How did life manage to piece together myriads of parts? At the very least, the first life forms on Earth needed a way to store and reproduce information. Only then can they make copies of themselves and spread around the world. Perhaps chemistry played a much more important role in the origin of life than previously thought.
One of the most influential hypotheses is that it all started with RNA, a molecule that can simultaneously record genetic records and trigger chemical reactions. The hypothesis of the "RNA world" manifests itself in many forms, but according to the most traditional, life began with the formation of an RNA molecule capable of reproducing itself. Her descendants developed the ability to perform many tasks such as making new compounds and storing energy. Over time, a difficult life followed.
However, scientists have found that self-replicating RNA is surprisingly difficult to create in the laboratory. They have succeeded, but the candidate molecules made to date can only reproduce RNA of a certain sequence or length. In addition, these RNA molecules themselves are quite complex, which raises questions about how they could have been formed by the will of a chemical accident.
Nick Hud, a chemist at the Georgia Institute of Technology, and his colleagues decided to go beyond biology and study the possible role of chemistry in the origin of life. Perhaps, before the emergence of biology, there was a preliminary stage of proto-life, in which only chemical processes created a "buffet" of RNA and RNA-like molecules. “I think there were quite a few steps that led to a self-replicating self-sustaining system,” says Hud.
In this scenario, various RNA-like molecules could be formed spontaneously, helping the chemical broth to simultaneously invent many of the details necessary for the development of life. Proto-life forms experimented with primitive molecular engineering, taking it apart piece by piece. The whole system worked like a giant crush. It was only when such a system was established that self-replicating RNA emerged.
At the heart of Hud's proposal is the chemical means of creating such a rich variety of proto-life. Computer simulations show that certain chemical conditions can produce a diverse collection of RNA-like molecules. The team is currently testing this idea with real molecules in the lab and hopes to present results soon.
Hud's group is paving the way for a number of researchers who challenge the traditional hypothesis of the RNA world and its dependence on biological, rather than chemical, evolution. In the traditional model, new molecular engineering was created using biological catalysts - enzymes - as is the case with modern cells. During Hud's proto-life stage, myriads of RNA or RNA-like molecules could be formed and altered using purely chemical means. "Chemical evolution could have helped start life without enzymes," says Hud.
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Hud and his colleagues decided to go further and assume that the ribosome, the only piece of biological engineering present in all living things today, came entirely out of chemistry alone. This is an unusual way of looking at things, since many believe that the ribosome was born by biology.
If Hud's team can create forms of proto-life in conditions that might have existed on early Earth, it can be assumed that chemical evolution may have played a much more significant role in the origin of life than scientists expected. "Darwinian evolution may have been preceded by a simpler form of evolution," says Niels Lehman, a biochemist at Portland University in Oregon.
Pre-Darwinian world
When most think about evolution, Darwinian evolution comes to mind, in which organisms compete with each other for limited resources and pass on genetic information to their descendants. Each generation undergoes genetic corrections, and the most successful offspring survive to pass on their genes. This mode of evolution prevails in modern life.
Karl Woese, the famous biologist who gave us the modern tree of life, believed that the Darwinian era was preceded by an early stage of life, ruled by completely different evolutionary forces. Woese believed that it would be almost impossible for a single cell to get everything it needs to live. Therefore, he envisioned a rich variety of molecules involved in communal existence. Instead of competing with each other, primitive cells shared molecular innovations. This pre-Darwinian broth created the ingredients needed for complex life, paving the way for the magnificent menagerie we see on Earth today.
Hud's model takes Woese's pre-Darwinian time vision even further back in time, providing primitive cells with the chemical means to create molecular diversity. One form of proto-life could devise a way to create the blocks it needed to create itself, another could find a way to get energy. This model differs from the traditional hypothesis of the RNA world in its dependence on chemical rather than biological evolution.
In the world of RNA, the first RNA molecules reproduced themselves using the built-in enzyme ribozyme, which is composed of RNA. In the world of Hud's proto-life, this task was carried out exclusively by chemical methods. The story begins with a chemical soup of RNA-like molecules. Most were short, as short chains would most likely form spontaneously, but there could be longer, complex molecules as well. Hud's model describes how longer molecules could be reproduced without the aid of an enzyme.
Hud believes that in the prebiotic world, the primary RNA broth went through regular heating and cooling cycles and became thick and viscous. The heat separated the bound RNA pairs, and the viscous solution kept the molecules apart for a while. Meanwhile, small segments of RNA, only a few characters in length, are attached to each long strand. These small segments were gradually stitched together, forming a new RNA strand corresponding to the original long strand. Then the cycle started again.
RNA replication chemical pathways
Over time, as the broth of a variety of RNA-like molecules expanded and grew, some of them acquired simple functions like metabolism. Likewise, pure chemical reactions could produce molecular diversity to create a pre-Darwinian cornucopia of Woese proto-life.
Hud's group has managed to complete the early stages of the reproduction process in the laboratory, although they have not yet learned how to glue short segments without resorting to biological tools. If they can overcome this obstacle, they will create a universal way of reproducing RNA.
However, some scientists doubt that chemically mediated reproduction will be good enough to reproduce the pre-Darwinian world that Hud describes. “I don’t know if I believe that,” says Paul Higgs, a biophysicist at McMaster University in Hamilton, Ontario, who studies the origins of life. "Everything has to happen quickly and accurately enough to create consistency." That is, this process must produce new RNAs faster than they are destroyed, and accurately enough to create approximate copies of template molecules.
Chemical changes alone are not enough to bring about life. The broth of proto-life still needed some sort of selection that would ensure that beneficial molecules would thrive and multiply. In their model, Hada's group suggests that the simplest proto-enzymes could have emerged and spread, which began to benefit their creators and society at large. For example, an RNA molecule that produced more building blocks benefited itself and its neighbors by providing them with additional raw materials for reproduction. Computer simulations carried out by Hud's group showed that this type of molecule could well take root. The one who enriches the broth is very useful.
Ribosomal roots
One possible glimpse of the pre-Darwinian world can be seen in the ribosome, an ancient piece of the molecular machinery that underlies our genetic code. It is an enzyme that translates RNA, which encodes genetic information, into proteins that carry out many chemical reactions in our cells.
The ribosome nucleus is composed of RNA. This makes the ribosome unique - the vast majority of enzymes in our cells are made up of proteins. Both the ribosomal nucleus and the genetic code are common to all living things, which indicates their existence at the very beginning of the evolution of life, possibly even before the Darwinian threshold was crossed.
Hud and his colleague Lauren Williams, also of Georgia Tech, point to the ribosome as supporting their theory of the chemically defined world. In a paper published last year, they made a controversial statement: the ribosome's core was created through chemical evolution. And they also suggested that it appeared even before the appearance of the first self-replicating RNA molecule. The ribosomal nucleus may have been a successful experiment in chemical evolution, they say. And after it took root in the pre-Darwinian broth, it crossed the Darwinian threshold and became an important part of all life.
Their argument relies on the relative simplicity of the ribosomal nucleus, formally known as the peptidyl transferase center (PTC). The job of the PTC is to put together amino acids, the building blocks of proteins. Unlike traditional enzymes, which speed up chemical reactions using “clever chemical tricks,” it works as a desiccant. He persuades two amino acids to bond by simply removing the water molecule. “It's such a poor way to nudge a reaction,” Lehman says. "Protein enzymes usually rely on more powerful chemical strategies."
Lehman notes that simplicity probably preceded power in the earliest stages of life. “When you think about the origin of life, you first need to think about simple chemistry; any process of the simplest chemistry is likely to be ancient, he says. "I think this is a more compelling argument than the fact that she belongs to all life."
Despite strong evidence, it is still difficult to imagine how the ribosomal nucleus could have been created as a result of chemical evolution. An enzyme that does more of itself - like an RNA replicator in the RNA world hypothesis - automatically creates a closed loop, constantly increasing its own productivity. In contrast, the ribosomal nucleus does not produce more ribosomal nuclei. It produces random chains of amino acids. It is unclear how this process should stimulate the production of more ribosomes.
Hud and his colleagues speculate that RNA and proteins developed in tandem, and whoever figured out how to work together survived. This idea lacks the simplicity of the RNA world, which postulates the existence of a single molecule capable of simultaneously encoding information and catalyzing chemical reactions. But Hud believes otherwise: it is complexity that adds elegance to the emergence of life.
“I think there has always been an over-emphasis on simplicity, that one polymer is better than two,” he says. “It might be easier to get specific reactions if the two polymers work together. It may have been easier for the polymers to work together from the start.”
Based on materials from Quanta Magazine