hostblog

 from New Scientist

Greg Hampikian  and Tim Anderson from Boise State university on working on the theory that there are certain possible sequences of DNA that are lethal to life and are speculating on the existence of ’suicide genes’. They have developed software that generates every possible sequence of nucleotides - the DNA ‘letters’ ACGT - and then compare them to sequence databases to identify those that aren’t present. Those that don’t occur in one species but do in others are termed “nullomers”, while those that aren’t found in any species are termed primes. Hampikian and Anderson are concentrating on the shortest absent sequences so as to minimalise the  chance of them being absent through chance - and up to now they have found 86 stretches of 11 nucleotides that are non existant in humans as well as a large number that have never been found in any species. As of yet they are not sure whether these sequences have any biological significance in living organisms but the consequences could be wide ranging if they do. Currently they are splicing these sequences into bacterial and human cells to see what happens…

The reason this article has grabbed my attention, apart form being generally interesting, is that it may have relevance to this project, or at least to a longer term development of it. During a brief presentation of my research a few days ago I was discussing the idea of encoding the microbial data and drawings in binary for transmission, however Stuart Nolan suggested encoding them in 4 base, or in other words the quarternery system of DNA - As, Cs, Gs and Ts. This data could then be synthesised as DNA and inserted into, for example, E Coli and presented as a form of cultural data encapsulation. I liked the idea of a small Sojourner type mobile robotic platform roaming around carrying a small screen and a culture of E Coli carrying the images and data within its DNA as an update on the Pioneer plaques and the Voyager golden record.

There are parallels here with the project Genesis by Eduardo Kac in which a section from the book of Genesis was encoded as DNA and its insertion into JM101 bacteria. The problem of genetic scrambling over generations encountered in this piece is currently one of the big problems faced by research into using bacteria as long term data storage solutions. I’ve no idea what the odds would be of ‘artist produced’ DNA containing one or more of these ’suicide genes’ but surely the longer the string you encode the more chance of it containing some meaningful pattern apart from what was intended. Maybe the chance side effect of encoding an image of Marsden moor along with the organic state of the organisms that made it might also enable the bacteria to grow to enormous size, develop real artistic talent then explode.

I can see that this blog is getting hits, not loads but some, and I’m curious about who is actually reading it. Drop me a quick line or make a comment and reveal yourself!

Another couple of hours carrying out basic lab chores in preparation for the coming experiments with calcite forming microbes suspending in alginate. Before we know we can do the alginate work we have to know that there are the correct microbes in the soil samples and we have to get them in a pure culture. To this end I spent the day plating out 12 petri dishes with B4 medium in the hope of bringing out cultures of these particular bacilli.

The first step was to do a serial dilution of 2 of the soil samples (soil sample 1 has been pretty much abandoned due to being composed of mostly decaying root matter) to get a relatively low concentration of microbes in a liquid. Bearing in mind that there can be millions of bacteria in one millilitre of pond water a petri dish could easily become swamped if the sample is not reduced enough. Serial dilution is a process in which 1g of the soil sample is mixed with a few millilitres of a phosphate solution called MRD - maximum recovery diluent. 1ml of this solution is then mixed with another vial of MRD and the process is repeated again and again until we end up with concentrations of 1:1000, 1:10000 and 1:100000. We then use another smaller pipette to extract 0.1ml of each of these concentrations and spread them evenly on the petri dishes.

The whole process of putting the tip on the pipette, shaking the vial, taking off the top, flaming the mouth of the vial, extracting the solution, replacing the top, removing the top of the next vial, flaming it, inserting the solution, putting the top back on, ejecting the tip of the pipette repeated over and over again becomes at once meditative and tedious. Every step, and there are many whether you are pouring agar into petri dishes, doing serial dilutions or plating out the samples, has to be meticulous and thorough. Missing out one step can mean having to start all over again. I’m sure being a lab assistant would be a very, very tedious job.

Anyway, I now have 12 petri dishes plated out with 3 concentrations of soil samples 1 and 2 in duplicate incubating nicely to see what grows. I should probably do something vaguely digital soon…

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Experiment number 1:

To use Thiobacilli cultured from the soil samples from walk 1 on Marsden moor to generate enough acid to etch into copper sheet.

The soil samples have been mixed with ground sulphur as a food source for the bacteria and are currently on the shaker in the lab to see what happens. Initial Ph testing of the samples has shown them to be between 4.2 and 5.5, a lot lower than was expected and low enough to cause possible difficulties in seeing the effects of the Thiobacillus. Anyhow, there is still a chance that they’ll pull the Ph further down to around 2 or 3 and we’ll be able to confirm their presence and do something with them. Otherwise I’ll just go and get some new samples from more reliable Thiobacilli rich areas.

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Ph testing

flasks on the shaker

Experiment number 2:

To use calcium precipitating bacilli species to lay down tracks of hardened calcite.

We aim to isolate and culture these bacilli (rod shaped bacteria) from the soil samples from walk 1 and immobilise them in alginate, a reaction between Sodium alginate and Calcium chloride. The cultured bacteria will be mixed into the sodium alginate and mixed with Calcium chloride which rapidly produces the thick jelly like substance alginate. Using a fine syringe we can lay this into tracks which will eventually be turned into stone like calcite but there is also the possibility of creating cast 3D objects. Alongside creating some nice stone visualisations of the landscape I quite like the idea of models of Pioneer, Voyager, Sojourner and the Arecibo dish made by moorland microbes.

Experiment number 3:

To encode the data and drawings produced by the bacteria in quaternery (4 base) and synthesise it into DNA.

The information and ‘cultural’ activities generated by the bacteria can be synthesised into DNA and placed into an E Coli carrier. Using basic bacterial transformation techniques the new DNA can be spliced into the DNA of the bacteria and cultured on form there. I’d love to build a mobile robot that presents the data and images on its screen while carrying a sort of time capsule containing all the data encoded into the genetic make up of the E Coli.

The problem with this experiment is that its pretty expensive, time consuming and notoriously hit and miss outside of expert labs. We’d be looking at spending around £500 for enough kit to have 40 goes at making it work without the guarantee that it would. Might have to leave this one on the back burner for a while. At the very least, though, I should be able to encode the data into quaternery and work out the DNA base pairs from there – and possibly even find out if there are any functioning genes hidden away within them.

Yesterday I did an 8 mile circular hike laden down with stills camera, video camera, sound recording equipment, GPS and sampling pots from Marsden across the moors and across the lines of the Standedge tunnels after driving out to visit 3 of the transmission masts not far from here. It rained pretty much non-stop but it was fantastic anyway. I did the walk with the aims of reconnecting myself with the landscape, getting some decent stills and video of the area and collecting some soil (mud) and water samples from which to cultivate the microbes that will hopefully be doing all the work one day soon. More musings and meditations on the meaning and experience of the big wet hike later, a few pictures for now.

the route

At last I made it out into the country side and set foot on a little bit of the landscape I’m planning to work with. Here’s a few moody shots from the area around Marsden and the entrance to the Standedge tunnels.

M13 - a great globular cluster in the constellation of Hercules. Contains several hundred thousand stars and has a diameter of about 145 light years, 25,100 light years from Earth. The target of the Arecibo transmissions of 1974.

M13 - a filamentous bacteriophage composed of circular single stranded DNA 6407 nucleotides long encapsulated in approximately 2700 copies of the protein P8, and capped with 5 copies of two different minor coat proteins (P9, P6, P3) on the ends. A non-lytic virus 900nm long and 9nm in diameter which has been studied for its uses in nanostructures and nanotechnology.

You would need somewhere in the region of 237,459,163,405,574,600,000,000,000 M13 phages laid end to end to reach from Earth to the M13 cluster. A few less if you started from the roof. Given the fact that every millilitre of seawater contains 10,000,000,000 phages of some description it shouldn’t be too hard to collect enough M13s…

some thoughts. not especially new thoughts, but thoughts related to my research…

Our relationships with and interpretations of nature are transforming rapidly and have in fact been transforming for pretty much as long as humankind can remember. Many things that we term as natural, such as a cow, a forest or a sunflower are actually nothing of the sort. We have been selecting and modifying the animals and plants we need since prehistory and have, for example, extrapolated the poodle from the jackal – no one has built a poodle from scratch but neither has the poodle evolved without interference. An Earth without humans would be an Earth without poodles.

Its not just that we have created species that are not strictly products of nature but that we have also created artificial environments which species have colonised. Of the 1,935 flowering plants on Hawaii, 902 are alien and are dominating the native species, in many instances to the point of extinction - but if we go to Hawaii today we will perceive a beautiful natural environment. Many altered environments are a byproduct of human migration as species hitch lifts on boats and planes but many have also been created purposefully but short sightedly with disastrous consequences for native life. The ecology of Australia is a famous example which has spawned, amongst other things the 2023 mile long rabbit proof fence and the chain reaction of events sparked by the introduction of the cane toad.

The altered landscapes left by the explosive development of the industrialised and industrialising world have created a huge number of opportunities for species to colonise new habitats. New microbial communities exist wherever there have been mine workings, factories or quarries – the altered chemistry of the environment provides for the chemical needs of bacteria, whose own chemical processes further alter the environment. As microbes are the foundation for all higher life we quickly create whole new viable ecosystems. Other industries have demanded the plantation of vast timber forests or the destruction of others. Rainforest transforms to savannah or to desert and organisms capitalise – with microbes always at the vanguard.

Since the isloation by Daniel Nathans and Hamilton Smith of restriction endonucleases in 1978 (for which they received the Nobel Prize) it has been possible to alter the biological make up of – theoretically – any living organism. We now have the capability to create, mutate and generate a vast number of new organisms for scientific, agricultural and industrial uses. Bacteria, plants and mammals have all been created or modified that will resist disease, develop disease, produce substances, resist freezing, glow in the dark, grow faster, not breed, live longer etc etc etc. These organisms have to be seen as a viable part of nature – they are alive, many of them alive, kicking and breeding outside of the laboratory. GM microbes are kept and cultured as essential tools in a huge variety of labs and many aspects of modern life we now take for granted would be impossible without them.

One of the ironies we are left to deal with after the wholesale ‘improvement’ of our lives, our planet and our industry is that we may not have a great deal of time left to enjoy it. Here the new organisms are coming into their own as a ray of hope. Every single living organism on planet Earth has evolved, or been modified, to exist and thrive in the conditions that exist here, from the surface dwellers that form most of the species we know to those in the pitch dark, acidic, hot and hugely pressurised conditions of deep ocean trenches and hot vents. The apparently inevitable need to investigate new ‘off-world’ environments as a migratory destination or an ‘Earth annex’ places more need on science to develop versions of our much loved post-natural tomatoes, cotton and chickens that can live in more extreme or unusual conditions than they are used to. NASA are spending a lot of money making this possible and the ISS is a veritable biological laboratory. Again microbiology is at the vanguard and as we begin to replace hope with expectation about finding microbial life in the ice of Mars or the deep seas of Titan we discover a viable ecological connection.

So is nature natural? At what point do we mark the boundary, the point of transition when nature stopped being natural? If what we have now and what we will have in the future is not natural, what is it? Of course, these things are only ‘post-natural’ if we see ourselves as humans as not being a part of nature. If a natural organism alters another natural organism, as many do, we see it as an entirely natural process. We are natural, we have altered ourselves and our environment – we may not like it but we cannot remove ourselves from the picture.

And using the also pretty cool planetarium software Stellarium I can see where M13 will appear at any time on any night - at least theoretically as its 25,100 light years away from earth. Here’s where it will be tonight (8th May 2007) at 9.39pm if you were looking in an Easterly direction from the DRU:

I’m not sure if I’m going to focus on this cluster for historical purposes or not to be honest, and I’m not even sure if I can transmit with anything like the power necessary to make it a meaningful attempt. But here it is anyway…

Thanks to Celestia I will now be spending the whole 3 months flying at many times the speed of light only occasionally slowing down to take in the sights. I’ve made a couple of images to justify my time in deep space and have managed to find a way to upload to my blog from a distance of 80 quintillion parsecs.

here i am just sailing past Voyager 2:

and this is the globular cluster M13 - target of the Arecibo transmissions: