Mathematical modeling reveals spontaneous emergence of self-replication in chemical reaction systems

Liu, Yu; Sumpter, David J. T.

doi:10.1074/jbc.ra118.003795

Cited by 27 publications

(35 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…each non-food molecule is generated at least as fast as it is used up), by Lemma 4.1 of [31]. Other dynamical aspects of RAFs concerning reaction rates have been explored in [7] and [32], and related dynamics have been explored recently by [22] and [28].…”

Section: 2mentioning

confidence: 99%

The structure of autocatalytic networks, with application to early biochemistry

Steel

Xavier

Huson

2020

Preprint

View full text Add to dashboard Cite

Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such selfsustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organisation of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualise RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide techniques to study and visualise the core aspects of primitive biochemistry.

show abstract

Section: 2mentioning

confidence: 99%

The structure of autocatalytic networks, with application to early biochemistry

Steel

Xavier

Huson

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…We first introduce one terminology: A chemical reaction network (CRN) comprises a set of reactants, a set of products, and how they are linked via reactions [34]. To investigate CRNs as broadly as possible, we employ the artificial chemistry framework that has been developed in a previous paper [35]. All of the CRNs that are constructed based on this framework satisfy basic physical principles such as mass conservation and thermodynamics, and some of them also correspond to real chemical systems.…”

Section: Theoretical Setupmentioning

confidence: 99%

“…• the criterion for "overproduction", i.e., there are some types of intermediate molecules, and the number of times it appears on the reactant side is less than that on the product side, • and the criterion for "no-over-intake", i.e., there is no type of intermediate molecules that the number of times it appears on the reactant side is larger than that on the product side, then it is irreducible self-sustaining (where intermediate molecules refer to those appear on both the reactant side and the product side of the whole CRN). Those CRNs refer to the "self-replicating" CRNs defined in [35], meaning that at least one type of molecules in this CRN is produced more than consumed so that if the resource is unlimited, the number of molecules can grow exponentially.…”

Section: Hypothesis: Two Extra Criteria Guarantee a Self-driven Crn Tmentioning

confidence: 99%

“…It is not an error but a poor legacy from a previous paper. The term "self-replicating" was used in the previous paper (ref 35) to refer to a particular property of a CRN, i.e., at least one type of molecules in this CRN is produced more than consumed. I admit that it may not be a good term to use in that paper, but here it is just for a reference and used once.…”

Section: Reviewer Comments 22mentioning

confidence: 99%

“…Here we recap main points of this framework [ 35 ]: (1) A molecule is denoted by an integer, ; (2) Only synthesis reaction and decomposition reaction are possible, and the sums of both sides should be equal, e.g., and ; (3) Each molecule has its own standard Gibbs energy of formation, and each reaction has its own Gibbs energy of activation, which together determine the reaction rate constant of each reaction.…”

Section: Theoretical Setupmentioning

confidence: 99%

See 2 more Smart Citations

On the definition of a self-sustaining chemical reaction system and its role in heredity

Liu

2020

Biol Direct

Self Cite

View full text Add to dashboard Cite

Background The ability to self-sustain is one of the essential properties of life. However, a consistent and satisfying definition of self-sustainability is still missing. Currently, self-sustainability refers to either “no-intervention by a higher entity” or “regeneration of all the system’s components”. How to connect self-sustainability with heredity, another essential of life, is another problem, as they are often considered to be independent of each other. Last but not least, current definitions of self-sustainability failed to provide a practical method to empirically discern whether a chemical system is self-sustaining or not. Results Here I propose a definition of self-sustainability. It takes into account the chemical reaction network itself and the external environment which is simplified as a continuous-flow stirred tank reactor. One distinct property of self-sustaining systems is that the system can only proceed if molecular triggers (or called, seeds) are present initially. The molecular triggers are able to establish the whole system, indicating that they carry the preliminary heredity of the system. Consequently, life and a large group of fires (and other dissipative systems) can be distinguished. Besides, the general properties and various real-life examples of self-sustaining systems discussed here together indicate that self-sustaining systems are not uncommon. Conclusions The definition I proposed here naturally connects self-sustainability with heredity. As this definition involves the continuous-flow stirred tank reactor, it gives a simple way to empirically test whether a system is self-sustaining or not. Moreover, the general properties and various real-life examples of self-sustaining systems discussed here provide practical guidance on how to construct and detect such systems in real biology and chemistry. Reviewers This article was reviewed by Wentao Ma and David Baum.

show abstract

Theoretical perspective on synthetic man‐made life: Learning from the origin of life

Peng,

Zhang,

Wang

et al. 2023

Quant. Biol.

Self Cite

View full text Add to dashboard Cite

Creating a man‐made life in the laboratory is one of life science’s most intriguing yet challenging problems. Advances in synthetic biology and related theories, particularly those related to the origin of life, have laid the groundwork for further exploration and understanding in this field of artificial life or man‐made life. But there remains a wealth of quantitative mathematical models and tools that have yet to be applied to this area. In this paper, we review the two main approaches often employed in the field of man‐made life: the top‐down approach that reduces the complexity of extant and existing living systems and the bottom‐up approach that integrates well‐defined components, by introducing the theoretical basis, recent advances, and their limitations. We then argue for another possible approach, namely “bottom‐up from the origin of life”: Starting with the establishment of autocatalytic chemical reaction networks that employ physical boundaries as the initial compartments, then designing directed evolutionary systems, with the expectation that independent compartments will eventually emerge so that the system becomes free‐living. This approach is actually analogous to the process of how life originated. With this paper, we aim to stimulate the interest of synthetic biologists and experimentalists to consider a more theoretical perspective, and to promote the communication between the origin of life community and the synthetic man‐made life community.

show abstract

Mathematical modeling reveals spontaneous emergence of self-replication in chemical reaction systems

Cited by 27 publications

References 55 publications

The structure of autocatalytic networks, with application to early biochemistry

The structure of autocatalytic networks, with application to early biochemistry

On the definition of a self-sustaining chemical reaction system and its role in heredity

Theoretical perspective on synthetic man‐made life: Learning from the origin of life

Contact Info

Product

Resources

About