Poetic Bacteria: the Gene-ius of Art!

We all know the expression Art imitating life, or even life imitating art but it is going above and beyond for life to incorporate art. Yet this is what one poet has done: He has created an original piece of "living poetry" in a lab in Canada.

According to the BBC Poet Christian Bok has encoded his verse into a strip of DNA and had it inserted into a common bacterium, E.coli.

Dr Bok used cryptography to embed his poem into the genetics of the bacterium, devising a chemical alphabet in which each letter is represented by a specific triplet of nucleotides (Adenine, Thymine, Cyttosine and Guanine). So, for example, the nucleotide sequence "ATA" codes for the letter "y" and GTG stands for the letter "n".
This enabled him to design a novel gene called X-P13, which was constructed specifically for the project. The poem's opening words, "Any style..." translate as ACG(A) GTG(n) ATA(y) AGT(space) AAG(s) TGC(t) ATA(y) GCC(l) TAT(e) in his gene's DNA sequence.

Dr Bok has no formal scientific training, but he taught himself molecular biology and computer programming for the purpose of this project.

Similar biochemical feats have been achieved before. American scientist Dr Pak Wong encoded the lyrics to It's a Small World After All into a strand of DNA and lodged it inside the bacterium Deinococcus radiodurans.

And when Dr Craig Venter, of the J Craig Venter Institute (JCVI) in Maryland and California, created the world's first manmade bacterial genome, he embedded his own name and those of his colleagues into its DNA; alongside quotes from James Joyce and from the Nobel prize winning physicist Richard Feynman.

But Dr Bok, who teaches in the department of English at the University of Calgary, has gone one step further than just encoding his code into DNA: he has induced his laboratory bacterium to give its own bio-poetry response.

DNA is essentially a template for constructing proteins. Proteins are strings of amino acids. There are 24 amino acids, each is represented by a triplet of DNA nucleotides. These are coded in reverse on the DNA strand. DNA is used to create Messenger RNA which is then used to create specific proteins.

Dr Bok's chemical cryptography is designed to work on two levels. Not only did he devise a cipher to link letters of the alphabet to specific nucleotides, but he also designed a second cipher to allow the ensuing protein to be decoded back into a brand new poem, by assigning a different set of letters to specific amino acids.

For example his first poem's opening words "Any style", once encoded into DNA, instructs the cell to build a protein that starts with the following amino acid string: threonine, valine, isoleucine, serine, lysine, cysteine, isoleucine, alanine, tyrosine, which can in turn be decoded to spell out the start of the bacterium's new poetic response "The faery..."

His scientific collaborator at the University of Calgary, Professor Sui Huang, has now succeeded in implanting the poem gene as a free floating chunk of DNA into E. coli and witnessed the bacterium express its own poetic protein response. His hope is that once embedded into the genetics of D. radiodurans, his biochemical text could continue to reproduce for billions of years - outlasting any other human artefact. However, he has no intention of releasing it into the wild.

"The only legacy we will leave is the background radiation of nuclear waste and the ecological and geological effects of climate change and that is not an appropriate one. By genetically engineering a poem into Deinococcus radiodurans I am producing something that will last over epochal time" he said

Dr Julian Parkhill of the Wellcome Trust Sanger Institute was sceptical of the chances for literary immortality. "His poem would be rapidly removed by natural selection, as it would confer no benefit on the host bacterium," he said. "Natural selection as literary criticism".

Professor Huang conceded that this is a very real possibility. "If the poem protein conveys even a slight disadvantage on the bacterium, the gene could be kicked out over time," he said.

"We don't know what the selection pressure would be for it to be kept, if it isn't too much of a burden the gene might stay".
And he argued that there was a scientific value to the project. "It shows how biology is just like information science," he said.
"There is already a poetry to nature and I see a parallel with the Xenotext project"

Well there you have it. Make of this story what you wi

Erdélyi töredék - Kovács András Ferenc

Transylvanian fragment

As on the walls of Transylvanian churches
Fresco fragments, tattered-shattered paintings,
Now long forgotten even by the Lord,
No longer tended by the nimble sunbeams -
Of such will we be: invisible,
Lying hidden in time’s corroding lime
Not even God knowing if we still exist,
Or how, why, under how many blind strata
Our callused faces lie, hoping for the heroic
Resurrection of wrinkles in a tear-dance or smile,
Should it subside without too much damage -
We’ll be like so many threadbare legends,
Salvaged pagans, meek martyrs and saints,
And hells, heavens, doomsday judgements,
Calvaries suffered and then hushed up,
And remnants of the images of Christ -
All these we’ll be, details merely, and crushed:
Not infant babes, Eastern sages or Marys,
But broken debris, misfortune’s odds and ends:
Not lost battles, but dark savage hoofs,
Retreating heels, flags, wounds and crucifixes -
All these we’ll be: hands raised for blessing,
Sweeping swords through the cool empty air,
Truncated tribes, nations, bodies and limbs,
And the wings of a hatchet or holy ghost
Shimmer above: eyes gouged, torn creases,
Fabrics and skin, ownerless aureoles,
A tossed up pile of haphazard bedlam -
These we’ll all be: crumbling artworks
Yet worthy exhibits within the confusion -
Who will explain our missing pieces,
Who will restore them to coloured wholeness,
Who will one day recognise in us
The signature of an unknown master?

(Translated by Dornacher, Kinga; Humphreys, Stephen)

This magnificent poem was sent to me by my friend and muse Saszet Agnes. It appears on a site called Babelmatrix, a site dedicated to bringing the literature of the Visegrad nations (Hungary, Poland and the Czech and Slovak republics) in translation to a wider audience.

It is a site well worth visiting if you have a love of literature.

A Philosophy Poetry Challenge -With great prizes!

I've decided that enough is enough: there are a number of intellectual pursuits that I simply can't get my head around: calculus and pholosophy are two that spring to mind imediately. While 'm sure that I can overcome my calculus block on my own I fear that there is no chance that I will ever be able to sit down and read the works of Schopenhauer, Hegel, Nietzsche or Lacan...

Gems of knowledge such as this by Lacan are a mystery to me: A geometry implies the heterogeneity of locus, namely that there is a locus of the Other. Regarding this locus of the Other, of one sex as Other, as absolute Other, what does the most recent development in topology allow us to posit?

Unless I can get my head around this I fear that the likes of Slavoj Zizek and Jacques Derrida will simply remain tedious pricks with no more relevance to the world than Jordan.

I therefore need help to overcome this block. Readers are therefore asked to explain philosophical concepts in verse form. All forms of verse are acceptable but the shorter the poem, the better - Haikus are particularly welcome!

There will of course be prizes for the best poems. The winner will receive a copy of the collected novels of Flann O'Brien. Second prize is the Third Policeman on audio book (read by the actor who played Bishop Brennan in Father Ted!).. Also up for grabs are three copies of the Poor Mouth (The novel that gave this blog its name)

All you need do is leave your poem as a comment... or poems, - you can enter as often as you like! . Closing date is 31 January

And now for some more Mad Madge

Again it's been a while since I posted a poem by 17th century Essex girl Margaret Cavendish (aka Mad Madge). Luckily for her posterity she was also the Duchess of Newcastle otherwise her great works may have been lost to the world. One of her favourite subjects was atomic theories. Here is a poem of hers dating back to 1652

The Bignesse of Atomes

MHEN I say Atomes small, as small can bee;
I mean Quantity, quality, and Weight agree
Not in the Figure, for some may shew
Much bigger, and some lesser: so
Take Water fluid, and Ice thats firme, [5]
Though the Weight be just the Bulke is not the same.
So Atomes are some soft, others more knit,
According as each Atome's Figured;
Round and Long Atomes hollow are, more slacke
Then Flat, or Sharpe, for they are more compact: [10]
And being hollow they are spread more thin,
Then other Atomes which are close within:
And Atomes which are thin more tender far,
For those that are more close, they harder are.

If you enjoyed this offering from Mad Madge on atomes then you can find an elephant's sufficency of her scientific poems here

Two poems by Alicia Partnoy

Survivor

I carry my rage like a dead fish,
limp and stinking in my arms.
I press it against my breast,
whisper to it,
people on the streets flee from me …
I don't know: is it the smell of death
that makes them flee
or is it the fear
that my body's warmth
might bring rage back to life?


Testimony

This microphone
with its cable coiling around it,
bows to me.
I walk up to it,
open my eyes
open
my book
open
my mouth.
That’s right, I open my mouth wide
and begin my story.
They say
I speak too softly,
that I am practically mumbling,
that they can’t hear
the screams piercing.
I open
my memory
like a rotten cantaloupe.

They say
I have not managed
to forcefully convey the pitiless rage
of the cattle prod.
They say that in matters such as this
nothing must be left
open
to the imagination or to doubt.
I take out
the Amnesty report
and begin speaking through that ink.
I urge: “Read.”
I, in my turn, coil around
my bowing accomplice,
this microphone.
I urge action as a prescription,
information as an infallible antidote
and, one every knot is untied,
I recite my verses.
I resist. I am whole.

This microphone
with its cable coiling around it,
bows to me.

Activist http://en.wikipedia.org/wiki/Alicia_Partnoy Alicia Partnoy spent over two years in detention during the Argentinian Dirty War, during which she was beaten, starved and sexually assaulted. Her novel The Little School is based on her experiences.

Forough Farrokhzad - Friday

Forough Farrokhzad (1935-1967)

My silent Friday,

My deserted Friday,

My Friday: sad, like old abandoned lanes.

My Friday:

The cold day of ailing, idle thoughts,

Moist day of long, evil bore,

loaded with grief,

grief for my faith, for my hope,

Oh, my Friday, this renouncing day

…

Oh, this empty room,

Oh, this gloomy house…

These isolating walls from attacks of youth,

These collapsing roofs on my slight daydream of light,

In this place of lone, reflection and doubt,

In this space of shade, text, image and sign.

My life, like a mysterious river,

streamed into those silent, deserted days,

so calmly with a lot of pride.

My life, like a mysterious river,

Streamed into those empty, gloomy rooms,

so calmly with a lot of pride.

Translation: Maryam Dilmaghani From the website Forough Farrokhzad The Sad Little Fairy

A bit of verse by a 17th century Essex girl

http://en.wikipedia.org/wiki/Margaret_Cavendish Margaret Cavendish (1623-1673), Duchess of Newcastle, was a prolific writer and poet. she was also interested in science produced several theories, including one which claimed that some people lived longer because their atoms were packed closer together. Anyway here is one of the Colchester Lass's musings on the nature of matter. Enjoy!

What is Liquid?

All that doth flow we cannot liquid name
Or else would fire and water be the same;
But that is liquid which is moist and wet
Fire that property can never get.
Then 'tis not cold that doth the fire put out
But 'tis the wet that makes it die, no doubt.

Forough Farrokhzad - Window

One window is sufficient
One window for beholding
One window for hearing
One window
resembling a well's ring
reaching the earth at the finiteness of its heart
and opening towards the expanse of this repetitive blue kindness
one window filing the small hands of loneliness
with nocturnal benevolence
of the fragrance of wondrous stars
and thereof,
one can summon the sun
to the alienation of geraniums.

One window will suffice me.

I come from the homeland of dolls
from beneath the shades of paper-trees
in the garden of a picture book
from the dry seasons of impotent experiences in friendship and love
in the soil-covered alleys of innocence
from the years of growing pale alphabet letters
behind the desks of the tuberculous school
from the minute that children could write "stone"
on the blackboard
and the frenzied starlings would fly away
from the ancient tree.

I come from the midst of carnivorous plant roots
and my brain is still overflowed
by a butterfly's terrifying shriek
crucified with pins
onto a notebook.

When my trust was suspended from the fragile thread of justice
and in the whole city
they were chopping up my heart's lanterns
when they would blindfold me
with the dark handkerchief of Law
and from my anxios temples of desire
fountains of blood would squirt out
when my life had become nothing
nothing
but the tic-tac of a clock,
I discovered
I must
must
must love,
insanely.

One window will suffice me
one window to the moment of awareness
observance
and silence.
now,
the walnut sapling
has grown so tall that it can interpret the wall
by its youthful leaves.

Ask the mirror
the redeemer's name.
Isn't the shivering earth beneath your feet lonelier than you?
the prophets brought the mission of destruction to our century
aren't these consecutive explosions
and poisonous clouds
the reverberation of the sacred verses?
You,
comrad,
brother,
confidant,
when your reach the moon
write the history of flower massacres.

Dreams always plunge down from their naive height
and die.
I smell the four-petal clover
which has grown on the tomb of archaic meanings.

Wasn't the woman
buried in the shroud of anticipation and innocence,
my youth?

Will I step up the stairs of curiosity
to greet the good God who strolls on the rooftop?

I feel that "time" has passed
I feel that "moment" is my share of history's pages
I feel that "desk" is a feigned distance
between my tresses
and the hands of this sad stranger.

Talk to me
What else would the one offering the kindness of a live flesh want from
you?
but the understanding of the sensation of existence.

Talk to me
I am in the window's refuge
I have a relationship with the Sun.

Translation: Leila Farjami

This website is dedicated to Forough. It is well worth a visit. It is the source of this and other Farrokhzad poems that have apeared here.

Gracefully she approached - Shimin Bebhahani

Gracefully she approached,

in a dress of bright blue silk;

With an olive branch in her hand,

and many tales of sorrows in her eyes.

Running to her, I greeted her,

and took her hand in mine:

Pulses could still be felt in her veins;

warm was still her body with life.

"But you are dead, mother", I said;

"Oh, many years ago you died!"

Neither of embalmment she smelled,

Nor in a shroud was she wrapped.

I gave a glance at the olive branch;

she held it out to me,

And said with a smile,

"It is the sign of peace; take it."

I took it from her and said,

"Yes, it is the sign of...", when

My voice and peace were broken

by the violent arrival of a horseman.

He carried a dagger under his tunic

with which he shaped the olive branch

Into a rod and looking at it

he said to himself:

"Not too bad a cane

for punishing the sinners!"

A real image of a hellish pain!

Then, to hide the rod,

He opened his saddlebag.

in there, O God!

I saw a dead dove, with a string tied

round its broken neck.

My mother walked away with anger and sorrow;

my eyes followed her;

Like the mourners she wore

a dress of black silk.

The Necklace - Simin Behbahani

Touched and deranged,

downcast and sad;

with veilless face,

and no chador;

heedless of arrest,

careless of the Guards.

For eyes she has

two red grapes

fallen off the bunch.

She's mad,

stark staring mad;

she's lost,

lost to herself,

lost to the world.

A straw in the wind,

she's drifting around.

A graveless body,

she's deadened to the world.

Round her neck she has

a pair of teardrops, a curse:

of a dead soldier boots

with laces tied together.

"What's that?", I said.

"My son", she said,

"sitting on my shoulders

with his boots on."

Forough Farrokhzad - To My Sister

Sister, rise up after your freedom,
why are you quiet?
rise up because henceforth
you have to imbibe the blood of tyrannical men.

Seek your rights, Sister,
from those who keep you weak,
from those whose myriad tricks and schemes
keep you seated in a corner of the house.

How long will you be the object of pleasure
In the harem of men's lust?
how long will you bow your proud head at his feet
like a benighted servant?

How long for the sake of a morsel of bread,
will you keep becoming an aged haji's temporary wife,
seeing second and third rival wives.
oppression and cruelty, my sister, for how long?

This angry moan of yours
must surly become a clamorous scream.
you must tear apart this heavy bond
so that your life might be free.

Rise up and uproot the roots of oppression.
give comfort to your bleeding heart.
for the sake of your freedom, strive
to change the law, rise up.

The Scholars

William Butler Yeats

Bald heads forgetful of their sins,

Old, learned, respectable bald heads

Edit and annotate the lines

That young men, tossing on their beds,

Rhumed out in love's despair

To flatter beauty's ignorant ear.


All shuffle there, all cough in ink;

All wear the carpet with their shoes;

All think what other people think;

All know the man their neighbor knows.

Lord, what would they say

Did their Catullus walk that way?

Forough Farrokhzad - The Conquest of the Garden

That crow which flew over our heads
and descended into the disturbed thought
of a vagabond cloud
and the sound of which traversed
he breadth of the horizon
like a short spear
will carry the news of us to the city.

Everyone knows,
everyone knows
that you and I have seen the garden
from that cold sullen window
and that we have plucked the apple
from that playful, hard-to-reach branch.

Everyone is afraid
everyone is afraid, but you and I
joined with the lamp
and water and mirror and we were not afraid.

I am not talking about the flimsy linking
of two names
and embracing in the old pages of a ledger.

I'm talking about my fortunate tresses
with the burnt anemone of your kiss
and the intimacy of our bodies,
and the glow of our nakedness
like fish scales in the water.
I am talking about the silvery life of a song
which a small fountain sings at dawn.
we asked wild rabbits one night
in that green flowing forest
and shells full of pearls
in that turbulent cold blooded sea
and the young eagles
on that strange overwhelming mountain
what should be done.

Everyone knows,
everyone knows
we have found our way
Into the cold, quiet dream of phoenixes:
we found truth in the garden
In the embarrassed look of a nameless flower,
and we found permanence
In an endless moment
when two suns stared at each other.

I am not talking about timorous whispering
In the dark.
I am talking about daytime and open windows
and fresh air and a stove in which useless things burn
and land which is fertile
with a different planting
and birth and evolution and pride.
I am talking about our loving hands
which have built across nights a bridge
of the message of perfume
and light and breeze.
come to the meadow
to the grand meadow
and call me, from behind the breaths
of silk-tasseled acacias
just like the deer calls its mate.

The curtains are full of hidden anger
and innocent doves
look to the ground
from their towering white heigh

From forughfarrokhzad.org

Later On

My death will come someday to me
One day in spring, bright and lovely
One winter day, dusty, distant
One empty autumn day, devoid of joy.

My death will come someday to me
One bittersweet day, like all my days
One hollow day like the one past
Shadow of today or of tomorrow.

My eyes tune to half dark hallways
My cheeks resemble cold, pale marble
Suddenly sleep creeps over me
I become empty of all painful cries.

Slowly my hands slide o’er my notes
Delivered from poetry’s spell,
I recall that once in my hands
I held the flaming blood of poetry.

The earth invites me into its arms,
Folks gather to entomb me there
Perhaps at midnight my lovers
Place above me wreaths of many roses.

Forough Farrokhzad 1935-1967

Another Birth

Another Forough Farokhzad poem. Read by Parvaneh Farid. I came across Farokhzad by accident only recently. Her life was cut short in a car accident in 1967. She was just 32. I can only imagine what she would have produced had she lived.

The Wind Will Take Us

In my small night, ah
the wind has a date with the leaves of the trees
in my small night there is agony of destruction
listen
do you hear the darkness blowing?
I look upon this bliss as a stranger
I am addicted to my despair.

listen do you hear the darkness blowing?
something is passing in the night
the moon is restless and red
and over this rooftop
where crumbling is a constant fear
clouds, like a procession of mourners
seem to be waiting for the moment of rain.
a moment
and then nothing
night shudders beyond this window
and the earth winds to a halt
beyond this window
something unknown is watching you and me.

O green from head to foot
place your hands like a burning memory
in my loving hands
give your lips to the caresses
of my loving lips
like the warm perception of being
the wind will take us
the wind will take us.


By Forough Farrokhzad (1935-1967)

Saluting the Sea Cucumber Part III

Not only does the sea cucumber have potential medical applications, it has also been immortalised in music and poetry.

In 2003 academic Robin Gill produced a 480 page book called Rise Ye Sea Slugs which brings together (possibly for the first time in English) around 1,000 haikus on the subject of our holothurian hero. Apparently they have been the subject of the Japanese poetry form for centuries this including this one from 1690:

This sea slug
is it too beastly for
proper monks?

And one from 1951 by Gijô

A few drinks
and I am a sea slug
out of water

(Taken from Danny Yee’s review of the book here). Wonderful stuff. I feel a purchase coming on!

More famous of course is Erik Satie’s composition Embryons desseches. The first movement is called holothurie and concentrates on the so-called purring of the holothurians (????). In his description on the score Satie wrote: “The Holothurian crawls across boulders and rocky surfaces. This sea-animal purrs like a cat; also, it produces disgusting silky threads. Light appears to have an incommodating effect on it.”

Make of that what you will. Sadly YouTube has no footage of it being played. It’s a shame also that no artist deigned to paint this versatile beast. Albrecht Durer painted a beautiful hare. I’m sure he could have done the Sea cucumber justice too!