Posts Tagged ‘protein’

Faced with the failure of the Stanley-Urey model to explain the origin of life, evolutionary scientists have been exploring the RNA World theory. With only the four nucleic acids required to form RNA rather than the twenty amino acids to form a protein, the chance probability tipped the advantage to the RNA-first theory, but that is not all.

In The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution, Richard Dawkins explains

“This is the RNA World. To see how plausible it is, we need to look at why proteins are good at being enzymes but bad at being replicators; at why DNA is good at replicating but bad at being an enzyme; and finally why RNA might just be good enough at both roles to break out of the Catch-22.”

The RNA World theory solved the chicken-or-the-egg Catch-22 conundrum. At least that was the hope. Notice Dawkins use of the word “plausible.” Building proteins requires information from DNA, but information in DNA cannot be processed without protein enzymes—the Catch-22.

The Catch-22 conundrum dogged origin of life research for decades. Like DNA, since RNA contains information. The discovery that certain RNA molecules also have enzyme activity to self-replicate paved the way to solving the Catch-22 puzzle. RNA acts like a protein at times, and at times like DNA.

The RNA World theory has emerged as the most popular natural mechanism for the origin of life. The National Science Foundation (NSF) now actively promotes the RNA World theory. NSF is a United States government agency; its medical counterpart is the National Institutes of Health.  

In association with Harvard University, the NSF RNA World theory initiative now exists for “Synthesizing Darwinian Chemical Systems.” Under the direction of Jack Szostak from the Center for Computational & Integrative Biology, Gerald Joyce from The Scripps Research Institute, and Steven Benner from The Foundation for Applied Molecular Evolution state -

“As both a storehouse of genetic information and a catalyst of metabolic reactions, RNA may have been the critical component that enabled the evolution of life”

The RNA World concept started in 1959 when Spanish Catalan biochemist Joan Oró synthesized adenine, a key component of RNA and DNA, from hydrogen cyanide, similar to a Miller–Urey experiment at high temperatures.

By the late in the twentieth century, origin of life researchers began to examine the RNA World theory. American physicist, biochemist, and molecular biology pioneer Walter Gilbert, in 1986, was the first to coin the term “RNA World” 

Gilbert envisioned a RNA-first model on primordial Earth. By the actions of natural selection on RNA, DNA and protein molecules theoretically formed with the DNA molecule evolving into an information role, the protein molecules evolving into a catalytic role.

Like the Miller–Urey experiment though, the lack of geological evidence for hydrogen cyanide in the fossil record emerged as a telltale sign. Even worse, hydrogen cyanide is a gas toxic to cellular metabolism. During the German Nazi regime, hydrogen cyanide was the gas-of-choice at Auschwitz.

To date, not one laboratory experiment with realistic early Earth elements and conditions has produced a single nucleic acid. In 1981, Francis Crick published Life Itself, a book critical of the RNA World theory. “It may turn out that we will eventually be able to see how this RNA world got started” Crick later wrote in 1993. “At present, the gap from the primal ‘soup’ to the first RNA system capable of natural selection looks forbiddingly wide”

Scripps Research Institute biochemist Gerald Joyce states that the “most reasonable interpretation is that life did not start with RNA.” The origin of life is so difficult a problem that German researcher Klaus Dose stated in 1988 that the RNA theory is “a scheme of ignorance. Without fundamentally new insights in evolutionary processes … this ignorance is likely to persist.”

Origin of life scientist, Robert Shapiro from New York University, a RNA World critic, notes – “no nucleotides of any kind have been reported as products of spark-discharge experiments or in the studies of meteorites.”

Stanley Miller, who performed the original Miller-Urey prebiotic simulation test points out problems with Oro’s simulation – “a high temperature origin of life involving these compounds [the RNA bases] therefore is unlikely.” The presumption of “bases, adenine, cytosine, guanine and uracil were readily available on the early earth,” Miller continues, is “not supported by existing knowledge of the basic chemistry of these substances.”

At the Salk Institute for Biological Studies, Leslie Orgel in 1994 noted – “Because synthesizing nucleotides and achieving replication of RNA under plausible prebiotic conditions have proved so challenging, chemists are increasingly considering the possibility that RNA was not the first self replicating molecule…”.

NASA lost enthusiasm for the RNA world, as well. In the Final Report issued after the “Astrobiology Workshop” in 1996 at Ames Research Center, California, concluded –

“It has been postulated that there was a time in protobiological evolution when RNA played a dual role as both genetic material and a catalytic molecule (“the RNA world”). However, this appealing concept encounters significant difficulties. RNA is chemically fragile and difficult to synthesize abiotically. The known range of its catalytic activities is rather narrow, and the origin of an RNA synthetic apparatus is unclear.”

“It goes without saying that the emergence of this RNA world and the transition to a DNA world imply an impressive number of stages, each more improbable than the previous one”, noted the eminent François Jacob in 1997 

In 1998, Leslie Orgel, senior research fellow and research professor at the Salk Institute for Biological Studies, where he directed the Chemical Evolution Laboratory, acknowledged that “we are very far from knowing whodunit” or what were the early environmental conditions on the Earth.

After 150 years running, how life spontaneously began, to which Darwin alluded, remains a mystery. The deputy editor of the journal Nature, and science writer, Nicholas Wade, reported in the New York Times in June 2000 “everything about the origin of life on the Earth is a mystery, and it seems the more that is known, the more acute the puzzle gets.”

Nearly twenty years later after Gilbert introduced the RNA World theory, the role of RNA in the origin of life remains elusive, if not improbable. In 2007, commenting in Proceedings of the National Academy of Sciences of the United States of America on a paper by Phillipp Baaske, Eugene V. Koonin, Senior investigator at the National Center for Biotechnology Information, National Library of Medicine, and National Institutes of Health noted -

“[RNA World] still is a hypothetical entity… the evolutionary path to the translation systems remains essentially uncharted.”

Richard Dawkins premise in The Ancestor’s Tale – “This is the RNA World. To see how plausible it is” – demonstrates how the common practice of word slighting in the evolution industry. The veiling of impossible as “plausible” reaches the edge of fraud—supported by US tax dollars.

Why Evolution is True, one of the best-selling books in support of evolution written by Jerry Coyne and endorsed by Richard Dawkins, conveniently fails to address one minor evolutionary issue—the origin of life. Reason: the origin of life problem is undermining the evolution industry.

The Stanley-Miller origin of life model was once the most popular theory, starting with the publication of The Planets: Their Origin and Development in 1952. Written by Harold Urey, the book speculates that life originated in early Earth’s atmosphere composed of ammonia, methane, and hydrogen—a reducing atmosphere without oxygen.

Harold Urey was awarded the Nobel Prize in Chemistry in 1934 for his work on isotopes. During World War II, Urey directed the Manhattan Project at Columbia University that lead to the development of the atomic bomb.

Urey’s model for the origin of life, however, was published without ever being tested. When challenged by his graduate student, Stanley Miller, they performed the now-famous Miller–Urey experiment.

After assembling a closed glass apparatus in Urey’s laboratory, Miller pumped out the air and replaced it with methane, ammonia, hydrogen, and water, creating a reducing atmosphere—without oxygen—a gas composition resembling the atmosphere of Jupiter. “By the end of the week,” Miller reported the water “was deep red and turbid.”

Just as Urey had predicted, chemical analysis of the resulting tar solution revealed several organic compounds, including glycine and alanine, the two simplest amino acids found in proteins—the building blocks of life. With amino acids spontaneously arising in early Earth’s atmosphere, the ensuing amino acid chance  interactions forming into proteins became recognized as the natural mechanism to explain for the origin of life.

Reference to the Miller–Urey experiment quickly found its way into almost every high school and college textbook starting in the mid-twentieth century as a natural explanation for the origin of life. According to Evolution 101, sponsored by the University of California, Berkley   

These experiments serve as ‘proofs of concept’ for hypotheses about steps in the origin of life — in other words, if a particular chemical reaction happens in a modern lab under conditions similar to those on early Earth, the same reaction could have happened on early Earth and could have played a role in the origin of life. The 1953 Miller-Urey experiment, for example, simulated early Earth’s atmosphere with nothing more than water, hydrogen, ammonia, and methane and an electrical charge standing in for lightning, and produced complex organic compounds like amino acids.

Since 1953, however, extensive investigations have demonstrated that the Earth’s atmosphere was not composed of ammonia, methane, and hydrogen. Rather than the anticipated reducing atmosphere, the Earth’s atmosphere was the opposite—oxidizing, containing oxygen.

Evolution 101, acknowledging atmosphere problems with the Miller-Urey experiment, adds - 

Now, scientists have learned more about the environmental and atmospheric conditions on early Earth and no longer think that the conditions used by Miller and Urey were quite right… These experiments yielded similar results – complex molecules could have formed in the conditions on early Earth.

While the formation of amino acids in the early atmosphere of the Earth is generally not considered a valid theory, what is the probability of complex molecules arising by chance?

 Evolution 101 uses the word “could” to explain the potential development of complex molecules developing on Earth. The fundamental question, however, is beyond “could.” The question centers on the “probability” of complex protein molecules forming by chance alone from amino acids. Any event “could” happen, but not all events are “probable”.  

Proteins consist of amino acids linked by peptide bonds. Since amino acids have roughly a 50:50 chance of forming peptide bonds to another amino acid, the probability of 4 amino acids forming peptide bond together is ½ X ½ X ½ X ½ = 1/16, or (1/2)⁴.

Since a simple protein usually consists of a chain of 150 amino acids, then the probability of forming the chain is (1/2)¹⁵⁰, or roughly 1 chance in 10⁴⁵. That is the number 10 with 45 trailing zeros.

Given that each amino acid has a mirror image, there is one left-handed and right-handed version for each amino acid, the probability of forming one simple protein from 150 amino acids is 1 chance in 10⁹⁰.

One of the most important functional aspects of a protein is the sequence of the amino acids. Since there are 20 biologically active amino acids, the probability of amino acids occurring in a functional is (1/20)¹⁵⁰, or roughly 1 chance in 10¹⁹⁵.

Origin of life scientist, Stephen C Meyer, in Signature in the Cell, gives a perspective to the probability of finding one functional protein in the universe - 

Another way to say that is the probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than finding a specified particle among all the particles in the universe.

Jerry Coyne and Richard Dawkins discretely circumvent the origin of life issue since the event probability was not by chance. Meyer concludes, 

For this reason, it would be vastly more probable than not that a protein functional would not have arisen by chance.

The evidence contradicts the central tenet of the theory of evolution—life by chance. Meyer’s logical conclusion concurs with Albert Einstein’s famous dictum:

God does not play dice with the universe.

One of the biggest questions in evolutionary molecular biology is—what is the chance that a single protein molecule could have actually been formed by mere random chance?

In principle, probabilities smaller than 1 over 1,050 are thought of as having a zero probability. Since an average-sized protein molecule is composed of 288 amino acids with 12 different types of amino acids, this protein can be arranged in 10,300 different ways, which is 10 followed by 300 zeros. Since 10,300 far exceeds 1,050, the probability of the formation of only one protein molecule by random chance is zero. Molecular biologist Harold Blum concludes that from the mathematical perspective, probability of a protein autonomously assimilating by chance is zero:

“The spontaneous formation of a polypeptide of the size of the smallest known proteins seems beyond all probability.”

In The Origin of Species, Charles Darwin concurs with Blum in the larger context,

“Mere chance, as we may call it, might cause one variety to differ in some character from its parents, and the offspring of this variety again to differ from its parent in the very same character and in a greater degree; but this alone would never account for so habitual and large a degree of difference as that between the species of the same genus.”

According to the February 27^th edition of Nature, more doubts now cloud the claim that dinosaur protein has been sequenced. Now a long-time critic has called for an independent review of the 2007 studies of ancient protein from a fossilized Tyrannosaurus rex after fresh analysis revealed traces of ostrich haemoglobin in the original samples.

In the contentious papers, researchers identified seven fragments from a protein called collagen, found in connective tissue, and said their sequences most closely matched the chicken version of the protein. The samples came from the fossilized femur of a T. Rex. As well as further strengthening the evidence for the link between dinosaurs and birds, the findings would make the protein the oldest ever to be sequenced. The work, published in Science, garnered headlines worldwide and met with considerable scepticism at the time, for good reason—fraud.

The hunt for Darwin’s “inconceivably great” missing links continues.