Schedule
Tuesday 19 July, 2022, 10:00 - 11:30 CEST, online (green room)
10:00 - 10:05
Richard Löffler - Introduction10:05 - 10:20
Shinpei Tanaka - Irregular/regular oscillatory behavior of a decanol droplet releasing surfactants around a paraffin droplet acting as their sink10:20 - 10:35
Pasquale Stano and Luisa Damiano - Synthetic (artificial) cells research: is impressive technical progress leaving important theoretical investigations one step behind?10:35 - 10:50
Nathaniel Virgo - A case for a slow, messy start to the origin of life10:50 - 11:05
Klara Hlouchova - Proteins from reduced alphabets: can they be useful?11:05 - 11:20
Tomoko Yamaguchi - Developing a visible detection method for early ribosome function11:20 - 11:30
Invitation to join the COST Action CA21169 - Information, Coding, and Biological Function: the Dynamics of Life (DYNALIFE)
Abstracts
Irregular/regular oscillatory behavior of a decanol droplet releasing surfactants around a paraffin droplet acting as their sink
Shinpei Tanaka
Graduate School of Advanced Science and Engineering, Hiroshima University, Japan
A droplet of surface active substance floating on the water surface changes the surface tension around it by releasing its surface active substance. Even if the release is centrosymmetric, the situation is unstable when the surface tension gradient is large enough. Then a slight motion of the droplet breaks the symmetry and the droplet starts self-propelling. When the surface tension gradient is not large enough, the droplet cannot break the symmetry and it will stay still. However, if there is a broken symmetry written in the environment, such as the existence of a sink of surface active substance, the droplet's self-propulsion can be sustained even under such a situation. Chemotaxis is probably a good example of the situation. In this study, we introduced such a broken symmetry using a mobile sink, that is, another droplet of different substance. Then two droplets form a source-sink relation and we observed that they exhibited significantly robust and sustained self-propulsion. Furthermore, we also observed several modes of motion, including rectilinear oscillation towards and away from each other. In this talk, I would like to show our experimental observations and discuss their behavior by proposing a simple mathematical model.
Synthetic (artificial) cells research: is impressive technical progress leaving important theoretical investigations one step behind?
Pasquale Stano(1) and Luisa Damiano(2)
(1) University of Salento, Lecce, Italy; pasquale.stano@unisalento.it
(2) IULM, Milan, Italy; luisa.damiano@iulm.it
In recent years the research on so-called “synthetic (artificial) cells” has been characterized by a momentum which was difficult to predict. In particular, the community of practicioners has grown significantly, also thanks to initiatives like the MaxSynBio consortium in Germany, the BaSyC (Building a Synthetic Cell) project in the Netherlands, the European Synthetic Cell Initiative (SynCellEU), the Build-a-Cell community in US, the fabriCELL project in UK, and Japanese programs such as CREST-PRESTO, or the events promoted by the Japanese Society for Cell Synthesis Research.
A very impressive acceleration on experimental studies on the construction of synthetic cells of different types can be identified just by looking at the number and quality of articles published on these subjects, very often in high impact-factor journals. This intense phase of research will probably attract many young and motivated scientists, who will pursue advanced studies in the next decades. Moreover, the combination of several approaches has produced a quite diversified research arena that literally shows the lively developments and the general enthusiasm around this topic – which is probably one of the most exciting among novel technologies. Synthetic cell technology, indeed, does not resemble anything previously existing and has the potentiality of driving a revolution in future science/technology.
Despite this impressive technical progress, it can be argued that important theoretical investigations related to what synthetic cells are and how they behave, how they can be “interpreted”, what is their epistemological role in scientific knowledge have not received sufficient attention. We refer, in particular, to a series of aspects that probably need dedicated studies in order to approach this fascinating research area from the theoretical side too. More in particular, synthetic cells can be considered as belonging to the wetware approaches to the “sciences of artificial”, whose aims focus on the understanding-by-constructing approaches.
For example, several open questions can be connected to the role played by synthetic cells as tools for investigating, e.g.:
Organizational theories of living systems
Understanding and distinguish types of relevance with respect to reference theories, such as autopoiesis, chemoton, (M,R)-systems.
Information theories
Application of syntactic (C. Shannon) vs semantic (D. MacKay - G. Bateson) theories, role of (cyber)semiotics (D. Nauta), emergence of meaning.
Complexity
Definition of synthetic cell complexity, possible ranking of synthetic cells.
Cybernetic Inheritance
Synthetic cells as a late product (and a reappraisal) of cybernetics (1st vs 2nd order) and systems theory.
Cognitive Sciences
Minimal cognition, mind-like characteristics, emergence of self.
Artificial Intelligence
Can synthetic cell research contribute to AI (and vice versa)? Implanting chemical AI devices in synthetic cells.
In this contributions we will briefly sketch what we believe are crucial aspects related to the above-mentioned issues, and present some preliminary ideas, based on our already-published and ongoing studies. An important take-home message will result: together with their impactful experimental results and potential applications, synthetic cells can play a major role in the exploration of theoretical questions.
A case for a slow, messy start to the origin of life
Nathaniel Virgo
ELSI, Tokyo, Japan
The origin of life presumably took a long time. Even if life appeared instantaneously on geological time scales, the chemical processes that led to it could still have played out over millions of years. In contrast, reactions in the lab tend to take place over hours or days at most, being tuned for high yields and manageable reaction rates. In this talk I will argue that chemistry that takes place at low temperatures and on long time scales might be qualitatively different from the fast, high-temperature reactions that we are most familiar with, especially for reactions that are "messy", producing a high diversity of products. These qualitative differences between fast and slow chemistry might be important for understanding the origin of life. This is because we expect slow kinetics not just to be slower but also to exhibit greater relative differences in reaction rates, with the consequence that selective effects should play a generally greater role. I will discuss theoretical results in favour of this idea, as well as a preliminary experimental investigation of prebiotic chemistry on time scales of a year or more.
Proteins from reduced alphabets: can they be useful?
Klara Hlouchova
Charles University and BIOCEV, Czech Republic
All extant cells known to humankind build proteins from the same 20 coded amino acids. However, the study of origins of life implies that earlier cells functioned with a smaller alphabet, before the fixation of the Central Dogma. That is intriguing within today’s biology where each of the 20 amino acids occupies a unique and seemingly indispensable role. This profound evolutionary transition in our cells’ history therefore raises urgent questions: how could early proteins support a protobiosphere and how easy or hard is it to build a functional protein from early vs. canonical alphabet? I will uncover the properties of proteins from early vs. canonical amino acids characterized by bottom-up approaches. Additionally, the effects of selected unnatural amino acid incorporation will be elaborated. We used highly combinatorial libraries composed of different amino acid repertoires as proxies of the sequences space available at distinct evolutionary periods. The ease of their expression and structure formation under different conditions were compared. Our work indicates that structured conformations were readily available already to early protein alphabets, capitalizing on interactions that are less frequent or rare in today’s biology.
Developing a visible detection method for early ribosome function
Tomoko Yamaguchi(1,2) , Shota Nishikawa (1,3) , Klara Hlouchova (2) and Kosuke Fujishima(1,3)
(1) Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
(2) Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
(3) School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
RNA and protein are both essential for life. However, origin and evolution of these biopolymers as well as the process of gaining function, remain elusive. Here we have focused on the evolution of the ribosome known as the molecular fossil of the RNA-protein world. Ribosome is an enormous molecular complex required for protein synthesis, while itself consists of three RNA components and dozens of ribosomal proteins. Ribosome is highly conserved in three domains of life. Especially, the core of the 50S ribosome is called Peptidyl transferase center (PTC) and is composed of highly conserved RNA with a catalytic function. It is hypothesized that ribosome evolved around this PTC gaining additional RNAs and peptides (Petrov et al., 2014). To experimentally validate this hypothesis, we are currently developing an in vitro method to visibly characterize the peptidyl transfer activity using different constructs of the PTC RNA, protein fragments and tRNA substrate amino acylated with fluorescent-labeled amino acids. If peptidyl transfer occurs, fluorescent signal will be transferred to another minihelix RNA substrate, thus visualized as a band shift on the gel. We look forward to share our preliminary experimental data and further discuss target primitive PTC structures to be tested.
Information, Coding, and Biological Function: the Dynamics of Life (DYNALIFE)
In the mid-twentieth century two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning cross-fertilisation was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids.
However, today, such synergy has not take advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges are not only of great theoretical relevance but also represent unavoidable milestones for next generation biology: from personalized genetic therapy and diagnosis, to artificial life, to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered long time ago in Europe, and that requires combined contributions from disciplines well outside the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. The successful achievement of these tasks requires a wide multidisciplinary approach, and Europe is uniquely placed to construct a world leading network to address such an endeavour. The aim of this Action is to connect involved research groups throughout Europe into a strong network that promotes innovative and high-impact multi and inter-disciplinary research and, at the same time, to develop a strong dissemination activity aimed at breaking the communication barriers between disciplines, at forming young researchers, and at bringing the field closer to a broad general audience.