our first 1000 steps on the human journey: chemical evolution

7/28/2019 Our First 1000 Steps on the Human Journey: Chemical Evolution

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OUR FIRST 1000 STEPS

ON THE HUMAN JOURNEY

R. S. HEYER

2005

VOLUME I. CHEMICAL EVOLUTION,

THE FIRST 100 STEPS


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DEDICATED

To those who have gone before,

To those who have shared the journey,

To those who are following or starting on the way,

And

To those I hope are yet to come.


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OUR FIRST 1000 STEPS

ON THE HUMAN JOURNEY

PREFACE

This project began in 1956 as an effort to form a more balanced and meaningful history of

humanity than high school and college courses and texts, periodicals, and private reading had

discovered, and to counteract the narrowness of accounts too limited in time, ethnicity, and culture, as

well as to focus on major themes rather than on "culture heroes" and passing rivalries.

From Sumerian historical texts purportedly written of city gods, the Shu Jing of China, the Vedas

of India, the monumental notices of rulers, from writers of private histories from Homer and Herodotus

to Ranke, Spengler, and more recent and current historical writing, a more balanced view began to

emerge in my mind. I began to collect maps from various sources showing the sequential rise of ever

larger culture areas and their empires, and the spread of world-wide cultural items such as pottery,

agriculture, architecture, the wheel, metallurgy, navigation, writing, the alphabet, etc.

Seeing that there was no truly balanced and unbiased world history, despite the numbers of

written histories, but only nationalistic, ethnic, and regionalistic histories, I felt a need for betterbalance, and began to plan the scope and method for creating one, filling in some of the content.

First, it must be species-wide.

Second, it must enumerate great steps toward social-systems improvement ultimately shared by

all or nearly all humans.

Third, the emphasis would be on these steps, how and when these cultural innovations were

achieved and spread, and not on nations, ethnicities, or any other divisions among humans.

Fourth, toward these goals, both terminology and content would have to differ from the

inadequacies of the traditional histories. As to content, individual personal names would be excluded

(as in a famous history of Rome, where no human is named, but one elephant is).1

Those culture heroes

are not what real history is about. Besides, those whose names became famous were merely points

along lines of advance to which many contributed but only one or a few are remembered for the workof all who went before and many who continued, and still continue, to refine the insights afterwards.

1Reference uncertain.

Some traditional divisive terms must be replaced with better terms. In place of "man" and

"mankind" in their broadest senses, "humans" or "humankind" are the terms used here for the Latin

word homo and the Greek word anthropos.

Having lived through the largest and most costly war in modern history (which was spurred by

nationalist propaganda and international ignorance), I felt we needed (and still need) to concentrate on

what we have in common, rather than on what divides us, of which people of small vision will constantly

remind us.

The next issue was how far back the history should go. Clearly, some events, which occurredbefore writing was invented, were later written and influenced still later history. Many histories in my

youth were starting to mention prehistory, but a one-volume book needed a starting date. In college I

ran across a small book on the Neolithic Revolution, of which I had not previously heard (it was not

mentioned in my college history or anthropology texts or classes). That was a logical starting point for

post-foraging history, and set the beginning boundary of the intended one-volume history slowly

assembling in my mind. This would be deeper in time than most histories, and would allow the

worldwide view needed, in addition to encouraging a longer-term perspective on human progress.


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That approach would require a new term for a period of 10,000 years, the time to be covered by

the contemplated history volume. Since my maps were arranged mainly by centuries, the concept of

100 centuries seemed suitable. I therefore coined the termcentadfor such a period as an antidote for

the near-sighted focus of most histories. That book on the Zero or Transition Centad is volume X of this

project, and permits a strictly forward progression of dates and times, with no confusing A.D. versus

B.C., with positive and negative dates, to muddle the mind and trouble the reader.

As increasing information gathered, my curiosity naturally arose about still earlier "steps" in our

history, whether cultural or biological, leading to the present 10-volume project, beginning from the

origin of life on Earth to the year 10,000 centad 0 (=2000 A. D.=1478 A.H.). If I do not live to see it

complete, I hope others may carry it on to completion, and draw from it the lessons it can provide.


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VOLUME I. STEPS 1-100:

CHEMICAL EVOLUTION

CHAPTERS TITLE STEPS PAGE

Chapter A. Introduction to the Series 1

Chapter B. Introduction to Volume I 10

Chapter C. Setting the Stage 22

Chapter D. Physical, Astronomical, and 1-10 44

Geological Evolution

Chapter E. Beginning Earth Chemistry 11-20 68

Chapter F. Early Earth Cycles, Beginnings 21-30 101

Of Chemical Cycles, and Rings

Chapter G. RNA and the First Bions 31-40 145

Chapter H. First Empire Grows 41-50 176

Chapter I. DNA, Thymine, and Amylation 51-60 208

Chapter J. Cheap Substitutes, Do It at Home, 61-70 248

And Recycling

Chapter K. Refining Proteins and Trying New 71-80 278

Ventures

Chapter L. Further Saccharide Achievements 81-90 320

Chapter M. Closing in on a Major Transition 91-100 349

Chapter N. Summary and Conclusions for Vol. I 396

Afterword 411

Bibliography 418

Glossary 423


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CHAPTER A.

INTRODUCTION TO THE SERIES

1. Purpose

The purpose of this project is to provide a perspective on human history that will be broader in

scope, longer in time covered, more balanced, more accurate, and sounder than previously available, by

tracing the progress of humans and their ancestors from their first origins to our own time (roughly the

end of the last century, millennium, and centad). While many of these ancestors are not usually

considered human today, each of them provided something that is still part of us today, and is therefore

pertinent to our history, to how we came to be here, and to what we are. Our goal in this project is to

point out what we have in common among all humans. For millennia we have heard too much

propaganda that tends to separate us and prevent us from a forming a union of peace, freedom,

fairness, and concern each for all and all for each.

2. Scope

This story is intended to apply to humans generally. Because we are made of elements created

by or in a series of long-gone stars, I cover briefly the typical origins and demise of stars, including the

origin of our Sun, which supplies most of the energy we now use (directly and indirectly). Because we

arose in and from the Earth, and still live on it, I touch on the origin of the Earth. Because we arose

from, depend upon, and consist mostly of chemical processes on Earth, I also touch on this, especially in

the first volume. The next several volumes mention some of our non-human ancestors and some steps

crucial to us that they took. The last two volumes bring us to modern humanity and its mainly cultural

history, ending with volume X, devoted to only the last 100 centuries.

I look here only at our own direct line of descent, and give only the highlights. So there is no

mention of any proposed origin for "the Universe", covered by many other books, and only the most

cursory and necessary references to physics, astronomy, geology, and chemistry in getting to ourearliest ancestors. This story does not cover the "gee whiz" kind of information about the biggest or

most fearsome animals, such as dinosaurs, because they are not our ancestors, and the unusual is not

our emphasis.

Perhaps a hundred million other forms of life could be traced in a similar way, each of with its

own comparable history, and each of them affects us and is affected by us, but they are mostly outside

the scope of this project.

3. Method and Structure

The series is divided into 10 sequential volumes, each with an introduction, a stage setting, and

10 chapters setting forth 10 steps each, in the order in which those steps occurred, as nearly as I can

determine. Each volume also ends with a chapter of summary and conclusions, followed by various

indices, such as a glossary of terms, a bibliography, etc.

The "steps", of course, do not cover all that happened, but really are important stages in our

development, mainly physical or chemical at first, biological in the middle period, and social and cultural

later, but in other ways too. The first volume refers to our chemical beginnings, the last only to our

recent experiences, behavior, and ideas. Each step's story includes a reference to its present residue in

us, if any, and an illustrative drawing or chart where practical.


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No personal names are included, no nations (except as locations), no dinosaur or other species

not part of our ancestry, and no ethnic references.

4. Terminology

Because of the scope of this project, specialized words are used by researchers in the particular

fields discussed. But my purpose is more general, so special terminology is avoided as much possible, so

as not to burden the reader unduly. Still the words I do use must be used consistently and ought to be

reasonably clear.

To keep our meaning and ideas clear, whether in science of any other subject, we have to

clarify, and to that end to coin our terms, at times, especially where current terminology is too unclear,

inconsistent, or laden with emotion to allow clear thinking and understanding. So I have tried to avoid

using technical terms in this project wherever possible and to use standardized terms where leaving out

the technical terms would be too awkward.

Even so, we need to use words for some basic ideas, and in a few cases standard English terms either do

not exist or present unnecessary problems. In those cases I have tried either to define ahead of time

precisely what words of my own invention or usage mean in these books, no matter what words are

more common. There are only a few of these.First of all, I use some existing words in a specific way here for a more rigorous scientific clarity:

Earth vs. earth

To avoid confusion, the name of our planet will start with a capital letter like the name

of any other planet, and "earth," not capitalized, means soil or the ground.

Human

Rather than "person" or "man", I use human so as to clearly include women and

children (but not human being, since we do not say canine being, feline being, etc.).

Universe

By this word I mean all of reality, not just some local part of it, nor some passing phase

of it. Some people speak of universes starting and ending, of parallel universes, and in one case

even of "universes" as the smallestunits of an imaginary structure, like a matrix, which he

proposed using as a method of reasoning. None of these proposed uses of the word "universe"

were really universal, but merely playing with the word, like the astronomer who outrageously

called galaxies other than the Milky Way "island universes" when they were first discovered.2

Wisely, his colleagues have abandoned his usage for a better one.

2The author is probably referring to the English astronomer, Sir William Herschel (1738-1822),

who was the first to observe stellar systems outside the Milky Way

(en.wikipedia.org/wiki/William_Herschel).

Society

"Society" here means a community of humans (or other bions) in a group, not just some

clique as the word is sometimes used elsewhere.


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Besides these definitions of usage here, two categories of usage coinages or adaptations are

included.

First, to encourage thinking in longer time periods than most conversations do, and to make

references to longer periods, I add a few new words:

Centad

I have coined this word to mean 100 centuries or 10,000 years, a meaningful period of human

behavioral history, by comparison with "century" and "decade.

Millad

I have coined this similar word to mean a period of a million years or 100 centads.

In addition, I have coined a word to refer to a single living organism:

Bion

I coined this word to refer to anything that was produced by template copying of a nucleic acid

and still retains the potential to function.Biology is sometimes defined literally as the "science of life," but there is no universally

convincing definition of life. One way around this difficulty is to list a dozen characteristics of

some of the larger forms of life.3 However, one or more of these characteristics may be found

where there is no life, and often some are absent when there is life. Life may be said to be

present when "several" of these criteria show up. This leaves open the question of how many

characteristics must be present before something may be termed alive. This approach led to

varying opinions between those who did not accept viruses as life and those who did. This

division of opinion is understandable because bacteria were originally discovered through

noticing the diseases they cause, by scientists feeding the unseen troublemakers to breed them

into visible colonies, and testing them chemically. When researchers found themselves unable

to repeat the process with viruses, some concluded that viruses were merely poisons and couldnot be alive.

3Compare the definition of biology from About.comonline: Biology is the science that deals with living

things (< Greek bios, "life"). The definition of life from Dictionary.com gives as the first meaning: the

condition that distinguishes organisms from inorganic objects and dead organisms, being manifested by

growth through metabolism, reproduction, and the power of adaptation to environment through changes

originating internally (dictionary.reference.com/browse/life).

Today, though, we are aware of what viruses are, how their processes resemble and

differ from the rest of biology, and the fact that they do reproduce by the same method as the

rest of biology. In fact the study of biology now routinely includes viruses, even though viruses

lack all the characteristics of life but reproduction. Thus, biology covers the study of things thatreproduce by copying nucleic acid strings through a template process based on a preexisting

string. That is the one and only until universal in biology. It is consistently (though not always

precisely) true and it never applies to non-biological events. So the unit of biology is thebion.

A bion (after the first one) is a single, distinct entitywhich came into existence through

the copying of a nucleic acid, or its complement, by atemplate-style process. That would

include, for examples, you or me or any other human, or any other animal, plant, fungus,

protistan (a single-celled organism such as an amoeba, alga, paramecium, etc.), or a bacterium,


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an archaean, a virus, or a past example or ancestor of any of these. The study of biology

therefore becomes simply the study of bions. A class or collection of individual bions constitutes

biota, a term already in wide use.

The term "bion" by itself will make the origin of bions easier to understand, as we shall

see, and avoid quibbles over undefined words. (Some people use the word "organism" for this

idea or a similar one, but others use the same word to mean "alive" which muddies thinking.

Others use the word biont, but again it assumes a wide range of biological processes which

cannot all have come into existence at the same time and thus also muddies thinking.)

Note that I do not say a bion must be able to reproduce; a particular living bion may not

be able to reproduce (i.e., it may be sterile). But it is still a bion if it was reproduced by the

method mentioned. Any particular bion may thus be a biological subject. This definition will

include all biota and no kinds of non-biological occurrences, objects, or processes.

Third, I attach a new meaning to a familiar word, and thus more properly adapt the usage of the

following term:

EmpireCategories of biota are customarily named, in order of inclusiveness, individuals,

species, genus, family, order, class, phylum, and kingdom, with "sub-" and "super-" (as in

subkingdom, superphylum, etc.) added where more terms are needed. These are medieval

words, but well established and practical categories. Biology has now shown itself to have

numerous kingdoms naturally grouped into still larger categories. Keeping to traditional terms

for medieval society, I add a still higher or broader set of biota called an empire, each of which is

composed of multiple kingdoms.

Other writers have sometimes used the word "realm" for this idea, but that word might

not translate well into other languages, because a realm was usually a kingdom, but might relate

to a grouping of any size, while an empire in history has normally included multiple kingdoms or

principalities. Of course, the particular word used is not crucial, but a clear definition isnecessary. So "empire" is what I use here for a group of multiple kingdoms, such as the

eukaryotes, which includes the animal, plant, fungus, and protistan kingdoms which are

separate but related.

The meanings of these terms will become clearer as we proceed.

5. No Evolutionary Leaps

Evidence is convincing from wide experience that evolution and heredity make changes in types

of biota by countless tiny changes, not great leaps, despite someones attempt in each generation to

propose the idea of macro-evolution (super-mutations) or a set of simultaneous, coordinated

mutations. A new name for this idea is presented with each generational repetition, but no evidence

has shown a genuine example.

Bacteria can spread one or a few mutations at a time, and viruses (and presumably the early

protobiota) have mutations (reproduction copying errors) more often than do more complex biota, but

aside from bacterial giving and receiving of existing gene mutations, every new mutation is single in one

individual, involves one or two molecular changes, and normally makes only a slight change, if the

offspring survive. Many mutations are in fact lethal, killing the offspring at some stage of development.


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We are not usually able to see the results of a series of mutations individually, preserved by natural

selection or sometimes by accident over generations, but only see the results.

Yet we do constantly see individual, single-molecule (part of one gene) mutations in all biota,

and often it is not difficult to recognize some of the factors that at times lead, over time, to dramatic

changes in species.

For these reasons, biota cannot have begun with multiple biological capabilities at their start.

Rather, the first biota could only have acquired their growing range of characteristics one mutation at a

time in an environment initially not requiring the full modern set of capacities needed in later times,

which were later acquired under the influence of a series of changing environments. We shall examine

the earliest steps in Volume I.

6. Knowledge

We humans often speak of what we know, but this word exaggerates the extent of our

possible understanding. All parts of the universe affect the behavior of all other parts. (Some writers

deny this, saying distant parts are too far away to affect nearby parts. This view ignores the fact that

intermediate parts are affected by both, and pass on that effect to other parts continuously.) The

universe is far larger and more complex, at least, than any of us, or all humans combined. Therefore, noone of us, nor all of us combined together, can fully comprehend the whole.

But if all things affect all things, and we cannot hold the whole universe in our minds, then we

cannot know completely any of the individual things of which it is composed. Hence, we never truly

know anything; we can only collect information about it, reason about it, and reach the most

perceptive (though necessarily incomplete) picture of that thing or matter of which we are capable at

the time. By combined and continuous common effort, we can gradually get closer to whole truth, but

we are never quite there. In real life, we have to settle for the best picture we can reach in our time.

Accordingly, absolute truth is not available in any of these (or any other) volumes. Those

dealing with the most recent history, with the aid of contemporary documents and more familiar

circumstances, are likely to be the most nearly accurate, but no one ever knows for certain about the

motives and internal mental processes of another, so even written, contemporary documentation maynot be accurate, and is often ambiguous.

Still, the last few volumes are likely to be the most accurate of the series. Because of the

remoteness of the time, the far more limited records from those earlier times, and the less familiar

circumstances, the first few volumes necessarily must be the most speculative, but I have tried to make

these as accurate as current circumstances allow. The volumes in the middle of the series also are likely

to fall in the middle category of relative (un)certainty. I hope the result will clarify some things.


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CHAPTER B. INTRODUCTION TO VOLUME I

1. OutlineThis first volume takes us through the origin and destruction of stars generally, the formation of

our star, the Sun, the whirling system of which it is the center and dominant part, the materials of whichit and we are composed, of the Earth, and of our first steps upon that Earth, which were largely chemical

steps. Neither fossils, rocks, nor atmosphere from that time have been reported as directly found by

humans, so this volume and the next two must be more speculative than later ones. Even so, much has

been fairly confidently inferred from what has been found, so the major outlines are probably rather

convincing, though no one, as noted earlier, can ever quite get the whole picture perfectly.

Chapter D begins our story, covering very briefly and simply the physics and astronomy of stars,

Sun, and early Earth, and the early geology of Earth, while most of the remainder (chapters E through M)

describes some chemical steps which led to the beginning of biological molecules and reproduction, the

bionic Earth, the planet-wide "cell," and, finally, the first empire of biota, theprotobiota, some early

steps beyond reproduction, and other early chemical processes which still are basic to life, including

ours. In addition, the book contains a chapter N, containing a summary and conclusions from the

previous chapters, as well as a glossary of terms, a bibliography, and an index.

The terms from our list in Chapter C that will be used in this volume include:

proton, a positively electrically charged particle whose mass is used as the basic unit ofmass (the Dalton);

electron, a negatively charged particle; neutron, a particle with no charge but mass similar to the proton; atom, which we shall explain briefly as we come to it; millad, a period of a million years; bion, the unit of biology, resulting (most of the time) from reproduction through the

copying of nucleic acid by a template process; and

protobion, a bion from first great category (empire) of bions that existed on Earth.We shall also meet a few terms from chemistry as they come up. They are also listed in the

glossary at the back of the book.

2. IssuesThree major issues have arisen in the creation of this volume. The first relates to the sources of

information and inferences about the history of biology. For tens of thousands of years, humans (even

Neanderthals) have noticed fossils, and have studied them more methodically for about two centuries,

at first for practical reasons (mining prospects), later to learn about evolution. In the last few years,

biochemical genetic analyses and comparisons, and virus studies, have added greatly to the picture. In

the past century, a small amount of chemical study of ancient rocks has provided further information

and insights. In addition to these sources, and what we know of chemistry generally (learned in othercontexts), an experiment on the inferred early atmosphere of the Earth was conducted.4

4This is the Miller-Urey Experiment: Miller, Stanley L. 1953. A Production of Amino Acids under Possible Primitive

Earth Conditions, in Science 117 (3046): 528-529; and Miller, Stanley L. and Harold C. Urey. 1959. Organic

Compound Synthesis on the Primitive Earth, in Science 130 (3370): 245-251. Doi: 10.1126/science.130.3370.245.

In this experiment, having evidence from rocks that free oxygen (not in molecules with other

atoms) was not present in Earths air on Earths surface before 1.9 billion years after the Earth became


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solid, and knowing that in the universe and in meteorites the most common elements were commonly

hydrogen (with one proton in each atom), carbon (with six protons), and oxygen (eight protons), and

also knowing that todays Earthly air is largely nitrogen (seven protons), the experimenter created an

artificial air containing these elements, but with the oxygen only present as part of molecules with one

or other of the other elements. Thus, his artificial air had carbon dioxide (which is known to come from

volcanoes), carbon monoxide, ammonia (nitrogen and hydrogen), methane (carbon with hydrogen),

water vapor (oxygen with some hydrogen), some free nitrogen, and some free hydrogen.

He placed this reconstituted ancient air into a flask, and energized it with electric shocks to

imitate lightning on a primeval Earth. He also connected the air flask to a water flask, which he

heated to boiling for two weeks. When the equipment and contents were allowed to cool, the products

were tested to see what molecules would be present. The products included water, methane,

ammonia, and some other of the original constituents. New molecules which had formed in this model

world included seven amino acids, including three that play a part in modern life throughout the Earth,

hydrogen cyanide (one atom each of hydrogen, carbon, and nitrogen), butaldehyde (a string of four

carbon atoms and one oxygen atom, with some attached hydrogen atoms), and several other molecules

of biological interest. Thus, he inferred, early Earth could and must have produced early biological

molecules, before there was any biology.

Some critics objected to his assumptions, the exact proportions of the ingredients (though notgenerally to their identities), and to the fact that besides the biological and pre-biological molecules

found in solution in the water flask (simulating an early ocean), a tarry residue also collected at the

bottom, which was beyond analysis by the techniques of the time. No one disagreed with hydrogen

being present, and free oxygen being absent, but some thought that the hydrogen would not have been

free on early Earth, and more combined oxygen would have been present.

It turns out from later experiments that these changes in air would not have made much

difference in the products.5 (The earliest Earth has been presumed to have started with a largely

hydrogen air, but when Earth was still hot at the surface and frequently pummeled by celestial objects

of all sorts in its earliest years, much of that hydrogen is believed to have been lost into space.) Cyanide

molecules could easily combine into organic bases, of the kind in nucleic acids, and the aldehyde strings

of carbon atoms with an atom of oxygen can hook their ends together, changing some of them intoring (also called cyclic) compounds called sugars, including ribose, also a vital part of the first nucleic

acid.

5See e.g. Oro, J. and S.S. Kamat. 1961. Amino-acid-synthesis from hydrogen cyanide under possible primitive

earth conditions, in Nature 190 (4774): 442-443. Doi: 10.1038/190442a0. More recently, Lazcano, A. and J.L.

Bada. 2004. The 1953 Stanley L. Miller Experiment: Fifty Years of Prebiotic Organic Chemistry, in Origins of Life

and Evolution of Biospheres 33 (3): 235-242. Doi: 10.1023/A:1024807125069. The Wikipedia article Milley-Urey

experiment states: Within a day, the mixture had turned pink in colour, and at the end of two weeks of

continuous operation, Miller and Urey observed that as much as 1015% of the carbon within the system was now

in the form of organic compounds. Two percent of the carbon had formed amino acids that are used to make

proteins in living cells, with glycine as the most abundant. Sugars were also formed.Nucleic acids were not formed

within the reaction. 18% of the methane-molecules became bio-molecules. The rest turned into hydrocarbons like

bitumen (en.wikipedia.org/wiki/Miller-Urey_experiment, accessed April 13, 2013).


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The Miller-Urey experiment (from Wikimedia).

As to the tarry mess, further geological and chemical studies of rocks have shown precisely that:

very long-chain hydrocarbon molecules (strings of carbon molecules with hydrogen molecules attached,

of different lengths, mixed together in the oldest rocks reported to have been discovered on Earth).

Importantly, the very oldest such rocks show such hydrocarbons formed by non-biological

processes, because they contain both possible forms of each of those molecules (i.e., both left-handed

and right-handed optical isomersin a racemic mixture, en.wikipedia.org/ wiki/Miller-

Urey_experiment). Those rocks were reported to be 4.1 billion years old, though some dispute the last

100 million years, so we may conclude 4.1 +/- 0.1 billion years old.6 Bions only make one of the two

possible forms of those molecules, which first appear in rocks about 3.9 billion years old (also +/- 0.1billion years), still long before any fossils that have been found.

(In addition, a recent rocket probe of Titan, the largest moon of the planet Saturn, proves that

its atmosphere of surrounding gases now essentially matches the experimental atmosphereor air

used in the experiments mentioned.7)

6Earth is now said to be 4.54 +/- 0.05 billion years old (en.wikipedia.org/wiki/Age_of_the_Earth). The oldest rocks

on Earth analyzed thus far are crystals of zircon from the Jack Hills of Western Australia, determined to be 4.404


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billion years old. See Wilde, S.A., J.W. Valley, W.H. Peck, C.M. Graham. 2001. Evidence from detrital zircons for

the existence of continental crust and oceans on the Earth 4.4 Gyr ago, in Nature 409 (6817): 175-178). See also

Wyche, S., D.R. Nelson, A. Riganti. 2004. 4350-3130 Ma detrital zircons in the Southern Cross Granite-Greenstone

Terrane, Western Australia: Implications for the early evolution of the Yilgran Craton, in Australian Journal of

Earth Sciences 51 (1): 31-45. Doi: 10.1046/j.1400-0952.2003.01042.x.

7

The Cassini-Huygens mission in 2004 determined the content of Titans atmosphere 98.4% nitrogen, 1.4%methane, 0.1-0.2% hydrogen. See Coustenis, Athena and F.W. Taylor. 2008. Titan: Exploring an Earthlike World.

Hackensack, New Jersey & London: World Scientific Publishing, p. 130.

Taking these items of information into account, we may and must reasonably infer that the first

steps in, on, or over the pre-biological Earth toward the beginning of biology must have been about as in

this and later experiments, and must have begun before four billion years ago, probably half a billion

years earlier. (Interestingly, the period for which substantial and recognizable fossils exist that one can

see with the naked eye is also about a half billion years.)

The second major issue is the categories used to describe the protobiota. In a single species, and

then only for sexually reproducing bions, the standard for deciding whether a group is or is not a single

species is whether the members of that species normally engage in sex with each other to reproduce,

and are able to do so successfully. Even then, all degrees of intermediate situations exist, such as where

a female horse and a male donkey can produce a mule, though most mules are sterile, with only an

occasional fertile mule, in contrast to a situation where a certain kind of flying insect living on the lower

portion of a set of high mountains can interbreed and reproduce with an apparently similar insect from

high on the mountain, producing fully fertile offspring, but generally prefer not to do so.7

7The Wikipedia article on Species notes situations where the standard definition breaks down:

By definition it applies only to organisms that reproduce sexually. Biologists frequently do not know whether two morphologically similar groups of organisms are

potentially capable of interbreeding.

There is considerable variation in the degree to which hybridization may succeed under naturalconditions, or even in the degree to which some organisms use sexual reproduction between

individuals to breed.

In ring species, members of adjacent populations interbreed successfully but members of somenon-adjacent populations do not (en.wikipedia.org/wiki/Species).

See de Queiroz, Kevin. 2005. Ernst Mayr and the modern concept of species, in Proceedings of the

National Academy of Sciences 102 (Suppl. 1): 6600-6607. Doi:10.1073/pnas.0502030102.

In categories larger than one species, no precise standard exists, but categories of different sizes

are nevertheless useful, and have been in use for a few centuries. Closely related species are grouped

together into genera (plural ofgenus), which may be grouped into still largerfamilies. An orderis a

group of families, while several orders may form a class. Several related classes make up aphylum.

Phyla are then grouped into kingdoms. (Hence references to species for non-sexual biota do not depend

on the interbreeding standard at all, and cannot depend on the more inclusive categories.)60 years ago, biologists tried to squeeze all biota into two kingdoms: plants and animals, even

though they already had enough information to see that much larger groupings were necessary, and

most of what were classified as plants were far less like plants than plants and animals are like each

other. It has since become recognized that fungi (such as toadstools and bread mold) constitute a third

kingdom, and single-celledprotista are a fourth. We also know, and knew 60 years ago, that all four of

these kingdoms are alike in some ways, having cells with their genetic material in a separate bag called a

membrane inside the cell, which itself also has a membrane. This internal bag within the cell (with its


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contents) is called a nucleus (totally different from the much tinier nucleus of an atom). All biota with

nuclei (plural of nucleus) in their cells are called eukaryotes. This category, consisting of four major

kingdoms, is here termed an empire.

More important than the name for this larger category is the fact that most bions are not

members of the empire of eukaryotes. Far more numerous are theprokaryotes, bions with a cell

membrane but no nuclear membrane, and therefore no true nucleus. These mostly single-celled bions

are much smaller, generally, than even single eukaryote cells. I group them together as the prokaryotes

and that term is generally recognized in biology. This second empire is known to be divided into two

groups, which therefore are at least separate kingdoms: the bacteria, well known, and the archaea,

discovered more recently. Some people would make these two kingdoms into separate empires from

each other, because they share relatively few genes, and therefore differ from each other far more than

humans differ from, say, yeast.

Another group of biota differs even more: theprotobiota. They are clearly a separate biological

empire, and differ rather fundamentally among themselves, into five or six distinct kingdoms. Some

scientists who work with protobiota regard them as related to the bions which they parasitize, but this

view misses the basics. Their structures and genetic systems are mostly utterly different from any biota

other than protobiota. These structures and genetic systems are far more fundamental than any

particular genes. So the genes do not indicate genetic relationships with other biota in this case, butonly variable adaptations to their environments, inside other bions in which they are now parasites.

So biology includes at least three empires: (1) the protobiota, (2) the prokaryotes, and (3) the

eukaryotes, and each of these empires consists of multiple kingdoms.

The third major issue is the nature of the fundamental or foundational step that marks the

beginning of real Earth biology. (Some writers have presumed to tell us what life may be like in places

other than on and around Earth, in one case even suggesting that computing machines could be a kind

of life because of their intelligence. This has been called astrobiology, generalizing from

information on Earth biology. This project appears a bit premature to me, since no unambiguous life has

ever been detected from elsewhere, and we do generally not yet have enough information on Earth-

based biology to start branching out into places we havent explored. Whether or not that project is

appropriate, it is not touched upon here.)Various proposals are mentioned below. None of them seem to have found the key, but some

suggest a related aspect of reality which seems likely to have played a part, as outlined below.

Among proposals by various writers on such a basic first crucial and founding step in, on, or near

Earth, are the following:

(1) One idea, generally no longer given much credence, is that Earth biology is derived frommigrating primitive forms which arose elsewhere.8 No evidence of such an event, no source

place, no suggestion of the mechanism or arising in that source place, or any reason for

supposing such a thing can happen has ever been found. Biology on Earth appears likely to have

started about as early in the existence of Earth as such existence was possible in the then-

existing conditions, composed of atoms available on Earth, and starting too simply to have likely

survived any space travel, even if some mechanism of launch on that journey could be found.

8This is the hypothesis termed panspermia (en.wikipedia.org/wiki/Panspermia). It suggests that life

exists throughout the Universe, distributed by meteoroids, asteroids and planetoids. See e.g. Mautner,

M. and G. Matloff. 1979. Directed panspermia: A technical evaluation of seeding nearby solar systems,

inJournal of the British Interplanetary Society32: 419.


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We may appropriately point out, though, that the Earth itself is composed largely of

atoms spewed out by past stars, so Earth and its inhabitants are, in a sense, composed of star-

dust from afar.

(2) One Scottish writer has proposed that the first genetic material was composed of clay crystals,which could evolve, organize the earliest biological processes, and finally be replaced by a

nucleic acid takeover.9 No evidence has been found to support this view. No present fossil form

has been reported to have been found functioning at all like this. No present bion shows any

sign of such an organism, nor has any experiment shown such an event to be possible. This does

not seem a worthwhile direction to pursue.

9I am uncertain who the Scottish writer is. But see Palacci, Jeremie, Stefano Sacanna, Asher Preska

Steinberg, David J. Pine, and Paul M. Chaikin. 2013. Living Crystals of Light-Activated Colloidal Surfers, in

Science 339 (6122): 936-940. Doi: 10.1126/science.1230020.Still, certain atoms, particularly metals, as well as certain compounds, can influence the

behavior of adjacent atoms, in the process called catalysis, as we shall see, and this sort of

mineral likely did, and in a controlled form, still does play a part in biology.

(3) Because early biochemists discovered protein and at first believed that protein was the essenceof life in a sense, and because protein is made of amino acids, which sometimes arrive inmeteorites and showed up in the (Miller-Urey) experiment mentioned above, some researchers

have suggested that Earth life started with proteins forming spontaneously and perhaps even

reproducing and evolving before nucleic acids were added.10

Unfortunately for this view, no one

has found proteins or other amino-acid compounds capable of performing any such steps, either

in nature or in a laboratory. This idea seems unhelpful in this form.

Even so, as in the previous examples, there may be this merit, that amino acids do form

in some meteorites, in the (Miller-Urey) experiments, and therefore presumably did so

somewhere in, on, or over the early Earth, perhaps in air or in the ocean; these amino acid

molecules do tend to join end to end, yielding small, usually circular sets of such molecules

(called peptides); and these peptides can in some instances influence the behavior of other

atoms and molecules, as we shall see. Thus they did likely play some role, just not the one

suggested.

10I am uncertain of the identity of these biochemists. But see Daniel P. Glavin, Andrew D. Aubrey,

Michael P. Callahan, Jason P. Dworkin, Jamie E. Elsila, Eric T. Parker, Jeffrey L. Bada, Peter Jenniskens,

Muawia H. Shaddad. 2010. Extraterrestrial amino acids in the Almahata Sitta meteorite, in Meteoritics

and Planetary Science 45 (10-11): 1695-1709. Doi: 10.1111/j.1945-5100.2010.01094.x.

(4) Colloids are mixtures of a fluid of one composition with particles of another composition, inwhich the particles do not truly dissolve in a chemical sense, but are so small that they do not

settle out, but remain in suspension, floating as if weightless in the fluid. Milk is an example:

milk is basically a fluid (water) with particles of fat and protein floating in it. In natural milk, theparticles of fat, being less dense than the water, tend to separate out, with time, floating to the

top and forming a cap of cream over the remaining milk.

The protein, however, interacts with the water and stays suspended, like a sort of

solution, but not a true chemical solution. Letting the milk stand for a week will still not result in

the milk protein settling out, so the milk stays white and opaque, unless bacteria enter and

cause spoiling or clabbering. (Colloidal suspensions are normally opaque, so you cannot see


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through them; true chemical solutions are normally clear, so you can see light through them,

although they may be colored.)

In the twentieth century, scientists first discovered the nature of colloids, and sizes

necessary for a particle to remain in colloidal suspension in certain particular fluids. This led to

homogenizing, which was breaking the cream down into particles small enough that they would

not settle out.

A Russian scientist, perhaps inspired by his new awareness of colloids and of colloidal

particles, invented the term coascervate for a tiny particle of (perhaps miscellaneous) material

which would remain floating (in suspension because of its light weight), as the first step to

biology.11 No evidence has been found that this was true in the early ocean, but various

molecules and atoms do sometimes attach themselves to surfaces, such as the bottom of the

ocean, grains of sand or clay, or floating debris, whether forming flat surfaces, floating colloidal

particles, or microscopic crevices in earth. This attachment is not, itself, biological action, but it

may increase the likelihood of one such adhering molecule meeting another on the same

surface or particle, or in such a crevice. Some such meetings likely did lead to chemical

interactions that started some biological processes or steps.

11

See Pollack, Gerald H., Xavier Figueroa, and Qing Zhao. 2009. Molecules, Water, and Radiant Energy:New Clues for the Origin of Life, in International Journal of Molecular Science 10 (4): 1419-1429. Doi:

10.3390/ijms10041419. They mention the term coascervate and cite Oparin, A.I. 1965. The Origin of Life

(2nd

ed.). New York: Dover.

(5) Some biologists think of the biological cell as the first crucial step, on several bases12:They do not think that nucleic acids can form without previous biologic mechanisms;

They consider that certain lipids (trios of chains of hydrocarbon compounds, around 14-

18 carbons long, attached to an acid, triglyceride), naturally and spontaneously (i.e., chemically)

join one another in water to form bubbles or globules (as we shall see later in more detail);

They consider the cell the smallest possible unit of life, and therefore necessarily the

first, one the grounds that what is living must be separated by a membrane from what is not

living.

12See, e.g., Moulton, Glen E. 2004. The Complete Idiots Guide to Biology. London: Alpha (a member of

Penguin Group), p. xxii: The next chapters establish the cell as the basic unit of function for all living

things.

This idea is unconvincing for several reasons. First, the necessity of a membrane is too

narrowly defined. Second, in the absence of previous life, it is unclear how enough lipid

molecules could be formed in the same area to make such a globule. Third, globules alone have

no means of copying themselves, evolving into biological forms, collecting the contents of

typical cells in their interior, or giving rise to cells. Finally, the simplest cell known is still far too

complex to have been formed at one time by a single event. No evidence exists to support thisproposal and no modern form (no proto-cell) has been found that is consistent with it, although

modern cells do have lipid external membranes.

(6) Some biologists consider that life, or at least the nucleic acids that contain the blueprint for it,cannot have existed until after metabolism was established. But there is no suggestion how that

might have happened, no such example is extant today of metabolism without genes, and there

seems to be no way that such a system could arise, evolve, or become complex enough to be

properly called metabolism. Further, such a system would provide no advantages to the


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molecules composing. Moreover, the word metabolism is a catch-all term that includes a wide

range of sequential and interwoven chemical steps which could not have arisen simultaneously

and cooperatively without some chemical assistance. Thus, there must have been an earlier

stage before metabolism was established.

(7) What we do have information about is that all biota now on Earth have been reproduced bytemplate copying of nucleic acids: virus particles or virions each have at least, and in some cases

consist entirely of, a nucleic acid molecule composed of a number of nucleotides strung

together in a chain, which may be ribonucleic acid (RNA) for the simpler ones or

deoxyribonucleic acid (DNA) for the more complex ones. All other biota are based on both of

these types of nucleic acid as the basic tools of both reproduction and genetic specification of all

the proteins, lipids, and other chemicals comprising both the structures and functions of these

biota, as we shall see.

Of these, RNA appears to have arisen first. It has not only the ability to reproduce (the

first step in biology) but also the ability to catalyze other chemical reactions. At first, then, RNA

could serve as both reproducer and built-in catalyst (the latter function later was largely

assumed by proteins). Even those biota which use DNA as their reproducer and the instructions

for making proteins still can perform those processes only with the aid of RNA. For these and

related reasons, most scientists who have specialized in the question of biological origin onEarth have concluded that RNA was the earliest and most crucial step, and still continually find

new functions which this versatile molecule performs in all of us.

On the other hand, some early chemical bits of what later came to be called metabolism

probably did arise in the period covered by this volume, and gradually increased the ability of

the new protobions to survive and increase in numbers.

From these several examples we may conclude of these various suppositions, as was

said of the famous blind men who tried to describe the nature of an elephant after their first

attempt to examine it, each touching a different part, that: each was partly in the right, and

all were in the wrong!13

13

A reference to the poem The Blind Men and the Elephant by John G. Saxe (in Woods, Ralph L., ed.1944. A Treasury of the Familiar. Chicago: Consolidated Book Publishers. Pp. 8-9). After each of six blind

men feels a different part of the elephant, pronouncing it to be like a wall (the side), a spear (a tusk), a

snake (the trunk), and so on, Saxe writes: And so these men of Indostan / Disputed loud and long, / Each

in his own opinion / Exceeding stiff and strong, / Though each was partly in the right, / And all were in the

wrong!

Looking Forward

This volume explores some aspects of how the prebiotic Earth reached the RNA stage, how it

progressed from that relatively simple beginning to create additional kingdoms and capabilities,

developed the genetic code, produced the first genetically generated peptides and proteins, enlarge its

most advanced genetic capability, and laid some foundations for the coming first cells. Volume II willcontinue with the evolution of cells, their differentiation, and their further history, as our ancestors kept

adding to what later became other ancestors and co-holders of Earth, even to ourselves.


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CHAPTER C. SETTING THE STAGE

Before we start this journey through our past, what facts, tendencies, and factors applied when

our story started, and still do?

Universe

We started, then, with the Universe containing and consisting of space, radiation, mass,

including stars of various sizes, spreading energy into space by the processes of nuclear fusion, various

planets, moons, planetoids (sometimes called asteroids), comets, meteors, rays, particles, dust, gasses,

etc., mostly gathered into spinning galaxies, clusters of galaxies, clusters of such clusters, and much

more. The Universe also contains tiny particles of various kinds, of which the rest is made, and now

(though not at the beginning of our story) contains us and all other biota, as well as our Sun and Earth

and the rest of the Solar System.

Systematics

The Universe is a system. A system is a whole made of many parts which all move or functionwith respect to each other, influence each other and the processes involving each other, and are

influenced by each other and by those processes and their results. We study these influences and

behaviors or phenomena under the title ofphenomenological sciences. The general titles of these

sciences are:

1. Physics

2. Chemistry

3. Biology

4. Sociology, and

5. Ecology.

Each such branch of science studies and tries to find general principles that apply widely, with

respect to particular aspects of reality, dealing with different kinds of interactions. Each such branch of

science also is the result of the interactions of the science listed before it. In theory, then, all other

sciences should be inferable from physics, the first. If we could calculate and reason well enough, we

could foresee and calculate all of chemistry from physics, biology from chemistry, and so down the list.

In practice, we cannot do that. Physics tells us some important things about chemistry, but we need

chemists to go beyond that. The same is true on down the list. Chemistry tells us much about biology,

biology about psychology and sociology, etc., but not everything. We have to use these separate

approaches (branches of science) to go beyond these predictable elements to get a digestible idea of

what is and how it works.

Thus, humans have only been able to get to the most basic aspects of each of the fields by

applying discoveries and principles derived from the previous ones. Beyond those most basic steps, we

must apply slightly different approaches as the branches become steadily more complex from physics to

ecology. Working separately at each of these five levels of complexity has enabled us to make many

discoveries that we could not forecast from the first. But of course reality is all one thing; we only divide

it up this way to cut some aspects of it into bite-sized bits that will fit in our limited minds.

Other sciences


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Some sciences, such as astronomy, psychology, and geology, seek more specialized kinds of information

relating to more particular objects, not universal principles. They often borrow techniques from the

other sciences for their purposes.

Recently (within the last century or so), humans have discovered certain more general principles

that apply in all of these branches of science. Systematics is a general property of reality, and applies in

all sciences, whether physics (e.g., meteorology or weather), chemistry (e.g., polymers and simultaneous

or sequential interactions among different molecules), biology, sociology, etc.

Firstly, we have found that the events or behavior of the parts of system are controlled by

behavioral tendencies have sometimes been calledforces or interaction behavior(or tendencies), and

that involve processes. We shall return to these ideas, but also specific frequent elements of systems

generally apply, regardless of the branch of science involved.

In computer and management systems, one such specific element is the idea offeedback.

Feedback is a means of control over a process. If we boil water in a pot or tea kettle, the result

is water vapor filling a much larger space than the water did. From a pot or kettle, the water vapor can

normally escape, and no problems arise unless the water boils away and the heat source melts the pot

or kettle. If the kettle has a whistle, when the water vapor is escaping rapidly, the speed of its escape

makes the whistle sound and the cook (if attentive), knows it is time to slow or stop the heating. This is

merely a signal, but an automatic one arising from the boiling itself, so no one needs to see the boiling.A steam engine goes further. When the steam presses hard on a little swinging door called a

valve, the steam pushes the valve open and escapes into open air, so the engine tank does not explode,

as it otherwise would from excessive steam pressure. Hence the machine system protects itself,

without any human intervention (unless the valve sticks, etc.). This is one sort of feedback mechanism.

Another is a sand dune. The wind blows the sand until it meets an obstacle or the wind changes

direction or dies down. The little pile of sand obstructs further sand blowing by later. The dune

therefore tends to move but also to grow. When the dune is high and steep, further sand blowing

against it tends to roll back down the dune, limiting its size. This, too, is feedback.

Other examples occur in chemistry and biology as well as in machinery and other physical

processes. When many chemical reactions can go in either direction, the reaction can be forced one

way by removing one resulting atoms or molecules of one kind as they form. For example, hydrogenmay combine with oxygen to make water, or water may be split into hydrogen and oxygen. If the

chemist or the situation allows the gases to escape, the water will all disappear, because the splitting

will dominate and the joining will fail (requiring other steps too). Similarly, if an animal does not eat for

long enough, it feels hungry and starts eating, continuing until it no longer feels hungry. If all the sub-

systems are well aligned, this balances food intake properly.

Likewise, societies and ecologies have some feedback mechanisms. If too many animals are on

the Earth, the use so much oxygen and give off so much carbon dioxide that this makes life harder for

themselves. But the extra carbon dioxide makes plants grow better, and plants then add oxygen back,

and, so far, life has continued. But none of these natural feedback mechanisms is perfect and the same

often proves true of manufactured machines. The system can work, but it can also break down.

Feed-forward

Sometimes a side effect of a process, instead of limiting may enhance that process. This is called

feed-forward. Both feedback and feed-forward may be either positive, enhancing the process, or

negative, limiting it. As a fire burns more fuel, it may spread and reach ever more fuel, increasing its

over-all size and temperature. This situation can cause run-away processes, unless limited by

exhaustion of fuel or countervailing processes that tend to restore balance.


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Another example is too many people in too small an area increasing the spread of diseases.

Biological systems and geological cycles tend to develop feedback and feed-forward aspects, keeping

the systems somewhat controlled, balanced, and adapted for survival, within limits. Of course, if the

limits are exceeded the entire system may change dramatically or fail altogether as happens from time

to time.

Subsystems and Modularization

A large and complex system commonly is divided into subsystems. All systems other than the

Universe are subsystems of the Universe and may have smaller subsystems within themselves. This

division into subsystems is sometimes called modularization because the subsystems are called

modules. Complex systems may contain a hierarchy of subsystems, whether natural or manufactured.

This is common in biology (including us), in sociology (in large organizations such as corporations,

governments, armies, and some voluntary service organizations), and in ecology.

A whirlwind or a fire is a system carried out by one or more processes. An airliner has in it a

lighting system, an electrical power system, a jet propulsion or propeller-engine system, a guidance

system, two or three communication systems, and procedures for service, loading, and unloading, etc.

A bion, a machine, and a nation-state often are systems with many subsystems and included processes.Systems can control themselves or be controlled by measuring devices, feedback processes,

sensing devices, and countervailing processes. For example, a steam engine can control its internal

pressure by having an outlet closed by a valve, which can open only when the inside pressure is strong

enough to overcome the resistance of a spring holding it shut. Opening allows some steam to escape.

When the pressure is low enough, the spring will close the valve.

If the steam passes through a tube back to a sensor operating the fuel feed, excessive pressure

may reduce fuel feed and thus indirectly reduce the pressure. This is an example of feedback, actively

operating a control process (reducing fuel intake) to reduce heat and thus pressure.

Living cells measure time by operating timing systems of two or more coordinated genes. When

the supply of one protein, which we shall callA, is too low and needs increasing, this condition activates

the gene for producing protein A, so the supply of this protein rises steadily. When the supply of Abecomes high, that condition triggers the other gene, which produces protein B. As B starts rising, it

signals the first gene to stop making A. Later, when B becomes high, that signals the first gene to start

making A again, and the second gene is signaled to stop making protein B. This system, modified in

various ways, creates many biological clocks that tell animals, plants, and perhaps fungi to behave as

though it is daytime or nighttime, even when they are cut off from sunlight, or left in artificial light all

the time. That is why most flowers (and people) come out in the morning and retire at night.

These biological clocks can be reset by light or darkness to adjust for seasonal or geographic

changes, but if we travel far enough and fast enough, or change our working shift, we often will not feel

right for a few days, and other biota also take time to reset their biological clocks.

That system is what tells us it is time to awaken or go to sleep, to eat meals or to stop, etc.,

although the mealtime and satiety feelings are also influenced by other signals, such as an empty or full

stomach, etc.

Another example is that satellites start being drawn by increasing gravity toward what they will

orbit, normally starting from a path that would not result in collision. As they draw closer, they pick up

speed, so, although they have fallen closer to the larger object, they reach a balance between the

forward speed producing centrifugal force or behavior (pulling the satellite away, like a ball on a string

whirled around one's head) and the centripetal force (gravity pulling the satellite toward the larger

object). If the smaller object reaches such a balance of behavioral tendencies, it just orbits the larger

object, as the Earth orbits the Sun, or the moon Titan orbits Saturn. Yet this is not a perfect or


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guaranteed orbiting or circling. The orbit may be disturbed by some third object. Ultimately, satellites

fall to the central object eventually, but may continue orbiting for billions of years, because there is little

friction in space. Still, there is some.

Systems and subsystems generally also have other general characteristics, and individual ones in

particular systems. One common one noted first by computer-system designers is pattern of "input,

processing, output". In some cases, input happens once, the process operates for a while, whether as

short as an explosion or as long as decay of an orbit, and then output occurs once or over a short time,

but other systems, like the Venusian water-sulphuric acid system described below, displays continuous

input and processing cycles with continuous output. Designers and users usually want continuous input

leading to continuing output, and, of course, biology and some other natural systems also need to

display that feature over considerable time.

Process

Processes go on in every system or subsystem. A process is a set of interactions among

participants in a system that lead in some direction, or circularly in a cycle among other processes, as in

the Venusian system just mentioned. A dune is built by wind against grains of sand, but limited in size

by gravity pulling the grains downhill and therefore by the steepness of the dune. Continuing wind maymove or destroy the dune.

In general, processes may behave in one or another of the following ways:

(1) A process may not proceed at all, despite the elements being present, either because of

interference by unhelpful or inhibitory elements, the wrong temperature, the wrong state of some

circumstance (moisture, aridity, direct contact, lack of trigger, need for missing energy source, type or

lack of solvent, etc.).

(2) The process may go to completion: A hill with water running down or wind blowing across it

may be worn down flat When sand is mixed in water, shaken, and left to stand, a tiny bit of the sand

may dissolve, but almost all will settle to the bottom. When a little salt or sugar is mixed in water and

shaken, it all dissolves. When a little sodium is dropped in a flask of hydrochloric acid, the sodium races

around the surface of the acid briefly, spitting bubbles in all directions until no free sodium is visible.When water in a pot boils long enough, eventually none is left.

(3) The process may be interrupted: In the examples of sand, salt or sugar, or sodium in a

container above, the vessel may break or its contents spill out for some other reason onto an interfering

surface. A bacterium may live normally until a toxic substance stops its life processes or a euchariotic

cell eats and digests it.

(4) The process may go to equilibrium: You may put some epsom salts in warm water to soak a

swollen foot, and stir the water until all the salt dissolves. Then you may add more salt and repeat. But

if you continue adding salt, it begins to collect on the bottom, sides, or top of the container or your foot,

no matter how long you stir. Why? This amount of water will only dissolve so much salt at this

temperature. If more salt is added beyond that, a few new molecules may dissolve, but an equal

number will settle out of the water. This is equilibrium, because the solution has reached a balance

between what it can dissolve and the amount already dissolved.

The same may happen without any visible effect, where a certain amount of two different kinds

of molecule are put in the solution, changing them partly to something else, but they only go so far, so

40% yields the desired result, but 60% remains what you started with. Individual molecules may

continue to change in the direction intended, but equal numbers of the product break up into the

original two kinds of molecule.

(5)..The process proceeds initially toward the expected end or goal, but the product or result is

eliminated by a further, unexpected process.


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(6) A process may be driven to continue by a continuous influx of new resources or whatever is

needed to keep it going. This situation is rarer than the other possibilities mentioned above and tends

not to continue indefinitely, but may continue for a long time, as we shall see. For example, a machine

may run as long as it has a power source, such as electricity, gasoline, or diesel oil. A bacterium may live

as long as it has available what it needs. Biota may continue to live and change on a planet as long as a

usable energy source is available, such as sunshine. Plants change carbon dioxide into food and animals

eat the plants and provide carbon dioxide. But if the Sun goes dark the plants die, the animals and fungi

starve. Sunlight "drives" most of life on Earth today.

A driven process, instead of evolving gradually by small changes resulting from copying errors or

imprecision in reproduction and differential survival, as normally in biology, may simply become cyclical.

On Venus, the great heat at the planetary surface boils water, which rises as vapor into the air or

atmosphere of the planet. Now, much of that atmosphere consists of sulfur dioxide. The Venusian

atmosphere is slightly cooler than the planet's surface, but warm enough so that the water vapor

combines with the sulfur dioxide to make sulfuric acid. Sulfuric acid is heavier than either sulfur dioxide

or water, so the acid rains down onto the surface again. The first part of the process repeats, sending

water and sulfur dioxide back into the air, and the cycle continues unchanging.

A general result of the science of systematics is that systems behave similarly and have similar

properties regardless of the particular science to which they are applied. Thus scientists often note thatfeatures of one science pop up again in another. Sometimes that is merely because the same systemic

process is at work, rather than any other connection between the two sciences. But it also is sometimes

the result of actual application of information from one science to the next more complex science, an

overlapping of sciences or parts of them. These two situations are quite different, a fact not always

recognized.

Emergent Behavior

Humans can learn some of the basics of any of the sciences of phenomena by reasoning from

certain information about the next more complex science, as the physics of electrical attraction and

repulsion help us understand the basic nature of chemical attraction and molecular formation. Butusually the more complex science cannot be fully understood from information learned in the simpler

science. Perhaps if our brains were more complex, we might make this leap more often, but usually

study of one of the more complex sciences depends mostly on information acquired from examining

directly the kinds of phenomena typically studied in that more complex science. This is due to what is

called emergent behavior. This phrase means we see this behavior within the phenomena studied by

the more complex science such as chemistry, biology, ecology, or sociology, but we would not have

predicted it from the simpler science (such as physics).

One example is our simple sand dune, mentioned above. Studying the characteristics of the

sand grain and applied wind (including friction, grain weight, etc.), we can predict the behavior of grains

at early stages in the process of building the dune. But an emergent property of the resulting dune, the

next higher level of organization, arises from its steepness on the windward side. At some critical point,

that steepness causes some sand grains to roll back down the dune. Nothing learned about individual

grains predicts that steepness, although the steepness is partly determined by the shapes of the grains,

which normally vary too much to be useful in making such predictions.

Similarly, the physics of electrical attraction tells us something about the attractions and

behavior of atoms and their formation into molecules at each point. But no one predicted from this

information the complicated behavior of large, complex proteins, DNA, and other biological molecules,

and how they interact in biology. That was discovered through biochemical studies. One result of

biochemical forces is that some bacteria have attached in their cell membranes a set of molecules that


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spin like a wheel (!), making a rotor which turns a whip-like flagellum. This in turn propels that

bacterium in a particular direction depending on chemical information coming in to the bion.

That information relates to the density of available food sources in the vicinity and of

obstructions and of harmful or toxic chemicals nearby. Internal processes connect the molecules that

receive the information with the rotor, influencing its motion to move the bacterium forward or

backward or to stay where it is. Our own behavior is still more complex and less likely to have been

predicted by the physics or chemistry of the body. This is emergent behavior.

Studies have shown that complex systems and processes can be steady, with results predictable from

input in a simple manner. Or those systems and processes may even be still. But they may also become

quite complex and dynamic, with output varying in response to input in very involved ways. Much of

biology consists of processes that are not particularly steady and proportionate but rather quite

variable, in fact often at the boundary between order and chaos. Chaos, in this sense, tends to be a

higher form of order, quite variable but calculable (if one has all the facts and knows how to interrelate

them, which is seldom true), resulting in, for example, seemingly irregular variations over time, but with

the danger that the whole system may collapse unexpectedly if pushed too far by circumstances.

An interesting example is an islands ecological system, isolated for a long time from other

interfering biota. Occasional birds, insects, and seeds come ashore and build up this system over time,

adapt to the environment and each other, and become quite robust and long-lasting, even thoughseasonal and weather factors tend to make population and propotions waver from year to year.

Then humans begin to arrive and bring a few additional animals and smaller numbers of plants

from time to time. The native species and ecology continue, seemingly unaffected, for a few more

generations. Then, unexpectedly, one more introduction finally pushes the entire ecology beyond its

ability to survive. The whole system collapses and most of its participants become extinct. This actually

happened in my lifetime. It is an example of what happens at times when we dismiss variation from

year to year as not being meaningful. The system had been in increasing stress and finally could no

longer survive. It was like the proverbial straw that broke the camels back. By itself, the final

introduction of a new species seemed trivial but it was part of a rising accumulation and could not be

accommodated.14

14This may refer to societal collapse on a remote Polynesian island. As noted in Jared Diamonds Tanner Lecture

for the Year 2000 (Ecological Collapses of Pre-industrial Societies, available at

www.sscet.ucla.edu/anthro/bec/papers/Diamond_Ecological_Collapses_of_Pre-industrial_Societies), a number of

such societies collapsed to the point that no humans survived. These include Henderson Island, Neck Island, and

Pitcairn Island prior to its settlement by mutineers from the Bounty (p. 4). Easter Island is the best documented

archeologically. There are now no native trees or land birds on Easter Island, though a few species of seabirds

survive on offshore stacks of rocks. When first discovered by humans, it was heavily forested, with at least six

species of land birds inhabiting it along with around 30 species of seabirds. The first Polynesian settlers began

clearing the forest for agriculture and hunting the birds. The human population increased rapidly to a density of

around 160 people per square mile. The island was completely deforested and all the land birds and most of the

seabirds became extinct, the topsoil eroded, sharply reducing agricultural output. Without the wood to build

canoes, the people had to stop much of their fishing as well. About three-fourths of the human population died by

the time of the final collapse. However, as Diamond observes, many Polynesian societies continued to flourish. So

other factors besides human activity were involved, including rainfall, volcanoes, and latitude (dry islands at high

latitudes with volcanic activity were the most fragile environments).

The Physics Stage Setting at our Beginning

Pertinent Particles
http://www.sscet.ucla.edu/anthro/bec/papers/Diamond_Ecological_Collapses_of_Pre-industrial_Societieshttp://www.sscet.ucla.edu/anthro/bec/papers/Diamond_Ecological_Collapses_of_Pre-industrial_Societieshttp://www.sscet.ucla.edu/anthro/bec/papers/Diamond_Ecological_Collapses_of_Pre-industrial_Societies


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The Universe includes parts and their interaction tendencies. The smallest parts with which we

need to be concerned are called particles, waves, and rays. We do not have space here to discuss all of

these. For our purposes, only a few are crucial to our story: protons, electrons, neutrons, and phota

(the plural ofphoton).

Phota (sometimes calledphotons) are units of electromagnetic radiation, such as light, heat, X-

rays, microwaves, radio waves, and gamma rays. These waves or rays have different wave lengths, and

the differences in wave lengths are what distinguish among them.

Heat and infrared waves are long, microwaves and ultraviolet rays are short, while other short waves

can be detected with some radios. Red radiation has longer waves than blue. Yellow is in between.

Because our Sun gives mainly yellow light, our eyes have adapted to seeing yellow in daylight better

than any other color. That is why yellow looks lighter and brighter in daylight than any other color

(except white, which is a combination of all wavelengths of light).

In very poor light, as at dusk, without artificial light, yellow seems darker and blue seems brighter,

because our day-vision light receptors cannot see well, and we rely on different, poor-light receptors,

which see blue better. I first noticed this as a small child, observing the wallpaper in my room in

twilight, without artificial light, watching the yellows in the pattern darken and the blues brighten as

evening darkened, and the reverse before dawn. Of course, optical scientists recognized this much

earlier.Our eyes see light and our skin feels heat. But we cannot detect the other rays except with

special instruments, such as radios, television sets, X-ray film, and the like. We can cook with

microwaves. Heat and light will mainly interest us here.

Protons and electrons are particles with equal but opposite electrical charges or natures, which

attract them to each other, like males and females. The charges are called positive and negative (any

two opposite titles would have been just as good: yin and yang or left and right, etc.). Neutrons have no

electrical charge.

Interaction Behavior

All the small parts (particles and subatomic waves) behave in ways suggesting four influences on(or reactions with) each other. Most of these influences are attractions, acting with varying strengths at

different distances between the particles being considered. The strongest of these influences or

attractions is simply called the strong force, influence, or interaction tendency. It is powerful enough to

hold protons and neutrons close to each other, at the tiny distances between them, in the center or

nucleus of an atom, even though protons at greater distances repel each other because of their like

electrical charges.

Within its short range the strong force is far stronger than any other force. Like all the

influences we are discussing, its strength or influence decreases as two such particles get farther away

from each other, and the decline of this interaction is very rapid, so the attraction is already weaker

than that of other forces at greater distances than those in an atomic nucleus.

The influence of the strong force between any two particles fades with the sixth power of the

distance between the two particles. For example, if the distance is doubled, the attraction between

them is reduced to 1/64 of its strength when the particles were closer (1/2 x 1/2 x 1/2 x 1/2 x 1/2 x 1/2 =

1/64). Consequently, the strong force, though the strongest in the universe at the closest distances,

becomes so weak that, at longer distances, other influences swamp its effect. For comparison,gravity,

more familiar to us, is a rather weak influence, but it weakens far more slowly, only in proportion to the

square of the distance (if the distance doubles, attraction becomes a quarter of what it had been: 1/4).

Hence gravity has by far the most influence at long distances.


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The weak force, though of course much weaker than the strong force, also is only important at

distances within the size of an atomic nucleus, and is also an attraction.

The third influence is called electromagnetism. It has two related effects: the simple electrical

aspect and the magnetic aspect. Its electrical aspect makes all positively charged particles (including

protons) attracted to all negatively charged particles (including electrons), and likewise all electrons are

attracted to all protons. So this aspect of this relationship is an attraction, like those above, and is

mutual, also like those above. Unlike these examples that we have considered, the electrical charge also

has a repulsive effect: protons repel each other, when beyond the distance at which the strong force

exceeds the electrical one, and likewise the electrons repel each other.

So naturally, protons not in a nucleus stay at a distance from each other, and electrons behave

similarly, but a proton and an electron attract each other, and so tend to team up in pairs. Mostly, they

do not attach to each other except in nuclei to form a neutron, but most electrons stay near the proton

with which they have paired. In this way, this attraction keeps electrons in the same atom with their

protons, but not in the nucleus. These electrons, formerly calledorbital electrons" are kept in certain

areas outside the nucleus but still in the atom. Those areas used to be described as orbits, like planets

orbiting the Sun, but more recently the region within the atom in which an electron stays is called an

orbital, which in this usage means a three-dimensional region a little like an orbit, often shaped rather

like a tear drop. The fatter end of this "tear drop" is where the electron is most of the time.Outside the range within which the strong force overwhelms all others, the electric force or

influence can be a powerful attractive or repulsive force at distances within the outer parts of atoms and

molecules, and therefore is very important in chemistry, the main process in this volume. The strong

force may be significant for slightly longer distances, but usually only for inches, except in weather

effects, such as lightning, which may extend somewhat farther.

The magnetic aspect of electromagnetism, like the electric aspect, has an attractive and a

repulsive effect. Magnetism arises from certain behaviors of electrons, including motion and

orientation, creating another set of opposites: we call them north and south (again, as with positive and

negative charges, these words in this context mean nothing more than that the two influences are

opposite to each other). North magnetic poles attract south magnetic poles, and vice versa, but north

poles repel other north poles, and south poles repel south poles. (We may say that magnetic fields offorce are circling in opposite directions between the two opposite poles, but we need not focus on what

that really means.) Magnetism will only play a slight role in this study, because we humans lack a

"magnetic sense", which some other animals, usually migratory, do have.

The fourth great influence in physics is gravity. Gravity appears only to attract.15

It is overcome

by the other three interaction influences at the short distances mentioned above in which they are

strongest, but its attenuation or weakening with distance is much slower than the others. Gravitational

attraction between two objects declines only in proportion to the square of the distance between them.

If a person jumps downward 10 feet, the landing may or may not break his bones, depending on

whether the jumper knows how to land, but if the jump is 20 feet down, damage is likely unless the

landing in onto a liquid or yielding surface. Therefore, for all large-scale phenomena, gravity is much

stronger and more important than the forces previously mentioned. So the gravity of large objects

billions and trillions of miles apart still affects each other and other things significantly.

15According to the theory of general relativity, gravity is not a force but a curvature of spacetime.

In summary of the four interaction tendencies, large and small objects are attracted or repelled

by all four of these influences, and in all directions, by different degrees depending partly on their

distances from each other. For electrical attractions and repulsions, not only distances apart but also


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differences between the numbers of electrons and protons in ea

our first 1000 steps on the human journey: chemical evolution

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