Universidad de Granada, Spain
More than 3.5 billion years ago, something interesting happened on Earth. Somewhere matter self-organized so that it was able to reproduce its complex state. Life had begun. Where and how that happened are questions whose answers, after many centuries, seem at last within reach. About four decades ago there were discovered hydrothermal vents at the bottom of the oceans; thirty years ago it was proposed that cool, alkaline vents ought to exist; the first of these were found in 2000, and there is now increasing evidence that submarine alkaline hydrothermal vents may have been the cradle of life on Earth. Such vents are geological examples of chemical gardens, self-assembled complex structures of membranes, tubes and vesicles resembling plants that are, however, completely abiotic, being produced by simple chemical precipitation reactions involving metal salts and anions such as silicates, carbonates, phosphates, cyanoferrates, and many more. Chemical gardens have been known about for centuries, and their complex morphology has from the beginning marked them out as having a possible relation with the living world. Today we know that chemical gardens are not in and of themselves alive, but that they may have served as reactors within which complex (bio)chemistry could begin; as vesicles constituting the first protocells. In this talk I shall outline how the modern interdisciplinary field of chemobrionics, emerging from chemical gardens and similar phenomena, and combining chemical reaction, fluid mechanics and osmotic processes, arose, and how it contributes to the present drive towards understanding where and how life on Earth began.
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, United States
Certain facets of life arise readily in a range of non-living systems. These include chemotaxis, homeostasis and reproduction, among others. Bone fide evolution is one of several grand but elusive goals for artificial life and origins researchers. It is also unclear what nonequilibrium driving forces could lead to the coalescence of biomolecular components into a recognisable cellular system. Here we present a promising direction that appeals to notions of information processing, computation and learning, abilities that fundamentally distinguish life from non-life. We propose two approaches: 1) the modelling and experimentation of chemical systems with learning abilities, and 2) the use of computational mechanics techniques to quantify the response of experimental and model systems to their external (dynamic) driving forces.
As well as the vast literatures of cybernetics, neuroscience and machine learning, there are also numerous examples of simple learning processes by the most primitive forms of life. There are also various studies alluding to the learning abilities of chemical systems (in addition to the rapidly growing field of DNA computing). Demonstrations of e.g., Hebbian learning in a simple chemical system such as oil droplets, would mark a significant step towards truly adaptive wet artificial life.
Furthermore, employing the mathematical framework of computational mechanics, one can calculate the statistical complexity of time series or even multi-dimensional data. This metric, among others, quantifies the ability of a system to compute on its inputs or boundary conditions. Given recent progress in messy chemistries and high throughput chemical experimentation, there remains a need for objective metrics with which to screen and analyse system responses. We propose that epsilon machine reconstruction offers an ideal method to compute complexity and information theoretic metrics that can be used to compare ensembles of chemical systems (either modelled or lab generated).
BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
OPTEC, Optimization in Engineering Center-of-Excellence, KU Leuven, Belgium
Introduction
A central question in the problem of the origin of life is how systems of interdependent components could arise in nature. Starting from Darwinian principles, a mathematical framework is developed to illustrate the conditions under which a homogeneous group of actors could diverge in the trait space to form a complex system. The mathematical model is rooted in the field of adaptive dynamics, an approach which utilizes evolutionary game theory to understand the evolution an asexually reproducing population in the trait space. The theoretical principles are subsequently applied to the problem of specialization of duplicated genes.
Methodology
A differential equation model is designed to describe the evolution of a homogeneous system under natural selection. The conditions for the arise of “branching lines”, lines in the trait space where a population will branch to a set of phenotypically different subpopulations are investigated. Also, an individual based model is used to explore the various evolutionary outcomes predicted.
Results
It is demonstrated that a generalist gene with low catalytic activity for a set of reactions can diverge, after duplication events, to a set of specialized genes, depending on the existence of a design conflict between the specialized functions.
Conclusion
Through this work, a mathematical argument is presented to support and expand the Escape from Adaptive Conflict model for the evolution of novel protein functions.
Keywords: Evolutionary branching, Evolutionary game theory, Adaptive dynamics, Functional divergence
University of Wisconsin, Madison, United States
Living chemical systems have two distinctive features; self-propagation (to grow, reproduce) and adaptive evolution (to get better at self-propagating over time). It is clear that these macroscale features of living systems are the result of non-linear chemical reaction systems both internal to life and between life and its chemical environment. But what is less clear is whether particular topologies or dynamical behaviors of nonlinear chemical reaction systems can be understood as equivalent to “self-propagation” and “adaptive evolution.”
To motivate this question, I will describe some results from prebiotic chemistry experiments we are conducting. When we incubate out-of-equilibrium synthetic prebiotic soups with minerals, we observe complex non-linear behavior. This includes oscillations of free inorganic phosphate concentration in the solution and non-monotonic changes in light absorbance and in surface features indicative of surface fouling with organics. Absorbance and phosphate concentrations are not closely correlated in these dynamics. In contrast, when we serially transfer a fraction of grain-soup slurry to a vial with fresh soup and grain for a fixed incubation period, we see macroscale behavior involving repeated boom and bust cycles. In this case, however, the booms correlate with both reduced phosphate and more organic fouling at the end of an incubation period. What do these patterns suggest?
The dynamic pattern seen in serial transfer experiment can be explained within the framework of either ecology or evolution. On the one hand, it could be seen as indicating the existence of a dynamically-maintained, surface-associated chemical system that increases in abundance until it exceeds the a “carrying capacity,” resulting in a “population” crash. Alternatively, might be that serial transfer selection for more and more heritable chemical states so that the system evolves directionally, with the bust pattern resulting from the emergence of self-propagating parasitic species. We would like help from workshop participants to decide whether these competing explanations are actually different and, if they are, how they could be distinguished if we fully understood the nonlinear chemistry of these soup-mineral mixtures. We are also wondering what the wet ALife community would need to see to conclude that such spontaneously-appearing chemical dynamics are hallmarks of a truly life-like system.
University of Glasgow, UK
Evolution, once the preserve of biology, has been widely emulated in software, while physically embodied systems that can evolve in populations of physically interacting chemical entities are very rare. Recently, we presented a liquid-handling robot built with the aim of investigating the properties of oil droplets as a function of composition via an automated evolutionary process. The robot made the droplets by mixing four different compounds in different ratios and placing them in a Petri dish, after which they were recorded using a camera and the behaviour of the droplets was analysed using image recognition software to give a fitness value. A fitness function discriminated based on movement, division and vibration over 21 cycles, and gave successive fitness increases. Analysis and theoretical modelling of the data yielded fitness landscapes analogous to the genotype–phenotype correlations found in biological evolution. Inorganic chemical cells (iCHELLs) are compartment structures consisting of polyoxometalates (POMs) and cations, offering structured and confined reaction spaces bounded by membranes. These precipitation structures are part of a wider class of materials covered by the field of chemobrionics. Having successfully built robotic systems to investigate oil droplet systems, we are now moving towards automated chemobrionic experiments.
School of Integrated Arts and Sciences, Hiroshima University, Japan
Liquid droplets are a natural model of a cell. So far various droplet systems have been utilized in an attempt to build life-like chemical systems [1]. They have attracted our interests especially when they exhibit a self-propelling nature and their life-like behaviors [2]. In this respect, it is important to know how much complexity these droplet systems can manifest [3].
We recently found that droplets could exhibit complex behaviors when many droplets are gathered together [4,5]. Our droplets consist of alkyl salicylate and paraffin liquid, so chemically they are simple. As a single droplet, they are propelled by inhomogeneous surface tension field made by themselves [6]. Their self-propulsion is sometimes uni-directional, and sometimes reciprocating. Time scale of the reciprocating motion is an order of a second. Interestingly, these modes of motion disappear gradually when many droplets coexist. Then there appears an oscillatory motion, where droplets oscillate as a cluster. The period of oscillation is an order of several hundreds seconds, much longer than the timescale of single droplet oscillation.
The mechanism of a single droplet motion is basically unbalanced surface tension around a droplet. However, it is not yet clear how this unbalanced surface tension field can induce both single droplet and multi droplets oscillatory motions. In this workshop, we would like to introduce our experimental results on the complex motions of these droplets, in order to discuss the physical mechanisms behind them. We also discuss the possibility to enhance the complexity even more using a mixture of chemically different droplets.
[1] J. M. Parrila-Gutierrez, S. Tsuda, J. Grizou, J. Taylor, A. Henson, and L. Cronin, Adaptive artificial evolution of droplet protocells in a 3D-printed fluidic chemorobotic platform with configurable environments, Nature Commun., 8, 1144 (2017).
[2] T. Toyota, N. Maru, M. M. Hanczyc, T. Ikegami, and T. Sugawara, Self-propelled oil droplets consuming "Fuel" surfactant, J. Am. Chem. Soc., 131, 5012-5013 (2009).
[3] N. Horibe, M. M. Hanczyc, and T. Ikegami, Mode switching and collective behavior in chemical oil droplets, Entropy, 13, 709-719 (2011).
[4] S. Tanaka, S. Nakata, and T. Kano, Dynamic ordering in a swarm of floating droplets driven by solutal Marangoni effect, J. Phys. Soc. Jpn., 86, 101004 (2017).
[5] J. Cejkova, K. Schwarzenberger, K. Eckert, and S. Tanaka, Dancing performance of organic droplets in aqueous surfactant solutions, Collids Surf. A, 566, 141-147 (2019).
[6] S. Tanaka, Y. Sogabe, and S. Nakata, Spontaneous change in trajectory patterns of a self-propelled oil droplet at the air-surfactant solution interface, Phys. Rev. E, 91, 032406 (2015).
1Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO) \\ University of Trento, 38123, Trento, Italy; 2Chemical and Biological Engineering, University of New Mexico, MSC01 1120, Albuquerque, NM 87131-0001, USA; martin.hanczyc@unitn.it
Liquid droplets possess some life-like behaviors and have been the subject of artificial life studies. Life-like behaviors such as fission, fusion and movement can be artificially re-created exploiting highly simplified chemical systems. We mainly focused our work on moving artificial life forms: chemotactic 1-decanol motile droplets. Chemotaxis is defined as a stimulated migration towards an increasing (or decreasing) chemical gradient, and 1-decanol droplets, formed in an aqueous medium containing decanoate at high pH, show chemotaxis when a chemical gradient is placed in the external aqueous environment. This kind of movement can be compared to already well-described system of eukaryotic chemotaxis. For example, Dictyostelium amoebae migrates along an increasing concentration of cyclic adenosine-3',5'-monophosphate (cAMP) (Ševčíková 2010). Čejková et al. showed in 2014 1-decanol chemotaxis towards a salt source (Čejková 2014). This system works even in mazes and can be exploited to transport non living objects (Čejková 2016). There is a challenge and benefit to begin to interface living and artificial systems to exploit potential synergies, increase robustness or increase the functionalities of both systems. We then attempted to interface the purely artificial decanol droplet system with living cells. We developed our artificial chemotactic system to make it compatible with natural living systems by creating a partially hydrophobic alginate capsule as a protective unit that can be precisely embedded in a droplet, transported along chemical gradients and deposited. This system was able to transport Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae. Both bacteria survived the transport (Holler 2018). We afterwards conceived the idea to develop this system to transport even mammalian eukaryotic cells. We decreased the decanoate pH from 12 to 7 and tried to transport mammalian cells inside our alginate capsules. We found out that lung cancer cells can be encapsulated in alginate hydrogels and survive. When in capsules incubated in DMEM, the cells secrete into their environment some compounds that lower the surface tension and act as surfactants. Some of the molecules secreted by the cells modulate the surface tension of the alginate capsule too. This surface modification allows the normally hydrophilic hydrogel capsule to associate efficiently and for an extended time with the hydrophobic 1-decanol droplets and makes the transport selective for live cells. Lung cancer cell lines showed surfactant release only when placed in our artificial transport system, thereby reinforcing the interface between the artificial and living systems. This is an example of not only how the interface between artificial life and biological life could be designed but how the one system can augment the other.
This work was financially supported in part by the European Commission FP7 Future and Emerging Technologies Proactive 611640 (EVOBLISS) and by the European Union's Horizon 2020 research and innovation program under grant agreement 824060 (ACDC).
· Ševčíková, H. Čejková, J. Krausová L., Přibyl M., Štěpánek F. and Marek, M. (2010) A new traveling wave phenomenon of Dictyostelium in the presence of cAMP. Physica D: Nonlinear Phenomena 239 879-888
· Čejková, J. Novak, M. Štěpánek, F. and Hanczyc, M.M. (2014) Dynamics of chemotactic droplets in salt concentration gradients. Langmuir 30 11937-11944
· Čejková, J. et al. (2016) Chemotaxis and chemokinesis of living and non-living objects. Springer, Advances in Unconventional Computing 256-260
· Holler, S. Porcelli, C. Ieropoulos, I. A. and Hanczyc, M. M. (2018) Transport of Live Cells Under Sterile Conditions Using a Chemotactic Droplet. Sci Rep 8:8408
Polish Academy of Sciences, Warsaw, Poland
Based on a mixture of camphor and camphene, combining the malleability of camphene with the strong surface activity of camphor, we produced a wax-like, self-propelled, material useful for experiments on surface active objects of arbitrary shapes[1]. We propose that one of the uses for this Material is to investigate the collective behaviour of active matter on a water surface. For example, we believe that it is possible to design a system which resembles clustering of cocci bacteria [2].
A series of experiments was performed, forming the mentioned material into many 1-2mm sized spheroids and depositing them on a water surface. An interesting collective behaviour was observed similar to [3].
As the spheroids continuously deposit camphor and camphene onto the water surface, they first exhibit spontaneous complex motion and second, they repel each other on longer ranges due to the resulting gradient in surface tension. Simultaneously, if the environment is crowded enough, they occasionally get close to each other (short range attraction) and collide. Since the material is quite sticky, most collisions will result in aggregation of multimers of spheroids. Over time the system goes through an evolution of several different cluster sizes and cluster conformations. At the stage when only three or less clusters are left (number depends on system boundary size and number of spheroids), these larger clusters change conformation by rearranging spheroid “arms” in their extremities. Eventually, after about 3-5 minutes, a single cluster is left to rearrange itself until a steady state has been achieved, where no further rearrangement takes place and the cluster moves on the water surface. This system exhibits some resemblance to the populations of bacteria, mentioned earlier, which arrange themselves in similar clusters [4]. Further work could consist of a large system and continuous feeding of spheroids to simulate growth.
Furthermore, we aim to use already existing models for long range repulsion and short-range attraction [5] to perform computer simulations on systems studied. The comparison between experiments and theory could be very fruitful as both our novel material-system as well as theory concern two-dimensional case and seem to be flexible regarding the shape of objects as well as sizes/shapes of the boundary. The simple experimental system, we have designed, allows for easy modification of the parameters mentioned above and so is presents a rare, fast verification of theoretical results.
[1] R. J. G. Löffler, J. Gorecki, and M. M. Hanczyc, “A novel hybrid camphor-camphene wax material for studies on self-propelled motion on water surface (In preparation),” 2019.
[2] J. Barenfanger and C. A. Drake, “Interpretation of Gram Stains for the Nonmicrobiologist,” Lab. Med., vol. 32, no. 7, pp. 368–375, 2003.
[3] J. Čejková, K. Schwarzenberger, K. Eckert, and S. Tanaka, “Dancing performance of organic droplets in aqueous surfactant solutions,” Colloids Surfaces A Physicochem. Eng. Asp., vol. 566, no. November 2018, pp. 141–147, 2019.
[4] F. Nojoomi, Q. B. Nejad, and S. D. Siadat, “Inactivation of vancomycin-induced unstable L-forms of Staphylococcus aureus by horse serum,” Int. J. Mol. Clin. Microbiol., no. 1, pp. 77–81, 2011.
[5] N. G. Almarza, J. Pekalski, and A. Ciach, “Effects of confinement on pattern formation in two dimensional systems with competing interactions,” Soft Matter, vol. 12, no. 36, pp. 7551–7563, 2016.
1University of Chemistry and Technology Prague, 2 Polish Academy of Sciences, Warsaw, Poland
In Richard's part of the practical workshop, participants will get the opportunity to explore the relationship between shape and trajectory for Marangoni effect self-propelled objects. For that they can form a piece of a 50-50 mixture of Camphor and Camphene in their hands, using rubber gloves, making arbitrary shapes. These can be placed on a water surface in a petri dish in order to observe the motion. Jitka's experiments will focus on artificial chemotaxis of decanol droplets in salt gradients.