28 September 2011

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


Don QuiScottie said...

And some people claim that I am engaged in deluded and pointless endeavours?... But you give me a worry Mr O'Donnell: typos encoded in DNA? My noble head is swirling somewhat at the possibilities... We have just hobbled past a place called Scotch Corner as we wander towards Romford, but it is not Scotch and it is not really a corner. And yet... people do claim that I am mad... And after more than a day in England I have yet to meet an Eng. And yet... people (such as Canadian Clod, I mean Claude), do claim that I make no sense... Look into yourselves, dear people, before accusing and abusing the Don.

jams o donnell said...

I know it is a rather curious way to express one's art!

I know Don the English are a strange breed that could do with the attention of a noble knight. Perhaps there would be more incentive to change if you let Rocinante have rest and saddled up on Ted.

Ted would be most agreeable if you explain to him that there will be plenty of opportunity to rend, tear and eviscerate!

Don QuiScottie said...

I am more concerned that Ted may intend to put his saddle on me. Is the original still mere pussycat size? It's the forty foot clones that worry me most, although the original is probably still the most dreadful. I can't believe that some people have not been paying attention and (according to their latest comment at Omnium) have no idea of the things we are on about. If people would pay attention they might realise that Taming typos and Terrible Tall Teds, Smiting Smileys and Wasting Windmills are the only activities that can possibly delay or even halt The End Times. I shall battle on alone though, even if some can't see what is right before them... I am indeed In-Sane, as in inside the state of sane, while everyone else seems just plain mad. Seanso, Shaunso and possibly you mysterious Master Jams (about whom I have growing suspicions) do have an inkling of In-Sanity too. Where is Shaunso when Jams is around? Hmmm, intriguing... and he does love to dress up.

jams o donnell said...

Ted is now 19 hands high and built like a destriere. that would give a Clydesdale a good kicking!

While he is evil he does like to provide the occasional pro bono service for the right kind of berserker.

Let them think we are all mad My dear Don. While they think we are harmless we can plot the downfall of nations!

Shaunso is not far away. He is relaxing with a bucket of whisky and seven or eight buxom serving girls

Don QuiScottie said...

Seven or eight? That sounds like Shaunso. The thick squire never could count.

jams o donnell said...

Ah he is cleverer than you think. He expends a lot of effort in drinking heroic quantities of the Water of Life and servicing ample wenches just to look like a pasty faced dullard in the morning!

Father Jack said...

Feck! Arse! Drink! Girls!

Sean Jeating said...


jams o donnell said...

The wisest words I have heard in ages father!

Sean, Shaunso said his last drinking session was just like that, except the girls wore less and he was drinking whiskey out of a bucket... oh and they were all singing the Ball of Kirriemuir instead of La Traviata!

susan said...

I must admit I don't see the point.

jams o donnell said...

I have to ask myself that too Susan!

SnoopyTheGoon said...

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

I shudder. Imagine the epitaph for humanity: "Killed overnight by an amateur poet's verse". Jeez...

jams o donnell said...

Haha what a fate for the planet Snoopy!