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Blockchain computing simulates early Earth
A new paper published Wednesday in the journal Chem highlights how blockchain technology could be useful for scientists who need extensive computing resources, and also makes news in prebiology.
Researchers Associated with Allchemy—an AI startup focused on drug discovery and computational synthesis—as well as Korea Institute for Basic Sciences and the Polish Academy of Sciencesthey claim to have been able to simulate a network of chemical reactions that could provide insights into how life formed on early Earth.
“It’s a very unusual marriage to combine chemistry, particularly prebiotic chemistry, with blockchain and distributed computing.”
—Sara Szymkuć, Allchimia
But there’s a twist: the researchers’ project used computing resources provided via Golem blockchain protocol to conduct complex chemical models. While cryptocurrencies are often used to solve complex mathematical problems, in this case the researchers started with an initial model of primordial molecules, such as ammonia and water, and then simulated a series of possible chemical reactions.
The system produced several generations of synthetic reactions, which could then be mined for potential cycles that appear to repeat, revealing chemical interactions that could potentially have played a role in the origin of life. The idea is reminiscent of a technological and 21st century breakthrough of the famous Urey-Miller experiment of 1953which sought to emulate Earth conditions and recreate organic molecules.
“These studies have allowed us to have more information [into what] could the first metabolic systems appear and how could they evolve into the metabolic cycles we have now,” explained Sara Szymkuć, a scientist who is also president and co-founder of Allchemy. “We found imitations of known cycles that used, for example, slightly different molecules or slightly different reactions. It could point us to certain directions to look at when we think about the evolution of early metabolic systems.”
The challenge, of course, is that digitally modeling these types of reactions requires an enormous amount of computing resources. During a previous project, researchers tried a similar approach, coding several prebiotic reaction rules known to produce synthetic generations of reactions. However, according to new research, the previous attempt may have been hampered by the limits computer resources placed on their calculations.
The project calculated over 4.9 billion “plausible prebiotic reactions” on over 3.7 billion simulated molecules.
This time, the team turned to Golem, a blockchain protocol that allows people to rent their computers, for the purpose of conducting complex calculations, in exchange for cryptocurrency. Allchemy and Golem Factory, a startup that delivers a CPU/GPU rental service, supported the research.
According to Szymkuć, the main advantage of using the cryptocurrency-based approach is financial. Renting similar assets from Amazon, he suggested, could have cost twice as much. There is also the question of time. Assembling the model via Golem, which ultimately involved about 400 machines, took about two months, Szymkuć said. By comparison, purchasing hardware with chips capable of completing these calculations could have taken at least six months, the paper notes.
“It’s a very unusual marriage to combine chemistry, especially prebiotic chemistry, with blockchain and distributed computing,” Szymkuć said. “What we also like about Golem is that it orchestrates the power needed to automatically perform calculations. We also didn’t have to make any major changes to our code.”
The resulting network, which they called the Network of Early Life, was immense, according to the article. The project calculated more than 4.9 billion “plausible prebiotic reactions” on more than 3.7 billion simulated molecules.
Ultimately, several hundred reactions were found to self-replicate, creating a promising basis for further studies. At the same time, the team claims to have established a new way of conducting scientific research that requires in-depth processing.
Soubhik Deba researcher who studied blockchain technologies at the University of Washington and now works for Autostratus, a cryptocurrency company focused on Ethereum, agreed that there are benefits to using blockchain technology for this type of research. He also claims that blockchain-based computing resources are less likely to be censored.
However, he says, there are caveats worth considering, including regarding safety and accuracy.
“Blockchains operate in Byzantine adversarial scenarios, where participants performing the calculations can simply submit incorrect calculation results[s]. Putting the right negative incentives in place to mitigate such adversarial behavior is really not easy,” Deb said. “Another big challenge is privacy, since the data to be processed is visible to everyone.”
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