Saturday, 14 June 2008

Without the Word - nothing

‘…several classes of facts…seem to me to proclaim so plainly, that the innumerable species, genera, and families of organic beings, with which this world is peopled, have all descended, each with its own class or group, from common parents.’ Charles Darwin, The Origin of Species, 1859

‘Why we are not like ET - Samples of DNA taken from humans, animals, plants, microbes and viruses have one thing in common: they form a double helix structure held together by four different chemicals called bases. And scientists from New Zealand and Sweden have now built a computer model to show that organisms are unlikely to evolve if their "life code" is written using more or fewer bases. The work could help our understanding of what to expect from alien lifeforms - if we ever come across them. Reading along the double helix, the sequence of the bases can be read off as a genetic code made of four letters - A for adenine, C for cytosine, G for guanine and T for thymine. This code carries the instructions for creating and maintaining life, but why not use two letters, or six or eight? ET in the famous Spielberg film was said to have six-base DNA and, on the face of it, Earth-bound life could have, too. The reason why not turns out to be in the way a prehistoric relative of DNA began to protect itself against copying errors. Paul Gardner, and colleagues…used a computer model to try to explain why four turned out to be the magic number. It is not entirely clear how life first began on Earth, but many biologists believe that before our current DNA-dominated world, there was an environment known as RNA World. RNA is a similar chemical to DNA but it is much less stable and so much less suitable for holding the blueprint information for building complex organisms. Supporters of the RNA World theory believe that RNA evolved from simpler chemicals and only later evolved into DNA. RNA would have existed in a constantly changing and reactive soup. Gardner and his colleagues built a computer model…to examine how RNA might have developed had it had two, six or eight bases, as well as the standard four. They found that four- and six-base RNA molecules were the most efficient at evolving into DNA. But four-base RNAs were the ones which were best suited to overcoming RNA's fundamental weakness: its susceptibility to making errors as it copies itself. The two- and eight-base RNAs seem to get stuck somewhere along the evolution process... But six-base RNAs could have survived if they had evolved a way of putting right the errors introduced by mutation. The research poses the question of what kind of DNA extra-terrestrial life might have if a similar process of evolution had taken place on a similar planet elsewhere in the Universe. "We found the margins between four- and six-letter alphabets to be low, so a percentage of independent lifeforms might incorporate six, or a different four. "But it is likely that the same principles that life on Earth are based on will be used elsewhere," Gardner said. If RNA-based lifeforms on other planets had developed the error-correcting techniques needed to repair the damage to their genetic code caused by mutation and degeneration, they may well have developed into something with six-base DNA. "I'd love to meet an organism with a six-letter alphabet. However, they'd probably take a lot longer to sequence," he said.’ Ivan Noble, BBC News Online, 2003

Without the Word - nothing

Without the Word, nothing
coming among uncultured

stars, under a dusty white Moon -
just stone bones adorning night’s

black charnel-house, silver
graves of collapsing matter.

In the whole Galaxy - Earth
heard, turning blue as an eye,

in the blink of aeons, marshalling
her creatures, her flowers, leaves,

from dreaming amoebae in the heart
of water; hearing the possible poems,

composing them in earth and light
metamorphosed into cells; skeleton,

flesh and wing, all her organic poetry -
laboured from the musical molecules.

Friday, 13 June 2008

‘LUCA’ – Last Universal Common Ancestor

‘Curiously, although his theory emphasized male-female distinctions, his description in the Origin always placed the primordial ancestor, or ‘the ancient progenitor’ outside, or previous to, gender or sexed system; an ‘it’, never a ‘he’ or ‘she’. Gillian Beer, Introduction to the Origin of Species 1859, Oxford University Press, 1988

‘Back before the dinosaurs, before the first fishes, before the first worms, before the first plants, before the first fungi, before the first bacteria, there was an RNA world - probably somewhere around four billion years ago, soon after the beginning of planet earth’s very existence and when the universe itsef was only 10 billion years old. We do not know what these ribo-organisms looked like. We can only guess at what they did for a living, chemically speaking. We do not what came before them. We can be pretty sure they once existed because of clues to RNA’s role that survive in living organisms today. These ribo-organisms had a big problem. RNA is an unstable susbstance which falls apart within hours. Had these organisms ventured anywhere hot or tried to grow too large they would have faced what geneticists call an error catastrophe – a rapid decay of the message in their genes. One of them invented by trial and error a new and tougher version of RNA called DNA and a system for making RNA copies from it, including a machine we’ll call the proto-ribosome. It had to work fast and it had to be accurate. So it stiched together genetic copies three letters at a time, the better to be fast and accurate. Each threesome came flagged with a tag to make it easier for the proto-ribosome to find, a tag made of amino acid. Much later, those tags themselves became joined togther to make proteins and the three letter word became a form of code for the proteins – the genetic code itself. (Hence, to this day the code consists of three letter words each spelling out a particular one of twenty amino acids as part of a recipe for a protein.) And so was born a more sophisticated creature that stores its genetic recipe in its DNA, made its working machines of protein and used RNA to bridge the gap between them. Her name was LUCA – the Last Universal Common Ancestor.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000

‘Last year has also witnessed the unveiling of the first molecular map of the ribosome, the cell's protein factory. This has given us startling new details about its structure and may boost support for RNA (ribonucleic acid) being the first "living" molecule on Earth.’ BBC Online

‘LUCA’ – Last Universal Common Ancestor

Even before DNA - RNA -
unstable, sucking more life

from the inchoate chemical world -
defining in the blurred creative soup

of transient genes, urging
to be, replicate - just stay.

Becoming ‘organic copier’;
stitcher, cutter and paster -

translator, builder, joiner,
fixer, connector - bridge.

Keeping itself patterned in DNA,
drawing order into possible life -

hearing the Word four billion years ago
in swimming silence, dim interpretation

of the frustrating invisibility of God -
call for creativity as a first principle;

making its own skeleton for us all,
boneless - yet imagined or dreamt.

Ur-gene, first gene; prettily named LUCA,
the ‘Last Universal Common Ancestor’ -

author of the code, writer of the three letter
words holding us in existence; maintaining

our fleshy shell, transforming wet molecules
to scaffold bone; metamorphosing chemistry

that wrote gold barley’s whiskered ear -
heaven-colour of blurred hummingbird,

shining armour of the patent beetle –
owl eye, eagle wing; old melancholy

hunchback sunflower studying earth.
The bridge translating coded stores -

DNA copied into RNA; reading the words,
translating into protein - building limb, fin,

finger, leaf; still reading ourselves,
making ourselves from glued code -

billion upon billion years rehearsing,
but never tiring, becoming dispirited;

like LUCA herself,
who wanted to be -

as earless leaves cramped
unborn within the branch

hear spring and sun.
As space and stars,

heard the Word,
dreamt of Earth.

LUCA not one, but many;
fountain of species, flood,

still printed in our word
with the worm and fish -

tree, bird -
water, star.

Thursday, 12 June 2008


‘RNA was the Word. RNA left behind five little clues to its priority over both protein and DNA. Even today, the ingredients of DNA are made by modifying the indredients of RNA, not by a more direct route. Also DNA’s letter Ts are made from RNA’s letter Us. Many modern enzymes, though made of protein, rely on small molecules of RNA to make them work. Moreover, RNA, unlike DNA and protein, can copy itself without assistance: give it the right ingredients and it will stitch them together into a message. Wherever you look in the cell, the most primitive and basic functions require the presence of RNA. It is an RNA-dependent enzyme that takes the message, made of RNA, from the gene. It is an RNA-containg machine, the ribosome, that translates that message, and it is a little RNA molecule that fetches and carries the amino acids for the translation of the gene’s message. But above all, RNA - unlike DNA - can act as a catalyst, breaking up and joining other molecules including RNAs themselves. It can cut them up, join the ends together, make some of its own building blocks, and elongate a chain of RNA. It can even operate on itself, cutting out a chunck of text and splicing the free ends together again. The discovery of these remarkable properties of RNA in the early 1980s… transformed our understanding of the origin of life. It now seems probable that the very first gene, the ‘ur-gene’, was a combined replicator-catalyst, a word that consumed the chemicals around it to duplicate itself. It may well have been made of RNA.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000

‘During the dearth and lack of those two thousand/ million years of death, one wishes primarily/ Just to grasp tightly, to compose, to circle,/ To link and fasten skilfully, as one/ Crusty grey bryozoan builds upon another,/ To be anything particular…To become godlike with transformation.’ Pattian Rogers, The Voice of the Precambrian Sea

‘Henceforth, for the animate, to last was to mean to change,/ existing both for one’s own sake, and that of all others,/ forever in jeopardy.’ WH Auden, 1907-1973, Unpredictable but Providential

‘The DNA makes a simpler molecule called RNA which interacts with ribosomes which churn out proteins based on the code in the genome. Some proteins then interact with a structure called the Golgi complex, which inspects packages and labels proteins before handing them over for distribution elsewhere in the cell.’ BBC, 2003

‘It is the classic case of chicken and egg: which came first, DNA or protein? It cannot have been DNA, because DNA is a helpless passive piece of mathematics, which catalyses no chemical reactions. It cannot have been protein, because protein is pure chemistry with no known way of copying itself accurately. It seems impossible either that DNA invented protein or vice versa. This might have remained a baffling and strange condundrum had not the word left a trace of itself faintly drawn on the filament of life. Just as we know now that eggs came long before chickens (the reptilian ancestors of all birds laid eggs), so there is growing evidence that RNA came before proteins. RNA is a chemical substance that links the two worlds of DNA and protein. It is used mainly in the translation of the message from the alphabet of DNA to the alphabet of proteins. But in the way it behaves, it leaves little doubt that it is the ancestor of both. RNA was Greece to DNA’s Rome: Homer to her Virgil.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000


Chemical Word -
spirit of life incarnate

in nascent chemistry -
guddling among Elements;

such light upon the water,
which will knit beams -

muscular feel of current,
into verdant dreams -

into molecular flesh,
swarming real green.

Print of the Word -
enshrined, infinite

while Earth lives.
Still star-sailing

whispering anywhere again -
hot rocks, mountains, water;

something found
out of darkness.

Communication of the Word,
translator of idea into flesh -

organic root; earth-nub;
realisation of the Word.

Active Principle of the Word -
original messenger, Olympian

bearing creativity;
life’s viral fires.

First Art of Chemistry -
first artist of the Word;

understanding desire
to be, to make, create,

for no reason but life,
expression and being.

Breaking - stitching
swarming molecules;

feeling something possible
will come into existence -

cradling one wet cell
dreaming of the flower

when no flower will be
for three billion years.

Why are men afraid to shout
these fabulous Earth miracles,

such shining, unlikely principles -
from mud and light will come us all.

RNA - understanding molecular creativity,
organic artistry, unextinguishable by time -

composer, conductor of chemicals
dreaming in water - such journey

to the white Poles, deserts, mountains,
from her bowl, sea-womb, light-seed -

spectacular travel to wing and eye,
breathing under still water, hooking

possibility from dark atoms of nothing;
connecting with star vibrations - dust.

Learner, teacher, catalysing knowledge;-
the Word driving a fantastic chemistry.

Wednesday, 11 June 2008

Your Hands are Stars

‘In a sense, human flesh is made of stardust.’ Nigel Calder, the Key to the Universe, BBC, 1977

Your Hands are Stars

Your hands are stars -
bright space molecules

fallen through this Universe
for black billenia. In darkness,

see they shine - learned dust-flesh;
spun white skeleton, light calcified.

Trees are alight with damp green stars,
leaf bones fragile as a mouse’s hand -

are sucking rain, sun,
from Earth’s wet halo.

When you touch me at night -
two silver prints like starfish.

Tuesday, 10 June 2008



‘To continue the linguistic, information-theory metaphor within which genetic theory was now to be formulated, the directed synthesis of RNA on DNA was termed transcription, and the synthesis of protein on the RNA was translation.’ Steven Rose, Lifelines: Biology, Freedom, Determinism, 1997

‘TRANSCRIPTION - The cell makes a copy of the gene whose message is to be interpreted. The copy is made of RNA, ribonucleic acid, a chemical similar to DNA. RNA has a different sugar in its sugar-phosphate backbone and is usually a single-stranded molecule. And wherever there is a T in DNA, there will be a U in RNA, also pairing with A. The enzyme that carries out this process of copying is called RNA polymerase. It can recognise the 'start here' and 'stop here' signals that appear in the DNA code, and catalyse the formation of an RNA molecule using bases, sugars and phosphate molecules from the nucleus. The RNA molecule created is called messenger RNA (mRNA) because it is responsible for carrying the message from the nucleus to the cytoplasm, the outer part of the cell, where the code in the mRNA will be translated into protein. The mRNA passes through the pores in the nuclear membrane, and makes its way to the part of the cell where proteins are made, called the rough endoplasmic reticulum (ER). Called 'rough' ER because, under the microscope, it has a bumpy, blobby appearance. The 'blobby' structures are ribosomes - the factories of the cell. Inside each ribosome are three different types of RNA molecule, called ribosomal RNA (rRNA).’

‘TRANSLATION - Ribosomal RNA is responsible for translation, in which the mRNA code is used to create a protein molecule. The mRNA message is 'read' in groups of three bases at a time. Each group of three bases is called a triplet, or 'codon'. There are 4 x 4 x 4 = 64 possible codons, or combinations of three bases. Most of the codons correspond to a specific building block of protein - an amino acid. Many of the amino acids have more than one triplet coding for them. Because there are more codons (64) than there are amino acids (20), the code is described as 'degenerate'. Three of the possible codons don't actually code for an amino acid; instead they indicate 'stop' signals. One codon (ATG - for methionine) is the 'start' signal for proteins. It is down to another RNA molecule, called transfer RNA (tRNA). Unfolded tRNA is roughly the same shape as a clover leaf. At one end of the 'leaf', are three crucial bases. These bases are called an 'anticodon' and are complementary to one of the codons on the mRNA molecule. When two bases will bind to each other, they are said to be complementary – the base A always binds to T, or (U in RNA) and C always binds to G. For the triplet GUC, the complementary codon would be CAG. These two codons would bind firmly together, with hydrogen bonds forming between each of the complementary bases. Each tRNA molecule becomes attached specifically to one of the 20 amino acids. As the protein is being formed, each codon on the mRNA molecule is read, one at a time. For each codon, the tRNA molecule with the complementary anticodon temporarily binds to the mRNA. The amino acid that is joined to the end of the tRNA molecule is brought in line with the growing polypeptide chain, and the amino acid links to the end of that chain. The tRNA disengages from the mRNA molecule, and the next codon on the mRNA molecule is available to be 'read'. The appropriate tRNA molecule is again joined to the mRNA molecule, and its amino acid joined to the polypeptide chain. The process of making a protein is called translation and is very similar to translating from one language to another - in this case from the four-letter language of DNA (interpreting all the full stops and starts of 'sentences') into the 20-letter language of proteins. ‘

‘Developmental biologists can observe genomic activiation taking place, more or less directly. For example, RNA contains the base known as uracil, whereas DNA contains thymine instead. If you add radioactive-labelled uracil to young embryos in culture you can see at that stage they start to incorporate it. They incorporate the uracil only when they start to make RNA – which, of course, signals the start of transcription.’ Ian Wilmut and Keith Campbell, Mammals Cloned, The Second Creation, Headline, 2001

‘Let/ there be/ amino acids,/ and there were: a slop/ of molecules in ancient seas,/ building cell walls to keep their/ distance, dividing, replicating, starting, to diversify, one growing oars, one rotors, one/ a wiry tail,/ lumping into clusters…’


‘Stellar dust has settled./ It is green underwater now in the leaves/ of the yellow crowfoot. Its potentialities/ Are gathered together under pine litter/ As emerging flower of the pink arbutus./ It has gained the power to make itself again/ In the bone-filled egg of osprey and teal.’ Pattian Rogers, The Origin of Order

‘In the beginning was the word. The word was not DNA. That came afterwards, when life was already established, and when it had divided the labour between two separate activities: chemical work and information storage, metabolism and replication. But DNA contains a record of the Word, faithfully transmitted through all subsequent aeons to the astonishing present…On the long arm of chromosome 1… if you read it carefully, there is a sequence of 120 letters - As Cs Gs Ts – that repeats over and over again. Between each repeat there lies a stretch of more random text, but the 120-letter paragraph keeps coming back like a familiar theme tune, in all more than 100 times. This short paragraph is perhaps as close as we can get to an echo of the original Word. This ‘paragraph’ is a small gene, probably the single most active gene in the human body. Its 120 letters are constantly being coped into a short filament of RNA. The copy is known as 5S RNA.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000


The word calling order -
being, instruments of life,

from malleable molecules,
colossal fires of existence;

atomic principles of freedom,
chaos. From spreading stars -

light and water -
green and blood;

simple amoeba heart
coagulating into fish,

a flower coming
to earth and light,

as decorative fulfilment,
wording of early script -

leaves, eyes, animal thud,
heavy on the written Earth;

evolved organic transcripts,
born in the first black belly.

Monday, 9 June 2008

Some Ingenious Gene Words for Growing Body Parts

Some Ingenious Gene Words for Growing Body Parts:

radical fringe;


sonic hedgehog -
pax, gap, even-skipped.

Fushi tarazu,
giant, knirps,


Porcupine -
Indian hedgehog,
desert hedgehog,

warthog, groundhog.

Shortarm1a, shortarm1b,