Investigating automated chemical evolution of oil-in-water droplets

One of the main unresolved questions in science is how non-living matter became alive in a process known as abiognesis, which aims to explain how from a primordial soup scenario containing simple molecules, by following a ``bottom up'' approach, complex biomolecules emerged forming the first living system, known as a protocell. A protocell is defined by the interplay of three sub-systems which are considered requirements for life: information molecules, metabolism, and compartmentalization. This thesis investigates the role of compartmentalization during the emergence of life, and how simple membrane aggregates could evolve into entities that were able to develop ``life-like'' behaviours, and in particular how such evolution could happen without the presence of information molecules. Our ultimate objective is to create an autonomous evolvable system, and in order tp do so we will try to engineer life following a ``top-down'' approach, where an initial platform capable of evolving chemistry will be constructed, but the chemistry being dependent on the robotic adjunct, and how then this platform can be de-constructed in iterative operations until it is fully disconnected from the evolvable system, the system then being inherently autonomous. The first project of this thesis describes how the initial platform was designed and built. The platform was based on the model of a standard liquid handling robot, with the main difference with respect to other similar robots being that we used a 3D-printer in order to prototype the robot and build its main equipment, like a liquid dispensing system, tool movement mechanism, and washing procedures. The robot was able to mix different components and create populations of droplets in a Petri dish filled with aqueous phase. The Petri dish was then observed by a camera, which analysed the behaviours described by the droplets and fed this information back to the robot. Using this loop, the robot was then able to implement an evolutionary algorithm, where populations of droplets were evolved towards defined life-like behaviours. The second project of this thesis aimed to remove as many mechanical parts as possible from the robot while keeping the evolvable chemistry intact. In order to do so, we encapsulated the functionalities of the previous liquid handling robot into a single monolithic 3D-printed device. This device was able to mix different components, generate populations of droplets in an aqueous phase, and was also equipped with a camera in order to analyse the experiments. Moreover, because the full fabrication process of the devices happened in a 3D-printer, we were also able to alter its experimental arena by adding different obstacles where to evolve the droplets, enabling us to study how environmental changes can shape evolution. By doing so, we were able to embody evolutionary characteristics into our device, removing constraints from the physical platform, and taking one step forward to a possible autonomous evolvable system.

Physicochemical complexity in complex chemical systems

Self-replication and compartmentalization are two central properties thought to be essential for minimal life, and understanding how such processes interact in the emergence of complex reaction networks is crucial to exploring the development of complexity in chemistry and biology. Autocatalysis can emerge from multiple different mechanisms such as formation of an initiator, template self-replication and physical autocatalysis (where micelles formed from the reaction product solubilize the reactants, leading to higher local concentrations and therefore higher rates). Amphiphiles are also used in artificial life studies to create protocell models such as micelles, vesicles and oil-in-water droplets, and can increase reaction rates by encapsulation of reactants. So far, no template self-replicator exists which is capable of compartmentalization, or transferring this molecular scale phenomenon to micro or macro-scale assemblies. Here a system is demonstrated where an amphiphilic imine catalyses its own formation by joining a non-polar alkyl tail group with a polar carboxylic acid head group to form a template, which was shown to form reverse micelles by Dynamic Light Scattering (DLS). The kinetics of this system were investigated by 1H NMR spectroscopy, showing clearly that a template self-replication mechanism operates, though there was no evidence that the reverse micelles participated in physical autocatalysis. Active oil droplets, composed from a mixture of insoluble organic compounds in an aqueous sub-phase, can undergo processes such as division, self-propulsion and chemotaxis, and are studied as models for minimal cells, or protocells. Although in most cases the Marangoni effect is responsible for the forces on the droplet, the behaviour of the droplet depends heavily on the exact composition. Though theoretical models are able to calculate the forces on a droplet, to model a mixture of oils on an aqueous surface where compounds from the oil phase are dissolving and diffusing through the aqueous phase is beyond current computational capability. The behaviour of a droplet in an aqueous phase can only be discovered through experiment, though it is determined by the droplet's composition. By using an evolutionary algorithm and a liquid handling robot to conduct droplet experiments and decide which compositions to test next, entirely autonomously, the composition of the droplet becomes a chemical genome capable of evolution. The selection is carried out according to a fitness function, which ranks the formulation based on how well it conforms to the chosen fitness criteria (e.g. movement or division). Over successive generations, significant increases in fitness are achieved, and this increase is higher with more components (i.e. greater complexity). Other chemical processes such as chemiluminescence and gelation were investigated in active oil droplets, demonstrating the possibility of controlling chemical reactions by selective droplet fusion. Potential future applications for this might include combinatorial chemistry, or additional fitness goals for the genetic algorithm. Combining the self-replication and the droplet protocells research, it was demonstrated that the presence of the amphiphilic replicator lowers the interfacial tension between droplets of a reaction mixture in organic solution and the alkaline aqueous phase, causing them to divide. Periodic sampling by a liquid handling robot revealed that the extent of droplet fission increased as the reaction progressed, producing more individual protocells with increased self-replication. This demonstrates coupling of the molecular scale phenomenon of template self-replication to a macroscale physicochemical effect.