Posts tagged Peter Arnott
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Don’t you think it’s strange?
Here’s a song we’re working on this afternoon…all together now:
Don’t you think it’s strange?
We are… Islands of order
In oceans of entropy
A concentrate of space time
That isn’t very likely
Molecular arrangements
Evolving sporadically
And Biased chains
Of crystaline identity
Bacterial colonies
Of dubious propinquity
And a lousy pack of bastards
Of our very own paternity
Don’t you think it’s strange
To be alive?
When we are…
(repeat until the end of time)
(Source: esrcgenomicsforum.blogspot.co.uk)
Saying It Out Loud
I’ve been quiet on the blog front of late…partly being away, but mainly because this has been a record of stuff I’ve been reading and I’ve started writing now. In fact, next week I go into rehearsals for Talent Night at The Fly Room…a one off genomic revue we’re doing at the Traverse on Thursday March 29th.
The idea is to road test some ideas…see what the response to the material I’m generating is…first by the actors, then an audience. It’s essential R and D for the play I’m writing, really.
I’m breaking my blog silence though, because I’ve been led to read something which I will be using in the script for Talent Night, but which illustrates perhaps my small contribution to the sociological arts embodied by the Genomics Forum.It’s what I call the Lasagne test and involves, once again, reading aloud.
Say there is an upcoming publication by researchers from Oxford and New York Universities on a human bio-engineering response to climate change. In the test, the bright young male sociologist takes his wife or girlfriend to a nice Italian restaurant. (I say male because only a male could have had the following idea).
He then reads this aloud to his girlfriend over the pasta course:
“Human ecological footprints are partly correlated with our size. We need a certain amount of food and nutrients to maintain each kilogram of body mass. This means that, other things being equal, the larger one is, the more food and energy one requires. While genetic modifications to control height are likely to be quite complex and beyond our current capacities, it nevertheless seems possible now to use preimplantation genetic diagnosis to select shorter children…what do you think, honey?”
If at this point, if he is picking lasagne out of his hair, which I confidently predict he will be, then it’s probably best not to publish.
(Interestingly, the making the population smaller option was also explored in 1962 by Mr Fantastic when he shrank the occupants of Planet X to save them from an asteroid in Fantastic Four 7 - only here the sociological narrative was more thought through.)
Read things aloud, folks…it’s a great way to test stuff. See you at the Traverse on March 29th.
From Peter Arnott’s Genotype blog
I’m exploring origins today…Reading Erwin Schrodinger’s seminal text from 1944 “What is Life?”, which seems, reading it at the end of my residency, eerily prescient of the genomic view of life…including the downgrading of the idea of “genes” in favour of a more holistic, four dimensional “thing in itself” version of that molecule of heriditary which can have existerd no more than theoretically for his audience in 1944…and harvesting quotations therefrom fro my March 29th event at the Traverse…
but I also came accross the above link to the very first Body/SciFi movie, J Searle Dawley’s 12 minute long adaptation of Frankenstein from 1910. Well worth a look…particularly at the “creation sequence” about four minutes in. Frankenstein doesn’t re-animate a corpse here, he grows a body from scratch…or rather, soup…and the phenotype self assembles behins a closed door…in a pot.
Oddly, that’s roughly how we might actually do it.
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.
Coolest Global Warming Ever
From Peter Arnott’s Genotype blog
Just a quick one…a link to a wonderful site I’ve just, to my shame, come across. A detailed graphic imagining of a globally warmed world (called Dubia, after George Dubya…)along with a bit of biological speculation by Chris Wayan.
And here, as a taster, is Europe…looks great, huh? This is what the world outside the library looks like, no question…
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.
Beginning with M
From Peter Arnott’s Genotype blog
http://www.ed.ac.uk/about/video/lecture-series/changing-world/stem-cells
A while ago I blogged about thinking of genomics in terms of things beginning with “M”. Memory was in there…so was machine…so was “mastery”. The above link is to a lecture given at Edinburgh University by Professors Siddharthan Chandran and Charles ffrench-Constant on Tuesday 9 November 2010.
These guys have just hit the news in a big way. Using the same kind of adult pluriopotent stem cells that gave us Dolly the Sheep - (that was breast tissue used to create a whole clone…breast…Dolly…Dolly Parton…breast…get it? Scientists are such BOYS!!!) - but, HUMAN adult pluripotent stem cells derived from human skin…and they’ve made human brain cells. Yup. Brain cells.
The medical potential of regenerating healthy brain tissue is literally mind blowing…many of the most devastating brain disorders from stroke injury to motor neurone disease and multiple sclerosis are based on damage to particular cell locations or cell types. This technology could be targeted to address these problems with only the most minor surgery. The same is of course true of every other organ, muscle…
Now…they haven’t made a brain, Dr Frankenstein…yet…But we do have to add an M to our list. “Miracle.” Honest.
Check out the lecture above.
Meanwhile, on the “memory” front, news from Australia that it took 24 million generations for something the size of a mouse (which was the size of the common ancestors of all today’s mammals before the dinosaurs pegged out) to evolve into something the size of an elephant…once the dinos were out of the way. This is being published in the Proceedings of the National Academy in the US…and when there’s a link available I’ll paste it.
http://medicalxpress.com/news/2012-01-health-inequalities-imprinted-dna.html
And mastery…or destiny, anyway…research in Glasgow describing the epigenetic poverty trap. Apparently the level of methylation of DNA in poor people means that poverty really does kill you, your children and your children’s children.
Put all this together - all these things beginning with M - and what do you get? No. I’m really asking.
Peter Arnott is Resident Playwright at the 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.
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.
Aristotle in the Cheeseshop
From Peter Arnott’s Genotype blog.
“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 bothered 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 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.
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.
Living in the Bacterial World
From Peter Arnott’s Genotype blog.
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 wepersist 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 beingsomething 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.
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.
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.
