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Rescuing the RNA World?, Part 1 (of 2)

New Research Provides Insight into a Creator’s Role in the Origin of Life

I remember watching Dudley Do-Right on Saturday mornings as a kid. A member of the Canadian Mounties, this cartoon hero displayed more heroism than smarts as week after week he took on his archenemy Snidley Whiplash. With sheer luck on his side, Dudley (and his horse named Horse) somehow managed to rescue his love interest Nell Fenwick from Whiplash’s dastardly schemes.

Recent work by chemists from the University of Manchester (U.K.) appears to have rescued one of the leading ideas for the origin of life, the RNA world hypothesis, from certain doom. Instead of relying on luck, these researchers applied “out-of-the-box” thinking. Through painstaking laboratory experiments, they discovered a novel, straightforward chemical route to one of the key building block materials required by the RNA world hypothesis.

This work not only makes an evolutionary explanation for the beginning of life more plausible, it also opens up a new avenue of research for the origin-of-life community. But, as exciting as this breakthrough appears, does it really bailout the RNA world scenario?

The RNA World Hypothesis

Many origin-of-life investigators think that RNA was the first replicator and information-harboring molecule, predating both DNA and proteins. As such, RNA took on the contemporary biochemical function of both DNA and proteins by operating as a self-replicator that catalyzed its own synthesis. According to the RNA world hypothesis, over time numerous RNA molecules possessing a wide range of catalytic activity emerged. Eventually, this environment transitioned to an RNA-protein world that–with the addition of DNA–finally gave way to contemporary biochemistry. (For a more detailed discussion on the central importance of the RNA world hypothesis to the origin-of-life paradigm, please see here.)

Validating the RNA World Hypothesis

In order to substantiate the RNA world scenario researchers need to establish the validity of several processes. These include:

  • reasonable prebiotic chemical routes that will generate the building blocks (nucleobases, ribose, and phosphate) of RNA;
  • reasonable prebiotic routes that will assemble these building blocks into ribonucleotides;
  • a reaction scheme that will chemically activate the ribonucleotides;
  • reasonable prebiotic routes that will assemble RNA from its building blocks into molecular chains long enough to form ribozymes.

Challenges Facing the RNA World Hypothesis

Scientists have identified possible routes to make ribose and the nucleobases, but these pathways have questionable relevance for the origin of life. While the reactions work well in the laboratory, the conditions of early Earth would have frustrated such processes.

For example, the only known plausible prebiotic route to ribose (and all sugars) is the Butlerow reaction (also known as the formose reaction). This reaction begins with the one-carbon compound formaldehyde, which researchers think would have been present on early Earth. In the presence of an inorganic catalyst (calcium hydroxide, calcium oxide, alumina clays, and so on), formaldehyde reacts with itself. The resultant products generate two, three, four, five, six, or more carbon sugars.

Though this route to ribose and other sugars exists, most researchers question its applicability to the origin-of-life scenario. Numerous side reactions dominate formose chemistry. As a consequence, this reaction yields over forty different sugar species with ribose as a minor component. If this reaction did operate on early Earth, it could never have yielded enough ribose to support an RNA world. Additionally, laboratory formose reactions are free of contaminants that would likely be present on early Earth. Ammonia, amines, and amino acids, for example, react with formaldehyde and the products of the formose reaction. On primordial Earth these side reactions would have consumed key reactants and frustrated the formation of ribose and other sugars.

Decomposition negatively affects ribose formation. Sugars decompose under alkaline and acidic conditions and are susceptible to oxidation. Even within a neutral pH range, sugars decompose. At 212 °F (100 °C), under neutral conditions, ribose’s half-life is seventy-three minutes. At 32 °F (0 °C), ribose has a half-life of forty-four years.

Similar problems confront origin-of-life researchers as they attempt to account for the genesis of the nucleobases. For example, chemists have discovered two possible pathways that produce cytosine. One route involves a reaction between cyanoacetylene and cyanate, and the other reaction begins with cyanoacetalydehyde and urea. These four compounds represent essential ingredients of early Earth’s supposed prebiotic soup.

Chemist Robert Shapiro demonstrated, however, that the two chemical routes lack any relevance. He points out the unlikelihood that cyanoacetylene, cyanate, cyanoacetaldehyde, and urea existed at sufficient levels on primordial Earth to effectively produce cytosine. Even if these compounds had occurred at appropriate levels, interfering chemical reactions would have consumed them quickly before cytosine could form. Cyanoacetylene rapidly reacts with ammonia, amines, thiols, and hydrogen cyanide. Cyanate undergoes rapid reaction with water. In the presence of water, cyanoacetaldehyde decomposes into acetonitrile and formate. When cytosine does form, it rapidly decomposes. At room temperature and with a neutral pH, cytosine breaks down, losing half its molecules in 340 years. At 32 °F (0 °C), its half-life is seventeen thousand years.

And even if a ready supply of ribose, nucleobases, and phosphates were present on early Earth, these compounds won’t react with each other to form ribonucleotides.

The weight of such problems is so burdensome that I heard the late Leslie Orgel actually say at a scientific conference that “it would be a miracle if a strand of RNA ever appeared on the early Earth.”

The Breakthrough

Traditionally, researchers divided possible prebiotic reactions into those that lead to sugars and those that yield nucleobases. Then they tried to find a way for the two products to eventually form ribonucleotides. But the Manchester chemists took a different tact. They looked for ways that the two prebiotic routes could intermingle.

This novel approach led to a breakthrough. The researchers discovered that activated ribonucleotides could readily form in the laboratory in just a few simple steps. The reaction of cyanamide and glycoaldehyde to form 2-amino-oxazole comprises a key to this reaction sequence. (Cyanamide is a material traditionally viewed as part of the chemical pathway to some of the nucleobases and glycoaldehyde is the first product in the formose reaction.) In turn, 2-amino-oxazole reacts with glyceraldehyde (formed when glycoaldehyde reacts with formaldehyde) to form a sugar derivative, pentose amino-oxazoline. This compound reacts with cyanoacetylene (one of the starting materials in the prebiotic synthesis of cytosine) to generate anhydroarabinonucleoside, which can react with pyrophosphate and urea to form an activated ribonucleotide. The new ribonucleotide is poised to react with other activated ribonucleotides to form RNA chains.

As promising as this chemistry is, the researchers noted a serious problem. In unbuffered reactions (in which the pH isn’t controlled), a large number of unwanted products result at each step in the pathway. As a consequence, 2-aminooxazole is present in the system only at low levels. The byproducts interfered with the remainder of the pathway and thwarted the generation of activated ribonucleotides.

In the face of this issue, the chemists discovered that including phosphate in the reaction mixtures eliminated many of the unwanted byproducts. Phosphate functions as both a catalyst and a buffer, controlling the pH of the reaction mixture. In other words, one of the key reactants in the last stage of the chemical route plays a role in earlier reactions, facilitating the production of ribonucleotides. The team also found that exposing the final reaction mixture to UV radiation selectively destroys unwanted byproducts as well, helping to increase the relative amount of ribonucleotides in the final product mixture.

Instead of thinking about sugar and nucleobase chemistries as separate, scientists from Manchester allowed the two chemistries to intermingle. This conceptual breakthrough allowed them to discover a very simple chemical route to produce activated ribonucleotides, which are chemically complex materials. In addition, the chemists allowed reactants from the final steps of the chemical pathway to intermingle with reactants in the early stages of the process. This, too, represents a conceptual advance in origin-of-life studies, and provides a reasonable way to “clean up” unwanted side reactions that otherwise would interfere with the production of the ribonucleotides. The use of UV radiation to “purify” the final product, too, is reasonable. UV radiation would have impinged on early Earth.

Without question, these chemists have made an important contribution to the evolutionary paradigm. Their work paves the way for others to approach problems in prebiotic chemistry in an unconventional way that might lead to other key advances. Still, have they really rescued the RNA world hypothesis?

Next time I will summon the help of another Saturday morning cartoon legend to demonstrate how this work actually turns the tables on chemical evolution and unwittingly provides support for intelligent design.

Part 1 | Part 2