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

From Peter Arnott’s Genotype blog.

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 bomboccurred 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 Honigsbaumwrote 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 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.


Filed under Genomics Peter Arnott Traverse Theatre Company

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

From Peter Arnott’s Genotype blog

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 publiclyfunded 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 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.

www.traverse.co.uk

Filed under Human Genome Project Genomics Traverse Theatre Company

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Breaking new ground: Jo Clifford’s Rehearsal Diary

From Jo Clifford’s blog.

This is my second day back in The Tree of Knowledge rehearsals.

It’s been an extraordinarily happy and productive day. Like all the others.

We’re now at the stage where we all know the play pretty well; and we can all co-operate on the business of making the changes that need to be made to make it better.

It’s such a joyful process.

I’m struck by the extraordinary change in me since I was last in Traverse rehearsals.

That was way back in 1992, or Light in the Village.

I happen to think that’s one of my best plays; but I can remember before the read through had even begun one of the actors coming up to me in great agitation and saying:

“I can’t say this line”.

It was the first line in the play:
“The story begins”.

“What’s my motivation?” he asked.
“To tell a story”
“Where am I coming from?”
“Off stage”.


He hated that. He was completely stuck in realism, and wanted me to remove all the story-telling aspects of the play.

I refused. He left the cast.

Soon after that, another cast member left. “Too difficult” he said.

And soon after that, I came down with pneumonia.

I felt guilty about it all; it was all my fault, i kept thinking, for being such a difficult writer.

”I could not appreciate myself at all. Only years later did I begin to understand that it wasn’t me being “difficult”.

It was me breaking new ground.

As I am now.

The Tree of Knowledge is at the Traverse Theatre from 8 - 24 December.

www.traverse.co.uk.

Filed under The Tree of Knowledge Traverse Theatre Company

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From Peter Arnott’s Genotype blog.

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 : 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 TheatreEdinburgh, Peter will be hosting a number of public engagements as he explores ideas and seeks inspiration for a genomics related play.

www.traverse.co.uk

Filed under Carl Sagan Peter Arnott Traverse Theatre Company Genomics

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The Tree of Knowledge Goes into Rehearsals

From Jo Clifford’s blog.

It’s a solemn kind of occasion, going into rehearsal.

I never quite know what’s going to happen. I want my contributions to be supportive and helpful, if they can be. Because life is so short and there’s quite enough suffering in it without adding more.

It makes me blush to think how terrible I was when I first began. I didn’t know what to do. But then no-one had told me. There was really no information about it at all. So I sat in the rehearsal room - which actually was the stage of the old Traverse, on the set of Chris Hannan’s “Elizabeth Gordon Quinn” - sat there not knowing what to do and feeling miserable.

I hated the sound of my play, and consequently spent a lot of time with my head in my hands. Which the actors took to mean that I hated what they were doing.

Which I didn’t.

And then if they ever asked me what such a such a line was for, I’d say “I don’t know”.

Because I didn’t.

None of this was very helpful. Afterwards I learnt to glue a smile onto my face, even if it was false, and even when I didn’t know what a line was doing somewhere, I’d always make something up.

Because that made everyone feel better. Including me.

But generally there’s no need to fake a smile these days. I love working with actors; and I learn so much.

And directors, too, I add hastily, and designers and stage managers and musicians and lighting designers and everyone involved.

My words are about to transform. Can’t wait to see what happens.

The Tree of Knowledge is at the Traverse Theatre from 8 - 24 December.

www.traverse.co.uk.

Filed under Jo Clifford Traverse Theatre Company The Tree of Knowledge Rehearsals

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The Tree of Knowledge Cast Announced: Gerry Mulgrew as David Hume, Joanna Tope as Eve and Neil McKinven as Adam Smith.From Jo Clifford’s blog.
There’s always this amazing moment when the play, that has really only had a kind of imaginary existence until this moment, starts to take on flesh and blood.I love it. It makes me so excited: because I can never “see” characters in my imagination. I can only hear them. And hear them speaking in very definite tones of voice, to be sure: but I never want these tones of voice to be duplicated by the actors.Because the mainly wonderful part of theatre making is that I create a script, using all my sensibility and skill, and give it to the actors, and the director, and the lighting designer, the set designer, the costume designer, the sound designer, the stage manager - all these amazing gifted people. And they apply all their sensibilities and all their skills and if we manage to work well together they just enrich the script immeasurably.And always in ways I never anticipated.And then the audience come along and do the same…The actors are: Gerry Mulgrew, as Hume, who is so alive and full of life’s joys in his presence and who I wanted to work with for years and years.Joanna Tope, as Eve, who was in one of my radio plays, and I can’t remember which, or who she played, or anything about it except she was wonderful. When she came for the audition what she did was so beautiful she made me cry. The part is incredibly difficult and makes great demands. She was equal to all of them.Neil McKinven, as Adam Smith, is someone I have worked with before, in Celestina I think. That was certainly, for all kinds of reasons, one of the unhappiest rehearsal processes I have ever been involved in. Mainly, it has to be said, because my wonderful partner Susie had suffered a stroke just before it started; and then was diagnosed with a brain tumour just before the show opened. In the midst of all this, it was lovely to work with Neil.I know they are three incredibly gifted artists. I can’t wait to work with them.
The Tree of Knowledge is at the Traverse Theatre from 8 - 24 December.
www.traverse.co.uk.

The Tree of Knowledge Cast Announced: Gerry Mulgrew as David Hume, Joanna Tope as Eve and Neil McKinven as Adam Smith.

From Jo Clifford’s blog.

There’s always this amazing moment when the play, that has really only had a kind of imaginary existence until this moment, starts to take on flesh and blood.

I love it. It makes me so excited: because I can never “see” characters in my imagination. 

I can only hear them. And hear them speaking in very definite tones of voice, to be sure: but I never want these tones of voice to be duplicated by the actors.

Because the mainly wonderful part of theatre making is that I create a script, using all my sensibility and skill, and give it to the actors, and the director, and the lighting designer, the set designer, the costume designer, the sound designer, the stage manager - all these amazing gifted people. And they apply all their sensibilities and all their skills and if we manage to work well together they just enrich the script immeasurably.

And always in ways I never anticipated.

And then the audience come along and do the same…

The actors are: 

Gerry Mulgrew, as Hume, who is so alive and full of life’s joys in his presence and who I wanted to work with for years and years.

Joanna Tope, as Eve, who was in one of my radio plays, and I can’t remember which, or who she played, or anything about it except she was wonderful. When she came for the audition what she did was so beautiful she made me cry. The part is incredibly difficult and makes great demands. She was equal to all of them.

Neil McKinven, as Adam Smith, is someone I have worked with before, in Celestina I think. That was certainly, for all kinds of reasons, one of the unhappiest rehearsal processes I have ever been involved in. Mainly, it has to be said, because my wonderful partner Susie had suffered a stroke just before it started; and then was diagnosed with a brain tumour just before the show opened. In the midst of all this, it was lovely to work with Neil.

I know they are three incredibly gifted artists. I can’t wait to work with them.

The Tree of Knowledge is at the Traverse Theatre from 8 - 24 December.

www.traverse.co.uk.

Filed under Jo Clifford Gerry Mulgrew Joanna Tope Neil McKinven The Tree of Knowledge Traverse Theatre Company David Hume Adam Smith