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.

Tuesday, 28 June 2011

Genomics Come all Ye to the Traverse Bar

So our first meeting is on Thursday. Our first "experiment". To be honest, a good part of the "experiment" is whether anyone shows up...or it becomes a meeting about meetings...

Anyway, I'm bringing along some juicy things to talk about, all connected to the same question -

Whose View Of Life?

I blogged earlier about Darwin, and Sean Carroll...and their view of life. The question is...what's yours? Does it depend which Church Pew or Lab Bench we sit at when it comes to assigning a sense of value to what science tells us is accidental? Where do you look for morality? Is there a gene for it? Or a kinship equation?

Let me put it this way:

I live in the world. We all live in the world. More or less inadequately. (Or maybe that’s just me...or Scotland). We do what we do. We do our best.

It’s not enough. It’s never enough. For our families, our societies or for ourselves. Never.

Why not? What, exactly, is the matter with us? Is there a design flaw? Or if we evolved this way, what’s that about? Is the lacking we sense in ourselves something we're stuck with...like tonsils?

We worry away at this. That’s why we build things, make things, write things…it’s why we rape continents, start wars, paint pictures…sequence genomes…It’s all questioning and not answering…why be human? Why live? Why do we die?

We attempt lots of answers to the same damn questions over and over again. Our attempts are what we call “culture” . That's why you will find exactly the same damn questions in every damn blog…in every damn thesis about every damned thing…and in the Epic of Gilgamesh, the first story ever written…

Every answer we come up with, we secretly suspect, is a lie, a con, something (anything) to get us through the night. We always intuit there's something more.

I suspect that’s roughly what Einstein did to get him through the night…and Mother Theresa…mind you, I think that’s what Himmler did too…
Why do we DO that?

The search for a reason…a shared search...however Hopeless…and not always Harmless. I think that’s what “genomics” is about for the non scientist (and the scientist)…especially as it aspires to being a science of “everything”

Anyway, I'm going to bring along some thought provoking hunks of text I've come across in the hope that we can start an argument...then go away and write FURIOUS poems and plays about it all.

Do come.

Traverse Bar, Thursday 30th, 2pm

Tuesday, 21 June 2011

Traverse Bar Thursday 30th June 2pm

Activity…all of this activity…on and on we go, trying to engage in good faith with all that we encounter…and what does it mean? What is it for? Where do we search for meaning to our lives? And why do we do that at all? Is that search built into us? What do we mean by that? Is it soul, God? Is it something that evolved in us, this consciousness lark? And if it is, is it adaptive? (That is it, does it work for us? And if it HAS been working for us so far, do our CO2 emmissions mean it's not going to be party time much longer?)

Not every capacity we evolve is good for us…We evolved the predisposition for cancer and heart disease as well as the capacity to run, jump and enjoy chocolate…

(We must have done…where does it come from otherwise?)

We, like every other phenotype on earth, are evolution making the optimal (naturally selected) use of available materials. The genome…which is nothing more than the sum of our stringy chromosomes considered holitically…is the bit we inherit directly from our parents…and it defines our limits and capacities.


Well, there are genetic fundamentalists as well as religious ones…but most of the things I’ve been reading of late would say “Probably not”

There is also memory…and cultural memory…

Mind you, some people put “cultural evolution” right alongside the physical…

Hum hum hum

Some people (I’m not one of them) have even created a unit of cultural inheritance and learned characteristics and abilities…Memes they call them…

Which is a metaphor that makes a similar sounding word to “genes” as far as I can make out…and not much else.

Whatever the metaphors, we are, a fair chunk of us anyway, defined by our inheritance…

So what about free will and all that?

Again, fundamentalists of all stripes don’t believe in any such thing…or rather, the religious fundamentalists argue that only God is truly free, while genetic fundamentalists argue that our bodies and the lives we live inside them are incidental to the immortal and invisible will to duplicate of our God like genomes…

I get the increasing sense the deeper I plunge into all this that there is a big old disconnect between how professionals in the gene trade think, and how the rest of us struggle to keep up.

I’ve no idea how I’m doing in bridging this gap…and would like to talk about it to the two constituencies of which I am professionally now a part….

One is theatre and scribbling folk who like to think about science, the other is science folk…who like to scribble...or read what other folk scribble

These conversations are the point of my being here.

If you fancy joining in…I’m starting a gene therapy group meeting on the last Thursday of every month in the Traverse bar. First one as above

I’ll bring along some stuff I’ve been reading…and just throw it in the mix…elicit some responses from whoever turns up…some of which I want to publish online via the Human Genre Project…the neat science and poetry website started by Ken MacLeod, my illustrious predecessor and science fiction novelist.

We can talk about science fiction too, if you like. Sometimes…and increasingly at the moment…I think it’s the only genre of modern writing that’s about what’s really going on.

Tuesday, 14 June 2011

The Metaphor in Question

"I live in a world of poetry," she said. "Everything seems significant to me. Everything has meaning. It's what gets me into trouble"

Una Persson in The Entropy Tango by Michael Moorcock.


History, besides BEING a metaphor
Is MADE of metaphors.

I want to EMPHASIZE that.

Evolution is a metaphor -
one that Charles Darwin
much resisted.

The word does not appear
In the eighteen fifty-nine
"Origin of Species"

("The survival of the fittest"
Didn't turn up till the fifth edition
and there as a quotation
from the work of Herbert Spencer)

Being classically educated
Darwin knew that "evolution"
means "a rolling out from"

He didn't like that a bit

Implicit in the word
is the idea that the organic present
has rolled
- progressively, Whiggishly
and inevitably –
from out of the past.

That’s what his predecessors (and successors)
Meant by the use of that metaphor
That's not what Darwin thought he saw
In the garden at Down
Or the volcanic lumps of the Encandatas

Niether did he see
The History of Life
As a ladder
From lower to higher

On his "entangled bank"
all life,
plant, insect, mould and duck
was exactly as "evolved"
as every other "form most beautiful"
Every bit as lovely...
Every bit as interesting


He didn't like his title either.

"Origin of Species" was a
publisher's echo of the earlier
(Best selling)
"Vestiges of Creation"
Robert Chamber's anonymous blockbuster
of 1844
To which, many people thought,
"Origins" was a sequel.

In Vestiges, Chambers talked
of "evolution"
of higher, better forms
succeeding, lower, simpler breeds
till at the pinnacle stood man
(white, male, possibly Scottish)
with mutton chops and a waistcoat -
a monkey's paw
fiddling in his pants

On the publication of Origins
(which didn't sell like hotcakes - or Vestiges)
Huxley, Darwin's bulldog, snapped at bishops.

But Huxley never accepted -
Descent with modification
Naturally selected in the struggle for existance -
as the engine of life's changes

But he, like Herbert Spencer,
Andrew Carnegie, and, yes
Adolph Hitler
"believed" in "Darwin"

Darwin the metaphor, that is.


In the beginning, then
Man created Darwin
just as Man created God

as a metaphor
out of metaphors

as a belief
a cause
an explanation


The Revd Adam Sedgewick
Who taught Charley his geology
broke his pupil's heart
when he wrote to Darwin
how he loved him
and how he hated his ideas.

But Sedgewick hated "Vestiges" more,
Despised it,
Assuming the anonymous author
to be a woman -
Like Eve, seeking out of vanity
For things she shouldn't know.

(Original Sin, also
Is a metaphor
But not for "knowing" No.
For "meaning"

Because till Eve took the apple
Nothing had a meaning
Everything had names for what they were.

So there was no need for metaphors
In the Garden.)


Pace Aristotle,
a human being (since Eve)
is a "meaning" reed

It must have happened first in Africa
Possibly with a yam or a banana

We've been in trouble ever since.

Meeting Up

Anyhoo…the next bit of my masterplan is to start meeting people and talking about this. If there’s anybody out there reading this, this means you…

Last Thursday of the month…June 30th…2pm … and the same in succeeding months…excepting August and December

I want to convene an informal group discussion around key texts I’ve dug up…Trav staff, writers’ groups, anyone else I can dig up…

(Burke and Hare made their contribution to the materiality of bodies and knowledge just round the corner, don't ya know)

The idea being to run a few of these ideas past and through some craniums (crania?) other than mine…to talk about this stuff not as people who UNDERSTAND genomes necessarily…

Just people who’ve GOT one…and are interested in what it means.

I’m posting a sort of poem I’ve written with some first thoughts a bit later on today…and we’ll see what kind of conversations we can get going.

Thursday, 9 June 2011

Last for now on Sean Carroll’s “Endless Forms most Beautiful”

Carroll’s essential tool kit genes…Hox Genes they’re called (for reasons he explains a lot better than I can…)

Anyway, it turns out these clever little monkeys have been around for what is effectively forever…so all the variations of all the bodies we see around us from wasps to whales…were sort of…(and here I’m getting foggier and need help) …potentially already there too.

In embryology (which is suddenly REALLY interesting again, having not been sexy for ages, according to Carroll) what these clever folk are finding out at the moment is that building bodies is largely a matter of time and space…of the same Hox Genes, the same toolkit… being switched on and off in the earliest stages of development in ALL animal embryos…so that your leg ends up THERE (if you’re a fruitfly) as opposed to THERE (if you’re Simon Cowell)…

And that switching OFF is possibly more important more of the time than switching ON.

(No…don’t put a leg there…or there…or there…or there…wait for it!…NOW)

This may be just bonkers, but doesn’t that view of life (as lots of no-es punctuated by well placed yes-es) rather tend to argue, or lie on similar lines, for and to Stephen Jay Gould’s proposed “inversion” of the cone of diversity as alluded to in my last post?

That evolution…natural selection…progressively favours simplicity? Maybe maybe.

That evolution is an arrow with no built-in direction? Bet your shirt on that one!

And doesn’t (as Carroll also thrillingly describes) the evolution of the same parts (from the same genes being expressed) into wings in one animal and gills in another…tend to point the same way?

That complexity has always BEEN there…

Just a thought.

Leading (me anyway) to lots of other thoughts…which I may berate you with when they’ve stopped swirling around my cranial cavity…

Meanwhile I hope that someone who’s cleverer than I am in these matters is reading this rubbish so they can electronically belt me over the head and tell me to stop being silly.

Or give me the Nobel Prize for my insight…either will do.

Next time...a bit of a poem...and almost immediately...a call to conversation!

Tuesday, 7 June 2011

Welsh Wonders

Another recommendation for reading…Stephen Jay Gould’s “Wonderful Life”…not an essay on the cinema of Frank Capra…but a radical, readable exposition on the fossils of early Cambrian creatures found by Thomas Walcott in the Burgess Pass in the Rockies more than a hundred years ago now…and reclassified in the 70s and 80s by Simon Conway Morris inter alia…

Gould uses the bizarre (to us) features of these creatures to propose a radical new model for evolution…that instead of the story of life on earth being one of simplicity evolving into complexity…we all of sudden STARTED complex…and have been getting simpler ever since…

(Conway \Morris’s own book on the Burgess Fauna – and more recent discoveries in China - The Crucible of Creation, I also recommend. Morris thinks that Gould’s use of the fossils to turn all of conventional evolutionary thought on its head is “premature” – which is science speak for “bollocks”)

I love a good fight, me.

A wee note…Cambrian means “Welsh”…because it was in Wales that rocks of that age were first ordered by geologists…though they didn’t know then WHAT age…and take a peek at Hallucigenia or Anomalocaris …(two of the oddities found by Walcott) and you think:

“ Wales…hum…isn’t that where they’re making Doctor Who?”

Thats Opabina with five eye stalks up there by the way...and Hallucigenia is the wee fellow with the spines bottom right...

Friday, 3 June 2011

Genes Forever

I’ll try to paraphrase some more of the cool stuff I’ve been reading…

Sean Carroll talks mostly in “Endless Forms Most Beautiful” about ten or so “Hox” genes…which biologists have been rather flabbergasted to discover are shared by ALL animals…everything…from flatworms to Simon Cowell.

What all these animals sharing the same essential body building tool kit means…from an evolutionary point of view…is that the common ancestor of all these bodies…phenotypes…already HAD many of the essential ingredients all animal life would ever need…genotypes…long before they were actually needed.

(It is also decisive proof, if more were needed in this day and age, that they all HAD a common ancestor…so yah boo to the Creationists)

That is, before the Cambrian Explosion 550 million years ago, when complex animal forms suddenly appear in the fossil record…many of the essential genes that make the amino acids that make the proteins that make the eyes and scales and legs and teeth and kidneys were already kicking about in the biomass - which till then consisted almost exclusively of the kind of blue green slime you clean off an old toilet…

(By the way, life on earth is still overwhelmingly bacteria…as it was exclusively in the beginning…and shall be exclusively again for almost all of the hereafter…till the sun blows up anyway)

Well WHY for goodness sake? Why have all the genetic material you need for building bodies, when there aren’t any bodies to build yet???

There is no “why”…is the answer that whispers on the pre-historic wind…that you can’t hear because there aren’t any trees for it to whisper through…

Just cos…

All of which I think goes to show that if the universe really was put together by a watchmaker, he wasn’t just blind…as Richard Dawkins would have it…but blind drunk.