Category Archives: Uncategorized

Complex experimental autocatalytic sets

In a recent paper, collaborators Andrew Griffiths and Niles Lehman and colleagues present new results on constructing and studying experimental autocatalytic sets consisting of ribozymes (catalytic RNA molecules). What is new in these results is that, unlike previous experimental systems, … Continue reading

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Peptide autocatalytic network dynamics

In a new paper that was just accepted in ChemPhysChem, collaborators Wim Hordijk and Gonen Ashkenasy study the dynamics of an experimental peptide autocatalytic set, using computer simulations, and show the influence of various factors such as network modularity, template … Continue reading

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Oregon Scientist of the Year: Niles Lehman

Collaborator Niles Lehman has been named 2018 Oregon Scientist of the Year by the OR Academy of Science for his ground breaking work in molecular evolution and the possible origins of life. Many congrats to Niles!

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Autocatalytic Sets and Chemical Organizations

In a new paper just published in the New Journal of Physics, collaborators Wim Hordijk and Mike Steel, together with coauthor Peter Dittrich, derive direct connections between autocatalytic sets and chemical organizations, and show how this connection can be used … Continue reading

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Spontaneous self-assembly of RNA

In a new paper in the journal ChemBioChem, collaborator Niles Lehman and colleague report on the spontaneous covalent assembly of short RNA fragments, on average <40 nucleotides in length. They show that a dehydration-rehydration sequence is the most effective means … Continue reading

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Emergence of native peptide sequences in prebiotic replication networks

In a recent paper in Nature Communications, collaborator Gonen Ashkenasy and co-workers report on their continued investigations related to the origin of life, analyzing a complex web of reactions in β-sheet peptide networks, and focusing on the formation of specific … Continue reading

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Three challenges for origin of life research

In a recent paper, collaborator Kepa Ruiz-Mirazo together with two of his former PhD students pose three challenges for origin of life research. In particular, they argue that “conceiving the process of biogenesis as the evolutionary development of highly dynamic … Continue reading

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Molecular cooperation at the origin of life

A new paper by collaborator Niles Lehman and co-authors investigates the types of cooperation possible in a real RNA system. As the authors write in their abstract: “Cooperation is essential for evolution of biological complexity. Recent work has shown game … Continue reading

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The origin of life as a cooperative effort

In a new popular science piece, collaborator Wim Hordijk contrasts the notion of a “selfish” RNA world with that of a possible “cooperative” origin of life in terms of autocatalytic sets. The article explains the concepts in an easy to … Continue reading

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Autocatalytic confusion clarified

In a new paper, collaborator Wim Hordijk explains and discusses the similarities and differences between various autocatalytic systems, in particular autocatalytic reactions, cycles, and sets. The relevance of these systems for possible origin of life scenarios is then also discussed, … Continue reading

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Autocatalytic sets in cognition and the origin of culture

The concept of autocatalytic sets has now also been used in cognition and the origin of culture. In a recent paper, collaborator Mike Steel and co-author Liane Gabora develop a novel idea that models of collectively autocatalytic networks, developed for … Continue reading

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Free online version of recent autocatalytic sets paper

A free (view-only) version of a recent paper on autocatalytic sets is now available online. This paper was published in the Journal of Mathematical Chemistry, and explores further theoretical and computational issues regarding autocatalytic sets, such as required levels of … Continue reading

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Autocatalytic Sets Talk

A recording of an introductory talk on autocatalytic sets in the context of the origin of life, as presented by collaborator Wim Hordijk, is now available on YouTube. This talk was presented at the eScience Center in Amsterdam, The Netherlands, … Continue reading

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Autocatalytic Sets and RNA Secondary Structure

The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. In a new paper, collaborator Wim Hordijk introduces … Continue reading

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Autocatalytic Sets Web-App

A basic but functional web-app is now available to analyze chemical reaction networks in terms of autocatalytic sets. The app allows one to type (or copy & paste) a reaction network (including catalysis) in a simple format, which is then … Continue reading

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Biodiversity is Autocatalytic

A new paper on autocatalytic sets was just published in the journal Ecological Modelling. In this paper, co-authors Roberto Cazzolla Gatti, Wim Hordijk, and Stuart Kauffman argue that biodiversity can be considered a system of autocatalytic sets, and that this … Continue reading

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Review paper on autocatalytic sets

A new paper on autocatalytic sets was just published in the journal BioSystems. In this paper, collaborators Wim Hordijk and Mike Steel review the work on autocatalytic sets they have done over the past decade or so. The paper is … Continue reading

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Stuart Kauffman Lecture

Stuart Kauffman recently visited the Konrad Lorenz Institute for Evolution and Cognition Research (KLI) in Klosterneuburg, Austria, where he presented a wonderful lecture entitled “Beyond Pythagoras: No Laws Entail Evolution”. In it, he stressed the importance of autocatalytic sets (as … Continue reading

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Autocatalytic Sets Arising

Much of the work on autocatalytic sets involves graph-theoretical analysis. The dynamical aspects have also been addresses, but are often harder to present. Recently, collaborator Wim Hordijk made a short movie showing autocatalytic sets arising and growing in “real time”. … Continue reading

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Funding for Autocatalytic Sets Research

Good news on the funding side! Collaborator Wim Hordijk has been awarded a senior fellowship at the Konrad Lorenz Institute for Evolution and Cognition Research in Klosterneuburg (near Vienna), Austria. Starting in March 2016, Wim will spend one year at … Continue reading

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Comment on autocatalytic sets

A short comment on a recent paper by Athel Cornish-Bowden was just published in the Journal of Theoretical Biology. In this recent paper, author Cornish-Bowden unfortunately misrepresents autocatalytic sets by providing an outdated description of this concept. In their comment, … Continue reading

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Prebiotic network evolution

A perspectives paper on prebiotic network evolution just appeared in the journal Molecular BioSystems. It discusses six key parameters likely to have been influential in the chemical evolution of reaction networks eventually leading to life. This discussion relies heavily on … Continue reading

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New paper on autocatalytic sets

A new paper on autocatalytic sets was just published in the journal Origins of Life and Evolution of Biospheres. In this paper, author Wim Hordijk applies the formal framework for detecting and analyzing autocatalytic sets to various computational models of … Continue reading

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Popular science article about autocatalytic sets

A new article describing and explaining our work on autocatalytic sets and the origin of life, written for a general readership, just appeared in the popular science magazine The Scientist. The article is written by collaborator Wim Hordijk and covers … Continue reading

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Algorithms for autocatalytic sets

A new paper published in the journal Algorithms for Molecular Biology focuses on algorithmic aspects of finding and analyzing autocatalytic sets. This paper presents recent joint work by collaborators Hordijk and Steel, with valuable contributions from graduate student Josh Smith. … Continue reading

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