Image: Nucleotides join to make the polymers, Deoxyribonucleic acid (DNA) & Ribonucleic acid (RNA). These two biomolecules are essential for all lifeforms on Earth.

The Organic Molecules & Processes Forming Life

(Essay #13, at 2-10-2026)          

This is the fourth Essay of six (#10 to #15) interrelated Essays on Earth’s geochemical origin of life and its subsequent Evolution. 
Here are the titles of those four Essays:

Essay #10 —The Processes of Evolution in Biology, Culture, & Technology
Essay #11 — Answering Evolution’s Critics
Essay #12 — Chemical Precursors to Life on Earth
Essay #13 — The Organic Molecules & Processes That Form Life (this Essay)
Essay #14 — Abiogenesis: Evolution of the First Life on Earth 
Essay #15 — Where Did Life First Begin: Warm Pools?  Black Smokers?

(Note to Readers: If you want bypass the chemistry, go to Essay #15.  It is the most  dramatic & colorful of the above six Essays. — JXM)

The first Essay above, Essay #10 — The Processes of Evolution & Their Meaning, is just as important as the five “biological” Essays listed above, because Essay #10 describes the evolution that is happening all around us, here and now, in three arenas: Biology, Culture, & Technology. 

It takes all six Essays to fully explain how the processes of evolution provide us with our complete human sense of, and appreciation for, Connectedness & Meaning based on Nature, Science, & History.

This Essay, Essay #13, addresses the key small organic molecules (monomers) in living things, how those small molecules chain together to become the key large organic molecules (polymers), and how those large molecules play essential roles in two basic Biological Systems — Cellular Respiration & Cellular Metabolism — inside living things.

But first, let’s look at the Earthly Resources and the Inorganic Compounds that make Life:

The 4 Earthly Resources Usually Needed to Make Life

1. Food — fuel that releases energy when organisms eat and digest substances or other organisms.
2. Water — Necessary for all living things.
3. A Gas – Usually, but not always, a gas such as oxygen (O2) or carbon dioxide (CO2) is taken from the water or from the air.
4. An Energy Source — such as Sunlight, Earth’s heat, the motion of the Earth, tides, and winds.

The above 4 Resources are the same for: a) entire organisms, b) for each of the single cells inside them, and c) for single-celled creatures that are themselves entire organisms (e.g., bacteria).

All organisms take in food and nutrients by eating other organisms and/or by absorbing nutrients directly from the soil; they take in (drink) water; and take in (inhale) oxygen and/or carbon dioxide from the air. In many animals and plants, all three inputs enter the circulatory systems, delivering them to the individual cells.

Much of the food for large organisms, of course, must first be broken down in digestive systems. The food needs to be broken down into simple molecules that individual cells can handle (metabolize). A common and important simple food molecule is the well-known sugar, glucose, which composed of Carbon, Hydrogen, & Oxygen.

The 6 Basic Inorganic Chemical Compounds of Life

In our previous Essay, #12, “Chemical Precursors to Life on Earth,” we discussed the Six Key Chemical Elements of life: Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur, and Phosphorus.

And we know from high school chemistry that chemical elements can combine to form chemical compounds. 

Below are the Six Basic Inorganic (generally, not-made by living organisms) Chemical Compounds of Life (as listed in the Simple Wikipedia article, “Origin of Life”): 

1. Methane (CH4)
2. Ammonia (NH3)
3. Water (H2O)
4. Hydrogen sulfide (H2S)
5. Carbon dioxide (CO2) or carbon monoxide (CO), and
6. Phosphate (PO4).    

Oxygen (O2) and ozone (O3), both highly important gases in today’s atmosphere, were either rare or absent on early Earth. They were created later, during and around the “Great Oxygenation Event,” which occurred between 850 and 540 million years ago. Experts say that in the early times of First Life, no organisms breathed oxygen as we do today! Thus, in scientific parlance, the earliest life on Earth appears to have been “anaerobic,” not “aerobic.” ¹

The Key Organic Compounds of Life

Organic compounds are generally (but not always) defined as any chemical compounds that contain carbon-hydrogen bonds. 

Methane (CH4) is an organic compound. Most organic compounds arise from biological processes. Methane is a component of natural gas that originates from the decomposition of ancient life under the intense heat and pressure of the Earth’s deep Interior.  Water, although abundant and critically important in living things, is not an organic compound because there is no carbon in its chemical formula, “H2O.”

Due to carbon’s ability to catenate (form chains with other carbon atoms), millions of organic compounds are now known; most of them are manufactured by biochemical systems within living organisms or by organic chemists to make plastics, fibers, pharmaceuticals, and petrochemicals. (For more, see the Wikipedia article on Organic Compounds.)

Although organic compounds make up only a small percentage of the Earth’s crust, they are of central importance because all known life is based on organic compounds. Living things incorporate inorganic carbon compounds into organic compounds through a network of processes (the carbon cycle) that begins with the conversion of carbon dioxide plus a hydrogen source like water into simple sugars and other organic molecules by organisms using light (photosynthesis) or chemical sources of energy.

The 4 Small (and the 4 Large) Key Organic Molecules of Life

More important for our purposes in this Essay are the “Key Small Organic Molecules” and the “Key Large Organic Molecules” of Life.

Each of the four Key Small Monomers of Life can chain together (“polymerize”) to form one of the four Key Organic Large macromolecules of Life. The macromolecules are typically composed of thousands of atoms!  Below is a list of The 4 Key Small & The 4 Key Large Organic Molecules of Life, and their Key Interactive Processes. The following list is central to this Essay #13.

Chains of Small Molecules Can Make A Large Macromolecule of Life

#1. Fatty Acid monomers chain together to form the macromolecules called Lipids. Then the lipids link together to make fats, oils, phospholipids, and waxes. Typically, phospholipids form the cell membrane, the boundary that separates the cell from its external environment. The cell membrane encloses and protects the cell’s interior chemistry. Self-enclosure, providing self-identity, and self-protection, are Key Processes of life. 

We discussed the Key Large Molecules called lipids and the cell membranes that they assemble in our earlier Essay, Chemical Precursors to Life on Earth (“Essay #12).  We also discussed two non-living systems that appear structurally analogous to lipids – sea foam and the mineral crystals found in geodes. In that Essay, we additionally looked at diatoms and seashells, which are non-living mineral creations of life.

#2.  Monosaccharide monomers link together to form the large Carbohydrate macromolecules. Carbohydrates (including sugars, starches, cellulose, and waxes) are “food molecules.” The simplest molecules of the sugars are the monosaccharides. They are the cellular food monomers for many organisms, including humans. A prime example is the monosaccharide glucose.

Eating is obviously a Key Process of Life.  At the cellular level, however, “breathing, eating, and digesting” are collectively called “Cellular Respiration.” The interacting processes of taking in food, extracting energy, and excreting waste are collectively referred to as metabolism for entire organisms and for the individual cells within them.

Dr. Hazen writes: “Every life form consists of discrete assemblages of molecules (cells) that are separated by a molecular barrier from the outside (the environment). These collections of chemicals have evolved two interdependent modes of self-preservation – metabolism (taking energy from food) and genetics (reproduction of a new, whole organism) – that together unambiguously distinguish the living from the non-living.” ²

Arvin Ash agrees, as he says in the first minutes of his online twelve-minute film presentation, “Abiogenesis – How Life Came from Inanimate Matter” (Sept 7, 2019). The Wikipedia article on Abiogenesis concurs as well.  And so does the book by J.X. Mason that you are now reading.

We need to describe how the key molecules arose, and then we need to explain how they began to work together in the first living cells (Abiogenesis), and how they continue to work in the Processes of Cellular Respiration and Cellular Metabolism, using flows of energy and supplies (e.g., oxygen, carbon dioxide, minerals, & nutrients).

#3. Amino Acid monomers chain together to build the cell’s large Protein macromolecules (called peptides & polypeptides), which are the workhorses of the cell. The proteins break down food, build up tissues, transport substances, and eliminate waste. Together, these processes are collectively known as cellular metabolism, a Key Biological Process of Life. In addition to their central role in protein synthesis, amino acids participate in several other processes, including the transmission of nerve signals and the construction of complex molecules from simpler ones (“biosynthesis”).

> Chains of linked amino acid molecules longer than 15 to 50 amino acids are called peptides. A polypeptide that contains more than approximately 50 amino acids is called a protein. As the main component of proteins, amino acids are the second-largest component of human muscles and other tissues. ³ (Water is the largest component.) Amino acids are the cell’s builders – they assemble all the proteins we find in living things.

> The key chemical elements in amino acids and proteins are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the “side chains” of certain amino acids. About 500 naturally occurring amino acids are known, and they can be classified in many ways. ⁴

> The amino acids and the proteins do most of the work in the cell, principally in the processes of cellular respiration and cellular metabolism. The proteins are also used for structural support, storage, transport, cellular communication, response to stimuli, movement, defense against infections, and elimination of waste. The proteins even build the RNA and DNA macromolecules needed for the process of reproduction in living things.

>  Proteins consist of one or more polypeptides arranged (“folded“) in a biologically functional pattern. ⁵ In modern cells, proteins are formed by the actions of tiny cellular “machines” called Ribosomes, which we will discuss more fully later in this Essay. Note: For more information, See the Wikipedia articles on Amino Acids and on Proteins.

      Three Fascinating Things About Protein Molecules:

1. Protein Folding

After being translated from a sequence of Messenger RNA into a linear or loosely coiled chain of amino acids, each would-be protein is an “unfolded” polypeptide. A protein isn’t functional until it has been folded from a random coil shape into its workable three-dimensional shape. (Catalytic proteins called “chaperones” can assist in protein folding.)

It is the three-dimensional shape of the folded protein that can present a certain surface that “fits with” the shape of another molecule. Only when the fit is achieved can the intended biochemical process proceed. This intricate chemistry supports the argument that life evolved naturally from non-living (inorganic) chemistry. ⁶ 

Drawing of a folded myoglobin Protein 

The above Artist’s Depiction of the folded structure of an oxygen-and-iron binding myoglobin protein, which is distantly related to the hemoglobin protein we have in human blood. (Think of “folding a protein as analogous to an Origami artist folding paper into a three-dimensional “crane” or “swan.”)  Note the rough similarity between protein-folding and the way that mineral crystals grow. It is also analogous to the way that silicate-clay crystals can act as templates for the formation of biomolecules, as we discuss in our section on The Silicate-Clay Model of cellular evolution, in Essay #4 of this series — Where Life Began: Warm Pools? Black Smokers?

2. There Are Misfolded Proteins Called Prions

Prions are misfolded proteins that are still able to transmit their misfolded shape onto normal proteins. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals. It is not known what causes the normal protein to misfold, but the abnormal three-dimensional structure is suspected of conferring infectious properties, causing nearby protein molecules to collapse into the same non-functional shapes. See “Prion: Infectious Particle,” Encyclopedia Britannica, online.  ⁷

Prions can form abnormal aggregates of proteins called amyloids, which accumulate in infected tissue and are associated with tissue damage and cell death. Amyloids are also responsible for several other neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease. ⁸

3. Protein Molecules Can Form Crystals

In the previous essay, Essay #12, we stated that crystals exhibit some of the characteristics of living things.  Now, we want to point out that regular arrays of proteins can form crystalline structures.

In protein crystallization, a regular array of individual protein molecules can be stabilized by crystal contacts. If the protein crystal is sufficiently ordered, it will diffract light. Some proteins naturally form crystalline arrays, like aquaporin in the lens of the eye. The “chaperone” molecules mentioned in the section just above are themselves large crystalline structures.

 Image: Crystalized Proteins

#4.  Nucleotide monomers link together to form large Nucleic Acid macromolecules. The nucleic acids then join to form the extremely long DNA and RNA macromolecules that are the self-replicating genetic “blueprints” that carry the instructions for reproducing new generations of the cell and/or the organism as a whole. The ability to self-replicate, to reproduce, is another of the Key Processes of life.

There are two Nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).  A single DNA molecule contains all of an organism’s hereditary information, its genetic code – the entire blueprint for building its structure and systems!  An RNA molecule is a DNA molecule “split lengthwise down the middle.” 

Nucleotides are composed of carbon, oxygen, hydrogen, and phosphorus. These chemical elements – C, O, H, & P (“chops”) — are the same as the elements that make up amino acids, except that nucleotides have added the chemical element phosphorus.  (Biochemists usually say that nucleotides consist of three “sub-units” of chemical elements: a sugar, a nitrogen base, and a phosphate group.)

Just as important as the addition of phosphorus is the fact that the molecules in nucleotides are arranged in different patterns from the molecules of amino acids. Their different three-dimensional, patterned shapes allow them to perform other functions inside the cell. (See our Essay, Nature Creates Patterns of Information & Beauty.)

The nucleic acids “DNA” and “RNA” are found in abundance in all living things. Inside each organism, they encode, store, and transmit the distinct construction information for assembling and operating that organism. They also transmit and express that information to the eggs or seeds of the next generation of the organism.

Crystalized DNA!

We just remarked that proteins can assume a crystalline form.  Here, we point out that DNA (deoxyribonucleic acid), the long, twin-ladder molecule that contains our genetic code, can also form a crystal.  Below is a black and white micro-photograph of a DNA crystal:

 
Image above:  “A star-like microstructure formed during DNA metallization” — Wikimedia, which also has many diagrams of DNA Crystals.

“DNA crystals form when a double helix is suspended in a liquid that evaporates. The crystals grow in patterns dictated by the information stored within the strands. Seen in cross-polarized light, they display a kaleidoscopic array of colors and shapes.  The huge range of crystal structures is amazing.” — Laura Mallonee, “Turns Out Crystallized DNA Is Crazy Pretty,” 2015, WIRED Magazine.  ⁹

We’ve now covered all 4 of the Key Small and all 4 of the Key Large organic molecules that accomplish the fundamental processes of Life.  We’ve also presented several fascinating facts about proteins and nucleic acids, including folding, misfolding, and crystallizing.  It is remarkable that all of the Key Molecules, Small & Large, are mainly composed of oxygen, hydrogen, nitrogen, and carbon, plus a bit of phosphorus. The different characteristics and powers of these molecules lie in how those chemical elements are arranged and connected.  As we say repeatedly in this book on Nature’s Continuing Creation,

       “The key to Nature’s Continuing Creation is combining components to create wholes that are remarkably new and different from their components.” — J.X. Mason

The 3 Key Fundamental Processes Inside Cellular Life: 

1) Cellular Respiration
2) Cellular Metabolism
3) Cellular Reproduction.
For the sake of brevity, this Essay will address only the first 2 of the Life’s Key Processes: 1) Cellular Respiration, and 2) Cellular Metabolism.  

Cellular Respiration (#1) and Cellular Metabolism (#2)

At the whole-organism level, “respiration” (a.k.a., “physiological respiration)” is the process of “breathing.” Animals breathe using lungs, fish breathe using gills, and plants breathe through their leaves, which have tiny pores called “stomata” that open and close to allow gases to pass in and out of the plant.

At the cellular level, however, whenever any individual cell of an organism takes in nutrients, water, oxygen, or carbon dioxide, that Key Process is called Cellular Respiration. Cellular Respiration is the “front-end” process of the larger Cellular Metabolism Process, which includes the intake of atmospheric gases (O2 and/or CO2), water, and food; digestion; the release of valuable energy; circulation; and excretion of waste.

Many cells also have specialized processes that are crucial to the organism’s overall functioning. Looking across all life’s creatures, these specialized processes include photosynthesis, circulation, breathing, producing hormones, vision, hearing, smelling, feeling, locomotion, information processing (e.g., thinking), flying, swimming, communicating, growing, defending against “germs,” and many more. 

The Cellular Metabolism of Green Plants

Green plants use the process of photosynthesis (energy flow from sunlight) along with water and nutrients in the soil to make monosaccharides (“simple sugars”). Green plants can store the energy present in monosaccharides by assembling them into larger carbohydrate structures such as cellulose, grains, fruits, nuts, and tubers.

Plants can also turn around and do the reverse. They can take in oxygen from the air to oxidize (“burn”) their own monosaccharides in the process of cellular respiration to grow the tissues of the plants (roots, leaves, stems, and flowers).  In this process, chemical energy flows when monosaccharides, such as glucose, are oxidized: the glucose molecule gives (“donates”) an electron to the oxygen molecule (which “accepts” the electron, thereby receiving the energy). This oxidation can take place at night, when the sun isn’t shining.

Nature is replete with exceptions. There are several carnivorous plant species that trap and digest animals, especially insects. These include the Venus Flytrap, the Cobra Lily, the Trigger Plant, the Portuguese Sundew, and the Moccasin Plant. (See, “Meet 12 Carnivorous Plants That Eat Everything from Insects to Mammals,” with photographs, written by Bob Strauss. https://www.thoughtco.com/plants-that-eat-animals-4118213.) 

The Cellular Metabolism of Animals (and Fungi)

The cells in animals (and in fungi) are unable to utilize the energy of sunlight to produce or perform any function.  Animals obtain the sun’s energy only indirectly, by eating green plants or other animals. Fungi get their indirect sun energy by secreting enzymes that decay nearby plants, animals, and other fungi… and then reabsorbing those enzymes.  

When animals eat plants, eat other animals, or eat fungi (e.g., mushrooms), they use the monosaccharides initially stored in plant structures for fuel, and they can also store them in their own structures, including the cells of bone, muscle, nerves, and fat. When these processes involve oxygen, they are called aerobic cellular respiration processes. When these processes do not involve oxygen, they are called anaerobic cellular respiration processes.

Cellular Metabolism in Two Early Kingdoms of Life: Archaea & Bacteria

In the U.S. and Canada, traditional biology classifications divide all Life into Six Kingdoms: Animal, Plant, Fungi, Protista, Archaea, and Bacteria.  We’ve covered Cellular Metabolism for the first two Kingdoms. (We’ll skip doing that for the fungi.)

But Earth is also home to “trillions-of-trillions” of other, usually microscopic organisms — Archaea and Bacteria — whose cells do not make or take in molecules of sugar as their basic cellular foodstuff. Instead, many of these microscopic creatures amazingly take in minerals like iron or sulfur. Then, some of these organisms use oxygen to obtain energy from food, e.g., they “rust” (oxidize) the iron, utilizing an aerobic cellular respiration process; and others use non-oxygen, anaerobic cellular respiration processes to release energy from minerals like sulfur.  

Fundamentally, every living organism is a thermodynamically open energy system that requires a set of additional inputs from outside sources: solar or thermal energy, food, water, minerals, and gases found in air or water, such as oxygen for animals and carbon dioxide for green plants. Each of these inputs must be a flow over time because their purpose is to sustain an organism’s life over time.  All these required chemical molecules (which can be simple or complex) ultimately come from non-living Earthly sources! This is persuasive evidence that life on Earth originated from geochemical processes.

A key takeaway is that life has developed various chemical processes to extract energy from different types of “food.” Life seeks, explores, tries, persists…  and then, if “frustrated,” life adapts and adopts. In other words, Life evolves.  And life does all this without any direction or control from a central authority… e.g., from “god…” unless “God” is simply another word for “Nature’s Continuing Creation.”

Apparent Steps in the Origin of Life  

Unicellular organisms are thought to be the oldest forms of life, with early protocells (“before living cells”) possibly emerging 3.8 to 4.0 billion years ago.  ¹⁰

First Life likely followed a direction of increasing organic-chemical complexity. This growing complexity would have taken several (likely interrelated & indistinct) chronological steps:

The Four Likely Steps of Organic-Chemical Complexity

Step A: The origin of biological monomers: fatty acids, amino acids, nucleotides, and sugars.
Step B: The evolution from free-floating molecules to membrane-contained molecules.
Step C: The assembly of biological polymers: Lipids, Amino Acids, and Nucleic Acids
Step D: The interaction of the molecules in working biological systems, such as cellular metabolism and reproduction.

Step A is both a late step in chemical evolution and the first step in biological evolution. It is truly a transition between chemical evolution and biological evolution.  We can almost say that for Step B as well. The metabolic and reproduction systems of Steps C and D, however, are in the realm of Earthly living things. Step D is the most challenging to trace, as it involves numerous interrelationships and unknowns.

The traditional four steps listed above may well have happened in a different order. For example, the creation of cell membranes in Step #C may well have happened first, since membranes can arise naturally in certain non-living chemical systems. Even more likely is that two or more of these steps took place together, reinforcing each other.

How Did First Life (Abiogenesis) Begin?

Were Amino acids the First Large Key Molecules to mark the beginning of Life?  

All Modern plants and animals, many fungi, and a few archaea require oxygen to “burn” their cellular food (sugars) and thus obtain their energy. However, today’s atmospheric oxygen (about 21% of our modern air) would have “burned away” any synthesis of Earth’s first organic molecules, which are the building blocks of modern life. Therefore, it has long been thought that the early Earth had a “reducing atmosphere,” meaning it contained almost no oxygen and was instead composed of gases such as hydrogen, carbon monoxide, methane, and hydrogen sulfide.

The GADV “Protein-World” Hypothesis 

Many scientists think that the lipids, amino acids, and proteins evolved before “Key Molecule #3,” the nucleotides. This view has been called the “Protein-World Model,” but today the preferred name is the “GADV Protein-World Hypothesis.” 

“GADV-protein world is a hypothetical stage of abiogenesis. GADV stands for the four one-letter codes of four amino acids, namely, glycine (G), alanine (A), aspartic acid (D), and valine (V), which are the main components of GADV proteins. In the GADV-protein World Hypothesis, it is argued that the prebiotic chemistry existing before the emergence of genes involved a stage where GADV-proteins were able to “pseudo-replicate.” This hypothesis is contrary to the RNA-world hypothesis.” — Kenji Ikehara  ¹¹

The “GADV Protein-World Model” is often paired with the “Warm Little Pond Model,” first set forth by Charles Darwin in the “Darwin Conjecture.”

“Darwin’s Conjecture”:  In an 1871 letter to Joseph Dalton Hooker, Charles Darwin proposed a natural process for the origin of life. Darwin suggested that the original spark of life may have begun in a “warm little pond,” with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc. Darwin further proposed that a protein compound would then be chemically formed, ready to undergo still more complex changes. ¹²

The “Little Warm Little Pond Model,” along with other competing models of First Life, are fully discussed in our Essay, Where Life Began: “Warm Pools? Black Smokers?,” which is Essay #4 in this series of 4 Essays on the origin of life.

A more recent and widely accepted hypothesis of First Life is that the Nucleotides and RNA evolved first, i.e., before the Lipids and before the Amino Acids. This is the “RNA-World Hypothesis,” which we will take up later in this Essay.  It is also possible that amino acids and RNA coevolved together!  Readers can also find out about the more recent (1899-1992) “Iron-Sulfur World Hypothesis” by reading the Wikipedia entry about it.  

Note: Today, many scientific theories and hypotheses — in all the sciences — are called “scientific models.”
Note:  In recent decades, laboratory work on the Origin of Life has dramatically increased across the world.  Many of these scientists have produced film-strip lectures on their findings and theories. There are over 20 such presentations available on YouTube as of August 2024. Some of these lectures include a good deal of chemistry, which some readers (including your author, J.X. Mason) will have trouble following. 

Creating Amino Acids in the Lab: Miller-Urey Experiments, 1950s

In the 1950s, several experiments by Drs. Stanley Miller and Harold Urey verified elements of the “Warm Little Pool” model when their now-famous lab experiment showed that the natural formation of organic molecular compounds was possible under the oxygen-less atmospheric conditions of the primordial Earth. These compounds included amino acids, which are the components of proteins. ¹³

Their experiments used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). The chemicals were all sealed inside a sterile 5-liter glass flask connected to a 500 ml flask half-full of water. The water in the smaller flask was heated to induce evaporation, and the water vapor was allowed to enter the larger flask. Electric sparks were fired between the electrodes to simulate lightning in the water vapor and gaseous mixture. The simulated atmosphere was then cooled, allowing the water to condense and trickle into a U-shaped trap at the bottom of the apparatus. ¹⁴

The liquid in the Miller-Urey U-shaped “trap-flask” contained three experiment-produced amino acids that are common in living things. Early Earth would have had all three of them. In fact, these basic building blocks now appear to be common throughout the universe, as we will discuss later in our section on Panspermia, in our Essay, Where Life Began: ‘Warm Pools?’ ‘Black Smokers’?

Social Reactions to the 1950s Miller-Urey Experiment

Social reactions to the early Miller-Urey experiment’s findings varied widely. On the one hand, religious Fundamentalists looked at Miller-Urey’s results and said something like, “Okay, they got a few amino acids, but how did the myriad amino-acid molecules in a living cell come about? They can’t explain that; therefore, God must have created them.”

On the other hand, Scientists said something like, “Okay, Miller and Urey successfully produced a few amino acids, but how did the myriad amino-acid molecules come about?  Let’s study chemistry and biology further and see if we can eventually explain it, and in the meantime, we can put forward plausible models of it that can guide our further investigations.”

These two points of view are still debated today, not just to answer the question of life’s origin, but in discussions of scientific topics of all kinds, including the origin of the Earth and the origin and evolution of human beings.

Updating the Miller-Urey Findings – 1967 & 2008

The Miller-Urey experiment inspired a good many other experimenters. Notably, in 1967, professors Juan I. Oro and A.P. Kimball found that many amino acids are formed from HCN and ammonia under the Miller-Urey experimental conditions. ¹⁵

Then, just as notably, a group of scientists in 2008 examined 11 vials left over from Miller’s experiments of the early 1950s. By using high-performance liquid chromatography and mass spectrometry, the group found more organic molecules than Miller-Urey had found. Their reenactment of Miller’s volcano-like experiment produced no less than 22 different amino-acid molecules. As Arvin Ash has said, “It turns out it’s pretty easy to form a number of organic molecules in a wide range of environments.” ¹⁶

Terminology — “Genomes, Chromosomes, & Genes“ 

A genome is an organism’s complete set of DNA. If we think of an organism’s DNA code as its complete “manual of written instructions,” then we can say those instructions are carefully organized into “chapters” (chromosomes), which are then organized into “paragraphs” (genes). The entire “instruction manual,” from start to finish, is called the genome. In almost every creature’s genome, chromosomes and genes are organized using the same double helix (spiral staircase) pattern.  There are 23 Chromosomes in the Human Genome.  The human genome contains between 19,000 and 20,000 protein-coding genes and about 63,000 genes in total. ¹⁷

The Evolution of the Nucleotides

Scientists hold that the Nucleotides (our Key Small Organic Molecule #3), which make the Nucleic Acids RNA and DNA, are products of chemical-organic evolution.  It is believed that the nucleotides, like the amino acids, emerged in the “primordial soup” – perhaps a pond on Earth’s surface (with or without a lightning strike), or possibly in an area of water around a hot or warm sub-sea hydrothermal vent (See our Essay, Where Life Began: ‘Warm Pools’? ‘Black Smokers’?)

Earlier in this Essay, we stated that the first nucleotides may have formed before the first amino acids, thereby placing the “RNA-World Hypothesis” before the “Protein-World Hypothesis.” Today, the RNA-World Model (i.e., RNA-World Hypothesis) is ascendant because many scientists believe that self-replicating nucleotides, linked together to form RNA (an “unzipped half” of DNA), could have originally performed two functions – RNA assembly and protein synthesis.

So, how did nucleotides originate?  Which came first, the amino acids or the nucleotides? Science doesn’t yet have the answers, but there are models (hypotheses) that are supported by scientific evidence.

Creating Nucleotides in the Laboratory

The Joan Oró i Florensa Nucleotide Experiments – 1960s

In the 1960s, experiments conducted by teams led by Professor Joan Oró i Florensa found that RNA and DNA nucleobases could be produced using simulated prebiotic chemistry with a non-oxygen, i.e., a “reducing,” atmosphere. For example, Dr. Oró i Florensa found that the nucleotide base adenine could be made from hydrogen cyanide (HCN) and ammonia in a water solution.

The Georgia Tech Nucleotide Experiments – 2016

Experimental studies led by Professor Nicholas V. Hud of The Georgia Institute of Technology in 2016 showed that plausible “proto-nucleotides” can be formed in simulated early Earth environments. ¹⁸

The Georgia team also reported that nucleotides they produced can form base pairs similar to the modern DNA base pairs (adenine, cytosine, uracil, and guanine) that are formed by modern nucleic acids. Furthermore, these experimentally produced nucleotides can self-assemble into large, stacked, noncovalent complexes, which could eventually facilitate the formation of RNA-like molecules.

Dr. Hud contends that such molecules could have later evolved to incorporate the bases now found in RNA. ¹⁹

The Czech Nucleotide [plus amino acids] Experiments – 2017

Recall that in our recent section on the emergence of amino acids, we described the Miller-Urey experiment done in the 1950s. Initially, the Miller-Urey experiment was thought to produce only amino acids. However, a 2017 study by researchers in the Czech Republic has shown that a modified version of the original experiment produces nucleotides as well as amino acids!

Their experimental setup was similar to the original Miller-Urey experiment, utilizing a simple reducing mixture of NH3, CO, and H2O.  However, in addition to electric discharge in water vapor, the Czech team also subjected the solution to powerful laser discharges to simulate the plasmas resulting from asteroid impact shockwaves. The results of the experiment demonstrated that all RNA nucleobases were synthesized, strongly supporting the emergence of biologically relevant chemicals in an Early Earth atmosphere. ²⁰

       “Clearly, one of the fundamental processes of Continuing Creation – Joining/Cooperating – was present at Abiogenesis, the creation of First Life on Earth!” — J.X. Mason 

How RNA Passes Information to Make New RNA and DNA

The DNA polymer molecule, often described as the “double-helix” nucleic acid, looks like a spiral ladder or a spiral staircase with a great many “rungs or steps.” Strings of nucleotides are chain-bonded to form the long twisting “outer rails” of the ladder.

Running between the two spiraling rails are the “steps” of the ladder. Each step is composed of a base pair of nucleotides selected from an inventory of five different nucleotides — adenine, cytosine, guanine, thymine, and uracil.  Each base-pair step in a DNA spiral staircase is composed of adenine-thymine (AT) or guanine-cytosine (GC). Each base pair in an RNA half-staircase is composed of adenine-uracil (AU) or guanine-cytosine (GC). These base pairs are the foundation of the “genetic code” that is woven into the DNA of all living things. (See the Wikipedia entries for Nucleic Acid Notation and Genetic Code.)

If a DNA molecule is alternatively pictured not as a spiral staircase or ladder, but as an extended “twisted zipper,” an RNA molecule can be thought of as an “unzipped half” of a DNA molecule.

When a DNA molecule “unzips,” and becomes two strands of RNA, each strand picks up free-floating nucleotides and attaches them to make the half-steps of the partial ladder into full steps. Then, a new ladder rail is added, joining up the outer ends of all the steps. In this manner, the original DNA ladder is replaced by two new DNA ladders. Then the cell divides into two new cells, each with its own double-helix ladder.

The codes in the DNA and RNA molecules are determined not by the nature of the chemicals in the DNA or RNA molecules, but by the order of the “rungs or steps” in the long, chained molecules. The order of the steps makes the code, just as the order of dots and dashes makes words using Morse Code, and the order of zeros and ones makes the code of a computer program.  

RNA Molecules “Give Birth” to “DNA Molecules”

Inside each organism, the long RNA half-ladder also delivers genetic “blueprints” that direct the cell on how to make its own amino-acid building blocks. The cell does this by transferring RNA “blueprints” to the cell’s ribosomes, which are the “molecular machines” that build amino acids. The RNA that does the delivery work in this process is called “Messenger RNA (mRNA).”

The human genome (having 23 chromosomes) is estimated to be about 3.2 billion base pairs long and to contain 20,000–25,000 distinct protein-coding genes. The human genome is very likely to contain ~3,200 Megabytes of information. ²¹

The Key Organic Molecules Work Together in Cellular Processes

For decades, it has been firmly established in biology that protein catalysis (the work of building proteins) in modern cells is reserved for special molecules called enzymes located in the ribosomes. The “blueprints” or “catalytic templates” used by enzyme molecules are segments of genetic nucleotide chains sent from a cell nucleus to the ribosomes in the form of messenger RNA (mRNA).

Cellular Catalysis and Enzymes

Chemical Catalysis

Catalysis is the process by which a substance (the catalyst) speeds up a chemical reaction without it being consumed or altered in the process. 

Catalysis happens quite often in non-living (inorganic) chemistry, as we discussed in our Essay, Chemical Precursors to Life on Earth (Essay #1 in our series of four). Enzymes are known to catalyze more than 5,000 biochemical reaction types. ²²

Biological Catalysis

In biology, catalysis is still “the process by which a substance (the catalyst) speeds up a chemical reaction without being consumed or altered in the process.” In living things, substances and molecules that can accomplish this remarkable feat are also referred to as catalysts, and they play a highly important role in cell biology. ²³  

Enzymes

In biology, enzymes are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called “substrates,” and the enzyme converts the substrates into different molecules known as “products.”  Almost all metabolic processes in the living cell need enzyme catalysis to occur at rates fast enough to sustain life. In living things, sequences of amino acids compose many cellular enzymes with the aid of organic catalysts.  Enzymes are known to catalyze more than 5,000 biochemical reaction types. ²⁴

Note: The critical operations of enzymes in both inorganic and organic settings are another piece of evidence suggesting that the cellular processes of life likely arose naturally from the processes of inorganic chemistry (… supernatural intervention was not required.)  — J.X. Mason

Ribosomes – “Tiny Cellular Machines”

Ribosomes are fascinating cellular structures that play a crucial role in protein synthesis.  In modern cells, ribosomes are “little cellular machines” that work between amino acids (our #2 key small organic molecules) and nucleic acids (our #3 key small molecules).  Interestingly, ribosome molecules are mostly made up of RNA, while they also manufacture most of the amino acids. Since Ribosomes are composed of both ribosomal proteins &* ribonucleic acids (RNA) working together, they are early instances of the Cooperation Process of Nature’s Continuing Creation!  — J.X. Mason

Ribosomes are not surrounded by a membrane, so they are not organelles, as are the much larger cell nucleus and cell mitochondria. Ribosomes are simple cell inclusions, as are pigment granules, fat droplets, and nutritive substances. Ribosomes are found in large numbers in the cytoplasm of living cells.  As we discussed earlier, the amino acids made by the cellular ribosomes build the structures and conduct the operations of most chemical processes inside the cells of all Earthly life forms.

“Each ribosome is a tiny cellular machine that moves along a particular segment of messenger RNA, using that segment’s sequence of genetic information as a template to manufacture a particular amino acid. It is as if the ribosome were ‘reading’ the RNA sequence ‘by braille.’ ” — S. Konikkat  ²⁵

How and Why Did Ribosomes Evolve?

Ribosomes make all amino acid molecules today. If early RNA could make amino-acid molecules by itself, how and why did ribosomes evolve? The answer to the “why” question is surely because ribosomes are faster and/or more efficient.

Scientists who support the RNA-World model think that the ribosome may have first originated as a complex of self-replicating RNA. Only later, when amino acids began to appear, did that complex evolve the ability to synthesize proteins. The early ribosomal RNA was able to take on the task of amino-acid synthesis because it already had the informational, structural, and catalytic functions that it needed to do this work efficiently ²⁶

But for RNA molecules to take hold, they would have needed an abundant supply of nucleotides, and scientists think that nucleotide-building RNAs evolved to provide these RNA building blocks. ²⁷

The enzymes that now synthesize protein inside ribosomes may have evolved to replace RNA manufacturing because they became more abundant and versatile. This is supported by the fact that the ribosomes’ own structure contains characteristics from both nucleotides and amino acids. ²⁸

Ribosomes are only one example of “Cellular Machines.”

Cellular Machines are multi-component macromolecules that carry out essential biological processes inside individual cells. There are hundreds of types of cellular machines at work inside cells. (See also the Wikipedia article on Cellular Manufacturing.)

1. One type of cellular machine are the ribosome, which we discussed above.
2. A second type of cellular machine is the macromolecules that make the tiny, whipping “tails” (flagella) that certain single-cell bacteria use to propel themselves through the water.   
3. A third type of cellular machine, existing in many cells, is the mitochondria, which use aerobic respiration to generate adenosine triphosphate (ATP), which is used throughout the cell as a source of chemical energy.  

Scientists who support the RNA-World model think that the ribosome may have first originated as a complex of self-replicating RNA. Only later, when amino acids began to appear, did that complex evolve the ability to synthesize proteins. The early ribosomal RNA was able to take on the task of amino-acid synthesis because it already had the informational, structural, and catalytic functions that it needed to do this work efficiently ²⁹

But for RNA molecules to take hold, they would have needed an abundant supply of nucleotides, and scientists think that nucleotide-building RNAs evolved to provide these RNA building blocks. ³⁰

The enzymes that now make protein inside ribosomes may have come to replace RNA-manufacturing because the enzymes became more abundant and versatile. This is supported by the fact that the ribosomes’ own structure contains characteristics from both nucleotides and amino acids. ³¹

New Fields of Study  

Let’s step to the side for a moment to mention two important Advances in the study of the cellular structures of Living Things.

1. The New Science of “Structural Cell Biology” 

The ability of modern electron microscopes to see the atomic structures of molecules has led to the new field of Structural Cell Biology. Powerful microscopy, crystallography, and computational tools are now able to generate testable atomic models of cellular machines. ³²

2. The New Engineering of “Synthetic Biology”

Another new field, Synthetic Biology, uses today’s understanding of cellular machines and other aspects of cellular biology to engineer new functions into living things, producing useful chemical compounds such as pharmaceuticals and biofuels. “This effort has already led to some astonishing successes, but much work, including standardization of techniques for manipulating genes, still needs to be done before cells can be as easily engineered as traditional machines.” ³³

Synthetic Biology Created a Vaccine for the COVID-19 Virus:  “In late 2020, synthetic biology successfully produced some of the first vaccines to fight the COVID-19 virus. Unlike traditional vaccines, which use weakened or inactivated versions of the germ they intend to fight, the new vaccines use laboratory-made Messenger RNA!  When injected into our arms, the new “mRNA” vaccines instruct some of our cells to make a harmless piece of “spike protein” on their own surfaces, like the spikes found on the surface of the COVID-19 virus. Next, our bodies’ overall immune systems recognize the spiky proteins as “foreign bodies,” and our immune systems begin making antibodies to kill the cells that have spikes. At the end of the process, our bodies have learned how to kill any and all cells that have spikes, thus protecting us against future infection from real COVID-19 viruses.” — Center for Disease Control ³⁴

3. Self-replication Among Non-Living (Inorganic) Chemicals!

While DNA and RNA are both organic molecules that can self-replicate, all the other organic molecules need help from adjacent molecular machinery. For example, amino acids get replicated, but only at the direction of RNA (an “unzipped” half of DNA), as we discussed above.

However, there are examples of inorganic chemical molecules self-creating outside of living organisms!  Here are two of those examples:

Example #1 — “Life makes more of itself. And now, so can a set of custom-designed chemicals. Chemists [Gerald Joyce and Tracey Lincoln] have shown that a group of synthetic enzymes replicated, competed, and evolved much like a natural ecosystem, but without life or cells… The researchers began with pairs of enzymes they had been tweaking and designing for the past eight years. Each member of the pairs can only reproduce with the help of the other member.” From there, Joyce and Lincoln added the enzymes into a soup of building blocks, “short strings of nucleic bases….and tweaked them to find the base pairs [that would allow the enzymes] to reproduce…. When the scientists put them in a bigger soup mix, a new set of mutants emerged that were better at replicating within the system. It worked almost like an ecosystem, but with just straight chemistry.”  —  Alexis Madrigal, “Self-Replicating Chemicals Evolve into Lifelike Ecosystem,” (See, Wired Magazine, 1/8, 1889. https://www.wired.com/2009/01/replicatingrna/.) 

Example #2 –“Although self-replication is usually associated with DNA, the behavior has been seen in very different-looking chemical systems – for example, in rotaxanes (tiny molecular assemblies shaped like a ring around an axle, where the axle is capped at each end to keep the ring from sliding off.) This raises the intriguing possibility of creating completely synthetic lifeforms that tick all three boxes for life: replication, the use, and storage of energy to perform… reactions that require outside energy while keeping all of these functions contained to protect them from parasitic lifeforms.” (See, Chemistry World Online: https://www.chemistryworld.com/news/self-replicating-molecules-show-signs-of-metabolism-for-the-first-time/4012152.article.)

Cellular Respiration & Cellular Metabolism

The Key Organic Molecules of Life Work Together in the Processes of Cellular Respiration and Cellular Metabolism.

When one of our human cells takes in oxygen (O2), water (H2O), and glucose (C6H12O6), this process is called Cellular Respiration. In fact, when the cell of any organism, unicellular or multicellular, takes in its “life supplies,” no matter what those supplies are, the process is called Cellular Respiration. ³⁵

When any living cell uses its inputs to do work – repairing, growing, transporting, moving, reproducing – that process is called Cellular Metabolism. Cellular metabolism also includes the processes by which energy is stored in body tissues for later use by the organism.

Metabolism is a Process, but not a process of Evolution. It is a process of homeostasis, of survival, of continuing life within each organism. (For more, see our Essay, The Processes of Evolution and Their Meaning.)

Note: While lungs and gills are sometimes said to do “respiration” for animals, here in this section we are talking about cellular respiration. And while every human being is said to have an overall “metabolism,” here we are talking only about cellular metabolism.

Aerobic (“uses oxygen”) Cellular Respiration

Cellular energy powers the cell as it performs all its metabolic activities. Cellular Respiration is the set of processes that take in food and release its energy; it is the “front-end” part of metabolism.  There are two types of respiration:  Aerobic respiration, which uses oxygen, and Anaerobic respiration, which does not use oxygen.

In aerobic cellular respiration, oxidation of organic “food” compounds takes place in the cell cytoplasm to produce energy. After respiration, the energy eventually goes into molecules of adenosine triphosphate (ATP). ATP is the “quick storage” of energy that is immediately ready for use by muscles, nerves, and all other cells.

To see how the aerobic respiration chemistry works, we will use glucose (the most abundant of the simple sugars) as our example of a food (fuel) molecule.

When humans inhale oxygen, we use it to accept electrons “donated” from the atoms in our food. In the aerobic respiration process, glucose (cellular “food”) is oxidized (“burned”). The oxidation of glucose releases chemical energy for the cell to use.  In chemistry, this is an example of a “Redox Reaction.” For example,

6 Glucose+ 6 Oxygen yields 6 Carbon-dioxide + Water + energy… i.e…. “C6H12O6 + 6O2    >Yields >    6CO2 + 6H20 + energy”
In this reaction, Glucose donates the electrons and Oxygen accepts the electrons. (See Khan Academy, “Introduction to Cellular Respiration and Redox.”)

This is called a “redox” reaction because the glucose (a simple sugar monomer molecule) is “oxidized” (takes on oxygen) to make carbon dioxide. The “acceptor molecule” for the electrons is oxygen, which becomes “reduced” to water. When the chemical bonds of the glucose molecule are broken, electrons move, releasing chemical energy (a form of electromagnetic energy) for the cell’s use. (Often, the cell will temporarily hold the energy in the “quick storage” form of Adenosine triphosphate (ATP).

Humans have an intuitive understanding of oxidation because we have seen fires using this process to burn paper and wood since we were children. Oxidation produces heat because the chemical bonds in the fuel contain more energy than the bonds in the water and carbon dioxide, which are the end-products of combustion.

 Below is more detailed biochemistry nomenclature for readers who have a further interest in oxidation (redox) reactions:

• • A “Redox Reaction” (Reduction-Oxidation) between two participants in a chemical reaction that involves the donation of electrons (energy) by one of the participants to the other. (Participants may be chemical elements or chemical compounds.)
  • The term “Oxidation” refers to the participant element that donates electrons (energy). The term “Reduction” refers to the element that accepts the electrons (energy).
  • An example of a Redox Reaction is when pure iron reacts with oxygen, forming iron oxide compounds such as rust and iron ores. The iron is “oxidized,” and the oxygen is “reduced.”
  • A blast furnace in a steel mill reverses that reaction, using carbon monoxide as a reducing agent (it accepts electrons and becomes reduced) to reduce the iron oxide ore (it donates electrons).   (See https://simple.wikipedia.org/wiki/Reduction_(chemistry)

Anaerobic (“doesn’t use oxygen”) Cellular Respiration

While our human cells get their energy through oxidation, that’s not how most scientists think the proto-cells and the cells of First Life got their energy. Why? Because the early Earth had little or no oxygen in its atmosphere or in the oceans.

Instead, the primordial atmosphere was mainly composed of gases spewed from volcanoes. The atmosphere included hydrogen sulfide, methane, hydrogen, and ten to 200 times as much carbon dioxide as today’s atmosphere. ³⁶

Readers will recall that Miller-Urey’s experiment used a glass vessel containing a similar (but not identical) “atmosphere” composed of water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). ³⁷ Whatever the actual mix, the early atmosphere was exceedingly hot. Any oxygen that had been present would have soon been used up by burning away many of the more populous hydrogen and hydrocarbon molecules.

This early Earthly atmosphere was quite suitable for organisms that employed a different type of cellular respiration, namely, anaerobic (non-oxygen-using) respiration. We know this type of respiration was possible on Early Earth because this method is still used today by many unicellular organisms, particularly the Archaea, which often live in modern Earth’s unique, sheltered environments where oxygen is either rare or not present at all. These modern environments include swamps, undersea hydrothermal vents, and sulfurous surface geysers, such as those found at Yellowstone National Park. 

Most scientists think that Earth’s first life, called the “Last Universal Common Ancestor,” had an anaerobic (non-oxygen-using) metabolism like so many of today’s archaea have. Today’s archaea would be descendants of the Original Ancestor. 

Of course, all of today’s aerobic (oxygen-using) organisms would also be descended from that same Original Ancestor, but first, they had to evolve an oxygen-based metabolism. Soon, we will discuss how that evolutionary switch most likely occurred.

Anaerobic respiration usually means that elements other than oxygen are the electron acceptors. Common replacements for oxygen are nitrates, iron, manganese, sulfur, sulfates, fumaric acid, and carbon dioxide. These electron acceptors have less ability to accept electrons than oxygen does. Since fewer electrons travel, less energy is released per reaction. Anaerobic respiration is, therefore, less efficient than aerobic respiration, except, of course, when oxygen is scarce. ³⁸ When oxygen did become prevalent on Earth, many ancient single-celled organisms evolved the ability to use aerobic metabolism – because it is much more efficient than anaerobic metabolism.  

“Sulfur Eaters” — An Example of Early Anaerobic Respiration

For purposes of illustration, let’s say that the First Cell (or even the first even earlier protocell) consumed raw, elemental Sulfur, probably from an undersea geyser, and used it as its electron acceptor.  If so, then Hydrogen was likely used as the electron donor. Here is the chemical equation for the anaerobic respiration of Sulfur by Sulfur-reducing microorganisms:

Hydrogen + Sulfur  > yields > Hydrogen-sulfide, i.e., H2 + S yields H2S

Hydrogen is the “food” or “fuel” that donates electrons, and Sulfur is the electron acceptor.
Since Sulfur has accepted electrons, it has been “reduced.”
Since oxygen is not involved, this is not a “redox reaction.” Instead, it is called a “sulfur-reduction respiration,” and is the “front door” to “sulfur-reduction metabolism.”

Note: Although sulfur is primarily found in sedimentary rocks and seawater, it is particularly important to living things because it is a component of many proteins. ³⁹

In our example, the end-product, hydrogen sulfide (H2S), is a gas having the foul odor of rotten eggs. Several types of bacteria and many archaea can reduce elemental sulfur. ⁴⁰

Similar microbes use inorganic sulfur compounds, such as Sulfide (SO3) and Sulfate (SO4), as electron acceptors. Sulfur and sulfate-reducing microorganisms can be traced back to 3.5 billion years ago and are among the oldest forms of microbes. ⁴²

Today, many species of archaea (and some bacteria) still use reduction reactions to survive and grow. We know them colloquially as sulfur-gas “breathers,” “iron-eaters,” and similar names. Of course, since these microbes have neither mouths nor lungs, they don’t really “eat” or “breathe.” The most correct expression would be to say they “consume,” or “take in” the chemical compounds they need to live. Sulfur-based metabolism has been found primarily in microorganisms from extreme environments, such as pockets, fissures, and hydrothermal vents that extend deep into the Earth. Previously unknown microorganisms have been found there in recent years.
⁴³

Elemental sulfur and sulfates remain abundant in the modern world, especially in and around deep-sea hydrothermal vents, hot springs, and other extreme environments. In July 2019, a scientific study of the Kidd Mine in Canada discovered sulfur-breathing organisms that live 7900 feet below the surface and which “breathe” sulfur to survive. These organisms are also remarkable due to their ability to consume minerals such as pyrite as a food source. ⁴⁴

Anaerobic Respiration of Organic Foods

Microbes also anaerobically break down organic matter, such as grains, grapes, and dead plants and animals. The microbes that “eat” grape and grain sugars use the anaerobic process of fermentation, which makes alcohol as a by-product. (Yeast, which is a well-known microbial fungus, can also do this.) These microorganisms “eat” dead swamp plants and landfill garbage, which often produce smelly hydrogen-sulfide gas as a by-product, as well as methane (from which they derive their name, methanogens). There are even bacteria in the human gut that use anaerobic chemistry to help us digest our food.

But these food types are organic, i.e., they were produced by other living things, and so it is chronologically impossible for them to have been First Life. By definition and logic, “First Life” had to get its nourishment from non-living, inorganic sources.     

Note: In many animals, including humans, a molecule of glucose, usually metabolized aerobically, can also be metabolized anaerobically when there is no oxygen available in the blood. However, the anaerobic path produces only one-third of the energy (measured in molecules of adenosine triphosphate, ATP) compared to the aerobic path.  ATP molecules are what directly fuel our cells. Additionally, the anaerobic path produces lactic acid instead of water and carbon dioxide; in animals, lactic acid can cause painful muscle cramps. Lastly, anaerobic metabolism can only use glucose and glycogen, while aerobic metabolism can also break down fats and proteins.  ⁴⁵

To gain increased energy efficiency, organisms eventually evolved the ability to use aerobic respiration. The aerobic pathway enabled them to access and deploy energy more efficiently. But the aerobic path of evolution wasn’t possible until Earth’s ocean had enough free oxygen (O2) dissolved in it, and/or Earth had enough free O2 floating in the air to make aerobic respiration possible. That great increase in atmospheric oxygen was made possible mainly by the cyanobacteria, which we discuss in our Essay, “The Rise of Multicellular Life.”

It is essential to recognize that multicellular animals, including humans, effectively utilize the increased energy derived from the aerobic respiration of their food. They (and we) use much of the energy for locomotion. Animal creatures can swim, crawl, walk, climb, swing, glide, and fly.  We do this to hunt for food, escape predators, outrun natural disasters, and escape wars and other forms of adverse competition. Of course, many bacteria and the grab-bag of tiny organisms called “protists,” also move around, but not as much as most animals do. (We plan to take up the Evolution of multicellular life in a future Essay.)

Here’s what Professor Hazen wrote in 2012 about his work with the Carnegie Institution, sponsored by NASA, about creating the 4 Monomers of Life in the laboratory:

“Our results, now duplicated and expanded in numerous labs, show beyond a doubt that a suite of life’s molecules can be synthesized easily in the pressure-cooker conditions of [Earth’s] shallow crust.  Volcanic gases containing carbon and nitrogen readily react with common rocks and seawater to make virtually all of life’s basic building blocks… “What’s more, these synthesis processes are governed by relatively gentle chemical reactions [oxidation and reduction] reactions, similar to the familiar rusting of iron… These are the same kinds of chemical reactions that life uses in metabolism…” — Professor Robert Hazen ⁴⁶

If the Carnegie Institution’s results have been (or will be) confirmed, they can provide strong support for the “Deep-Hot Model” of the Origin of Life.  We will talk more about that model (and other models) in our Essay, Where Life Began: “Warm Pools?” “Black Smokers?” — the last Essay in our series of 4 Essays.

How the Key Organic Molecules Work Together

This is the section where we discuss how all four of the key monomers — the lipids, amino acids, nucleotides, and various food molecules — evolved to work together to form the First Living Organism.

Many scientists think that inside the earliest functioning cells, the “protocells,” the second and third of our Key Molecules, i.e., the nucleotides and the amino-acids, worked together using a simpler version of DNA, namely Messenger-RNA (mRNA), to do two essential jobs: (1) store and transmit genetic information, and (2) direct the construction of amino-acids. This has become an important hypothesis of the Origin of Life, called the “mRNA Model,” or simply, the RNA World Model.

The “RNA-World” Model

Now we’re equipped with sufficient information to lay out the “RNA-World Hypothesis,” (“RNA-World Model”), which is the most important rival to the “GADV Protein-World Model” presented earlier in this Essay:

In modern living things, RNA is created from DNA when the DNA “unzips” along its long center to form two strands, each half of an RNA molecule. Then, segments from one of the halves, called “Messenger-RNA” or “mRNA,” travel to the cell’s ribosomes and “conceptually give them the ‘blueprints’ for constructing specific proteins. Lastly, special enzymes in the ribosomes manufacture the proteins.

But there likely were no ribosomes at the time of the early protocells, because ribosomes are complex, too complex to have been made by protocells.  

Then, in 1982, it was discovered that the simpler (“unzipped”) half of DNA, called RNA, is capable of doing, all by itself, both of the following two jobs: 

1. RNA can store and carry the genetic instructions for the next generation, and
2. RNA can also direct the protein manufacturing work that enzymes now do in modern organisms. ⁴⁷

This discovery led Professor Walter Gilbert of Harvard to propose, in 1986, that in the distant past, Earth’s first cells used RNA as both genetic material and as the catalytic molecule for constructing proteins. In contrast, in modern cells, these functions are divided between DNA and ribosomal enzymes. 

“RNA-World” is a hypothetical early stage in the very early evolutionary history of First-Life on Earth, in which self-replicating RNA molecules proliferated inside the earliest living cells before the evolution of DNA.

The RNA-World model (hypothesis) argues that life on Earth began with a simple RNA molecule that could copy itself without help from other molecules. Because early RNA was now thought to have done both these two jobs – manufacture proteins and pass genetic information on to the next generation — many, even most, scientists began to think life as we know it began in an “RNA-World,” i.e., an early world which had no DNA or proteins in it. ⁴⁸

The RNA-World Model argues that RNA did both the work of modern DNA and the work of modern ribosomes. And there likely were no ribosomes at the time of the early protocells, because ribosomes are relatively complex, too complex to have been made by protocells. Since RNA is simpler than DNA, proponents of the RNA-World model believe that the first RNA likely evolved before the first DNA.

The online Khan Academy has an excellent online lesson and written presentation about the “RNA World Model.”  (See: https://www.khanacademy.org/science/ap-biology/natural-selection/origins-of-life-on-earth/a/rna-world.)

It is proposed that the first strands of RNA weren’t very stable and degraded quickly. But some were more stable than others. These more stable strands grew longer and bonded nucleotides more quickly. Eventually, the nucleotide strands grew faster and easily broke down, and this was RNA’s foot in the door. RNA could do the repair/replacement work. Over millions of years, these RNAs multiplied and evolved to create an array of RNA machines, including ribosomes, that are the basis of life as we know it today. ⁴⁹

Of course, still more alternative Models to the first cellular Life have been proposed, other than the GADV-Protein and mRNA models, but we will not take them up in this Essay. ⁵⁰ Even so, the evidence for an early RNA-World Model is strong enough that the hypothesis has gained wide acceptance. ⁵¹

Why Did DNA Evolve at all?

So, assuming RNA happened first, why did DNA evolve to replace RNA as the safe-keeping molecule for genetic information?  Well, DNA has better stability and durability than RNA, and this alone may explain why it became the predominant information storage molecule in all modern organisms. ⁵²

Notes: The term “RNA-World” is sometimes used to refer to the entire modeled chain of evolution, from the first nucleotide to RNA, to Ribosomes and proteins, to DNA. Among other things, this overall model explains how nucleotides and RNA, on the one hand, evolved to work together with amino acids and proteins; on the other hand, all of which result in the grand configuration of interlocking systems we see in modern living cells.

Many of the steps or links in the RNA World model have not yet been fully explained and require additional research. They will be challenging to nail down because the earliest living cells on Earth left no fossil record.

There are more than three million differences between your genome and anyone else’s. On the other hand, we are all 99.9% genetically the same. (By contrast, we are only about 99% the same as our closest relatives, chimpanzees.) ⁵³

21st Century Efforts to Create First-Life in the Laboratory

Early in the twenty-first century, research groups have already determined ways of creating rudimentary versions of cellular metabolism and have transplanted hand-crafted genomes into living cells.

In 2009-10, Professor Gerald Joyce, working in his laboratory at The Scripps Research Institute, produced a self-sustaining and self-replicating chemical system in glass containers (in vitro).  Moreover, this system was capable of exponential growth, and it featured changing proportions of the original chemicals.

However, all of Dr. Joyce’s new chemical molecules were exact copies of the old molecules, so there was no evolution of novelty; no ability to mutate. The system could not combine those chemicals in new ways to adapt to changes in its environment; it could not evolve.  ⁵⁴

Note: In September 2017, researchers from 17 laboratories in the Netherlands formed the group, Building a Synthetic Cell (BaSyC), which aims to construct a “cell-like, growing and dividing system” within ten years, according to biophysicist Marileen Dogterom, who directs BaSyC and a laboratory at Delft University of Technology. The project is powered by a $21.3 million Dutch Gravitation grant. ⁵⁵

Note: As of 2018, various laboratories around the world had successfully done several things:

• Artificially produced cell-like lipid microspheres and micro-injected them with amino acids.
• Made a rudimentary artificial mitochondrion (a cellular machine that manufactures the ready-energy ATP molecules that provide ready energy on demand, quickly delivering power to animal muscles).
• Isolated 17 natural enzymes from 9 different organisms that together can perform photosynthesis more simply and efficiently than real photosynthesis can.
• Isolated a relatively small number of the most critical genes from a simple bacterium and had that “minimal genome” boot up a free-living, slow-growing organism. ⁵⁶ 

______________________________
           — J.X. Mason   ContinuingCreation.org

Footnotes to this Essay:

1. J.F. Kasting, “Earth’s Early Atmosphere, 2-12-1992, Science, Vol. 259, Issue 5097, pp. 920-926.  DOI: 10.1126/science.11536547.
2. Robert M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2013, Penguin Books, p. 128, paraphrased.
3. M.C. Latham, “Chapter 8. Body composition, the functions of food, metabolism, and energy,” 1997, Chapter 8: Human nutrition in the developing world. Food and Nutrition Series, 1997, No. 29.
4. I. Wagner and H. Musso, “New Naturally Occurring Amino Acids,” November 1983, Angewandte Chemie International Edition in English. 22 (11): 816–828. doi:10.1002/anie.198308161.
5. K. Saladin, Anatomy & Physiology: The Unity of Form and Function (6th ed.), 2011,. McGraw-Hill. p. 67. ISBN 9780073378251. See also: “Proteins,” IUPAC Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”), 1997, online corrected version, 2006, doi:10.1351/goldbook.P04898. See also: “What are Peptides,” Zealand Pharma A/S. Archived from the original on 4-29-2019.
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46. Robert Hazen, Ibid., p. 135.
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54. Robert Hazen, Ibid. pp. 129-30.
55. Kendall Powell, “How Biologists are creating life-like cells from scratch: Built from the bottom up, synthetic cells and other creations are starting to come together and could soon test the boundaries of life,” Nature, News Feature 11-7-2018.”
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