Comparative Genomics
“Comparative genomics is going to be the single most important tool going forward in analysing genomes.” Sir John Sulston, Director, Wellcome Trust Sanger Institute, UK
‘For understanding evolution, comparative genomics will add a hitherto unimaginable comprehensiveness to the study of relationships between species.’ Adam Rutherford, Editor, Nature
‘...if every form which has ever lived on this earth were suddenly to reappear… all would blend together by steps as fine as those between the finest existing varieties.’ Charles Darwin, The Origin of Species, 1859
‘All genomics is rapidly becoming comparative genomics and we are often asked to define the members of gene families across multiple species and to examine the processes underlying their evolution.’ MRC, HGU
‘One of the most powerful general approaches for unlocking the secrets of the human genome is comparative genomics, and one of the most powerful starting points for comparison is the laboratory mouse, Mus musculus.’ Nature, 2003
‘We identified 1,308 groups of proteins, each containing at least one predicted orthologue in each species and many containing additional paralogues. The 1,308 groups contained 3,129 human proteins, 1,445 fly proteins, 1,503 worm proteins and 1,441 yeast proteins. These 1,308 groups represent a conserved core of proteins that are mostly responsible for the basic 'housekeeping' functions of the cell, including metabolism, DNA replication and repair, and translation.’ International Human Genome Sequencing Consortium, Nature
"Almost all the proteins that you and I have probably exist in varying forms in the chicken. You can say this is true in almost all higher organisms. The differences become apparent in the slight variations in when and where the genes are expressed - that creates the unique organism.’ Dr Hans Cheng, US Department of Agriculture's Avian Disease and Oncology Laboratory, Michigan, US
‘..a better proof of this cannot be given than a circumstance mentioned by Agassiz, namely, that having forgotten to ticket the embryo of some vertebrate animal, he cannot now tell whether it be that of a mammal, bird, or reptile…The points of structure, in which the embryos of widely different animals of the same class resemble each other, often have no direct relation to their condition of existence.’ Charles Darwin, The Origin of Species, 1859
‘Although the scientists suspected we have fewer genes than originally thought, they were still surprised to learn we have only twice as many as a fly.’ Horizon, BBC
“We share 99% of our genes with mice, and we even have the genes that could make a tail.” Dr Jane Rogers, Head of Sequencing, Sanger Institute, UK
‘It is a fact that 75% of our genetic make-up is the same as a pumpkin.’ BBC Science News
‘The comparison demonstrated that the same phenomenon of gene conversion appeared to be at work more than 5 million years ago, when humans and the non-human primates diverged from each other. "The comparison between human and non-human primate chromosomes confirming the finding shows the power of comparative genomics," Dr. Collins said. "Without the ability to compare the genetic material across species, it would have been difficult for the team to test their hypothesis." NHGRI now funds a number of genome sequencing projects on model organisms, including the dog, the chimp, the chicken and the honeybee. The mouse, rat and fruit fly sequencing projects are essentially completed…’ National Human Genome Research Institute
‘Dead, she became space-earth/ Broken to pieces./ Plants nursed her death, unearthed her goodness… He used familiar hands/ Incriminating many,/ And he borrowed mouths, leaving names/ Being himself nothing / But a tiger’s sigh, a wolf’s music/ A song on a lonely road/ What it is/ Risen out of mud, fallen from space/ That stares through a face.’ Ted Hughes, Seven Dungeon Songs
‘The model organisms used in genomics have, in general, small genomes and short generation times. Investigations into organisms such as the fly and the worm,and the mouse and the rat yield a great deal of information that can be relevant to humans and animals. Often experiments that can be performed on model organisms would be impractical or unethical in higher organisms. For plants, the model organism is a small weed called Arabidopsis.’ Demystifying Genomics, Medical Research Council, UK
Comparative Genomics
The invisible zoo -
imagined menagerie,
distilled to essential pattern;
possible animals snuffling
at the cage of nothing,
wishing for skin
in the starless place.
There is hunger in the darkness
for eyes,
like the lover’s ache for presence -
sea sparkles with lights of coming fish;
wanting in water
for feather skeletons,
silver scales tiled -
in air nests,
birds dream of amazing arms.
A zoo contained on the head of a pin -
more books bound in Life’s shining library;
empty shelves groaning
to record the Leopard, Tiger, Polar Bear,
before their stories, written for a billion years -
embroidered poetry of hotly spotted fur,
fiery stripes and snow-spun -
become oral, legend, mythology.
Gather them all in,
before their words return to the mud -
having written the tiger,
who could begin again with the worm?
We are burning the books of the world;
illuminated pages and master copy -
manuscript and disk.
Gather them all in -
lay them here to sleep
in the tiny library of the world -
keepers to watch over them,
safe from being’s thieves,
the pirates of existence;
New-Noah, a scientist,
recording their essential letters,
preserving the ancient grammar -
fresh librarians waiting in the wings
to mother them - protect, celebrate -
from the moment they might be;
to lend them to the Earth, people
who have read, and understood themselves -
humans who will this time love them properly.
In difference, similarity -
mouse and fish are sleeping
in my figured skin and bones -
the vibrating cat warming my lap
pads in my pink, sheepskin feet -
my evening owl-eyes widen round,
see courtesy of sterile spooky moon.
We are flowers from the same stem -
even the very perfumed, skirted blooms,
earth’s ornaments, her party pleasures -
are sisters branching from the same root.
All form unfurling; petal, flesh, colour,
hair; finger, fur and claw - one blood -
one root, watered by millennia -
species, slow explosions thrown
from the communal, creative core -
incremental difference infitessimally
printing until Earth’s paper runs out -
struggle of invention tires, after eyes.
A world of freaky living mirrors
to bizarrely recognise ourselves;
in disguise more easily understood -
us without the bullshit, ornate mess,
humble in our feathers and fur, fins;
under mothering worm, our muscle.
Slowly explosive, the writing genes –
Creation’s slow, silent bombs, strung
glittering here on shorter, tidier threads;
jewels set in shadows, misunderstood -
seeing ourselves more clearly
through the transparent mouse;
fish-bone, bird-wing, tree-leaf,
even hearts of flowering plants.
We learn of ourselves much faster
by reading a mouse’s starry whisker;
scales have fallen from our related eyes,
to witness old poems printed in our skin -
sketches of flesh, leaf, star, bone,
drawn on the communal skeleton.
The world is stripped to the story of itself -
and all Earth’s dreaming creatures scripted;
we take our rightful place, proudly
hand in hand with cowering mouse,
burrowing with mother worm,
swimming with sisterly fish -
remembering our old wings,
we figure ourselves as angels -
rising as bundled light-sheaves;
animal shape-shifters emerging.
"We can now start seriously investigating how it is that humans, who we think are so complex, can manage with only a relatively modest number more genes than worms and flies…The challenge for scientists is to explain how a sophisticated human can be built from around 30,000 genes, fewer than for a grain of rice, and only a few hundred more than a mouse.” Martin Bobrow, Professor of Medical Genetics, University of Cambridge, UK.
‘Two prominent families are involved in the control of development. The human genome contains 30 fibroblast growth factors (FGFs), as opposed to two FGFs each in the fly and worm. It contains 42 transforming growth factors compared with nine and six in the fly and worm, respectively. These growth factors are involved in organogenesis, such as that of the liver and the lung. A fly FGF protein, branchless, is involved in developing respiratory organs (tracheae) in embryos. Thus, developmental triggers of morphogenesis in vertebrates have evolved from related but simpler systems in invertebrates.’ International Human Genome Sequencing Consortium
‘Model organisms have a unique value in genomics. Not only are many of the genes from disparate organisms very similar, but their genes are often grouped in the same way on chromosomes.’ Demystifying Genomics, Medical Research Council, UK
‘What is true of mice is just as true of people. Flies and people are just variations on a theme of how to build a body that was laid down in some worm-like creature in the Cambrian period. They still retain the same genes doing the same job… this incredible conservation of embryological genetics took everybody by surprise... the similarity is so mind-blowing that when it first came to light few embryologists believed it… Geneticists can knock out a gene in a fly by deliberately mutating it, replace it by genetic engineering with the equivalent gene from a human being and grow a normal fly… Human Hox genes can rescue their fly equivalent, as can Otx and Emx (mouse) genes. Indeed, they work so well that it is often impossible to tell which flies have been rescued with human genes and which with fly genes. Genes are just chunks of software that can run on any system; they use the same code and do the same jobs. Even after 530 million years of separation, our computer can recognise a fly’s software and vice versa.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000
‘A corollary of the highest importance may be deducted from the foregoing remarks, namely, that the structure of every organic being is related to the most essential yet often hidden manner, to that of all other organic beings.’ Charles Darwin, The Origin of Species, 1859
Genetic tools under the skin
Under the skin,
like the bone of a star,
star of a leaf,
structures of green chemistry -
purple heart plum,
flower muscles
levering petals,
morning and evening;
under iron, corpuscles,
brutal red poetry of blood -
tools used by variation, adaptation,
selection; unchanged for billennia.
‘The finished sequence of human chromosome 6 reveals an abundance of biological information previously buried within the draft of the human genome, and illustrates the increasing power of comparative genomics.’ Nature, 2003
‘The genome is a dynamic structure, continually subjected to modification by the forces of evolution. The genomic variation seen in humans represents only a small glimpse through the larger window of evolution, where hundreds of millions of years of trial-and-error efforts have created today's biosphere of animal, plant and microbial species. A complete elucidation of genome function requires a parallel understanding of the sequence differences across species and the fundamental processes that have sculpted their genomes into the modern-day forms. The study of inter-species sequence comparisons is important for identifying functional elements in the genome. Beyond this illuminating role, determining the sequence differences between species will provide insight into the distinct anatomical, physiological and developmental features of different organisms, will help to define the genetic basis for speciation and will facilitate the characterization of mutational processes. This last point deserves particular attention, because mutation both drives long-term evolutionary change and is the underlying cause of inherited disease. The recent finding that mutation rates vary widely across the mammalian genome raises numerous questions about the molecular basis for these evolutionary changes. At present, our understanding of DNA mutation and repair, including the important role of environmental factors, is limited. Genomics will provide the ability to substantively advance insight into evolutionary variation, which will, in turn, yield new insights into the dynamic nature of genomes in a broader evolutionary framework.’ A Vision for the Future of Genomics Research, US National Human Genome Research Institute, 2003
‘It is a fact that 75% of our genetic make-up is the same as a pumpkin. Although we like to think we are special, our genes bring us down to Earth. DNA is what ties the entire living world together. It may well account for the extraordinary diversity among organisms but it also serves to underline their common origins - we all evolved from the same soup of chemicals. So while a complete map of the human genome - our particular collection of genes - will be extremely useful when it is finished in the next few years, that will not be the end of the story. Once we have the map, we will need something to compare it with. And that is the goal of an emerging field of research called comparative genomics. By studying non-human genomes, we gain insight into our own.’ Monise Durrani, BBC Science
‘I find I incorporate gneiss and coal and long-threaded moss and fruits and grains and esculent roots/ And am stucco’d with quadrapeds and birds all over/ And have distanced what is behind me for good reasons,/ And call any thing close again when I desire it.’ Walt Whitman, Leaves of Grass: 31
‘Comparison of genome sequences from evolutionarily diverse species has emerged as a powerful tool for identifying functionally important genomic elements. Initial analyses of available vertebrate genome sequences have revealed many previously undiscovered protein-coding sequences. Mammal-to-mammal sequence comparisons have revealed large numbers of homologies in non-coding regions, few of which can be defined in functional terms. Further comparisons of sequences derived from multiple species, especially those occupying distinct evolutionary positions, will lead to significant refinements in our understanding of the functional importance of conserved sequences. Thus, the generation of additional genome sequences from several well-chosen species is crucial to the functional characterization of the human genome.’ A Vision for the Future of Genomics Research, US National Human Genome Research Institute, 2003
Conservation, preservation
of the ancient chemistry -
agonisingly slow sequences
hauled from earth and time,
blue building beads of water,
bright scribbling of equations,
doodlings over skeleton and fin -
clues to why we surrendered wings.
Shall I dare to believe the mouse is my brother
Shall I dare to believe
the mouse is my brother,
worm and shrew old mothers?
I was dinosaur, bird - flower?
Can I have faith in such miracles,
trust these white-coated disciples.
‘Metaphorically, comparative genomics allows one to read evolution's laboratory notebook. In the roughly 75 million years since the divergence of the human and mouse lineages, the process of evolution has altered their genome sequences and caused them to diverge by nearly one substitution for every two nucleotides (see below) as well as by deletion and insertion. The divergence rate is low enough that one can still align orthologous sequences, but high enough so that one can recognize many functionally important elements by their greater degree of conservation. Studies of small genomic regions have demonstrated the power of such cross-species conservation to identify putative genes or regulatory elements. Genome-wide analysis of sequence conservation holds the prospect of systematically revealing such information for all genes. Genome-wide comparisons among organisms can also highlight key differences in the forces shaping their genomes, including differences in mutational and selective pressures.’ Nature, 2003
I live in the Church of Nature
I live in the wild Church of Nature;
my fellow celebrants, congregation -
laughing otter, imperial stag,
keening eagle, shining seal;
our feet in grey North Sea -
antlers, arms, wings, fins
uplifted, similarly praising.
The sun is our chandelier,
bloody rowan, our cross -
still dripping blood to earth.
Our humming purple altar
is laden with rung heather,
golden honey being sung by bees,
on white cloths of mountain snow.
Come evening, sacrament, host,
chalice of silver light, turning
salmon-gold in fiery celebration
of sky and sea’s late communion -
now our pure, domed blue ceiling
is painted with cherubic clouds -
my brethren and I united,
by love, peace, and genes.
‘Genes shared with fly, worm and yeast - IPI.1 contains apparent homologues of 61% of the fly proteome, 43% of the worm proteome and 46% of the yeast proteome. We next considered the groups of proteins containing likely orthologues and paralogues (genes that arose from intragenome duplication) in human, fly, worm and yeast…Briefly, we performed all-against-all sequence comparison for the combined protein sets of human, yeast, fly and worm. Pairs of sequences that were one another's best matches in their respective genomes were considered to be potential orthologues. These were then used to identify orthologous groups across three organisms. Recent species-specific paralogues were defined by using the all-against-all sequence comparison to cluster the protein set for each organism. For each sequence found in an orthologous group, the recent paralogues were defined to be the largest species-specific cluster including it. The set of paralogues may be inflated by unrecognized splice variants and by fragmentation… We identified 1,308 groups of proteins, each containing at least one predicted orthologue in each species and many containing additional paralogues. The 1,308 groups contained 3,129 human proteins, 1,445 fly proteins, 1,503 worm proteins and 1,441 yeast proteins. These 1,308 groups represent a conserved core of proteins that are mostly responsible for the basic 'housekeeping' functions of the cell, including metabolism, DNA replication and repair, and translation…In 564 of the 1,308 groups, one orthologue (and no additional paralogues) could be unambiguously assigned for each of human, fly, worm and yeast. These groups will be referred to as 1-1-1-1 groups. More than half (305) of these groups could be assigned to the functional categories shown… Within these functional categories, the numbers of groups containing single orthologues in each of the four proteomes was: 19 for cellular processes, 66 for metabolism, 31 for DNA replication and modification, 106 for transcription/translation, 13 for intracellular signalling, 24 for protein folding and degradation, 38 for transport, 5 for multifunctional proteins and 3 for cytoskeletal/structural. No such groups were found for defence and immunity or cell-cell communication…’ International Human Genome Sequencing Consortium
How humbling, how funny -
man’s guts, misplaced pride,
cultivation of aggression, chest-thumping
wars, domination, dictatorship, destruction;
his shifting fashion - art, music, wine,
singing and cooking, poetry and sport,
should find himself brother to the worm,
wedded to a flower, dung-beetle cousin -
sister to the smallest bird pecking nuts
ferociously in a winter garden - child
of the singing whale speared by his hand,
one with a shivering wee mouse he kills.
Even a single act of cruelty to these - his kin,
corrupts his shared genetic code, ancient disk;
affects expression of communal genes,
where gifts of fear abide among love.
‘The 1-1-1-1 groups probably represent key functions that have not undergone duplication and elaboration in the various lineages. They include many anabolic enzymes responsible for such functions as respiratory chain and nucleotide biosynthesis. In contrast, there are few catabolic enzymes. As anabolic pathways branch less frequently than catabolic pathways, this indicates that alternative routes and displacements are more frequent in catabolic reactions. If proteins from the single-celled yeast are excluded from the analysis, there are 1,195 1-1-1 groups. The additional groups include many examples of more complex signalling proteins, such as receptor-type and src-like tyrosine kinases, likely to have arisen early in the metazoan lineage. The fact that this set comprises only a small proportion of the proteome of each of the animals indicates that, apart from a modest conserved core, there has been extensive elaboration and innovation within the protein complement…..The relatively small proportion of vertebrate-specific multicopy families suggests that few new protein domains have been invented in the vertebrate lineage, and that most protein domains trace at least as far back as a common animal ancestor.’ International Human Genome Sequencing Consortium
‘Finally, the olfactory receptor genes comprise a huge gene family of about 1,000 genes and pseudogenes. The number of olfactory receptors testifies to the importance of the sense of smell in vertebrates. A total of 906 olfactory receptor genes and pseudogenes could be identified in the draft genome sequence, two-thirds of which were not previously annotated. About 80% are found in about two dozen clusters ranging from 6 to 138 genes and encompassing about 30 Mb (INCLUDEPICTURE "../../../../../Application%20Data/Documents%20and%20Settings/Owner/Application%20Data/Microsoft/THE%20HUMAN%20GENOME/nature%20part%204%20genes_files/409860a0_r_4_files/glyph(2).gif" \* MERGEFORMAT 1%) of the human genome. Despite the importance of smell among our vertebrate ancestors, hominids appear to have considerably less interest in this sense. About 60% of the olfactory receptors in the draft genome sequence have disrupted ORFs and appear to be pseudogenes, consistent with recent reports, suggesting massive functional gene loss in the last 10 Myr.’ International Human Genome Sequencing Consortium
Once, I could smell you
Once, I could smell you
with my olfactory genes -
the way dogs smell ghosts,
badness on a man’s hands;
rabbits snatch samples
of twitchy evening air,
deer hammer rusty hillsides
at humans the size of mice.
Now I must rely
on mutated sense -
tapping into that lost percentage –
60% wrecked, sunk pseudo-genes,
wiring for special occasions,
when other darkness warns.
I will surreptitiously sniff
hair, skin, fingers, mouth,
for news of your iron-red heart;
clues to your unskinned nature -
strings of chemical messages,
strung about you like tinsel -
hung on the air’s simple molecules;
you are written, found out - undone.
‘Plants and animals, too, can have similar genes: a fungal resistance gene in the weed Arabidopsis is also used by the fruit fly to combat a fungus. This conservation of genes and their organisation means that characterisation of a gene, or a whole genome, in one species immediately provides important clues both about gene function in related species, and about the nature and function of individual genes more widely.’ Demystifying Genomics, Medical Research Council, UK
‘The DNA of a camel was once in the sea, but it hasn’t been there for 300m years.’ Richard Dawkins, Unweaving the Rainbow, Penguin, 1998
‘Say from what simple springs began/ The vast ambitious thoughts of man…’ Mark Akenside, 1721-70, Hymn to Science
“The work also raises philosophical questions about the planet we share with creatures surprisingly similar to ourselves.” Martin Bobrow, Professor of Medical Genetics, Cambridge University, UK
From star-death, gases, we have risen
From star-death, gases, we have risen -
original shining dust where light, water,
came - hearing the Word - coagulating
life from fertile chaos, invisible purpose;
from the dreaming cell enclosing space -
becoming one; differentiating, replicating
with invented magic device - from muddy
palette, colours separating, brush forming;
life willing itself into existence - writing
more recipes, aspiring to such blind love
powering the cosmos; slowly firing Earth,
building her many creatures, all moulding
from her humble soil, aquatic beds.
From death and atrophy, compost
of millennia, her heart is like rays;
fish, bird, flower, animal coming -
mammal, human, lending millennia -
experimentation, parenthood; refining,
being different, exploring life’s byways,
devastating streams, laboured beauties -
until these calm moments of reflection -
when basking summer sighs in sweating
leaves on scratching thin brown fingers -
when my expression of the Genome feels
such kinship with the trees’ green palms,
star skeleton to skeleton against the blue;
understanding now how wing and fin, tail,
are sleeping still within this holy scheme -
particular, expressed in time - yet sewn
into the whole, as one; more shimmering
embroidery upon the cloth of life, invisibly
black among blank heavens - deaf moons -
like a focusing of stars, bright web centre,
no more capable of being apart than eyes -
always part, comforted by life, kinship; such
impersonal love as drives the new lime leaves,
even knowing these leaves will die as red,
incandescent stars to the end; and leaving
the same star print as my hands on earth -
autographed bones returning to mud, water.
‘…genes do not operate in isolation. They are in constant dialogue with the rest of the cell, which in turn responds to signals from the other cells of the body, which in the end are in touch with the world at large…The dialogue between the genes and their surroundings is understood to some exent but we need to know far more. This dialogue controls the development of an organism from a single cell into a sheep - or indeed into a human being or an oak tree…the dialogue shapes the processes of differentiation…The dialogue between genes and their surroundings continues after the animal is born and throughout life…once we understand how the genes interact with their surroundings – the nature of the dialogue – then, truly, we will begin to appreciate how bodies really work, and develop… that understanding is science.’ Ian Wilmut, The Second Creation, Headline, 2001
‘To lay the logarithmic spiral on/ Sea-shell and leaf alike, and see it fit,/…how secret that is, and how privileged/ One feels to find the same necessity/ Ciphered in forms diverse and otherwise/ Without kinship – that is the beautiful/ In Nature as in art…’ Howard Nemerov, Figures of Thought
‘Hast thou ever raised thy mind to the consideration of EXISTENCE, in and by itself, as the mere act of existing? Hast thou ever said to thyself thoughtfully, IT IS! heedless in that moment, whether it were a man before thee, or a flower, or a grain of sand? Without reference, in short, to this or that particular mode or form of existence? If thou hast indeed attained to this, thou wilt have felt the presence of a mystery, which must have fixed thy spirit in awe and wonder.’ Samuel Taylor Coleridge
From strings of time, star molecules
From strings of time, star molecules,
we have woven ourselves in water -
spinning light’s instant shining fibres,
we have knitted miraculous existence.
From stars, light, water-words,
we have made ourselves cells -
in the fabulous agony of creation,
swum, crawled, fought and flown;
learned climbing, standing, walking,
begun to understand the art of love -
knowing ourselves now as leaf,
fish, tiger, penguin, bat, mouse;
holding the very soil, worm,
in Primate palm, recognising,
here is our mother, basic chemistry;
hearing the voice that called us all.
Marvellous Metaphor! ‘Eukaryotic cells – the kinds that human beings have, and sheep, and oak trees – are wonderfully complex. If each prokaryote cells is compared to a house, then each eukaryote cell is like a city. Though the light microscope, the ‘standard’ eukaryotic cells looks like a fried egg…’ Ian Wilmut, The Second Creation, Headline, 2001
‘By viewing Nature, Natures Hand-maid, Art,/ Makes mighty things from small beginnings grow…This I fore-tel, from your auspicious care,/ Who great in search of God and Nature grow:/ Who best your wise Creator’s praise declare,/ Since best to praise his works is best to know…’ John Dryden, Annus Mirabilis, 1631-1700
‘We are descended not from one ancestral LUCA, but from the whole community of genetic organisms.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000
Behold the Leaf in my Hand
Behold the leaf in my hand,
its green five-fingered palm -
our starry skeletons are laid
one upon the other, saying -
look how we are webbed -
like bats, the foot of a bird;
how time has bent blood
and bone and water thus -
grown beauty, grace,
from root-light, time;
shining chemistry
among molecules.
‘I have been pointing out the imaginative visions which underlie those sciences with a view to breaking the habit of polarisation that separates them radically from the humanities, producing an unwinnable ‘war of the two cultures’…This feud saddles the young with a painful and unnecessary dilemma, forcing them to specialise on one side or the other of the divide – a choice which they have to make much earlier and much more completely in English-speaking countries than they do in most European ones. It should be obvious that, in trying to close this culture-gap, I am not attacking science but emphasising its importance in our culture…Science is not an isolated, autonomous, omnipotent castle but an organic part of our total world-view. That is why we all need to be conscious of it. The visions that underly it ought to get far more attention than they now do in discussions both of literature and of the physical sciences themselves.’ Mary Midgley, Science and Poetry, Routeledge, 2003
‘Every department of knowledge we see excellent and calculated towards a great whole. I am so convinced of this that I am glad at not having given away my medical books, which I shall again look over.’ John Keats, Letter 64, 1818
Every atom, every molecule
Every atom, every molecule
amid the moving universe
is linked to one another;
every star, every planet,
human, eagle, wolf -
dreaming flower, leaf,
chained within reality -
where energy is canvas,
life art, unfinished -
overprinted; painted
movement after subtle movement
through time’s littered galleries -
each crimson streak, vermilion hue,
cobalt, flashing feather; eye, beak -
patent husk that closed a beetle,
black curling tongue of butterfly;
each star-haired dandelion seed,
armoured scale a dinosaur shed -
each bone, amoeba, tusk, fin -
elephant, swan-wing, flea, hair;
each rabbit-tail and lizard-skin,
each unhinged petal, fallen leaf,
framed within the endless halls;
named and gilded, remembered,
celebrated - for each has played
some effervescent part, makes up
some fragment of the glowing whole -
some golden shade, fine predatory line,
some chiaroscuro, one species to another;
shading, hatching, re-working of design -
but lose a single feather from that robin
on the winter fence, soft molecule of red
from that symbolic breast,
Christmas will be altered;
snow less pure, dense, threatened -
part of Creation bleeding to death.
I looked into the galleries; empty, white,
unlocked rooms – shadows on the wall -
unhung clean spaces where creatures
should have been - labels reading –
‘Removed by Man, never to return’;
no renovation, replacement possible.
Shuddering, I made to close the doors,
but wind which claims all emptiness -
that sings among the musical stars,
goes weaving like a world lament,
already was, Pibroch in the space;
now beneath my feet - crackling
like a shattered egg, fault lines
running from the blank frame
of just one rainforest leaf burned,
joining now with all other cracks -
thunderous clouds, Hollywood storm -
what new horrors might come from loss
of a tropical frog, pink flamingo,
tiger fur-flames, or lion sun-ruff –
scoffers, imagine, just one jumper-stitch
dropped, endless embroidery thread cut,
that had run to the start of the world -
earth, sea, before light, up to the stars.
What devastation coming as I ran,
as if fleeing - shutting eyes, ears -
might fill the empty pictures, and harmony,
even in browning molecules, spilled blood -
come right again, re-write such brutal labels;
re-instate Earth’s works, as stolen by thieves.
Not one letter in the script is spare,
wasted; not one word unimportant -
no broken string of life can lead reality;
ropes of light to every unfilled darkness -
for every atom, molecule,
amid the dancing universe
is linked to one other -
every star, every planet;
human, eagle, wolf -
dreaming flower, leaf;
love now dripping from such wounds
like gentle haemorrhage of mercury -
life’s essential sap,
her original blood.
‘During the Age of Reason… this muddled antithesis of scientific reality versus everyday illusion lined up with a whole constellation of other crude antitheses – science versus literature, intellect versus imagination, analysis versus synthesis, expert versus amateur, man versus woman, adult versus child – thus distorting the whole picture of life and making many of its practical problems look insoluble.’ Mary Midgley, Science and Poetry, Routeledge, 2003
‘Some of these cultural effects come as much from the behavioral aspects of the HGP as from the genomic sequences themselves. The sharing of new information, even before its assembly into publishable form, has spurred efforts to share other kinds of research tools and has encouraged the notion of making the scientific literature freely accessible through the Internet. The contribution of scientists in many countries to the sequencing of many genomes, including the human genome, has inspired efforts to develop gene-based sciences - from basic genomics to biotechnology - throughout the world, including the poorest developing nations. Indeed, the World Health Organization, the United Nations, and the World Bank have all contributed recently to the growth of the ideas that science is both possible and valuable in all economies and that science can be a means to help unify the world's population under a banner of enlightenment, demonstrating a virtue of globalization.’ Harold Varmus, Nature, 2003
‘The word 'partnership' appears numerous times intentionally. We expect to have partnerships not only with other public funding sources, such as the other 26 NIH institutes and centres, but also with many other governmental agencies, private foundations and private-sector organizations. Indeed, public-private partnerships, such as the SNP Consortium, the Mouse Sequencing Consortium and the International HapMap Project, provide powerful new models for the generation of public data sets with immediate and far-reaching value. Thus, many of the most exciting opportunities in genomics research cross traditional boundaries of specific disease definitions, classically defined scientific disciplines, funding sources and public versus private enterprise. The new era will flourish best in an environment where such traditional boundaries become ever more porous.’ A Vision for the Future of Genomics, National Human Genome Research Institute, US, 2003
All strictures, boundaries, single vision
All strictures and boundaries, single vision –
art’s rosy blinkers - ornate, many-coloured;
or gleaming frames of chilled steel science -
constructed; restricting niches cut in a whole.
That noose with which we hanged our God
was woven in our minds; man-made fibres
for the stifled god that we had fashioned -
limited; absolutely, arrogantly described;
when the star is of stone, gas, ice, white
fire, but also light, five-pointed symbol -
nexus of wishes, lamp for sailors, epitome
of cold beauty sparkling in space portraits;
night-dust of wonder, depressed perspective -
not one, but all these real, interlinking aspects.
Yet we have shown the Genome as exhibition
of humanity; gone back to roads, paths, fences,
before even understanding, knowing how
we have been imprisoned, cut off, isolated
from all the other earthly creatures - kin -
how hippies got it right…! Earth is mother;
animals and flowers, our sisters and brothers,
not in foolish gooey sentiment, but science -
not wishful syruping, but in fact; now flexible,
not brittle, overly defined as was, inaccurately.
Re-thinking is required if healing is to come;
saving Earth is not baking wholemeal bread,
porridge-coloured jumpers, henna’d tresses -
not protest, but sense; urgent, necessary, right.
‘There are patterns. Organisms all have their relations and their place in a context – they can exist only within quite special circumstances.’ Mary Midgley, Science and Poetry, Routeledge, 2003
‘The opossum shrimp was introduced in Flathead Lake in Montana and in other lakes and reservoirs in the USA to provide an extra food source for economically important salmon. Unfortunately, the introduced shrimps ate so many native small crustaceans, which were the primary food source of salmon, that the salmon fishery collapsed. The loss of salmon as a food source adversely affected populations of bald eagles and grizzly bears.’ BBC, 2006
‘…the extreme individualistic model of selfhood – the social atomism which underlies social contract thinking - treats each self as independent, an object like a billiard-ball radically cut off from its fellows…It is a solitary atom gyrating in a social void, a radically solitary rational entity moving among a crowd of others with whom it has no real connection. This is a world which does not easily find room for non-rational humans such as babies and a world which can scarely accommodate non-human nature at all. The Buddhist self, by contrast, lives in a world without frontiers and must recognise a great range of other beings, human and otherwise, as literally continuous with itself.’ Mary Midgley, Science and Poetry, Routeledge, 2003
All is divided because we cannot see the whole;
carving existence until it fits our mental plate -
subject and animal, knowledge and love,
like an over exuberant clerk filing madly,
obsessively, as time goes on and the papers
increase, and he locks away whole sections
but for the few; too specialised, too difficult
for you, so you must let it go, no comment -
no say, no wondering, no challenge, thinking;
just dull acceptance, science fiction, outrage,
misunderstanding; when a new synthesis
is required, fresh foundations, structures -
for experts in one thing are not experts
in everything, whether scientist or poet,
citizen, cleric. As the greater picture
is of one world, one frame of being
where all come beautifully embroidered
at their time; all must be acknowledged
as connected, as important – for each
is made by four billion years of work,
as each is born alone, but still connected
to the whole, each must know; to wonder.
‘He hangs between… In doubt to deem himself a God, or Beast…’ Alexander Pope, 1688-1744, An Essay on Man
‘And out of the ground made the Lord God to grow every tree that is pleasant to the sight and good for food; the tree of life also in the midst of the garden, and the tree of the knowledge of good and evil.’ Genesis 2, The Bible
“What am I? Or from whence? For that I am/ I know, because I think; but whence I came,/ Or how this Frame of mine began to be,/ What other being can disclose to me?/ I move, I see; I speak, discourse, and know,/ Though now I am, I was not always so./ Then that from which I was must be before:/ Whom, as my Spring of Being, I adore…’ John Dryden, The State of Innocence and Fall of Man: An Opera: 1631-1700
‘But there went up a mist from the earth, and watered the whole face of the ground. And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.’ Genesis 2, The Bible
‘A first pass into this type of large-scale evolutionary biology is presented with the study of gene birth and death in humans. Of course, this newly discovered genomic plasticity, notably the duplicated genes within the segmental duplications, presents the ideal 'evolutionary putty' for positive selection. Very recent duplications appear to account for about 1200 genes, most of these occurring within larger gene clusters.’ European Journal of Human Genetics, 2005
Coming from the Clay
So we did come from the clay -
but not on a single exulted day;
we are the living work of art,
pulled slowly from the heart -
God, the catalyst, creator, artist -
from the earth we were practised.
‘Deem not thyself from harm secur’d/Pholas!* in rock or oak immur’d/ Or more tenacious clay;/ Howe’er thy wish to live retir’d,/ Unseen, unsought, and unadmir’d,/ Yet by they tempting beauty fir’d,/ We bring thee forth today.// Gracefully striate is thy shell,/ Transverse and longitudinal,/ and delicately fair;/ But why that magic luster bright?/ For sure thou art no erudite,/ Studious to trim the lamp by night,/ Or breathe the vesper prayer.’ *Pholas: the piddock, which has the faculty of burrowing into sand and soft rock.’ Sarah Hoare, 1777-1856, Poems on Conchology and Botany
‘…who doth not see in daily practice/ Art can beget bees, hornets, beetles, wasps,/ Out of the carcasses and dung of creatures;/ Yea, scorpions of an herb, being rightly placed?/ And these are living creatures, far more perfect/ And excellent than metals…’ Ben Jonson, 1572-1637, The Alchemist
‘ …for scientific knowledge itself, atomism seemed to promise a most reassuring kind of simplicity and finality – a guarantee that the world would prove intelligible in the end in relatively simple terms, once it had been split up into its ultimate elements. In fact, understanding the world seemed to be essentially a matter of simplifying it so as to locate these ultimate units…. But…on