A simpler source of life

The formation of systems of energy-consuming chemical reactions between small molecules as a first step to the formation of life is more likely than the conventional idea, according to which large molecules, such as RNA, capable of replicating themselves suddenly appeared

On the same subject

Revolution - not evolution

Life began with a drop of fat

They knew the beginning of life

They knew how to create life in the laboratory

By Robert Shapiro

The chances of the sudden appearance of a large self-replicating molecule, such as RNA, are extremely low. It is more likely that life began as a system of chemical reactions between small molecules, whose driving force was energy.
Extraordinary discoveries inspire extraordinary announcements. James Watson said that immediately after he and Francis Crick discovered the structure of DNA, Crick "flew to the Eagle pub to tell everyone within earshot that we had discovered the secret of life." The structure they discovered, an elegant double helix structure, almost deserved such enthusiasm. The relationships between the components of the coil made it possible to store information in a language in which four chemicals, called bases, play the role of the letters of the alphabet.

Moreover, the information is packaged in two long chains, each of which determines the content of the other. This arrangement suggested a replication mechanism: the two strands of the DNA double helix can separate and new building blocks of DNA carrying the bases, called nucleotides, are organized along the separated strands and connect to each other. Instead of one double coil, two were now created, each one an exact copy of the original coil.

Watson and Crick's structure led to a tremendous flood of discoveries about the way living cells function today. These insights also raised speculations about the origin of life. Nobel laureate H. G. Muller wrote that the material from which the genes are composed is "living matter, the contemporary representative of the first life". These first living things were imagined by Carl Sagan as "primitive genes, independent and naked animals found in a mixed solution of organic matter." (In this context the term "organic" describes compounds that contain carbon atoms bound together, whether these compounds are found in living things or not.) Scientists have proposed many different definitions of life. Mueller's comment is consistent with what is called NASA's definition: life is a chemical system with independent existence capable of undergoing Darwinian evolution.

Richard Dawkins detailed the character of the earliest living being in his book "The Selfish Gene": "At a certain moment a molecule was created by chance in a special way. We will call her the 'replicator'. It may not have been the largest or most complicated molecule around, but it had an extraordinary property: it could make copies of itself." When Dawkins wrote those words, thirty years ago, the DNA molecule was the most likely candidate for this role. The researchers then turned to other molecules as the earliest replicator. But I and other researchers believe that this model, called the "replicator-first model", is a fundamentally flawed model for explaining the origin of life. We prefer an alternative idea that seems far more plausible.

The rule of the RNA
Very quickly complications began to arise regarding the DNA-first theory. Replication of DNA cannot occur without the help of several proteins - members of a family of large molecules that are chemically very different from DNA. Both types of molecules, DNA and proteins, are built from subunits connected to each other and form a long chain, but DNA is built from nucleotides, while proteins are built from amino acids. The proteins are the maintenance workers of the living cell. Enzymes, the most famous subgroup of proteins, act as accelerators, they accelerate chemical processes that without the enzymes would occur too slowly to support life. Proteins used by living cells today are built according to instructions coded in DNA.

The last sentence evokes the old riddle: who came first, the egg or the chicken? DNA stores the prescription for building proteins. But this information cannot be retrieved or copied without the help of proteins. If so, which large molecule appeared first - the protein (the chicken) or the DNA (the egg)?

A possible solution appeared when attention was diverted in the direction of a new hero - RNA. The molecules in this diverse group are also composed, like the DNA molecules, of nucleotide building blocks, but RNA has many roles in our cells. Certain RNA molecules transfer information from the DNA to the ribosomes, which are the sub-cellular structures that create the proteins (and are themselves built mainly from another type of RNA). RNA molecules, in their various functions, can take the form of a double helix similar to DNA or the form of a folded single strand, similar to a protein.

In the early 80s, scientists discovered ribozymes, enzyme-like substances made of RNA. It seemed that a simple solution to the riddle of the chicken and the egg had been found: life began with the appearance of the first RNA molecule that could copy itself. In 1986, Nobel Laureate Walter Gilbert wrote in a pioneering article in the journal Nature: "It is possible to imagine a living world containing only RNA molecules that serve as catalysts for their own synthesis... Therefore, the first stage of evolution occurs through RNA molecules that carry out the chemical catalyzing operations needed to assemble themselves from a soup of nucleotides." According to this view, the first self-replicating RNA molecule, which was created from inanimate matter, performed all the different roles that RNA, DNA and protein molecules perform today.

Several other signs support the idea that RNA appeared during the evolution of life before proteins and DNA. For example, there are many small molecules, called cofactors, that play a role in the chemical reactions that enzymes catalyze. These molecules often have an RNA nucleotide associated with them that has no clear function. In the past, it was believed that such structures are "molecular fossils", remnants of the time when RNA ruled alone, without DNA or proteins, in the biochemical world.

However, these and other clues only support the conclusion that RNA preceded DNA and proteins. They do not provide any information regarding the origin of life before the world of RNA, in a period that may have included additional stages and other living beings that ruled the dome. Adding to the confusion is the fact that various researchers use the term "RNA world" in reference to both ideas. I will use the term "RNA-first" here to describe the claim that RNA was involved in the formation of life, and I will distinguish it from the claim that RNA only preceded DNA and proteins.

The soup pot is empty
In front of the RNA-first hypothesis stands a question that poses a huge challenge: How did the first RNA molecule that replicated itself appear? Major obstacles prevent us from accepting Gilbert's description according to which RNA was created from a still soup of nucleotides.

Nucleotides, the building blocks of RNA, are complicated organic substances. The molecule of each of them contains 3 subunits: sugar, phosphate (phosphate ion) and one of four nitrogen-containing bases. Each of the RNA nucleotides therefore contains nine or ten carbon atoms, many nitrogen and oxygen atoms and a phosphate group, all connected to each other in a precise three-dimensional pattern. There are many alternative ways to connect these atoms that create thousands of additional possible nucleotides that are also able to easily connect to the normal nucleotides. But these alternative nucleotides are not found in the RNA molecules in the cells. The number of possible nucleotides is dwarfed by the hundreds of thousands, and perhaps even millions of stable organic molecules that are similar in size but are not nucleotides.

The idea that, despite this, suitable nucleotides are formed draws its inspiration from the well-known experiment published by Stanley L. Miller in 1953. He passed an electric spark through a mixture of simple gases, then thought to represent the atmosphere of the early Earth, and saw that amino acids were formed. Amino acids were also identified in the Murchison meteorite that fell in Australia in 1969. Nature must have been generous in providing these particular building blocks. Some writers concluded from these results that all the building blocks of life could easily be formed in experiments similar to Miller's and that these materials would be present in meteorites. But that is not how things are.

Amino acids, such as those created in experiments similar to Miller's, are much simpler molecules than nucleotides. They are characterized by two chemical groups, an amine group (nitrogen and two hydrogens) and a carboxylic acid (carbon, two oxides and hydrogen), both attached to the same carbon atom. Of the 20 amino acids that make up natural proteins, the simplest amino acid contains only two carbon atoms. Seventeen amino acids from the entire series contain 6 carbon atoms or less. The amino acids and other important substances produced in Miller's experiment contained only 2 or 3 carbon atoms. In contrast, no nucleotides of any kind have been reported to have been created in electrical breakdown experiments or discovered in meteorites. Apparently the still nature tends to create rather small molecules containing few carbon atoms and therefore it has no preference for the creation of the nucleotides necessary for life of our kind.

To save the RNA-first concept from this fatal flaw, its proponents developed a new scientific field called prebiotic synthesis. They tried to show that it is possible to produce RNA and its components in the laboratory through a series of carefully controlled reactions, using conditions and relevant starting materials, according to their opinion.

This is not the place to expand on the disadvantages of prebiotic synthesis. The problems that the approach raises raise this analogy: imagine in your mind a golf player, who, after finishing threading the ball into the 18 holes of the course, assumes that the ball will be able to play itself, without the player himself, and complete the course by himself. After all, the actor demonstrated that there is a possibility that the event will happen. Now all that remains is to assume that a combination of natural forces (earthquakes, winds, tornadoes and floods, for example) can cause the same result, provided the time is long enough. It is not necessary to break any physical law in order for RNA to be formed spontaneously, but the chances of this are zero.

Some chemists have proposed that a simpler replicating molecule, similar to RNA, appeared first and dominated life in the "pre-RNA world". According to them, this replicator could catalyze chemical reactions similar to RNA. But so far no traces of this supposed ancient replicator have been found in the processes of modern biology. RNA probably occupied all the functions of this replicator and catalyst at some point in time after its appearance.

And even if nature had provided a primordial soup of suitable building blocks, whether nucleotides or simpler substitutes, the likelihood that these building blocks would spontaneously connect to each other and produce a replicating molecule is infinitely lower than even the likelihood of the creation of the appropriate soup itself. Let us assume that in some way a suitable mixture of the building blocks is formed under conditions that allow their connection into chains. These building blocks will be accompanied by a multitude of defective units that will enter the growing chain and destroy the possibility of it being used as a replicator. It is enough for the simplest defective unit to have only one "arm" and it will connect to only one neighboring building block, instead of two, so that the chain does not grow.

Theoretically, the indifferent nature would connect the units randomly and produce a huge number of short chains whose growth has stopped, instead of the longer chain, with a uniform backbone, needed to support the functions of replication and catalysis. The probability of the success of this last process is so small and negligible that its occurrence, even once in the visible universe, can be considered an extraordinarily lucky coincidence.

Small molecules create life
Nobel laureate Christian de Dube called for "the rejection of all cases whose probability is so small and immeasurable that they can be called miracles, phenomena that go beyond the realm of scientific investigation." We must abandon the idea that DNA, RNA, proteins and other large complex molecules participated in the creation of life. Still nature provides us, instead, with a variety of mixtures of small molecules with which we must work.

Fortunately, an alternative set of theories dealing with these substances has been around for several decades. These theories use a thermodynamic rather than a genetic definition of life. The definition was presented by Carl Sagan in the Encyclopaedia Britannica: a domain region will be considered alive if order increases in it (entropy decreases) through a series of circular processes driven by a flux of incoming energy. This approach, based on small molecules, is rooted in the ideas of the Soviet biochemist Alexander Oparin. Different ideas that explain the origin of life according to this approach differ only in their exact details. I will present here five accepted requirements (and add some ideas of my own).

1. A boundary is needed that separates the living from the inanimate. Life is distinguished by its high degree of organization, yet the second law of thermodynamics requires that the universe move in the direction where disorder, or entropy, increases. However, there is a loophole in this law, which allows entropy in a limited region to decrease, provided there is a greater increase in entropy outside that region. When living cells grow and multiply, they convert chemical or radiant energy into heat energy. The released heat increases the entropy of the environment and compensates for its decrease within the living systems. The border keeps the world divided into small pockets of life within a still environment in which they must sustain themselves.

Today, sophisticated double membranes (membranes), made of materials classified as lipids, separate living cells and their environment. Most likely, at the beginning of life, some natural feature served the same purpose. The work of David W. Diemer of the University of California at Santa Cruz supports this idea. He saw membrane-like structures in meteorites. Other ideas proposed natural boundaries that are not used by life today, such as membranes of iron sulfide, rocky surfaces (where electrostatic forces separate certain molecules from their surroundings), small ponds, and suspensions in the air (aerosols).

2. An energy source is needed to drive the organizing process. To live we consume carbohydrates and fats which we react with oxygen we breathe. Microorganisms are more versatile and can use minerals instead of food or oxygen. In all cases these are processes called redox reactions. In reactions, electrons pass from an electron-rich substance (the reducer) to an electron-poor substance (the oxidizer). Plants can capture sunlight directly and utilize it for life functions. Cells in special circumstances use other forms of energy - for example, a difference in the degree of acidity on both sides of a membrane. It is possible that other forms of energy, such as radioactivity or sudden temperature changes could be used by life elsewhere in the universe.

3. A coupling mechanism must link the release of energy with the organizing process that creates life and sustains it. Release of energy does not necessarily result in a useful result. Energy is released when fuel is burned in the combustion chamber of a car, but the car will not move unless the energy is used to turn the wheels. For this, a mechanical connection, or coupling, is required. Every day, each of us breaks down kilograms of a nucleotide called ATP in our body cells. The energy released in this reaction is used to drive the processes necessary for our biochemistry, processes that without it would occur too slowly or would not occur at all. The coupling is achieved through an intermediate common to both reactions and the process is catalyzed by an enzyme. One of the assumptions of the small molecule approach is that conjugated reactions take place in nature and that there are primitive catalysts sufficient for the beginning of life.

4. A network of chemical processes must be created that allows adaptation and evolution. We have now come to the heart of the matter. Imagine, for example, an energetically favored redox reaction that drives the transformation of an organic substance, A, into another organic substance, B, within the region bounded by the partition. I call this key process the "preventive response", as it serves as the driving force of the entire organizing process. If B simply returns and becomes A, or leaves the bounded area, it will not be a path leading to a higher level of organization. Conversely, if there is a multi-step chemical pathway that converts B back to A, say from B to C, to D, finally to A, then the steps in this circular pathway (or cycle) will be favored, because they regenerate the stock of A and allow continued useful release of energy through the reaction of the mineral [see box on page 27).

Branching reactions will also occur, such as a two-way reaction that turns material D, which is in the circuit, into material E, which is not part of it, and vice versa. Since the chemical cycle continues to operate, the reaction in the direction in which substance E becomes substance D will be favored because it introduces substance into the cycle and maximizes the release of energy that accompanies the driving reaction.

The chemical cycle will also be able to adapt to changing conditions. When I was a child I was fascinated by the way the water flowing from a leaky faucet found its way down the hill to the nearest sewer opening. If fallen leaves or discarded trash blocked their path, the water would accumulate until another way around the obstacle was found. Similarly, if a change in the degree of acidity in the environment were to inhibit any step in the pathway from B to A, one of the substances would accumulate until another chemical pathway was found. Further changes of this type will turn the original circuit into a network of processes. This investigation of the chemical "landscape", by way of trial and error, may also lead to the appearance of compounds that can speed up important steps in the cycle and thus increase the efficiency with which the network of processes utilizes the energy source.

5. The reaction network must grow and multiply. In order to survive and grow, the network must absorb material at a faster rate than the rate at which it loses it. Diffusion of substances participating in the network reactions, which leads to their exit to the outside world outside the domain area, is an entropically favored process, and therefore it will occur at a certain rate. Some side reactions can create gases that will be released or insoluble tar-like substances that will settle out of the solution. If the rate of these processes exceeds the rate at which the network absorbs material from the environment, the network will be eliminated. Decomposition of the external fuel will also result in a similar result. One can imagine that the early Earth had many such beginnings, involving alternative driving reactions and alternative external energy sources. Finally, a particularly durable preventive response took root and sustained itself.

Eventually, a method of reproduction must also be developed. If our network of processes finds a home in a fatty membrane, physical forces can tear it apart after it has grown enough. (Freeman Dyson of the Institute for Advanced Research in Princeton, New Jersey described such a system as a "garbage bag world" in contrast to the "beautiful and orderly picture" of the RNA world.) A domain system functioning within a rock may overflow and flow into nearby pores. The splitting into separate units, whatever the mechanism may be, protects the system from complete extinction due to a devastating local event. Once these independent units are established, they can develop in different ways and compete with each other for the raw materials. In doing so, we made the transition from life that arose from inanimate matter through the action of an energy source, to life that adapts to the environment through Darwinian evolution.

The paradigm shift
Systems of the type I described are often classified under the heading "metabolism-first" (or "metabolism-first"), a title that implies that they do not include a mechanism of heredity. In other words, they do not contain a molecule or structure that clearly enables the replication of the information stored in them (their heredity) and its transmission to their descendants. However, a collection of small objects contains the same information as a list describing those objects. For example, my wife gives me a grocery shopping list. The collection of grocery items that I return to you contains the same information that the list contains. Doron Lantz from the Weizmann Institute of Science in Israel gave the name "compositional genome" to the heredity stored in small molecules, instead of in a list like DNA or RNA.

The approach of small molecules to the source of life requires several requirements from nature (a bounded area, an external energy source, a preventive reaction linked to the energy supply, a network of chemical reactions that includes this reaction and a simple mechanism of replication). However, these requirements are of a general nature and the likelihood of their existence is infinitely greater explaining the sophisticated multi-step pathway required to create a replicator molecule.

Many theoretical papers over the years have put forward various proposals for exchange-materials-first, but only a few experimental works have been presented to support them. In those cases where experiments were published, they were usually used to demonstrate the feasibility of individual steps in a proposed circuit. The most new information came from Gunter Wachtershauser and his colleagues at the Technical University of Munich. They presented parts of a circuit in which the connection and separation of amino acids are carried out in the presence of metal and sulfur compounds that were used as catalysts. Oxidation of carbon monoxide to carbon dioxide provides the energy that drives the process. The researchers have not yet demonstrated the operation of a complete circuit or its ability to sustain itself and undergo further evolution. A conclusive experiment demonstrating these three properties is needed to validate the small molecule approach.

The main initial task of such an experiment is the identification of driving reactions - a reaction between small molecules (like A and B in the previous example) coupled to a common energy source (like the oxidation of carbon monoxide or a mineral). Once a reasonable preventive response is identified, it will not be necessary to specify the rest of the system in advance. It will be possible to put the selected ingredients (including the energy source) into a suitable reaction tank along with a mixture of other small molecules that are usually produced by natural processes (and were, most likely, common on the surface of the ancient Earth). If a stable network of chemical reactions is created that is capable of evolution, it will be observed that the concentrations of the substances participating in the network will increase and change over time. New catalysts that increase the rate of key reactions may appear, while the amount of irrelevant substances will decrease. The reaction vessel will need an input facility (which will allow a renewed supply of energy and raw materials) and an outlet facility (which will allow the disposal of waste products and materials that are not part of the chemical network).

In such experiments it will be easy to identify failures. The energy may be consumed without creating noticeable changes in the concentration of other materials, or the materials will turn into tar that will clog the equipment. The success of such an experiment may demonstrate the first steps on the way to life. These steps do not have to reproduce those that did happen on the surface of the ancient Earth. More important is that the general principle will be demonstrated and made available for further research. It is possible that there are many possible paths to life, and the choice between them is dictated by the conditions of the local environment.

An understanding of the initial steps that led to life will not reveal what the actual specific events were that led to the organisms that exist today, based on DNA, RNA, and proteins. And yet, since we know that evolution is not capable of predicting the events of the future, we can assume that the first nucleotides that appeared in the metabolic processes were used for some other purpose, perhaps as catalysts or as storehouses of chemical energy (the ATP nucleotide is still used for this purpose today). A chance event or some circumstance led, perhaps, to the joining of the nucleotides to create RNA. The most obvious role of modern RNA is to serve as a structural component that helps in creating bonds between amino acids in the synthesis of proteins. It is possible that the first RNA was used for the same purpose but without a preference for certain amino acids. Many additional evolutionary steps are required to "invent" the complex mechanisms for the replication and synthesis of certain proteins that we observe in life today.

If the general paradigm of the small molecule approach is confirmed, our expectations about life in the universe will change. A very unlikely beginning of life, as in the RNA-first scenario, suggests that we are alone in the universe. In the words of the biochemist Jacques Mono: "The universe did not conceive life and the biosphere did not conceive man." Our number just came up in the Monte Carlo roulette."

The alternative of small molecules, on the other hand, corresponds to the views of the biologist Stuart Kaufman: "If all this is true, the existence of life is much more likely than we assumed. Not only is the universe our home, but it is also very likely that we share it with neighbors we have not yet met."

Overview The origin of life
The theories regarding the way in which life arose from inanimate matter are divided into two comprehensive groups: "replicator-first" theories, according to which a large molecule capable of replicating itself (such as RNA) was created by chance, and "metabolism-first" theories, according to which molecules Small ones created a network of chemical reactions linked to an energy source and undergoing evolution.

Proponents of the "replicator-first" theories must explain how such a complicated molecule could have formed before the evolutionary process got underway.

Proponents of "metabolism-first" must show how a network of chemical reactions capable of growth and evolution could have formed in the early days of the Earth.

About the authorRobert Shapiro is a retired professor of chemistry and senior research scientist at New York University. Published by himself or with colleagues more than 125 articles, mainly in the field of DNA chemistry. Shapiro specifically studied the ways in which the chemistry of the environment can damage hereditary material and cause changes that can lead to mutations and cancer.

Frequently asked questions from readers
Robert Shapiro answered questions posed by readers on the Scientific American English blog. Here is an edited selection of questions and answers.

Does the exchange-of-materials-first hypothesis point to a single source of life or multiple sources independent of each other?- JR

Answer: Many sources seem to be a more practical assumption in the exchange-the-materials-first scenario. Gerald Feinberg and I discussed in our book Life Beyond Earth, published in 1980, the possibility of alien life (life not based on DNA, RNA and other biochemistry familiar to us). Researchers at a conference hosted by Paul Davis at Arizona State University in December 2006 concluded that undiscovered alien life may exist even on the surface of our planet. Using the usual culture materials, it is difficult to grow and make cultures of most microorganisms, which can be observed under a microscope, and a significant part of them therefore remains uncharacterized. Alien microbes can possibly exist in living environments that are too extreme for even the most resistant forms of life known to us.

Why should we demonstrate metabolism-first in vitro? Is it not possible to simulate them using a computer program? –Dave Ivanoff

A: Stuart Kaufman, Doron Lantz and others used computer simulations to demonstrate the feasibility of self-sustaining feedback loops. Such simulations did not specify the exact chemical mixtures and reaction conditions necessary for the establishment of chemical networks. We still don't know all the reaction pathways open to mixtures of simple organic compounds, much less know the thermodynamic constants. Even if this information were available, most chemists would not be convinced by a computer simulation but would demand an experimental demonstration.

The fact that all biological molecules have the same chirality requires some explanation - John Holt
A: If the chemical reaction carried out using a mineral, which drives the reaction circuits I discussed in the article, prefers only one form of the mirror image of the chemical substance A, then the product B and other compounds in the cycle would also have only one form of the mirror image. Control of chirality becomes essential when small molecules join together to form large molecules. A modern enzyme may contain 100 amino acids, linked together, and all of them having the same chirality (they are called L amino acids). If they were replaced, at sensitive sites within the enzyme, with D amino acids, which are the mirror image of the L forms, the spatial form of the enzyme would change and its function might disappear.

The answer of an RNA-first researcher
Stephen A. Benner of the Westheimer Institute of Science and Technology in Gainesville, Florida claims that the RNA-first model is alive and well.

Even if some of the researchers declare that the RNA-first model to explain the origin of life is dead because the probability of the spontaneous appearance of an RNA molecule is beyond imagination, scientific research actually offers support for this model.

Let me first acknowledge the fact that most organic molecules turn into something like asphalt when bombarded with energy (such as lightning or heat from volcanoes), a material more suitable for paving roads than for reducing vitality. But the metabolism-first models, even if supported by some real chemical substance, also have to deal with this paradox: the molecules active enough to participate in metabolism are also active enough to break down. There are no easy solutions.

Like many others, my research group returned to the scientific imperative: to conduct an actual laboratory experiment to learn how RNA could have appeared on Earth.

The sugar ribose, the Rabbi of the BRNA, provides an example lesson of how a problem that was declared "unsolvable" is actually only "not yet solved". For a long time, ribose remained "impossible" to produce through prebiotic synthesis (reactions between mixtures of molecules whose existence on the surface of the prebiotic Earth is probable), since it contains a carbonyl group - a carbon atom with a double bond to an oxygen atom. The carbonyl group gives the molecule both "good" reaction options (the ability to participate in metabolism) and "bad" (the ability to form a tar-like substance). About ten years ago, Stanley L. Miller concluded that the instability of ribose arising from the carbonyl group "prevents the use of ribose and other sugars as prebiotic agents... and hence ribose and other sugars were not components of the first genetic material."

But prebiotic soups need a soup bowl made of minerals, not a Pyrex chemical beaker. One interesting "soup bowl" is found today in "Death Valley" in California. In the ancient Valley of Death the environment was alternately wet and dry, rich in organic molecules left over from the cloud of matter that formed the earth and also (most importantly) full of minerals containing the element boron. Why is the pit important? Because it stabilizes carbohydrates like ribose. Moreover, if you mix together boron oxide (borate) and organic compounds common in meteorites and expose them to a lightning strike, beautiful amounts of ribose are formed from formaldehyde and the resulting ribose does not decompose.

The fact that a problem that was declared "unsolvable" was found to have such a simple solution does not prove that the first life form certainly used RNA to carry out genetics. But it should stop us a bit at a time when we are advised to abandon research directions just because some problematic bits of them have not yet been resolved.