Chemists use the blockchain to simulate over 4 billion chemical reactions essential to the origins of life
Cryptocurrency is usually “mined” through the blockchain by asking a computer to perform a complicated mathematical problem in exchange for tokens of cryptocurrency. But in research appearing in the journal Chem on January 24, a team of chemists have repurposed this process, asking computers to instead generate the largest network ever created of chemical reactions which may have given rise to prebiotic molecules on early Earth.
This work indicates that at least some primitive forms of metabolism might have emerged without the involvement of enzymes, and it shows the potential to use blockchain to solve problems outside the financial sector that would otherwise require the use of expensive, hard to access supercomputers.
“At this point we can say we exhaustively looked for every possible combination of chemical reactivity that scientists believe to had been operative on primitive Earth,” says senior author Bartosz A. Grzybowski (http://grzybowski-group.net/default.asp) of the Korea Institute for Basic Science and the Polish Academy of Sciences.
To generate this network, the researchers chose a set of starting molecules likely present on early Earth, including water, methane, and ammonia, and set rules about which reactions could occur between different types of molecules. They then translated this information into a language understandable by computers and used the blockchain to calculate which reactions would occur over multiple expansions of a giant reaction network.
“The computer takes the primordial molecules and the accepted prebiotic chemistries. We coded it into the machine, and then we released it onto the world,” says Grzybowski.
Grzybowski’s team worked with chemists and computer-specialists at Allchemy, a company that uses AI for chemical synthesis planning, to generate the network using Golem, a platform that orchestrates portions of the calculations over hundreds of computers across the world, which receive cryptocurrency in exchange for computing time.
The resulting network, termed NOEL for the Network of Early Life, started off with over 11 billion reactions, which the team narrowed down to 4.9 billion plausible reactions. NOEL contains parts of well-known metabolic pathways like glycolysis, close mimics of the Krebs cycle, which organisms use to generate energy, and syntheses of 128 simple biotic molecules like sugars and amino acids.
Curiously, of the 4.9 billion reactions generated, only hundreds of reaction cycles could be called “self-replicating,” which means that the molecules produce additional copies of themselves. Self-replication has been postulated to be central to the emergence of life, but the vast majority of its known manifestations require complex macromolecules like enzymes.
“Our results mean that with only small molecules present, self-amplification is a rare event. I don’t think that this type of self-replication was operative on primitive earth, before larger molecular structures were somehow formed,” says Grzybowski. “We see emergence of primitive metabolism, but we don’t see self-replication, so maybe self-replication appeared later in evolution.”
“If you asked me two years ago, I’d be thinking we’d need years for this type of work,” says Grzybowski. “But for a fraction of the cost, in two or three months, we finished a task of 10 billion reactions, 100k times bigger than we did previously.”
This work not only advances what we know about early prebiotic chemistry, but it also demonstrates how science can be made more accessible to researchers at smaller universities and institutions.
“Our system of education is based on elite universities mostly in the western world. It’s very hard for the developing world to even compete with these universities because they don’t have access to supercomputers,” says Grzybowski. “But if you can distribute computing in this way for a fraction of the cost, you can give other people opportunities to play.”
While the network generated in this work was performed on hundreds of computers around the world, Grzybowski suggests that this method can be used at institutions without having to pay out cryptocurrency tokens to the computers performing the calculations.
“With a platform like Golem you can connect your institution’s network and harness the entire idle power of its computers to perform calculations,” says Grzybowski. “You could create this computing infrastructure without any capital expenditure.”
Grzybowski hopes that repurposing the blockchain in this way can revolutionize the way we perform large scale calculations across the world and change how we see the value of cryptocurrency.
“I hope people in computer science can figure out how can we tokenize cryptocurrencies in some way that can benefit global science,” says Grzybowski. “Maybe society could be happier about using cryptocurrencies, if you could tell people that in the process we could discover new laws of biology or some new cancer drug,” says Grzybowski.
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Development of all codes and algorithms described in this work described was supported by internal funds of Allchemy, Inc. and Golem Factory, GmbH. Analysis of pathways and writing of the paper by Bartosz Grzybowski was supported by the Institute for Basic Science, Korea. Grzybowski has no financial stake in Golem although he is a stakeholder of Allchemy. Additional information about declarations of interest can be found in the paper.
Chem, Roszak et al. “Emergence of metabolic-like cycles in blockchain-orchestrated reaction networks” https://cell.com/chem/fulltext/S2451-9294(23)00611-3
Chem (@Chem_CP) is the first physical science journal published by Cell Press. A sister journal to Cell, Chem, which is published monthly, provides a home for seminal and insightful research and showcases how fundamental studies in chemistry and its sub-disciplines may help in finding potential solutions to the global challenges of tomorrow. Visit https://www.cell.com/chem. To receive Cell Press media alerts, contact press@cell.com.
JOURNAL
Chem
METHOD OF RESEARCH
Computational simulation/modeling
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
Emergence of metabolic-like cycles in blockchain-orchestrated reaction networks.
ARTICLE PUBLICATION DATE
24-Jan-2024
Chemistry professor R. Graham Cooks expands research of water droplet interfaces that offer the secret ingredient for building life
R. Graham Cooks, the Henry B. Hass Distinguished Professor of Chemistry, and his postdoctoral researcher Lingqi Qiu have experimental evidence that the key step in protein formation can occur in droplets of pure water, and have recently published these findings in the Proceedings of the National Academy of Sciences (PNAS).
In this key step, amino acids are dehydrated (they lose water) even though they are in a water solution, a paradox that is resolved by the fact that these droplet surfaces are unusually dry and highly acidic. Under these conditions, amino acids connect to each other to create peptides, a fundamental step toward forming proteins and, eventually, living organisms.
A crucial aspect of the discovery is that the natural "left-handed" structure of amino acids is maintained throughout this process. This leads to the formation of pure chiral peptides with the same "L" handedness. The authors identified a specific compound, oxazolidinone, as a crucial intermediate in this reaction.
Further, they found that this dehydration reaction is not confined to microscopic droplets. It also happens on a larger, centimeter scale, as demonstrated in a lab experiment starting from the oxazolidinone intermediate. This larger-scale reaction mirrors the microdroplet chemistry and is also analogous to the well-studied wet-dry cycles that are suggested to occur in hydrothermal pools and seashores. This connection links peptide formation in aerosols and in more extensive, prebiotic environments.
The study adds to the body of evidence that the surface of water drops represents a uniquely active physical and chemical system. Present are very high electric fields and extreme acidity that drives dehydration of amino acids to form peptides. Studies of the chemistry at water droplet interfaces offer new insights into the early stages of life's chemical evolution.
The authors acknowledge valuable discussions with Purdue research associates Dylan T. Holden and Nicolás M. Morato. They also acknowledge the financial support from the Multidisciplinary University Research Initiative of the Air Force Office of Scientific Research (FA9550-21-1-0170) via Stanford University (sub-award 62741613-204669) and also support from the National Science Foundation (grant CHE-1905087).
Related Link: The fountain of life: Water droplets hold the secret ingredient for building life
JOURNAL
Proceedings of the National Academy of Sciences
ARTICLE TITLE
Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets
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