MAKING_LIFE 2014–2015

We Are The Only Chance

Our morning started with a interesting and quite in depth lecture by Rupert Mutzel - "Panspermia or Not"

Important to note the operational definition of life: "The characteristic that distinguishes organisms from inorganic substances and dead objects" (Wikipedia), it doesn't really say anything about life.  Referring to the article "Nothing makes sense in biology except in the light of evolution" by Theodosius Dobzhansky (1964) we discuss that the phenomena observed can only make sense under the framing of evolution, contrasting to the religious view.

Rupert's lecture led us to discuss The Last Universal Common Ancestor, LUCA, which is our limiting factor, it is how the basis of all life and 'unity' is understandable as a consequence of common descent. Hacking biology can give a chance to other organisms and species that cannot survive without our intervention, we are their only chance. It could be said that natural selection blocks innovation.

 

Strategies he went through for creating artificial life forms including BioBricks, Moore’s law in DNA sequence analysis and chemical gene/genome synthesis, Synthetic Biology by trial and error?... but Nature knows “how to” - we call it evolution.

 

Adopting "Darwin’s Dampfmaschine" in which each generation the living organisms are just a way of gene amplification, scientists design the devices that go through directional evolution for the bacteria.

 

Rupert's research involves continuous culture devices and is a combination of elements of the Chemostat (nutrient flow is constant) and Turbidostat (nutrient flow is conditional to cell density - selecting those who grow faster). Originally, they were designed for experimental evolutions. The real game is - who is the one who is left in the system in the end -> those that have not disappeared. The problem is continuous cultivation of cells in chemostats or turbidostats invariably selects for adhesive, static variants.

 

Rupert’s experiment is trying to use the technique of experimental evolution to evolve new bacteria that can use modified thymine (thymine with a -CH2 modified to -Cl, which is non-existing in nature). Rupert is using on and off pulses, switching between giving the bacteria thymine (non-stressed) v.s. chloride modified thymine (stressed) to let the bacteria go through evolution. Where in the end he successfully evolved bacteria that can use modified thymine within a few hundred generations. In the end there are even bacteria strands that cannot endure thymine.

  Is the system selected by growth? In each case it can link to growth of the organisms

A new form of life?

Could it have been created in vitro?   How many mutations to get there?  About 10,000- 400 hundred generations.   Why hasn't it happened in Nature?  May be it is and has - this is evolution.   Constraint propagation (“frozen accident”): Natural selection blocks innovations, problems in natural systems, there are too many wild types, one will never get the chance to recover from the lower status. How could it be done differently? Xenobiology Here we were discussing experimental evolution, with Rupert's example of modifying bacteria with a thymine base with Cl adding chloride instead. How can we make E. coli grow on chloride?  This experiment shows that it is possible to modify a bacteria to become something else. But what happens later, after?  The lifespan of computers are short, can we read the data later, how will we read it in the future.  
  Today's experiments: 000 Experiment by Oron, Inoculation: anaerobic bacteria from mouth Using blood plates and salt plates to grow bacteria from teeth and gum.  
001 Experiment By Andy, Part 1, Halophile Salts
The halophiles we use are stored in salt crystal form. They have the gvpA gene which forms gas vesicles (Vac+). This determines the colour of the growth.      

• 5 ml medium in each tube, take 25ml in total for 5 tubes


• Add salt crystals into the medium


• Inoculate at 42 degrees


 

      002 Experiment by Andy, Part 2, Halophile Plates       Using 25% salt medium to grow Halobacterium NRC-1.    

• Each person has three plates, marked streak, spread, and control group.


• Streak plate, use inoculation loop, dip into the bacteria medium to streak the plate to form single colonies.


• Spread plate, pipet some medium onto the plate, then spread it using a spreader.


• Control plate, just put anything onto the plate to prove that nothing grows.


 

      003 Growing Rupert’s experimental evolved E. coli       Growing the experimental evolved E. coli using minimum salt medium. At concentrations of 0 M, 0.6 M, 1.2 M, and 1.8 M NaCl.   Strands including wild type E. coli (marked type ‘B’), and experimentally evolved (‘A’) bacteria flown directly from Berlin with Prof. Rupert.        

1. Label the 4 Falcon tubes: Final salt concentration, strain ID, date, group ID.


2. Distribute growth media from the 0 M and 1.8 M NaCl media into these tubes in order to have 6 ml final medium each, containing 0, 0.6, 1.2, 1.8 M NaCl. Keep the rest of the 0 and 1.8 M NaCl media until final analysis as sterile controls.


3. Inoculate each tube with a lapful of bacteria scraped from an agar plate. (For ‘A’, use a lots of material. Because they have been selected as hard to grow on the surface, they don’t grow well on the agar plate, all we can see are really small colonies).


4. Screw the cap loosely in order to allow for air to pass, fix with adhesive tape.


5. Incubate at 30C until friday with good aeration (shaker)


6. Inspect tubes for growth.


 

The Discussion 

We finished the day with a long discussion about the themes we have covered so far. Stephen started the conversation with questions concerning Andy's approach to the lab coat. The response that for an artist a lab coat is a ceremonial item brought up the question of how the clothing you wear affects your experience and/or how you engage with a situation.  The playfulness that was discussed in Rupert's talk is brought out in a thinking by doing process and the lab coat is also part of this process. It is clear that we cannot reach significant conclusions in our week long workshop but what we can do is think as we do - it's about the doing not the result. This hands on approach can help when developing conceptual thinking around this subject, the process that you follow gives you the tools to be able to converse about this.

After this we moved onto criticism of some of the approaches that had been brought up earlier in the day i.e. BioBricks. Rupert's approach is different  and involves altering the environment to enable certain characteristics to evolve from the top down and bottom up. The environment, the relationship between the organism and the environment. Can bio-organism be designed as circuit? Rupert has a well defined goal and he just sets up a pathway to get there. It is not just feedback, there is a pattern. If evolution is evolving randomly then they are evolving individually, they will never get to exactly the same point, but close, they still have the same patterns and a lot of over-crossing.  It is important to remember that the environment is the selective force that alters the behaviour, we are creating changes and alternations within diets, for example. Laura then states something beautiful "When we change the world we change also and when we change, the world also changes". The environment is always acting on us.

We end the day with Oron opening the question about ethics, the use of language i.e. Nature, as a limiting force and the contrast in thinking concerning Western and Eastern philosophy and nature perceived in a religious context. How do we proceed when we will never have a shared ethic across the world. In the end of our discussion Oron asks "What is responsibility?" for us to consider.

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