Posts tagged Genomics

From Peter Arnott’s Genotype blog

Well…the last act of my residency (per se) is on Thursday Night at the Trav…and, having just played some blues harmonica loud enough to disturb some scholars…sorry…I can safely say that “Talent Night in the Fly Room” isn’t what I expected it would be when we started rehearsal.

We started last Monday with roughly ninety pages of material…three hours worth or so…mostly quotations from the most important sources I’ve been looking at, all the way from TH Morgan to Erwin Schrodinger…to Max Delbruk…and a couple of songs and sketches, sure.

But under laboratory conditions text is tested to destruction…the reality test of having actors in the room with the ideas, and the anticipation of an audience being there alters the shape and feel of the work, and forces it towards reality…or at least, into the version of reality that we can share, we’re down to what I hope is a tight little, right little show.

Something like the laboratory process of rehearsal is going to be the thrust of a more academic presentation I’ll make at the Genomics Conference in London at the British Library in April: to wit, have I learned anything about the way the specifically dramatic arts…(as opposed to music or poetry) relate to scientific ideas and processes?

Well, maybe. In the meantime, the show is the thing. And here is the lyric to a little tango number I’ll be doing:

If you want spider silk from goats
You tweak the genome
If you want diesel fuel from oats
Just use the genome
If you’re feeling all alone
There’s no one we can’t clone
From any chromosome
Just ask the genome.

We make brain cells from your armpit
And the genome
If you’re sick we’ll make you fit
We’ll use the genome
We’ll insert those nano-bots
And end up which god knows what
Don’t put up with what you’ve got
Call in the genome

Nothing comes from nothing
Not even genomes
All history is written
In our genomes
Material machines
Tell you what existence means
All your fears and all your dreams
Are in your genome

Miracles are every day
Just provided you can pay
Though the price might be obscene
Depending on your genes

All the birds and all the bees
Have all got genomes
Every virulent disease
Has got a genome
We’ve all got the same ancestor
Who was a such a wise investor
In the chemical congestor
Of the genome

Click here for more information on Talent Night in the Fly Room, Peter’s Genomics inspired revue at the Traverse on Thursday 29 March. 

(Source: esrcgenomicsforum.blogspot.co.uk)

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)

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.

Click here for more information on Talent Night in the Fly Room, Peter’s Genomics inspired revue at the Traverse on Thursday 29 March. 

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.

Click here for more information on Talent Night in the Fly Room, Peter’s Genomics inspired revue at the Traverse on Thursday 29 March. 

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.

From Peter Arnott’s Genotype blog.

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 genetics 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 cyanobacterialsurvival, 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 beenmuch, 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 abovwe so below…uncertainty at every scale, convergence and homogony and happenstantial selection are evetrywhere 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.

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