To personify Nature, the best choice is an artist’s rendition of Mother Nature, or “Gaia”

Abiogenesis: Evolution of First Life on Earth

(Essay #14, at 6-23-25) 

This is the third of our four (#12 to #15) interrelated Essays on Earth’s geochemical origin of life and its subsequent Evolution.
Here are the titles of those four Essays:

Essay #12 — Chemical Precursors to Life on Earth
Essay #13 — The Organic Molecules & Processes that Form Life
Essay #14 — Abiogenesis: Evolution of First Life on Earth 
Essay #15 — Where Life Began: Warm Pools?  Black Smokers?

Another of our Essays is also quite important — “The Processes of Evolution in Biology, Culture, & Technology” — because it describes the kinds of evolution happening all around us, here and now, in biology, culture, and technology.  It explains how all these processes provide us with secular-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.  However, the universe exists, and evolutionary processes are at work on Earth. As these processes evolve, they generally become more complex, as they likely do on other planets when planetary conditions are suitable.  (For more on Deism, see our Essay, “Forerunners to Our Path & Practice.”)

In any case, the above four Essays about the Origin of Life are integral to the Book of Continuing Creation. Charles Darwin’s “On the Origin of Species,” published in 1859, and all the evolutionary science that followed are forerunners to this book about Nature’s Path of Continuing Creation.

At the time of this writing (2024), there are up-to-date published sources available that brilliantly present the latest scientific knowledge about the Origin of Life. Listed below are four sources that readers may want to turn to before (or while) they read our series of four Essays.

         Recommended Outside Sources

> 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. ¹

> Abiogenesis – How Life Came from Inanimate Matter. This 12-minute short film, made and narrated by polymath Arvin Ash, presents the basic story with clarity and superb moving illustrations. This film is available on the Arvin Ash website, arvinash.com. ²

> 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. ³

The current Wikipedia article on Abiogenesis is a detailed review of the current scientific knowledge 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.”).

The above-recommended outside sources indicate that the scientific community’s intense focus on the Origin of Life will constantly update our knowledge over the next decades. Our four Essays in Nature’s Continuing Creation draw on all of the above sources and a good number of others.

Note: 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 suggests that between 4.1 and 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 essential ingredients for life. ⁴

We Oppose Fundamentalist, Biblical Creationism 

(Note: This Section is largely repeated from Essay #12, “Chemical Precursors to Life on Earth.”)

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 produce 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 also say that the odds of creating a protein molecule by chance are only 1 in 10 to the 45th power. ⁵

The Religious Creationists fail to recognize three things: First, chemicals can combine to make organic molecules. Second, organic molecules can combine to make more complex inorganic molecules. Third, #1 and #2 happened, step by step, over hundreds of millions of years.   

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 open to new knowledge.  Biblical Creationism is often closed to new knowledge; it seems to be afraid of what it does not know.

Biblical creationists charge that we have “faith” in science, that we have made a religion out of science, and 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 Nature’s Continuing Creation 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 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?  ⁶

People who are determined to keep their traditional faith in a supernatural God should ask themselves this: Which is more powerful, more creative?

1. A God who decrees human life into existence, or…
2. The Sum of all the Interacting Processes of Continuing Natural Creation. Processes that include the laws & rules of physics, chemistry, and biology, such that intelligent life will emerge from them on at least some of the six billion Earth-like planets all across the Milky Way Galaxy.

We Also Oppose “Progressive Evolution”

Some readers may accuse the Book of Continuing Creation of being another argument for orthogenesis — the biological hypothesis that organisms have an innate tendency to evolve in a definite direction toward some goal (a teleology) due to an internal plan that aims at an outcome. A more modern term for orthogenesis is Progressive Evolution. ⁷

However, a trend is not a goal, and certainly not a predetermined one. We 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.

A more modern term for orthogenesis is Progressive Evolution. ⁸ 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 create larger and more efficient paths of energy flow.  

We agree with Professors Bejan and England. We do not see increasing complexity as a goal.  Or as an inevitability. We view it as a tendency when the environment is right, 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.)

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. Nevertheless, we know that life did recover, and it continued to evolve, including the eventual evolution of mammals and humans. ⁹

Comparing This Essay to our “Processes of Evolution” Essay

Our related Essay, The Processes of Evolution & Their Meaning, is likely just as important as the four Essays in our first list because it describes the evolution that is happening all around us, here and now, in biology, culture, and technology.  All three of those arenas provide us with evidence of evolution and its meaning.

While we understand that a Deist “Clockmaker-God” may have started the universe, we can’t prove it up or down.  However, the universe exists, and evolutionary processes are at work on Earth. As these processes evolve, they generally become more complex, as they likely do on other planets when planetary conditions are suitable.  (For more on Deism, see our Essay, “Forerunners to Our Path and Practice.”)  In fact, Darwin’s On the Origin of Species, published in 1859, and all the evolutionary science from then until now, are forerunners to this book about Nature’s Continuing Creation.

A Quick Review of “Emergence”

We will use the word “emergence” several times in this Essay. In fact, our primary objective is to demonstrate that First Life likely originated from geochemical processes. “Emergence” is an important concept in modern science, and we discuss it at length in our Essay, “Complex Systems, Evolution, & Transcendence.”  Some Readers may elect to pause and read that Essay 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 individual cells can pump blood or see a tree.
— Water is composed of oxygen and hydrogen, but neither of these gases has the liquidity of water on Earth’s natural surface pressure and temperatures. 

Life Arose from Non-Living Chemistry

While there is no single, generally accepted theory of the origin of life, all credible proposals suggest that life, under natural conditions, could have evolved through a slow process of chemical and molecular evolution, resulting in simple forms of life over a long period of time. This chemical evolution was probably the biggest hurdle for life to have occurred on Earth. ¹⁰

Once this happened, biological evolution took over and relatively quickly resulted in an exceptional diversity of life forms. We observe this in the fossil record of early Earth, and, of course, we see it on Earth today.  Do we have proof that this is how life originated?  No… at least not yet. Is it plausible?  Absolutely.  ²⁵

Still, respected scientists such as Stephen Meyer and James Tour argue that even a single living cell exhibits such an astounding, incredibly complex organization that it cannot be explained by laboratory assemblies of energized chemicals. They think that a cell’s complexity and coordinated complexity can only be explained by “intelligent design.” To quote one of them, “A code requires a Coder.” But the two Doctors admit they have no idea where the intelligent design came from. From an equally complex universe?  From an overarching mind? From “The Tao?”  No one knows, and we humans may never know.  Both these men think, however, that Darwinian Evolution is the right explanation for how fish, plants, and intelligent human life evolved from a single-celled “First Organism.” (See Peter Robinson’s filmed interview of Drs. Meyer and Tour, “Beyond Evolution: Unraveling the Origins of Life,” published online (YouTube) by the conservative Hoover Institution located on the campus of Stanford University.)  See also our own Essays #13, #14 & #15, listed in our Table of Contents.  

The Essential Features & Processes of Life

(This section is repeated from our Essay #12.)  

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, and evolve. Living things are composed of either a single cell or multiple cells, and they 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:

Life…
> Constructs and maintains a boundary that separates it from the outside.
> Channels a flow of energy through itself (i.e., it is a thermodynamically open system).
> Maintains homeostasis (we have a 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 – Life can change over time in response to changes 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, e.g., to its food. The food cannot enter the organism (nor waste exit it) unless the boundary is semi-permeable.

Note: The boundary must be semi-permeable. It admits some new things and not others. There is an 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.

“Trees of Life” = Trees of Biological Classification (Taxonomy)

So, life comes from geochemistry. 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. Let’s look ahead at the “Big Picture” of Today’s evolved Life, by means of schematic drawings called “Trees of Life.”

      Left: “Evolutionary Tree” of the 6 Domains of Life.           Right: A detailed Tree of the 3 Earliest Domains  

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 above drawing on the left 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.

> Bacteria are ubiquitous, mostly free-living organisms that often consist of one biological cell. 

> Prokaryotes — A domain of Single-cell organisms lacking a nucleus and lacking all other membrane-bound organelles (e.g., chloroplasts).
> Archaea —  A domain of single-cell organisms that for various reasons are not bacteria.
> Eukaryotes  — The domain of all organisms whose cell or cells have a membrane-bound nucleus (i.e., the nucleus has its own cell-wall.) 
> Protists —  A “grab-bag” of organisms who are not animals, nor land plants, nor fungi.  The amoeba and the slime mold are well-known protists.
> Fungi — A Kingdom (a major group within a domain) that includes yeasts, molds, and mushrooms. 

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 (and out of the Human Species) on the upper right of our Tree.  (For more, see our Essay, “Cyborgs, Transhumanism, & Immortality.”)

As of this writing, (2024), there is a wonderful online diagram, “All the Biomass of Earth, in One Graphic,” showing the incredible modern diversity of Life on Earth (over 8.7 million species) broken down by the biomass weight in gigatons of carbon, “Gt-C,” and split out into these 7 groups:

• Plants, 450 gigatons of carbon (Gt-C)
• Bacteria, 70 Gt-C
• Fungi, 12 Gt-C
• Archaea, 7 Gt-C
• Protists, 4 Gt-C
• Animals, 2.6 Gt-C
• Viruses, 0.2 Gt-C

Of course, if we counted the number of individual organisms in each group, we would get a much different distribution.  We leave it to our readers to hunt down that information, as they wish.

Abiogenesis: From Inorganic Chemistry to Organic Chemistry

               “Abiogenesis is when chemistry turned into biology” — Dr. 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 biological evolution. However, if we contend that grand evolution encompasses geology, chemistry, biology, culture, and technology, as we do here in the Book of Continuing Creation, then Abiogenesis is part of that grand evolution. ²⁶

Abiogenesis (informally, “the origin of life”) is the natural process by which life has arisen from non-living matter, particularly from chemical precursors and chemical processes.  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. ²⁷

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.)

To Explain “First Life,” Look 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,  conceptual integrity, which attests to the fact that all life has descended from a single Original Common Ancestor. ¹¹

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 geochemistry. By the same logic, the simplest organisms living today are likely descendants of the very simple First Organism. The simplest organisms we have today are the bacteria and the archaea, at the base of the Tree of the 6 Domains of Life.

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 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. They are microscopic creatures that swim around in water. Typically, only 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. (Multi-celled organisms efficiently share their cell walls with the cells on all sides of them.)

Modern Archaea were first discovered in hot springs and salt lakes, and later 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 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) that conduct specialized processes. Therefore, all archaea and bacteria are classified as prokaryotes. Cells that do have such internal enclosed organelles are classified as eukaryotes. (However, most prokaryotes do have an irregular, unbounded region that contains DNA, known as the nucleoid. ¹² In the nucleoid region of each cell, most prokaryotes have a single, circular chromosome, in contrast to eukaryotes, which typically have linear chromosomes. ¹³

Nutritionally, prokaryote species can utilize a wide range of organic and inorganic materials to power their metabolism, including sulfur, cellulose, ammonia, or nitrite. Today, prokaryotes are ubiquitous across the Earth, even in the most extreme environments. (See the Wikipedia article, “Unicellular Organism.”)

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 — their 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. ¹⁴

As we shall discuss in this set of four Essays, there were likely non-living chemical systems that 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. Also 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).  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. ¹⁵

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. ¹⁶

All other Earthly life – protists, fungi, plants, and animals — evolved out of the bacteria, out of the archaea, or directly out of the Original (or “Un-named”) Ancestor. For more details, 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, the chimpanzee species, the 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 in Biology, Culture, & Technology.”)

What Defines Life?  What Do All the Organisms in all the Domains 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?

Chemistry’s Definition of Life

As we said in the Essay, “Chemical Precursors to Life on Earth,” Robert M. Hazen, Professor of Earth Science at George Mason University, 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, Ibid. p. 128]

A panel at the Scripps Research Institute, chaired by Dr. Gerald Joyce, Professor of Chemical Biology at The Salk Institute, came up with an excellent one-sentence statement of chemistry’s definition of Life, which Joyce later amended to become: “Life is a self-sustaining chemical system capable of incorporating novelty and undergoing Darwinian evolution.” ¹⁷

The First life must have started from non-living matter – because, by definition, “First life” could only be preceded by “non-life.” ¹⁸ The earliest protocells (“pre-living cells”) may not have met all the definitional requirements for life. They may have lacked one or more of the Key Processes of Life. And the chemical systems that evolved even earlier than the first protocells may have barely hinted at what would evolve later.

Autocatalysis — Same for Inorganic & 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 Wikipedia’s article, “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.” ⁵⁰

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

In Essay #1, “Chemical Precursors to Life on Earth,” we discussed Chemical catalysis. Catalysis also happens inside living things. 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. ⁴⁹

Carbon’s natural ability to grow by chaining its own molecules and by combining with other elements shows the tendency of pre-biological, 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.” ¹⁹

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 that 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 human blood is salty because we 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. ²⁰

The Six Basic Chemical Compounds (Molecules) 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: ²¹

• 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 discuss in our Essay, “The Processes of Evolution — In Biology, Culture, & Technology.” Science finds that in the early times around First Life, no organisms breathed in oxygen as we animals do today. ²²

Organic Compounds

Organic compounds are generally 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 that arises from the decomposition of ancient life under the heat and pressure of the 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.  ²³

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 variety 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. (See the Wikipedia article, “Macromolecule.”)

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

#1. Lipid molecules – Lipid 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.  Self-enclosure, providing self-identity and self-protection, is a Key Process of life. The lipids also have other jobs within a cell.

#2. Amino-acid molecules – Amino-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 molecules – Nucleotide 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 energy in 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 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 a food, but they do it without oxygen in a process called fermentation. Fermentation is a type of anaerobic (“non-oxygen-using”) respiration process.

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 (anaerobic) 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.  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 in the form of 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.” ²⁴

In our previous Essay, Essay #2 of this series, we discussed “The Organic Molecules & Processes that Form Life.”

Here in Essay #3, 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) geochemistry. These four types of molecules 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. 

And after that, in Essay #4, we will talk about the 8 Models of Where Life First Began — Warm Pools? “Black Smokers. These 8 models describe the real-world geological forces and locations one (or more) of which or more of which 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. ^{53 25}.

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. ²⁶

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 Secular-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. ⁵⁵ 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).

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. ⁵⁶

The “Salt Problem”

Until recently, 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. ²⁷

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.” ²⁸

Later, in multicellular organisms, encapsulation of each cell protects it from its neighbors, which could be ill, aging, or just functionally different. As we’ve said, 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 intercellular transportation and communication, which are 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.

The Evolution of Beauty

Let’s briefly step aside to remark on The Evolution of Beauty. The diatoms, mineral crystals, and seashells we talked about in Essay #1 in this series of four, “Chemical Precursors to Life on Earth,” 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 flowers, the plumage of birds, the fur of animals, the coloration of tropical fish, and coral reefs. 

Birds & Flowers Evolved Beauty

Some 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 talked about Chemical catalysis in Essay #1 of this Series, “Chemical Precursors to Life on Earth.”

Biologists have written best-selling books on the Evolution of Beauty, including these two:
> Professor Sean B. Carroll’s Endless Forms Most Beautiful: The New Science of Evo-Devo and the Making of the Animal Kingdom (2005, W.W. Norton.)
> Professor Richard O. Prum’s The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World – and Us (2017, Doubleday, 2017. 

Key Molecule #2 – Amino Acids: How a Cell Does Its Work

Now we turn to the second of the 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. ²⁹

Short chains of amino acid molecules are called peptides, and a polypeptide is a longer chain of between 15 and 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. ³⁰

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

Proteins

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. ³¹

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 “mRNA” (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.  ³²

Diagram of a Folded Protein (myoglobin)

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 of cellular evolution. 

Large catalytic molecules called chaperones often assist in 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, causing nearby protein molecules to collapse into the same shape. ³³

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. ³⁴

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, light, heat, electricity, etc. Darwin further proposed that a protein compound was then chemically formed, ready to undergo still more complex changes. ³⁵

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, the atmosphere was made up of gases such as hydrogen, carbon monoxide, methane, and hydrogen sulfide.

The Miller-Urey Experiments – 1950s

In the 1950s, 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. ³⁶

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. The simulated atmosphere was then cooled, allowing the water to condense and trickle into a U-shaped trap at the bottom of the apparatus. ³⁷

The resulting 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.

Social Reactions to The Miller-Urey Experiment

Social 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 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, not just to the question of life’s origin, but to scientific progress of all kinds, including the origin of the Earth and the origin of human beings.

Updating the Miller-Urey Experiment – 1960s

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. ³⁸

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.” ³⁹

Key Molecule #3 in the Origin of Life – Nucleotides

The “nucleotides“ are our third “Key Monomer.”  Nucleotides are simple molecules (monomers) that join to form long molecular chains (polymers), known as nucleic acids – specifically, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).  A single DNA polymer molecule contains all of an organism’s hereditary information, its genetic code – the entire blueprint for building its structure and systems. An RNA molecule is a DNA molecule “split lengthwise down the middle.”

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

Just as important as the addition of phosphorus is the fact that the molecules in nucleotides are arranged in different patterns from the molecules of amino acids. Their different three-dimensional shapes or patterns enable them to perform various functions within 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 internal operations of the cells, 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 lengthy “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 complete steps. Then, a new ladder rail is added, joining up the outer ends of all the steps. In this manner, the original DNA ladder is replaced by two new DNA ladders. Then the cell divides into two new cells, each with its own double-helix ladder.

The codes in the DNA and RNA molecules are determined not by the nature of the chemicals in the DNA or RNA molecules, but by the order of the 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 in turn 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 genetic code, can also be a crystal. Laura Mallonee writes that  “DNA crystals form when a double helix is suspended in a liquid that evaporates. They grow in patterns dictated by the information stored within the strands. Seen in cross-polarized light, they display a kaleidoscopic array of colors and shapes.  The huge range of crystal structures is amazing.” ⁴⁰

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” that direct the cell on how to make its own amino acid building blocks. The cell does this by transferring RNA “blueprints” to the cell’s ribosomes, which are the “molecular machines” that build amino acids. The RNA that does this delivery work is called “messenger RNA (mRNA).”

The human genome of 23 chromosomes is estimated to be about 3.2 billion base pairs long and to contain 20,000–25,000 distinct protein-coding genes. ⁴¹

The Origin of Nucleotides

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

The nucleotides that make up 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. (See our 4th Essay in this series, Where Life Began: Warm Pools?  Black Smokers?)

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

The Joan Oró i Florensa Nucleotide Experiments – 1960s

In the 1960s, 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 a 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. ⁴²

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. ⁴³

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 1950s. 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, utilizing a simple reducing mixture of NH3, CO, and H2O. However, in addition to electric discharge in water vapor, the Czech team also subjected the solution to powerful laser discharges to simulate the plasmas resulting from asteroid impact shockwaves. The results of the experiment demonstrated that all RNA nucleobases were synthesized, providing strong support for the emergence of biologically relevant chemicals in an Early Earth atmosphere. ⁴⁴

Ribosomes — “Tiny Cellular Machines”

Now, we want to take a moment to discuss ribosomes because, in modern living cells, they work in between our first key molecule, amino acids, and our second key molecule, nucleotides. More specifically, ribosomes are mostly composed of RNA, and they manufacture most amino acids.  As we discussed earlier, the amino acids produced in this manner form the structure and conduct the operations of most chemical processes within the cells of all life forms. 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.

For decades, it has been firmly established in biology that protein synthesis (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.” ⁴⁵

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 called catalysts, and they are of immense importance in chemistry and biology. In biology, sequences of amino acids assemble the enzymes with the aid of catalysts. ⁴⁶  It is essential 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.

Cellular Machines and Structural Cell Biology

Modern ribosomes are an example of “cellular machines.” Cellular Machines are multi-component macromolecules that carry out essential biological processes inside individual cells. Another type of cellular machine is the macromolecules that construct the little tails (flagella) that certain bacteria use to propel themselves through water. There are hundreds of types of cellular machines at work inside cells. ⁴⁸

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.” ⁴⁹

Synthetic Biology Creates a Vaccine for the 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 aim to combat, the new vaccines utilize laboratory-made mRNA.  When injected into our arms, the new mRNA vaccines instruct some of our cells to produce a harmless piece of “spike protein” on their own surfaces, similar to the spikes found on the surface of the COVID-19 virus. Next, our body’s overall immune system recognizes the spiky proteins as “foreign bodies,” and our immune system begins 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. ⁵⁰

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 phosphorus 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 occur outside of life, in the realm of inorganic chemistry?  Yes, it does!  We addressed these phenomena in our prior Essay, “Essay #1 in this series, “Chemical Precursors to Life on Earth.” — JXM

Key Molecules for Life #4 – Food Molecules for Energy

This also brings us to the fourth of our 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 the air. 

Let’s start by examining what we humans (giant multicellular 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.  A common Important 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 is called Cellular Respiration. ⁵¹

When any 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.

Cellular Metabolism is a Process, but not really a process of Evolution.  Evolution is about change, whereas metabolism is about maintaining what is already there.  Metabolism is a process of homeostasis, self-maintenance, and the continuation of life within each organism, essential for survival. (For more, see our Essay, The Processes of Evolution and Their Meaning.)

Note: While lungs and gills are said to perform “physiological respiration” (breathing) in animals, in this section, we are referring to cellular respiration.  Also, while every human being has a measurable overall “Basal Metabolic Rate (BMR),“ in this Essay we are talking about cellular metabolism.

Aerobic (“uses oxygen”) Cellular Respiration

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

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

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

When humans inhale oxygen, we use it to accept electrons “donated” from the atoms in our food. In the aerobic respiration process, the glucose (cellular “food”) is oxidized (“burned”). The oxidation of glucose releases chemical energy that the cell can 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, online, “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 witnessed fires using this process to burn paper and wood since childhood.  Oxidation produces heat because the chemical bonds in the fuel contain more energy than the bonds in the water and carbon dioxide, which are the end-products of combustion.

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

• • A “Redox (Reduction-Oxidation) Reaction” between two participants is a chemical reaction that involves the transfer of electrons (energy) from one participant 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) 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 obtained 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. ⁵²

Readers will recall that the Miller-Urey experiment used a glass vessel containing a similar (but not identical) “atmosphere” composed of water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). ⁵³ Whatever the actual mix, the early atmosphere was exceedingly hot. Any oxygen that had been present would have soon been used up by burning away many of the more populous hydrogen and hydrocarbon molecules.

This early 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, such as those found at Yellowstone National Park. https://en.wikipedia.org/wiki/Anaerobic_respiration

Most scientists think that Earth’s First Life, the “Last Universal Common Ancestor (LUCA),” had an anaerobic (non-oxygen-using) metabolism like so many of today’s archaea have. Today’s archaea would be descendants of the Original Ancestor. Of course, all of today’s aerobic (oxygen-using) organisms would also be descended from that same Original Ancestor, but first, they had to evolve an oxygen-based metabolism. 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 less ability to accept electrons than oxygen. Since fewer electrons travel, less energy is released per reaction. Anaerobic respiration is, therefore, less efficient than aerobic respiration, except, of course, when oxygen is scarce. ⁵⁴ When oxygen did become prevalent on Earth, many ancient single-celled organisms evolved the ability to use aerobic metabolism, because it is a much more efficient use of energy. 

An Example of Early Anaerobic 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 was likely used as the electron donor.

Note: Although sulfur is primarily found in sedimentary rocks and seawater, it is critically important to living things because it is a component of many proteins. ⁵⁵

“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 donates electrons, and Sulfur is the electron acceptor.
Since the 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 rotten eggs. Several types of bacteria and many archaea can reduce elemental sulfur. ⁵⁶ 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. ⁵⁸

Today, many species of archaea and bacteria continue to utilize 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 have been found there in recent years.  ⁵⁹

Elemental sulfur and sulfates remain abundant in the modern world, especially in and around deep-sea hydrothermal vents, hot springs, and other extreme environments.  In July 2019, a scientific study of the Kidd Mine in Canada discovered sulfur-breathing organisms that live 7900 feet below the surface and which “breathe” sulfur to survive. These organisms are also remarkable due to their ability to consume minerals such as pyrite as a food source.  (See the ‘Black Smokers’ section of our Essay, “Where Life Began: ‘Warm Pools’? ‘Black Smokers’?”  ⁶⁰

Anaerobic Respiration of Organic Foods

Microbes also anaerobically break down organic matter, such as grains, grapes, dead plants, and dead animals. The ones that “eat” grape and grain sugars use the anaerobic process of 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 produce smelly hydrogen sulfide gas as a by-product, as well as methane (from which they get their name, “methanogens”). There are even bacteria in the human gut that utilize anaerobic chemistry to aid in food digestion.

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, which is usually metabolized aerobically, can also be metabolized anaerobically when oxygen is not available in the blood. However, the anaerobic path only produces one-third of the energy (measured in molecules of adenosine triphosphate, ATP) as the aerobic path.  ATP molecules are what directly fuel our cells. Additionally, the anaerobic path produces lactic acid instead of water and carbon dioxide; in animals, lactic acid can cause painful muscle cramps. Lastly, anaerobic metabolism can only use glucose and glycogen, while aerobic metabolism can also break down fats and proteins. ⁶¹

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 them and/or Earth had enough free O2 floating in the air to make aerobic respiration possible. That great increase in O2 was made possible mainly by the cyanobacteria.

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

Creating the Four “Key Molecules” of Life:  On Earth & In Lab  

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 ⁶²

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 our fourth and last Essay of this series, “Where Life Began: ‘Warm Pools’? ‘Black Smokers’?”

How the Four Key Molecules Work Together

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

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

This has become an important hypothesis for the Origin of Life called the “mRNA Model,” or “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 long strands 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 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 Khan 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. ⁶³

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. ⁶⁴

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. ⁶⁵

Of course, alternative chemical paths to original life have been proposed. ⁶⁶ Even so, the evidence for an early RNA-World Model is strong enough that the hypothesis has gained wide acceptance. ⁶⁷

How and Why Did Ribosomes Evolve?

If early RNA could make amino acid molecules by itself, how and why did ribosomes (which are tiny amino acid factories) 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 ⁶⁸

However, 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. ⁶⁹

The enzymes that now make protein inside ribosomes may have come to replace RNA manufacturing because the enzymes evolved 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. ⁷⁰

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. ⁷¹

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 require 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. (By contrast, we are only about 99 percent the same as our closest relatives, chimpanzees.) ⁷²

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

Early in the twenty-first century, research groups have already determined ways of creating rudimentary versions of cellular metabolism and 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 evolve.  ⁷³

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. ⁷⁴

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, to quickly power 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. ⁷⁵

_______________________________

               — J.X. Mason.   ContinuingCreation.org

Footnotes:

1. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books.
2. Arvin Ash, Abiogenesis – How Life Came from Inanimate Matter, 9-6-2019, a video film, www.arvinash.com 
3. 1974, Bantam Books. Taken from Essays that originally appeared in the New England Journal of Medicine between 1971 and 1973.
4. 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.”
5. Arvin Ash, “How Did Life Begin? Abiogenesis. “Origin of Life from Nonliving Matter,” a video film, now on YouTube, 09-6-2019, www.arvinash.com
6. Science Daily, June 16, 2020, from Univ. of British Columbia, www.sciencedaily.com/releases/2020/06/200616100831.htm.
7. 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.
8. 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.
9. 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.
10. Arvin Ash, The Video Film — “Abiogenesis: How Life Came from Inanimate Matter, 9-6-19, at www.arvinash.com
11. Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, 2015, W.W. Norton & Co., pp.1 and 4-5.
12. Nancy Kleckner, J.K. Fisher, and Mathieu Stout, “The bacterial nucleoid: nature, dynamics and sister segregation,” 12-01-2014, Current Opinion in Microbiology.
13. “Eukaryotic Chromosome Structure, Science Primer, scienceprimer.com.
14. 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, F.U. Battistuzzi, A Feijao, and S.B. Hedges, “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. 
15. Robert M. Hazen, Ibid., p. 134.
16. https://opentextbc.ca/biology2eopenstax/chapter/structure-of-prokaryotes-bacteria-and-archaea/#:~:text=The%20timelines%20of%20divergence%20suggest,diverged%20from%20the%20archaean%20line.
17. Hazen, pp.129-130.
18. Arvin Ash, Ibid.
19. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books, p. 131.
20. 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.
21. From the Simple Wikipedia article on “Origin of Life.”
22. J.F. Kasting, “Earth’s Early Atmosphere, 2-12-1992, Science, Vol. 259, Issue 5097, pp. 920-926.  DOI: 10.1126/science.11536547.
23. 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.
24. Robert M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2013, Penguin Books, p. 128, paraphrased. Arvin Ash also agrees, as he says in his twelve-minute film presentation, Abiogenesis – How Life Came from Inanimate Matter (Sept 7, 2019). The Wikipedia article on Abiogenesis concurs as well.
25. Tom Herrmann and Sandeep Sharma, “Physiology, Membrane,” 3-2-2019, StatPearls, SIU School of Medicine, Baptist Regional Medical Center, PMID 30855799.
26. Arvin Ash, “Abiogenesis – How Life Came from Inanimate Matter,” a video film, 9-6-2019, www.arvinash.com
27. Arvin Ash, Abiogenesis, Ibid.
28. 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, Proceedings of the National Academy of Sciences.  https: doi.org/10.1073/pnas.m 1900275116.
29. 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.
30. 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.
31. 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.
32. 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, “Folding Proteins in Fatal Ways, December 2003, Nature. 426 (6968): 900–4, bibcode:2003 Nature.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.
33.  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.
34. 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.
35. First Life on Earth Archived 2012-06-29 at ArchiveToday, 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.
36. Arvin Ash, “Abiogenesis,” Ibid.
37. 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.
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42. Celia Henry Arnaus, “How the First Nucleotides Might Have Formed on Earth,” Chemical & Engineering News, 4-27-2016.
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44. Their results were published in the 2017 Proceedings of the National Academy of Sciences PNAS 2017; 4-10-2017, DOI: 10.1073/pnas.1700010114.
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46. https://www.britannica.com/science/catalysis/Biological-catalysts-the-enzymes.

48. The ability of electron microscopes to see the atomic structures of molecules has led to the new field of Structural Cell Biology. Powerful microscopy, along with crystallography and computational tools, are now able to generate testable atomic models of cellular machines. ⁴⁷ https://www.cell.com/trends/cell-biology/fulltext/S0962-8924(06)00020-1.

49. http://sitn.hms.harvard.edu/flash/2011/issue88/.
50. https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html.
51. https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-respiration-ap/a/fermentation-and-anaerobic-respiration.
52. https://forces.si.edu/atmosphere/02_02_01.html#:~:text=When%20Earth%20formed%204.6%20billion,carbon%20dioxide%20as%20today’s%20atmosphere.
53. https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment#:~:text=The%20Miller%E2%80%93Urey%20experiment%20(or,of%20life%20under%20those%20conditions.
54. https://simple.wikipedia.org/wiki/Anaerobic_respiration.
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61.  https://en.wikipedia.org/wiki/Anaerobic_organism#:~:text=An%20anaerobic%20organism%20or%20anaerobe,that%20requires%20an%20oxygenated%20environment.
62. Robert Hazen, Ibid., p. 135.
63. https://www.umassmed.edu/rti/biology/role-of-rna-in-biology/
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72. “Genome Variations: How Different is One Human Genome from Another?” Jan 15, 2003, www.genomenewsnetwork.org.,resources, Ch. 4_1.
73. Robert Hazen, Ibid. pp. 129-30.
74. Kendall Powell, “How Biologists are creating life-like cells from scratch: Built from the bottom up, synthetic cells and other creations are starting to come together and could soon test the boundaries of life,” Nature, News Feature 11-7-2018.”
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