F Rosa Rubicondior: Abiogenesis News - Scientists Harness The Massive Computing Power of Blockchain Technology To Show How Metabolic Processes Arose

Thursday 25 January 2024

Abiogenesis News - Scientists Harness The Massive Computing Power of Blockchain Technology To Show How Metabolic Processes Arose

Chemists use the blockchain to simulate over 4 billion chemical reactions essential to the origins of life | ScienceDaily

As though to give a two-fingered salute to those creationist frauds who tell their dupes that scientists are turning their back on materialism and accepting that magic creation is a better explanation for abiogenesis and evolution than the operation of the laws of chemistry and physics, scientists from the Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland with colleagues in IBS Center for Algorithmic and Robotized Synthesis, Ulsan, South Korea, have used the massive computing power of blockchain technology to simulate all possible reactions between pre-biotic chemicals such as water, methane and ammonia and their products, and shown that simple metabolic processes such as the citric acid cycle can arise without enzymes.

A few of these metabolic cycles were found to be capable of self-replication (believed to be a prerequisite for evolution) but these were comparatively few in number, so the scientists believe they may not have played a significant part on early abiogenesis.

These primitive metabolic processes could have provided the necessary energy for more complex processes to evolve including enzymes, each of which, if it catalyzed the reactions in the metabolic cycles, would have given it additional advantage and been quickly incorporated into the process.

the The scientists have published their findings in the Cell Press journal Chem and explain their research in a Cell Press news release.

First, a brief AI explanation of blockchain technology and its use in cryptocurrencies:
What is a blockchain and how is it used in cryptocurrency? A blockchain is a decentralized and distributed digital ledger that records transactions across a network of computers in a secure, transparent, and tamper-resistant manner. It consists of a chain of blocks, where each block contains a list of transactions. These transactions are grouped together and added to the chain in a linear, chronological order. Here's a basic overview of how a blockchain works:
  1. Decentralization: Unlike traditional centralized databases, a blockchain is decentralized. It is maintained by a network of nodes (computers) that participate in the validation and consensus process.
  2. Blocks and Transactions: Transactions are grouped into blocks. Each block contains a unique identifier called a cryptographic hash, which is generated based on the information in the block and the hash of the previous block in the chain.
  3. Consensus Mechanism: In order to add a new block to the chain, there needs to be a consensus among the nodes in the network. Different blockchain networks use various consensus mechanisms to achieve this, such as Proof of Work (used by Bitcoin) or Proof of Stake.
Now, regarding cryptocurrencies:
  • Creation of Digital Assets: Cryptocurrencies are digital or virtual currencies that use cryptography for security. These currencies are often created through a process called mining, where powerful computers solve complex mathematical problems to validate and add new transactions to the blockchain.
  • Transaction Validation: When someone initiates a cryptocurrency transaction, it is broadcast to the network. Nodes on the network verify the transaction using consensus mechanisms, ensuring that the sender has the necessary funds and that the transaction is valid.
  • Immutable and Transparent Ledger: Once a block is added to the blockchain, it is extremely difficult to alter the information within it. This immutability ensures the integrity of the transaction history. The transparent nature of the blockchain allows anyone to view the entire transaction history of a particular cryptocurrency.
  • Decentralization of Authority: Cryptocurrencies operate on a peer-to-peer network, eliminating the need for central authorities like banks. This decentralization is a key feature of many blockchain-based cryptocurrencies, providing users with more control over their funds and reducing the risk of censorship or manipulation.
The most well-known example of a blockchain-based cryptocurrency is Bitcoin, but there are numerous other cryptocurrencies with different features and use cases, all built on blockchain technology. Ethereum, for instance, introduced the concept of smart contracts, which are self-executing contracts with the terms of the agreement directly written into code on the blockchain
. In the Cell Press news release, the scientists say:
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 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."
Sadly, the full paper in Chem is behind an expensive paywall and only the Highlights and Abstract are available:
  • The largest-known network of prebiotic reactions propagated on a blockchain platform
  • Emergence of primitive forms of metabolism from basic prebiotic feedstocks
  • Cross-talk between reaction cycles and competing side reactions
  • Self-replication unlikely to guide emergence of life at the level of small molecules


This theoretical work harnesses the power of an open-access, blockchain-based platform for distributed computing to generate the largest-known network of prebiotic reactions and then to trace within this network (1) synthetic routes to biotic molecules and (2) reaction cycles and their unions that could have defined some elements of primitive, non-enzymatic metabolism. The calculation of this network, spanning >4.9 billion plausible prebiotic reactions and >3.7 billion molecules, was orchestrated automatically over hundreds of machines worldwide, each machine bidding its dynamically adjustable computing power in return for Golem cryptocurrency tokens, which underlie this platform and are traded at major cryptocurrency exchanges. In a broader context, this work illustrates how (1) blockchain-based technology can find new productive uses outside of the financial/security sector, whereas (2) scientists can benefit from this technology by gaining access to computing resources they would normally not have at their disposal.

What this shows is that from a few different precursor atoms and molecules that would all have been available on pre-biotic Earth, the billions of interactions between them and their products, over time, could easily produce simple metabolic cycles like simplified forms of the citric acid cycle, that would have provided the energy needed to build proteins, some of which could have catalysed the reactions in the cycles, speeding them up and refining them even further.

Over time, this process would have led to enzyme-dependent metabolic processes and the mechanism for producing self-replicating, free-living systems enclosed in a glycolipid cell membrane, in other words, simple living cells such as archaea and bacteria.

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