The RNA World Hypothesis Explained and Unexplained by Kathleen Hamrick Will Brooks, Ph.D.

http://apologeticspress.org/APContent.aspx?category=12&article=2317

The RNA World Hypothesis Explained and Unexplained

by	Kathleen Hamrick Will Brooks, Ph.D.

[Editor’s Note: The following article was written by A.P. auxiliary staff scientist Will Brooks and one of his students. Dr. Brooks holds a Ph.D. in Cell Biology from the University of Alabama at Birmingham and serves as Assistant Professor of Biology at Freed-Hardeman University.]

One of the goals within the discipline of biology is to define life. This goal, however, is no simple task. While we can have an intuitive understanding of what it means to be alive, forming this understanding into a precise definition of life poses a dilemma for scientists. Life comes in many shapes, sizes, colors, and forms, so placing all these variations of life into one nice definition is seemingly impossible. To circumvent this problem, scientists have defined life by stating characteristics shared by all life forms. To be considered “alive,” a system of molecules must possess each of these characteristics. Examples include (1) the ability to sense and respond to stimuli, (2) the ability to acquire and utilize materials for energy, (3) the ability to store genetic information in the form of DNA, and (4) the ability to self-replicate. All living organisms share these basic characteristics, and those systems of molecules which lack even one of these basic characteristics is not considered to be a living organism.

Deoxyribonucleic acid (DNA) is the genetic material used by all living organisms to code for life. DNA can be thought of as the genetic fingerprint of each organism because it is unique to each species of organism. During the process of self-replication, this genetic code is duplicated and identical copies (discounting rare instances of mutation) are given to each progeny of an organism, maintaining the fingerprint and thus the identity of that organism. The function ofDNA as the genetic material of an organism is to provide a code for the production of another group of molecules known as proteins. Proteins serve a host of functions for an organism. They are known, appropriately, as the workhorses of a cell, because they carry out the vast majority of organismal tasks, including catalysis.

A catalyst is any substance capable of increasing the speed of a chemical reaction. Within each living organism on Earth, millions of chemical reactions take place every minute. The majority of these reactions are prompted by a very large group of protein catalysts known as enzymes. These enzyme-mediated chemical reactions range from those used to synthesize various metabolites to those used to break down ingested foods. By serving as enzyme catalysts, proteins play a crucial role in all living organisms. For without enzymes, organisms would be both unable to break down the food that they ingest and unable to make the necessary metabolites needed to sustain life.

While the vast majority of functional enzymes within living organisms are proteins, scientists have discovered that another group of molecules, known as ribonucleic acids (RNAs), are also capable of catalyzing some chemical reactions (Kruger, et al., 1982). RNAs are very similar in structure to DNA, differing only in the type of sugar used to form the molecules—DNAutilizes deoxyribose and RNA utilizes ribose. While DNA is the vital genetic code that is passed down between parents and offspring, RNA also plays an important role. Ribonucleic acids are a messenger system that carries the DNA code from the cell’s nucleus, the home ofDNA, to the cellular cytoplasm where proteins are synthesized. These are known as messengerRNAs (mRNA). Furthermore, another group of RNAs, known as ribosomal RNAs (rRNAs), is used along with proteins to build the cellular structure known as the ribosome, which is the cellular location at which proteins are made. So, RNA plays several related roles in the process of protein production: (1) it carries the genetic code from DNA to the ribosome, (2) it helps form the structure of the ribosome, and (3) it functions in catalysis.

While there are a few other examples (reviewed in Fedor and Williamson, 2005), the catalytic properties of RNA are best seen in the ribosome. When proteins are synthesized by an organism’s cells, small units known as amino acids are chemically linked together to form a long, linear chain. This chain of amino acids is known as a polypeptide or protein. The chemical bond that links together each amino acid in the chain is called the peptide bond. Because each of the 20 amino acids are very similar in structure, the same peptide bond is formed between every unit of the polypeptide chain. The chemical reaction that forms this peptide bond requires catalysis. The protein-rRNA complex that we know as the ribosome has long been known to serve as the site as well as the catalyst in forming the peptide bond. But, scientists were surprised to discover that the protein component only serves as a structural element of the ribosome. It is the RNAcomponent of the ribosome that serves as the catalyst (Nissen, et al., 2000). This catalyticRNA has thus been termed a ribozyme.

Later it was discovered that yet another group of RNAs, the small nuclear RNAs (snRNA), were also capable of catalyzing a chemical reaction (Valadkhan and Manley, 2001). When produced by the cell, mRNA must undergo a series of maturation steps before it is fully functional as a genetic message (Alberts, et al., 2002, pp. 317-327). One of these steps toward maturity is the process of splicing. Newly synthesized mRNA contains large regions, spread throughout its length, that do not directly code for protein production. These non-coding regions are called introns. To make the mRNA mature and functional as a code, each intron must be removed from the mRNA and the remaining coding regions, known as exons, must be linked or spliced back together. These “cut-and-paste” events occur within the cell’s nucleus within a structure that we call the spliceosome. Like the ribosome, the spliceosome is a large complex of both protein and RNA, in this case snRNA. Amusingly, these protein-RNA complexes have been dubbed small nuclear ribonucleoproteins or “snurps.” Interestingly, scientists found that not protein, but RNAs were responsible for catalyzing the chemical reactions that take place during these splicing events. RNAs were carrying out chemical reactions on other RNAs.

Scientists were very excited by these revolutionary findings. Now, they had a single type of molecule, RNA, that possessed two very important properties. First, it was very similar in structure to DNA and thus theoretically could also store genetic information. Second, it could function as a catalyst like proteins. In 1986, Walter Gilbert coined the phrase “RNA World” and initiated what is now known as the RNA World Hypothesis (Gilbert, 1986). This hypothesis on the origin of life states simply that because RNA has the dual ability to both store genetic information and catalyze chemical reactions, it must pre-date DNA and proteins, both of which supposedly evolved after and perhaps from the RNA.

The RNA World Hypothesis is widely accepted by evolutionists, because it provides an alleged solution to a long-recognized problem in evolutionary theory. Consider how proteins are made by a cell. First, DNA which holds the genetic code is converted into RNA through a process known as transcription. This process is similar to how one would copy a letter from one piece of paper onto another sheet. The contents of the letter remain unchanged, only the medium—the paper—has changed.RNA carries this information to the ribosome, where it is read and used as a code to make a protein through a process known as translation. This process can be compared to translating the copy of the letter from one language into another. Nucleic acid (DNA and RNA) is changed into another molecule altogether: protein. This linear progression of DNA to RNA to protein is known in biology as the Central Dogma of Molecular Biology (Alberts, et al., 2002, p. 301). Of the three components in the path, only DNA has the capacity to be replicated. So, while DNA stores the genetic code and can be replicated, it cannot perform any chemical reactions. And, while protein can perform chemical reactions, it cannot store genetic information. So, in evolutionary thinking, which came first—DNA or protein? Making the problem even more difficult, DNA relies upon proteins during its own replication. DNA does not self-replicate of its own accord. It must have protein enzymes to facilitate this process. So, what came first—the chicken or the egg? DNA or protein? Each relies upon the other. You should begin to see howRNA might solve this problem. If RNA can both store genetic information and catalyze chemical reactions, and if it evolved first, we have a single molecule that stores information and can catalyze its own replication, a self-replicating genetic material.

In order to prove this theory plausible, a set of conditions must be created to favor the spontaneous formation of RNA molecules without the aid of a biological catalyst. This would have had to be the starting point for an RNA world. One necessary component for RNAformation would be a steady supply of nucleotides, the building blocks of RNA. Scientists speculate these nucleotides were created from other small molecules present, or were generated in space before arriving on earth. Ribose, the sugar used in RNA, is assumed to have arisen from formaldehyde via the formose reaction. The mystery of the addition of nucleotides onto a ribose backbone remains unsolved by scientists attempting to create conditions of a primitive Earth (Müller, 2006, 63:1279-1280). Once these RNA molecules were formed completely by chance, they would have to have possessed or evolved the ability to catalyze reactions leading to self-replication. After sustaining itself through several replications, the RNA would then need to gain the ability to create a barrier between the extraneous materials surrounding it, in order to isolate the beneficial products from those proving non-functional. Thus, a membrane of sorts would have had to evolve and be maintained (Müller, 63:1285-1286). These steps are only the basics, proving the task much too complicated to occur by mere chance.

In all known organisms living today, DNA and not RNA is the genetic material. DNA has advantages over RNA which make it a more suitable molecule to store the very important genetic code. First, DNA is a double-stranded molecule while RNA is single-stranded. The double-stranded nature of DNA gives it the ability to be replicated in a much simpler series of steps. When DNA is replicated, each of the two complimentary strands serves as a template on which to build another strand. The result is that in one step, each strand of DNA is replicated to produce four total DNA strands or two identical double helices. RNA, however, is single-stranded. In order for it to be replicated, two sequential rounds of replication would be required. First, a complimentary strand would need to be synthesized from the original parental strand. Only then could that new complimentary strand be used to re-make the parental strand. As stated before,DNA and RNA differ in the sugar which makes up the molecule’s backbone. Deoxyribose, the sugar used in DNA, differs from ribose used in RNA, by lacking one organic functional group known as alcohol. The absence of this alcohol group greatly increases the stability of DNA overRNA. In ribonucleic acids, this
–OH group is capable of initiating chemical reactions which favor breakdown of the RNAmolecule. For these and other reasons, DNA is a much more stable and preferable genetic material. This is made obvious by the fact that all living organisms use DNA, not RNA, as their permanent storage medium of genetic information. It also indicates that RNA would be an unsuitable medium by which to initiate life.

Evolutionists would have us to believe that non-living elements and molecules joined together and developed increasing biological capabilities. Those who believe in intelligent design reject this hypothesis, insisting that neither RNA nor living cells are able to evolve spontaneously. While some disagreement exists among those in the evolutionary community on the time frame for such alleged reactions to occur, the consensus is that, given large amounts of time, single-celled bacteria were formed. But all known biological principles militate against this notion. Even billions of years could not provide mechanisms for the reaction products to evolve advantageous characteristics and form DNA and cell proteins, let alone create strings of RNA nucleotides, arriving at just the right sequence in order to code for a functional protein. The four nucleotide bases that form RNA (adenine, guanine, cytosine, and uracil) can be arranged in an exponential array of combinations and lengths. For an actual, functional protein to be coded, a precise sequence of nucleotides must be obtained. Forming the code for even one protein by evolutionary means is impossible, without even considering the necessity of the number that work together in a single cell.

There is no scientific evidence to suggest that RNA is spontaneously being created and capable of forming pre-cellular life today. While some artificial ribozymes have been created in the laboratory (reviewed in Chen, et al., 2007), there are still significant holes in reproducing anRNA world to support the hypothesis. The ribozymes created artificially lack the abilities to sufficiently process themselves, and there is no evidence of them producing large quantities of advantageous nucleotide sequences. Moreover, no system has ever created cellular life. There is even significant debate among scientists over the conditions and constituents of a “prebiotic Earth” model.

The RNA World Hypothesis is simply another attempt by scientists to explain the origin of life to the exclusion of the divine Creator. Given the absolute impossibility of life originating from the reactions of non-living matter, it can be justified that RNA did not predate other biological molecules. All biological molecules were created together to work in concert. RNA was designed to be the essential intermediate between DNA and proteins, making our cells capable of sustaining life as it was created. The designer of this system must be the intelligent Designer, the God of the Bible.

REFERENCES

Alberts, Bruce, et al. (2002), Molecular Biology of the Cell (Oxford: Garland Science).

Chen, Xi, et al. (2007), “Ribozyme Catalysis of Metabolism in the RNA World,” Chemistry and Biodiversity, 4:633-656.

Fedor, Martha and James Williamson (2005), “The Catalytic Diversity of RNAs,” Nature Reviews Molecular Cell Biology, 6(5):399-412.

Gilbert, Walter (1986), “The RNA World,” Nature, 319:618.

Kruger, Kelly, et al. (1982), “Self-splicing RNA: Autoexcision and Autocyclization of the Ribosomal RNA Intervening Sequence of Tetrahymena,” Cell, 31(1):147-57.

Müller, U.F. (2006), “Re-creating an RNA World,” Cellular and Molecular Life Science, 63:1278-1293.

Nissen, Poul, et al. (2000), “The Structural Basis of Ribosome Activity in Peptide Bond Synthesis,”Science, 289:920-930.

Valadkhan, Saba and James Manley (2001), “Splicing-related Catalysis by Protein-free snRNAs,” Nature, 6857:701-707.