“Abiogenesis:” Evolution of the First Life on Earth

Abiogenesis: Evolution of the First Life on Earth 


This is Essay #3 of our four interrelated Essays on Earth’s geo-chemical origin of life and its subsequent Evolution.
Here are the titles of those four Essays:

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

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

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

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

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

         Recommended Outside Sources

    1. 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
    2. Abiogenesis – How Life Came from Inanimate Matter. This short 12-minute film, made and narrated by polymath Arvin Ash, lays out the basic story with clarity and superb moving illustrations. This film is available on the Arvin Ash website, arvinash.com2
    3. The Lives of a Cell: Notes of a Biology Watcher, written in lyrical prose by Dr. Lewis Thomas, MD, who was then President of the Sloan Kettering Cancer Center in New York. 3 
    4. The current Wikipedia article on Abiogenesis is a detailed review of the current science in this area. It complements the other three sources with authoritative information supported by 358 footnotes citing scientific research papers. (Biogenesis means “beginning out of life;” A-biogenesis means “beginning out of not-life.”) .

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 two decades. Our four Essays in Nature’s Continuing Creation will be drawing 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 shows that 4.1 to 3.7 million years ago the surface environment of Mars had liquid water and may have been habitable for microorganisms. A 2018 study found that 4.5 billion-year-old meteorites found on Earth contained liquid water along with prebiotic complex organic substances that may be ingredients for life. 4

We Oppose Fundamentalist, Biblical Creationism 

Note: This Section is largely repeated from Essay #1, “Chemical Precursors to Life.”

When biblical creationists criticize biological evolution, they like to point out that placing all the parts of a watch in a vat of water and stirring them up does not make an assembled, working watch.
They cite a paper by Fred Hoyle and Chandra Wickramasinghe which calculates that the probability of all the chemicals in a simple bacterium arising on their own by chance is 1 in 10 to the 40,000th power. They also say that the odds of creating a protein molecule by chance is1 in 10 to the 45th power
.
5

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

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

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

A lot remains unknown about the Origin of Life on Earth. But as more evidence comes to light, we see more evolutionary steps.  Of course, every piece of new evidence also creates more so-called “evolutionary gaps” in the minds of religious creationists.  We see more pieces of evidence; they see more “gaps” between the pieces of evidence. Science is about discovery.  It welcomes new questions because they lead to new knowledge.  Science is openness to new knowledge.  Biblical Creationism is often closed to new knowledge; they seem to be afraid of what they do not know.

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

People who are determined to keep their traditional faith in a supernatural God should ask themselves this: which is more powerful, more creative:
1. A God who decrees human life into existence, or…
          2. The Sum of all the Interacting Processes of Continuing Natual Creation? Processes that include the all the laws & rules of physics, chemistry, and biology such that intelligent life will emerge from them                  on 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 orthogenesisthe biological hypothesis that organisms have an innate tendency to evolve in a definite direction towards some goal (teleology) due to some internal mechanism or “driving force.” According to this theory, the largest-scale trends in evolution demonstrate an absolute goal such as increasing biological complexity. A more modern term for orthogenesis is Progressive Evolution. 7

But a trend is not a goal, and certainly not a pre-ordained goal. We and do see Progressive Evolution all around us in the sense that energy flow-throughs are made more efficient and the structures that arise are more complex. But those processes could end if we were hit by a large meteor, or if Humans destroy the biosphere.  Note: A more modern term for orthogenesis is Progressive Evolution.) 8

In the modern day, Professors Adrian Bejan and Jeremy England independently argue that there is a driving (but not inevitable) force behind increasing complexity, and that is the force of energy trying to find more, larger, and more efficient paths of energy flow.  

We agree with Professors Bejan and England. We do not see increasing complexity as a goal.  Or as an inevitability. We see it as a tendency when environments are 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. 9 Nevertheless, as we all know, life did recover, and it continued to evolve, including the eventual evolution of mammals and humans.


Comparing This Essay to Our Processes of Evolution Essay

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

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

Both our “Processes Essayand this “Abiogenesis Essay” are integral to this book about Nature’s Continuing Creation.  Darwin’s On the Origin of Species, published in 1859, and all the evolutionary science from then until now are forerunners to this book about Nature’s Continuing Creation.

 

A Quick Review of “Emergence”

We are going to use the word “emergence” several times in this Essay. In fact, our main thrust is to show that First Life likely emerged out of geochemistry“Emergence” is an important concept in modern science, and we discuss it at length in our Essay, Complexity and Continuing Creation.  Readers may want to pause and read 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 those gases, by themselves, have the characteristics of water. Water’s very liquidity emerges only when O and H2 combine (at one atmosphere                   of pressure and 33-to-211 degrees F).

 

Life Arose from Non-Living Chemistry

Image:  Mother Nature Creates Through Her Process of Emergence

While there is no single generally accepted theory of the origin of life, all credible proposals show that life, under natural conditions, by a slow process of chemical and molecular evolution, could have plausibly resulted in simple forms of life over a long period of time, and that this chemical evolution was probably the biggest hill to climb for life to have occurred on Earth  10

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

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

What are the Essential Features and Processes that Constitute Life?

(This section of our Essay #3 is repeated from our Essay #1.)  

One widely accepted definition of “Life” says that living organisms are open systems that have energy flow-through, perform metabolism, maintain homeostasis, can grow, respond to stimuli, adapt to their environment, reproduce, can evolve, are composed of a single cells or multiple cells, and have a life cycle from birth to death.

Re-stated as a list, this definition says that something is alive, it is a living organism, if (1) it is composed of one or more cells, (2) it has a life cycle – it is born, and it eventually dies, and (3) it does all of the following things:

  • Constructs and maintains a boundary that separates it from the outside.
  • Channels a flow of energy through itself (i.e., it is a thermodynamically open system).
  • Maintains homeostasis [good description below]
  • Has a metabolism – It takes in nutrients, extracts energy, and excretes waste.
  • Moves and/or grows.
  • Adapts to its environment.
  • Responds to stimuli.
  • Evolves – it can change over time in response to change in its surroundings.

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

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

 

The Tree of Life — Biological Classification (Taxonomy)

Let’s look ahead at Big Picture of Today’s evolved Life, by means of a schematic drawing called a Tree of Life.

The “Evolutionary Tree” of the 6 Domains of Life

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

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

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

As of this writing, (March, 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 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 bio-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 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.  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 compounds27

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 the Evolution of “First Life,” We Start by Looking at Today’s Simplest Organisms

Evolutionary biologists overwhelmingly maintain that all life evolved from a single species, the “First Organism” or the “Original Common Ancestor.”  The strongest evidence for a single “first organism” species is that the DNA of all living things is highly similar. [Cellular] Processes as distinct as respiration, fermentation, and photosynthesis all share a common basis, a conceptual integrity, which attests to the fact that all life has descended from a single Original Common Ancestor. 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 geo-chemistry. 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 our 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 the bacteria evolve because we spend fortunes inventing new antibiotics to combat new strains of bacteria that are infectious. (We also spend large sums of money to combat new infectious strains of viruses and fungi.)

Bacteria and Archaea Are Today’s Simplest Organisms

All the Bacteria and Archaea are single-celled, and each cell is enclosed by a cell membrane. 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 then came to be found everywhere on Earth. Archaea are important in the human gut and mouth, where they aid digestion. Interestingly, none of the Archaea are pathogens or parasites, which is quite a contrast with many species in the Bacteria Domain.

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

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

Note: Most prokaryotes do have an irregular, unbounded region that contains DNA, known as the 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 material to power their metabolism, including sulfur, cellulose, ammonia, or nitrite. Today, prokaryotes are ubiquitous across the Earth, even in the most including extreme environments 14

 

The “First Organism” or “Original Ancestor”

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

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

Gene sequencing studies are used to reconstruct the archaea and bacterial ancestry trees (phylogeny), and these studies indicate that the most recent common ancestor of bacteria and archaea was probably a single-celled extreme-heat-loving (hyper-thermophilic) organism that lived about 4.2 billion–3.6 billion years ago, probably near an underwater volcanic vent or hot springs. The earliest life on land may have been bacteria some 3.22 billion years ago. 15

As we shall discuss in this set of three Essay, there were likely non-living chemical systems which existed and replicated even before the advent of the Original Ancestor.  These “pre-living” systems are often called protocells.  (Not to be confused with proteobacteria, which are entirely different. 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).  And it is interesting to note that many archaea are able to survive the coldest, hottest, most saline and most acidic environmental conditions that Earth throws their way. 34 16

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. 17

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

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

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

What Defines Life?  What Do All 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 Essay #1, Dr. Hazen maintains that “Chemistry provides a firmer foundation for defining life, for all living things are organized molecular systems that undergo chemical reactions of astonishing intricacy and coordination.” [Hazen p. 128]

A panel at the Scripps Research Institute, chaired by Dr. Gerald Joyce came up with an excellent one-sentence 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.” 18

First life must have started from non-living matter – because, by definition, “First life” could only be preceded by “non-life.” 19 The earliest protocells (“pre-living cells”) may not have met all the definitional requirements for life. They may have lacked one of more of the Key Processes of Life. And the chemical systems that evolved even earlier that the first protocells may have barely hinted at what would evolve later.

Autocatalysis — Same Definition for Both Inorganic and Organic Chemistry

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

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

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

Autocatalytic Networks and RAFs

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

“Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life’s origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is so far lacking. [In this paper] we identify “Reflexively Autocatalytic Food-generated Networks (RAFs)” — self-sustaining networks that collectively catalyze all their reactions embedded within microbial metabolism…. [RAFs] indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.” 50

 

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

In Essay #1, 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-biologic, non-living systems to form ordered structures, grow them, and increase their complexity.

However, as Professor Hazen writes, “Carbon cannot have undergone the remarkable progression from geochemistry to biochemistry by itself. All of Earth’s great transformative powers – water, heat, lightning, and the chemical energy of rocks – were brought to bear in life’s genesis.” 20

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

Other Chemical Elements Play Important Roles in Life on Earth

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

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

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

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

Calcium is a silver-gray metal that’s the fifth-most abundant element in the human body. It plays a vital role in electrolytes, cell biochemistry, neurotransmission, the contraction of all muscles, and fertilization. Calcium is important for protein synthesis and bone formation. Seashells are made of calcium carbonate, in the mineral form of calcite or aragonite. Animals build their shells by extracting the necessary ingredients—dissolved calcium and bicarbonate—from their environment. 21

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: 22

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

Note: Molecular oxygen (O2) and ozone (O3), both important parts of today’s atmosphere, were either rare or absent on early Earth. They were created later, in and around the Great Oxygenation Event, which we will take up later in this Essay. At the early time of First Life, it is thought that no organisms breathed oxygen as we do today. 23

Organic Compounds

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

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

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

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

Further below, we will talk about the Key Molecules of life.

Apparent Stages in the Origin of Life. 

Unicellular organisms are thought to be the oldest form of life, with early protocells (“before real living cells”) possibly emerging 3.8–4 billion years ago.  24

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

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

Step #A is both a late step in chemical evolution and the first step in biological evolution. It is truly a transition between chemical evolution and biological evolution.  We can almost say that for Steps #B and #C as well. The metabolic and reproduction systems of Stage #D, however, are clearly in the realm of living things. Stage #D is the tough one to trace, containing many interrelationships and many unknowns.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

An important take-away is that life has evolved to use many different chemical processes with which to take energy from different kinds of “food.” Life seeks, explores, tries, persists, and adapts, and adopts.  In other words, Life evolves.  And life does all this without any direction or control from a central authority.  More generally, every living organism is an open energy system that requires a varying set of additional inputs from outside sources: food, water, minerals, and gases found in air or water such as oxygen for animals and carbon-dioxide for green plants. Each of these inputs must be a flow over time because their purpose is to sustain an organism’s life over time.  All these required chemical molecules (which can be simple or complex) ultimately come from non-living Earthly sources. This is persuasive evidence that Abiogenesis on Earth arose from geochemistry.

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

Dr. Hazen writes: “Every life-form consists of discrete assemblages of molecules (cells) that are separated by a molecular barrier from the outside (the environment). These collections of chemicals have evolved two interdependent modes of self-preservation – metabolism and genetics –that together unambiguously distinguish the living from the non-living.” 25 Arvin Ash also agrees, as he says in the first three in his twelve-minute film presentation, Abiogenesis – How Life Came from Inanimate Matter,” (Sept 7, 2019). And the Wikipedia article on Abiogenesis concurs as well.

In our previous Essay, Essay #2 of this series, we discussed The Molecules that Form Life.

Here in Essay #3, in this the sections below, we look at each of our “Four Key Molecules of First Life,” and we describe how they emerged naturally from inorganic (non-living) geo-chemistry. These Four typed of molecule are more complex than the monomer molecules we talked about above.

After those sections, we will consider how likely it was for all those monomers to assemble and function together, chemically. ? or was this in Essay #2 ? 

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 that brought all the chemistry together.

 

Key Molecule #1 in Creating Life — Lipids:  

Every living thing is either a single cell or a group of cells (rose bushes and humans are huge, organized groups of cells). Every one of these cells is enclosed by a cell membrane. Inside each cell membrane, interacting molecules carry out the chemical processes of life, such as the oxidation (“burning”) of food sugars to generate energy, or the assembly of protein molecules to build muscle tissue. 53.26.

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. 27

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

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

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

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

Cell membranes are formed by a layer of lipid molecules. 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

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

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

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

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

The “Salt Problem”

Until recently, however, scientists discounted the idea that lipid spheres in water could have been the first protocell membranes, because the water we are talking about was most certainly seawater, and the salt in seawater tends to destroy lipid structures. Science concluded that lipid spheres could not exist in the oceans. 28

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.” 29

Later, in multicellular organisms, encapsulation of each cell protects each cell 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 inter-cellular transportation and communication – critical for the health of the larger organism.

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

The Evolution of Beauty

Let’s briefly step aside to remark the Evolution of Beauty. The diatoms, mineral crystals, and seashells we talked about in our last Essay, Essay #1, 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 Have 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, 

Biologists have written best-selling books around this topic, including Professor Sean B. Carroll’s Endless Forms Most Beautiful 30 and Professor Richard O. Prum’s The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World – and Us. 31

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

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

The key elements of an amino-acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino-acids. About 500 naturally occurring amino- acids are known and they can be classified in many ways. 32

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

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

As the main part of proteins, amino-acids are the second-largest component (water is the largest) of human muscles and other tissues. 33

Beyond their role in proteins, amino acids participate in a number of processes such as transmitting nerve signals and in building complex molecules out of simple ones (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. 34

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

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

Protein Folding

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

A protein isn’t functional until it has been folded from a random-coil shape into its native three-dimensional shape. It is the three-dimensional shape that is able to present a certain surface that “fits with” the shape of another molecule. Only when the fit is accomplished can the biochemical process move forward.  35

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

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

 

Protein Crystals

   Crystalized Proteins

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

Prions – Misfolded Proteins. Prions are misfolded proteins with the ability to transmit their misfolded shape onto normal proteins. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals. It is not known what causes the normal protein to misfold, but the abnormal three-dimensional structure is suspected of conferring infectious properties, collapsing nearby protein molecules into the same shape. 36

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. 37


Were Amino-acids the First “Key Molecule” to Evolve?

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

Darwin’s Conjecture

In an 1871 letter to Joseph Dalton Hooker, Charles Darwin proposed a natural process for the origin of life. Darwin suggested that the original spark of life may have begun in a “warm little pond,” with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. Darwin further proposed that a protein compound was then chemically formed ready to undergo still more complex changes. 38

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

The Miller-Urey Experiments – 1950’s

In the 1950’s, several experiments by Drs. Stanley Miller and Harold Urey verified that the natural formation of organic molecular compounds was possible under the oxygen-less atmospheric conditions of the primordial Earth. These compounds included amino-acids, which are the components of proteins. 39

Their experiments used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). The chemicals were all sealed inside a sterile 5-liter glass flask connected to a 500 ml flask half-full of water. The water in the smaller flask was heated to induce evaporation, and the water vapor was allowed to enter the larger flask. Continuous electrical sparks were fired between the electrodes to simulate lightning in the water vapor and gaseous mixture, and then the simulated atmosphere was cooled again so that the water condensed and trickled into a U-shaped trap at the bottom of the apparatus. 40

The liquid in the Miller-Urey U-shaped trap contained three experiment-produced amino-acids that are common in living things. Early Earth would have had all three of them. In fact, these basic building blocks now appear to be common throughout the universe, as we will discuss later in our section on Panspermia.

Societal Reactions to The Miller-Urey Experiment

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

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

These two types of reactions are still applied today, and not just to the question of Life’s origin, but scientific progress of all kinds, including the origin of Earth and the origin of human beings.

Updating the Miller-Urey Experiment – 1960’s

The Miller-Urey experiment did inspire many others. Notably, professors Juan I Oro and A.P. Kimball found that many amino-acids are formed from HCN and ammonia under these conditions. 41

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.” 42

Key Molecule #3 in the Origin of Life – Nucleotides

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

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

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

Nucleotides join to make DNA

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

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

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

How RNA Passes Genetic Information to a New Generation

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

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

The codes in the DNA and RNA molecules are determined not by the nature of the chemicals in the DNA or RNA molecules, but by the order of the steps in those molecules. The order makes the code, just as the order of letters makes the words of a language, and the order of zeros and ones makes the code of a computer program. 

Related Terminology:  A genome is an organism’s complete set of DNA. If we think of an organism’s DNA code as its complete “manual of written instructions,” then we can say those instructions are carefully organized into “chapters” (chromosomes), which are then organized into “paragraphs” (genes). The entire manual from start to finish would be the genome. Almost every creature’s genome, chromosomes and genes are organized in the same way.

Crystalized DNA

Earlier, we remarked that proteins can assume a crystalline form. DNA, the long twin-ladder molecule that contains our genetics code, can also be a crystal.  “DNA crystals form when a double helix is suspended in liquid that evaporates. They grow in patterns dictated by the information stored within the strands. Seen in cross-polarized light, they display a mind-bending kaleidoscope of color and shape.  The huge range of crystal structure is amazing.” 43

How RNA Passes Construction Information for Making Amino-acids

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

The human genome (23 chromosomes) is estimated to be about 3.2 billion base-pairs long and to contain 20,000–25,000 distinct protein-coding genes. 44

The Origin of Nucleotides

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

The nucleotides that make the nucleic acids DNA and RNA appear to be products of evolution.  It is believed that the first nucleotides, like the amino-acids, emerged in the “primordial soup” – perhaps a pond on Earth’s surface (with or without a lightning strike), or possibly in an area of water around a hot or warm sub-sea hydrothermal vent.

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

The Joan Oró i Florensa Nucleotide Experiments – 1960’s

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

The Georgia Tech Nucleotide Experiments — 2016

Experimental studies led by Nicholas V. Hud of Georgia Institute of Technology (GIT) in 2016 showed that plausible proto-nucleotides can be formed in simulated early Earth environments. 45

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. 46

The Czech Nucleotide Experiments – 2017

Recall that in our recent section on the emergence of amino-acids, we described the Miller-Urey experiment done in the 1950’s. Originally, The Miller-Urey experiment was thought to produce only amino-acids.

However, a 2017 study by researchers in the Czech Republic has shown that a modified version of the original experiment produces nucleotides as well as amino acids.

Their experimental setup was similar to the original Miller-Urey experiment, using a simple reducing mixture of NH3 + CO and H2O. But in addition to electric discharge in water vapor, the Czech team also subjected the solution to powerful laser discharges to simulate the plasmas resulting from asteroid impact shock waves.

The results of the experiment demonstrated that all RNA nucleobases were synthesized, strongly supporting the emergence of biologically relevant chemicals in an Early Earth atmosphere. 47

Ribosomes — “Tiny Cellular Machines”

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

For decades now, it has been firmly established in biology that protein catalysis (the work of building proteins) in modern cells is reserved for special molecules called enzymes located in the ribosomes. The “blueprints” or “catalytic templates” used by the enzyme molecules, are segments of genetic nucleotide chains messengered out of the nucleus as messenger-RNA (mRNA). Each ribosome is a tiny cellular machine that moves along a particular segment of the mRNA, using that segment’s sequence of genetic information as a template to manufacture a particular amino-acid. It is as if the ribosome were “reading” the RNA sequence “by braille.” 48

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

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

Since ribosomes are not surrounded by a membrane, they are not organelles like the much larger nucleus and mitochondria are. Ribosomes are simple cell inclusions, as are pigment granules, fat droplets, and nutritive substances. Ribosomes are found in large numbers in the cytoplasm of living cells.

As we discussed earlier, the amino-acids made in this manner build the structure and conduct the operations of most chemical processes inside the cells of all life forms.

Cellular Machines and Structural Cell Biology

Modern ribosomes are an example of “cellular machines.” Cellular Machines are multi-component macro-molecules that carry out essential biological processes inside individual cells. Another type of cellular machine are the   macro-molecules that make the little tails (flagella) that certain bacteria use to propel themselves through the water. There are hundreds of types of cellular machines at work inside cells. 50

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.” 51

Synthetic Biology Creates a Vaccine for the Covid-19 Virus

Covid-19 Virus

                      Covid-19 Virus

In late 2020, synthetic biology successfully produced some of the first vaccines to fight the COVID-19 virus. Unlike traditional vaccines which use weakened or inactivated versions of the germ they intend to fight, the new vaccines use laboratory-made mRNA.  When injected into our arms, the new mRNA vaccines instruct some of our cells to make a harmless piece of “spike protein” on their own surfaces, like the spikes found on the surface of the COVID-19 virus. Next, our bodies’ overall immune systems recognize the spiky proteins as “foreign bodies,” and our immune systems begin making antibodies to kill the cells that have spikes. At the end of the process, our bodies have learned how to kill any and all cells that have spikes, thus protecting us against future infection from real COVID-19 viruses. 52

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

Does “self-replication” or “reproduction” ever occurs outside of life, in the realm of inorganic chemistry?  Yes, it does!  We addressed these phenomena is our prior Essay, “Essay #1 in this series, Chemical Precursors to First Life.

Key Molecules for Life #4 – Food Molecules for Energy

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

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

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

Cellular Respiration and Cellular Metabolism

When one of our human cells takes in oxygen (O2), water (H2O), and glucose (C6H12O6), this process is called Cellular Respiration. In fact, when the cell of any organism, unicellular or multicellular, takes in its “life supplies,” no matter what those supplies are, the process in called Cellular Respiration. 53

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

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

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

Aerobic (“uses oxygen”) Cellular Respiration

Cellular energy powers the cell as it performs all its metabolic activities. Cellular Respiration is the set of processes that take in food and releases its energy; it is the “front-end” part of metabolism.

There are two types of respiration: Aerobic respiration, which uses oxygen; and anaerobic respiration, which does not use oxygen.

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

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

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

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

(See Khan Academy, 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 seen fires use this process to burn paper and wood since we were children.  Oxidation produces heat because the chemical bonds in the fuel contain more energy than the bonds in the water and carbon dioxide that are the end-products of combustion.

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

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

(See https://simple.wikipedia.org/wiki/Reduction_(chemistry) )

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

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

Instead, the primordial atmosphere was mainly composed of gases spewed from volcanoes. The atmosphere included hydrogen sulfide, methane, hydrogen, and ten to 200 times as much carbon dioxide as today’s atmosphere. 54

Readers will recall that the Miller-Urey’s experiment used a glass vessel containing a similar (but not identical) “atmosphere” composed of water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). 55 Whatever the actual mix, the early atmosphere was exceedingly hot. Any oxygen that had been present would have soon be used up by burning away many of the more populous hydrogen and hydrocarbon molecules.

This early atmosphere is quite suitable for organisms that do a different type of cellular respiration, namely non-oxygen-using anaerobic respiration.  We know this type of respiration was possible, because this method is still used today by many unicellular organisms, principally Archaea, that often live in unique sheltered environments where oxygen is either rare or not present at all. These modern environments include swamps, undersea hydrothermal vents, and sulfurous surface geysers like those at Yellowstone. https://en.wikipedia.org/wiki/Anaerobic_respiration

Most scientists think that Earth’s First Life, the “Last Universal Common Ancestor,” had an anerobic (non-oxygen using) metabolism like so many of today’s archaea have. Today’s archaea would be descendants of that Original Ancestor. Of course, all of today’s aerobic (oxygen using) organisms would also be descended from that same Original Ancestor, but first they had to evolve an oxygen-based metabolism. Shortly, we will talk about how that evolutionary switch most likely happened.

Anaerobic respiration usually means that elements other than oxygen are the electron acceptors. Common replacements for oxygen are nitrates, iron, manganese, sulfur, sulfates, fumaric acid and carbon dioxide. These electron acceptors have lesser ability to accept electrons than oxygen has. Since fewer electrons travel, less energy is released per each reaction. Anaerobic respiration is therefore less efficient than aerobic respiration; except, of course, when oxygen is scarce.  56 When oxygen did become prevalent on Earth, many ancient single-celled organisms evolved the ability to use aerobic metabolism – because it is much more efficient. 

An Example of Early Anerobic Respiration

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

Note: Although sulfur is primarily found in sedimentary rocks and sea water, it is particularly important to living things because it is a component of many proteins. 57

“Sulfur-eaters” – Anaerobic Respiration of Sulfur

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

Note that since oxygen is not involved, this is not a “redox reaction.” Instead, it is called a “sulfur-reduction respiration,” and is the “front door” to “sulfur-reduction metabolism.”

In our example, the end-product, Hydrogen-sulfide (H2S), is a gas having the foul odor of a rotten eggs. Several types of bacteria and many archaea can reduce elemental sulfur. 58

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. 60

Today, many species of archaea and bacteria still use reduction reactions to survive and grow. We know them colloquially as sulfur-gas “breathers” “iron-eaters,” and similar names. Of course, since these microbes have neither mouths nor lungs, they don’t really “eat” or “breathe.” The most correct expression would be to say they “consume,” or “take in” the chemical compounds they need to live. Sulfur-based metabolism has been found largely in microorganisms from extreme environments, and previously unknown microorganisms found there in recent years. 61

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 which live 7900 feet below the surface, and which “breathe” sulfur in order to survive. These organisms are also remarkable due to consuming minerals such as pyrite as their food source. 62

Anaerobic Respiration of Organic Foods

Microbes also anaerobically take in organic foods – such as grains, grapes, dead plants and animals. The ones that “eat” grape and grain sugars use the anerobic process fermentation, which has alcohol as a by-product. (Yeast, which is a microbial fungus, can also do this.) The microbes that “eat” dead swamp plants and landfill garbage often have smelly hydrogen sulfide gas as a by-product, as well as methane (from which they get the name methanogens). There are even bacteria in the human gut which use anaerobic chemistry to help us digest our food.

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

Note: In many animals, including humans, a molecule of glucose, usually metabolized aerobically, can also be respirated anaerobically, when there is no oxygen available in the blood.  But the anaerobic path only produces one-third the energy (measured in molecules of adenosine triphosphate, ATP) as the aerobic path. ATP molecules are what directly fuels our cells. Also, the anerobic path produces lactic acid instead of water and carbon-dioxide; and in animals, lactic acid can cause painful muscle cramps. Lastly, anaerobic metabolism can only use glucose and glycogen, while aerobic metabolism can also break down fats and protein. 63

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

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

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

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

“Our results, now duplicated and expanded in numerous labs, show beyond a doubt that a suite of life’s molecules can be synthesized easily in the pressure-cooker conditions of [Earth’s] shallow crust.  Volcanic gases containing carbon and nitrogen readily react with common rocks and seawater to make virtually all of life’s basic building blocks…“What’s more, these synthesis processes are governed by relatively gentle chemical reactions [oxidation and reduction] reactions, similar to the familiar rusting of iron… These are the same kinds of chemical reactions that life uses in metabolism…” — Professor Robert Hazen 64

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

How the Four Key Molecules Work Together

This is the section where we talk about how all 4 of the Key Monomers — the lipids, amino-acids, nucleotides, and the various food molecules evolved to work together to make the First Living Organism.

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

This has become an important hypothesis of the Origin of Life called the “mRNA Model,” or simply as the RNA World Model.

The “RNA-World” Model

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

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

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

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

  1. RNA can store and carry the genetic instructions for the next generation, and
  2. RNA can also direct the protein manufacturing work that enzymes now do in modern organisms. 65

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. 66

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. 67

Of course, alternative chemical paths to original life have been proposed. 68 Even so, the evidence for an early RNA-World Model is strong enough that the hypothesis has gained wide acceptance. 69

How and Why Did Ribosomes Evolve?

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

Scientists who support the RNA-World model think that the ribosome may have first originated as a complex of self-replicating RNA. Only later, when amino-acids began to appear, did that complex evolve the ability to synthesize proteins. The early ribosomal RNA was able to take on the task of amino-acid synthesis because it already had the informational, structural, and catalytic functions that it needed to do this work efficiently 70

But for RNA molecules to take hold, they would have needed an abundant supply of nucleotides, and scientists think that nucleotide-building RNAs evolved to provide these RNA building blocks. 71

The enzymes that now make protein inside ribosomes may have come to replace RNA-manufacturing because the enzymes came to be more abundant and versatile. This is supported by the fact that the ribosomes’ own structure contains characteristics from both nucleotides and amino-acids. 72

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. 73

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

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

There are more than three million differences between your genome and anyone else’s. On the other hand, we are all 99.9% the same, DNA-wise. (By contrast, we are only about 99 percent the same as our closest relatives, chimpanzees.) 74

Twenty-first Century Efforts to Create First-Life in the Laboratory

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

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

However, all of Dr. Joyce’s new chemical molecules were exact copies of the old molecules, so there was no evolution of novelty; no ability to mutate. The system could not combine those chemicals in new ways to adapt to changes in its environment; it could not evolve75

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. 76

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

  1. Artificially produced cell-like lipid microspheres and micro-injected them with amino-acids.
  2. Made a rudimentary artificial mitochondrion (a cellular machine that manufactures the ready-energy ATP molecules that provide ready energy on demand quickly power to muscles).
  3. Isolated 17 natural enzymes from 9 different organisms that together can perform photosynthesis more simply and efficiently than real photosynthesis can.
  4. Isolated a relatively small number of the most critical genes from a simple bacterium and had that “minimal genome” boot-up a free-living, slow-growing organism. 77  doi: https://doi.org/10.1038/d41586-018-07289-x

END OF THIS ESSAY

  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 Colombia, 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., pp1 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. See the Wikipedia article on Unicellular Organism.
  15. 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
  16. Robert M. Hazen, Ibid., p. 134.
  17. https://opentextbc.ca/biology2eopenstax/chapter/structure-of-prokaryotes-bacteria-and-archaea/#:~:text=The%20timelines%20of%20divergence%20suggest,diverged%20from%20the%20archaean%20line.
  18. Hazen, pp.129-130.
  19. Arvin Ash, Ibid.
  20. Robert. M. Hazen, The Story of Earth: The First 4.5 Billion Years, from Stardust to Living Planet, 2012, Penguin Books, p. 131.
  21. 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.
  22. From the Simple Wikipedia article on “Origin of Life.”
  23. J.F. Kasting, “Earth’s Early Atmosphere, 2-12-1992, Science, Vol. 259, Issue 5097, pp. 920-926.  DOI: 10.1126/science.11536547.
  24. 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.
  25. Robert M. Hazen, The Story of Earth: The First 4.5 billion Years, from Stardust to Living Planet, 2013, Penguin Books, p. 128, paraphrased.
  26. Tom Herrmann and Sandeep Sharma, “Physiology, Membrane,” 3-2-2019, StatPearls, SIU School of Medicine, Baptist Regional Medical Center, PMID 30855799.
  27. Arvin Ash, “Abiogenesis – How Life Came from Inanimate Matter,” a video film, 9-6-2019, www.arvinash.com
  28. Arvin Ash, Abiogenesis, Ibid.
  29. Arvin Ash, Abiogenesis, Ibid. See also, Caitlin Cornell, Roy Black, Mengjun Xue, et al., “Prebiotic Amino-acids Bind to and Stabilize Prebiotic Fatty Acid Membranes,” Edited by David Weitz, 1-8-2019, Harvard University, Proceeds of the National Academy of Sciences.  https: doi.org/10.1073/pnas.m 1900275116.
  30. Endless Forms Most Beautiful: The New Science of Evo-Devo and the Making of the Animal Kingdom, 2005, W.W. Norton.
  31. Professor Richard O. Prum, The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World – and Us,  2017, Doubleday.
  32. 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.
  33. 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.
  34. 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.
  35. J.M. Berg, J.L. Tymoczko, and L. Stryer,  (2002). “Protein Structure and Function,” 2002, Biochemistry, W. H. Freeman. ISBN 978-0-7167-4684-3.  See also, D.J. Selkoe,

    Diagram of a Folded Protein (myoglobin)

    The Folded Structure of myoglobin protein

    “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.

  36.  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.
  37. 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.
  38. First Life on Earth Archived 2012-06-29 at Archive.today windmillministries.org, Retrieved on 2008-01-18.  See also: Letters of Charles Darwin, written in 1871, published in Darwin, Francis, ed., 1887, The Life and Letters of Charles Darwin, Including an Autobiographical Chapter, Volume 3, London: John Murray.
  39. Arvin Ash, “Abiogenesis,” Ibid.
  40. 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.
  41.  Oró J, Kimball AP (August 1961). “Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide”. Archives of Biochemistry and Biophysics. 94 (2): 217–27. doi:10.1016/0003-9861(61)90033-9. PMID 13731263. See also,  Oró J, Kamat SS (April 1961). “Amino-acid synthesis from hydrogen cyanide under possible primitive earth conditions”. Nature. 190 (4774): 442–3. Bibcode:1961Natur.190..442O. doi:10.1038/190442a0. PMID 13731262. S2CID 4219284. See also, Oró J (1967). Fox SW (ed.). Origins of Prebiological Systems and of Their Molecular Matrices. New York Academic Press. p. 137.
  42. Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (October 2008). “The Miller volcanic spark discharge experiment”. Science. 322 (5900): 404.  Bibcode:2008Sci…322..404J. doi:10.1126/science.1161527. PMID 18927386. S2CID 10134423. See also, “Lost’ Miller–Urey Experiment Created More Of Life’s Building Blocks”. Science Daily. October 17, 2008. Archived from the original on October 19, 2008. Retrieved 2008-10-18.
  43. Laura Mallonee, “Turns Out Crystallized DNA Is Crazy Pretty,” 2015, WIRED Magazine, https://www.wired.com/2015/08/linden-gledhill-crystalized-dna/.
  44. L.A. Moran LA (2011-03-24). “The Total Size of the human genome is very likely to be ~3,200 Mb,” 3-24-11, Sandwalk.blogspot.com. Retrieved 2012-07-16. See also, “The Finished length of the human genome is 2.86 Gb,” Strategicgenomics.com, 6-12-2006-06,  Retrieved 2012-07-16. See also, International Human Genome Sequencing Consortium (October 2004). “Finishing the euchromatic sequence of the human genome,” October 2004, Nature. 431 (7011): 931–45. Bibcode:2004Natur.431..931H. doi:10.1038/nature03001. PMID 15496913.
  45. Celia Henry Arnaus,“How the First Nucleotides Might Have Formed on Earth,” Chemical & Engineering News, 4-27-2016.
  46. Celia Henry Arnaud, “How the first nucleotides might have formed on Earth,” Chemical and Engineering News, 4-27-16, referencing the publication: “Spontaneous Formation and Base Pairing of Plausible Prebiotic Nucleotides in Water,” by Brian J. Cafferty, David M. Fialho, Jaheda Khanam, Ramanarayanan Krishnamurthy & Nicholas V. Hud, Nature Communications, volume 7, Article number: 11328 (2016).  DOI: 10.1038/ncomms11328).
  47. their results were published in the 2017 Proceedings of the National Academy of Sciences PNAS 2017; 4-10-2017, DOI: 10.1073/pnas.1700010114.
  48. S. Konikkat  (February 2016). “Dynamic Remodeling Events Drive the Removal of the ITS2 Spacer Sequence During Assembly of 60S Ribosomal Subunits,” February 2016, in S. cerevisiae (Ph.D. thesis). Carnegie Mellon University. See also E.W.  Weiler and L. Nover, (2008). Allgemeine und Molekulare Botanik (in German). Stuttgart: Georg Thieme Verlag. p. 532. ISBN 978-3-13-152791-2. See also J. de la Cruz J, K. Karbstein, and J.L. Woolford, (2015). “Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo”. Annual Review of Biochemistry. 84: 93–129. doi:10.1146/annurev-biochem-060614-033917. PMC 4772166. PMID 25706898.
  49. The ability of electron microscopes to see the atomic structures of molecules has led to the new field of Structural Cell Biology. Powerful microscopy plus crystallography and computational tools are now able to generate testable atomic models of cellular machines. 49 https://www.cell.com/trends/cell-biology/fulltext/S0962-8924(06)00020-1.

  50. http://sitn.hms.harvard.edu/flash/2011/issue88/.
  51. https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html.
  52. https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-respiration-ap/a/fermentation-and-anaerobic-respiration.
  53. https://forces.si.edu/atmosphere/02_02_01.html#:~:text=When%20Earth%20formed%204.6%20billion,carbon%20dioxide%20as%20today’s%20atmosphere.
  54. https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment#:~:text=The%20Miller%E2%80%93Urey%20experiment%20(or,of%20life%20under%20those%20conditions.
  55. https://simple.wikipedia.org/wiki/Anaerobic_respiration.
  56. https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.4%3A_Nutrient_Cycles/16.4F%3A_The_Sulfur_Cycle
  57. Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl DA (2014). Brock Biology of Microorganisms. Benjamin-Cummings Pub Co. pp. 448–449. ISBN 978-0321897398. See also, R. Rabus, TA Hansen, and F Widdel, “Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes,” 2006, The Prokaryotes, 2006, Springer Publishing, pp. 659–768. doi:10.1007/0-387-30742-7_22. ISBN 978-0-387-25492-0.
  58. https://en.wikipedia.org/wiki/Sulfate-reducing_microorganisms, 59 LL Barton and GD Fauque, “Biochemistry, Physiology and Biotechnology of Sulfate-Reducing Bacteria,” Advances in Applied Microbiology, 2009, pp. 41–98. doi:10.1016/s0065-2164(09)01202-7. ISBN 9780123748034. PMID 19426853.
  59.  https://en.wikipedia.org/wiki/Sulfur-reducing_bacteria#:~:text=Acidithiobacillus%20are%20chemolithoautrophics%2C%20Gram%2Dnegative,and%20nitrogen%20from%20the%20atmosphere.
  60. https://www.google.com/url?sa=i&url=http%3A%2F%2Fwiki.biomine.skelleftea.se%2Fwiki%2Findex.php%2FSulfate_reducing_bacteria&psig=AOvVaw0lzzAafSRHXcc93VaXn8L-&ust=1613421722267000&source=images&cd=vfe&ved=0CAIQjRxqFwoTCKjI5bae6u4CFQAAAAAdAAAAABAD, footnotes 2, 12, 13, and 14.
  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/
  64. Christopher Packham, “Researchers Produce all RNA Nucleobases in Simulated Primordial Earth,” 4-21-2017, Phys.org News, https://phys.org/news/2017-04-rna-nucleobases-simulated-primordial-earth.html. See also, Walter Gilbert, “The RNA World,” February 1986, Nature 319 (6055): 618. Bibcode:1986Natur.319..618G. doi:10.1038/319618a0. S2CID 8026658.
  65. Khan Academy, RNA World AP.BIO: SYI‑3 (EU), SYI‑3.E (LO), SYI‑3.E.2 (EK)
  66. BH Patel, C Percivalle, DJ Ritson, CD Duffy, and JD Sutherland, “Common Origins of RNA, Protein and Lipid Precursors in a Cyanosulfidic Protometabolism,”April 2015, Nature Chemistry. 7 (4): 301–7. Bibcode:2015NatCh…7..301P. doi:10.1038/nchem.2202. PMC 4568310. PMID 25803468.
  67. Nicholas Wade, Nicholas (May 4, 2015). “Making Sense of the Chemistry That Led to Life on Earth,” 5-4-2015, The New York Times.  See also, SD Copley, E Smith, and HJ Morowitz, “The Origin of the RNA World: Co-evolution of Genes and Metabolism,” Bioorganic Chemistry. 35 (6): 430–43. doi:10.1016/j.bioorg.2007.08.001. PMID 17897696.
  68. M. Root-Bernstein M and R. Root-Bernstein, “The Ribosome as a Missing Link in the Evolution of Life,” February 2015, Journal of Theoretical Biology. 367: 130–158. doi:10.1016/j.jtbi.2014.11.025. PMID 25500179.
  69. “The RNA Origin of Life,” NOVA Labs, https://www.pbs.org/video/nova-labs-rna-origin-life/. See also, Kahn Academy, “The RNA Origin of Life,” https://www.khanacademy.org/science/ap-biology/natural-selection/origins-of-life-on-earth/v/originoflife.
  70. Liang Shen and Ji Hong-Fang, “Small Cofactors May Assist Protein Emergence from RNA World: Clues from RNA-Protein Complexes,” 2011, PLOS ONE. 6 (7): e22494. Bibcode:2011PLoSO…622494S. doi:10.1371/journal.pone.0022494. PMC 3138788. PMID 21789260.
  71. R.J. Mackenzie, “DNA vs. RNA – 5 Key Differences and Comparison,” 12-18-2020, Genomics Research from Technology Networks.
  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.”
  75. Kendall Powell, How biologists are creating life-like cells from scratch, Nature Magazine, Nature 563, 172-175 (2018) https://www.nature.com/articles/d41586-018-07289-x

Leave a Reply

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