...which is what I think I've been going on about.

Anyway...

Cooperation and cheating, appearance and reality. An old story. Well...it's even older than you think.

I've been finding that "genomics" is altogether more nuanced, altogether more altogether than the hype threatened and promised. Genetics and environment interact unpredictably at all parts in the life cycle. Though this has the advantage of being true, it's a lot harder to sell. At the same time though, there is a holistic, fractional, metaphysic arising...a sameness, a conditionality which I find attractive. And I find it all over the place.

For instance, and to tie this entery together with stuff I wrote in earlier posts about human altruism and its viccissitudes, it turns out that it may well be that the only thing that has saved us from extinction (so far) may be that bacteria, like people, seem to have choices; to be able to choose to collaborate in groups or compete within groups. To "cheat"

(This harks way back in the blog to when I was writing about the problem of human altruism as tragically played out in the life and death of Geoprge Price...ie if we are all Darwinian individuals solely driven by reproductive genetic self interest, what makes us give money to Save the Whale? inter alia?)

I quote again...from up to the minute research:

"It has been suggested that bacterial cells communicate by releasing
and sensing small diffusible signal molecules in a process commonly
known as quorum sensing (QS). It is generally assumed
that QS is used to coordinate cooperative behaviours at the population
level. However, evolutionary theory predicts that individuals
who communicate and cooperate can be exploited. Here
we examine the social evolution of QS experimentally in the
opportunistic pathogen Pseudomonas aeruginosa, and show that
although QS can provide a benefit at the group level, exploitative
individuals can avoid the cost of producing the QS signal or of
performing the cooperative behaviour that is coordinated by QS,
and can therefore spread."

(Diggle et al. Nature September 2007)

Bacteria, having been around long before us and being dominant in life on earth now and long after we've all succumbed to whatever it turns out to be in the long list of things we're going to have available for us to succumb to...cooperate and cheat. Just like we do. And if they got it together, we'd be a meat store...

Gives a man pause, shore nuff. I wonder how I could sell THAT?


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, 22 November 2011

Aristotle in the Cheeseshop





"Aristotle's doctrines were a very strong and lasting influence in the history of the world because of their compatibility with observation. For us, as for Aristotle, it is the sun and the stars that rise and set...As we proceed on our daily tasks it does not appear to us that the Earth is moving at high velocity. If we drop a stone and a feather from a high cliff into the sea then of course the stone reaches the sea before the feather does. "



Bernard Lovell. In the Centre of Immensities.



I'm such an amateur, in both senses of the word. I look back over the stuff I've written on this blog since May, and sometimes I catch the sound of myself pontificating away at the Traverse Bar...and I think "Who do you think you're fooling?"



My job was supposed to be to respond creatively to the philosophical/social/political challenge of the genomic view of life. I was supposed to come up with a drama. Instead I'm doing this over weight and unconvincing Bronowski impersonation, regurgitating half digested information I've just come across as if I've known it all the time.



A playwright is an actor with a pencil.



But then when I read something like the above written by one of the most famous 20th Century British astronomers, and it makes me feel a bit better. See, I had a chemistry teacher at school who once told me I was "as stupid as Aristotle"...which even aged twelve and still basically reading Marvel Comics to the exclusion of all else, struck me as a peculiar put down.



(He'd asked me to name an element. And I'd said "Fire"...based on information about a character in The Fantastic Four, as it happens...and that's when he hit me with the above epithet. I wish I could say it became my school nickname, but it didn't. Not the "Aristotle" bit anyway.)



Stephen Jay Gould wrote a lot about the arrogance of the "now". The assumption that because the scientific world view has been so successful that previous thinkers from other, older times must have been wilfully thick not to see what now seems so obvious...when had these god bothered ivory tower dwellers taken the trouble to look out of the window, had they observed empirically like they should have done, they'd have quite clearly seen what we can clearly see.



Lovell's point is that if we look out of the window we only see what Aristotle saw...that we have to learn how to see the earth going round the sun, or the chemistry that fuels digestion...or, just maybe, that neutrinos, once in a while, seem to beat photons in a hundred yard dash...



We don't live, except intellectually, in the world as it is. We live in reality as an evolved element of it. We have to engineer reality in order to understand it, and understand it in order to engineer it. And for a non scientist like myself, for the bit of me that's a writer, what my attempt to assimilate the genomic "view of life" amounts to is an extraordinary enriching of available metaphors. Honest to God, it's like waking up in a sweetshop (or even better, a cheese shop). I don't know where to start.



Which is why, I think, what I've come up with as a scenario reflects that sense of both richness and disorientation. It's going to be publicised in the next Traverse Brochure, and will try out some ideas which may or may not become the play I write. Briefly, it's about librarians trapped with the total information of the universe at their disposal...but who've forgotten how to read.



I know...iffy...but it feels how I feel and you've got to start somewhere.



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.







Queequeg's Coffin or The Lifeboat


Before I get going, I want to think about this image for a second. This was how it was chosen to "market" the project for sequencing the human genome. We are contained and confined and defined by it. That's what it says. The gene is the essential us. Every branch of knowledge falls into its helical embrace.

Shudder!




Like every other "View of Life", genomics seems to me to be capable of being used in two ways: the way of Ahab or the way of Ishmael. A restless wish to master and control the experience of being alive... against a rather fluffier, more accepting, more systemic sense of being part of a continuum which we cannot seek to master. Religion, I think, has similarly bipolar potential.


What is wrong in the image above (and with almost all religions) is the idea that it's all about us. Take us out of the centre of the image, and genomics, I think, offers "us" liberation, not confinement. Freedom, not definition.

Like all good ideas, genomics is capable of being at least two opposite metaphors at the same time. But if you listen to the hype, genomics is all about mastery. Taking the stuff of life and making of it the raw material for commerce, for technical innovation. Oddly, the promise of total control of our biological destiny is the way this idea of life's interconnections and interdependence has been sold to us.

Now I'm all for enhancing our quality of life through an enhanced technical capacity. I don't believe I suffer from residual "essentialism", from any idea that life, as such, is sacred and not to be messed with. Far from it. If anything, my own "View of Life" is more rigorously material and relativist the more I find out about it through this residency. A molecule is just a molecule.

It's "mastery" I distrust as a metaphor for how we should regard ourselves and our relationship with nature. It's "truth" I distrust as a metaphor for our intellectual interactions with stuff. Including human nature. I don't think it's a coincidence that the financial technocrats whose delusions currently afflict us are referred to as the "masters of the universe", even if they had the plastic toys rather than the gods in mind. The track record of mastery in its financial manifestation is poor and the future prospects for that "view of life", if anything, are worse.

Bruce McKibben, in "the End of Nature", one of the founding texts of modern environmentalism, put forward the idea that our metaphor of being actors upon a stage...humanity in nature...was no longer tenable. Specifically, that "man made global warming" undermined our "stewardship" of this ball of rock and water we call home. That we are living in the Anthropocene era...that we are causing such fundamental changes in the climate, (and, if the 1 October edition of New Scientist is to be believed, in earth's geology as well) that we need to adjust our thinking to a different kind of reality. A different metaphor, in our terms. To quote David Cameron, that we are all in it together. But we have to mean it.

The temptation is to see ourselves as the devil. But we're no more the devil than we're God. It's the separateness of the ideas of "human" and "natural" that is being rendered incoherent by the new demands on us for living in the world consciously.

Genomics, I think, fundamentally challenges both sides of the "Human/Nature" dialectic. It integrates our biology fundamentally and practically with biology tout court. It fosters, as does the threat of environmental catastrophe, a systemic way of thinking about "life" which radically de-centres humanity, humbles us, in fact, while at the same time demanding of us urgent self-protection. To see ourselves as an accidental and temporary evolutionary product dramatises the contingency of our civilisation. Both terms, both metaphors - human and nature - are now of questionable utility in getting us to do what we need to do.

A very narrow window for "life as we know it" opened at the receding of the ice from the middle east 10 000 years ago that can just as easily and dramatically find itself closing. Human exceptionalism, like American exceptionalism, is a fantasy in the mind of Michelle Bachman. Rather the reverse of exceptionalism is more and more overwhelmingly the case, both in terms of how we hope to survive as a "civilisation" and of how we see ourselves, what metaphors we use to describe and think about ourselves.

I suspect that the fact that climate change denial joins manifest destiny and "the right to life" on every Republican platform is itself a response to the slippage of mastery as a tenable image of our relationship with nature and with each other. Fundamentalists of all stripes are insisting so loudly that "we are who we say we are" that one suspects that they secretly doubt it.

My last three blogs have all been heading in the direction of some sort of synthesis. Between Cezanne's renunciation of the joys of perspective, to Andrew Knoll's bacteria-centric model of "life" to Carl Sagan's celebration of the immensity of time, I think there is a liberating and emotional connection.

We are time and environment limited. Only by learning how not to be God, only by learning that we are not the centre of everything can we learn to be the centre of ourselves. We have to learn a new way to value ourselves and each other that not only does not seek to deny our contingency and material commonality with "nature" but takes inspiration and purpose not from our imaginary strength and uniqueness, but from our actual, demonstrable weakness, fragility and dependence.

For this purpose, may I offer a small selection of equivalences in the hope of their utility.

Complexity is evidence of improvisation
Natural selection is intelligent chance.
God is Dice.
Mastery is illusion.
We do not and cannot live in the world the way it really is.
Metaphors are how we make things useful to us.
To observe is to act upon the world.
There is no one but ourselves who cares to save us.
The measure of everything is everything
The measure of "man" is whatever we want it to be
Ishmael survived.
Ahab went down with the whale.

Shantih Shantih Shantih


Oh...quick recommendation, next time you hear someone describe Hitler as a Darwinist, (and hence Darwin as Hitler), send them this.


http://coelsblog.wordpress.com/2011/11/08/nazi-racial-ideology-was-religious-creationist-and-opposed-to-darwinism/






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, 15 November 2011

Om - Traverse Bar 4pm November 24th



Ah, Carl Sagan! There was a TV series in which no one said "I've had an incredible journey to discover just how much I care about cauliflowers"...and which actually WAS a journey.

It moves and does not move
It is far and near likewise
It is inside all this
It is outside all this

Whoever sees
All beings in the self (atman)
And the self in all beings
Does not shrink away from it.

For the one who knows
In whom all beings have become self
How can there be delusion or grief
When he sees oneness?





(Isa Uphanishad trans by Valerie J Roebuck - image of Mandala of Vajradhatu )

By "it" is meant, I think, what Carl Sagan called Cosmos, and what I call "reality" - or at least I'm calling it reality right now.

The thing about Hinduism, or one of the things, is that it eschews the Western hierarchy of Appearance as being less than Reality...which dichotomy underpins the languages of Western Philosophy and Science. Hence Hinduism's attraction to the great underminers of that tradition from the West itself from Schopenhauer on.

I'm doubtless going out on a limb here, but I'm starting to think of the different levels of "reality" in our biology, of the genomic perspective, as being related to this perspective, at least on the level of emotion... my emotion, anyway. So here goes:

Maya, or "illusion" as it is usually rendered in English, is the only way we ever see or understand or act upon anything. We intuit another level of reality, brahman, which is only ever accessible through the extinction of all desire. Including the desire for understanding. Hence our apparent God-like command of information is only ever apparent.

(Yes...this stuff does go round in circles...and doesn't get you anywhere except to a different part of the circle. The point being that is there is no such thing as a "point"...ask Max Planck if you don't believe me!)

To speak in terms of rude practicality, we can only sequence or read a genome by turning it into a not-genome...by cutting it up and cloning a bit of it at a time. Genomes as such and in situ cannot be read. Even here uncertainty is an absolute. We are never detached in our observation...to observe is to act. Language, including "scientific" language, does not DESCRIBE the universe, it acts within it - it interacts with it.

I trust this is sufficiently obscure.

Life, considered from the imaginary, objective viewpoint of a God-like observer, consists, so far as we can tell, of bacteria with temporary variants. This "life" exclusively exists, so far as we know for sure, only on a oblate sphere in the middle of nowhere, a fly-speck of chemical activity on a chunk of matter almost wholly surrounded by void.

Matter itself is anomalous...most of what we call the universe is empty of it. Life is an anomalous and insignificant subset of an anomalous subset of "reality"...or of "Brahma" if you like.

But Maya...illusion...is where we live. Our only possible relationship to reality is to live in it. Our only possible ambition is to live in it better.

Which is why it is useful to explore atoms and some of their special and unlikely arrangements in the form of molecules of DNA. In case they turn out to be useful, including "useful" in the sense of understanding where and what and for how short a time we "are". And what a statistically inestimable privilege it is.

(That's as near to religion and meaning as we can ever get...call it Jaweh or Krishna...what does it matter?)

Genes are not the "truth" of us. Truth as a concept is and only ever can be useful to us. Nobody and nothing else. Understanding life in terms of genes, and now genomics, is useful. True is something else again.

(Don't get me started)

Our sense of wonder...and inadequacy...in the face of the infinite, has been and will continue to be expressed in our explorations of what we call "reality", what the Vedas call "brahma".

But Maya...that is, our lives...will also continue to be the only actual measure of how useful, or not, reality is to us. And our decisons are only ever about how this unearned, accidental wealth of ours can be properly and most pleasantly distributed.

Anyway...that's the kind of stuff I've been thinking about...and would like to discuss in the Traverse bar on Thursday next.

ps Incidentaly, RIP Lynn Margulis, who as Lynn Margulis Sagan put forward the first model fior the evoltion of complex celled life - endosymbiosis - or one single celled creature living inside another - in 1967

pps : The resemblance between this image of a human genome from the University of Maryland and the Mandala above, is of course purely coincidental.

(as above, so below)

Do come.







Peter Arnott is Resident Playwright at the ESRC Genomics Forum April 2011 - April 2012. Appointed in partnership with 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.

Living in the Bacterial World

You recognize this fella? Sure, it's the tree of life as sketched by Charles Darwin in "red transmutation notebook B" early in the 1840s. Famously, the words "I think" are clearly and charmingly visible up in the top left corner.



Darwin was lovably and maddeningly diffident. Afflicted with afflatus, he was always reluctant to discuss the implications of his work in print, let alone in public. But this scratchy graphic, with the figure "1" standing for the common ancestor of us all, ranks with Crick and Watson's model of the double helix as the icon of a materialist, historical understanding of what we persist in calling "life."




I've cut and pasted another and more recent version of this famous graphic at the bottom of this post. This one is derived from the microbiologist Karl Stetter, and reflects his research priorities as much as Darwin's did his. I saw it first in a cracking book by Andrew H Knoll called "Life on a Young Planet" which joins the book list I'm going to be posting as recommended reading at the end of this residency (once I've read them all myself!).




Knoll and Stetter are enthusiasts for the small and slimy end of things. You'll note that what we think of as "life" most of the time occupies a mere sliver of the diagram. Up there at the top right, look. Plants and animals and fungi. Overwhelmingly we are living, say Knoll and Stetter, in a bacterial world. And we always have been.




Shaded in red down at the bottom is a great big idea about the origins of life. What all our ancestors had in common, as well as the rudimentary chemistry of life in their combinations of RNA, DNA and amino acids, was thermophilia. . Most of what we know these days as "archaea" still live in hot springs and at oceanic thermal vents and under the earth's crust, which, while not recommended as holiday destinations, may well be where most of what we call "life" still lives. They all liked it hot




They also liked (and like) it without oxygen, which was lucky, as there wasn't any yet...or not much. Oxygen was poison to them. They excreted it as a waste product when they'd done munching on Carbon Dioxide. Which is lucky for us. Life itself, on a microbial scale, created, eventually, the conditions for large scale agglomerations of tissue like you and me and the elephants...and the fruit flies...but only after most life had derived energy from light and heat. Photo and Chemo-synthesis.




Darwin was famously flummoxed by the fact that life, or the fossils/traces of life, seemed to appear quite abruptly in the ground. It seemed that complex animal life, (overwhelmingly trilobites in Darwin's day and ours) were suddenly just there! Darwin's tree of ancestry demanded a root...at least one...that had to extend in time back beyond that borderline where hard bodied fossils had been found...that explosion of complexity in the Cambrian epoch, which we now know to have been around 480 million years ago.




That invisible ancestral world is where Andrew Knoll lives. And it's a riveting and exciting place to explore. Especially when one comes to understand that the earliest life yet found is in rocks in Greenland that have miraculously survived uncrushed by tectonic forces that have now been dated (using the wonder radioactive decay clock of Zirconium) as being something like 3.8 BILLION years old.




That's right, Martha. Plants and animals and fungi only arrived on earth eight ninths of the way to the present day. We are all Eucarya...that is, our cells have a nucleus surrounded by another membrane. And these two cell areas have precisely demarcated duties when it comes to memory (our genomes live on strands called chromosomes that live in the nucleus) and the more energetic activities of energy storage and expenditure -and reproduction -which all happen in the outer part of the cell, the protoplasm.




The overwhelming biomass of planet earth was and remains procaryotic, single-celled life with its genome nicely arranged on a single, circular chromosome. And nothing like us would work in the present, or would ever have evolved in the past, without "life" - that is, bacteria - working away at the heart of it.




It's not just "Yakult", you know.




You'll also notice a whole third kingdom on here. These "archaea" were discovered to be distinct from bacteria through genetics. They look pretty similar, even under a microscope. But they ain't according to their genomes. More recently, they've been found to be closer to us genetically than bacteria are, hence more recent shared ancestry. There is some other big news tucked away at the bottom of the chart.




Though our shared ancestors in the hottest world seemed to have used that heat to split into the three main kingdoms...two procaryotic, one eucaryotic...it seems that THEIR common ancestor arrived when it was cooler. 50 degrees or so. So that is now the temperature range in which these clever folk are seeking the materialist holy grail of what's called "abiogenesis" - where stuff that wasn't "life" became "life".




DNA, you see...couldn't possibly have evolved from RNA in those sort of temparatures. It seems that it had to have evolved before a mass extinction event, (which left only the thermophiles), and to have carried our chemical building blocks unused through the whole boiling epoch so that it could then be used as the information store that could make bodies.




Just as at the KT boundary, which killed the dinosaurs, and at the Great Permian Dying, the mass destruction of most life was as essential to evolution as all the cuddly stuff, like sex.




A final twist in the hierarchy is that the whole project of sequencing the human genome involves a heating and reheating of the source material...and so depends on using an enzyme called DNA Polymerase (to mark, isolate and multiply a selected snip of bases from a chromosome) that is derived from Thermus Aquaticus, a heat loving bacterium that lives in the hot Springs at Yellowstone, and can therefore survive the process.




(Thermus Aquaticus? Sounds like Monty Python made that up)


All this is fantastically challenging to my idea of "reality" at a far more fundamental level than I was expecting, and weird analogies with my equally patchy understanding of Hindu scriptures are starting to intrude uncomfortably on what I'm still pleased to call my "consciousness".




One thing for sure, "life" will never escape from quotation marks ever again.











Goodbye to Bright Ideas Fellow - Mairi Levitt

by Mairi Levitt  - Genomics Forum Bright Ideas Fellow
Senior Lecturer, Department of Politics, Philosophy and Religion, Lancaster University, www.lancs.ac.uk/fass/faculty/profiles/Mairi-Levitt

This is the final week of my Bright Ideas Fellowship but the point about coming here for 2 months was, of course, to make contacts and develop research ideas.  So once I get the bright collaborative ideas into final shape, with help from colleagues in the law school, a research proposal (or two!) will emerge.  I will then have plenty of reasons to come back - assuming  I get the money.

Just as I am beginning to feel optimistic I see some news from one of the major funders about 'demand management'. This translates as the steps being taken to reduce the number of applications so they don't have to wade through so many and the success rate looks more respectable.  But, even if the funding doesn't materialise, it has been a productive time - I have learned a lot more about criminal law, analysed data and given a seminar.  One article is nearly completed, 2 more planned out and an idea sketched out for an edited book (after a very good meal at the Grain Store!).

So thanks to all at the Forum including Margaret and the lunch group, the creative duo I shared a room with (Peter, resident playwright and Pippa, writer in residence) and both Steves for letting me come.  So to end with some snippets from my research on people's ideas about genes and responsibility ....  freewill is about having and making choices. We all live within a complex network of environmental and genetic influences but some will find it harder to control their behaviour than others. Those who commit violent crimes must take responsibility for what they have done and (except perhaps in cases of insanity or extreme mental illness) must be treated as responsible by the courts for the legal system to work. But...  to the assertion that 'genes are not destiny' respondents made different additions: genes are not destiny 'and never will be' ; 'but might be [much] more important in the future' ; 'must never be seen that way because of the consequences

Wednesday, 9 November 2011

"Eyeless" in Aix

                     "This is What I See" becomes replaced by a question: "Is This What I See?"

Cezanne famously painted the same views over and over, obsessed with changes in light and atmosphere. As this residency goes on, and as I obsessively ask myself, over and over, "What is Genomics?" - I go through a rotation of answers. It's a set of techniques, it's the social and intellectual implications of those techniques - and I am eventually coming round to my own "perspective". Or rather, renunciation of any such thing.

Genomics is a way of seeing the world by being in it. It challenges ideas about scientific "reality" as something out there waiting to be discovered and both integrates "being" with "seeing" and renounces, like Cezanne did, the idea of mastery. Of the viewer as a one eyed stationary God looking at a world they do not inhabit.


Which brings me to "Eyeless".

Like most of the first identified genes, "Eyeless" is defined double negatively. It was the absence of "Eyeless" that made a fruitfly that was without eyes. It's on chomosome 4 of a fruitfly and was identified in the "Fly Room" - the Palo Alto lab of TH Morgan, the first great explorer of the connection between molecules found in the nuclei of cells...and how bodies were made, how those things we now call genes are "expressed."

In the 1990s, Eyeless in Fruitflies was one of the first genes to be sequenced and identified as being "homologous" with genes in...well...lots of things. Including us. These days, having sequenced the genomes of mice and people AND fruitflies (inter alia), we call it a Hox gene for short. Its ubiquity as a molecule in the cell, and as an eye making agent in developing animals as ancestrally diverse as flies and mice - whose last shared ancestor was kicking about a LOOOOOONNNNNGGGG time ago- argues for its extreme ancientness.

Indeed, the gene for making eyes may have been around, as a molecule (or bit of a molecule) for much longer than there have been things with sufficient complexity and size to grow an eye - or leg or spleen - at all.

The eye was once thought to be the proof above all of an intelligent designer. It turns out to be an elementary adaptation to light...at least as old and established as photosynthesis in the earliest plant life.

We - you and I - in this view, are accidental agglomerations of molecules that just happen to paint pictures and think thoughts - themselves activities no more or less miraculous than gravity and breathing.

Perspective...it's not reality. "Reality" is a place that only exists for animals big enough brained to imagine it. Making a theory, interpreting the points of light above our heads as distant-in-space/time nuclear reactors - may well be "accurate" or "useful" as ways of seeing.

But that is all they are, ways of seeing and imagining. And, in the case, here and now, of what we call"genomes", manipulating.

We only live twice...one life for ourselves, and one for our dreams.




Peter Arnott is Resident Playwright at the ESRC Genomics Forum April 2011 - April 2012. Appointed in partnership with 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, 1 November 2011

Shh...You Know Who....


"Among its many roles during development, Sonic Hedgehog patterns spinal cord and limb bud tissue differentiation and controls midbrain and ventral forebrain neuronal differentiation"

"The Sonic network functions as a genetic switch"

"Drosophilia hedgehog and Sonic Hedgehog, one of its three Mammalian homologs are canonical secreted signalling factors that regulate cell function and fate...)"

(Quotations from The Sonic Hedgehog Signalling System as a Bistable Genetic Switch by Lai, Robertson and Schaffer - Biophysical Journal Vol 86 May 2004)

One of the first "How it works" genes to be identified, Shh, as it's called, was found on Chromosome Seven of humans having been previously found on the genome of fruit flies (Drosophilia). Fruit flies are the workhorses of genetic research, and have been since TH Morgan first started battering their chromosomes before the First World War. The poor little blighters have been lured with rotting bananas ever since and irradiated, sliced and unnaturally selected for interesting mutations.

Saturday, 22 October 2011

Thursday 27th October 4pm at the Traverse Bar - some things beginning with M we might talk about.

Just a few things to think about for our next wee chat. First, a TED talk on personalised medicine...the genome as Machine...Medicine...Material...all the Ms...







And here's a nice blog I've found run by biologists in Australia

http://www.bioedge.org/index.php/site

And last a nice chat given in Edinburgh last year on the genome as Memory.








As for the genome as "Molecule"...as Thing in Itself...here's something on evolution and the nature of truth from pragmatist philosopher Richard Rorty which I'm trying to get my head around:

"To see the employment of words as the use of tools to to deal with the environment rather than as an attempt to represent the intrinsic nature of that environment is to repudiate the question of whether human minds are in touch with reality. No organism is ever more or less in touch with reality...to rid our thinking of the vestiges of Cartesianism, to become fully Darwinian in our thinking, we need to stop thinking of words as representations and to start thinking of them as nodes in the causal network which binds the organism together with its environment"

My contention on Thursday, ladies and gentlemen, is that what he means is that everyone needs to start thinking like playwrights. Language as ACTION!!!!

See you then.

Peter Arnott is Resident Playwright at the ESRC Genomics Forum April 2011 - April 2012. Appointed in partnership with 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.

Thursday, 20 October 2011

Paddling Upstream at the Genomics Forum

Traverse Bar...4pm ...Thursday 27th October!

Back in April when I started this blog, I seem to remember claiming I had a handle on the Genomics...on the science...but was a bit less clear on what the Forum itself was about. The first part of the sentence wasn't true, as it happens...I had a lot more very enjoyable reading and questioning to do...I think I'm making progress...but I want to take this morning to think aloud a bit about the Forum itself.

And I'm about to make another reckless claim or six.

The Forum is made up of social scientists...not biological scientists. Which means that society...ie you people...is the problem under consideration.

The political impetus behind the establishment of the Forum had a headline rationale, and a political imperative that were parallel but not identical. The headline impetus for its establishment was the enormous technical, commercial, philosophical and social potential of the sequencing of the "human genome". It would be interesting, it was felt, to study how "society" might engage with the new science as it unfolded in terms of information, products and possibilities, ideas and innovations.

The narrower political interest...the problem to be solved or at least addressed...derived from the public relations disaster of GM Crops in the UK and the EU in the last decade. It was felt that anti-GM activists of various ideological orientations had persuaded the "public" to be afraid...Frankenstien Foods...all that. And that this artificially engendered anxiety was capable of "getting in the way" of progress. This is where the idea of "Upstream Engagement" came from. The idea being that if you SLOWLY and CAREFULLY explain to people why they should be happy a bit earlier on, then they will be happy. If the little darlings feel involved...they may even give their positive consent. Or at least be less swayed by Luddite Propaganda.

"Upstream Engagement" would involve people in the issues in a "softer" way...more nuanced...through hiring the likes of me, for example...the Forum would create audiences...and better informed, more responsible citizens for future consultation.

In the Metaphor is the Meaning. The river's still gonna go where it's gonna go. But it's easier if the flotsam LIKES it...that's possibly a bit unkind. And it makes me and writing plays and doing public events and such a sort of tributary, I suppose.

It was all very New Labour...democracy as massage....but things are changing here as well as in the wider world, not least because public conflicts on the GM scale have been elided...but more because of the change of government, leave alone of the economy. So, the Forum won't exist in its current form quite soon. There are different political priorities. A refocusing and a reforming is well underway...resumes are flying around.

But the Genie of the Genome is out of the bottle. The impact of the new technology and new knowledge, as I can testify from my own research has indeed been, and is going to be, enormous and complex. But the mood music, even in genomics, is fatalistic more than messianic these days. We have a "public" who feel helpless to influence anything, being swatted around the head by the hidden hand of the market, and we have little belief that any other hand will be guiding research and development of anything at all, let alone of something with so much potential power. Protest against this and other powers, too, is visceral and anguished rather than articulate and focused. We occupy Wall Street and Dale Farm without any expectation of doing any more than spreading a bit of discomfort and embarrassment before we die...

And that is the greater and un-massageable reason why the Luddites won last time...on GM Foods in the UK and Europe...and why for all the talk of Upstream Engagement, the last thing that the commercial and scientific powers (or those who pay their wages) want now, or will tolerate in future, is "public engagement" in any more than a cosmetic sense. (As a distraction for us and a necessary cost for them.) This is not a chat about reason anymore, it's a fight about fear...and the gloves are coming off.

The current climate does not and will not admit of any of "engagement" for very much longer. The "debate" is not really a debate between "progress" and "dignity"...in the field of genetic medicine, for example. It's a tension between imperatives, and between instincts, and, consisting of any more than shouting and weeping, actual constructive democratic oversight of power is a luxury we can no longer afford.

(Democracy is becoming such a problem...don't these noisy, feckless people in Greece understand anything about banking?)

The Forum exists as a place for research and debate...for argument, for reasonable conversations. Reasonable conversations, I think, are history. As the climate changes and the oil runs out, we will look back with helpless nostalgia to a time when we thought that destiny was maybe democratic...and that the future was in our hands.

Which brings me to my wild claim, if those weren't wild enough. We are not afraid because we have been PERSUADED to be afraid. We ARE afraid. We are afraid of the motivation and competence of those in charge. We do not think they are honest. In turn, they think we're stupid and untrustworthy. They think we're "in the way."

They're right about that. Frightened people are not rational. But we're right too. Science is a social practice...progress IS a metaphor. There is still a role for epistemology as we man the barricades.

And metaphors are stories we tell about things to make us feel better. Even if we're scientists. And personally, "in the way" is where I feel comfortable. Metaphorically, anyway.

And THAT is what the play is going to be about! And what the second half of my residency is going to be rehearsing and refining. The conversation continues next Thursday at Four pm in the Traverse Bar.

For a more reasonable (but enjoyably sceptical) take on "Upstream Engagement" from Joyce Tait, one of the Forum's founding dignitaries, see below.

http://www.nature.com/embor/journal/v10/n1s/pdf/embor2009138.pdf

Peter Arnott is Resident Playwright at the ESRC Genomics Forum April 2011 - April 2012. Appointed in partnership with 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.

Monday, 10 October 2011

The RNA Tie Pin Club

I'm reading James Watson's 2003 Book "DNA The Secret of Life" with which Katherine Mendlesohn at the Traverse was good enough to gift me before my showing there the other week, and lots of responses to it, and to its style, occur to me. I've just finished the first chapters on the "heroic" (my word) era...which are a reminder of not only the physical and chemical questions that Crick and Watson, Franklin and Wilkins were asking, but of the physical processes of research itself...of the distinction between the Gene/genome as "model" and as "molecule"...of the thing in itself...and what you need to do to it before it gives up its "secrets".


This is the original paper they wrote in "Nature" as published in April 1953. The first thing that strikes you, of course, is how short it is, how pithy for such an earth shaping discovery.

Now, we're used to a mythology of instantly shifting paradigms...and assume that after April 1953, no one ever thought of life the same way again...just as we also tend to assume that no one thought of life the same way again after November 1859 and the Origin of Species.

But only a moment's reflection is needed to realize that this is bollocks - that's Hollywood. That's not how things really happen. The full implications of neither event have nothing like fully really permeated our culture. (The very moment I use a phrase like "our culture" more questions get begged than answered.)


Truth is that NOBODY got it...or almost nobody....not for a while. What needed to happen even in the world of science was that this theoretical model for inheritance had to be physically demonstrated and explained...which meant that a pathway had to be found from the splitting and copying of the DNA molecule on the chromosomes inside the nucleus to the manufacture of proteins by amino acids in the ribosomes of the cell... (in the "other" bit of the cell, the cytoplasm) ...all this had to be tested for, confirmed and explained.

Ain't no DNA in ribosomes...what is there, however, is RNA, a similar molecule, now thought to be the senior synthesising molecule...

(RNA WORLD was Crick's idea - the idea, now widely accepted, that RNA made life first and that DNA evolved from it)

...RNA, which, in the meantime had to be shown somehow to transcribe and carry the "information" from the DNA to the amino acids which make the proteins which make the bodies...

RNA being necessary to life in the distant past and still necessary now demonstrates, incidentally, that evolution has thrown the cellular system together with the same disregard for "design principles" as our bigger more familiar "bodies" - which are obviously jerry-built botch jobs... the more that the cell is understood the more it is clear that it too is an accumulation of improvisations on a theme of adaptation.

Took till about 1966 to fix the process in more than a handful of minds as being the way things actually were.

In the meantime, in 1954, James Watson and George Gamow (one the great characters of 20th century science...and, like Crick, a refugee from nuclear physics to biology post Hiroshima) formed the RNA Tie Pin Club...assigning each member one of the twenty amino acid acronyms...and a tie -pin...marking their mission to think about how all this might work.

The club numbered Crick and Watson and Gamow as members, of course...and other figures who became legendary in Molecular Biology, like Sydney Brenner...but also Richard Feynman and Edward Teller...who were, of course, physicists.

There was plenty of room in this very tiny, very elite club for these luminaries...and both the elitism and the smallness of the group are redolent of the way things actually happen in science.

It was just the two of them at the very beginning, in the Cavendish Laboratory in January 1953...gazing with a wild surmise... then Maurice Wilkins and Rosalind Franklin...who were two of the only other people on earth fully qualified to see what this "model" of replication meant...then there were the twenty members of the RNA club...

And then there was DNA recombination in 1973...and the first regulatory and commercial implications till there was commercial genetic engineering by the 90s...then the sequencing of the genomes of humans and e-Coli and potatoes etc etc etc

And now the club, in a way, is a much more open, much more amorphous gathering of social scientists and politicians and even playwrights trying to work out what it all means...asking ourselves are we using our specialisms to interrogate the meaning of genomics...or is genomics, rather more disturbingly, that is interrogating us.

Is it possible for any of us to go on with any of our ethical and moral enterprises without being given pause by the questions asked of us by "This View of Life"?

And most of us, still, when it comes to an overview of the science and its development, are next door to clueless...while the number of people with a comprehensive, nuanced overview of the Science of Genomics, and of its rampantly expanding technology -leave alone of its implications as process and story, as well as information...is still a pretty tight little group. Perhaps there is no one who can see the whole thing anymore, so intense is the field's own specialization.

Most of Watson's 2003 book, though, seems to be about the human story of the science - not just ideas, but how those ideas were sweated for, negotiated and sold. I'm looking forward to reading his take on the politics...and boy were there politics...of the genetic industry as it developed in the 70s...and culminated with the evangel according to Bill, Craig and Tony in the White House in the year 2000 ...just before Bin Laden and the banks between them cancelled the future.

Another day, another day...

In any case, here is the man himself, maybe still wearing his tie pin, maybe a candidate for the maybe mythical role I describe, telling his own story in his own scurrilous style, at the opening of Ted Talks in 2005.











Peter Arnott is Resident Playwright at the ESRC Genomics Forum April 2011 - April 2012. Appointed in partnership with 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.

Friday, 7 October 2011

Adam's Tummy Button


Entirely contradicting what I said in my last entry that I'd be talking about this time, I'm going to put a bit of a footnote to my performance last week at the Traverse, where we were exploring the good old God vs Darwin chestnut once again. First by a bit of back reference to my previous residency at the National Library of Scotland and the archive of Darwin's publisher John Murray.

I also apologise to anyone trying to read this about how strange it looks...the images are straining "Blogger" technology...which is oddly apposite.

Thursday, 6 October 2011

'Lighting up '

by Mairi Levitt  - Genomics Forum Bright Ideas Fellow
Senior Lecturer, Department of Politics, Philosophy and Religion, Lancaster University, www.lancs.ac.uk/fass/faculty/profiles/Mairi-Levitt

It is week 4 of my bright ideas fellowship and the light bulb on top of my head has lit up a few times already!  I am getting used to a blank diary that I can fill with reading, thinking, coffee drinking and discussions.  In fact today I managed to be late for the only meeting I had not arranged myself. The Forum's team got together and I was ensconced in the university library law section reading about automatons in Scots law…well it might have been relevant to behavioural genetics  (‘an external factor not self-induced’, that you could not forsee, that ‘results in a complete alienation of reason’ etc).  But actually it doesn’t seem to be relevant after all since your genetic make-up is internal not external and the research I’m interested in shows correlations with problem behaviours not  ‘a complete loss of self control’.

I share a room with Peter Arnott (playwright and most prolific blogger at the Genomics Forum) and he has not only read one of my journal articles (on genetics and crime) but wants me to come to an open meeting at the Traverse theatre in his Translating the Genome series to discuss it.  Nice to be able to say yes without checking whether it clashes with teaching or other university duties.   I could also spend each and every day in the National Library overdosing on a few of the 14 million items which can be brought to your desk and recommended for the coffee and free newspapers when you need a break. But I only have 5 weeks left after this one so I need to narrow down my interests a bit….why did I say I’d only come for 2 months?!

-------------------------------
Mairi will be holding a seminar on ‘Whatever genes one has it is preferable that you are prevented from going around stabbing people’: Genes, environment and responsibility for behaviour at the Genomics Forum on Thursday 3 November, please email forum@genomicsnetwork.ac.uk to register.

Wednesday, 5 October 2011

Start From Anywhere or All Roads Lead to Genome.

I haven't posted for a week or so...partly because last week I was rehearsing and then performing my Men and Monkeys event...which went well, I think. But I'm not sure how much it tells me about what to do next. As witness my resorting to the appalling title of this post.


It's just that the thing about this subject matter is that the point of entry can be anywhere...you will eventually get around to everything no matter where you start...so where do you start?

Does that make sense?


Take the fact that the UK Police between them now have a DNA database, potentially...of 5 million people...and that the standard DNA mouth swabs that get taken when you get arrested could...with the merest tweak to Data Protection Law...get tested for a mitochondrial enzyme called Monoamine Oxidase A (MAOA)...whose absence (or low-activity) in the cytoplasm is a fairly good predictor for random acts of violence...especially when the possessor has himself (usually him) taken a few beatings down the years...


The information is already there...so why not test for it...it's not that we'd automatically lock people up...so what harm is there in KNOWING...?

Mairi Levitt from Lancaster University is visiting the forum just now...this is her area...and I think I've persuaded her to come and talk about it next time we convene our Traverse Bar discussion group...watch this space...


In the meantime...I'm spoiled for choice for other stuff to write about...and I honestly think I just want to throw it all up in the air in a room with a bunch of actors and say "You Pick One!"


Because the neat thing about everything being connected to everything else is that it doesn't matter where you start...in the end you'll cover all the bases...


(That's a nucleotide joke)


You might start with the 20th Century's leading Eureka! moment... Jim Watson ...possibly in his bath...in January 1953...cutting out bits of cardboard representing said nucleotides and noticing how the shapes of Gs and Ts and Cs and As coincide in an alluringly simple and repeating fashion ...then taking his new jigsaw to show his pal Francis Crick down in the Cavendish...who saw how the mapping worked really well if you ran the chains of bases in opposite directions...


and hey presto...bingo...whatever...they'd discovered a blueprint, invented an icon, envisaged a machine, an industry, an understanding...every metaphor all at once in a flash of structural and functional and conceptual perfection...and they ran downstairs to the Eagle to get pissed...and a very nice pub it is too.


You could start from there. You'd end up with juvenile delinquents' mitochondria eventually. But should us non scientists start at all is the question I'm suddenly confronted with.

Check this:


http://www.uabgrants.org/


It's a link to somewhere just 40 drunken seconds down the road from the Eagle. It's a new scheme being run from The Faraday Institute and St Edmund's College Cambridge.


"The aim of the interdisciplinary Programme is to investigate contemporary non-scientific uses and abuses of biological thought (beneficial, benign or negative) in the domains of philosophy, the social sciences, the media, religion and politics. Collaborative projects between those engaged in the biological sciences and investigators from other disciplines are particularly welcomed"

There's an essay competition and grant funding available...and as a serial abuser of biological thought myself, I must say it sounds most interesting. I might offer myself as a test subject.


Of course, even a playwright might have to point out that scientists themselves have been known for the odd abuses of science ... but maybe that's an essay topic.


Anyway, next time...Does DNA "know" how to make bodies the same way I "know" my pin number...or the way that I "know" that the quality of mercy is not strained...or neither of the above...answer me that one, if you can!



Peter Arnott is Resident Playwright at the ESRC Genomics Forum April 2011 - April 2012. Appointed in partnership with 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.