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How a computer is helping scientists discover the origins of life

Where did we come from?

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Life on Earth is, as far as we know, an extremely rare occurrence in the universe. It is arguably one of the most astounding and beautiful processes, but scientists know surprisingly little about how a desolate, primordial Earth transformed to support life as we know it.

Using a few basic building blocks, like water, ammonia, or methane, previous research has been able to tease out a few possible timelines for how these ingredients transformed into the complex chemistry we know today. But the sheer number of possibilities becomes too much to calculate the deeper you go into the process.

New research published today in the journal Science takes a different approach. In this study, scientists turned to computers to solve this extremely human problem.

Using a chemical synthesis software called Allchemy, the team has uncovered three important forms of chemical evolution that likely lead to life.

Long before humans — or even single-cell microbes — walked the Earth, scientists believe our world was a fiery, disorganized mess composed of just a few key chemical compounds, including water, nitrogen, cyanide, ammonia, methane, and sulfur.

Focusing on these six compounds, the scientists behind this new study sought to uncover the chemical domino effect that led to the creation of the amino acids life on Earth depends upon.

While scientists have identified how individual molecules or organic chemical reactions may have emerged from Earth's primordial goo, there's less known about what this picture looked like as a whole. To get past this challenge, Allchemy takes basic primordial molecules and uses a prediction algorithm to explore the thousands of different potential pathways for how they might have led to the creation of life.

"Although hundreds of organic reactions have been validated under consensus prebiotic conditions, we still have only a fragmentary understanding of how these individual steps combined into complete synthetic pathways to generate life’s building blocks," write the authors. "[And] which other abiotic molecules might have also formed."

"As you can imagine, the number of combinations in which these molecules can react, and the products they produce, how they then can react with each other and so on and so on, can be very very huge," explains Bartosz Grzybowski, a lead author and professor of chemistry at UNIS, in a video describing the research. "There are also molecules that might have emerged that for some reason life has not chosen."

"The question is: which molecules were chosen, how and why not the other ones?"

When it comes to creating life as we know it, the process is a little complex.Science

Crunching the numbers — To answer this fundamental question, the researchers designed Allchemy to think like a chemist. In addition to teaching the algorithm the basic rules of chemistry, the researchers also trained their forward-synthesis algorithm to use previously published chemical reaction mechanisms in its calculations as well.

The algorithm starts with water, nitrogen, cyanide, ammonia, methane, and sulfur, and then a chemist using the algorithm can choose how many future iterations of these base chemicals they want to explore. One or two iterations are still calculable by hand, but up to four, five, or even seven iterations soon bloom to thousands of possibilities, as the study's graphs show. Up to seven generations can be processed in roughly two hours on a standard desktop computer, they say.

In seven generations of this synthesis, the researchers identified 82 biotic molecules known to exist today, and over 36,000 other molecules that could have been created under the same conditions but, for one reason or another, did not come together to create life.

A reason why just a few biotic molecules rose above the rest may be that they are more water-soluble and have stronger hydrogen bonding, helping them build larger structures, the researchers say.

Emerging patterns — The researchers also identified three key patterns that contributed to the evolution of complex molecules:

  1. Molecules within the network can act as catalysts for downstream reactions
  2. Molecules can produce surfactants (i.e. compounds that lower surface tension) relevant to primitive forms of biological compartmentalization
  3. Molecules undergo self-replicating cycles

Identifying these patterns could help scientists better understand why certain synthesis pathways lead to life, while others do not.

What's next — The Allchemy software is available for free to the public and research communities at large. The researchers behind it hope the powers of their software will continue to grow via crowd-sourcing. Establishing a better understanding of how chemical life on our own planet evolved is not only important for chemists and biologists trying to understand life on Earth, but may also answer questions about how extraterrestrial life could have emerged as well.

Abstract: The challenge of prebiotic chemistry is to trace the syntheses of life’s key building blocks from a handful of primordial substrates. Here we report a forward-synthesis algorithm that generates a full network of prebiotic chemical reactions accessible from these substrates under generally accepted conditions. This network contains both reported and previously unidentified routes to biotic targets, as well as plausible syntheses of abiotic molecules. It also exhibits three forms of nontrivial chemical emergence, as the molecules within the network can act as catalysts of downstream reaction types; form functional chemical systems, including self-regenerating cycles; and produce surfactants relevant to primitive forms of biological compartmentalization. To support these claims, computer-predicted, prebiotic syntheses of several biotic molecules as well as a multistep, self-regenerative cycle of iminodiacetic acid were validated by experiment.
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