Violence... The story so far

Latest Revision: 17 June 2010

Our jungle/savanna heritage plays a role in human violence. This page provides that backdrop.

"...we grasp the central idea of it all as so simple, so beautiful, so compelling that we will say to each other, 'Oh how could it have been otherwise!' How could we all have been so blind for so long!" John Wheeler

A note on substance and style for the thoughtful:

Most writers on evolution describe events as if atoms, molecules, codons, DNA, chromosomes, bacteria, archaea, eukarya, primitive species, all have minds of their own individually and collectively. They do not. It is just more fluid, lively, and comprehensible to write in such a style. Human understanding and motivations are lacking at the root levels of life. Nevertheless, it is easy to project ourselves into the simplest of molecules and their tendencies to join and "flock together" and buck nature's tendency toward increasing entropy. This basic blueprint fits society as well. So nature itself exhibits patterns we can "understand" intellectually and "identify with" emotionally. On that basis, let us proceed.

To contemplate nature and how things evolve is a magnificent revelation in vastness, in time, in smallness, where quantum probabilities reign, and in how nature's laws organize the constituents into these things collectively called life. The most predictable thing about the universe is: Nature is ever changing in its presentation, yet never changing in how it works. The laws of nature are immutable within our time frame and domain of perception. Those laws brought reproducing life into being--eventually with five senses along with locomotion, memory, intelligence, and emotions. We share all these traits with many other species; our skill sets and behaviors differ from other species only in degree and not always for the better.

Our genes provide us with the temperament we are born with. They provide the foundation of our beginning personality and may contain various degrees of such traits as energy, love, sociability, affection, compassion, intelligence, or dominance. These traits collectively combine such that societies come into being that reflect composites of those making up a society.

This page provides a snippet of the vast amount of coherent evidence supporting how life and the above situation came about, given what we now know of nature.

Nothing seems to come free -- with no strings attached. Everywhere we look, the state of things depends on the state of things next door, above, or below. This seems to be true from the tiniest subatomic particles to the grandest structures in the universe and possibly even the universe itself. The universe may not be what it seems if dimensions we cannot see exist, as some theorists, and Einstein's law of gravity itself, suggest. In the grand scheme of things, life on earth seems too minute to matter. That life happened is evidence of an awesome power manifest in nature and the evolution of life. We had no say in this, yet here we are. Of course that is an important issue to each of us.

Furthermore, mutations take more steps backward than forward. But the forward products--whether a "lifeless" atom, chemical, snippet of life, or life itself--survive as the next rung up the ladder of evolution because they are more fortunate or fit in some way. They are better able to compete for food, to reproduce, survive hard times and temperature extremes, to develop antibodies that thwart attacks (by infection) from much earlier species on lower rungs. In evolving in one direction, species may lose functionality that is not used. Whales and dolphins lost all ability to walk on land; fish living in dark caves lost eyesight.

And yes, emphatically, it is all possible through chance alone--given the statistics of huge-huge numbers of participating atoms (something like ten followed by 38 zeros) in the biosphere over four billion years--to accomplish awesome degrees of organization. Reducing these opportunities for chemical reactions to atom-seconds one gets a number like ten followed by 55 zeros for reactions to happen. Possible opportunities for chemical reactions are simply too huge to even estimate. Of course most chemical reactions require much less than a second to accomplish; so I deal in magnitudes here. Keep these features in mind as you read what follows.

If there was any initial "Intelligent Design," it was in the creation of the natural laws in the first place, not their necessary consequences. However, intelligent design (lower case) is fully evident when we selectively breed animals, genetically modify and engineer crops while fighting illnesses and extending life in new ways guided by the fundamental laws of nature. It is also evident when humanity finds new ways to kill people and commit genocide. In short, humanity has reached a stage where it is changing the natural probabilistic course of evolution as we know it to date; it is using human design of limited intelligence. It might be eons, if ever, before nature would achieve the same results. Food crops naturally developing resistance to pests, herbicides, drought, saline soil, competing weeds, and improved nutrition for humans might never be driven by natural processes without human intervention. These things are now routine in our lives; humanity has reached a stage where it modifies our natural state to make living more comfortable. Humanity has accomplished all this in the mere blink of an eye of geologic time.

For a further perspective, consider: From the time Homo sapiens became a species, it still took another 155 millennia for living creatures to reach any real understanding of biological nature. Biotechnology is the 21st Century's modernization; we must guide its direction and use the results wisely in furthering peace and harmony on earth. Clones are here; they had to come before new species or the reconstruction of old ones. The latter will come in due course as such things are possible -- given time. Humanity itself is now directing evolution as part of evolution itself! What humanity has yet to accomplish is a level of "morality" that simply holds: "All people are created equal." Do not all such people deserve an equal share in opportunities and in what the biosphere has to offer?

Our mastery of chemistry does not equate to God-like power -- that would only become evident if a law of physics could be arbitrarily altered. Chemistry is the necessary result of the laws of physics, not the other way around. Even though humanity can control its destiny to a limited extent, it can only do so as part of nature itself.

To our ancestors of antiquity, virtually every element of modern society would seem miraculous in a biblical view. None are. However, as Stephen Hawking wrote, what we now know, limits what God can possibly be. Whatever created the laws of nature (and the universe) is a far more powerful and unknowable "God" than any God of tradition.

This essay is meant to be a salute to the handiwork of that creator--handiwork we see in the very nature of Nature. We see no conflict between religion and science. They are very different things, addressing quite different needs in quite different ways. They do share one thing in common however: Each can be, and has been, politicized by extremists to the detriment of humankind!

See: Answers for what the fossil record says and BIG QUESTIONS for some timeless queries.



As marvelous as Darwinian evolution is, it pales in scale (in terms of mass and energy) as part of another evolution, that of star formation and how the precursors of "life" themselves evolved from the beginning--some 13.4 billion years ago according to current thinking. Our own solar system was born some 4.7 billion years ago.

Stars form from clouds of hydrogen and other gases that become unstable gravitationally. When huge masses of gases collapse under gravitation, enough heat and pressure are generated to ignite fusion reactions that sustain their "burning" and thus create stars. Hydrogen fusion into helium then becomes self-sustaining until the hydrogen fuel runs out.

Hydrogen is the simplest of atoms. It consists of a proton which is positively charged, and an electron which is negatively charged. The proton and electron are bound together electro-statically, so the charge on each atom is neutral. Hydrogen can also accommodate one or two neutrons in its assembly. Neutrons are neutral uncharged nucleons; a neutron may be thought of as a proton and electron "fused" together. Unless bound together with other nucleons in an atomic nucleus, a neutron alone in space shortly decays into a proton and electron.

Stars get their energy from lightweight elements fusing into heavier elements. Atoms of increasing complexity are forged from simpler atoms by the fusion process as stars ignite and burn. For example, four hydrogen atoms fuse into helium, and hydrogen and helium together can fuse into lithium. Another example is that three helium atoms can fuse into carbon; four can fuse into oxygen. Charged particle fusions are said to occur in all these cases. When hydrogen is involved in the fusion, proton capture is said to take place. These events may be called the p-process. Energy is released with each such fusion contributing its fair share of stellar power.

Many of the elements that comprise life are forged in stars. Some of the foregoing fusion processes produce neutrons which can be captured by other atoms or decay back to hydrogen. When an atom absorbs too many neutrons, it undergoes a beta decay by converting an excess neutron into a proton. The atom moves up one notch in the periodic table to the next atomic number. This is called the s-process. Very gradually, but very surely, heavier atoms are forged during each star's lifetime.

These processes may occur in slow, roundabout ways. Each step produces energy. For example:

A proton collides with and is absorbed by carbon 12 producing nitrogen 13 (the number of protons in the nucleus defines the atomic number; the number following the element name indicates its mass number or isotope).

Nitrogen 13 emits a positron (an "electron" with opposite charge is emitted converting a neutron into a proton) becoming carbon 13.

Carbon 13 collides with and absorbs a proton to become nitrogen 14.

Nitrogen 14 is impacted by a proton which it absorbs to form oxygen 15.

Oxygen 15 emits a positron to become nitrogen 16 as described above.

Nitrogen 16 immediately decays by emitting a helium 4 atom (with two neutrons and two protons in its nucleus) leaving a carbon 12 atom behind.

In this way, carbon recycles itself in the sun as the concentration of helium slowly builds up over eons. Hydrogen, carbon, and oxygen make up most of the bulk of each living organism on earth.

Nuclear fusions release successively less energy as the proton number created increases up to 26, that of iron. Upon reaching iron, further fusions do not release energy; they require energy. Stars die long before they can turn into iron. Stars of the size of our sun simply use up their hydrogen and helium fuels and then collapse into white dwarfs.

Lithium, beryllium, and boron (atomic numbers 3,4, and 5) are so easily fused into heavier atoms in stellar interiors that their concentrations forever remain very low. However they are forged in the interstellar medium by reactions with high energy cosmic rays or by neutrino spallation reactions on carbon, nitrogen and oxygen (atomic numbers 6, 7, and 8).

As hydrogen is exhausted, stars like our sun begin burning helium, slowly at first, then at increasing rates. That accelerating process produces still higher temperatures. Stars burning helium bloat and enlarge into huge red giants. The earth itself will burn to a cinder long before our sun completes that process in 4-5 billion years. In the case of our sun, it will contract after bloating and become a white dwarf, retaining most of its present mass.

White dwarfs are stable unless they are in a neighborhood where they can accrete (grow or condense) matter. When that happens, they become unstable and explode as a type 1a supernova, spewing elements mostly heavier than iron into the void around them. Two white dwarfs may collide or join and give rise to a supernova. There are also subtypes of supernovas generally listed as types 1b or 1c.

A supernova explosion is so hot and intense that atoms multiples more massive than iron are forged with mass numbers well over 200 times that of hydrogen. Atomic numbers up to 92, and higher, come into being during the explosion. So many neutrons are present that elements are forged so fast that their proton numbers move many notches up the periodic table in split seconds. This "explosive forging" of new elements is called the r-process.

Stars six to 25 times larger than our sun die violently in supernova explosions. These stars exhaust their fuel rather quickly. At the end, they first collapse, then explode with unimaginable heat and pressure leaving neutron stars behind instead of white dwarfs. In contrast with white dwarfs, these type II supernova explosions fill the void with elements mostly lighter than iron elements like carbon, nitrogen, oxygen, and sulfur. These elements of course are the staff of life. So-called neutron stars or even black holes are left behind after supernova explosions of stars 25 or more times larger than our sun.

Our interest in the supernovas lies in the material blown off into the interstellar medium. This material has the seeds of life in new germinations of stars and planetary systems.

Life-forming and heavy elements made by the above processes began to appear very early in the history of the universe, some 275 million years after the big bang according to Volker Bromm of the Center for Astrophysics. It seems that the first progenitor stars were some 200 times as massive as our sun; they became supernova in that relatively short time. Evolution, first stellar, then towards life as we know it has been proceeding ever since for 13-14 billion years.



Supernova explosions are truly humongous demonstrations of physics. Among them, they distribute all the elements needed for life into the vastness of space where gravity wells, coolness, and chemistry await. Widely dispersed clouds of gas result from supernovas. As the clouds cool, dust particles of the heavier elements and their combinations form. These cool dusty clouds consist of the sod and fertilizer for generating life. Our solar system arose from the ashes of the exploding nuclear furnaces in the following way:

First a huge and dusty hydrogenic cloud of stellar ashes collapses under the influence of gravity to form a new second or later generation star, one that contains all the elements needed for life. In fact, our sun is comprised of over 80 elements, most of them with higher proton numbers than iron. That is how we know it is a second (or third) generation star.

As a star is born during gravitational collapse of gaseous dusty clouds, some of the material from the cloud ends up in orbit around the star. Such material is characterized by high angular momentum and tends to accrete and reside in a flat disk orbiting around the central star. This is a common occurrence during star formation. In the disk, heavy elements from the cloud condense into solid materials that accrete into dust, rocks, metals, liquids, and, out beyond a certain distance, ices.

Planetary systems arise in the first place because most atoms simply like each other, gravitationally and chemically. Dust and gravel accrete into asteroids which can grow into proto-planets. Proto-planets further accrete into planets of various size at various distances from the host star (the sun in our case). As the mass and gravity of these solid materials grow they sweep up most of the remaining material in their orbital zones. The craters of the moon, Mercury, Venus, Mars, asteroids, and the outer planet moons attest to the violence and consistency of it all. Water, which life cannot exist without arrived on Earth and Mars when comets from the far reaches of the solar system where they picked up condensed water in the form of ice collided with Earth, dumping their loads of water that eventually covered most of the planet.

Energy supplied by the central star maintains temperatures on some planets that allow the continued presence of liquid water. Two features of chemistry then begin to operate: love of one element for another that leads to creation of complex assemblies (molecules) and the ability to recreate that complexity long before life germinates and becomes sustainable in a thermal gradient maintained by the central star. If the central star lives a very long time and is at a proper distance from such planets, life would indeed arise. But molecules of increasing complexity and organization must first form. Here's how.

At low temperatures, atoms combine with other atoms to form molecules. Most notably, hydrogen and oxygen combine to form the molecule we know as water. This is also the process by which common salt arises from the union of sodium and chlorine, atoms forged eons earlier by living and exploding stars. Beach sand comes into being when silicon and oxygen meet and combine in rocks which are then worn away by weather, turning them into their constituent minerals for transport by rivers and wind to the sea shore. All the other minerals form in similar fashion.

When two or more elements join, we say a chemical reaction has occurred. Such reactions occur because of the way atoms are built up from simpler constituents. Every atom consists of at least one proton and one electron. Protons are massive particles that carry a positive charge while electrons are very light particles that carry a negative charge. The number of protons an element has determines its atomic number and that number also defines how many electrons an element has in its rest state. In the simplest atom of all, hydrogen, a single electron is bound to a proton by their mutual electrical (electrostatic) attractions. An early visualization of their bound geometry was by analogy with the solar system, the electron simply orbits the proton, circling forever. That view has given way to a more sophisticated view where probabilities of location in various energy levels explain the atomic spectra unique to each element.

What we are concerned about here is why atoms like each other as they surely do. The answer lies in the fact that the number of electrons in each of the several orbitals or shells (energy levels) possible is limited. However, each orbital likes to be full. Two electrons fill the first shell for example. Helium represents such an atom. While hydrogen wants to fill its outer orbital, helium remains satisfied. Hydrogen is thus chemically reactive; helium is not. The atom with three electrons is lithium. Having an extra electron outside the helium core, lithium wants to react with other elements. The degree to which the outermost orbital is filled governs the chemical behavior of each element. The number of protons in an atom is defined as its atomic number, which is always equal to the number of electrons present in an atom at rest. As the atomic number increases, the number of electrons needed to fill the outermost orbital undergo a systematic increase as follows: 2, 8, 8, 18, 18, 32. At the point where each orbital fills, "noble gases," Helium, Neon, Argon, Krypton, Xenon, and Radon form. All other elements, including those higher than radon, are either trying to give electrons to another element, or borrow some to fill its own outer orbital, or both.

Of the 92 naturally occurring elements on earth, only the six "noble gases" are loners in that they do not effectively react with other atoms. They disdain strong bonds with any other elements, even among themselves. Their electronic orbitals about the nucleus are filled, leaving no place for another atom to attach by sharing, receiving or donating an orbital electron.

The pertinent point here is that all other atoms, as in the lithium example above, with unfilled outer orbitals, are "uncomfortable." They are always on the lookout for other atoms with which they can borrow, give up electrons to fill their outer orbitals to create an "ionic bond." Stated another way, atoms donate electrons to fill another atom's outer orbital, or accept electrons from another atom to fill their own.

In some cases, they share electrons, as in carbon, where 4+4=8 satisfies the outer orbital needs of both participating atoms. In this event, a covalent bond is said to have formed. A third bonding type is the metallic, where each metal atom resides in a "sea" of electrons. Whatever the bonding type, atoms like each other.

The degree to which one atom likes another is called the "Free Energy" of their combination, the molecule. The free energy is free only in a restricted sense; it is the "useful energy" released when the atoms involved become bound to one another--it is not the total heat released. Like boulders rolling down a hill, falling into a "gravity well," except for the noble gases, all atoms in the universe are always looking for an "energy well" to fall into so as to release some of their potential (free) energy.

This basic tendency for atoms to form molecules is true of all elements except the noble gases. To iterate, for all substances, the natural attraction atoms have for one another has been named the free energy of formation. Each molecule, however simple or complex, has it own unique free energy of formation.

Complex molecular structures can arise spontaneously; this is nature's way in creating building blocks. Building blocks then join up with other building blocks. This happens because molecules, no matter how complex, like each other just as atoms do, so they join up in ever-increasing complexity. This is especially true of hydrocarbons and carbohydrates, the staff of life.

When atoms combine the assembly is given the name molecule. Carbon is the most unique and in many ways the most fascinating of elements. It contains four electrons in its outer orbital. Carbon would as soon give away as receive electrons, but it has a very strong preference for simply sharing electrons. As you might imagine, carbon chemistry is extremely complex in the number of compounds and structures it can form and participate in. Carbon bonds covalently with four hydrogen atoms. Carbon-based molecules are called organic molecules. Just as atomic complexity increases with the number of electrons, so also organic molecules have a huge potential for complexity based on the CH4 ensemble. Carbon atoms also share electrons with other carbon atoms as in CH3CH2CH3, Propane. When pure carbon is compressed in such a way that it must share electrons with itself, diamond, the hardest of all known molecules, forms.

Organic molecules consist of some number of atoms of carbon and hydrogen along with oxygen and/or other elements. Complex organic molecules can form from simpler ones. Ammonia, NH3, which consists of one nitrogen atom and three hydrogen atoms, forms by the process described above. Methane, CH4, forms in a similar way. Both NH3 and CH4 have been identified in the spectra of other planets. The Cassini mission to Titan, a moon of Saturn, verified and extended the planetary list to include N, CO, CH4, C2H4, C3H4, C4H2, HCN, HC3N, and C2N2, life precursors. While Titan is a cold, presumably lifeless, place, it nevertheless harbors "chemical seeds" that can grow in complexity and ultimately join in the replication dance called life. Could life happen on Titan? We should know within this century.

Mix these molecules with water vapor and hydrogen (also naturally present) in the presence of cosmic rays and lightning discharges and the molecules comprising the staff of life begin to form. After some time amino acids such as Glycin (NH2-CH2-COOH), alanin (CH3-CH(NH2)-COOH) and more complex forms arise out of the shattered fragments. Amino acids, nitrogenous organic compounds, are the building blocks of proteins. And proteins are the next step up the ladder of evolution and complexity.

Stanley Miller and Harold Urey duplicated nature in their laboratory in 1951 at the University of Chicago. They mixed hydrogen, water, methane and ammonia together--all occur naturally. They then added electric arcs--lightning on the lab scale, for a few days. A bright yellow-red soup resulted that contained more than a dozen amino acids. In one crucial experiment, Miller and Urey used the gases emitted by volcanoes. In that case, they found every single amino acid found in living organisms--every single one!

Fast forward to 1969. A meteorite landing in Australia was analyzed for organic compounds. Every amino acid Miller and Urey found was also present in the meteorite! This key finding converted skeptics to new ways of thinking about life. Life's most basic building blocks arise naturally in outer space, and also here on earth. That is to say, given the immense number of stars with planets out there, life on other worlds is a virtual certainty.

We now know that carbon has been playing these games for at least 10.5 billion years. A 28 July 2005 news release from Cal Tech:


Recently, astronomers, at the Robert C. Byrd Green Bank Telescope (GBT) identified sugar molecules in space. The first sugar found was Glycolaldehyde, a simple molecule, an 8-atom sugar. It can combine with other molcules to form ribose and glucose. Ribose is a building block for both RNA and DNA. Combining with itself into more complex structures, glycoaldehyde forms methyl formate and acetic acid--which had been found in interstellar clouds of gas earlier. We quote the latest finding:


Being conservative, scientists often use qualifiers such as perhaps, may, or possible, when projecting extensions of their work. That is as it should be. On this page, we take a similar approach. But we also employ well known science, such as the free energy of formation of compounds and its associated equilibrium constant, to predict with virtual certainty how molecular complexity increases with time. Miller's experiments demonstrated just that fact in a very brief period of time under set conditions. Given the vast range of environments earth possesses, and has possessed over the immense time it has existed, it is obvious that anything that can happen naturally, eventually will--if it has not already. Moreover, well-known catalytic processes dramatically shorten the time needed to establish new levels of complexity. So while life has not yet been created in the lab, it can happen, and likely will this century.

Ordinary sugar has the composition of 12 carbons, 22 hydrogens, and 11 oxygens, (C12H22O11). Alcohol, the kind we drink, is even more simple. It is made up of two carbons, six hydrogens, and one oxygen (C2H6O) where the bonding electrons add up to sixteen, all essentially shared). Other elements present may join the fun in a similar fashion. Complex molecules comprised of hundreds of hydrogen, carbon, nitrogen, oxygen, and other light atoms arise the same way, all because atoms like each other. In cases where a surplus of the light elements is present, the conditions required for life can be created. When nitrogen is present, ammonia can form. Mixed with light hydrocarbons, ammonia and nitrites can evolve into amino acids, purines, sugars and other building blocks of life.

There are uncounted numbers of combinations that carbon can join in with other elements. When hydrogen, carbon, and oxygen react, they like to go around in chains, rings, and more complex shapes. Carbon is unique because of the diversity and complexity of molecules it can form. The scientific disciplines of organic chemistry, biology, and their sub-disciplines all rest on this diversity. Life itself relies on the chemical diversity of carbon, and of course on the presence of water and a number of other molecules.

Cosmic rays churn the present-day soup as they did the primordial one, breaking molecular bonds between atoms. Volcanoes, geysers, deep-sea vents, meteoric in-fall, lightening, and other high-energy events can have the same result. Broken bonds are active sites for creating new bonds with different atoms or molecules. All the conditions needed for building up new and complex but uniquely different assemblies are always present. Even before life as we know it came into being on earth, inanimate molecules had ways of recreating their kind as well as evolving new more complex molecules from their fragments if they happened to meet "death;" from an energetic natural-event such as those listed above.

From many such events, one can only conclude that chemical evolutionary steps toward life on earth occurred in supernova ejecta as it condensed into a dust cloud before our solar system arrived in its present state. These basic molecular building blocks, amino acids, have "seeded" all the other planets and their moons as well. Life independent of earth could surely arise anywhere in the universe over a few billion years from such seeding in the presence of liquid water and a steady supply of energy such as from a star--and there are "gazillions" of stars. Some of the chemical pathways have now been elucidated, increasing optimism that yet more missing links will be discovered. (See page 54 in the September 2009 issue of Scientific American for more.)

Assemblies of molecules and snippets of hydrocarbons, reacting with other elements, eventually reach a point of being able to replicate themselves. We also know that certain metals such as platinum can speed up (catalyze) chemical reactions. Catalysis can dramatically shorten the period of evolution from one compound to the next. The presence of excess hydrogen also facilitates the formation and reformation of organic compounds the precursors of life. All that is needed is an energy gradient one that can be tapped to supply a ready supply of component materials that can lead to more-complex reactions involved in life itself.

Since this page was first written, long-lived alkaline ocean hydrothermal vents have become the most-likely sources for life-precursor reactions. Early in earth history, its atmosphere was devoid of oxygen. Atmospheric oxygen became common only after photosynthesis enabled by chlorophyll plant evolution—some three billion years later. What was needed early on was simply an energy gradient, or reaction potential to create precursors related to real life. The annals of science since the mid-twentieth century now point to alkaline hydrothermal vents such as those in the Lost City. For details, see Science, 6 June 2014, VOL 334, Issue 6188.

Energy-releasing chemical reactions are at the core of the living process of all organisms. These bioenergetic reactions have myriad substrates, but their main by-product today is adenosine triphosphate (ATP), life’s primary currency of metabolic energy. Bioenergetic reactions have been running in a sequence of uninterrupted continuity since the first prokaryotes arose on earth more than 3.5 billion years ago, long before there was oxygen to breathe.

The two-page article is primarily an overview of 15 papers addressing how inorganic reactions start with hydrogen ions and carbon dioxide, both naturally present, with help from transition metals, to tap available energy. Sodium and ferrous ions are also naturally present and they In that process, phosphorylation at the substrate level is used to convert adenosine diphosphate (ADP) to ADT. Methane and acetate are “by-products” in a sense. But they go on to create methanogens and acetogens and both are found in alkaline hydrothermal vents. The hydrothermal vents contain vast volumes of micro-compartments with equally vast surface areas upon which organic compounds can adsorb and thus enhance their presence.

…The chemistry of hydrothermal vents id vastly unexplored, and H2-dependent anaerobic autotropes are only beginning to relinquish their bioenergetic secrets. Energy-releasing processes that link the two might shed new light on biology’s biggest question.

In every reaction, thermodynamic equilibria governs as described above and elsewhere. But even uphill reactions can still move forward provided a means for concentrating products is present. These authors, William Martin, Filipa Sousa, and Nick Lane, explain how this and other details come about. Go to the Science article for a more-authoritative rendition and references.



The fact that atoms and molecules like each other, makes complexity a given. The free energy, coupled with the constant energy from the sun, are the fundamental driving forces in the biosphere driving evolution. Evolution is therefore seen to be a fundamental law of nature.

Among the molecular fragments that form as soon as a primordial "soup" cools are the sugar phosphates. The element phosphorus is comprised of 15 protons, 15 electrons and 17 neutrons. Deep beneath the sea in vents driven by magma deep in the earths mantle, sugar phosphates came into being along with nitrogen bases. These molecules eventually combined to form RNA, the first self replicating molecule. RNA is more resistant to harsh ultraviolet radiation from the sun than the sugar phosphate, so it survived preferentially. The nitrogen bases shield them from disruption. In this and other ways, RNA is more stable than the molecules from which it sprang. From this platform of security, life sprang.

Molecules like each other for the same reason individual atoms do; by joining, they minimize free energy of formation, just as rocks or water tend to move down a hillside into the valley or gravity sink, their potential energy is dissipated. Two chains of molecules can get together and form strings, purely by happenstance , because the new configuration reduces the free energy. Or they might form spirals for "rope", two of which can form a double helix. Any of these might have appendages or sites that other molecules (or atoms) can latch onto. Put all of them together in a soup (an ocean with thermal vents loaded with minerals for example) and it is no stretch at all for the imagination to see how RNA and DNA can arise from molecular ropes. Proteins and enzymes can also arise from the many possible mixtures. Add to these the fact that elements such as nitrogen, phosphorus, sodium, chlorine, iron, potassium, and calcium like to play the molecule game of love, too.

The exact details of how his "primordial soup", a term now outdated, led to RNA have been the subject of intensive research ever since Watson and Crick shook the world of biology with their solution to the structure of DNA. The full story is so amazing, it deserves a page of its own. It turns out the the "Smokers" (sea floor vents of steam and other gases such as hydrogen and carbon dioxide) provide the novel acidic environment for the most primitive of life forms to come into being. As these vents cool over the eons they turn alkaline. Along with that slow cooling, organisms adapt to the lower temperatures and and thanks the the cooler vent's alkalinity, evolve further to degrees that allow life to spread beyond the local confines of their origin. As the earth's core cools, water seeps down and reacts with certain rocks to form serpentine which in the vagaries of the inner-earth churning, is reheated and releases water and other chemicals into the so-called hydro-thermal vents that are alkaline when they emerge from the sea floor. For how this fascinating start plays out, see: Life Ascending by Nick Lane. The many fascinating details lie far beyond our overview here. This book is in the "can't-put-down" class. in short, the deep ocean vents not only provide the all-important thermal gradients, but also the concentrations and catalysts necessary to create life robustly in its three ultimate forms, archaea, bacteria, and euckarya. The latter demonstration will surely occur this century. To venture a prediction here: It will turn out that life is today is still being created in the deep ocean vents.

Since Lane's remarkable summary, Craig Ventnor has created a new species of bacteria, using only mail-order chemicals. That achievement, as remarkable as it seems, falls far short of creating life from scratch. But such was inconceivable before Watson and Crick, not to mention Mendel and Darwin.

Researchers at the university of Manchester employed systems chemistry to show how ribonucleotides can be synthesized from early-earth, prebiotic, geochemical models. The key inorganic chemical is inorganic phosphate in the presence of organic cyanamide, cyanoacetylene, glycolaldehyde, and glyceraldehyde. (See Nature, vol 459, 14 May 2009, p239 for the details.) Notably, the presence of radiation enhances the the chemical sequence by destroying unwanted by products. The importance of this discovery is that activated ribonucleotide molecules are the building blocks of RNA that can polymerize without enzymes into larger molecules, snippets of RNA. Another link in the chemical pathway to life has now been forged. This event will surely generate a flood of research. Watch for it.

The complexity of possible organic molecules multiplies again and again and is truly enormous, like a flea, or a human body for just two examples. The underlying chemical law is grossly simple compared with the vast number of possible combinations of carbon compounds. Certain sections of DNA are so tightly bound that they maintain their identity through hundreds of millions of generations. Such stretches are known as haplotypes. How do we know? It can be no other way when homo shares haplotypes with species, whose concestor (common evolutionary ancestor) with us existed hundreds of millions of years ago.

A huge mass of evidence for evolution ties all of life together in a code of just 64 "words", or codons, having 21 meanings--comprised of 20 amino acids and one all-purpose "punctuation mark." A codon is a specific combination of three amino acids that code for a specific protein. A specific sequence of codons gives rise to a specific gene, an expression of a feature in an organism. A chromosome is a segment of DNA containing a large number of genes. A genome, a human for example, is the entire sequence of DNA giving expression to a human. Each human being is comprised of some 20,000 to 30,000 genes depending on the source of information. That is far fewer than was expected by many before the human genome was decoded.

All living things are made up of DNA in this same structure. This 64 word language is found to be universal, unchanging. Now for the punch line: Amino acids seem to be everywhere in the cool parts of the universe, wherever chemistry operates. Amino acids are found in all terrestrial life, in meteorites, in interstellar clouds. The twenty found in life comprise only 10 - 27 atoms, each. See page nine of Dr. Karen Kolehmainen's report NSCI 314 for more. For yet more on how the most-primitive life forms carried forward, see the excellent and fascinating book "The Ancestor's Tale" by Richard Dawkins, Oxford University.

The forgoing step may seem too formidable to recreate in the lab. But Craig Vintner, who first decoded the human genome, has reproduced the DNA of a simple bacterium, Mycoplasma genatalium from just four bottles of inert substances. It contains 582,970 base pairs. It remains to see if his strand of DNA can replicate itself. The odds that once seemed so formidable are being reduced dramatically by a long list of scientists from several disciplines who have made life origin(s) their life-work.

There are two basic schools of thought: metabolism first and RNA first. (See Robert Shapiro, "A Simpler Origin for Life," Scientific American, June 2007, p 47.) Each school cites impressive progress; yet neither has won the day.

The metabolism first scientists see four requirements that must be met:

• Energy must be available; radiation from the sun for example.
• The energy must drive chemical reactions.
• A network of chemical reactions must form that allows increased complexity.
• The network of reactions must draw material into itself and the "compartments" must replicate.

All of these requirement are met int the acidic sea-floor black smokers and the alkaline hydrothermal vents. See Dramatic Visual for a movie on the steps of replication on the molecular level.

Like their simpler counterparts, self-replicating elements, once formed, join with others much like themselves. This happens simply because cells like other cells, to minimize the free energy, while the sun continuously makes up for waste heat lost (entropy) while supporting the process. One can imagine two slightly damaged cells combine to "heal" the damage and be doubly complex! All living cells consist of hydrogen, carbon, nitrogen, oxygen, phosphorus and sulfur.

After life migrated out of the alkaline hydrothermal vents, evolution added animation and the five senses to the tools by which organisms work. RNA combinations with proteins eventually evolved into the biosphere and life as we know it. That process was gradual, one or only a very few mutations evolve at a time. Each generation belongs to the same species as fore bearers and offspring alike. What drives speciation is dispersion in geography or other barrier, and/or time. Species that inhabit a continent that splits and slowly drifts apart are separated from their species and each evolves slowly in different directions. Mutations are random events, first this way, then that, with only favorable mutations lasting long. A mountain chain arising mid-continent would have the same effect for many species as for a continent that becomes separated by an ocean.

Modern species, such as the salamanders Ensatina eschscholtzii and Ensatina klauberi became separate species just this way. In the Sacramento Valley, California, there is just one species Ensatina in its northernmost extent. Proceeding south, along the eastern and western edges of the Central Valley of California, the species progressively diverge genetically. At the Southern extreme, the species do not mate. But all neighbors mate with their neighbors from one end of the "loop" to the other. They are truly a "ring species." Only the most remote do not mate!

The herring gull that lives in the northern latitudes similarly migrated from Europe to North America and on to east Asia (or the other way around) only to meet up with its distant fore-bearers as a separate species. Many species, whose histories are not traceable, but hybridize, doubtless have a common ancestor from which they sprang relatively recently in evolutionary time.

We see the same effect in Homo sapiens, except that speciation never came close to being accomplished. Yet, separation and evolution reached the point where "races" distinguishable by form and color came into being. However, the most divergent of people, are still much more closely related to each other than are the typical Chimpanzee, Gorilla, or field mouse related to their own kind. In terms of geologic time, Homo sapiens is a very young species, whose genetic divergence only began perhaps only 8,000 generations ago.

These examples are factual evidence of speciation and how it works. Separate species, mating naturally with their own kind by definition, can be connected "continuously" by numerous individual breeding groups separated from neighbor groups only by a few mutations in a "chain" that extends over several hundred kilometers. In a parallel direction, a modern example of speiciation comes from animal breeding. Dogs have been bred of such disparate size that they could not breed naturally--even though the instinct to do so is still there.

These observations deny that there are, or even can be a missing link in the origins of species. Again Richard Dawkins provides the authority. He has an immense amount of DNA data fitting observations about how nature works. All this from just 20 codons and a punctuation mark!

Two features drive most speciation: ecological gradients and distance, though neither is a sufficient condition. The salamander speciation occurred simply by separation; distance prevented mating except with local partners. The ecological gradient is much more obvious and is equivalent to distance when it is extreme as when species become divided by rivers, glaciers, new mountain ranges or continental drift. Only recently has it been realized that even minor gradients in the environment are sufficient to create new species. Lake water depth has been shown to cause fish speciation in Cameroon and Nicaragua. In like manner, differences in soil acidity on Howe Island caused the founding palm species to separate into two species.

But evolution can also occur in a dish. Luis Ariza in the December 2007 issue of Scientific American explained how. Some 70 years ago, J.B.S. Haldane had the audacious idea that mutation offers a trade off. He observed that people in Africa who inherit sickle-cell anemia resist the regions big killer--malaria, and survive better than their normal brethren. Hence he postulated that infectious disease can drive evolution. From the tenets of the science, it obviously does. But until recently, no one had actually observed the feat in a test tube.

Spanish researchers in 2001, however, observed just such an event. They studied the effects of an infectious bacterium, Pseudomonas aeruginosa, on a nematode, Caenorhabditis elegans. Normally the bacteria kill the nematode in short order. The researchers were stunned to discover that in one of 152 trials, the opposite happened. The nematodes ate the bacteria. In looking into the reason the researchers found at least seven changes in proteins between the two groups. This is ordinarily enough to declare the two groups of nematodes to be separate species. The researcher do not go that far, only saying they are close. It seems from here that it will be only a matter of time until the bacteria eaters encounter a further change sufficient for the most cautious scientist to agree, that, yes indeed, a new species has now evolved before our eyes in the laboratory.

Back to the story.

It may seem mind boggling that evolution of otherwise inert substances occurred well before life formally arose. Daniel Dennet in his Darwin's Dangerous Idea explains all this and more in both an entertaining and authoritative way. This is all factual; no "belief system" is required. Rather a belief system could well retard the development of science as it did during the Inquisition and still is today wherever authoritarians and/or conservative religions manage to limit thinking by individuals in their societies.

With the ability to decipher genomes, it now appears that life did indeed form as a single event, which was then followed by two significant differentiations that led to the taxonomies of today. In this way, three basic domains of the DNA tree of life, the bacteria, archaea, and the eukaryota, arose. They differ greatly from one another. Bacteria are typically one-celled microorganisms that multiply by simple cell division and under a microscope appear to be spherical, rod like, or spiral in form. Archaea are similar except that they inhabit extreme environments, like fumaroles (hot volcanic sulfurous vents) and analogous deep sea vents. Their metabolism differs from that of bacteria. Eukaryota are more complex. They are multi-cellar, and have the evolutionary advantage of od sexual reproduction. Multi-cellularity offers orders-of-magnitude to the ability of an organism to differentiate into new species.In this way the many branches of plants and animals we see today came into being. Life to most people is comprised of eukaryota.

From University of Arizona, Tucson: A bacterium living in special cells inside an insect has the smallest genome of any known cellular life form. Carsonella ruddi has only 159,662 base pairs of DNA; the genome is less than half the size previously thought to be the minimum necessary for life. "It's the smallest genome -- not by a bit but by a long way," said co-author Nancy A. Moran, UA Regents' Professor of ecology and evolutionary biology and a member of the National Academy of Sciences. "It's very surprising. It's unbelievable, really. We would not have predicted such a small size. It's believed that more genes are required for a cell to work." An organism's genome carries all of the instructions it needs to make the proteins required for life. Carsonella's genome codes for 182 proteins. The human genome, by comparison, contains about 3 billion DNA base pairs and codes for about 35,000 proteins. This finding does not prove this is the minimum cell size at the dawn of life, it could have lost some of its genes after becoming parasitic on insects. Most recently, Craig Vintner, the pre-imminent pioneer in genome studies, has studied this issue by altering and selectively removing genes. He also turned up an astonishing result. The minimum number of genes needed for self replication in bacteria is merely about 100.

Archaea can be quite small as well. From the Proc. National Academy of Science: The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in co-culture with the crenarchaeon Ignicoccus. Ribosomal protein and RNA-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. The N. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. It is the smallest natural microbial genome sequenced to date, and also one of the most compact, with 95% of the DNA predicted to encode proteins or stable RNAs. Its limited biosynthetic and catabolic capacity indicates that N. equitans' symbiotic relationship to Ignicoccus is parasitic, making it the only known archaeal parasite. Unlike the small genomes of bacterial parasites that are undergoing reductive evolution, N. equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome."

Eukaryota, multi-celled units of life, embrace all other forms, the fungi, plants, and animals of all lands and seas for example. In terms of cell complexity, life progressed from Bacteria through Archaea to Eukaria. But that is not necessarily all there is to it.

Bacteria and Archaea were the first steps up the ladder of life. Bacteria even evolved the capacity to communicate chemically to coordinate attacks on others and a willingness to commit suicide resulting in greater good for the community. Later, Bacteria and Archaea likely came together in a fusion event to create a third basic form of life, the Eukarya, to which humans belong. (Nature, Vol 435, 26 May 2005.)

All three domains take part in the carbon cycle on the earth's crust. In terms of DNA, the Bacteria and Archaea differ from each other and from us to far greater degrees than we ourselves differ from pine trees, salamanders, mosquitoes, and the like. Eukariota are sub-classified of course as plants, animals, fungi, & protists.

The most primative Eukarya known are the comb jellies. Other early Eukarya were typically sponges, blobs of multi-celled creatures, adept at pushing simpler organisms aside or feasting on them. About 600 million years ago, a single event gave life a huge boost. While sponges and simpler life recognized no left and right or up and down symmetries, the newly evolved bilaterians did know left from right. From that moment forward, the Eukaryan fauna (animals) grew in size and competitiveness such that they came to dominate the earth. Having dual organs gave them new advantages. New modes of locomotion evolved. Two eyes proved superior to having only one. Brains with two hemispheres were more adaptable than brains having only one. The bilaterians came some fifty-million years before the so-called Cambrian explosion.

Back now to the very early life story once cells came into being.

At what point life can be said to exist depends on one's definition, most fundamentally RNA self-replication might be that point. From there, evolution gave organization to fossils and lineage to the domain, phyla, class, order, family, genera, and species that comprise the trunks, branches, twigs, and leaves of the trees of Eukariota life.

There is an intimate connection where all systems of atoms seek to minimize the free energy of the assembly and produce the macro expression of evolution. Atomistic systems work together. And so life begins, evolves, and continues to evolve. The process is well understood. Evolution has been demonstrated not only in nature but in the laboratory as well. Its salient features have been repeatedly demonstrated.

In and of itself, a virus may be the simplest living molecule built with complex hydrocarbon-based compounds that can reproduce itself. Viruses are snippets of DNA or RNA surrounded by a coat of protein. The polio virus, for example, is a million times less complex than a human cell, but it can reproduce itself given the right environment, just as the human cell can. In that sense, a polio virus meets one definition of living matter. All life as we know it requires special conditions and a continuous external source of energy. Our sun and our biosphere comprise the special conditions required to sustain the human species.

The 12 July 2002 issue of the New York Times reported the creation of an attenuated but live polio virus created from inert snippets of DNA by a team of scientists led by Dr. Eckard Wimmer, a professor at Stony Brook. Polio has a genome of some 7000 bases (units of DNA and RNA analogous to atoms in a molecule). Wimmer and associates started with commercially available DNA snippets 50-100 bases long. Their human-made virus reproduced itself in mice, meeting one simple test of liveness. While this feat has not been repeated and does not qualify as a complete re-creation of life from random mixtures of atoms, it demonstrated one step in the chain of events leading to life on earth, the very essence of evolution.

As life evolved, assemblies of cells began to move around, feebly and mindlessly at first, but with ever more speed and precision. Neural structures evolved that could not only sense exterior conditions but command movement toward or away from food or danger. Such structures survived to evolve simply because their sensing ability to avoid danger gave them more time to reproduce and crowd out some of the earlier forms. From this point forward new features arose. The basic equations for evolution of life involve sensing, locomotion, guidance, and survival of the fittest, those organisms most adaptable to new conditions multiply and mutate again to the point that their forebears become obsolete.

Neural structures eventually became complex enough to remember past experiences. At this moment, "awareness" dawned. In our times, quite primitive organisms can be trained in various tasks and to those extents can be said to be aware, if not yet self-aware. Honeybees do not need training. They are naturally aware and can communicate their memories to their fellow workers.

How the foregoing and other processes work in detail to ultimately create life and new species are continuing subjects of research, as well as discussion and legitimate arguments that always attend new scientific developments. The matter of replenishing the energy needed by each life unit to maintain itself is solved in various ways. The sun is always bathing the earth with an excess of energy, so there are no thermodynamic barriers to continued existence and evolution of life. When the sun bloats into a red giant, before burning out, life as we know it will, too, at least in our local vicinity of the universe.

Meanwhile, another source of energy is life itself, otherwise known as the food chain (part of the carbon cycle in the biosphere). Energy needed to support life in nature is carefully used again and again.

Predators and scavengers of various kinds evolved to help maintain this balance. At the same time, vultures, bacteria, and other life forms devour the carcasses of the dead and dying. In the process of finding food, many species evolved instincts (genetic memory) for avoiding predators or poisons, and to communicate the approach of danger.

This was a crucial evolutionary development. Species with an instinct for avoiding or surmounting trouble survived. (Instinct still survives in our own species, only we now call it a hunch, premonition, intuition, or even deja vu.) There is no obvious morality here, only survival of the fittest. Movement, speed, strength, fierceness, and intelligence reign in the animal world.

Survival-by-fitness rules apply to all forms of life. Speed, strength, and fierceness eventually give way to or are augmented by smarts in allowing "thinking species" to survive.

Having smarts, gives fast and strong animals a huge edge. As smarts became smarter, the need for strength and speed diminished, but agility remained important. In this way, nature evolved the hominids from which Homo sapiens (us) arose. The "handy man" Homo habilis could only spawn and give way first to the likes of Homo neanderthalensis and then "knowing man" Homo sapiens. Homo sapiens inexorably became supreme. Neanderthals were our equal in brain case, but their line was extinguished during the last ice age. No one knows why for sure. They were stouter, so perhaps their survival depended less on the herding instinct. Equally possible, they may have been gentle creatures, like the bonobos, and no match for the more aggressive sapiens. Or it could have been lost habitat or disease that led to their demise. The latest thinking on this issue is that they were assimilated. What is fairly certain is that they were primarily meat eaters, and as such possibly could not compete with sapiens and their more varied diet. Their oral communication ability may have been more limited than our is. An ability to speak fits the fact that Homo neanderthalensis began leaving sophisticated tools behind only after making contact with Homo sapiens.

The genome of Homo neanderthalensis is now known to include fair skin and red hair. So they were similar to us in many ways, and genetically our closest relatives. The DNA evidence now indicates, with nearly 100% of its genome now deciphered, that Homo neanderthalensis and Homo sapiens were closely enough related to have been able to reproduce.

In any event, some degrees of speed, strength, and fiercen