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, 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.


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.


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.


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.