OUTDATED – Flows of Energy Assemble Molecules into Life – OUTDATED

OUTDATEDFlows of Energy Assemble Molecules into LifeOUTDATED


This Essay is now OUTDATED.  Do not show it to Readers.  But retain it as a reference for J.X. Mason


Essay #1 — Chemical Precursors to Life on Earth
Essay #2 — The Molecules that Form Life
Essay #3 — Abiogenesis: Evolution of the First Life on Earth 
Essay #4 — Where Did Life First Begin: Warm Pools?  Black Smokers?


The fundamental process of Nature’s Path of Continuing Creation is this: When a steady flow of energy encounters a receptive environment, it weaves patterns and creates systems of increasing Complexity.

Most biologists agree that all organisms living today evolved from a single primitive one-celled lifeform. 1 The consensus holds that this “First Life” emerged by natural geo-chemical processes about 3,900 million (3.9 billion) years ago.  Yet many questions remain to be answered.

The concept of “Mother Nature,” has evolved from biology, consciousness, and human culture.

This Essay explains how the first living thing on Earth could emerge naturally from the processes of chemistry coupled with the favorable conditions available to it here on this planet. Our point of view is in accord with philosophical Naturalism, which holds that only natural causes are taken seriously.

Before life began there must have been a process of chemical change, a process of chemical evolution happening before the process of biological evolution. 2 This is consistent with Nature’s Path of Continuing Creation’s definition of evolution as a set of linked processes that start with the Big Bang and cosmic evolution, continue with geo-chemical evolution, then biological evolution, and include the human-agented evolution of culture and technology.

When biblical creationists criticize biological evolution, they like to point out that placing all the parts of a watch in a vat of water and stirring them up does not make an assembled, working watch. They cite a paper by Fred Hoyle and Chandra Wickramasinghe which calculates that the probability of all the chemicals in a simple bacterium arising on their own by chance is 1 in 10 to the 40,000th power. They say that the odds of creating a protein molecule by chance is1 in 10 to the 45th power. 3

But this argument is an over-simplification. It ignores the fact that sophisticated life forms like current-day bacteria, or even a complex protein molecule, almost certainly did not arise spontaneously from a mix of chemicals. They arose from simpler, incremental steps that had a much higher chance of occurring.  Proteins, for example, are made out of simpler amino-acids. 4

The biblical creationists also ignore that fact that there are about 4×1047 molecules of water in Earth’s oceans. So, even if there was one amino-acid molecule among 1 million water molecules, that would still be 1041 amino-acid molecules that had the opportunity to interact with each other, in numerous environments, in numerous places, and in numerous trials over millions of years, to eventually produce proteins. 5

The relevant probability is not the chance of hundreds of complex chemicals coming together to form a modern-day bacterium, but the probability of 10 or 20 chemicals coming together to form the precursors of life, precursors that can then chemically evolve over time to form the simplest kind of life form, one that likely looked nothing like any evolved life form we recognize today. 6

More fundamentally, a recent well-reviewed book by Dr. Bobby Azarian tells us that wherever energy flows (e.g., from hot to cold) it can drive natural systems to self-organize into structures which are able to move more energy through faster. For example, when water runs out of a bathtub, it adopts the organized structure of a whirlpool to empty the tub more quickly. Quite a few inorganic chemical systems do this, and so do the structures we call living organisms. This fact has led a majority of NASA astrophysicists to conclude that the emergence of life may be widespread across the millions of Earth-like planets and moons in our own galaxy, the Milky Way. (Bobby Azarian, The Romance of Reality: How the Universe Organizes Itself to Create Life, Consciousness, and Cosmic Complexity, 2022, BenBella Books.)

Readers May Want to Start with These Outside Presentations  

At the time of this writing (May, 2021) there are up-to-date sources available which brilliantly present our scientific knowledge about the Origin of Life.  Listed below are four sources that readers might want to turn to before they read this Essay.

  1. Abiogenesis – How Life Came from Inanimate Matter. This short 12-minute film, made and narrated by polymath Arvin Ash, lays out the basic story with clarity and superb moving illustrations. This film is available on the Arvin Ash website, arvinash.com. 7
  2. The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, by Robert M. Hazen. In chapters 6, “Living Earth,” and 7, ”Red Earth,” Dr. Hazen tells general readers, in expressive language, how the chemicals and conditions on early Earth interacted to produce and assemble the components of the first single-celled organism.  8
  3. The Lives of a Cell: Notes of a Biology Watcher, written in lyrical prose by Dr. Lewis Thomas, MD, who was then President of the Sloan Kettering Cancer Center in New York. 10
  4. The current Wikipedia article on Abiogenesis, (May, 2021) is a detailed review of the current science in this area. It complements the other three sources with authoritative information supported by 358 footnotes citing scientific research papers. (Biogenesis means “beginning out of life;” A-biogenesis means “beginning out of not-life.”)

These four recommended sources indicate that the scientific community’s intense focus on the Origin of Life will constantly update our knowledge over the next two decades. Our Essay here will be drawing on all four of the above resources, and a good number of others.

Scientific study of the Origin of Life has accelerated in recent years, partly due to NASA’s interest in the possibility of life on other worlds. Evidence shows that 4.1 to 3.7 million years ago the surface environment of Mars had liquid water and may have been habitable for microorganisms. A 2018 study found that 4.5-billion-year-old meteorites found on Earth contained liquid water along with prebiotic complex organic substances that may be ingredients for life. 11

A lot remains unknown about the Origin of Life on Earth. But as more evidence comes to light, we see more evolutionary steps.  Of course, every piece of new evidence also creates more so-called “evolutionary gaps” in the minds of religious creationists.  We see more pieces of evidence; they see more “gaps” between the pieces of evidence. 

Science is about discovery.  It welcomes new questions because they lead to new knowledge.  Science is openness to new knowledge.  Fundamentalist, Biblical Creationism is closed to new knowledge; they are afraid of what they do not know.

Biblical creationists charge that we have “faith” in science; that we have made a religion out of science; that we want to make “science” into a God.  No, we are not doing those things.  We don’t have faith, we have confidence in the scientific method and optimism about its ability to find answers and solve problems.  We do not reject the possibility of God-the-Creator, we simply hold that Creation is more accurately described by scientific knowledge about the Processes of The Growing, Organizing, Direction of the Cosmos than it is by the anthropomorphic verses in the Bible, the Koran, or in the Bhagavad Gita. 

People who are determined to keep their traditional faith in a supernatural God should ask themselves this: which is more powerful, more creative: a God who decrees human life into existence, or the Sum of all the Interacting Processes of Nature’s Continuing Creation? Processes that include the rules of physics and chemistry such that intelligent life will emerge from them on some of the six billion Earth-like planets all across the Milky Way Galaxy? 12

This Essay Compared to Our Processes of Evolution Essay

This Essay about life’s origin may be less important than our related Essay, The Processes of Evolution & Their Meaning, because the latter describes the evolution that is happening all around us, here and now. It explains how those processes provide us with spirituality – our sense of connectedness and meaning.

While we understand that a Deist “clockmaker-God” may have started the universe – we can’t prove it up or down.  But the universe is here, the evolutionary processes are working here on Earth, and as these processes grow, they generally become more elaborate… as they likely do on other planets when planetary conditions are adequate.  (For more on Deism, see our Essay, Forerunners to Our Spiritual Path.

In any case, both our “Processes” Essay and this “Origin of Life” Essay are integral to the Book of Continuing Creation. Darwin’s On the Origin of Species, published in 1859, and all the evolutionary science from then until now are forerunners to this Book of Continuing Creation.

Life Arose from Non-Living Chemistry

While there is no single generally accepted theory of the origin of life, all credible proposals show that life, under natural conditions, by a slow process of chemical and molecular evolution, could have plausibly resulted in simple forms of life over a long period of time, and that this chemical evolution was probably the biggest hill to climb for life to have occurred on Earth. 13

Once this happened, biological evolution took over and relatively quickly resulted in exceptional diversity of life forms. We see that in the fossil record of early Earth, and of course, we see that on Earth today.  Do we have proof that this is how life came about?  No… at least not yet. Is it plausible?… absolutely.  14

So, life comes from geo-chemistry. But before we look at how chemistry transitions to become life, let’s take a large scale look at a chart covering all of life, and then take a closer look at the simplest forms of life that are still living today.

The Tree of Life — Biological Classification (Taxonomy)

We can step back and look at the Big Picture of Life by means of a schematic drawing called a Tree of Life.

Tree of The 6 Domains of Life

Living things are classified into an evolutionary order of successively evolved groups called taxa, and the science of biological classification is called Taxonomy. When taxa are drawn on a page, they form a Tree of Life, with the oldest and simplest organisms at the bottom of the tree trunk.  Life then spreads upward and outward into successively smaller and newer branches. The roughly 11 trillion different species living on Earth today would each occupy a single “leaf” at the end of a tiny twig on this tree.

The drawing at the side shows that there are six huge groupings – called Domains — of living organisms on Earth. Each Domain is a grouping of millions of individual species. The names of all Six Domains are: Bacteria, Archaea, Protists, Plants, Fungi, and Animals.

In more detailed Trees of Life, we would see that the six Domains branch into biological Kingdoms; which in turn branch into Phyla. After the Phyla there are successively more, smaller, and newer types of branches as follows: Classes; Orders; Families; Genera; and Species.

Note: If computers evolve their own intelligence, self-sufficiency, and ability to reproduce, they might someday be classified as a new “Seventh Domain of Life,” sprouting out of the Animalia Domain on the upper right of our Tree.  (For more, see our Essay, Cyborgs, Transhumanism, and Immortality.)

We Start by Looking at Today’s Simplest Organisms

Evolutionary biologists overwhelmingly maintain that all life evolved from a single species, the “First Organism” or the “Original Common Ancestor.” The strongest evidence for a single “first organism” species is that the DNA of all living things is highly similar. [Cellular] Processes as distinct as respiration, fermentation, and photosynthesis all share a common basis, a conceptual integrity, which attests to the fact that all life has descended from a single Original Common Ancestor. 15

The sciences of evolution and genetics also tell us that “First-Life” (also called the “Common Ancestor”) began with the simplest of all organisms, because that organism would have been the easiest to self-construct using the processes of geo-chemistry. It follows that the simplest organisms living today are likely descendants of the First Organism. The simplest organisms we have today are the bacteria and the archaea, at the base of our Tree.

So, to find the origin of life, we need to focus on the Bacteria and the Archaea, which are the two huge Domains at the base of our Tree’s trunk. The Archaea and Bacteria still exist today; in fact, they are flourishing, and each domain contains hundreds of thousands of individual species.  Moreover, they continue to evolve.  We know the bacteria evolve because we spend fortunes inventing new antibiotics to combat new strains of bacteria that are infectious. (We also spend large sums of money to combat new infectious strains of viruses and fungi.)

Bacteria and Archaea Are Today’s Simplest Organisms

All the Bacteria and Archaea are single-celled, and each cell is enclosed by a cell membrane.  (Multi-celled organisms efficiently share their cell walls with the cells on all sides of them.) They are microscopic creatures that swim around in water. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. A few species of archaea have additional, unusual shapes.

Modern Archaea were first discovered in hot springs and salt lakes, and then came to be found everywhere on Earth. Archaea are important in the human gut and mouth, where they aid digestion.  Interestingly, none of the Archaea are pathogens or parasites, which is quite a contrast with many species in the Bacteria Domain.

Years ago, it was thought that the archaea were a type of bacteria, but genetic analysis has revealed their genes to be quite different. For example, some bacteria and some archaea have flagella – tiny whip-like tails that propel the creatures through the water – but the two domains differ in how the flagella are structured.

Archaea and bacteria do not have any organelles — membrane-enclosed structures inside themselves (such as a nucleus, mitochondria, or chloroplasts) which conduct specialized processes. Therefore, all archaea and bacteria are classified as prokaryotes. Cells that do have such internal enclosed organelles are classified as eukaryotes.

Note: Most prokaryotes do have an irregular, unbounded region that contains DNA, known as the nucleoid16 In the nucleoid region, most prokaryotes have a single, circular chromosome, in contrast to eukaryotes, which typically have linear chromosomes. 17

Nutritionally, prokaryotes species can utilize a wide range of organic and inorganic material to power their metabolism, including sulfur, cellulose, ammonia, or nitrite.[9] Today, prokaryotes are ubiquitous across the Earth, even in the most including extreme environments. 18

The “First Organism” or “Original Ancestor”

While the bacteria and archaea are genetically different, they are similar enough to persuade scientists that both domains are descended from a single “Last Universal Common Ancestor, LUCA.” (We will just say, “Original Ancestor,” or “First Organism,” in this Essay.) Of course, there may have been many generations of those Original Ancestors, but no fossils of them have yet been found.

The First Living Cell, the First Living Organism, must have been a prokaryote. Why? Because evolution generally proceeds from simplicity to complexity, and prokaryotes are simpler than eukaryotes. 

Gene sequencing studies are used to reconstruct the archaea and bacterial ancestry trees (phylogeny), and these studies indicate that the most recent common ancestor of bacteria and archaea was probably a single-celled extreme-heat-loving (hyper-thermophilic) organism that lived about 4.2 billion–3.6 billion years ago, probably near an underwater volcanic vent or hot springs. The earliest life on land may have been bacteria some 3.22 billion years ago. 19

As we shall discuss in this Essay, there were likely non-living chemical systems which existed and replicated even before the advent of the Original Ancestor.  These “pre-living” systems are often called protocells.  (Not to be confused with proteobacteria, which are entirely different. And not to be confused with viruses, which are non-living segments of genetic material that have broken off and float around to infect the genetic material of other living organisms.)

The “First Great Divergence”

No one knows which domain evolved first – the archaea or the bacteria.  It may be that many generations of the “First Organism” preceded both of those domains.

Most geologists agree on one thing: for about 500 million years following the formation of Earth, conditions were extremely hostile to Life (as we know it).  And it is interesting to note that many archaea are able to survive the coldest, hottest, most saline and most acidic environmental conditions that Earth throws their way. 20

At some point in ancient geologic time, likely between 4.2B and 3.1B billion years ago, the archaea diverged from the “common ancestor.” The bacteria perhaps diverged a bit later, at between 3.2B and 2.5B years ago. Together, these two events are sometimes called the “First Great Divergence” in evolution. 21

All other Earthly life – protists, fungi, plants, and animal — evolved out of the bacteria, out of the archaea, or directly out of the Original (or “Un-named”) Ancestor. For more detail, see the excellent and well-illustrated Wikipedia article entitled Prokaryote.

The Process of Divergence is common in all stages of evolution. Two or more species can evolve out of a common ancestor species. For example, the Human species, chimpanzee species, gorilla species and others all evolved out of, “diverged from,” a common ancestor.

We can also see the process of divergence at work in cultural and technological evolution. Today’s modern romance languages – including Italian, French, Spanish, Portuguese, and Romanian — evolved out of and diverged from the older and now extinct Latin language that was spoken by the ancient Romans. In the story of the electric light, we saw that the neon light, fluorescent light, arc light and other “species” evolved out of “Edison’s” incandescent lightbulb. (For more, see our Essay The Processes of Evolution and Their Spiritual Meaning.)

What Defines Life?  What Do All Organisms Have in Common?

Before we describe how Life emerged from chemistry, we need to define the word, “Life.”
What are the essential features and processes that constitute Life, across all species and all domains?

Biology’s Definition of Life

  • One widely accepted definition of “Life” says that living organisms are open systems that have energy flow-through, perform metabolism, maintain homeostasis, can grow, respond to stimuli, adapt to their environment, reproduce, can evolve, are composed of a single cells or multiple cells, and have a life cycle from birth to death.
  • Re-stated as a list, this definition says that something is alive, it is a living organism, if (1) it is composed of one or more cells, (2) it has a life cycle – it is born, and it eventually dies, and (3) it does all of the following things:
  • Constructs and maintains a boundary that separates it from the outside. (However, the boundary must be semi-permeable — capable of taking “good” things in, and excreting wastes.)
  • Channels a flow of energy through itself (i.e., it is a thermodynamically open system).
  • Maintains homeostasis [good description below]
  • Has a metabolism – It takes in nutrients, extracts energy, and excretes waste.
  • Moves and/or grows.
  • Adapts to its environment.
  • Responds to stimuli.
  • Evolves – it can change over time in response to change in its surroundings.

We can clearly see how interdependent all these functions are. An organism cannot move unless it has a boundary that separates it from its environment. It cannot move, self-maintain, grow, or reproduce without an energy flow. The organism can’t access energy without sensing and/or traveling to an energy source – to its food. The food cannot get into the organism (nor waste get out of it) unless the boundary is semi-permeable.

Note:  The boundary is semi-permeable.  It admits some new things and not others.  There is inherent tension between these two things: homeostasis and evolution. Things strive to stay the same, yet they evolve. Energy flows through day-to-day, but does not destroy the organism… until the organism dies, and makes way for newborns that may display evolved features and abilities.

Chemistry’s Definition of Life

Dr. Hazen maintains that “Chemistry provides a firmer foundation for defining life, for all living things are organized molecular systems that undergo chemical reactions of astonishing intricacy and coordination.” [Hazen p. 128]

A panel at the Scripps Research Institute, chaired by Dr. Gerald Joyce came up with an excellent one-sentence definition of Life, which Joyce later amended to become: “Life is a self-sustaining chemical system capable of incorporating novelty and undergoing Darwinian evolution.” 22

First life must have started from non-living matter – because, by definition, “First life” could only be preceded by “non-life.” 23 The earliest protocells may not have met all the definitional requirements for life. They may have lacked one of more of the Key Processes of Life. And the chemical systems that evolved even earlier that the first protocells may have barely hinted at what would evolve later.

Are Viruses Alive?

What about viruses?  Aren’t they alive?  Sort of alive?

Viruses are not fully alive, because they have no mechanisms for metabolism or reproduction. Nor do they have a cell membrane, just a coating. Viruses are pieces of genetic material (RNA or DNA) that have broken away from an organism and float around in air and water. When they contact the cells of another fully alive organism, they infect them. Inside, they hijack that organism’s metabolic and reproductive systems, tricking the host organism into producing copies of virus which then escape into the world to infect the cells of other fully alive victims. Viruses are usually classified as “near-living.”  (Nick Lane, The Vital Question, Ibid., p. 53-4.)

Note:  Viruses are parasites.  But so are human beings.  Everything we eat was first a part of some other organism.  We “harvest” (often meaning “kill”) that organism before we eat it.   So, like viruses, we “parasitize” our environment.  On the other hand, the green plants we eat need us as much as we need them – we are co-dependent, each breathing in the other’s exhalations.

Abiogenesis: From Inorganic Chemistry to Organic Chemistry

Abiogenesis is when chemistry turned into Biology”
                  — Lawrence Krauss. 

Chemical evolution preceded biological evolution. The transition between the two is called abiogenesis.  Note that Abiogenesis is technically not part of biological-evolution, because by definition, abiogenesis took place before all bio-evolution.  However, if we contend that grand evolution encompasses geology, chemistry, biology, culture, and technology, as we do here in our book about Continuing Creation, then Abiogenesis is part of grand evolution. 24

Abiogenesis (informally, the origin of life) is the natural process by which life has arisen from non-living matter, particularly from chemical precursors.  Specifically, life arose from chemical compounds that contain carbon that is bonded to hydrogen. Since these chemicals continue to be deployed within living organisms, they are called organic compounds. 25

There is no “standard model” for Abiogenesis. Instead, there are several theoretical models, each one supported by evidence from geology, chemistry, molecular biology, and cell biology. We will discuss each of these models later in this Essay.

Note: The expression, “Scientific Model” has largely replaced the older “Scientific Hypothesis.”  The word “model” is thought to better convey the fact that all chains of scientific reasoning must remain open to the discovery of new facts and/or verification by new experimental results. For a larger discussion, see “Hypothesis, Model, Theory, and Law,” ThoughtCo, at https://www.thoughtco.com/hypothesis-model-theory-and-law-2699066.

The Six Key Chemical Elements of Life on Earth

From the mightiest blue whale to the most miniscule paramecium, life takes dramatically different forms. Nonetheless, all organisms are built from the same six essential elemental ingredients: carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur (“CHNOPS”). 26 Among these six are the four elements that are both the most prevalent in the human body and the most common elements in the universe: Hydrogen, oxygen, carbon, and nitrogen.

One thing that makes nitrogen, hydrogen and oxygen good is that they’re abundant. They also exhibit acid-base effects, which allows them to bond with carbon to make amino-acids, fats, lipids and the nucleobases from which DNA and RNA are built. 27

Life on Earth is Carbon-based

“Everyone agrees that the element carbon played a starring role.  No other element has such rich molecular designs or such diverse molecular functions. Carbon atoms possess an unmatched ability to bond to other carbon atoms as well as to myriad other elements – notably hydrogen, oxygen, nitrogen, and sulfur – with up to four bonds at once.

Carbon can form long chains of atoms, or interlocked rings, or complex branching arrangements, or almost any other imaginable shape.  It thus forms the backbone of proteins and carbohydrates, of fats and oils, of DNA and RNA. 28

Only carbon-based molecules appear to share the twin defining characteristics of life: the ability to replicate and the ability to evolve.  Every morsel of food we eat, every medication we take, the bodies of every living thing, are loaded with carbon.”  29

Earlier, we mentioned that crystals and crystal formation have several of same features as life and living systems. It is not surprising, then, that carbon is both the basis for life, and carbon can also form brilliant diamond crystals outside of living systems.

Progressive Evolution

Some readers may accuse this book about Nature’s Continuing Creation of being another argument for orthogenesis — the biological hypothesis that organisms have an innate tendency to evolve in a definite direction towards some goal (teleology) due to some internal mechanism or “driving force,” such as “the Hand of God.”  We hold that the largest-scale trends in evolution do demonstrate a trend of increasing biological complexity

But a trend is not a goal, and certainly not a pre-ordained goal. We and do see Progressive Evolution all around us in the sense that energy flow-throughs are made more efficient and the structures that arise are more complex. But those processes could end if we were hit by a large meteor, or if Humans destroy the biosphere.  (Note: A more modern term for orthogenesis is Progressive Evolution.) 30

In the modern day, Professors Adrian Bejan and Jeremy England independently argue that there is a driving (but not inevitable) force behind increasing complexity, and that is the force of energy trying to find more, larger, and more efficient paths of energy flow.  We will talk more about this in the chemical Evolution sections of this Essay.

We do not see increasing complexity as a goal.  We see it as a tendency, but never a certainty. A set of viruses could conceivably wipe out all of today’s humans, or even all mammals. It is also true that today’s “simple” microbes continue to evolve, and do so quite rapidly, although none of them come close to evolving the complexity of a human being, crow, or octopus. (For more, see the Wikipedia article on Orthogenesis.) On the other hand, estimates of the number of Earth’s current species range from 2 million to 11 million. (See the Wikipedia article on “Global Diversity.”)

History and biology also show that the tendency toward greater complexity can be thwarted. For example. in the period known as The Great Dying (the Permian-Triassic Extinction Event), an estimated 81% of all marine species, 70% of all terrestrial vertebrate species, and a huge but uncalculated percentage of insect species all went extinct, likely due to changes in the atmosphere and the seas. 31 Nevertheless, as we all know, life did come back and it continued to evolve.

Carbon’s natural ability to grow by chaining its own molecules and by combining with other elements shows the tendency of pre-biologic, non-living systems to form ordered structures, grow them, and increase their complexity.

However, as Professor Hazen writes, “Carbon cannot have undergone the remarkable progression from geochemistry to biochemistry by itself. All of Earth’s great transformative powers – water, heat, lightning, and the chemical energy of rocks – were brought to bear in life’s genesis.” 32

For decades, many futurists and science-fiction writers have speculated that on other planets in other solar systems, life might be based on silicon rather than carbon. Silicon is right below carbon on the Periodic Table of Elements, and silicon has almost as many ways to combine with other elements as carbon has. On Earth, silicon has already shown its versatility as the central element in the workings of electronics and computers. When computers “wake up” and become conscious entities in an expected event dubbed the Technological Singularity, they may become a “new species of life.”  For now, however, most scientists still place their bets on carbon as being central to all life across the cosmos. (For more on the Technological Singularity, see our Essay, Cyborgs, Transhumanism, and Immortality.  Also, see the Wikipedia article, Hypothetical Types of Biochemistry.)

Other Chemical Elements Play Important Roles in Life on Earth

Magnesium is the eleventh most abundant element by mass in the human body and is essential to all cells and some 300 enzymes. Hundreds of enzymes require magnesium to function.

Iron is a chemical element, a metal, and a naturally occurring metal mineral that is a critical part of hemoglobin, a protein which carries oxygen dissolved in our blood from our lungs throughout our bodies. It is the iron in our blood that makes it red. It helps our muscles store and use oxygen. Iron is also part of many other proteins and enzymes.

Sodium and Chlorine are each highly dangerous as raw elements. Sodium is explosive in the presence of water. Chlorine is a poisonous, lung-burning gas.  But with an easily added electron, chlorine becomes the far more prevalent chloride. Sodium and chloride readily combine to make common table salt, which is an important component of our blood. (Our blood is salty because we are evolved from fish in the sea.)  

Sodium-chloride is an example of the Path of Continuing Creation’s Principle that when simple things are combined, a new thing is often created that is quite different from its components. 

Calcium is a silver-gray metal that’s the fifth-most abundant element in the human body. It plays a vital role in electrolytes, cell biochemistry, neurotransmission, the contraction of all muscles, and fertilization. Calcium is important for protein synthesis and bone formation. Seashells are made of calcium carbonate, in the mineral form of calcite or aragonite. Animals build their shells by extracting the necessary ingredients—dissolved calcium and bicarbonate—from their environment. 33

The Six Basic Chemical Compounds of Life

We know that chemical elements can combine to form chemical compounds. The basic chemical compounds from which life is thought to have formed are: 34

  • Methane (CH4),
  • Ammonia (NH3),
  • Water (H2O),
  • Hydrogen sulfide (H2S),
  • Carbon dioxide (CO2) or carbon monoxide (CO), and
  • Phosphate (PO4).

Note: Molecular oxygen (O2) and ozone (O3), both important parts of today’s atmosphere, were either rare or absent on early Earth. They were created later, in and around the Great Oxygenation Event, which we will take up later in this Essay. At the early time of First Life, it is thought that no organisms breathed oxygen as we do today. 35

Organic Compounds

Organic compounds are generally any chemical compounds that contain carbon-hydrogen bonds.

By this definition, methane (CH4) is an organic compound. Most organic compounds arise from biological processes. Methane is a component of natural gas arising from the decomposition of ancient life under the heat and pressure of deep Earth.  Water (H2O) would not be an organic compound, because there is no carbon in it.

Due to carbon’s ability to catenate (form chains with other carbon atoms), millions of organic compounds are now known; most of them manufactured by biochemical systems within living organisms, or by organic chemists making plastics, pharmaceuticals, or 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. (See Wikipedia article, “Organic Compound.”)

Further Below, we will talk about the Key Molecules of life:

Apparent Stages in the Origin of Life. 

Unicellular organisms are thought to be the oldest form of life, with early protocells (“before real living cells”) possibly emerging 3.8–4 billion years ago.  36

 We take the approach that First Life likely followed a direction of increasing complexity. This direction of increasing complexity would have taken several (likely interrelated and indistinct) steps:

Step #A: The origin of biological monomers: fatty acids, amino-acids, nucleotides, and sugars.
Step #B: The assembly of biological polymers.
Step #C: The evolution from free-floating molecules to membrane-contained molecules.
Step #D: The interaction of the molecules in working systems of 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 Steps #B and #C as well. The metabolic and reproduction systems of Stage #D, however, are clearly in the realm of living things. Stage #D is the tough one to trace, containing many interrelationships and many unknowns.

We must note that the traditional four steps listed above may 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.

The Origin of Life Requires 3 Kinds of Simple Molecules in the Organism… plus Food Molecules for Energy

To see how Abiogenesis (The Origin of Life) works, we start by breaking it down into its principal components.

Despite the incredible varieties of life we see today; at the fundamental level all living things require the four simple molecules listed below, which are called the “Four Monomers of Life.”  (Per Step #A above)

A monomer is a small molecule that becomes a subunit when combined with similar subunits to form larger chains of molecules called “polymers.”

Each of the four Monomers of Life can link together (polymerize) to form large macromolecules called lipids, amino-acids, and nucleotides. These macromolecules are typically composed of thousands of atoms. (Carbohydrates, a food/energy source, are also macromolecules.) wiki on macromolecule]

The 4 Key Monomer Molecules of First Life, and their Key Processes:

#1. Lipid moleculesLipid monomer molecules link together to make fats, oils, phospholipids, and waxes. Usually, phospholipids form the cell membrane, the boundary that separates it from the outside world. The membrane encloses and protects the cell’s interior chemistry. The lipids also have other jobs within a cell. Self-enclosure, providing self-identity and self-protection, are a Key Process of life.

#2. Amino-acid moleculesAmino-acid monomers chain together to build the cell’s large protein molecules, which are the workhorses of the cell. The proteins break down food, build up (and constitute) tissues, transport substances, and eliminate waste. Together, those processes are called metabolism, which is one of the Key Processes of Life. (In addition, the proteins even build the RNA and DNA molecules needed for reproduction.

#3. Nucleotide moleculesNucleotide monomers combine together to form nucleic-acids. The nucleic-acids form the exceedingly long DNA and RNA molecules that are the self-replicating genetic blueprints that carry the instructions for reproducing new generations of the cell and/or of the organism as a whole. DNA and RNA are self-replicating, organic molecules. The ability to self-replicate, to reproduce, is another of the Key Processes of life.

#4. Food molecules — In the modern world, the simplest molecules of sugar, the monosaccharides, are the basic cellular food monomers for many organisms, including humans. A prime example is the monosaccharide, glucose.

Green plants use the process of photosynthesis to make monosaccharides. Then, at night when the sun doesn’t shine, their cells use oxygen to “burn” the monosaccharides as fuel in a process called cellular respiration. Energy moves 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). The green plants can also store the energy in the monosaccharides by assembling them into carbohydrate structures such as cellulose, grains, fruits, nuts, and tubers.

When animals eat the plants (or eat each other), they use the monosaccharides originally stored in the plant structures for fuel, and they can also store them in their own structures including as bone, muscle, nerves, and fat. When these processes involve oxygen, they are called aerobic respiration processes.

The cells of other modern organisms also use plants as food for their energy source, but they do it without oxygen in a process called fermentation. Fermentation is a type of anaerobic respiration processes.

Earth is also home to billions of other organisms whose cells do not make or take in molecules of sugar as their basic cellular foodstuff. Instead, and amazingly, they take in minerals like iron or sulfur.  Some of these organisms use oxygen to get energy from the foodstuff (e.g., they “rust” the iron, an aerobic process), and some use non-oxygen (anerobic) processes to release energy from minerals like sulfur.  Whenever any organism takes in “food” at the cellular level, that Key Process is called Cellular Respiration, and it is the “front-end” portion of Cellular Metabolism.

An important take-away is that life has evolved to use many different chemical processes with which to take energy from different kinds of “food.” Life seeks, explores, tries, persists, and adapts, and adopts.  In other words, Life evolves.  And life does all this without any direction or control from a central authority.  More generally, every living organism is an open energy system that requires a varying set of additional inputs from outside sources: 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 Abiogenesis on Earth arose from geochemistry.

Among the more than nine million known organic compounds, four major categories of organic molecules listed above — lipids, amino-acids, nucleotides, and the flows of various energy and supplies (e.g., sugars and minerals) — are found in all living things. If we want to describe how life first emerged, we need to describe how each of these four arose, and then we need to describe how they began to work together in the first living cell.

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 and genetics –that together unambiguously distinguish the living from the non-living.” 37 Arvin Ash also agrees, as he says in the first three in his twelve-minute film presentation, Abiogenesis – How Life Came from Inanimate Matter,” (Sept 7, 2019). And the Wikipedia article on Abiogenesis concurs as well.

In the sections below, we look at each of our “Four Key Molecules of First Life,” and we describe how they emerged naturally from inorganic (non-living) geo-chemistry. These Four typed of molecule are more complex than the monomer molecules we talked about above.

After those sections, we will consider how likely it was for all those monomers to assemble and function together, chemically.

After that, we will talk about the Models of Where, When, and How the Earliest life took place. These models describe the real-world geological forces and locations that brought all the chemistry together.

Key Molecule #1 in Creating Life — Lipids:  

Every living thing is either a single cell or a group of cells (rose bushes and humans are huge, organized groups of cells). Every one of these cells is enclosed by a cell membrane. Inside each cell membrane, interacting molecules carry out the chemical processes of life, such as the oxidation (“burning”) of food sugars to generate energy, or the assembly of protein molecules to build muscle tissue. 38.

How did these cell membranes arise from non-living chemical molecules?

Before life arose, picture the four chemicals essential for abiogenesis as floating in water, because life started in water. (The human body is itself 70% water.) Pre-life chemicals would not have been able to perform their functions unless they were protected from outside intrusion from other “foreign” chemicals and intrusions. 39

Life cannot exist unless it is able to separate itself from the world around it. There must be a boundary that separates the living creature from the non-living environment around it.  Without a boundary – an outer cell membrane — the outside world would contaminate and disrupt the delicate molecular chemistry within the cell. Compartmentalization was also necessary for the right interior chemical molecules to get close enough to each other to carry out their interactions.

In the language of physics, without such a boundary, the law of entropy (the Second Law of Thermodynamics) says that the cell’s organization and energy would dissipate out into the wider world and disappear. Similarly, in the realm of technology, every machine that successfully generates useful energy – a car’s motion, steam used to heat a building, electric current — has one or more boundaries that serve the same purpose. The boundary controls the energy, forcing it along a mechanical path, a controlled exit, that accomplishes work. An example is the steam boiler driving a piston in a locomotive.

If there are no boundaries, there are no differences.  Without differences, there is no information, no variation… and therefore, no Creation.  In essence, all Creation is the production of a difference that did not exist before. For more on this fundamental concept of our entire Spiritual Path, see our Essay, Patterns of Information – How Nature’s Creation Works.)

 The hollow lipid spheres that occur naturally in chemistry are the same as the hollow lipid spheres that are critical to the existence of all cellular life. This clear continuation of chemistry into biology demonstrates that the creation of First Life was not done by a sudden command from a mythical, anthropomorphic God, but rather from the self-assembling, evolutionary Processes of Nature’s Continuing Creation: The Growing, Organizing, Direction of the Cosmos.     

Cell membranes are formed by a layer of lipid molecules. 40 A lipid is any of various chemical compounds that are insoluble in water. They include fats, greases, waxes, and oils. Lipids are mostly composed of Oxygen and Hydrogen. Sometimes a Nitrogen group is present. Cholesterol is a well-known lipid.

Lipid molecules have a bulbous head on one end and a “tail” of acids on the other end. The bulbous end is “water-loving” (aquaphilic), while the trailing end is “water-hating” (aquaphobic).

Liposomes and Micelles

Lipids like to coagulate, head next to head and tail next to tail, forming a uniform layer. Since the bulbous heads are wider than the acid tails, a lipid layer will naturally curve in on itself to form a sphere. The bulbous heads face outward, and the acid tails dangle on the inside.

The formation of these layers and spheres is an automatic process of self-assembly – no outside direction or manipulation is required. 

Because of their simplicity and ability to self-assemble in water, it is likely that these simple lipid membranes predated other forms of early biological molecules. 41

Lipids naturally encapsulate small volumes of water.  If that water contains the other monomers of life we listed above, the amino-acids and the nucleotides, then the sphere could be called a protocell, which is a non-living pre-cursor to the first living cell(s). This possibility is in fact one of the main models (theories) about how Life began. And as we have said, the cell membranes of all organisms living today are still composed of lipid layers.

When there is water both outside and inside the sphere, the lipids can form a double-layered (bi-layered) sphere: One layer has its bulbous heads facing outside to the world, and a second layer has its heads facing inward toward the interior. Between those two layers, all the trailing chains of the molecules end up facing toward each other. The whole assembly is like a peanut butter sandwich rolled into a hollow ball. Some “bread” faces outward and some inward, while the “peanut butter” is sandwiched in between the two spheres of bread.  In biology, these spheres are called micelles, and if they are bi-layered they called vesicles. A vesicle man-made in the laboratory, e.g., for use in the intravenous delivery of drugs, is called a liposome.

Lipids Can Form Naturally Outside of Living Things

Where did the lipids come from?  It had been thought that lipids could only be made by living organisms.  But recent experiments show that when CO, carbon-monoxide (simulating an ancient atmosphere) and H2O, water (simulating a little warm pool) are heated up with minerals currently found in Earth’s crust, lipids can form… on their own.  42

 When lipids are placed in water, the hydrophobic (water fearing) tails aggregate to form micelles and vesicles, with the hydrophilic (water loving) ends facing outwards.43

Primitive cells likely used self-assembling fatty-acid vesicles to separate chemical reactions and the environment. Because of their simplicity and ability to self-assemble in water, it is likely that these simple membranes predated other forms of early biological molecules. 44 As a result, some biologists tend to equate the words “micelle” and “vesicle” with the term protocell.

The “Salt Problem”

 Until recently, however, scientists discounted the idea that lipid spheres in water could have been the first protocell membranes, because the water we are talking about was most certainly seawater, and the salt in seawater tends to destroy lipid structures. Science concluded that lipid spheres could not exist in the oceans. 45

But in 2019, researchers at the University of Washington showed that [even in saltwater] lipid spheres do not disassemble if they are in the presence of amino-acids. As Arvin Ash says, “So, there is a synergy, almost a symbiosis, between the lipids and the amino-acids – they help each other survive in salty oceans. The cell membrane, now stable, allows the amino-acids to concentrate and join to form proteins.” 46

Later, in multicellular organisms, encapsulation of each cell protects each cell from its neighbors, which could be ill, aging, or just functionally different. For both unicellular and multicellular organisms the cell membranes must be semi-permeable so that food can get in and waste can be excreted out. Semi-permeability also permits inter-cellular transportation and communication – critical for the health of the larger organism.

Lipid layers also encapsulate enclosed bodies called vesicles that eukaryotic cells have inside them. The larger and more important of the vesicles – e.g., nucleus, mitochondria, and chloroplasts – are called organelles.

Lipid Spheres Often Form Outside Living Organisms

Our aim in this Essay is to show how the chemistry of Life can arise from non-living, inorganic chemistry.  Evidence of this is seen in the fact that lipid spheres are often found in non-living locations of the natural world.

Sea Foam and Soap Bubbles

Spherical Lipid enclosures frequently stack together to form sea foam and soap bubbles. Their spherical shape, and their tendency to self-assemble in layers are natural. There is no outside manipulation, no outside intelligence giving them directions to do this. 47

Sea foam and soap bubbles are made of lipids that had an organic origin as animal fats and algae, including disintegrating seaweeds.

Sea foam, or spume, is created by the agitation of seawater, when it contains concentrations of dissolved organic matter. Due to its low density and persistence, foam can be blown by strong winds blowing from the sea and reaching tidal pools on the beach. 48

In ancient Babylon and Sumer, people made soap by mixing ashes with water and fat and boiling them.  Their soap was actually a soap solution, or soapy water. A froth of small soap bubbles looks a lot like a slice of living tissue looks under a microscope.  49

Just like the lipid membranes we discussed above, “A soap molecule consists of a polar ionic hydrophilic (water “loving”) end, and a non-polar hydrophobic (water “hating”) end. When dissolved in water, the soap molecules arrange themselves in the form of roughly spherical aggregates of 60 or so molecules, called surfactant micelles.

The Walls of Geodes Enclose Crystals

Geodes are another example of inorganic chemicals – rock minerals, in this case – that form enclosures permitting ordered structures to grow inside them. Beautiful crystals can grow from slow precipitation on the inside of the hollow rocks, creating geodes. While it is forming, every geode is completely enclosed by a protecting rock barrier-wall which acts a lot like the cell membrane that surrounds every living cell.

Geode Containing Amethyst Crystals

Geode Containing Amethyst Crystals

While sea foam and soap bubbles are still made of lipids, which usually have had their origin in some sort of formerly living organism, rock geode crystals are clearly not byproducts of living things. Yet, geology is able to form enclosures that permit ad protect ordered structures to grow inside them, just like living cells do. Later in this Essay, we will describe the Silicate-clay Crystals Model (Hypothesis) for the Origin of Life.

The crystals inside geodes form by the partial filling of geological vesicles (hollow cavities) in volcanic and sub-volcanic rocks with minerals deposited from hydrothermal fluids such as mineral-rich water.

Note: Forts and castles and ancient cities and kingdoms also have surrounding walls. So do wasps’ nests, and insect cocoons. The “keep,” the inner fort inside a medieval castle wall, is like the nucleus in a eukaryotic cell.

Many crystals in geodes are shaped like hexagonal columns that point inward toward the center of the geode. Often, such a six-sided column will begin to taper to a faceted point. How is that “decided”? How does each of the six faces “know” to start doing that at the same time, so that the point is reached at the center of the column? The crystal has no brain with which to decide or to know; but the behavior is clearly life-like.

Crystals in General Are Like Living Organisms

The same lifelike growth, symmetry, and apparent coordination can be seen in crystals that form outside geode enclosures. In many ways, all crystals behave like living things.  Later in this Essay, we will discuss how inorganic crystal faces may have been the templates on which organic molecules were first able to form.

A crystalline structure is any structure of molecules or atoms that are held together in an ordered, three-dimensional arrangement. (Non-Crystalline structures are called amorphous.) 50

Like living things, we know that crystals grow over time. They often grow out of a slow flow of mineral-rich dripping water in underground caves. Water flow and/or evaporation provide the energy flow. Crystals often take place when the water is supersaturated with dissolved minerals.

A sudden trigger – like a landing speck of dust, can trigger a cascade of crystallization. (For more about triggering systems, See our Essay, Complexity and Continuing Creation.)

Crystal growth in minerals is a non-organic, but structured, emergence.  It is a kind of “chemical evolution,” involving lattices, templates, and the repetitive reproduction of layers. (See the articles on Crystal Structure and Crystallization in Wikipedia.)

Crystals Are Not Alive, But They Are Able to Form a Structure and Grow

Crystals consist of a regular, geometric lattice of atoms.  Each crystal lattice can grow if it is placed in water laced with the same chemical components. The adjacent free-floating atoms bump into and automatically attach themselves to the crystal edge, enlarging the crystalline form.

Even outside of geode enclosures, mineral crystals are one type of lifelike geo-chemical systems. We will discuss crystals more in our sections on aminos-acids and on ribonucleic acid (RNA).

Crystals may have irregularities where the regular atomic structure is broken, and when crystals grow, these irregularities may propagate, creating a form of self-replication of crystal irregularities. 51

This quick description of crystals, both inside and outside of geodes, show us that there are natural systems in geology and inorganic chemistry that, while clearly not alive, not even biological, have features that are analogous to the features of living organisms.  We might call them “Lifelike” geo-chemical systems.

There Are Crystals Inside Living Things

Not only do crystals act like living things, key molecules of living things — amino-acids, proteins, nucleic-acids, RNA and DNA – can all adopt important crystalline structures.  52

Diatoms Make Silica Cell Walls that Are Similar to Crystals

Since quartz crystals and many other mineral crystals are primarily made of silica (i.e., of silicon-dioxide) it worth noting that tiny single-celled living creatures called diatoms form their outer cells walls using silica. In other words, diatoms make their outer walls out of a mineral that also makes up rocks. 

Diatoms are a type of micro-algae found in oceans, waterways, and soils worldwide. Like green plants and green algae, diatoms convert light energy to chemical energy by photosynthesis, although this shared capability evolved independently in both lineages.

Diatoms generate about 20 to 50 percent of the oxygen produced on the planet each year,53 Diatoms take in over 6.7 billion metric tons of silicon each year from the waters in which they live, and constitute nearly half of the organic material found in the oceans. The shells of dead diatoms can reach as much as a half-mile (800 m) deep on the ocean floor. 54

Diatoms Have Silicate Cell Walls

The silica cells walls of diatoms are called frustules. These frustules have structural coloration due to their photonic nanostructure, prompting them to be described as “jewels of the sea” and “living opals.” The frustule is both hard and porous and is coated with a layer of organic substance composed of several types of polysaccharides. 55

The frustule’s structure is usually composed of two overlapping sections that allow for some internal expansion room and is essential during the reproduction process. The frustule also contains many pores and slits that provide the diatom access to the external environment for processes such as waste removal and mucilage secretion.

Seashells Are Mineral Structures Made by Living Creatures

Analogous to the outer walls of diatoms, seashells are also mineral. Thus, while we usually think of minerals as something that organic processes use to make living things, seashells are the opposite – they are minerals made by living organisms. Seashells, however, are not crystalline.

The Evolution of Beauty

Diatoms, like mineral crystals, seashells, and flowers, display many geometric shapes and/or colors. These shapes and patterns show that evolution, when conditions are right, is quite capable of producing geometrical beauty.

Humans also find beauty in the plumage of birds, the fur of animals, and the coloration of tropical fish and coral reefs. Some

Birds and Flowers Have Evolved Beauty

biologists argue that there is a tendency in evolution toward beauty, primarily because it influences the selection of mates. It is also possible that the evolution of flower-beauty to attract birds, co-evolves with the evolution of bird-beauty to attract mates. The two evolutionary mechanisms reinforce each other. Working together, both trends would produce more flowers and more birds. If so, this co-evolution is very much like catalysis in chemistry, because the mutual reinforcement stimulates the speed of production. We talk about catalysis later in this Essay.

Biologists have written best-selling books around this topic, including Professor Sean B. Carroll’s Endless Forms Most Beautiful 56 and Professor Richard O. Prum’s The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World – and Us.  57

Liquid Crystals

Liquid crystals (LCs) are a state of matter which has properties between those of conventional liquids and those of solid crystals. For instance, a liquid crystal may flow like a liquid, but its molecules may be oriented in a crystal-like way.” (See the Wikipedia article on Liquid Crystal.)

“Examples of liquid crystals can be found both in the natural world and in technological applications. Widespread Liquid-crystal displays use liquid crystals. Many proteins and cell membranes are liquid crystals. Other well-known examples of liquid crystals are solutions of soap and various related detergents, as well as the tobacco mosaic virus, and some clays.” (Wikipedia article on Liquid Crystal.)

In 2007, a team led by the University of Colorado at Boulder and the University of Milan discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth. 58

CU-Boulder Physics Professor Noel Clark said the team found that “surprisingly short segments of DNA, life’s molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that “self-orient” parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA-like or RNA-like molecules in a prebiotic ‘soup’” solution of ancient organic molecules. 59

Supra-molecular Assemblies

We can generalize even further. Liquid crystals and soap bubbles are both examples of Supramolecular assemblies. So are biological membranes, liposomes, colloids, biomolecular condensates, lattices, micelles, and even helical liquid crystals such as RNA and DNA. 60 In such ensembles, their chemical composition is not solely responsible for their unique properties. Rather, their unique properties also depend heavily on their specific ordered spatial structures. For more on this topic, see our Essay, Complexity and Continuing Creation.

All these structures are held together by loose (noncovalent) chemical bonds are weaker than the bonds that hold atoms together to construct a molecule. All these structures are held together by loose (noncovalent) chemical bonds, which are weaker than the bonds that hold atoms together to construct a molecule. There are so many structures and systems today that are alive, or at least act like they are alive, that a modern interdisciplinary branch of science, Supramolecular Chemistry, studies all of them together. 61

Supramolecular Chemistry specializes in non-covalent interactions. These weak and reversible forces—such as hydrogen bonds, hydrophobic forces, van der Waals forces, and metal–ligand coordination—are key to understanding biological processes and self-assembling systems. 62

Key Molecule #2 in Creating Life – Amino-acids: How a Cell Does Its Work

Now we turn to the second of Four Key Components of Abiogenesis (the Origin of Life), which are amino-acids. Amino-acids can chain themselves together to build the cell’s large protein molecules, which are the workhorses of the cell.

The key elements of an amino-acid 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. 63

Short chains of amino-acids molecules are called peptides, and a polypeptide is a longer chain of between 15 to 50 amino-acids.

The amino-acids are the cell’s builders – they make the proteins.  The amino-acids and the proteins do most of the work in the cell, principally including its metabolism.

As the main part of proteins, amino-acids are the second-largest component (water is the largest) of human muscles and other tissues. 64

Beyond their role in proteins, amino-acids participate in a number of processes such as transmitting nerve signals and in building complex molecules out of simple ones (biosynthesis).


A polypeptide that contains more than approximately 50 amino-acids is known as a protein. Proteins consist of one or more polypeptides arranged (‘folded”) in a biologically functional way. 65

In modern cells, proteins are formed within tiny cellular “machines” called Ribosomes, which we will discuss more fully a bit later.

The proteins break down food and build up tissues. They are used for structural support, storage, transport, cellular communication, response to stimuli, movement, defense against foreign substances, and elimination of waste. Together, most of these processes are part of the grand process called cellular metabolism. The proteins even build the RNA and DNA molecules needed for reproduction. (See the Wikipedia article on Amino-acids.]

Protein Folding

Each protein exists first as an unfolded polypeptide, after being translated from a sequence of Messenger RNA into a linear, loosely coiled chain of amino-acids. At this stage, the protein polypeptide lacks any stable (long-lasting) three-dimensional structure.

A protein isn’t functional until it has been folded from a random-coil shape into its native three-dimensional shape. It is the three-dimensional shape that is able to present a certain surface that “fits with” the shape of another molecule. Only when the fit is accomplished can the biochemical process move forward.  66

Note the similarity between protein-folding and the way that mineral crystals naturally grow.  It is also analogous to the way that silicate-clay crystals can act as templates for the formation of biomolecules, as we discuss below in our section on The Silicate-Clay Model cellular evolution.

Large catalytic molecules called chaperones assist protein folding.” This fact further supports the argument that life evolved naturally from non-living (inorganic) chemistry.

Protein Crystals

   Crystalized Proteins

Interestingly, proteins can take on crystalline structures.  The “chaperone” molecule just mentioned is itself a huge crystalline structure “The crystal structure of the chaperonin is a huge protein complex.

Prions – Misfolded Proteins. Prions are misfolded proteins with the ability 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, collapsing nearby protein molecules into the same shape. 67

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. 68

Were Amino-acids the First Key Molecule to Evolve?

Many scientists hold that the amino-acids and proteins evolved before “Key Molecule #3,” the nucleotides. This view is sometimes called the “Protein-World Model,” which can be paired with the “Warm Little Pond Model.” A more recent and more accepted model is that the Nucleotides and RNA evolved first, i.e., before the amino-acids.  It is also possible that amino-acids and RNA coevolved together.  We will discuss these and other models later in this Essay.

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, lights, heat, electricity, etc. Darwin further proposed that a protein compound was then chemically formed ready to undergo still more complex changes. 69

Modern living things, both animals and plants, require oxygen to “burn” their cellular food (sugars) and thus obtain their energy. However, today’s atmospheric oxygen would have “burned away” any synthesis of Earth’s first organic molecules, which are the building blocks of life. Therefore, it has long been thought that early Earth had a “reducing” atmosphere, meaning it contained almost no oxygen. Instead, it was made up of gases such as hydrogen, carbon monoxide, methane, and hydrogen sulfide.

The Miller-Urey Experiments – 1950’s

In the 1950’s, several experiments by Drs. Stanley Miller and Harold Urey verified 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. 70

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. Continuous electrical sparks were fired between the electrodes to simulate lightning in the water vapor and gaseous mixture, and then the simulated atmosphere was cooled again so that the water condensed and trickled into a U-shaped trap at the bottom of the apparatus. 71

The liquid in the Miller-Urey U-shaped trap 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.

Societal Reactions to The Miller-Urey Experiment

Societal reactions to the Miller-Urey experiment varied widely. On the one hand, religious Fundamentalists looked at Miller-Urey’s results and said, “Okay, they got a few amino-acids, but how did but how did the myriad of 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, “Okay, Miller and Urey successfully produced a few amino-acids, but how did the myriad of known 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 types of reactions are still applied today, and not just to the question of Life’s origin, but scientific progress of all kinds, including the origin of Earth and the origin of human beings.

Updating the Miller-Urey Experiment – 1960’s

The Miller-Urey experiment did inspire many others. Notably, professors Juan I Oro and A.P. Kimball found that many amino-acids are formed from HCN and ammonia under these conditions. 72

Additional Updating to Miller-Urey — 2008

In 2008, a group of scientists 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. They found that Miller’s volcano-like experiment had produced the most organic molecules — 22 amino-acids. 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.” 73

Key Molecule #3 in the Origin of Life – Nucleotides

The nucleotides are our third “Key Monomer.”  Nucleotides are the simple molecules (monomers) that join to make the long molecular chains (polymers) named nucleic-acids – specifically, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).  A single DNA polymer molecule contains all 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 phosphorous. These chemical elements – C, O, H, & P — are the same as the elements that make up amino-acids, except nucleotides have added phosphorous.  (Biochemists usually say that nucleotides consist of three “sub-units” of chemical elements: a sugar, a nitrogen base, and a phosphates group.)

Just as important as the addition of phosphorous is the fact that the molecules in nucleotides are arranged in different patterns from the molecules of amino-acids. Their different three-dimensional shapes or patterns allow them to do different jobs inside the cell.

Nucleotides join to make DNA

The nucleic-acids DNA and RNA are found in abundance in all living things. Inside each organism, they encode, store, and transmit the distinct design information of that organism. They also transmit and express that information to the interior operations of the cell, as well as to the next generation of the organism.

The DNA polymer molecule, often described as a “double-helix,” looks like a spiral ladder with a great many “rungs.” Strings of nucleotides are bonded to form the long twisting “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 ladder is composed of adenine-thymine (AT) or guanine-cytosine (GC). Each base pair in an RNA half-ladder 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.)

How RNA Passes Genetic Information to a New Generation

If a DNA molecule is alternatively pictured not as a spiral ladder, but as a long “twisted zipper,” an RNA molecule can roughly 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 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 steps in those molecules. The order makes the code, just as the order of letters makes the words of a language, and the order of zeros and ones makes the code of a computer program. 

Related Terminology:  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 manual from start to finish would be the genome. Almost every creature’s genome, chromosomes and genes are organized in the same way.

Crystalized DNA

Earlier, we remarked that proteins can assume a crystalline form. DNA, the long twin-ladder molecule that contains our genetics code, can also be a crystal.  “DNA crystals form when a double helix is suspended in liquid that evaporates. They grow in patterns dictated by the information stored within the strands. Seen in cross-polarized light, they display a mind-bending kaleidoscope of color and shape.  The huge range of crystal structure is amazing.” 74

How RNA Passes Construction Information for Making Amino-acids

We’ve said that DNA contains all the genetic information of an organism and passes it on to the next generation. Just as importantly, inside each organism, the long RNA half-ladder also delivers genetic “blueprints” directing the cell how to make its own amino-acid building blocks. The cell does this by passing RNA “blueprints” to the cell’s ribosomes, which are the “molecular machines” that build amino-acids. The RNA that does this delivery work is called “messenger RNA” (mRNA).

The human genome (23 chromosomes) is estimated to be about 3.2 billion base-pairs long and to contain 20,000–25,000 distinct protein-coding genes. 75

The Origin of Nucleotides

So, how did nucleotides originate?  And which came first, the amino-acids or the nucleotides? Science continues to pursue the answers to these questions.  We don’t yet have answers, but we do have models that are supported by scientific evidence.

The nucleotides that make the nucleic acids DNA and RNA appear to be products of evolution.  It is believed that the first 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.

Today, the RNA-World Model (i.e., RNA-World Hypothesis) is ascendent because many scientists think that the nucleotides, chained together to form RNA (a simpler form of DNA), could have originally performed both functions – protein building and genetic coding. 

The Joan Oró i Florensa Nucleotide Experiments – 1960’s

In the 1960’s, the previously mentioned experiments conducted by teams led by Professor Joan Oró i Florensa found that  RNA and DNA nucleobases could be obtained through simulated prebiotic chemistry with an non-oxygen, i.e., a reducing, atmosphere. For example, Dr. Oró 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 Nicholas V. Hud of Georgia Institute of Technology (GIT) in 2016 showed that plausible proto-nucleotides can be formed in simulated early Earth environments. 76

The Georgia team reported that the 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. 77

The Czech Nucleotide Experiments – 2017

Recall that in our recent section on the emergence of amino-acids, we described the Miller-Urey experiment done in the 1950’s. Originally, 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, using a simple reducing mixture of NH3 + CO and H2O. But 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 shock waves.

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. 78

Ribosomes — “Tiny Cellular Machines”

Now we want to take a moment to discuss ribosomes, because in modern cells they work in between our first key molecule, amino-acids, and our second key molecule, nucleotides.  More specifically, ribosomes are mostly made out of RNA, while on the other hand they make (manufacture) most amino-acids.

For decades now, 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 the enzyme molecules, are segments of genetic nucleotide chains messengered out of the nucleus as messenger-RNA (mRNA). Each ribosome is a tiny cellular machine that moves along a particular segment of the mRNA, 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.” 79

Note: Catalysis is the process by which a substance speeds up a chemical reaction without being consumed or altered in the process. Substances that can accomplish this remarkable feat are termed catalysts and are of immense importance in chemistry and biology. In biology, sequences of amino-acids compose the enzymes with the aid of catalysts.  https://www.britannica.com/science/catalysis/Biological-catalysts-the-enzymes.

It is important to know that catalysis also happens quite often in non-living (inorganic) chemistry. This is yet another piece of clear evidence showing that the cellular processes of life arose naturally from the processes of standard inorganic chemistry. Supernatural intervention is not required.

Since ribosomes are not surrounded by a membrane, they are not organelles like the much larger nucleus and mitochondria are. 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 in this manner build the structure and conduct the operations of most chemical processes inside the cells of all life forms.

Cellular Machines and Structural Cell Biology

Modern ribosomes are an example of “cellular machines.” Cellular Machines are multi-component macro-molecules that carry out essential biological processes inside individual cells. Another type of cellular machine are the   macro-molecules that make the little tails (flagella) that certain bacteria use to propel themselves through the water. There are hundreds of types of cellular machines at work inside cells. 81

Synthetic Biology

Another new field, Synthetic Biology, uses our 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.” 82

Synthetic Biology Creates a Vaccine for the Covid-19 Virus

Covid-19 Virus

                      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 mRNA.  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. 83

We have now described the first three of the four monomers that are key in starting life – lipids, amino-acids, and nucleotides. It is remarkable that all three are mostly composed of oxygen, hydrogen, nitrogen and carbon (plus a bit of phosphorous in the third of them). The different characteristics and powers of these molecules lie in how those chemical elements are arranged and connected.  As we say repeatedly in the Book of Continuing Creation, the key to creation is the combining of components to create wholes that are remarkably new and different. 

Does “self-replication” or “reproduction” ever occurs outside of life, in the realm of inorganic chemistry?  Yes, it does!  We addressed these phenomena is our prior Essay.    

Key Molecules for Life #4 – Food Molecules for Energy

This brings us to the fourth of Four Key Components of the Origin of Life (Abiogenesis), which are the various molecules that cells bring in from outside to fuel the cell’s housekeeping, repair, and construction. In other words, we are talking about “food” molecules, water, and often (but not always) some gas such as oxygen or carbon-dioxide from the sea or from the air.

Let’s start by looking at what we humans (giant multi-celled creatures composed of trillions of cells) take in on behalf of our individual cells.  We take in (eat) food, we take in (drink) water, and we take in (breathe) oxygen from the air. All three of those inputs go into our bloodstream, which delivers them to our individual cells.

The food, of course, must first be broken down in our stomachs and intestines, because it has to be turned into simple molecules that the individual cells can handle.  An important and common molecule is the simple sugar, glucose.

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 in called Cellular Respiration. 84

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

6 Glucose+ 6 Oxygen yields 6 Carbon-dioxide + Water + energy
C6H12O6 + 6O2  produces 6CO2 + 6H20 + energy
In this reaction, Glucose donates the electrons and Oxygen accepts the electrons.

(See Khan Academy, “Introduction to Cellular Respiration and Redox.”)

It is called a “redox” reaction because the glucose (a simple sugar monomer) is “oxidized” to 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 ATP.)

Humans have an intuitive understanding of oxidation because we have seen fires use 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 that are the end-products of combustion.

Note — Below is more detailed biochemistry nomenclature for readers who have an interest:

  • A “Redox (Reduction-Oxidation) Reaction” between two participants ia 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 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. 85

Readers will recall that the 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). 86 Whatever the actual mix, the early atmosphere was exceedingly hot. Any oxygen that had been present would have soon be used up by burning away many of the more populous hydrogen and hydrocarbon molecules.

This early atmosphere is quite suitable for organisms that do a different type of cellular respiration, namely non-oxygen using anaerobic respiration.  We know this type of respiration was possible, because this method is still used today by many unicellular organisms, principally Archaea, that often live in 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 like those at Yellowstone. https://en.wikipedia.org/wiki/Anaerobic_respiration

Most scientists think that Earth’s First Life, the Last Universal Common Ancestor,” had an anerobic (non-oxygen using) metabolism like so many of today’s archaea have. Today’s archaea would be descendants of that 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. Shortly, we will talk about how that evolutionary switch most likely happened.

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 lesser ability to accept electrons than oxygen has. Since fewer electrons travel, less energy is released per each reaction.
Anaerobic respiration is therefore less efficient than aerobic respiration; except, of course, when oxygen is scarce.  87 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. 

An Example of Early Anerobic Respiration

For purposes of illustration, let’s say that the First Cell (or even the first protocell) consumed raw, elemental Sulfur and used it as its electron acceptor.  If so, then Hydrogen wa likely used as the electron donator.

Note: Although sulfur is primarily found in sedimentary rocks and sea water, it is particularly important to living things because it is a component of many proteins. 88

“Sulfur-eaters” – Anaerobic Respiration of Sulfur

Here is the equation for the anaerobic respiration of Sulfur by Sulfur-reducing microorganisms:
Hydrogen + Sulfur yields Hydrogen-sulfide
H2 + S yields H2S
Hydrogen is the “food” or “fuel” that is donating electrons, and Sulfur is the electron acceptor.
Since Sulfur has accepted electrons, the Sulfur has been “reduced.”

Note that 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.”

In our example, the end-product, Hydrogen-sulfide (H2S), is a gas having the foul odor of a rotten eggs. Several types of bacteria and many archaea can reduce elemental sulfur. 89

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. 91

Today, many species of archaea and 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 largely in microorganisms from extreme environments, and previously unknown microorganisms found there in recent years. 92

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 Kidd Mine in Canada discovered sulfur-breathing organisms which live 7900 feet below the surface, and which “breathe” sulfur in order to survive. These organisms are also remarkable due to consuming minerals such as pyrite as their food source. 93

Anaerobic Respiration of Organic Foods

Microbes also anaerobically take in organic foods – such as grains, grapes, dead plants and animals. The ones that “eat” grape and grain sugars use the anerobic process fermentation, which has alcohol as a by-product. (Yeast, which is a microbial fungus, can also do this.) The microbes that “eat” dead swamp plants and landfill garbage often have smelly hydrogen sulfide gas as a by-product, as well as methane (from which they get the name methanogens). There are even bacteria in the human gut which 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, “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 respirated anaerobically, when there is no oxygen available in the blood.  But the anaerobic path only produces one-third the energy (measured in molecules of adenosine triphosphate, ATP) as the aerobic path. ATP molecules are what directly fuels our cells. Also, the anerobic path produces lactic acid instead of water and carbon-dioxide; and 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 protein. 94

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 oceans 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 O2 was made possible largely by the cyanobacteria, which we will discuss in our following Essay, The Rise of Multicellular Life.

It is important to understand that multicellular animals, including humans, make good use of the “triple energy” they get from the aerobic respiration of their food. They (we) use much of the energy for locomotion. Animal creatures can swim, crawl, walk, climb and swing, glide, and fly.  We do this to hunt for food, escape predators, outrun natural disasters, and to escape wars and other forms of adverse competition.  (Of course, many bacteria and protists also move around, but not as much as most animals do.) We plan to will take up the Evolution of Multicellular Life in subsequent (as yet un-published) Essay.

To summarize, what can we say about the creation of the four Key Molecules of Life? 

Here’s what Professor Hazen wrote in 2012 about his work with the Carnegie Institution (and sponsored by NASA) to create the Four 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 95

If the Carnegie Institution’s results continue to be confirmed, they provide strong support for the “Deep-Hot Model” of the Origin of Life. We will talk more about that model (and other models of life’s origin) later in this Essay.

How the Four Key Molecules Work Together

This is the section where we talk about how all 4 of the Key Monomers — the lipids, amino-acids, nucleotides, and the various food molecules evolved to work together to make 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 important 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 as the RNA World Model.

The “RNA-World” Model

In modern living things, RNA is created from DNA when the DNA “unzips” down its long center to form two strings of RNA. Then, segments from one of the halves, Messenger-RNA (mRNA), travel to the cell’s ribosomes and give them the “blueprints” for specific proteins. Lastly, special enzymes in the ribosomes manufacture the proteins.

The mRNA Model points out, however, that there likely were no ribosomes at the time of the protocells, because ribosomes are quite complex.  Instead, the Model argues that the mRNA did both the work of modern DNA and the work of modern ribosomes.

Since RNA is simpler than DNA, model proponents think the first RNA likely evolved before the first DNA. This idea is central to the widely accepted “RNA-World Model” (i.e., RNA-World Hypothesis). The Kahn Academy has an excellent online lesson and written presentation about “RNA World’ —  Go to https://www.khanacademy.org/science/ap-biology/natural-selection/origins-of-life-on-earth/a/rna-world

In 1982, it was discovered that the simpler (“unzipped”) half of DNA, called RNA, is capable of doing, alone, both of these 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. 96

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 protein-constructing molecule, whereas in modern cells these functions are divided between DNA and ribosomal enzymes.

The RNA-World model also argues that life on Earth began with a simple RNA molecule that could copy itself without help from other molecules. “RNA-World” is a hypothetical early stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA.

To repeat, because early RNA is now thought to have done both these jobs – manufacture proteins and pass genetic information on to the next generation — most scientists think life as we know it began in an RNA-World; a world which at first had no DNA or proteins even in it. 97

It is proposed that the first strands of RNA likely 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, RNA strands grew faster than they broke down—and this was RNA’s foot in the door. 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. 98

Of course, alternative chemical paths to original life have been proposed. 99 Even so, the evidence for an early RNA-World Model is strong enough that the hypothesis has gained wide acceptance. 100

How and Why Did Ribosomes Evolve?

If early RNA could make amino-acid molecules by itself, how and why did ribosomes evolve?

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 101

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. 102

The enzymes that now make protein inside ribosomes may have come to replace RNA-manufacturing because the enzymes came to be more abundant and versatile. This is supported by the fact that the ribosomes’ own structure contains characteristics from both nucleotides and amino-acids. 103

How and Why did DNA Evolve?

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. 104

Note: Sometimes, the term “RNA-World” is 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 resulting 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 await additional research. They will be difficult 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% the same, DNA-wise. (By contrast, we are only about 99 percent the same as our closest relatives, chimpanzees.) 105

Twenty-first 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 of transplanting hand-crafted genomes into living cells.

In 2009-10, Professor Gerald Joyce’s 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 evolve106

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. 107

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

  1. Artificially produced cell-like lipid microspheres and micro-injected them with amino-acids;
  2. Made a rudimentary artificial mitochondrion (a cellular machine that manufactures the ready-energy ATP molecules that provide ready energy on demand quickly power to muscles);
  3. Isolated 17 natural enzymes from 9 different organisms that together can perform photosynthesis more simply and efficiently than real photosynthesis can;
  4. 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. 108  doi: https://doi.org/10.1038/d41586-018-07289-x

Chemical Evolution

Science tells us that before life began there must have been a process of chemical change, a process of chemical evolution that preceded the process of life’s biological evolution. 109 While the details are still unknown, the prevailing scientific hypothesis is that the transition from non-living to living entities was not a single event, but an evolutionary process of increasing complexity that involved “chemical evolution.” Chemical Evolution is a new term, and while it has various definitions, it covers the chemical creation of the Three Four Monomers we discussed above – lipids, amino-acids, nucleotides, and the various food molecules.

As Dr. Nick Lane has written, “…The distinction between a ‘living planet – one that is geologically active – and a living cell is only a matter of definition. There is no hard and fast dividing line. Geochemistry gives rise seamlessly to biochemistry.” 110

Professor Robert Hazen expressed a similar viewpoint when he wrote: “Molecular evolution, not intelligent design, is by far the fastest and most reliable path to achieving function. (That’s why we say that if God created life, she’s smart enough to have used evolution.)” 111 This premise is consistent with the Book of Continuing Creation’s definition of evolution as a set of linked processes that start with the evolution of stars and planets (if not earlier) and go all the way through the “human-agented” evolution of culture and technology.

Inorganic Chemistry, by Itself, Often Behaves a lot Like Life:

The modern term “chemical evolution” has to do with the inorganic (non-carbon-based) molecules that are the precursors of life. We will talk about them shortly.

However, simple observation of Nature, plus some high school chemistry and geology, reveal instances of non-biologic growth and pattern formation that seem very much like the growth and patterns found in

This River Delta is structurally similar to Branching in Lungs

biological organisms. Many of us have observed that the branching patterns of river tributaries and the branching patterns of river deltas are highly similar to what trees do with roots and branches, and to the branching patterns of veins and arteries in human bodies.(See our Essay, Patterns of Information – How Creating Works.)

The mathematical series known as the Fibonacci Sequence (where, starting with “1, 1, 2, 3, 5, and 8…” each new integer is the sum of the previous two integers) produces the decidedly inorganic spirals of countless great rotating galaxies. And this same number sequence also produces the organic spiral arrangement of the seeds in sunflowers, and the spiral shape of a snail’s shell. (See our Essay, Mathematics and Continuing Creation.)

High School chemistry taught us that the 92 natural chemical elements have combined to produce thousands of inorganic chemical compounds. Then, a subset of those same elements continue on, working with geology, to evolve organic chemistry with its even larger cornucopia of organic compounds and millions of different living species, each occupying a different niche in the environments of Earth.

Amazingly, the human body is up to 60% water (H2O) by weight, and all four of the “Key Monomers” discussed in this Essay– lipids, amino-acids, nucleotides, and (for aerobic organisms) monosaccharides — are mostly composed of the same chemical elements: carbon, hydrogen, oxygen, sulfur, and sometimes potassium.  But those elements are arranged in different patterns that make the cornucopia of organic compounds found in living things. 112

What is “Chemical Evolution”? 

As we mentioned, the term “chemical evolution” has not been clearly defined. 113

  • Some scientists adopt a narrow definition and say that chemical evolution is mostly about the following three types of processes seen in the life-like chemistry that can be found among inorganic molecules: 1) molecular self-replication, 2) self-assembly, and 3) autocatalysis. Some of these people elect to include the formation of lipid spheres (e.g., sea foam) in this definition.
  • Other scientists take a broader view. They say that Chemical evolution is the formation of complex organic molecules from simpler inorganic molecules through chemical reactions in the oceans during the early history of the Earth. “It was the first step in the development of life on this planet. The period of chemical evolution lasted less than a billion years.” [dictionary.com]

This second definition is almost the same as the definition of Abiogenesis, which we talked about earlier. But this definition of chemical evolution has organic molecules as its endpoint, whereas Abiogenesis has an actual First Living Organism as its endpoint.  114

Where Do We Come Out on the Definition of Chemical Evolution? 

The theme of our book, Nature’s Path of Continuing Creation, is that Evolution is the grand construction of complexity from the Big Bang all the way through the evolution of cultures and technology. 

Yes, this grand construction can be divided into stages for ease of discussion, but in fact all the stages, steps, and processes are highly interrelated.  Moreover, there are many principles and processes of evolution that are common to all its steps and stages.  A key example is the principle that the combination of things that are identical (or at least similar) can result in the creation of something amazingly new and different.  (For more on this principle and others, see our Essay, The Processes of Evolution – and Their Spiritual Meaning.)

Chemical Catalysis

Catalysis is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst. Catalysts are not consumed in the catalyzed reaction but can act repeatedly. Often, only very small amounts of catalyst are required to achieve a quick and/or massive result. 115

Chemical Catalysts are often used to speed up commercial chemical processes. The global demand for commercial chemical catalysts in 2010 was estimated at approximately US$29.5 billion. 116

Three Examples of Catalysis in Inorganic Chemistry:

  1. The “Contact Process” speeds up the manufacture of sulfuric acid: When sulfur-dioxide gas is passed, together with air, over a solid vanadium-oxide catalyst, its conversion into sulfur trioxide is speeded up.
  2. The Haber Process uses iron as a catalyst to speed the reaction of hydrogen and nitrogen to make ammonia.
  3. The exhaust gases of cars are passed over transition-metal catalysts inside catalytic convertors.   The catalysts increase the rate of chemical reactions that turn exhaust pollutants such as carbon monoxide and unburnt fuel into gases and vapors that are less toxic.

When catalysts play a role in the processes of living cells, they are performing biochemistry — chemistry and biology at the same time. In the biochemistry of living organisms, enzymes are protein-based catalysts that act in the processes of cell metabolism. Most biocatalysts are enzymes, but other non-protein-based classes of biomolecules also exhibit catalytic properties. (See https://en.wikipedia.org/wiki/Catalysis#Illustration.)

The many instances of chemical catalysis demonstrates that inorganic non-living systems can self-organize, and can self-reproduce, in a way that is a harbinger of the ways that living organisms self-organize and reproduce.

An Example of a Catalyst in All Living Cells — The Citric Acid Cycle

The Citric Acid cycle, also called the Krebs Cycle, is a complex series of catalytic chemical reactions used by all aerobic organisms to release stored energy through the oxidation of carbohydrates, fats, and proteins. The net result of these reactions is the production of adenosine triphosphate (ATP) which is used to drive actions such as muscle contraction, nerve impulse propagation, and chemical synthesis. 117

Autocatalysis — Same Definition for Both Inorganic and Organic Chemistry

A single chemical reaction is said to be autocatalytic if one of the reaction products is also a catalyst for the same or a coupled reaction that happens later. This definition holds for both inorganic chemistry and organic chemistry happening inside living organisms.

A set of chemical reactions can be said to be “collectively autocatalytic” if a number of those reactions produce, as reaction products, catalysts for enough of the other reactions that the entire set of chemical reactions is self-sustaining given an input of energy and food molecules (For more, see autocatalytic set).

Catalysts act as scaffolds and templates for new constructions of themselves. In this way, they are like crystals.

Autocatalytic Networks and RAFs

In a 2019 paper abstracted for the Proceedings of Biological Sciences entitled “Autocatalytic Chemical Networks at the Origin of Metabolism,” Bioengineer and Science writer Joana C. Xavier writes:

“Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life’s origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is so far lacking. [In this paper] we identify “Reflexively Autocatalytic Food-generated Networks (RAFs)” — self-sustaining networks that collectively catalyze all their reactions embedded within microbial metabolism…. [RAFs] indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.” 118

Geochemical Evolution — Before Life Evolved

Some say that biological evolution is not the same as chemical evolution because only biological evolution is driven by “natural selection,” a weeding-out process favoring those organisms that have the best chance of survival and reproduction. 

However, the chemical compounds that appear on Earth, and their states of matter (solid, liquid, or gaseous), clearly evolved from Earth’s planetary environment.  They were selected by our planet’s distance from the sun, by its volcanic activity, gravity, temperature, pressure, and its mineral composition.

Earth evolved both its atmosphere, and its oceans.  As the result of gravity and geo-chemistry, Earth’s atmosphere is made up of 78% nitrogen and 21% oxygen, not 96% carbon-dioxide like Venus and Mars, or nearly all hydrogen and helium like Jupiter.  Earth’s modern atmosphere evolved to contain 20% oxygen as the result of trillions millions of cyanobacteria discharging their photosynthetic “waste oxygen” into the air during prehistoric eons.  (We will further discuss this transformation in a sequel Essay.)    

We tend to think of living creatures, even the most primitive of microbes, as the “heroes” of the early biological evolution story.  But bacteria and archaea organisms have no brain, make no decisions, have no consciousness with which to “struggle.”  Instead, we should view the processes of evolutionary creation as the hero, the protagonist of the story, even though they also have no central brain.  And this is true not just for biological evolution, but for geological and chemical evolution as well. 

The Driving Force for All Types of Evolution is Increasing Energy Efficiency

If “Natural Selection” is not the driving force behind evolution, what is?

Two well-known scientists – Professors Adrian Bejan and Jeremy England — argue that the driving force is the same in both chemo-evolution and bio-evolution. That driving force is the tendency toward increasing energy-flow efficiency in all open thermodynamic systems, whether they are living or not living. The Book of Continuing Creation agrees with them.

Professor Adrian Bejan’s Constructal Law

In their book Design in Nature, Bejan, with co-writer J. Peder Zane, argue that Earth’s process of evolution uses (creates) microorganisms because they increase the constructive efficiency of energy flow. 

  • Adrian Bejan is Professor of Mechanical Engineering at Duke University, and the author, with J. Peder Zane, of Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization (2013) and many other books. Dr. Bejan has received 16 honorary doctorates from universities in 11 countries. 119

The driving force for both chemical and biological evolution is the drive for constructive energy efficiency. The selection mechanism, for both chemo and bio evolution, is the environment. The “environment” can be geologic and completely inorganic, or it can be almost purely organic, or it can be a mix of the two.    

There is evolution in both geology and chemistry.  In geology, the flow of water across the land evolved to develop small tributaries that gather water into rivers, because that is the most energy- efficient way to gather and move water from high mountains to the low shore. A river delta is much like the branching bronchial tubes in our lungs. They are each the most efficient ways to exhale carbon-dioxide and dispel river water, respectively.

Many animals were selected for swimming by the existence and the nature of Earth’s oceans.  Birds, bats, and some species of dinosaur were naturally selected for flying by the existence and the nature of Earth’s atmosphere.  Why? Because those modes of travel – swimming and flying – provide the most energy-efficient way for those creatures to find and eat foods that were present in those two environments.

Jeremy England’s Theory of Increasing Energy Efficiency

As we have discussed, scientists have had trouble figuring out what could have driven chemicals to evolve the complexity needed for biological functioning. But in 2014, Dr. Jeremy England, physics professor at MIT, showed mathematically that the driving…force for chemical evolution may be hidden in physics… “From a physics point of view, the one thing that distinguishes living things from non-living things is their ability to capture energy and convert it into a fuel which is then burned or undergoes some other chemical reaction to make heat.” 120

  • Jeremy England holds a PhD in Physics from Stanford. He was an Assistant Professor of Physics at MIT until joining the biological products firm GlaxoSmithKline in 2019 as Senior Director of Artificial Intelligence and Machine Learning.

Dr. England talks about what he calls “dissipative” systems. But that’s a clumsy term borrowed from physics that has too many misleading connotations us here. What England talks about are better described as “energy flow-through systems.”  121

An energy flow-through system is a thermodynamically open system that builds a dynamic structure. 122

The structure does this by exchanging energy and matter with its environment. A tornado may be thought of as an inorganic energy flow-through system:  it takes in wind from two or more sides, makes a funnel structure by circling the wind around and around, moving the air faster and faster, and focusing it on a small area of land or sea. Energy flow-through systems stand in contrast to Energy-conservating systems.  123

Trees are organic, biological flow-through systems that raise water to the sky more efficiently than normal evaporation into the atmosphere does, thereby speeding up Earth’s water cycle.

An example of an organic, living energy flow-through structure would be a human being. A human being starts as a fertilized human egg (zygote) that exchanges energy and matter with its environment.  As it does so, it increases the size, complexity, and power of its structure (a human body, a human life), until it ultimately disintegrates (dies) and its heat and organization disperse. “From dust to dust.” (Ecclesiastes 3:20; also in The Funeral Service in the Book of Common Prayer.) 124

In the realm of chemistry, England argues that when exposed to an external source of energy, such as the sun, any group of molecules will restructure themselves to flow-through more energy more efficiently. This, he says, is the driving force for chemical evolution. Over time, this force can result in living organisms, such as those we see today – organisms that are super-efficient at flowing-through energy for constructive purposes. 125.

When oxygen became prevalent in Earth’ seas and atmosphere, many species shifted their respiration chemistry from anaerobic to aerobic processes because the latter is far more as efficient at producing energy (ATM molecules) for construction, repair, motion, and communication within the cell [reference this Essay, earlier]

The presence of atmospheric oxygen permitted the evolutionary rise of oxygen breathing animals. They arose via the processes of evolution because aerobic oxidation produces more energy (or produces the same amount of energy more efficiently) than does anerobic reduction.

We can say that efficient gathering, transporting, and distributing energy for constructive purposes is pretty much a restatement of our own definition of Life, which is: Order, organization, pattern, or structure arising from natural processes (including human-agented ones) and powered by an energy flow – such as sunlight, volcanic heat, motion, and electro-chemical radiation. 

As we have discussed in this Essay, metabolism is all about energy flow. 126 Note the inherent tension between these things: homeostasis and evolution. Energy flows-through, but does not destroy the organism, at least for the span of its lifetime.

A Review of Emergence

We’ve used the word “emergence” several times in this Essay. In fact, our main thrust is to show that First Life likely emerged out of geo-chemistry. “Emergence” is an important concept in modern science, and we discuss it at length in our Essay, Complexity and Continuing Creation.  Readers may want to pause and read it now.

Emergence occurs when an entity is observed to have properties that its parts do not have on their own; properties or behaviors which emerge only when the parts interact in a wider whole.”
— Wikipedia on Emergence

Emergence is the creation of a whole that is qualitatively quite different than the sum of its parts. A bicycle emerges from the union of its parts – wheels, frame, handles, seat, pedals, and so on.  None of those parts, by themselves, can enable a rider to ride down a road. A human body is composed of cells, but none of those cells can pump blood by themselves or see a tree.  Water is composed of oxygen and hydrogen, but neither of those gases, by themselves, have the characteristics of water. Water’s very liquidity emerges only when O and H2 combine (at one atmosphere of pressure and 33-to-211 degrees F).

— The concept, “Mother Nature,” has evolved from biology, consciousness, and human culture

Models of Where, When, and How First Life Arose

So far, we’ve only discussed evolutionary paths that were likely to have been followed in creating the precursors for life, i.e., the Four Key Molecules. But gathering those precursors together does not necessarily mean that it will all function together to do enclosure, respiration, metabolism, and replication. Protocells might only do three of the four, or protocells might perform all four but in primitive ways. In other words, the earliest protocells might have been more like chemical systems than living systems. 127

How did we get just the right sequences of physics, geology, and chemistry to produce a functional First Organism?  What sort of general (and local) environment was required? What materials needed to be at hand? What sort of energy supply?  What temperature and what pressure?

There is not much evidence about how Life got from amino-acids free-floating in water to the first single-celled, membrane-enclosed proto-bacteria, (or proto-archaea) but there are several models (hypotheses) describing where and how First Life was “put together.” Each model has significant support in the scientific community.

One thing all the models will show us is that early life was adaptable. Life is a strong seeker, a powerful explorer. Life finds a way! Not always, but often, and if not often, often enough!  This amazing adaptability has resulted in an incredible diversity of single-celled life forms, and portends even greater abundance of diversity in the realms of multicellular plant and animal life, as we shall see in our next Essay.  

“Extremophiles” — Microbes That Live in the Harshest Environments

Before we look at the eight models, consider where present-day archaea and bacteria are living.  Since they are the simplest organisms we have today, maybe First Life started out in one (maybe more than one) of those environments.

What we find is that modern microbes live in virtually all Earth’s environments today. And since “all” our environments includes some extremely harsh ones, we need to look at those; especially since life most likely started in the early Archaean Eon, when Earth’s intense volcanic activity produced tremendous heat and subterranean pressure.

In fact, most chemotrophs (including the ones we discussed earlier that consume inorganic elements like sulfur and iron) are extremophiles — bacteria and archaea that live in hostile environments, including those of deep Earth.

Since early Earth was much more inhospitable than it is today, this suggests that the first archaea, and/or the first protocells, were also extremophiles. Examples of these Archean Eon extremophile types are as follows:

  • Thermophiles – heat-loving.
  • Psychrophiles – cold-loving.
  • Alkaliphiles – love alkaline conditions.
  • Acidophiles — love acidic conditions
  • Piezophiles, — love high pressure (in the deep oceans or earth).
  • Halophiles – love high salt concentrations.
  • Thermoacidophiles – love both heat and acid. (These are archaea that live around acidic hot springs and in dumps of acidic mine waste.)

It is now known that extremophiles (microorganisms with extraordinary capability to live in the harshest environments on Earth) can specialize to thrive in the deep-sea, ice, boiling water, acid, the water core of nuclear reactors, salt crystals, toxic waste and in a range of other extreme habitats that were previously thought to be inhospitable for life.128

Living bacteria found in ice core samples retrieved from 3,700 meters (12,100 ft) deep at Lake Vostok in Antarctica, have provided data for extrapolations to the likelihood of microorganisms surviving frozen in extraterrestrial habitats or during interplanetary transport. Also, bacteria have been discovered living within warm rock deep in the Earth’s crust. In the laboratory, Metallosphaera sedula bacteria have been grown on meteorites. 129

This variety of acceptable habitats is a good segue to our next section, which talks about the various places on Earth where The Origin of Life may have taken place.

The 8 Models of How and Where First Life Came Together

There are Eight models of where, when, and How First Life got its start.

  1. The Little Warm Pool Model
  2. The Hollow Lipid Spheres or “Protocell” Model (maybe a corollary to warm pool model)
  3. The Iron-Sulfide Cavities or “Tiny Pockets in Rocks” Model
  4. The Clay Hydrogel Model
  5. The Silicate-clay Crystal-surface Templates Model (Cairns-Smith Clay Model).
  6. The Deep-hot Biosphere Model
  7. The Deep-Sea Model (maybe a corollary to Deep-Hot model)
  8. The Panspermia Model

We are going to look at each of these models in turn. The numbers on this list are simply for reference. There is no real chronology or order of importance here. At present, science has no consensus about which of these eight models are the more probable.

There could well have been some combination of two or more of the models. For example, The Warm Little Pool Model (#1) and The Hollow Lipid Spheres Model (#2) may have been two stages of a single model. It is also possible that different models were followed in different geographic locations on Earth.

The Deep-Hot Biosphere Model (#6) could have taken place before one or more of the others, and The Deep-Sea Model (#7) may be an extension or a variant of The Deep-Hot Biosphere Model (#6).  Panspermia, Model #8, could have preceded all the others. Each of the models supposedly results in one single protocell.  In short, perhaps the eight models ought to be called partial models.

Notice that the important “RNA-World Model” is not on this list. That’s because RNA-World is not really about a particular environment on Earth where life most likely started, nor is it about where and how First Life got its molecular food.  RNA World could have happened in any one of the above location-and-food-source models; although it is most often associated with The Silicate-Clay Crystals Model, because, as we shall see, that model provides “templating.”

Whatever the order, the variety of these eight models, all of which have evidence backing them up, testifies to Life’s power to “find a way.”

As Dr. Ian Malcolm, a character in the film Jurassic Park, says: “If there’s one thing the history of evolution has taught us, it’s that life will not be contained. Life breaks free, it expands to new territories, and crashes through barriers painfully, maybe even dangerously, but, uh, well, there it is… Life will find a way.” 130

1. The “Little Warm Pond” Model of First Life

Darwin suggested that simple chemicals in small or shallow bodies of water might spontaneously form organic compounds in the presence of energy from heat, light, or electricity from lightning strikes. These organic compounds could then have replicated and evolved to create more complex forms. 131

Darwin’s “little warm pond” or “little warm pool” remains one of the most suggestive explanations for the origin of life. A classic experiment performed by Harold Urey and Stanley Miller in the 1950s brought the problem of the origin of life, and the “little warm pool,” into the laboratory. 132

The Miller-Urey experiment tried, in part, to simulate Darwin’s small pond of water. But was the original Pond(s) a freshwater pond or a tidal saltwater pool?  Was there a body of water that was calm and peaceful anywhere on Earth during the Hadean Eon?  Wouldn’t a strike of lightning or volcanic action (both simulated by Miller-Urey) disrupt the calmness of the water? Wouldn’t a pool or a pond be too spacious and therefore unable to bring the 4 monomers of life close enough together to form chains and become polymers?

Although Miller had made some of the most essential compounds of life, his experiment did not explain how they and other building blocks – such as nucleotides, which make up DNA – first came together in an ordered way, to form the complex molecules necessary for life. 133

2. The “Hollow Lipid Spheres” Model of First Life

The Hollow Lipid Spheres model is really a corollary to the Warm Little Pond model. If a little warm pond was too big to bring the earliest organic molecules sufficiently close to each other, or provided insufficient protection from outside chemicals and currents, some scientists contend that Hollow Lipid Spheres would have been able to do those two things, because such spheres are often microscopic.

3. The “Iron-sulfide Cavities,” or “Tiny Pockets in Rocks” Model of First Life

Earlier, we explained how organic spheres composed of self-assembling lipid (fat) molecules could have been the first membranes that enclosed the chemical reactions of the single-celled First Organism.

However, some scientists feel that such a lipid membrane would not have been strong for long enough to allow the earliest simple molecules (monomers) that were the building blocks of life to come together and start functioning as a “team.”

The Iron-sulfide Cavities model contends that First Life did not have to form cell membranes (let alone sturdier outer cell walls), because tiny pockets and fissures in iron-sulfide minerals served to confine and protect each cell’s interior cytoplasm.

We know that hot springs on the ocean floor naturally deposit honeycombs made of the mineral iron-sulfide which are shot through with tiny air pockets a few hundredths of a millimeter across. Drs. William Martin and Michael Russell argue that these pockets are the ideal places for life to get started. 134

The iron-sulfide cavities model is clearly complementary with the Deep-hot and/or Deep Ocean models (#6 and #7) discussed below. Taken together, the iron-sulfide plus the surrounding heat may also have speeded up the chemical reactions that join inorganic molecules together into organic ones.

These combined models also argue that life could have started in this way at many locations and could have persisted under many conditions. 135

Of course, one could conceptually combine the lipid model and the mineral pocket model, arguing that First Life got started in iron-sulfide pockets, and then laid their own cells walls up against the inside walls of the iron-sulfide pockets.

Note:  Many Living cells have cell walls in addition to cell membranes. Cell walls are usually, tougher, thicker substances that form just outside the cell membrane. The walls provide additional protection from the outside environment and can also lend structural strength to the cell.  Bone tissue incudes cells whose walls are partly made of calcium. The cell walls of tree trunks and branches are made tough by cellulose, an organic polymer molecule composed of linked sugar units. [wiki on cellulose 3 and 4] Whether cell walls evolved after or along with cell membranes is outside the scope of this Essay.

4. The Clay “Hydrogel” Model of First Life

Clays are thought to do two things, and we will talk about each of them as separate models for the emergence of First Life:

  1. They may isolate and protect proto-organic molecular reactions (e.g., allow chaining), and
  2. They may provide scaffolds and templates for fledgling organic molecules to cling to.

The first of these two models is called the Clay Hydrogel Model, and the second is called the Silicate-clay Crystal-surface Templates Model. This section of the Essay is about the first of these two models.

Professor Dan Luo of the Kavli Institute for Nanoscale Science at Cornell, “proposes that in early geological history, clay hydrogel provided a confinement function for biomolecules and biochemical reactions.” 136

Luo and his team knew that in simulated ancient seawater, clay forms a hydrogel — a mass of microscopic spaces capable of soaking up liquids like the tiny pockets in a sponge. Over billions of years, chemicals confined in those spaces could have carried out the complex reactions that formed proteins, DNA and eventually all the machinery that makes a living cell work. Clay hydrogels could have confined and protected those chemical processes until the membrane that surrounds living cells developed.

“To test the idea, Dr. Luo and his team demonstrated protein synthesis in a clay hydrogel in the laboratory. This experiment showed that synthetic hydrogels could be a non-living, “cell-free” medium for protein production.  137

“The researchers believe that when the spongy material is filled with amino-acids plus DNA, the right enzymes, and a few bits of cellular machinery, they could be able to make the proteins for which the DNA encodes, just as might be done in a vat of living cells. 138

“As supporting evidence, geological history shows that clay first appeared — as silicates leached from rocks — just at the time biomolecules began to form into protocells — cell-like structures, but incomplete — and eventually membrane-enclosed cells. The geological events matched nicely with biological events.” 139

As we know, other scientists previously suggested that tiny balloons of fat or polymers (lipid spheres) might have served as precursors of cell membranes. But clay may be a more promising possibility because biomolecules tend to attach to its surface, and theorists have shown that cytoplasm — the interior environment of a cell — behaves much like a hydrogel. And, Luo said, a clay hydrogel better protects its contents from damaging enzymes (called “nucleases”) that might dismantle DNA and other biomolecules.

5. The “Silicate Crystals” or “Clay Surfaces” Model of First Life

We’ve already discussed how the hard, geometric surfaces of non-living mineral crystals can form and maintain ordered shapes and can make themselves grow.  Order and growth are characteristics of living things, even though crystals are clearly not living!  This suggests that crystals may have been inorganic precursors of life.  There is evidence that this is so.

We have also seen that the “Little Warm Pool Model” suggested that the earliest amino-acids and nucleotides formed in water solutions. But a minority school of scientists say that these monomers, free-floating in water, would have had little chance of combining into the long polymer strands of proteins, RNA, and DNA respectively.

The “Silicate Crystals” or “Clay Surfaces” model suggests that complex organic molecules arose gradually by using silicate crystal surfaces as a template or scaffold. This theory holds that the early simple organic molecules would cling to adjacent layers of a silicate crystal substrate. There, they could join up with others to make longer polymer molecules. In other words, the organic cells may have used the inorganic crystals as a scaffolding or substrate on which to build their “working molecules” – the peptides, proteins, and nucleotides. Or perhaps the crystal surfaces were the templates for linking up chains of peptides, and building the first cell membranes or walls. (See https://sites.google.com/site/originsoflifecarlmont/clay-theory.)

Conceivably, such silicate-clays could have acted as tiny “chemical factories” for processing organic materials into the more complex molecules from which the first life arose. (See  https://sites.google.com/site/originsoflifecarlmont/clay-theory.)

Going further, it is suggestive that silicate-clay crystals can replicate by splitting apart, with one “mother” crystal giving rise to one or more “daughter” crystals. Each crystal can even have its own peculiarities, which it can pass on to its daughter crystals – much like the way the way living things inherit traits from their parents. And sometimes, when a crystal breaks apart, new quirks can be introduced, for instance because of the stress of breaking. This is similar to the processes of reproduction and genetic mutation, which creates new traits in living things.  140

If the “Clay Surfaces” Model holds true, clay mineral crystals were a link between the worlds of inorganic evolution and biological evolution. 141

What Are “Silicate-Clay Crystals”?

Clay, like any silicate, is made up of crystals. Crystals can grow and accumulate out of solutions.  Silicate minerals are the most common of Earth’s minerals, and include quartz, feldspar, and mica.  When common clay is examined under a microscope, it is seen to be composed of tiny silicate mineral crystals. Within each crystal, atoms are arranged in a structure that repeats in a tightly-packed, regular pattern.

An individual silicate crystal in a clay suspension naturally forms and extends itself by attaching “loose” atoms from the watery clay around it, similar to the way that a snowflake forms and grows in a cloud consisting of cold water-vapor. Generally, once a crystal formation starts to take on a shape, it continues to grow along that same pattern. 142 When these crystals are held in a watery suspension, they take on the plasticity characteristic of clay.

The Earliest Silicate-Clay Model

In 1949, the Irish scientist J.D. Bernal suggested that clay minerals may have created a meeting place for life’s first molecules. 143 In the mid-1960’s, organic chemist Alexander Cairns-Smith published a controversial book, Seven Clues to the Origin of Life, laying out his hypothesis that self-replication of clay crystals in solution might have provided a simple intermediate step between biologically inert matter and organic life.

The Cairns-Smith theory also contended that when silicate-clays dry out, flakes of them can be blown about by the wind. If they land somewhere where they again become wet, the pre-organic molecules within them could have resumed their processes in a new location. In this way, pre-life could have spread around large areas of land. [sites.google.com Clay Theory. (See the website https://sites.google.com/site/originsoflifecarlmont/clay-theory.)

Through the next four decades, however, diverse laboratory investigations of silicate clays mediating peptide bond formation had only limited success. The peptide molecules that formed in the laboratory were “over-protected” in the laboratory environment, and thus showed no evidence of inheritance or metabolism.

Contemporary Research on the Silicate-Clays Model – Creating Peptides and Nucleotides

A 2009 study at the Rensselaer Polytechnique Institute in Troy NY did show that current-day RNA could have formed on the surface of clays, which act like a catalyst to bring RNA together. 144

In December 2017, a revised theoretical model developed by Erastova and collaborators[37] suggested that peptides could form at the interlayers of layered clays such as so-called “green rust” in early Earth conditions. According to this model, drying of the layered material should provide the energy and co-alignment required for peptide bond formation. Then, a re-wetting should allow mobilization of the newly formed peptides, and a repopulation of the interlayer with new amino-acids. This mechanism would lead to the formation of peptides that are over 12 amino-acids-long after 15 to 20 consecutive washes. 145

Going Further – Crystal Layers May Have Templated the Genetic Code in DNA

Cairns-Smith’s theory went a lot further than the formation of peptides and nucleotides lying along a silicate crystal surface. He also proposed that a DNA molecule might have arisen as a cross-section down through a set of crystal layers: “In that respect,” the layers are “like a DNA molecule, which has base pairs platelets stacked on top of each other. It is the sequence of this stacking which creates the information.” 146

Rebecca Schulman, a bio-engineer at Johns Hopkins University in Baltimore, Maryland, was able to design a laboratory system in which information is coded in a crystal structure. Rather than using naturally-occurring minerals, Schulman used crystals made of nanometer-scale tiles that were made of DNA.  Schulman found, first through computer simulation and then by experiment, that the DNA tiles could stack up in a particular pattern, effectively encoding information in a crystal structure. She had found a way to represent and copy information, in crystal form. 147

[Picture Citations:  http://universe-review.ca/I11-02-clay.jpg ]

The “Diamond Variation”

Andrei Sommer of the University of Ulm in Germany proposes that a specific type of crystal – the “hydrogenated diamond” – may have been the crystal that was most able to host the Origin of Life on its surface. It is totally non-toxic and completely biocompatible,” he says. “Hydrogenated diamonds” have gained a rigid outer coating of hydrogen atoms from local gas-emitting volcanoes during Earth’s volcanic age.  When a hydrogenated diamond is wetted, the water molecules line up on the surface as if they were frozen into a crystal layer (an analogy might be static electricity making all the hairs on your head stand up. 148

Surprisingly, these crystal water layers do not disappear when the hydrogenated diamond is fully immersed in water. Because this is the only natural material known to exhibit this behavior, Sommer’s team proposes that small organic molecules in the primordial soup landed on hydrogenated diamonds and were helped by its robust crystal water layers into linking together to form proteins and DNA. 149

Support for this idea comes from a recent study that found that certain nucleobases (the building blocks of DNA and RNA) form an organized pattern on the surface of graphite, which is chemically similar to diamond. 150

Summary Comments on the Silicate-Clays Models

The “Silicate Crystals” or “Clay Surfaces” model holds a minority position today. Most scientists who work on the problem of life’s origin focus instead on how simple sugars, amino-acids, and other organic chemicals came together to form nucleic acids and proteins. 151

On the other hand, Professor Robert Hazen, says this: “Many of life’s most vital molecular building blocks stick to virtually any natural mineral surface…. [including amino-acids, sugars, and the components of DNA and RNA]….What’s more, when several molecules compete for the same piece of crystal real estate, they often cooperate and yield complex surface structures of their own.” 152

If crystals do provide the order life needs to arise, that has implications for the possibility for life beyond Earth. Mineral crystals should be common on rocky worlds, even if those planets have chemical environments quite different from our own. 153

6. “Deep-Hot Biosphere” Model of First Life

In 1992 the astrophysicist Thomas Gold proposed the theory that life first developed not on the surface of the Earth, but several kilometers below Earth’s surface, and widely distributed across the Earth .154

The discovery in the late 1990s of nanobes (filament structures that are smaller than bacteria, but that may contain DNA, found in deep rocks) [33] may support Gold’s theory. Gold’s theory posited that the main flow of food to these extremophiles came from primordial methane gas rising out of Earth’s interior mantle.

In a paper called, “The Deep Hot Biosphere,” Gold wrote that “This model holds that the first living things were single-cell microorganisms that were the ancestors of both bacteria and archaea. Gene sequencing studies can be used to reconstruct the bacterial phylogeny (ancestry trees), and these studies indicate that the most recent common ancestor of bacteria and archaea was probably a hyperthermophile (extreme heat-lover) that lived about 2.5 billion–3.2 billion years ago, probably near an underwater volcanic vent or hot springs.

If Gold’s model is correct, the earliest life on land may have been organisms some 3.2 billion years ago. 155

It is also reasonably well established that microbial life is plentiful, today, at depths in the Earth up to five kilometers below the surface. Most of them are extremophile (“loving harsh conditions”) archaea, rather than bacteria, which typically live in more temperate zones near and at the surface. Studies reveal a rich subterranean ecosystem that is almost twice the size of all the world’s oceans. Scientists estimate this subterranean biosphere is teeming with micro-organisms totaling hundreds of times the combined weight of every human on the planet. 156

Methanogens (anaerobic microbes which generate methane as a by-product) have been found in several extreme environments on Earth, including hot dry deserts and buried under kilometers of ice. Microbes making methane were found in a glacial ice core sample retrieved from about three kilometers under Greenland by researchers from the University of California, Berkeley. They also found a constant metabolism able to repair macromolecular damage at temperatures ranging from 293 to –40 °Fahrenheit.  157

There is also molecular, microscopic, and metagenomic evidence that [“iron-eating”] cyanobacteria predominate in deep subsurface rock samples from southwestern Spain. Results suggest that they may play an important role as primary [food] producers within the deep-Earth biosphere. 158

Thermophiles Living around Hot Springs, Geysers and Fumaroles

A thermophile is an organism—a type of extremophile—that thrives at high temperatures between 106 and 252 °F.  Thermophiles are usually microbes, and many are archaea. Thermophiles are found in the decaying plant matter of peat bogs and compost.

Hyperthermophiles are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as the hot springs, geysers, and fumaroles of Yellowstone Park. Hyperthermophiles isolated from hot springs in Yellowstone National Park were first reported by Thomas D. Brock in 1965. Since then, more than 70 species have been established. Many of the hyper-thermophilic archaea require elemental sulfur for growth, including anaerobes that use the sulfur instead of oxygen as an electron acceptor during cellular respiration.

Research has shown that some minerals can catalyze the stepwise formation of hydrocarbon tails of fatty acids from hydrogen and carbon monoxide gases—gases that may have been released from hydrothermal vents or geysers. Since vesicle (lipid sphere) formation requires a higher concentration of fatty acids, some scientists suggest that protocell formation started at land-bound hydrothermal vents such as geysers, mud pots, and fumaroles where water evaporates and concentrates the solution. 159

Thermophiles and hyperthermophiles demonstrate how hardy life can be, and they imply that life can arise on other planets that are not in Earth’s so-called “Goldilocks Zone” of moderate temperatures and pressures. (For more, see: the Wikipedia article, Extremophile.)

7. The Deep-Sea Model of First Life

Today, many thermophile and hyperthermophile microbes flourish in and around the hot volcanic vents at the bottoms of our

A deepsea “Black Smoker”
Hydrothermal Vent

deepest oceans, where Earth’s tectonic plates meet. They form large microbial communities surrounding these undersea vents, making them the primary food source for an entire food chain of more complex multi-cellular creatures, including shrimp and giant tube worms that can be up to 6 feet tall. Many scientists hold that life began in and around these deep-sea hydrothermal vents.

“Black Smokers”

We’ve said that organisms that do chemosynthesis can use inorganic electron donor sources such as hydrogen sulfide, elemental sulfur, ferrous iron, molecular hydrogen, and ammonia or organic sources.

“Black Smokers,” formally known as Hydrothermal Vents, were first discovered in 1979 on the East Pacific Rise, which is the main tectonic plate boundary the runs down the middle of the South Pacific Ocean, and then curves west almost to the tip of India.  160

The most extreme thermophiles, hyperthermophiles, live on the superheated walls of deep-sea hydrothermal vents, requiring temperatures of at least 194° Fahrenheit for survival. An extraordinary heat-tolerant hyperthermophile is “Strain-121,” has been able to double its population during 24 hours in an autoclave at 121 °C (hence its name). 161

The deep-sea organisms discovered around these vents have no access to sunlight, and no hope of doing photosynthesis. Instead, the diverse ecological communities surrounding these vents depend on nutrients found in the dusty chemical deposits and hydrothermal fluids thrown up by the undersea vents. Compared to the surrounding sea floor, however, these communities have a density of organisms 10,000 to 100,000 times greater than the surrounding ocean floor.

Biological Communities Around Deep-sea Vents

The chemotrophic bacteria around the deep-sea vents grow into a thick mat which attracts other organisms, such as shrimp-like amphipods and copepods, which graze upon the bacteria. Larger organisms, such as snails, clams, limpets, shrimp, crabs, tube worms, sea snails, slugs, fish (especially eelpout and cutthroat eel), and octopuses form a food chain of predator and prey relationships above the primary consumers.

Giant Tube Worms
Around Hydrothermal Vents

Giant Tube Worms, which may grow to over 6.6 ft tall in the largest species, often form an important part of the community around a hydrothermal vent. They have no mouth or digestive tract, and like parasitic worms, absorb nutrients produced by the bacteria in their tissues. About 285 billion bacteria are found per ounce of tubeworm tissue. Tubeworms have red plumes which contain hemoglobin. Hemoglobin combines with hydrogen sulfide and transfers it to the bacteria living inside the worm. In return, the bacteria nourish the worm with carbon compounds.


Over 300 new species, including microbes and multicellular animals, have been discovered at hydrothermal vents, including more than 100 gastropod species (sea snails and slugs). 163

The ecological communities around deep-sea vents can sustain such vast amounts of life because at the bottom of the communal food chain are large populations of chemotrophic bacteria that consume water from the hydrothermal vents that is rich in dissolved minerals. A large population of bacteria consumes the sulfur compounds in that water, particularly hydrogen sulfide (a chemical highly toxic to most known organisms) and uses chemosynthesis to produce abundant organic material.

Undersea hydrothermal vents are now often found near volcanically active places, areas where tectonic plates are moving apart at spreading centers, ocean basins, and hotspots. Black smokers (as well as related white smokers) are now known to exist in the Atlantic and Pacific Oceans, at an average depth of 2100 meters. The most northerly black smokers are a cluster of five named Loki’s Castle, discovered in 2008 on the Mid-Atlantic Ridge between Greenland and Norway. 164

Active hydrothermal vents are thought to exist on Jupiter’s moon Europa, and Saturn’s moon Enceladus, and it is speculated that ancient hydrothermal vents once existed on Mars. 165

Biology Has Chemosynthesis and Photosynthesis.  What About “Thermosynthesis?”

Did the microorganisms growing around under-sea hydrothermal vents ever use thermosynthesis, i.e., the heat from those vents, to drive their constructive metabolism?  While there is little concrete evidence of this, Professor Anthonie Muller at the University of Amsterdam has proposed a theoretical mechanism (a model) by which this could have taken place. The components of the biological thermosynthesis machinery would be related to today’s process of ATP synthesis. It also resembles the process by which organic molecules adhere to the surfaces of clay crystals.

Muller proposes that this simple type of energy conversion may have sustained the origin of life, including the emergence of the RNA World. Thermosynthesis also permits, theoretically, a simple model for the origin of photosynthesis. However, no organisms are known at present that use thermosynthesis as a source of energy. 166

Deep-Sea “Iron-Eaters”

In the deep oceans, there are also iron-oxidizing bacteria that derive their energy needs by oxidizing ferrous iron (Fe2+) to ferric iron (Fe3+). [wiki on panspermia]

8. The Panspermia Model of First Life

The discovery of under-sea chemosynthesis revealed that terrestrial life, life on planet Earth, need not be sun-dependent; it only requires water and an energy gradient in order to exist. [wiki on panspermia]

In addition, the discovery of deep-sea ecosystems, along with advancements in the fields of astrobiology, observational astronomy, and discovery of large varieties of extremophiles, opened up a new avenue in astrobiology by massively expanding the number of possible extraterrestrial habitats; and also the possible transport of hardy microbial life through vast distances. 167

 Note: This section of our Essay is largely paraphrased from the Wikipedia article Panspermia, as it appeared in February 2021. The footnotes citing that article’s sources are included at the end of this Essay.

“The chemistry leading to life may have begun shortly after the Big Bang, 13.8 billion years ago, during a habitable epoch when the Universe was only 10 to 17 million years old. Though the presence of life has been confirmed only on the Earth, some scientists think that extraterrestrial life is not only plausible, but probable or inevitable. 168

“From the early 1970s, it started to become evident that interstellar dust included a large component of organic molecules. Interstellar molecules are formed by chemical reactions within sparse interstellar or circumstellar clouds of dust and gas. The dust plays a critical role in shielding the molecules from the ionizing effect of ultraviolet radiation emitted by stars. 169

“The Panspermia Model of First Life is the hypothesis that life exists throughout the Universe, distributed by space dust, meteoroids, asteroids, comets, and planetoids. Distribution may have occurred spanning galaxies, and so may not be restricted to the limited scale of solar systems. 174

“Comets and other icy outer-solar-system bodies are thought to contain large amounts of complex carbon compounds (such as tholins) formed by these processes, darkening the surfaces of these bodies. We know the early Earth was bombarded heavily by comets, possibly providing a large supply of complex organic molecules along with the water and other volatiles the comets contributed.” 175

A 2017 paper from McMaster University in Canada and the Max Planck Institute in Germany showed that the building blocks of RNA could have polymerized in the early Earth using organic molecules from meteorites and interplanetary dust in shallow ponds. The wet/dry cycle of these ponds, they showed, was conducive to RNA polymerization. 176

In January 2018, a study (See https://en.wikipedia.org/wiki/Earliest_known_life_forms) found that 4.5 billion-year-old meteorites found on Earth contained liquid water along with prebiotic complex organic substances that may be ingredients for life. 177

Looking Ahead to Our Next Essay, The Rise Of Multi-cellular Life

In a sequel Essay, likely to be named “The Rise of Multicellular Life,” we will talk about the significant evolutionary events that happened relatively soon after the early single-celled archaea and bacteria had a good foothold on Earth.

For the first time, we have a fossil record to document many of organisms that evolved. For example, we see a fossil record of large bacterial colonies called “mats,” and we have clear evidence of the silica shells left by the diatoms (a species of single-celled protists).

Here is a partial list of the topics we expect to cover in our next Essay, The Rise of Multicellular Life:

  • Evolution of whiptails on bacteria: greater motility
  • The formation of colonies, including some very extensive “mats” of microbes and algae floating on surface waters.
  • The engulfment of some microbes by other larger microbes, with the captured organisms becoming what we now call organelles, including the cell nuclei, mitochondria, and chloroplasts. These enclosures provide the host cell with specialized functions and assume a symbiotic relationship with the host.
  • Evolution of Eukaryotes — Cells that have “captured” other cells to do special functions.
  • The cyanobacteria almost single-handedly create Earth’s oxygenated atmosphere
  • The slime mold: How a single-celled creature can evolve amazing capabilities
  • Networks of transport and communication within colonies.
  • The specialization of cells within a colony
  • The specialization of cells within an organism
  • Photosynthesis among algae and true plants
  • Form changes over life cycles.
  • Sexual Reproduction: An Acceleration of Evolution

  1. Emily Singer, “Mongrel Microbe Tests Story of Complex Life,” 11-30-2015, Quanta Magazine, re-reported in Scientific American https://www.scientificamerican.com/article/mongrel-microbe-tests-story-of-complex-life/.
  2. Guenther Witzany, “Crucial Steps to Life: From Chemical Reactions to Code Using Agents,” 2006, BioSystems. 140: 49–57. doi:10.1016/j.biosystems.2015.12.007. PMID 26723230.
  3. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, a video film, 9-6-2019, www.arvinash.com
  4. Arvin Ash, Abiogenesis How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com
  5. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com
  6. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com.
  7. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com
  8. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books.
  9. 1974, Bantam Books. From Essays that originally appeared in the New England Journal of Medicine between 1971 and 1973. 9 Lewis Thomas, The Lives of a Cell: Notes of a Biology Watcher, 1974, Bantam Books, The Viking Press.
  10. Arjun Berera, “Space Dust Collisions as a Planetary Escape Mechanism,” 11-6-2015, Astrobiology.7 (12): 1274–1282. arXiv:1711.01895. Bibcode:2017AsBio..17.1274B. doi:10.1089/ast.2017.1662. PMID 29148823. S2CID 126012488. See also Wikipedia, Earliest Known Life Forms. See also Wikipedia, “Life on Mars.  
  11. Science Daily, June 16, 2020, from Univ of British Colombia. www.sciencedaily.com/releases/2020/06/200616100831.htm.
  12. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com
  13. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com
  14. Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, 2015, W.W. Norton & Co., pp. 1 and 4-5.
  15. Nancy Kleckner, J.K. Fisher, Mathieu Stouf, et al“The bacterial nucleoid: nature, dynamics and sister segregation” 12-01-2014, Current Opinion in Microbiology. Growth

    and development, 127.137.137. doi:10.1016/j.mib.2014.10.001PMC 4359759PMID 25460806.

  16. “Eukaryotic Chromosome Structure,” | Science Primer”. scienceprimer.com.
  17. Wikipedia article on Unicellular Organism.
  18. M. Di Giulio, “The Universal Ancestor and the Ancestor of Bacteria Were Hyperthermophiles,” Dec 2003, Journal of Molecular Evolution. 57 (6): 721–30. Bibcode:2003JMolE..57..721D. doi:10.1007/s00239-003-2522-6. PMID 14745541. S2CID 7041325. See also, FU Battistuzzi, A Feijao, and SB Hedges SB, “A Genomic Timescale of Prokaryote Evolution: Insights Into the Origin of Methanogenesis, Phototrophy, and the Colonization of Land,” Nov, 2004, BMC Evolutionary Biology. 4: 44. doi:10.1186/1471-2148-4-44. PMC 533871. PMID 15535883.

    See also, Martin Homann, et al.. “Microbial Life and Biogeochemical Cycling on Land 3,220 Million Years Ago,” 7-23-2018, Nature Geoscience. 11 (9): 665–671. Bibcode:2018NatGe..11..665H. doi:10.1038/s41561-018-0190-9. S2CID 134935568. All noted sources are from the Wikipedia article on Bacteria, https://en.wikipedia.org/wiki/Bacteria

  19. Robert M. Hazen, Ibid., p. 134.
  20. https://opentextbc.ca/biology2eopenstax/chapter/structure-of-prokaryotes-bacteria-and-archaea/#:~:text=The%20timelines%20of%20divergence%20suggest,diverged%20from%20the%20archaean%20line.
  21. Hazen, pp.129-130.
  22. Arvin Ash, Ibid.
  23. Arvin Ash, “Abiogenesis – How Life Came from Inanimate Matter,” a video film, 9-6-2019, www.arvinash.com
  24. Juli Peretó, “Controversies on the Origin of Life,” 2005, International Microbiology. 8 (1): 23–31. PMID 15906258. See also, David Warmflash and Benjamin Warmflash, “Did Life Come from Another World?,” Scientific American, November 2005, 293 (5): 64–71. Bibcode:2005SciAm.293e..64W. doi:10.1038/scientificamerican1105-64. PMID 16318028.
  25. https://www.livescience.com/32983-what-are-ingredients-life.html.
  26. https://www.livescience.com/32983-what-are-ingredients-life.html#:~:text=Nonetheless%2C%20all%20organisms%20are%20built,phosphorus%20and%20sulfur%20(CHNOPS)

  27. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books.
  28. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books, p. 131.
  29. Stephen J. Gould, The Lying Stones of Marrakech: Penultimate Reflections in Natural History, 2001, Vintage, pp. 119–121. ISBN 978-0-09-928583-0. See also, Ernst Mayr, Toward a New Philosophy of Biology: Observations of An Evolutionist, 1988, Harvard University Press. p. 499. ISBN 978-0-674-89666-6.
  30. https://en.wikipedia.org/wiki/Permian%E2%80%93Triassic_extinction_event#:~:text=The%20Permian%E2%80%93Triassic%20extinction%20event%2C%20also%20known%20as%20the%20P,approximately%20251.9%20million%20years%20ago.
  31. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books, p. 131.
  32. Linus Pauling Institute, Oregon State University, Corvallis, Oregon. 9-1-2017. See also, “Calcium: Fact Sheet for Health Professionals,” 7-9-2019, Office of Dietary Supplements, U.S. National Institutes of Health.
  33. From the Simple Wikipedia article on “Origin of Life.”
  34. J.F. Kasting, “Earth’s Early Atmosphere, 2-12-1992, Science, Vol. 259, Issue 5097, pp. 920-926.  DOI: 10.1126/science.11536547.
  35. See the Wikipedia article on Unicellular Organism. See also, Andrew Pohorille, and David Deamer, “Self-assembly and Function of Primitive Cell Membranes,” Research in Microbiology 6-23-2009. 160 (7): 449–456. doi:10.1016/j.resmic.2009.06.004. PMID 19580865.
  36. Robert M. Hazen, The Story of Earth: The First 4.5 billion Years, from Stardust to Living Planet, 2013, Penguin Books, p. 128, paraphrased.
  37. Tom Herrmann and Sandeep Sharma, “Physiology, Membrane,” 3-2-2019, StatPearls, SIU School of Medicine, Baptist Regional Medical Center, PMID 30855799.
  38. Arvin Ash, “Abiogenesis – How Life Came from Inanimate Matter,” a video film, 9-6-2019, www.arvinash.com
  39. Arvin Ash, “Abiogenesis,” Ibid.
  40. Arvin Ash, “Abiogenesis,” Ibid.
  41. Arvin Ash, “Abiogenesis,” Ibid.
  42. Ann Taylor and Scott Feller, the entry for “Lipids” in Chemistry Explained, online at http://www.chemistryexplained.com/Kr-Ma/Lipids.html.
  43. Andrew Pohorille and David Deamer, “Self-assembly and Function of Primitive Cell Membranes,” 6-23-2009, Research in Microbiology, 160 (7): 449–456. 
  44. Arvin Ash, Abiogenesis, Ibid.
  45. Arvin Ash, Abiogenesis, Ibid. See also, Caitlin Cornell, Roy Black, Mengjun Xue, et al., “Prebiotic Amino-acids Bind to and Stabilize Prebiotic Fatty Acid Membranes,” Edited by David Weitz, 1-8-2019, Harvard University, Proceeds of the National Academy of Sciences.  https: doi.org/10.1073/pnas.m 1900275116.
  46. Arvin Ash, “Abiogenesis,” Ibid.
  47. Katerina Schilling and Mattias Zessner, “Foam in the Aquatic Environment,” Water Research, 10-1-2011, 45 (15): 4355–4366. ISSN 0043-1354. PMID 21757217.
  48. Wikipedia article on soap
  49. Marauo Davis, “What Is Crystalline Structure,” 5-31-2020. Study.com. https://study.com/academy/lesson/crystalline-structure-definition-structure-bonding.html.
  50. “The Idea that Life Began as Clay Crystals is 50 Years Old,” BBC.com. 2016-08-24. Retrieved 11-10-2019.
  51. Elena Boldryeva, “Crystalline Amino-acids: A Link Between Chemistry, Materials Science and Biology, a paper in Models, Mysteries and Magic of Molecules, J.C. Boeyens and J. Ogilvie, eds., 2008, Springer Dordrecht, DOIhttps://doi.org/10.1007/978-1-4020-5941-4_7. See https://link.springer.com/chapter/10.1007%2F978-1-4020-5941-4_7
  52. “What are Diatoms?” Diatoms of North America. Archived from the original on 25 January 2020. Retrieved 28 January 2020.
  53. P. Treguer, D.M. Nelson, A.J. Van Bennekom, et. al., “The Silica Balance in the World Ocean: A Reestimate,” 1995, Science. 268 (5209): 375–9. Bibcode:1995Sci…268..375T. doi:10.1126/science.268.5209.375. PMID 17746543. S2CID 5672525.
  54. F.E. Round and David J. Chapman, Eds., Progress in Phycological Research: 1991, vol. 7.
  55. Endless Forms Most Beautiful: The New Science of Evo-Devo and the Making of the Animal Kingdom, 2005, W.W. Norton.
  56. Professor Richard O. Prum, The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World – and Us,  2017, Doubleday.
  57. “Liquid Crystal Life,” Astrobiology Magazine, 11-30-2007.  https://www.astrobio.net/origin-and-evolution-of-life/liquid-crystal-life/.
  58. “Liquid Crystal Life,” Astrobiology Magazine, 11-30-2007.  https://www.astrobio.net/origin-and-evolution-of-life/liquid-crystal-life/.
  59. H.Schneider, “Binding Mechanisms in Supramolecular Complexes,” 2009, Angew. Chem. Int. Ed. Engl, 48 (22): 3924–77. doi:10.1002/anie.200802947. PMID 19415701.
  60. J. Lehn, Supramolecular Chemistry,1993, Wiley, VCH. ISBN 978-3-527-29311-7.
  61.   https://softbites.org/2018/02/15/discovery-of-liquid-crystals-in-short-dna/.
  62. 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.
  63. 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.
  64. 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.
  65. J.M. Berg, J.L. Tymoczko, and L. Stryer,  (2002). “Protein Structure and Function,” 2002, Biochemistry, W. H. Freeman. ISBN 978-0-7167-4684-3.  See also, D.J. Selkoe,

    Diagram of a Folded Protein (myoblobin)

    Folded Structure of Myoblobin protein

    “Folding proteins in fatal ways, December, 2003, Nature. 426 (6968): 900–4, bibcode:2003 Natur.426..900S. doi:10.1038/nature02264. PMID 14685251. S2CID 6451881. See also B. Alberts, D. Bray D, K. Hopkin, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, “Protein Structure and Function,” Essential Cell Biology (Third ed.), 2010, Garland Science. pp. 120–70. ISBN 978-0-8153-4454-4.

  66.  Prion Diseases, https://www.hopkinsmedicine.org/health/conditions-and-diseases/prion-diseases. See also, “Prion: Infectious Particle,” Encyclopedia Britannica. Retrieved 15 May 2018. https://www.britannica.com/science/prion-infectious-agent.
  67. C.M. Dobson, “The Structural Basis of Protein Folding and its Links with Human Disease,” Feb. 2001, Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences. 356 (1406): pp. 133–45. doi:10.1098/rstb.2000.0758. PMC 1088418. PMID 11260793. See also: Todd E. Golde, David R. Borchelt, Benoit I Giasson, and Jada Lewis,. “Thinking Laterally About Neurodegenerative Proteinopathies,” 5-01-2013, Journal of Clinical Investigation. 123 (5): pp. 1847–1855. doi:10.1172/JCI66029. ISSN 0021-9738. PMC 3635732. PMID 23635781.
  68. First Life on Earth Archived 2012-06-29 at Archive.today windmillministries.org, Retrieved on 2008-01-18.  See also: Letters of Charles Darwin, written in 1871, published in Darwin, Francis, ed., 1887, The Life and Letters of Charles Darwin, Including an Autobiographical Chapter, Volume 3, London: John Murray.
  69. Arvin Ash, “Abiogenesis,” Ibid.
  70. Stanley L. Miller and Harold C. Urey, “Organic Compound Synthesis on the Primitive Earth.” 1959, Science. 130 (3370): 245–51. Bibcode:1959Sci…130..245M. doi:10.1126/science.130.3370.245. PMID 13668555. See also, Lazcano and J.L. Bada, “The 1953 Stanley L. Miller Experiment: Fifty Years of Prebiotic Organic Chemistry,” 2004, Origins of Life and Evolution of Biospheres.” 33 (3): 235–242. Bibcode:2003OLEB…33..235L. doi:10.1023/A:1024807125069. PMID 14515862. S2CID 19515024.
  71.  Oró J, Kimball AP (August 1961). “Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide”. Archives of Biochemistry and Biophysics. 94 (2): 217–27. doi:10.1016/0003-9861(61)90033-9. PMID 13731263. See also,  Oró J, Kamat SS (April 1961). “Amino-acid synthesis from hydrogen cyanide under possible primitive earth conditions”. Nature. 190 (4774): 442–3. Bibcode:1961Natur.190..442O. doi:10.1038/190442a0. PMID 13731262. S2CID 4219284. See also, Oró J (1967). Fox SW (ed.). Origins of Prebiological Systems and of Their Molecular Matrices. New York Academic Press. p. 137.
  72. Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (October 2008). “The Miller volcanic spark discharge experiment”. Science. 322 (5900): 404.  Bibcode:2008Sci…322..404J. doi:10.1126/science.1161527. PMID 18927386. S2CID 10134423. See also, “Lost’ Miller–Urey Experiment Created More Of Life’s Building Blocks”. Science Daily. October 17, 2008. Archived from the original on October 19, 2008. Retrieved 2008-10-18.
  73. Laura Mallonee, “Turns Out Crystallized DNA Is Crazy Pretty,” 2015, WIRED Magazine, https://www.wired.com/2015/08/linden-gledhill-crystalized-dna/.
  74. L.A. Moran LA (2011-03-24). “The Total Size of the human genome is very likely to be ~3,200 Mb,” 3-24-11, Sandwalk.blogspot.com. Retrieved 2012-07-16. See also, “The Finished length of the human genome is 2.86 Gb,” Strategicgenomics.com, 6-12-2006-06,  Retrieved 2012-07-16. See also, International Human Genome Sequencing Consortium (October 2004). “Finishing the euchromatic sequence of the human genome,” October 2004, Nature. 431 (7011): 931–45. Bibcode:2004Natur.431..931H. doi:10.1038/nature03001. PMID 15496913.
  75. Celia Henry Arnaus,“How the First Nucleotides Might Have Formed on Earth,” Chemical & Engineering News, 4-27-2016.
  76. Celia Henry Arnaud, “How the first nucleotides might have formed on Earth,” Chemical and Engineering News, 4-27-16, referencing the publication: “Spontaneous Formation and Base Pairing of Plausible Prebiotic Nucleotides in Water,” by Brian J. Cafferty, David M. Fialho, Jaheda Khanam, Ramanarayanan Krishnamurthy & Nicholas V. Hud, Nature Communications, volume 7, Article number: 11328 (2016).  DOI: 10.1038/ncomms11328).
  77. their results were published in the 2017 Proceedings of the National Academy of Sciences PNAS 2017; 4-10-2017, DOI: 10.1073/pnas.1700010114.
  78. S. Konikkat  (February 2016). “Dynamic Remodeling Events Drive the Removal of the ITS2 Spacer Sequence During Assembly of 60S Ribosomal Subunits,” February 2016, in S. cerevisiae (Ph.D. thesis). Carnegie Mellon University. See also E.W.  Weiler and L. Nover, (2008). Allgemeine und Molekulare Botanik (in German). Stuttgart: Georg Thieme Verlag. p. 532. ISBN 978-3-13-152791-2. See also J. de la Cruz J, K. Karbstein, and J.L. Woolford, (2015). “Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo”. Annual Review of Biochemistry. 84: 93–129. doi:10.1146/annurev-biochem-060614-033917. PMC 4772166. PMID 25706898.
  79. The ability of electron microscopes to see the atomic structures of molecules has led to the new field of Structural Cell Biology. Powerful microscopy plus crystallography and computational tools are now able to generate testable atomic models of cellular machines. 80 https://www.cell.com/trends/cell-biology/fulltext/S0962-8924(06)00020-1.

  80. http://sitn.hms.harvard.edu/flash/2011/issue88/.
  81. https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html.
  82. https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-respiration-ap/a/fermentation-and-anaerobic-respiration.
  83. https://forces.si.edu/atmosphere/02_02_01.html#:~:text=When%20Earth%20formed%204.6%20billion,carbon%20dioxide%20as%20today’s%20atmosphere.
  84. https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment#:~:text=The%20Miller%E2%80%93Urey%20experiment%20(or,of%20life%20under%20those%20conditions.
  85. https://simple.wikipedia.org/wiki/Anaerobic_respiration.
  86. https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.4%3A_Nutrient_Cycles/16.4F%3A_The_Sulfur_Cycle
  87. Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl DA (2014). Brock Biology of Microorganisms. Benjamin-Cummings Pub Co. pp. 448–449. ISBN 978-0321897398. See also, R. Rabus, TA Hansen, and F Widdel, “Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes,” 2006, The Prokaryotes, 2006, Springer Publishing, pp. 659–768. doi:10.1007/0-387-30742-7_22. ISBN 978-0-387-25492-0.
  88. https://en.wikipedia.org/wiki/Sulfate-reducing_microorganisms, 90 LL Barton and GD Fauque, “Biochemistry, Physiology and Biotechnology of Sulfate-Reducing Bacteria,” Advances in Applied Microbiology, 2009, pp. 41–98. doi:10.1016/s0065-2164(09)01202-7. ISBN 9780123748034. PMID 19426853.
  89.  https://en.wikipedia.org/wiki/Sulfur-reducing_bacteria#:~:text=Acidithiobacillus%20are%20chemolithoautrophics%2C%20Gram%2Dnegative,and%20nitrogen%20from%20the%20atmosphere.
  90. https://www.google.com/url?sa=i&url=http%3A%2F%2Fwiki.biomine.skelleftea.se%2Fwiki%2Findex.php%2FSulfate_reducing_bacteria&psig=AOvVaw0lzzAafSRHXcc93VaXn8L-&ust=1613421722267000&source=images&cd=vfe&ved=0CAIQjRxqFwoTCKjI5bae6u4CFQAAAAAdAAAAABAD, footnotes 2, 12, 13, and 14.
  91.  https://en.wikipedia.org/wiki/Anaerobic_organism#:~:text=An%20anaerobic%20organism%20or%20anaerobe,that%20requires%20an%20oxygenated%20environment.
  92. Robert Hazen, Ibid., p. 135.
  93. https://www.umassmed.edu/rti/biology/role-of-rna-in-biology/
  94. Christopher Packham, “Researchers Produce all RNA Nucleobases in Simulated Primordial Earth,” 4-21-2017, Phys.org News, https://phys.org/news/2017-04-rna-nucleobases-simulated-primordial-earth.html. See also, Walter Gilbert, “The RNA World,” February 1986, Nature 319 (6055): 618. Bibcode:1986Natur.319..618G. doi:10.1038/319618a0. S2CID 8026658.
  95. Khan Academy, RNA World AP.BIO: SYI‑3 (EU), SYI‑3.E (LO), SYI‑3.E.2 (EK)
  96. BH Patel, C Percivalle, DJ Ritson, CD Duffy, and JD Sutherland, “Common Origins of RNA, Protein and Lipid Precursors in a Cyanosulfidic Protometabolism,”April 2015, Nature Chemistry. 7 (4): 301–7. Bibcode:2015NatCh…7..301P. doi:10.1038/nchem.2202. PMC 4568310. PMID 25803468.
  97. Nicholas Wade, Nicholas (May 4, 2015). “Making Sense of the Chemistry That Led to Life on Earth,” 5-4-2015, The New York Times.  See also, SD Copley, E Smith, and HJ Morowitz, “The Origin of the RNA World: Co-evolution of Genes and Metabolism,” Bioorganic Chemistry. 35 (6): 430–43. doi:10.1016/j.bioorg.2007.08.001. PMID 17897696.
  98. M. Root-Bernstein M and R. Root-Bernstein, “The Ribosome as a Missing Link in the Evolution of Life,” February 2015, Journal of Theoretical Biology. 367: 130–158. doi:10.1016/j.jtbi.2014.11.025. PMID 25500179.
  99. “The RNA Origin of Life,” NOVA Labs, https://www.pbs.org/video/nova-labs-rna-origin-life/. See also, Kahn Academy, “The RNA Origin of Life, https://www.khanacademy.org/science/ap-biology/natural-selection/origins-of-life-on-earth/v/originoflife.
  100. Liang Shen and Ji Hong-Fang, “Small Cofactors May Assist Protein Emergence from RNA World: Clues from RNA-Protein Complexes,” 2011, PLOS ONE. 6 (7): e22494. Bibcode:2011PLoSO…622494S. doi:10.1371/journal.pone.0022494. PMC 3138788. PMID 21789260.
  101. R.J. Mackenzie, “DNA vs. RNA – 5 Key Differences and Comparison,” 12-18-2020, Genomics Research from Technology Networks.
  102. “Genome Variations: How Different is One Human Genome from Another?,” Jan 15, 2003, www.genomenewsnetwork.org.,resources, Ch. 4_1.
  103. Robert Hazen, Ibid. pp. 129-30.
  104. 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.”
  105. Kendall Powell, How biologists are creating life-like cells from scratch, Nature Magazine, Nature 563, 172-175 (2018) https://www.nature.com/articles/d41586-018-07289-x
  106. Juli Peretó, “Controversies on the Origin of Life, 2005, International Microbiology. 8 (1): 23–31. PMID 15906258. Archived from the original (PDF) on 24 August 2015. See also, Wikipedia article on Abiogenesis.
  107. Nick Lane (Professor of Evolutionary Biochemistry at University College, London), The Vital Question: Energy, Evolution, and the Origins of Complex Life, 2015, W.W. Norton, p.27.
  108. Hazen, Ibid. p. 147.
  109. See, “What is the Body Made Of,” online at New Scientist.
  110. K Ruiz-Mirazo, C. Briones, and A. de la Escosura, “Chemical Roots of Biological Evolution: The Origins of Life as a Process of Development of Autonomous Functional Systems,” 4-26-2017, Open Biology, The Royal Society Publishing.
  111. Guenther Witzany, Guenther (2016). “Crucial Steps to Life: From Chemical Reactions to Code Using Agents,” 2016, Biosystems. 140: 49–57. doi:10.1016/j.biosystems.2015.12.007. PMID 2672323*0. See also, Elizabeth Howell, “How Did Life Become Complex, And Could It Happen Beyond Earth?, 12-8-2016, Astrobiology Magazine.
  112. Richard I. Masel, Chemical Kinetics and Catalysis, 2001, Wiley-Interscience, ISBN 0-471-24197-0. See also: Louise Lerner, “7 Things You May Not Know about Catalysis,” Argonne National Laboratory, 2011. 
  113.  “Market Report: Global Catalyst Market,” (2nd ed.), Acmite Market Intelligence.
  114. J.M. Lowenstein, Methods in Enzymology, 1969, Volume 13: Citric Acid Cycle, Academic Press. ISBN 978-0-12-181870-8. https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20946. See also L. Kay and P.D. Weitzman, Krebs’ Citric Acid Cycle: Half a Century and Still Turning,1987, Biochemical Society, p. 25. ISBN 978-0-904498-22-6. See also Hazen, Ibid., p. 143.
  115. Joanna C. Xavier, et al., https://pubmed.ncbi.nlm.nih.gov/32156207/.  See also https://royalsocietypublishing.org/doi/10.1098/rspb.2019.2377.
  116. A. Bejan and J. P. Zane, Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization, 2013, First Anchor Books, flyleaf.
  117. Arvin Ash, “Abiogenesis,” Ibid. See also, Jeremy England, “Statistical physics of self-replication,” 2013, The Journal of Chemical Physics (AIP),  http://dx.doi.org/10.1063/1.4818538.
  118. Natalie Wolchover, “A New Physics Theory of Life,” 1-28-2014, Scientific American.
  119. Arvin Ash, “Abiogenesis,” Ibid.
  120. Arvin Ash, “Abiogenesis,” Ibid.
  121. Arvin Ash, “Abiogenesis,” Ibid.
  122. Natalie Wolchover, “A New Physics Theory of Life,” Scientific American, 1-28-2014. See also Santi Tafarella, “Dissipation-Driven Adaptive Organization: Is Jeremy England The Next Charles Darwin?,” 1-28-2014, Prometheus Unbound  See also Arvin Ash, “Abiogenesis,” Ibid.
  123. Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, 2015, W.W. Norton pp. See Lane, 58-62.
  124. Arvin Ash, “Abiogenesis – How Life Came from Inanimate Matter,” a video film, 9-6-2019, www.arvinash.com
  125. Wikipedia article on “Panspermia,” particularly footnotes 163 through 169.
  126. Wikipedia article on “Panspermia,” particularly footnotes 171 through 173.
  127. Jurasic Park, motion picture, 1993, Amblin Entertainment, Universal Studios; Dr. Malcolm was played by Jeff Goldblum;, after the 1990 novel of the same name by Dr. Michael Crichton.
  128. https://www.encyclopedia.com/science/science-magazines/did-life-earth-begin-little-warm-pond.
  129. https://www.encyclopedia.com/science/science-magazines/did-life-earth-begin-little-warm-pond.
  130. Martha Henriques, “The Idea that Life Began as Clay Crystals Is 50 Years Old” 8-24-2016, BBC.
  131. W. Martin and M. Russell, “On the Origins of Cells: A Hypothesis for the Evolutionary Transitions from Abiotic Geochemistry to Chemoautotrophic Prokaryotes, and From Prokaryotes to Nucleated Cells,” Philosophical Transactions of the Royal Society, B, published online at Nature.com. doi:10.1098/rstb.2002.1183 (2002). https://www.nature.com/news/2002/021202/full/news021202-2.html.
  132. John Whitfield, “New Theory for Origin of Life: Mineral Cells Might Have Incubated First Living Things,” Nature, 12-4-2002, doi:10.1038/news021202-2. See also, Roldane, N. Hollinsworth, et al., “Bio-inspired CO2 Conversion by Iron Sulfide Catalysts Under Sustainable Conditions,” Royal Society of Chemistry, 3-24-15. https://pubs.rsc.org/en/content/articlehtml/2015/cc/c5cc02078f.
  133. D. Luo, D. Yang, S. Peng, and G.Q. Lu, “Enhanced Transcription and Translation in Clay Hydrogel and Implications for Early Life Evolution,” Scientific Reports, 11-7-2013; https://www.nature.com/articles/srep03165.
  134. Paraphrased from Bill Steele’s article, “Before Cells, Biochemicals May Have Combined in Clay,” 11-7-2013, Cornell Chronicle, Cornell University.
  135. Bill Steele, Ibid.
  136. Bill Steele, Ibid.
  137. Martha Henriques, “The Idea that Life Began as Clay Crystals is 50 Years Old,” 8-24-2016, BBC.
  138. Leslie March, “Life’s Crystal Code,” 3-19-2009, www.space.com.
  139. https://sites.google.com/site/originsoflifecarlmont/clay-theory. See also Martha Henriques, “The Idea that Life began as clay crystals in 50 years old, 8-24-2016, BBC.
  140. Leslie Mullen, “Life’s Crystal Code,” www.space.com.
  141. Arvin Ash, “Abiogenesis,” a video film, Ibid.
  142. V. Erastova, MT Degiacomi, D. Fraser, and HC Greenwell, “Mineral Surface Chemistry Control for Origin of Prebiotic Peptides,” December 2017, Nature Communications. 8 (1): 2033. Bibcode:2017NatCo…8.2033E. doi:10.1038/s41467-017-02248-y. PMC 5725419. PMID 29229963.
  143. Leslie Mullen, “Life’s Crystal Code,” www.space.com]
  144. Martha Henriques, Ibid.
  145. Michael Schirber, “Diamonds May Be Life’s Birthstone,” Space.com, 9-25-2008,  https://www.space.com/5882-diamonds-life-birthstone.html.
  146. Michael Schirber, Ibid.
  147. Michael Schirber, Ibid.
  148. Leslie Mullen, “Life’s Crystal Code,” www.space.com, 3-19-2009.]
  149. Robert Hazen, Ibid., p.138.
  150. Leslie Mullen, “Life’s Crystal Code,” www.space.com, 3-19-2009.
  151. D.R. Colman, S. Poudel, et.al, The Deep, Hot Biosphere: Twenty-five Years of Retrospection,” Proceeding of the National Academy of Science, (PNAS), 7-03-2107, https://www.pnas.org/content/114/27/6895. See also, https://doi.org/10.1073/pnas.1701266114.
  152. Martin Homann, et al., “Microbial life and Biogeochemical Cycling on Land 3,220 Million Years Ago,” 7-23-2018, Nature Geoscience,11 (9): 665–671. Bibcode:2018NatGe..11..665H. doi:10.1038/s41561-018-0190-9. S2CID 134935568; from the article, “Bacteria,” on Wikipedia, https://en.wikipedia.org/wiki/Bacteria.
  153. Jonathan Watts, “Scientists Identify Vast Underground Ecosystem Containing Billions of Micro-organisms,” The Guardian, 12-10-2018, https://www.theguardian.com/science/2018/dec/10/tread-softly-because-you-tread-on-23bn-tonnes-of-micro-organisms.
  154. HC Tung, NE Bramall, PB Price, 2005, “Microbial Origin of Excess Methane in Glacial Ice and Implications for Life on Mars,” Proceedings of the National Academy of Sciences, 102 (51): 18292–6. Bibcode:2005PNAS,10218292T. doi:10.1073/pnas.0507601102. PMC 1308353. PMID 16339015.
  155. F. Puente-Sanchez, A. Arce-Rodrigues, et al., Viable Cyanobacteria in the Deep Continental Subsurface, Proceedings of the National Academy of Sciences, 10-1-2018, https://www.pnas.org/content/115/42/10702. From Wikipedia, “Earliest Known Life Forms.”
  156. Carl Zimmer, “What Came Before DNA,?” Discover Magazine, 6-26-04.
  157. Sean Chamberlin, “Black Smokers and Giant Worms,” 1999, Fullerton College, Retrieved 2-11-2011. See also, Brent C. Christner, 2002, “Detection, Recovery, Isolation, and Characterization of Bacteria in Glacial Ice and Lake Vostok Accretion Ice,” 2002, Ohio State University.
  158. Office of Legislative Affairs, “Microbe from Depths Takes Life to Hottest Known Limit,” 8-14-2003, National Science Foundation, https://www.nsf.gov/od/lpa/news/03/pr0384.htm.
  159.   A.V. 22  Sysoev, A. V.; Kantor, Yu. I. (1995). “Two new species of Phymorhynchus (Gastropoda, Conoidea, Conidae) from the hydrothermal vents” (PDF). Ruthenica. 5: 17–26. From the Wikipedia article, “Hydrothermal Vent.”
  160. “Extremes of Eel City,” Astrobiology Magazine. 28 May 2008. See also, A. V. Sysoev and Y.I. Kantor, (1995). “Two New Species of Phymorhynchus (Gastropoda, Conoidea, Conidae) From the Hydrothermal Vents,”1995, at Ruthenica. 5: 17–26. See also, S. Botos, “Life on a Hydrothermal Vent,” Hydrothermal Vent Communities.
  161. Live Science Staff, “Boiling Hot Water Found in Frigid Arctic Sea,” LiveScience, https://www.livescience.com/9588-boiling-hot-water-frigid-arctic-sea.html.
  162. Kenneth Chang, “Conditions for Life Detected on Saturn Moon Enceladus,” 4-13-2017, New York Times. See also, “Spacecraft Data Suggest Saturn Moon’s Ocean May Harbor Hydrothermal Activity,” NASA, 3-11-2015. See also, M. Paine, “Mars Explorers to Benefit from Australian Research,” 5-15-2001, Space.com. Both references from Wikipedia article, “Hydrothermal Vent.”
  163. For 19 separate footnote references to Dr. Muller’s scientific papers on this topic, see the Wikipedia article on Thermosynthesis.
  164. C. Mileikowsky, F.A. Cucinotta, J.W. Wilson, et al., “Natural Transfer of Microbes in Space, Part I: From Mars to Earth and Earth to Mars,” 2000, Icarus, 145 (2): 391–427. Bibcode:2000Icar.145..391M. doi:10.1006/icar.1999.6317. PMID 11543506.
  165. From Wikipedia article on “Panspermia.”
  166. A. Dalgarno, A. “The Galactic Cosmic Ray Ionization Rate,” 2006, Proceedings of the National Academy of Sciences. 103 (33): 12269–73. Bibcode:2006PNAS..10312269D. doi:10.1073/pnas.0602117103. PMC 1567869. PMID 16894166. See also, Laurie Brown, Abraham Pais, and A.B. Pippard, “The Physics of the Interstellar Medium,” 1995, Twentieth Century Physics (2nd ed.), p. 1765. ISBN 978-0-7503-0310-1.
  167. Seth Shostak, “Comets and Asteroids May Be Spreading Life Across the Galaxy – Are Germs From Outer Space the Source of Life on Earth?,”10-26-2018, NBC News. See also, Idan Ginsburg, M. Lingham, and Abraham Loeb, “Galactic Panspermia,” 11-19-2018, The Astrophysical Journal Letters. 868 (1): L12. arXiv:1810.04307v2. Bibcode:2018ApJ…868L..12G. doi:10.3847/2041-8213/aaef2d. S2CID 119084109. 170

    “Although computer models suggest that a captured meteoroid would typically take some tens of millions of years before collision with a planet, there are documented viable Earthly bacterial spores that are 40 million years old that are resistant to radiation, and others able to resume life after being dormant for 100 million years, suggesting that lithopanspermia life-transfers are possible via meteorites exceeding 1 m in size.171 Edward Belbruno; Amaya Moro-Martı´n, et.al., “Chaotic Exchange of Solid Material between Planetary [Systems],” 2012, Astrobiology. 12 (8): 754–74. arXiv:1205.1059. Bibcode:2012AsBio..12..754B. doi:10.1089/ast.2012.0825. PMC 3440031. PMID 22897115. See also, “Impacts ‘More Likely’ to Have Spread Life from Earth,” 8-23-2011, BBC. See also, Yuki Morono, Motoo Ito, et. al., “Aerobic Microbial Life Persists in Oxic Marine Sediment As Old as 101.5 Million Years,” 7-8-2020, Nature Communications. 11 (1): 3626. Bibcode:2020NatCo..11.3626M. doi:10.1038/s41467-020-17330-1. ISSN 2041-1723. PMC 7387439. PMID 32724059. 172

    “Conditions similar to those of the Miller–Urey experiments are present in other regions of the solar system, often substituting ultraviolet light for lightning as the energy source for chemical reactions. The Murchison meteorite that fell near Murchison, Victoria, Australia in 1969 was found to contain over 90 different amino-acids, nineteen of which are found in Earth life. 173 M.A. Line, “Panspermia in the Context of the Timing of the Origin of Life and Microbial Phylogeny,” 2007, International Journal . Astrobiol. 3. 6 (3): 249–54. Bibcode:2007IJAsB…6..249L. doi:10.1017/S1473550407003813. See also,  Wickramasinghe, D. T.; Allen, D. A. (1980). “The 3.4-µm Interstellar Absorption Feature,” Nature. 287 (5782): 518–19. Bibcode:1980Natur.287.518W. doi:10.1038/287518a0. S2CID 4352356. See also,

    Allen, D. A.; Wickramasinghe, D. T. (1981). “Diffuse Interstellar Absorption Bands Between 2.9 and 4.0 µm,” 1981, Nature. 294 (5838): 239–40. Bibcode:1981Natur.294..239A. doi:10.1038/294239a0. S2CID 4335356.

  168. D.T. Wickramasinghe, and D.A. Allen, D. A. (1983). “Three Components of 3–4 μm Absorption Bands,” 1983, Astrophysics and Space Science, 97 (2): 369–78. Bibcode:1983Ap&SS..97..369W. doi:10.1007/BF00653492. S2CID 121109158. See also, Fred Hoyle, Chandra Wickramasinghe & John Watson, Viruses from Space and Related Matters, 1986, University College Cardiff Press.
  169. Arvin Ash, “Abiogenesis,” Ibid.
  170. Queenie H.S. Chan, et al. (10 January 2018). “Organic Matter in Extraterrestrial Water-bearing Salt Crystals,” 1-10-2018, Science Advances. 4 (1, eaao3521): eaao3521. Bibcode:2018SciA….4O3521C. doi:10.1126/sciadv.aao3521. PMC 5770164. PMID 29349297.  See also, Staff, Lawrence Berkeley National laboratory, 1-10-2018, “Ingredients for Life Revealed in Meteorites that Fell to Earth – Study, Based in Part at Berkeley Lab, Aso Suggests Dwarf Planet in Asteroid Belt May Be a Source of Rich Organic Matter”AAAS – EurekAlert. Retrieved 11 January 2018.

Leave a Reply

Your email address will not be published. Required fields are marked *