Bacteria

“It's remarkable that some of our genome seems to have jumped from bacteria into vertebrates without going through the evolutionary trail of most of the rest of the DNA. That indicates that periodically in the lives of people, DNA actually jumps from bacteria into us.” David Baltimore, Nobel Prizewinner, President, California Institute of Technology, US

‘Hundreds of human genes appear likely to have resulted from horizontal transfer from bacteria at some point in the vertebrate lineage. Dozens of genes appear to have been derived from transposable elements.’ "International Human Genome Sequencing Consortium" International Human Genome Sequencing Consortium, Nature, 2001

‘Remarkably, a couple of hundred genes found in humans are more similar to bacterial genes than to anything seen in yeast, worm, fly or plants. And they appear to have been transferred from a range of bacterial species. The same genes are found in other vertebrate species, indicating that they were introduced into the genome of a common ancestor and were retained during evolution of the vertebrate lineage. Is this a case of bacterial genes hitchhiking an evolutionary ride, or is there something in it for us? Most of the inherited genes encode enzymes and have been sequestered into specific pathways, such as stress responses and metabolism of environmental chemicals, suggesting that they have been adapted to important physiological functions. The relatives of the gene encoding monoamine oxidase (an enzyme of the mitochondrial outer membrane), for example, appear to be bacterial in evolutionary origin. Monoamine oxidase is involved in the metabolism of neurotransmitters, and is a target for important psychiatric drugs. The physiological functions in humans of the other bacterially derived genes remain to be determined.’ Richard Gallagher and Carina Dennis, Wellcome Trust, 2001

‘It can be argued that bacteria are the pinnacle of evolution, as they represent the most numerous species on earth. Humans, like other species, will continue to evolve as we have in the past.’ Ref

‘…the human species is by no means the pinnacle of evolution….The black-smoker bacterium, living in a sulphurous vent on the floor of the Atlantic ocean and descended from a stock of bacteria that parted company with our ancestors soon after Luca’s day, is arguably more highly evolved than a bank clerk, at least at the genetic level.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000

‘Each of us is a city of cells, and each cell a town of bacteria. You are a gigantic megalopolis of bacteria.’ Richard Dawkins, Unweaving the Rainbow, Penguin, 1998

‘An interesting category is a set of 223 proteins that have significant similarity to proteins from bacteria, but no comparable similarity to proteins from yeast, worm, fly and mustard weed, or indeed from any other (nonvertebrate) eukaryote…We did not identify a strongly preferred bacterial source for the putative horizontally transferred genes, indicating the likelihood of multiple independent gene transfers from different bacteria. Notably, several of the probable recent acquisitions have established (or likely) roles in metabolism of xenobiotics or stress response. These include several hydrolases of different specificities, including epoxide hydrolase, and several dehydrogenases. Of particular interest is the presence of two paralogues of monoamine oxidase (MAO), an enzyme of the mitochondrial outer membrane that is central in the metabolism of neuromediators and is a target of important psychiatric drugs. This example shows that at least some of the genes thought to be horizontally transferred into the vertebrate lineage appear to be involved in important physiological functions and so probably have been fixed and maintained during evolution because of the increased selective advantage(s) they provide.’ International Human Genome Sequencing Consortium

“This again reminds us of the unity of life - the fact that genes are not purpose-made for each organism, but rather evolution keeps on re-using its inventions over time. And it was known that this occasionally happened, but suddenly the scale is much greater - there's hundreds of genes that have come that way. Some people might find that scary, that we're exchanging DNA with bacteria all the time. We have to get used to this idea. Nature is not very prophylactic in what it does.” Sir John Sulston, Head, UK Human Genome Project, Newsnight transcript, BBC

‘Bacteria by contrast, exhibit a far wider range of metabolic variations than eukryotes… We, however, use just one of their many metabolic designs for energy production, namely that of aerobic respiration, the speciality of mitochondria.’ Microcosmos: Four Billion Years of Microbial Evolution, Lynn Margulis and Dorion Sagan, 1987

’The ancestors of mitochondria, when they lived on their own, evolved biochemical tricks that we call aerobic respiration. We eukaryotes now benefit from this advanced chemical wizardry because our cells contain the decendents of the bacteria discovered them. On this view there is an unbroken line of descent from modern mitochondria back to ancestral bacteria living free in the sea. When I say ‘line of descent’, I literally mean that a free-living bacterial cell divided into two, and at least one of those divied into two, and so on until we reach every one of your mitochondria, continuting to live in your cells.’ Er… Lynn Margulis and Dorion Sagan, Microcosmos: Four Billion Years of Microbial Evolution, 1987, or Richard Dawkins, Unweaving the Rainbow, Penguin, 1988 – oops.

Transfer of Bacteria

Teaching us to breathe below - above water -

from sea coming to us when we were dreams

in the darkness; tutoring passionately, quietly -

quaint metabolisms of stress, neurotransmitters;

skills with air, ability with bright brother-world,

insisting genetically all must be one - adaptable,

even these most humble servants; but never ever

underestimate bacteria - these tiny peacemakers

are genetic troops for good, assimilated, fully

integrated - at peace, enriching, co-operating -

but entering also as foes; raven-winged,

small black angels - even as devil-genes

written with the marks of death -

anti-Word, evil evolved; organic,

extant for all these millennia,

defying penicillin, medicine’s

evolving swords - bad molecules

that can never become part of us;

reformed, re-habilitated,

as some people stay bad. 

‘Where do our genes come from? Mostly from the distant evolutionary past. In fact, only 94 of 1,278 protein families in our genome appear to be specific to vertebrates. The most elementary of cellular functions - basic metabolism, transcription of DNA into RNA, translation of RNA into protein, DNA replication and the like - evolved just once and have stayed pretty well fixed since the evolution of single-celled yeast and bacteria.’ David Baltimore, Nature

It seems a bit miserable to be made of bacteria

It seems a bit miserable to be made of bacteria -

Makes you feel dirty, hoaching, somewhat inferior,

A bustle of bacteria not just up your posterior,

But spread throughout your entire interior -

Though before you go and drink down Dettol,

Allow the Genome’s proper message to settle –

Without the help of all these bugs,

We might have stayed bigger mugs -

And it’s not just the help with building brains,

From stuff more commonly found in drains -

The very metabolism of neuro-transmitters,

Adapted from them, such helpful critters -

Dealing with chemicals found outside,

I’d think twice before I was snide -

Without these bacteria brewed from the sea,

You wouldn’t be breathing, or drinking tea;

Without these biochemical wizards -

We might still be worms, flies, lizards.

So think on that next time you swim,

(and obviously don’t go near Vim) -

Some of the pleasure felt in your limbs,

Isn’t just because you once had fins -

All of you once lived in this water -

No wonder you feel quite like an otter;

Your blood and germs from salty soup,

Rose up from Nature’s mighty gloup -

Like Venus rising, from bugs and all -

So remember Pride cometh before a fall;

Don’t diss your humble bacterial roots -

Forget their art, good evolutionary fruits.

‘Hundreds of genes appear to have come from bacteria – one of which is a major pathway for depression. We don't understand the mechanism of transfer, and indeed it's possible that the bacteria have picked up our genes rather than the other way round – though this seems less likely. But either way it's a tremendous reminder of the unity of life, and of the fact that we don't live in a cocoon isolated from other species.’ Wellcome Trust

THE TREE OF LIFE IS UPSIDE DOWN

‘As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides, many a feeble branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth and covers the surface with its ever branching and beautiful ramifications.’ Charles Darwin, The Origin of Species, 1859

‘There has been this notion since Aristotle's time of this great chain of being with humans at the top and then less complex life at the bottom. But while that might seem intuitive to some people, it doesn't appear to be borne out by the data.’ BBC, UK

‘The tree of life as it appears in virtually every textbook may be upside down… it now looks as if bacteria came later, highly specialised and simplified descendants of the Lucas… it is we that have retained the primitive molecular features of the Lucas in our cells; bacteria are much more highly evolved than we are.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000

The tree of life is upside down       

The tree of life is upside down -       

the roots are the topmost branches;

we did not come from bacteria,

some of us became bacteria -

evolving better and better

survival techniques amid

huge extremes of heat and cold -

challenges of sulphur and dust.

Honing and streamlining, stripping

everything superfluous to survival;

anti-artist colonising everywhere,

even interiors of flesh machines.

We live in the Empire of Bacteria -

they are the purified Imperial Army,

pinnacle of Evolution’s ruthless streak;

miniscule dictators of the ornate world.

‘Geneticists have drawn up the most accurate tree of life yet and pinpointed what they believe to be the organism from which all other life on Earth evolved. Scientists construct tree of life "maps" to show how different organisms evolved over millennia, and split into the myriad species that have emerged on Earth. But previous versions have been beset with uncertainties, not least because microbes near the bottom of the tree swap DNA, making them hard to classify. The new tree uses genetics to work out for certain where on the tree different organisms should be. In creating it, the researchers were able to cast back to see what lay at the bottom of the evolutionary tree, an organism dubbed the "last universal common ancestor" from which all other life sprung. The researchers found that our oldest ancestor was very similar to disease-causing bugs of today. It lived in a much hotter environment, had a single membrane to keep it intact, and falls into the same group of well-known pathogens, Bacillus, Listeria, Staphylococcus, Enterococcus, Clostridium and Streptococcus. The tree will help researchers classify unnamed organisms and reveal how they evolved... Dr Ciccarelli and her team created the tree by first identifying 36 genes that are common to species in each of the three categories of life: bacteria, single celled organisms called archaea and the eukaryotes, which includes multi-celled organisms such as animals, plants and fungi. By combining the set of common genes with information from the genomes of 191 fully sequenced species, the researchers were able to work out precisely how one species was related to another...’ Ian Sample, Science Correspondent, Guardian newspaper, UK, 2006

‘Before ever land was,/ Before ever the sea,/ Of soft hair of the grass,/ Or fair limbs of the trees,/ Or the flesh-coloured fruit of my branches,/ I was, and they soul was in me//…The tree many-rooted/ That swells to the sky/With frondage red-fruited,/ The life-tree am I;/ In the buds of your lives is the sap of my leaves: ye shall live and not die.’ Algernon Charles Swinburne, 1837-1909

“It’s the first time all three domains of life have been brought together. You can compare the speed of evolution of different organisms and you can easily see that the pathogens evolve very fast, which makes sense because they have to adapt to the host's defences.” Francesca Ciccarelli, European Molecular Biology Laboratory

The tree of life is never still

The tree of life is never still -

her breezes are always change;

wind from the birth of the world

whispers her twitching branches -

her light is stars,

hung like fruit -

ripe, white, sparkling.

Invention, adaptation

are her grown golden rings,

green fire in invisible sap -

understanding the red-black plum

into formation of beating muscle;

patiently transforming clear sea

into a mystery of red salt blood;

her twigs bearing leaves, fingers -

branches, buds, arms, fins, wings;

her torso is elephant, tree and man,

her bark is scale and skin - feather.

Her peacock eyes are rainbow-hued,

where fiery pupils open and close -

showing us glimpses of the original fire,

white explosion at the heart of darkness -

a hand of light beckoning, coaxing;

word sounding - like a first music -

coaching star dust and gases - carbon;

coagulating cells’ wild creative spirit,

dancing plasticity, dreaming possibility,

into orchestrated expression; something

emergent, explosive worship of diversity -

but speaking always of the Earth and stars,

water and uncomprehended soul;

force yearning, haunting nothing,

noplace, until Earth’s dreaming blue embryo,

suspended - maintaining the notion of dream

creating reality - something touchable;

that one day we will hold to our breast,

every molecule newly born,

wet with the signs of birth -

written like the bright word on the forehead

of every man, also coming among branches -

in his palm, the leaf; bat, star -

at spring his fingertips bloom

white flowers like hawthorn blossom,

red blood rimming the finger-eyes -

sea that was beaten with iron,

remembers tides and Moon -

hung left above the tree, in the eyes

of owls, lemurs, wolves, bushbabies;

overhead directly, the integrated Sun,

her energy streams in strange words -

equations, theories, new hypotheses -

love for Earth’s tree, hot yellow word

of her essential love - her salmon-blood

word of gentle evening, illusory resting;

sighing under an opening canopy of stars -

whose jealousies of Earth are compounded

by thirst, frost, acid and stormy temperament,

the hopelessness of shining without gardens -

but ameliorated by kinship with flesh -

all molecules recycling, journeying on

their share of that living light;

photosynthesising of tree leaf -

love, light, and water -

theories of RNA, DNA,

struggling in that water -

practicalities of chemistry

expressed with art -

energy of creativity.

The Tree of Life had known of nothing else,

her branches might climb back to Heaven -

but now among the evening of the Tree,

leaves which only glow with spirit-light,

their creatures gone, extinct, removed -

these rightful branches, breathing fruits;

small starry lights that once prefigured flowers

that never came among these sullied meadows,

poisoned hedgerows, adulterated hills -

choking fish leap silver, back and forth

like shooting stars, dropping dew like tears

upon the sighing Tree – of filleted Mercury

that is the sickening of coagulated light.

The first brown leaf is set in static gold,

monument to her murdered, stolen leaves,

unnatural autumn; as black shadows slash

among the deepest, dearest branches,

the mutated roots of air combusting –

flames erupt among the mother Tree -

her green tongues burning into absence

of the word - anti-oxygen, blind to life;

the stinking processes of bad chemistry,

smoking black, consuming - anti-Genome;

the abomination of soil, pollution of light.

The Tree still shimmers, shifts, compensates;

sprouting endless, generous fruit and bounty,

but each twisted, broken twig,

family branch corrupted, blank,

accumulates a wound -

bleeding fungal darkness

that is the timeless child of nothing;

sister of death, waiting in the wings,

allowed yet further - closer, nearer

to the mysterious spark, pilot-heart;

such abundance and history sustaining

for now her still groaning canopies -

her art of Evolution driven

from first stars and water -

the voice that called her irresistibly,

as piper, lullaby, marching tune, jig; 

hiding the canker, hurt in original root -