Origin of Life Theory, The Gap

by Richard William Nelson | Jun 20, 2010

In The Origin of Species, along with natural selection, Charles Darwin (pictured left) included an unexpected explanation for the origin of life. In the six editions between 1859 and 1872, the last sentence he ventured on an origin of life concept, noting —

“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one.”

Surprisingly, beginning with the second edition published a few months later in 1860, Darwin included “Creator” in the sentence, stating —

“There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.”

This second edition sentence remained unchanged in all the later editions. Darwin used the term “Creator” seven times in the first edition, and nine times in the last in 1872. However, Darwin’s origin of life concept placed a teleological gap in an otherwise non-teleological theory of natural selection.

Darwin’s Private Letter

In an 1871 letter to long-time colleague Joseph Dalton Hooker (pictured right), he shared his personal belief. It was quite different —

“I am always delighted to see a word in favour of Pangenesis, which some day, I believe, will have a resurrection… But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes.”

In this same letter to Hooker, however, Darwin included a warning —

“At the present day such matter wd (would) be instantly devoured.”

By the early twentieth century, the rediscovery of Gregor Mendel’s inheritance laws gave new life to Darwin’s struggling natural selection theory. However, progress in developing origin of life concepts had lagged, remaining separate from natural selection studies.

Modern Synthesis

The synthesis of Mendel’s inheritance laws with natural selection became known as the “Modern Synthesis” theory of evolution by mid-century. During this time, the emergence of new technologies introduced new methods to explore Earth’s vast and mysterious biosphere.

However, an evolutionary theory to explain the origin of new species without an explanation for the origin of life is incomplete. By modern scientific standards, while Darwin was explanation-rich, his theory was explanation-incomplete and mechanically evidence-poor.

Origin of Life

A scientific explanation for the origin of new species without one for the origin of life is one of Darwin’s non-teleological gaps. Without a scientific explanation for the origin of life, any explanation of how natural selection works is irrelevant. As Darwin makes clear, natural selection can only act to preserve and accumulate what already exists —

“Natural selection can act only by the preservation and accumulation of beneficial variations.”

The title of his book, The Origin of Species, implies that the book is about the origin of species. However, the book only explains the origin of new species, not a natural origin of species process. Downplaying the significance of the gap, in the letter to J.D. Hooker in March 1863, Darwin privately argued —

“It is mere rubbish thinking at present of the origin of life.”

The gap, however, was anticipated to be resolved eventually. The emerging advances in the sciences and technology fueled confidence in discovering a scientific explanation for the origin of life.

By the mid-twentieth century, advances in geochemistry and cosmochemistry opened new avenues of study. Chemists finally had the laboratory tools to simulate the formation of biomolecules, a step toward understanding the origin of life.

Study Framework

Harold C Urey

Harold Clayton Urey (1893-1981) emerged as one of America’s leading physical chemists studying the chemical systems in Earth’s solar system. In 1952, Urey (pictured) left) published his most influential book, “The Planets: Their Origin and Development.”

In the book, Urey explained how the conditions of early Earth could naturally form organic compounds from prebiotic molecules — without atmospheric Oxygen. Generally, any large chemical compound containing a carbon–hydrogen or carbon–carbon bond is known as organic.

In a reducing atmosphere, Urey envisioned early Earth containing methane (CH₄), ammonia (NH3), hydrogen (H2), and water (H2O) vapor. In this reducing atmosphere, Urey envisioned early Earth naturally forming biological organic molecules without atmospheric Oxygen (O2).

Urey provided the first rigorous chemical model of early Earth’s atmosphere — a model that made prebiotic chemistry experimentally testable. For his innovative work, in 1934. Urey was awarded a Nobel Prize for Chemistry.

In 1952, Urey met 23‑year‑old graduate student Stanley Miller at the University of Chicago. Together they designed a method to test Darwin’s “warm little pond” hypothesis. Miller’s chemical synthesis expertise complemented Urey’s elemental atmospheric expertise.

Together, they were the first to experimentally demonstrate how life may have emerged from simple molecules and energy, naturally. What became known as the Miller–Urey experiment emerged as the most iconic experiment in origin of life research.

Stanley Miller

While in Oakland High School, Stanley Miller was nicknamed “a chem whiz” and later followed his brother to the University of California at Berkeley to study chemistry.

Miller enrolled in the University of Chicago PhD program in September 1951. He searched for a thesis topic and met professors, preferring theoretical problems rather than laboratory experiments, which tended to be repetitive and tedious.

Initially, Miller worked with the theoretical physicist Edward Teller on the synthesis of elements. Then, Urey approached Miller in September 1952 with a fresh research project.

Urey’s project to test whether organic synthesis was possible in a reducing environment, such as the primitive Earth’s atmosphere, intrigued Miller. As did the opportunity to work with Urey, a legend.

Laboratory Experiment Testing

Working together, Miller eventually persuaded Urey to experiment using electric discharges in reducing gases to induce organic compound synthesis. Darwin had speculated —

“But if (& oh what a big if) we could conceive in some warm little pond with… light, heat, [and] electricity.”

Using a closed glass apparatus in Urey’s laboratory, Miller pumped out the air and replaced it with methane, ammonia, hydrogen, and water. This oxygen-free prebiotic reducing atmosphere resembles the atmosphere of Jupiter. With an electrical arc applied, the solution began to turn pink on the first day. Within the first week, Miller reported —

“By the end of the week, [the resulting solution] was deep red and turbid.”

As Urey had theorized, chemical analysis of the resulting tar solution revealed several organic compounds. These included glycine and alanine, the two simplest amino acids found in proteins—the building blocks of life.

The Miller–Urey experiment soon became the most iconic experiment in origin of life research, empirical support for Darwin’s “warm pond” speculation. The experimental tests were inferred to support a natural explanation for the origin of life, essential for a non-teleological theory of evolution.

 ‘Proofs of Concept’ Inferences

The Miller–Urey experiment quickly found its way into science textbooks. The early experimental findings seemed to resolve Darwin’s origin of species gap, inferentially. According to Evolution 101, at the University of California, Berkeley —

“These experiments serve as ‘proofs of concept’ for hypotheses about steps in the origin of life.”

The experiment showed that building blocks of life can emerge from simple chemistry—this elevated origin of life concepts from philosophical speculation to experimental science.

Urey’s atmospheric model and Miller’s experiment became the foundation of modern prebiotic chemistry, known as abiogenesis. The experimental inferences influenced academic developments in the emerging fields of geochemistry, planetary science, and astrobiology.

Urey’s Atmospheric Assumption

Later in the twentieth century, however, subsequent investigations have indicated that the Earth’s atmosphere differs from Urey’s assumptions. Earth’s early oxygen concentrations are now known to have been higher, with only a weakly reducing or neutral atmosphere.

Rather than an oxygen-free atmosphere, Earth’s early atmosphere resembled our current atmosphere. 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.”

This distinction matters because prebiotic oxygen would have destroyed the reducing gases and reactive intermediates required for amino acid formation. Oxygen oxidizes methane, ammonia, hydrogen, and amino‑acid precursors, preventing the natural formation of peptides and proteins.

Prebiotic oxygen destroys reducing gases by oxidizing and destroying key molecules, including methane, ammonia, and hydrogen. Prebiotic chemistry requires reducing conditions; oxygen destroys the natural formation of amino acids and eventually proteins.

The Miller–Urey experiment produced eleven amino acids, and later reanalysis of Miller’s preserved samples (2008) identified more than twenty. Although the experiment used a gas mixture more reducing than modern models support, it demonstrated that biologically relevant molecules can form under plausible early‑Earth conditions.

Great Oxygen Event

The Great Oxygen Event (GOE) refers to the rise of atmospheric oxygen. The rise in oxygen is attributed to photosynthesis by Cyanobacteria, a group of autotrophic gram-negative bacteria of the phylum Cyanobacteriota.

The phylum’s photopigments absorb the red- and blue-spectrum frequencies of sunlight to split water molecules into hydrogen ions and oxygen. Eventually, algae, land plants, decomposition, and weathering of rocks stabilized global atmospheric oxygen concentrations to 20.95%. This concentration is essential for complex life, forests, fire, climate, and biogeochemical cycles to coexist.

Since the GOE is a historical event and not directly observable, methodological studies must use epistemic reasoning. Epistemic reasoning is the method of inferring truth from incomplete, indirect, or historical evidence. It evaluates the reliability, limits, and assumptions behind logical conclusions.

Epistemic Reasoning

Epistemic reasoning, however, runs the risk of developing a logical fallacy. These fallacies arise when assumptions are mistaken, frameworks are improperly mixed, evidence is indirect, and historical reconstructions cannot be experimentally tested.

Specifically, integrating biological and geological conclusions, as is common in GOE studies, carries a risk of circular reasoning. As an example –

• • Premise (Biology): Certain fossils represent organisms that once lived during a specific time period.
  • Assumption (Geology): The presence of those fossils in a layer implies the layer was formed during the organism’s timeframe.
  • Conclusion: Stratigraphic layers (geology) can be dated based on their observed fossil content (biology).

The circular reasoning is –

• • Fossil’s age is inferred from the layer, or
  • Layer’s age is inferred from the fossil

Epistemic reasoning even when following a logical process, but the conclusions may be a logical fallacy. This explains why “scientific” conclusions drawn in GOE studies remain open for debate until empirically tested. Commenting on the scientific status of the GOE, Jason Olejarz at Harvard University noted in a Nature Communications article in 2021 –

“The Great Oxygenation Event… records the initial rise of O₂ to permanent prominence in the atmosphere and surface ocean… debate continues about the physical and/or biological drivers.”

Science writer and editor for the University of Chicago News, Steve Koppes, noted in September 2022 –

“The origin of life on Earth stands as one of the great mysteries of science. Various answers have been proposed, all of which remain unverified.”

Miller-Urey experiment demonstrated that some biological molecules naturally emerge from early Earth’s presumed atmospheric molecules. However, the experiment did not demonstrate the emergence of life’s essential biological compounds.

Probability of Biological Compounds

The probability of essential biological compounds emerging from early Earth’s presumed atmospheric molecules can be mathematically calculated. Aside from genetics, the most important biological compounds for life are peptides and proteins.

A peptide consists of a short chain of amino acids linked together by peptide bonds, sometimes known as “mini-proteins.” Proteins are defined as one or more polypeptides folded into a functional 3D structure. However, the probability of these naturally linking and folding together by chance challenges basic molecular evolutionary assumptions.

A single amino acid is just an amino acid, not a peptide. Since a peptide requires at least one peptide bond, a peptide requires a minimum of two amino acids. However, nature’s simplest life form, Archaea, has hundreds of peptides, while bacteria have a minimum of 400 to 500 peptides.

Calculating Probability

Amino acids have a 50:50 chance of forming a peptide bond to another amino acid. Therefore, the probability of 4 amino acids forming a peptide bond together is ½ X ½ X ½ X ½ = 1/16, or (1/2)4 = 6.26%. But two amino acids alone are not known to form a living entity.

The simplest known living entity has hundreds of more peptides. However, the probability by chance of a life form emerging with just 150 linked amino acids can be mathematically calculated –

• • Probability of forming the chain is (1/2)¹⁵⁰, or roughly 1 chance in 10^-45.
  • This is 10 with 45 trailing zeros, yielding a probability percentage of 0.000000000000000000000000000000000000000000007006%.

In essence, the probability of consistently forming chains of 150 amino acids by chance is effectively impossible in practical scenarios. The assumption, however, is that each type of amino acid used in the peptide is the same, but it isn’t.

Each type of amino acid is a chiral molecule, meaning each molecule has a mirrored image, a left-handed and a right-handed version. Therefore, the probability of forming a chain of 150 amino acids increases from 1 chance in 10^-45 to 10^-90.

Origin of life scientist Stephen C Meyer (pictured left), in Signature in the Cell, gives a perspective on 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.”

Evolutionary Scientists and Chance

Evolutionary scientists have varying views on the origin of life, even Richard Dawkins and Jerry Coyne (pictured right). Dawkins and Coyne are highly influential atheist advocates, along with Christopher Hitchens and Daniel Dennett.

Coyne has served as Vice President and President of the Society for the Study of Evolution, and was elected to the American Academy of Arts and Sciences. Dawkins, a British evolutionary biologist, zoologist, and science communicator, published two highly influential books, The Selfish Gene (1976) and The Blind Watchmaker (1986).

Surprisingly, Coyne, in Why Evolution is True, argued that calculating probabilities is misguided, even though envisioning life emerging as a direct result of chance-given chemistry. Coyne’s book has been one of evolution’s best-selling books, and considers evolutionary biology –

“… more like the fine arts of science.”

Dawkins, in The Genetic Book of the Dead, views the origin of life as emerging by chance, driven by replicators and crude early peptides, without modern proteins. Ironically, in Climbing Mount Improbable (1996), Dawkins never quantified any of nature’s chance probabilities.

However, neither Coyne nor Dawkins quantifies chance by calculating its probability. Probability is simply the quantitative measure of chance – this is what makes science distinct from philosophy.

Coyne and Dawkins’ explanations are persuasive, logical, and popular, but not scientific. Science is founded on documented repetitive empirical observations with consistent measurements.

Currently, the absence of a scientific explanation for the origin of life remains a lethal gap in Darwin’s “Origin of Species” theory. Natural selection, as written by Darwin, has never been a scientific molecules-to-the-Munster’s theory.

Darwin, however, wisely concluded The Origin of Species with the following sentence –

“There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one.”

Genesis

The Genesis account written by Moses is compatible with the scientific evidence. Meyer’s assessment aligns with Albert Einstein’s (pictured left) famous dictum during the Scientific Revolution:

“God does not play dice.”

The origin of-life gap insures that the theory of evolution will remain in a theory in crisis, further intensifying Darwin’s Dilemma.

“Origin of Life Theory, The Gap” is a category Origin of Life article.

Darwin Then and Now is an educational resource on the intersection of evolution and science, highlighting the ongoing challenges to the theory of evolution.

Move On

Explore how to understand twenty-first-century concepts of evolution further using the following links –

• • The Understanding Evolution category showcases how varying historical study approaches to evolution have led to varying conclusions. Subcategories include –
    • Studying Evolution explains how key evolution terms and concepts have changed since the 1958 publication of The Origin of Species.
    • What is Science explains Charles Darwin’s approach to science and how modern science approaches can be applied to different investigative purposes.
    • Evolution and Science feature study articles on how scientific evidence influences the current understanding of evolution.
    • Theory and Consensus feature articles on the historical timelines of the theory and Natural Selection.
  • The Biography of Charles Darwin category showcases relevant aspects of his life.
  • The Glossary defines terms used in studying the theory of biological evolution.