Researchers from Stony Brook University’s Laufer Center for Physical and Quantitative Biology and Lawrence Berkeley National Laboratory in Berkeley, California, proposed a mechanism that could help explain the origins of life.
In a paper named “Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers” that was published in Proceedings of the National Academy of Sciences in July 2017, the researchers presented a potentially universal computational model that can test mechanisms that might explain the transformation of non-living chemicals into the building blocks of life.
If the theoretical mechanism that passed their computational model is proven to be true, it will be indicative of “how the earliest stages of life rose from just simple chemicals four billion years ago, before the Earth had any biology on it at all,” said Dr. Ken Dill, co-author of the study and a distinguished professor of chemistry and physics at the university.
What we know so far about prebiotic chemistry, or abiogenesis – a natural process of life emerging from a soup of chemicals – is that basic chemical reactions can explain short monomer (molecule) units linking together to form dimers, trimers and so on. However, it is still a mystery what activated the proceeding of those short polymers (large molecules) to next-level, longer chains of protein-like polymers (complex molecules).
In short, what makes chemicals, which seek equilibrium and permanence, convert to biology that strives to survive and develop under the earth’s basic conditions? Dill used the analogy of pearl necklaces to explain the mechanism that might have the answer. Imagine, in nature, you have red beads that are like oil and blue beads that are like water, and you get them in a random order. Basic chemical reactions can only hold five or six beads together at a time, but at least a few hundred beads need to be connected to each other in a specific order to form more complex forms of life that evolve over time.
This is where the researchers’ proposed mechanism comes in. They found that with enough red beads on a string, those beads will fold into a “landing pad” structure, just like oil does in water. This, in turn, would allow the beads to connect to other short strings and form longer and longer chains of molecules. Those “landing pad” structures are essentially the catalysts that start the formation of elongated polymers, which have a unique arrangement.
“We don’t have proof that it’s right,” Dill said, “there’s a lot of work to be done experimentally to prove or disprove this.”
Dr. Ronald Zuckermann, co-author of the paper, is planning on testing the theory with National Energy Research Scientific Computing Center supercomputers at Lawrence Berkeley National Laboratory.
“We are planning in the next phase of the work to corroborate our experimental findings using these computers, to study the ability of certain sequences to fold and perform simple catalytic functions,” Zuckermann, who also serves as the director of Biological Nanostructures User Program at the Molecular Foundry, a nanoscience research facility, said.
Zuckermann has high hopes for future implications of this work. He thinks it could lead to humans eventually making more stable artificial proteins that can perform complex tasks, synthetic antibodies that do not need refrigeration and nanoscale drug delivery vehicles. These are the long-term goals he focuses on in his research and in his collaboration with Dill.
According to Dill, his inspiration for the project came from his lifelong interest in the origins of life. He commended the hard work of Dr. Elizaveta Guseva, who is the lead author of the study and current business associate at Gartner, a research and advisory firm. Guseva did not reply to our request for comment.
As for the origin of life line of work, Dill acknowledges that it is hard to make an impact – mostly because these are abstract ideas that predict beginning-of-life processes, which are often not experimentally testable.
“But this particular model gives you very specific recipes for how to test itself,” Dill said. “Experimentalists can go off now and figure out if we got it wrong or right.”