Posts Tagged ‘probability’

Self-organization is hot, once again.

Critical of his own work, in a letter to Hugh Falconer in October 1862, Charles Darwin wrote, “I look at it as absolutely certain that very much in the Origin will be proved to be rubbish; but I expect and hope that the framework will stand.”

For Darwin, the origin of life was the result of spontaneous generation. The twenty-first century version is now more popularly referred to as abiogenesis, or self-organization. Continue Reading

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.

Charles Darwin in a letter Joseph Hooker in February 1871 speculated that life might have originated in “some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a proteine compound was chemically formed ready to undergo still more complex changes”.

Darwin’s speculation went untested until the Miller–Urey experiment in 1952 at the University of Chicago. Stanley Miller and Harold Urey successfully produced some of Darwin’s “proteine compounds” by building on Alexander Oparin‘s and J. B. S. Haldane‘s hypothesis that the primitive conditions on Earth were favorable to the chemical reactions that synthesized organic compounds from inorganic precursors. Oparian and Haldane’s favorable conditions required a nitrogen-rich reducing atmosphere without oxygen.

The Miller-Urey experiment advanced the question to center stage—were the conditions of primitive Earth the same as proposed by Oparin and Haldane? Was early Earth nitrogen-rich? Was oxygen absent?

Since 1952, research on the actual chemical conditions of the primitive Earth has been on the investigative frontlines of origin of life research. After over 50 years, the consensus is inconclusive. Wikipedia, under the topic of “Origin of Life” in, now more commonly referred to as “Abiogenesis,” concludes: “There is no truly ‘standard model’ of the origin of life. Most currently accepted models draw at least some elements from the framework laid out by the Oparin-Haldane hypothesis.”

Irrespective of primitive Earth conditions, an even more challenging question emerges—what is the statisitcal probability for functional proteins to arise de novo from the “prebiotic soup” of amino acids by chance? 

Stephen Meyer, in his new book entitled Signature in the Cell, reviews the extensive research into answering this daunting question on chance. Based on the works of Robert Sauer at MIT, Douglas Axe at Cambridge University, and British cosmologist Sir Fred Hoyle, Meyer, concldues that “the improbability of generating the necessary proteins by chance—or the genetic information to produce them—to balloon beyond comprehension.”

Meyer writes, “The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebioitc soup is no better than 1 chance in 10¹⁶⁴.” Meyer continues, “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, trillion times smaller than the odds of finding a single specific particle among all the particles in the universe.”

The evidence for the probability of origin of life arising from Darwin’s “warm little pond” seems to have vanished beyond the realm of any possibility—regardless of any early Earth scenario.

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.”