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 intermediate compounds and template-assisted replication. Specifically, they show that the enrichment of one ‘‘master sequence’’ is a result of a collective network behavior manifested by multiple template-assisted processes. They suggest that their findings may shed light on molecular evolution processes that led to current biology.

J. Nanda, B. Rubinov, D. Ivnitski, R. Mukherjee, E. Shtelman, Y. Motro, Y. Miller, N. Wagner, R. Cohen-Luria and G. Ashkenasy. Emergence of native peptide sequences in prebiotic replication networks. Nature Communications 8: 434, 2017.

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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 and integrated protocell populations provides the most appropriate framework to address the difficult problem of how prebiotic chemistry bridged the gap to full-fledged living organisms on the early Earth.” The authors explicitly advocate “taking dynamic, functionally integrated protocell systems (rather than complex reaction networks in bulk solution, sets of artificially evolvable replicating molecules, or even these same replicating molecules encapsulated in passive compartments) as the proper units of prebiotic evolution.”

Their article was published earlier this year in the Beilstein Journal of Organic Chemistry.

B. Shirt-Ediss, S. Murillo-Sánchez and K. Ruiz-Mirazo. Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research. Beilstein Journal of Organic Chemistry 13: 1388-1395, 2017.

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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 theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. […] We discuss implications for understanding cooperation as a driver of complexification in the origin of life.”

This interesting new work was just published as an open access article in the journal Life.

C. Mathis, S. N. Ramprasad, S. I. Walker and N. Lehman. Prebiotic RNA network formation: A taxonomy of molecular cooperation. Life 7(4): 38, 2017.

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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 understand way, including several illustrative examples. This popular science piece is published in “This View Of Life” (TVOL), the online magazine of the Evolution Institute.

Wim Hordijk. The origin of life: A selfish act or a cooperative effort? TVOL, 18 September 2017.

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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, with an emphasis on the role that autocatalytic sets may have played in this.

Wim Hordijk. Autocatalytic confusion clarified. Journal of Theoretical Biology (in press), 2017.

A (free) preprint is also available from the author’s website.

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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 understanding the origin and organization of life, may also help explain the origin of the kind of cognitive structure that makes cultural evolution possible. A very interesting and novel idea, taking autocatalytic sets far beyond chemistry & origin of life, and into the social sciences.

Liane Gabora and Mike Steel. Autocatalytic networks in cognition and the origin of culture. Journal of Theoretical Biology 431:87-95, 2017.

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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 catalysis under various catalysis distributions, and how to deal with inhibition.

The paper can now be read online for free, but not downloaded.

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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, on 9 March 2017. It presents a general and high-level introduction to the theory and main results of autocatalytic sets. Thanks to the eScience Center for making this recording available! A link to a PDF of the lecture slides is included in the video description.

Watch the full video here (45mins):
Autocatalytic Sets Talk

 

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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 a novel computational model of chemical reaction networks based on RNA secondary structure, and analyzes the existence of autocatalytic sub-networks in random instances of this model. The main results are that (i) autocatalytic sets are highly likely to exist, even for very small reaction networks and short RNA sequences, and (ii) sequence diversity seems to be a more important factor in the formation of autocatalytic sets than sequence length. These findings could shed new light on the probability of the spontaneous emergence of an RNA world as a network of mutually collaborative ribozymes.

Wim Hordijk. Autocatalytic Sets and RNA Secondary Structure. Journal of Molecular Evolution, online first, 2017.

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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 analyzed for the presence of various types of autocatalytic sets with the click of a button. The web page also contains links to PDFs with some basic background information. The app is still under development, and will be updated and expanded over time, but the main functionality is there.

Here is the link to the web page containing the app:
http://www.math.canterbury.ac.nz/bio/RAF/

With thanks to Prof. Mike Steel for making this web page and background information available, and Dietrich Radel for the implementation.

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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 view offers a possible answer to the fundamental question of why so many species can coexist in the same ecosystem.

R. Cazzolla Gatti, W. Hordijk and S. Kauffman. Biodiversity is Autocatalytic. Ecological Modelling 346:70-76, 2017.

 

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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 written as a general overview and introduction, without the technical details. References throughout the paper point to the more technical articles where the original work was published.

W. Hordijk and Mike Steel. Chasing the tail: The emergence of autocatalytic networks. BioSystems, 2016.

 

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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 instances of “Kantian wholes”). His full lecture can now be viewed on YouTube.

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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”. This visualization makes certain dynamical aspects more clear, especially some issues that are hard to present in a scientific article.

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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 this institute, specifically to continue his work on autocatalytic sets and the origin and organization of life, including the ongoing collaborations that make up the COOLscience Club. He also hopes to start new collaborations, in particular to try and extend the theory of autocatalytic sets to the fields of ecology and economics.

The KLI is an institute for the advanced study of natural complex systems, and supports theoretical research primarily in the areas of evolutionary developmental biology and evolutionary science. It  is funded by a private trust and receives additional support from the Province of Lower Austria. The institute has close ties with many of the higher education institutions in Vienna and Lower Austria as well as with a number of international institutions with similar aims.

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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, collaborators Wim Hordijk and Mike Steel try to rectify this by presenting a more complete and up-to-date overview of recent work on autocatalytic sets, both theoretical as well as experimental.

W. Hordijk and M. Steel. Comment on “Tibor Gánti and Robert Rosen” by Athel Cornish-Bowden. Journal of Theoretical Biology, 2015.

 

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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 earlier results, both theoretical and experimental, on autocatalytic sets. The authors of this paper include collaborators Niles Lehman, Stuart Kauffman, Sara Walker, and Wim Hordijk

P. Nghe, W. Hordijk, S. A. Kauffman, S. I. Walker, F. J. Schmidt, H. Kemble, J. A. M. Yeates and N. Lehman. Prebiotic network evolution: six key parameters. Molecular BioSystems 11: 3206-3217, 2015.

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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 chemical reaction networks that have been described in the literature. It is shown how previous alternative definitions of autocatalytic sets all seem to fall short one way or another, but that the formal framework known as RAF theory is able to capture all of them, allowing for a complete analysis of the emergence and (potential) evolution of autocatalytic sets across all these different models. This suggests that RAF theory can be used as a standard formalism.

W. Hordijk. Evolution of autocatalytic sets in computational models of chemical reaction networks. Origins of Life and Evolution of Biospheres, 2015.

 

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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 the main concepts and achievements, from Stuart Kauffman’s original idea (in the early 70’s) to the recent confirmation that the metabolic network of E. coli forms an autocatalytic set.

A free online version of the article is available.

 

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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.

W. Hordijk, J. I. Smith and M. Steel. Algorithms for detecting and analysing autocatalytic sets. Algorithms for Molecular Biology 10:15, 2015.

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Autocatalytic sets in E. coli metabolism

A new autocatalytic sets paper was just published in the Journal of Systems Chemistry. In this paper, co-authors Sousa, Hordijk, Steel, and Martin show that the metabolic network of E. coli forms an autocatalytic set. They also perform several analyses to investigate the robustness and modularity of this set. These results provide the first real (and formal) proof that living systems are indeed autocatalytic sets.

F. L. Sousa, W. Hordijk, M. Steel and W. F. Martin. Autocatalytic sets in E. coli metabolism. Journal of Systems Chemistry 6:4, 2015.

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Permission to use Escher image

We now have official permission from the M.C. Escher Company to use part of Escher’s ‘Metamorphosis II’ print in the banner of our website. We felt that the left part of this image forms an appropriate graphical metaphor for how the chaotic primordial soup “metamorphosed” into structured chemical networks, which eventually gave rise to living entities, all in an almost inevitable and highly organized way.

The original (full) image can be seen on the website of the M.C. Escher Company. With thanks for their kind permission.

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Interview with Kauffman

A whirlwind interview with Stuart Kauffman appeared in Scientific American recently, as part of John Horgan’s weekly column. Horgan seems to be stepping back a bit from his earlier, rather harsh, criticism of complexity science. This interview covers a wide spectrum of scientific topics, including the work on autocatalytic sets by Kauffman and others from our collaboration.

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New paper out

A perspectives paper on “autocatalytic sets and boundaries” was just published in the Journal of Systems Chemistry. In this paper, co-authors Hordijk & Steel explore the relationship between autopoietic systems, the chemoton model, and autocatalytic sets in more detail. They also describe a possible mechanism for the emergence of higher-level autocatalytic sets by considering “boundaries” (such as cell membranes) as additional catalysts.

W. Hordijk and M. Steel. Autocatalytic sets and boundaries. Journal of Systems Chemistry 6:1, 2015.

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Preliminary website available

A preliminary version of the COOLscience Club website is now available. Please check back regularly for updates.

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