Exploring astrobiology using in silico molecular structure generation

Abstract

The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, ‘animate’ matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic ‘chemical space’. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of ‘chemical spaces’ beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems.This article is part of the themed issue ‘Reconceptualizing the origins of life’.

Systems protobiology: origin of life in lipid catalytic networks

“…Similarly, it is pointed out that ‘Biochemistry, as we know it, occupies a minute volume of the possible organic “chemical space”. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components' [ 45 , p. 1].…”

“…In an example of a repertoire of N G = 100, composomes would appear only in micelles, whose sizes are compatible with N MAX = 100 [ 90 ]. With a much larger amphiphile diversity, say N G = 10 6 , likely to prevail at life's origin [ 45 ], much larger assemblies, such as small (0.2 µm) vesicles (a size consistent with total molecular count of 10 6 ), might portray replication/reproduction behaviour. We note that GARD dynamics of such large molecular counts has not been explored to date, yet such large counts are relevant to GARD's evolvability and emergence in a planetary context (see §§ 7.2 and 13).…”

Re-conceptualizing the origins of life

“…The models have enormous range, from purely computational chemistry of interacting programs [53,54] to models that seek explicit approximation of real chemistry. Meringer & Cleaves [57] and Andersen et al [58] are both on the latter side of the spectrum. Meringer and Cleaves use chemistry to motivate the construction of graph-based structure generation, aiming to understand the prebiotic formation of the chemical playing field, the universe of compounds used by biology, with an eye towards the potential design of novel (i.e.…”

Formation and Delivery of Complex Organic Molecules to the Solar System and Early Earth

“…From the analysis of organic matter in meteorites and other Solar System objects, we now know that abiotic synthesis can create a wide range of organic compounds far beyond those found on Earth. This hints that the degree of complexity and diversity of prebiotic organics is much larger than previously thought (Meringer and Cleaves 2017). It is therefore not surprising that there still remains a number of unexplained astronomical spectral phenomena, as the carrier of these phenomena may be organic compounds that we are unfamiliar with in the terrestrial environment.…”