Chapter D.

Steps 1-10 Physical, Astronomical, and Geological Evolution

Step 1. Gravity draws protons toward each other in space. To simplify, let us start with a single proton traveling through space. Gravity between it and other protons or larger assemblages of matter will alter the path of each, bending that path as a dip in a surface alters the path of a rolling marble or ball. Thus, gravity gathered (and continues to gather) protons (hydrogen nuclei) from space into growing collections of all sizes. Such a collection can at first be just a few protons moving along a few feet or miles apart. Normally they do not touch because they tend to pull away if they get too close. This avoidance is called electromagnetic repulsion, interaction, or force. But even a few protons moving along a few feet apart have more gravity together than a lone proton, so other protons that are totally alone, or only near one other proton, will come closer to the larger group nearby, or near the path of the proton. As the group grows larger, it adds more gravity, and that lets it pull in protons from still farther away. As the number of protons becomes quite large, the total gravity of the bunch pulls them ever closer to each other and attracts still more. If they meet electrons, which protons attract like magnets, they pull the electrons in and the electrons get even closer to the protons. Electrons tend to pair up with the protons, each electron traveling around or surrounding the heavier proton. Together, this pair is called an atom. This kind of atom is a sample of what is called element number one (because it includes only one proton), or, more commonly, hydrogen.

Elliptical orbits of electrons in an idealized atom (from Microsoft Word Clip Art).

If a collection of protons or atoms grows large enough, and especially if it picks up enough electrons to balance the number of protons, these little particles will move close enough together to form into a gas or sometimes even a kind of thick dust. (If gravity draws many protons and other material together into diffuse "clouds", detectable in the spaces among stars, the protons or atoms may typically approximate 100 per cubic centimeter.) If it keeps growing, as it often does passing through space, some of the closest atoms may even collect into particulate matter. If enough of these collect, it may form a cloud, or a comet, or even grow up to a planet size. If it grows enough, i.e., if one too many protons is added, we have what chapter C termed emergent behavior: the cloud, or a portion of it, will

2
begin to "fall" toward the common center of mass of the cloud. This falling and massing cause the area affected to begin to circle around the center of the cloud. As each atom or proton is drawn toward the common center of the cloud, its previous path will skew this fall away from the center; but as it moves toward passing the center, if its speed is slow enough and the center has enough mass, the proton may reach a point at which the force of gravity exactly matches the tendency to keep going in a straight line, leading it whirl around the center. If it gets closer than that, it may be drawn into the center and join with it. Planets, moons, comets, and other satellites follow orbits around the central celestial body. These orbits are not perfect circles, but ellipses. An ellipse is a smooth curve with two centers or foci instead of one. The central body will be located at one of these centers. If the two foci of an orbit are near each other, as with the eight larger planets of our Solar System, the orbit seems almost circular. If the foci are farther apart, the orbit becomes a more elongated ellipse, as with the orbits of Pluto and comets. The dust cloud thus becomes a whirling mass of protons or atoms, perhaps with other particles, gaining speed as it shrinks in volume, like a spinning skater drawing in the arms to spin faster. If the total spinning mass is great enough, much of that mass may even become a star, as seems to have happened to much of the stuff that each of us is made of. (Before the star forms, we may call such a spinning cloud a pre-solar system.) A body with the mass of Jupiter, the largest planet in our Solar System, is not large enough to become a star. Planets have now been indirectly detected that are even larger than Jupiter, orbiting stars other than our Sun. If the central mass does not grow larger than 80 Jupiters, it may form a star briefly, bursting into a giant thermonuclear fusion reactor and radiating light and heat, but then quickly fizzles out and becomes a brown dwarf, a dead star. The smallest known star has a mass 96 times that of Jupiter (about a tenth of the mass of our Sun). So the boundary between a celestial mass becoming a star, whether for a significant time or not, lies between 80 and 96 Jupiter masses. A star 96 times more massive than Jupiter (or larger) is able to continue its fusion until other processes take over and thus does not become a brown dwarf. Step 2. Stars and Atoms. The increase in gravity of these collections of protons, when they get to star size, finally pulls the individual protons so close together, increases their speed of motion so much, and therefore produces so much pressure that some of the protons come within the effective range of the strong force, which fastens the protons together into groups of four, and even changes their nature a little, most often changing roughly half of them enough to make that half lose their electrical charges, presumably by capturing electrons among them to neutralize two of the proton electrical charges. The result of such a union of four protons, called atomic or nuclear fusion, is a tight, lasting group of two unchanged protons and two former protons now changed to neutrons. This group may be spewed out from a star as a single block of matter called an alpha ray. When an alpha ray slows down enough to pick up two electrons to balance the electrical charge of its two remaining protons, it becomes an atom of helium. This type of atom is said to belong to element number 2, because it has two protons (i.e., helium). This number of protons which have remained such in any atomic nucleus is called the atomic number of that atom and is what makes some substances like each other and unlike other substances. This new atom therefore consists of two parts: (1) a nucleus of two protons and two neutrons (and an electrical charge of +2), which is balanced by (2) an electron cloud consisting of

3
two electrons (hence a charge of -2). The electrons used to be described as orbiting the nucleus, but the orbits seem to be three-dimensional, hence moving around the nucleus on all sides and as if they were all around at the same time, so physicists now say the electrons travel in an orbital. They describe the position of the electron at any one time as merely statistical, so that the electron acts as though it is in all parts of its path at the same time. That seems strange, but it seems to work mathematically for now. This first star process, called nuclear fusion, has been detected working for at least 14 billion years so far, and probably far longer, and still goes on in the remaining stars, changing hydrogen (with one proton in its nucleus) to helium (with two protons and two neutrons) and making mainly the light, but also heat, radio, and other waves that come from stars, including our Sun. This provides the energy that allows us to live. Step 3. Further star processing of atoms. Helium atoms, once formed in a star, may, as mentioned above, be cast out as alpha rays, but most of them are created at or near the center of the star, where the heat, pressure, and proton closeness (mass density) are greatest, and most of them stay there for long periods of time, gradually building a growing core of helium atoms in the center of the star. How long a star shines, and how long each of the processes in it last, are believed to depend on how large the star is. The biggest stars process their matter fastest and thus burn out the fastest, sometimes in millions of years. The Sun is estimated to have lit up roughly 4.5 billion years ago and is expected to last several billion years more. A star with less than 60% of the mass of the Sun becomes a white dwarf star. White dwarfs continue to form new helium nuclei until finally the star collapses, blasting much material away, and compressing the densest part into an extremely tight collection of neutrons, into which the rising stellar heat had converted all protons in some of its helium nuclei, thus forming a sort of giant atomic nucleus consisting entirely of neutrons, extremely compact. The rapid spinning of the small, remaining celestial object, and the final processes of this star type, have created a neutron star, which emits primarily only X-rays, only in a limited beam, so that the spinning may be detected by the sweep of the beam across Earth (if the neutron stars orientation is exactly perfect for our detection), sometimes thousands of times in a second. A star the size of the Sun, a main sequence star, and similar ones from more than 60% of the Sun's mass up to a several times as massive as the Sun, start the same way and may carry on that process for billions of years, but in time they collect enough helium in the cores to begin a second round of fusion. This happens when about 10 percent of the hydrogen has been used up. In this next round, in the center of the already collected helium atoms, the heat, density, pressure, and temperature rise enough, helped by the great energy constantly produced by the equivalent of myriads of nuclear fusion bombs exploding all the time, that the most central helium nuclei begin to fuse with each other to form a larger atomic nucleus containing four protons and four neutrons. That is the Beryllium nucleus. A few of these larger nuclei may survive, but most of these join with another helium nucleus (alpha particle) to make a total of six protons and six neutrons, the nucleus of the atom or element with atomic number 6, and a mass of 12 daltons, i.e., as much as 12 protons would have. This atom is called carbon, of crucial importance to us. In this process even a few atoms of element 8 may form, of course with eight protons. Like the other examples so far, it happens that this new nucleus also has as many neutrons as protons, and the result is oxygen, also crucial to us. Chemists formally compress this information by using these symbols for the first four common atoms:

4
1 1H 4 2He 12 6C

Hydrogen Helium Carbon Oxygen

16

8O

In each of these symbols, the subscript number to the left and below shows the number of protons in the atom. This is the atomic number. We could consider that number as identifying which element this is and just say atomic number 1, or 2, or 4, or 6, but most elements were discovered before people knew about protons, so it is still customary to include the letter symbol for the element. You may just concentrate on remembering the atomic number and ignore the name if you wish, but most find names easier to remember. The superscript at the upper left of each of these symbols is the total mass of the atom, which is simply the sum of its protons and neutrons. As these larger atoms are formed in a star with a mass around that of the Sun (up to several times more), the star swells up, its surface cools, and it becomes a red giant star. If the star is multiple times more massive than the Sun, it uses up its hydrogen faster, and in its final stages it may make still larger atomic nuclei. In the process of making those nuclei already mentioned, a main-sequence star may also make small amounts of nuclei that amount to intermediate steps toward one mentioned. Some of these intermediates will be unstable and convert to something else, but a small proportion will lead to stable atomic nuclei, such as lithium (Li, atomic number 3), and nitrogen (N, atomic number 7).
Period Group 1 Group 2 Group 3 Group 4 Group 5 Group 6 Group 7 Group 0

0 1 2 3a 3b 3c 4

+1 *11H1+ *63Li1+ *2311Na *3919K *29Cu

+2
8 2+ 4Be *2412Mg *4020Ca2+

+3
3+ 5B *2713Al 45 21Sc *5626Fe 70 31Ga 10

4 *126C4 ?2814Si 48 22Ti

73 32Ge

-3 *147N-3 *3115P 41 23V *5927Co ?7533As

-2 *168O-2 *3216S 52 24Cr *12251Sb *9642Mo

-1
-1 9F *3517Cl 18

0
4 0 2He 20 0 10Ne 40 18A

*6530Zn

*25Mn 59 28Ni 80 * 35Br *12753I

36Kr 131 54Xe

84

Chart 1. The early rows of the Periodic Chart of the Elements, showing the kinds of atoms known on Earth, identified by their atomic symbols (letters), atomic numbers (subscript), and atomic weights (superscript). Atomic numbers 37-41 and 43-52 are not shown here because they are not known to be included in biota. Question marks on Si and As indicate we do not need them for life now but both were probably crucial to the origin of life and for its nature. Not shown here are the rest of the 90 natural elements found on Earth, nor any of those created in laboratory experiments.

The elements (atoms) actually needed in humans are listed below along with their symbols:
Element Symbol Element Symbol Element Symbol Element Symbol

Hydrogen Lithium Carbon Nitrogen Oxygen Sodium

H Li C N O Na

Magnesium Aluminum Phosphorus Sulfur Chlorine Potassium

Mg Al P S Cl K

Calcium Manganese Iron Cobalt Copper Zinc

Ca Br Fe Co Cu Zn

Antimony Bromine Molybdenum Iodine

Sb Br Mo I

Chart 2. Elements now needed in humans bodies.

Step 4. Supernovae. In stars 20 to 30 times the mass of the Sun, the greater mass causes more rapid heating, faster fusion, and, after creating helium, carbon, oxygen, and smaller amounts of incomplete atomic nuclei of intermediate sizes, it forms neon and begins to fuse these into other, bigger nuclei. Ultimately, the star explodes as a supernova, and in this explosion (which lasts some time) the carbon and oxygen fuse into still larger atomic nuclei. The next atoms formed in significant numbers are magnesium (Mg, 12 protons, so atomic number 12), sulfur (S, atomic number 16) and calcium (Ca, atomic number 20), as well as combinations of just-made, large nuclei such as carbon, oxygen, etc., with additional helium nuclei. Similar combinations occur between nitrogen (N, atomic number 7) and two helium nuclei (He, atomic number 2), giving sodium (Na, atomic number 11), and in similar ways, between various alpha particles (He, atomic number 2), protons, and neutrons, to give aluminum (Al, atomic number 13), a lot of silicon (Si, atomic number 14), phosphorus (P, atomic number 15), chlorine (Cl, atomic number 17), and potassium (K, atomic number 19). (These can also be seen in order in Chart 1.) Beyond calcium, the process changes. Inside the great outer layer of hydrogen which makes up most of a star, we have seen that a core of helium gradually builds. As larger molecules accumulate in the center of this core, a second, inner core of carbon builds up, and then a smaller one of oxygen, with some nitrogen. When this second, inner core is large enough, the largest nuclei then present collect at its center, to create still further successive cores (much smaller at each level) where larger interactions occur. But when oxygen nuclei are fused with each other, they do not directly form larger molecules; instead, they shatter, creating a shower or stew of helium atoms, protons, and neutrons, which then combine with other molecules to create new fusions. Further, larger nuclei are formed, as well as the intermediate ones. On one hand, the regular, one-helium-at-a-time growth of nuclei does not continue past calcium, but on the other hand smaller amounts of larger nuclei do grow from this new multiple-particle process. The same process also creates many odd nuclei of the same element with extra neutrons, the socalled isotopes. So, for example, there is standard aluminum with 13 protons and 13 neutrons, and another form, an isotope of the first, still with 13 protons (still aluminum), but with 14 neutrons. The next several elements past those we have discussed are not very stable in the extreme conditions of an exploding supernova, so the amounts of them never build up very high, until the iron group is reached. Iron (Fe, atomic number 26), cobalt (Co, atomic number 27), and nickel (Ni, atomic number 28) are more stable, and are formed in these supernova

6
explosions, so we have significant amounts of them available. This occurs when Si (silicon) nuclei fuse to form Ni (nickel), which then loses parts, leaving cobalt and iron. Those elements formed by these processes are ultimately strewn through space by the later stages of the supernova explosion. Those not surviving to that stage may still get into space in more modest amounts by turbulence in star cores which eject considerable material, in star disruptions from encounters with other stars, and perhaps in still larger celestial bodies. At any rate, on Earth, about 90 elements exist. Each element is a collection of atoms with the same atomic number (the same number of nuclear protons), but some, especially larger ones, have differing numbers of neutrons. Charts 1 and 2 show some of the atoms found on Earth, and name those necessary for human life, and most biotic life. Step 5. Multiple Stellar Fusion Cycles. The same protons and atoms go through the same experience, time after time, building a total of about 90 lasting kinds of atoms, and constantly building new blobs of collected matter in space, such as stars, clusters of stars, galaxies of many stars and clusters, planets, moons, comets, planetoids (also called asteroids: tiny planets), down to dust and individual atoms wandering in space, and up to clusters of galaxy clusters. Some of these objects we can still see in our sky, while others have long ago been destroyed and replaced by others. Most remain invisible to us. The galaxies bunch together into bigger galaxies, clusters of galaxies, and these into still larger groupings, with larger spaces separating the larger groupings. Away from stars, the protons and other atomic nuclei often meet electrons. Electromagnetic interactions among these tiny bits of stuff push lone protons and protons in atomic nuclei away from other protons and nuclei, electrons away from electrons, but electrons toward protons. So, if they are not smashed together in stars and larger objects, nuclei will not normally join to make a bigger nucleus in more open space, unless they run into each other extremely forcibly, as in an atom smasher that people build. But if nuclei meet electrons, the electrons will often stay close to the nucleus, a little like a planet circling a sun, or a ball on a string swung around by a person. (A line of electrons pushing each other to get to a nucleus is called an electric current, or just electricity. We cannot see it, but we know it can give us a shock or make our light bulbs shine and our toasters heat. Notice that the light bulb also heats and the toaster coil also shines.) Each nucleus tends to collect about as many electrons as it has protons, to balance its electric charge. The combination of a nucleus with its electrons is called an atom. So we call this kind of nucleus an atomic nucleus. Atoms are important to us because we are made of them, as is everything solid, liquid, and gaseous, even air. These balancing electrons are important to us because they are the foundation of chemistry. But before we come to that, we should note that the atoms and separately traveling protons, neutrons, and electrons, after being built up in and expelled from an exploding star tend again to collect in space under the influence of gravity and sometimes magnetism, forming new stars, and being recycled. In the new star the process begins again, over time building up some kinds of atoms, shattering others, and enriching the mix. This process must have happened many times over to create all the materials composing our Earth and ourselves, eve up to uranium (atomic number 92, with 92 protons, often with 146 neutrons, but sometimes only 143), presumably recycled through multiple stars before reaching such lofty numbers of

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nuclear particles. The proportions of those created have probably had some influence on the proportions and numbers of various kinds of atoms of which we are composed today. Step 6. Milky Way. Multiple billions of years ago a collection of stuff formed in space. We call it the Milky Way Galaxy, because its many stars and dust clouds make a faint, whitish haze across the night sky when our air is very clear, as though some giant had spilled a little milk across our sky. That galaxy whirls around a dense center, where maybe the heaviest atoms are being made, and a star called a supermassive black hole is believed to reside. (It is not actually a hole, but an extremely dense and massive collection of matter.) Our galaxy is part of a vast bunch of galaxies. Within it are many stars and dust clouds. Step 7. Formation of the Solar System. Within the Milky Way Galaxy, billions of years ago, gravity drew enough atoms, bits of dust, and perhaps larger bits of stuff, near each other to form a whirling cloud, hundreds of millions (perhaps a billion) of miles across. As its gravity pulled it all closer together, this huge cloud changed. The bits of it began to join up into a great mass in the center with a number of smaller blobs circling around the center. The central part, as described above, gradually grew massive and dense enough to fuse protons into helium nuclei, becoming our Sun, and to shine. At the same time, the other blobs consolidated into the planets, moons, comets, and so on, of our solar system. One of those new planets was our Earth, on which we have always lived and depended. We still do. Meteorites have indicated that the Solar system formed into something like its present nature about 4.55 billion years ago (older books say 4.6, newer ones usually say 4.5; the difference is not a change in view, but unwillingness to put the second figure after the decimal point, because of uncertainty in the calculations).16 This indicates when the crust of the Earth mainly hardened.
16

The United States Geological Survey (USGS) website has in-depth information about the age of the Solar System and how it was determined, using radiometric dating: All rocks and minerals contain long -lived radioactive elements that were incorporated into Earth when the Solar System formed. These radioactive elements constitute independent clocks that allow geologists to determine the age of the rocks in which they occur (geomaps.wr.usgs.gov/parks/gtime/ageofearth.html#date). Some of the radioactive elements used for the calculation of age are uranium, potassium, rubidium, samarium, and thorium. See also USGS publications (pubs.usgs.gov/gip/geotime/age.html): The results [of radiometric dating of meteorites] show that the meteorites, and therefore the Solar System, formed between 4.53 and 4.58 billion years ago. Thus, variation between the figures of 4.5 and 4.6 billion years, both due to rounding off, derives from differences in the particular elements measured. For additional information, see Dalrymple, G. Brent. 1991. The Age of the Earth. Stanford, CA: Stanford University Press.

The planets collected themselves through gravity, bringing together much of the matter circling the Sun near a particular orbit where the local concentration of mass was greatest, as faster-moving particles caught up with slower ones in nearby orbits. This process has gradually built up the planets and cleared the spaces between adjacent planets somewhat, most rapidly nearest the Sun, where planets travel fastest along their orbits, and more slowly farther out. The least massive parts of the Solar System, of course, tended to become segregated out to its edges, including the Oort cloud, believed by many astronomers to have formerly existed between the orbits of Uranus and Neptune, but now out 1,000 times farther from the

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Sun than the Kuiper belt, which lies beyond the orbit of Neptune.17 This cloud and belt consist of isolated atoms, molecules, larger particles, comets, and possibly a few heavier bodies, composed of light material such as hydrogen, helium, carbon, and oxygen (hydrogen and oxygen often combining to form water ice).
17

See Morbidelli, Alessandro. 2005. Origin and Dynamical Evolution of Comets and Their Reservoirs at arXiv:astro-ph/0512256.

The Kuiper belt is a flat and nearly circular (technically an ellipse, as suggested above), like the orbits of the eight largest inner planets, but the Oort cloud is a sphere, as the outer edge of the original dust cloud was. Pluto's orbit is still more oval than that of the other planets, and lies in a different plane, perhaps reflecting Pluto's slower adherence to the pattern of the other planets, because of its great distance from them, or perhaps its later arrival in the Solar System from elsewhere.18 The objects in these outer clouds are mostly icy comets, and some have very elongated orbits that bring them closer to the Sun periodically, perhaps from the influence of the gravity of the four large, outer, gas giant planets on the orbits of the comets.
18

In 2006, the International Astronomical Union reclassified Pluto as a dwarf planet, a class of object distinct from a planet. It is not only smaller than the other planets but also smaller than some moons (our Moon, Io, Europa, Ganymede, Callisto, Titan, and Triton) (nineplanets.org/pluto.html).

Step 8. Early Earth geology. The hot Earth slowly sorted its atoms by mass or weight, first as it was collecting and consolidating. As with stars, at first the pressing together of the material making up our Earth (and the remaining energy from the previously separate motions of its parts) made it so hot that the inside melted. The decay of radioactive atoms trapped in the Earth also added to its heat, and a little more heat came from the Sun when it began to shine. That melting let the heavy atoms sink further toward the center of the earth, and the lighter ones move toward the surface. In a while, much of the center seems to have become largely iron and nickel, with even heavier atoms, though some heavy atoms stayed close enough to the surface to be mined later. But this process did not end. Even now, the inner Earth slowly churns its soft core. The separation was never complete. Some heavy material still exists on top, and the heat of the interior has always made it spill out on top sometimes, like the water bursts in boiling oatmeal, making volcanoes which continue to spill out on the surface some lava newly pushed up from deep in the Earth. Still, the nickel-iron core does not spill onto the surface, but at times heats parts of the next higher layer, the rocky mantle, causing it to melt and push up through the lightest layer, the thin crust on top. Lighter atoms like carbon came to the crust, and often through it in volcanoes and geysers. Medium-weight atoms like silicon collected into a sort of coating or skin for our Earth, now called the crust, while the lightest atoms, like argon, oxygen, hydrogen, nitrogen, and maybe chlorine, were able to float around as gas or air just above this skin, but mostly held near it by gravity. The very lightest atomshydrogen, with only one protoncould and can slip away from the Earth, especially when it was hot. If our Earth had a large hydrogen atmosphere early on, as some students think, much of that hydrogen slipped away early. Earth now has only a little more than enough hydrogen to make up our water and biology.

9. New Moon and Cooling. Then, about 4.5 billion years ago (50 million years after the formation of the Earth), an early planet about the size of Mars crashed into the Earth, knocking much of Earth into space. This debris is believed to have formed an orbiting collection of pieces of the outer Earth, which gradually consolidated into the Moon. That is the explanation for the Moon's being much less dense than Earth (Earth's densest materials are deepest inside).19 Then, the smaller things in Sun's solar system, including Earth's moon, and probably our Earth began to cool on the outside. The smaller worlds cooled faster, while Earth and a few other bodies still have hot centers and volcanoes. As they cooled, their outer skins became quite solid and mostly hard.
19

There are several hypotheses of the Moons formation, of which this is the most widely held (Canup, R. and E. Asphaug. 2001. Origin of the Moon in a giant impact near the end of the Earths formation, in Nature 412 (6848): 708-712. Doi:10.1038/35089010).

(This happened because what we call "cooling" is actually dancing atoms slowing down. Most of the time, atoms move. Something is hot if its atoms are moving fast, cold if its atoms are moving slowing. If atoms move fast enough, they can slip past each other. If gravity pulls them hard enough, they stay close together but can slide past each other, like marbles filling a bowl. In the gravity of Earth, when we tip a bowl of marbles far enough, they slip past each other, slide out, and fall on the floor. When we do the same with a bowl of milk, the atoms or molecules slip past each other, slide out, and fall on the floor in the same way. Stuff in which the atoms or molecules are freely able to do that is called "liquid" and can pour.) If atoms move so slowly that they cannot pass each other, they usually stick together to make a solid, which does not pour. Sometimes some stuff is part way between these two conditions, and stays together but gravity or another force can bend or shape it. If atoms move so fast that they fly past each other in all directions, they make a gas, like air. Where there is not much air pressure, there is no liquid. Where atoms or molecules can move past each other freely, but air pressure keeps them near Earth's surface, they form a liquid, which can pour. If atoms move so lowly that they cannot pass each other, they usually stick together to make a solid which does not pour. Sometimes a substance is partway between these two conditions and stays together but gravity or another force can bend or shape it. If atoms move so fast that they fly past each other in all directions, they make a gas, like air. Where there is not much air pressure, there is no liquid. Where atoms or molecules can move past each other freely but air pressure from gravity keeps them near Earths surface, they form a liquid which can pour. 10. Further Early Earth geology and meteorology. So, in early Earth, the solid iron became so hot that it turns into a liquid, but the skin became cool enough to become solid. As Earth cooled, the atoms of a few gasses slowed down so much that they changed to liquids and fell to the earth, i.e., they rained. The Ocean and various rivers and ponds formed. Evaporation of water to lift it into the air as a vapor and consolidation of that vapor back into rain created a great cycle which still continues, providing an endless supply from limited resources, through recycling. Wind, as well as rain (and sleet and snow) began to wear down the high places on the crust, but continents formed from the lightest kinds of rock (with lighter atoms like aluminum, sodium, etc., combined) and slid around on top

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of the rest of the crust, pushed by upwelling lava coming through the thinnest parts of the crust, arranged along deep-Ocean trenches. The resulting collisions among parts of the upper crust forced some parts of that crust to slide over a piece against which they were pushed, while the other slid beneath and sank back into the mantle, to be recycled by the heat and pressure below. These processes continue today, causing earthquakes, landslides, tsunamis, and other events that are troublesome to us but providing resources that were necessary to create biology and that remain necessary. When atoms dance very fast, they zip past each other with little or no interaction. When they dance very slowly, they do not touch each other very often and touch so gently they hardly notice, so they often continue along on their ways. But if the temperature is just right the atoms dance at just the right speedthen some atoms will stick together for a while. A cluster of atoms stuck together in that way is called a molecule. A molecule is like a team of atoms dancing together as partners. An important thing that happened as Earth's outside cooled was that the atoms slowed down to just the right temperature to take partners and form molecules of atoms dancing together. That change is important to us because it let us live, since we are made of molecules. All the atoms in our bodies are dancing with partners in molecules. Sometimes the dancing atoms change partners, join partners, or leave partners. Chemistry is the process of joining, leaving, or changing atom partners in a molecule. That is what the next part of this story is about. So chemistry began on Earth at latest by about 4.5-4.4 billion years ago, and we cannot understand what we are, or how we became what we are, without knowing this part of the story. However, it is hard for most people to get a feel for billions of years, so let's invent some new words and think of it this way. We understand seconds, hours, days, weeks, months, and years. We understand decades, centuries, and millennia. A century is 100 years. Most of us have at some time counted to 100, or at least we can. So let's call a hundred centuries (100 x 100 = 10,000 years) a centad (from Latin cent- hundred). Then we can call 100 centads (100 x 100 x100 = 1,000,000 years) a millad. So we can say that Earth's outside solidified and chemistry began 45 hundred millads ago. Between the hot, molten, and churning iron-group core and the cold surface or crust lies a third layer of Earth, the mantle. This is made of minerals (oxygen, silicon, aluminum, and various other elements, especially metals), at an intermediate temperature. The boundaries between these layers are not smooth and constant, but irregular both in space and time. A region hotter than the rest, down in the mantle, tends to be more turbulent than the rest, to heat the surface, and periodically to squeeze out onto the surface as hot steam, as other gasses (especially carbon dioxide), as particles like cinders, and as molten rock, called magma, which then cools and hardens. In addition, the underlying heat breaks the crust in places into sections called tectonic plates, and pushes these plates about the surface as the heat of a burner on the stove makes the fluid part of creamed wheat roil and push "plates" of relatively solid meal about, over the surface, causing them to bump into and crumple one another, pile up, etc. In just such a way, the heat deep in the Earth pushes the plates of crust about on the surface, making them move from place to place on Earth, collide with each other, push over each other, crumple up into mountains, etc. New material comes up mostly along the lowest, thinnest parts of the Earths crust, as you might expect, and these thinnest parts trace the deepest parts of the Ocean. When one tectonic plate pushes over another, one is pushed up into mountains while the other is forced

11
back down into the mantle, where it softens, is compressed and chemically slightly changed, and from where it ultimately appears again, unrecognizable, somewhere else. (The rock that is heated, melted, and erupts in volcanoes, whether on the Ocean bottom or on an island or continent, or is melted underground and later found at or near the surface, is called igneous rock, often grainy and full of crystals. On the surface it may be worn down or eroded by wind and water, changed by chemical events, and it collects again to consolidate as a new kind of rock, sedimentary. When it is buried deep enough in the crust, pressure may change its density, texture, appearance, and other qualities, in which case it is called metamorphic rock. If a bit of crust is recycled through the mantle in the process of plate tectonics, as described, it is too deep to be recognized as metamorphic rock. Instead, it is again igneous. All of these things happened to the Earth and on it. None of us were there 4500 millads ago, but only after those changes occurred could biology begin. And even more was necessary, as we shall see. Chapter D. Supplement: Recent Discoveries Because a large part of this volume was complete before the following information became available, and because this new information is neither critical to what has been covered in this chapter nor been fully evaluated, the following new information is presented here in its current form without integration into the original text. Recently, astronomers have reported discoveries of the following previously unknown planets beyond the orbit of Pluto, which was previously thought to be the most distant planet from the Sun, showing their tentative working names, their distances from the Sun in astronomical units (AU, i.e., their distances times the distance of the Earth from the Sun), their sizes or masses, as now estimated, and their numbers of moons, as so far determined: 1. 2003 EL61 is the current code for an object the size of Pluto, found beyond Pluto at 52 AU, within the Kuiper Belt (which extends to 70-72 AU from the Sun); it is the most elongated orbiter of the Sun that is this large, has two known moons, and is currently believed (on real but limited evidence) to have a rocky core with a skin of ice. One of the moons also seems to be composed largely of ice. It has been inferred from this that this moon arose in a manner similar to our Moon. As a substitute for the cold, statistical code name, I remember it as three-fourths P(luto).20 2. Buffy, a bit smaller than Pluto (P-b) and also within the Kuiper Belt, is estimated to be 58 AU from the Sun, and has an orbit tilted 47 degrees from the plane in which the eight major inner planets orbits lie, a greater such tilt than any of the other newly discovered planets.21 3. Sedna has a mass about 1/3 that of Pluto (P/3), orbits beyond the Kuiper belt at 76 AU from the Sun, and spins faster than any other object orbiting the Sun (one complete spin in four hours instead of our 24, though it is much smaller than the Earth). If the hypothesized Oort Cloud really exists, probably Sedna is the first planet found within it.22 4. Xena is the first object found beyond the orbit of Pluto but larger than Pluto (1.5 times as large, hence 1.5 P), and spends most of its time within the Kuiper belt, but, because of an oblong orbit, is now at 97 AU, more remote than any other celestial object so far detected orbiting our Sun.23

12
Astronomers have proposed at least two possible implications from these recent discoveries, but the data is still too limited to draw any firm conclusions. Perhaps it all suggests merely that (1) the original cloud of particles and other debris from which the Solar System grew was (or became after nearby cloud regions produced other stars and moved away) roughly that the remote, more concentrated, and closer Kuiper Belt objects orbits have not yet fully rounded out and conformed to the single plane of the major planets, because of the remoteness of the four newest-found planets, (2) that the central part of the original cloud has rounded and conformed (almost) to a single plane, and (3) that the outer portions of the original cloud always were tenuous (and have increasingly become more so), as some matter has been drawn inward toward our Sun, and some may also have leaked away into farther space. We shall see how future discoveries add to our picture as they happen.
20

2003 EL61 was officially named Haumea, after the Hawaiian goddess of childbirth, by the International Astronomical Union (IAU) in 2008. This dwarf planet was discovered in 2004 by Mike Brown of California Institute of Technology and his team at the Palomar Observatory as well as in 2005 by the team of J.L. Ortiz at the Sierra Nevada Observatory in Spain (en.wikipedia.org/wiki/Haumea_(dwarf_planet)). 21 Buffy is a temporary name for 2004 XR 190, discovered as part of the Legacy Survey on the Canada France Hawaii Telescope (www.space.com/1876-solar-system-crazier.html). 22 The IAU has not officially determined that Sedna is a dwarf planet but it may be one (en.wikipedia.org/wiki/90377_Sedna). Its orbit is extremely elliptical, reaching 937 AU at the farthest point from the Sun and 76 AU at its closest approach. Astronomers still disagree on its location in the Oort cloud in 2013. It was discovered in 2003 by Mike Brown of the California Institute of Technology, Chad Trujillo of the Gemini Observatory, and David Rabinowitz of Yale University 23 In 2006, the International Astronomical Union renamed the dwarf planet Xena. It is now known as Eris after the Greek goddess of discord (http://www.caltech.edu/content/dwarf-planet-formerlyknown-xena-has-officially-been-named-eris-iau-announces). Eriss moon is now called Dysnomia, after a daughter of Eris who was the goddess of lawlessness. These names were suggested by the discoverers, Mike Brown of the California Institute of Technology, Chad Trujillo of the Gemini Observatory, David Rabinowitz of Yale University, and the engineering team of Keck Observatory. Although a little larger than Pluto, Eris is still a dwarf planet.

13 Chapter E. Steps 11-20 Beginning Earth Chemistry

Step 11. The dance of the atoms and start of Earths chemistry. Atoms are always in motion. This motion is sometimes called the dance of the atoms. What we call temperature is merely the tempo of that dance. When this dance is very fast and wild, atoms usually do not take partners, and no chemistry occurs. When Earths crust fell to a temperature below a few thousand degrees, some slower moving, heavier atoms began to take partners. As the surface cooled further, many atoms began to take partners. That was the beginning of Earth chemistry. (If the tempo becomes too slow, atoms meet each other less often, so they interact less often, to, to us, more slowly. Also, if they move very slowly, it is because they lack sufficient energy to move more quickly. Much chemistry requires energy to launch it.) Also, if the tempo of the dance becomes still slower, liquids begin to solidify, losing access to other atoms; ice can interact with non-water atoms and molecules if it comes in contact with them, but only the surface of the ice can do so. So temperatures (or the dance tempo) must be just right for us and much of biology, i.e., the narrow range of temperatures above that of water freezing and below water boiling, between 0 and 100 degrees Centigrade (32-212 degrees Fahrenheit). Chemistry consists of atoms taking partners, changing partners, and abandoning partners in their continuous dance. The three most abundant elements in the crust of the Earth mixed and often combined with each other and with other elements also in the crust. Those three elements consist of all of the atoms of three types: oxygen (atomic number 8), silicon (14), and aluminum (13). So most of Earths crust is made of silicon dioxide molecules, each with one silicon atom and two atoms of oxygen (written as SiO2), sometimes also combined with aluminum in the same molecular team. Step 12. The structure of atoms. How and why do the atoms make these choices? To answer that question, we must examine the structure and nature of atoms generally. Now we already are aware that an atom consists of two main parts: (1) a tiny nucleus in which the strong force holds together all the protons and neutrons of that atom, and (2) a larger area around the nucleus where the electrons are. We are also aware that the protons have a particular kind of electrical force or interaction tendency that we call positive, while the electrons each have an equal but opposite tendency which we call negative. Any neutrons in the atom will also be in the nucleus but will have no electric charge; they will be electrically neutral. Because protons attract electrons and the other way around, such a nucleus will tend to attract a number of electrons equal to the number of its protons (if they are available and if the attraction is not overwhelmed by some stronger attraction from elsewhere). Each of these electrons will tend to locate itself within a region known as its orbital, surrounding the nucleus. A hydrogen atom, for example, has only one proton, so by itself it will attract just one electron. A helium atom, however, has two protons (and two neutrons) so the protons will attract two electrons. Each electron will occupy its own orbital. But both electrons (and their orbitals) will occupy the same shell, a three-dimensional region around the nucleus that includes both orbitals.

14
If an atom has more than two electrons, the orbitals of the two electrons closest to the nucleus will occupy the same shell which thus includes both orbitals. Any further orbital electrons locate in a second shell, outside the first one. Lithium, for example, has three protons and three orbital electrons (as well as usually three neutrons). The first two will each have an orbital within the first and smallest shell. The remaining electron will occupy a different orbital in a larger shell. Again, carbon atoms each have six protons and (usually) six neutrons, so a neutral carbon atom (no net electric charge) has six electrons, two in the inner shell and four more in the outer shell. Likewise, nitrogen (with seven protons and seven electrons) has the same two shells, with again two electrons in inner one, but five in the outer shell. In the same way, oxygen (eight protons, eight electrons) has six of its eight electrons in the outer shell and neon (10 protons, 10 electrons) has eight of its electrons in the second shell. If an atom has more electrons than that, though, it still cannot have more than eight electrons in the second shell and so must add a third shell. If the third shell fills up to eight electrons, it must add a fourth shell. More electrons can be added to the fourth shell but if two electrons are in the fourth shell, the next electrons will be added back to the third shell until the third has 18 electrons! Only then can more be added to the fourth shell. Still further electrons lead to still more complicated electron arrangements, which the reader can see in the accompanying diagrams. In any case, chemistry is affected mainly by the electrons in the outermost shell, which are called the valence electrons. A lesser influence is atomic weight, approximately the sum of protons and neutrons in an atom. Lighter-weight atoms combine with other atoms more readily into molecules, even pushing away competitor atoms of heavier atomic weight. In certain atoms with large numbers of protons and electrons (and neutrons), an electron from the second largest shell will sometimes slip into the outer shell and affect chemistry, but not in most of the elements that concern us here. Step 13. Valence and choice of atomic teammates. From what has been said, we know that chemistry depends largely on the valence electrons, those in the outermost shell of an atom. In an atom such as hydrogen (atomic number 1) or helium (2), only one shell exists, and it can hold only one or two electrons. Those are the valence electrons for those two kinds of atom. Generally, the remaining kinds of atoms, numbers 3-92 (and higher for artificial ones), no matter how many shells an atom has or how many electrons are in some of the intermediate shells (which varies with the total number of electrons in the atom), the outermost (valence) shell cannot regularly have more than eight electrons. From chart for step 3 in chapter D, part of the standard periodic table of the elements found in most chemistry texts), as well as the diagrams for step 12 in this chapter, the reader can see that the atoms are arranged in eight numbered columns. I have arranged them slightly differently from the usual way, so the number of the column is the number of valence electrons these atoms have, except for the last column. That column is normally called the zero (0) column, but it really contains atoms whose outermost (valence) electrons are as many as that shell can have. In other words, that might be called the full column, because atoms listed there have a full outermost electron shell. The reader can also see the total number of electrons in a neutral atom in this chart by looking at the number shown in superscript to the left of the symbol. So hydrogen (atomic number 1) has a small numeral one, helium (atomic number 2) has a small superscript 2 (which

15
is full for the innermost shell). For those two atoms, a 1 or 2 for outermost (valence) electrons appears to the upper right of the symbol. Again, neon (atomic number 10) has a full outermost shell of eight electrons, while sodium (Na) has only one electron in its outermost shell, with a numeral one above and to the right of the symbol, and falls in column 1 of the chart. Likewise, aluminum (atomic number 13), carbon (6), nitrogen (7), and oxygen (8), like sodium, do not have full outer shells. Why do we care about this? Because atoms whose outermost shell is full cannot have any more electrons. Because chemistry is caused by valence electrons, atoms with full outer shells normally do not take part in chemistry. There are a few exceptions, but those do not play a part in biology. A full outer shell, however, is why helium and those elements listed under it cannot burn (as burning is a chemical process) and is thus safe for use in zeppelins (dirigibles) and toy balloons. How do atoms join dance teams (molecules)? There are several ways, called bonds, but the basic idea is that atoms join together to fill their outermost shell of electrons. They tend to do what is needed to get a full outer shell. If they normally have four valence electrons, as carbon (C) and silicon (Si) do, they can team up with other atoms to add four more electrons. They may do so by sharing electrons with each other. For example, sodium (Na) has one valence electron. Carbon has four. Neither have eight alone. But if four sodium atoms with one valence electron each join one carbon atom, the total valence electrons equal eight, and all can share in this common full set of valence electrons. This sharing, which becomes one full outer shell for all five atoms in common, is what binds them together as a molecule (4 Na x 1 + 1C x 4 = 8). This particular combination, though, is not common. Likewise, another carbon atom, also with its own four valence electrons, can team up with four hydrogen atoms, each with one valence electron (its only electron). Thus, again, the four carbon electrons and one electron more from each of four hydrogen atoms total eight valence electrons which can be pooled and shared and this sharing binds the five atoms together into one molecule, called methane. This molecule is important in our story, as we shall see. In both of the last two cases, the sodium or hydrogen atoms space themselves equally far apart around the carbon atom to make this sharing easy. Such a sharing is called a covalent bond. In a similar fashion a sodium atom with its one valence electron can share that electron with a chlorine (Cl) atom, which, as can be seen from the chart in step 3, is in column VII and thus has seven valence electrons (7 + 1 = 8). Notice here that the sodium atom in the chart shows a + by the number of valence electrons. That means it has one valence electron. But chlorine has an almost full valence shell; it needs just one more electron, so it behaves, in a way, as though it has one vacancy or space for a missing valence electron, which needs filling in with an electron from some other atom. This is shown by putting -1 to the right of the symbol (i.e. in right superscript). We see that the atom has seven valence electrons because its symbol is listed in column 7, but it needs one more to have a full valence shell, which has the equivalent of one vacancy for another electron. In the same fashion the reader can see that the elements listed on the left side of the chart all have a few valence electrons available for partners (shown by + and 1, 2, or 3), while those on the right generally have a few vacancies for more valence electrons (shown by and 1, 2, or 3). Thus, a large proportion of the elements listed on the left (which are called metals) join with elements on the right (non-metals) to make molecules. The molecule of a sodium atom (metal +1) and a chlorine atom (nonmetal -1) is technically named sodium chloride (the metal

16
part being named first usually), but is commonly known as the ordinary table salt so prevalent in food products, a necessity for cellular life including ours. We may think of these positive and negative numbers as the hands that our atomic dancers hold to keep their teams or molecules of atoms dancing together. So the positive and negative numbers shown beside the atomic symbols are called valence numbers. If a positive valence is balanced a negative valence, the number of hands needed to be held to make a dance team (molecule) will match and the team can dance together. Just dancing nearby is not enough; they must hold all of each others hands to make a stable and coherent dance team/molecule. (Each molecule normally has a name and chemists follow standard rules to select and recognize such names.) Metals normally do not form molecules by joining with each other (rather only with nonmetals) and thus do not chemically join each other. But they may be physically mixed with each other in an alloy. Nonmetals may join chemically with metals and even with each other or other atoms like themselves (e.g., oxygen and nitrogen, when not joined to some other kind of atom, normally bond with copies of themselves, shown as N2 and O2. Atoms of hydrogen, too, can pair up between themselves, and so these elements are all classed as nonmetals.) Some other examples are included in the table for this step. We should also note that if we add one to the row number in which an atom listed, in this chart, we can see how many shells the atom has (which appears above row three). Starting there and going down, the situation is more complicated than is necessary to explain for the purpose of this project and difficult to show accurately in a small space. What of the middle atoms in the first and second rows of this chart (carbon and silicon)? They have four valence electrons, i.e., four vacancies for more. This is shown by the 4 beside the symbols C and Si. This also means they can join either metals or nonmetals, or copies of themselves. They are also fairly abundant. The result is that silicon plays a large part in rocks on Earth, mostly in combination with oxygen as silica (SiO2), which can be found in numerous lifelike formations because it is able to form such complex molecules. Similarly, carbon, because of the same ability form long chains of itself and very complex molecules with many other kinds of atoms, is crucial to biology on Earth, including us. Step 14. Chemical Bonds. Several different kinds of chemical bonds among atoms forming molecular teams have been discovered, but all are based on the idea of valence mentioned above, derived from the electrical attractions and repulsions of protons in the nuclei and electrons, mainly the valence electrons in the outermost shell of each atom. First, there are the covalent bonds, in which two or more atoms share their electrons, which we might call the sharing or pooled-electron bond. These are the strongest in most situations. They can be even stronger if, instead of holding just one hand of the other atom in a pair (like carbon and hydrogen in methane, CH4), a pair of atoms hold two hands, like iron (Fe+2) and sulfur (S-2) joining to make ferrous sulfide (FeS), which may be shown as Fe=S to represent, with two parallel lines, the two bonds. An even stronger case occurs when each atom bonds with three hands of the other, as in hydrogen cyanide (HCN), where three hands of the nitrogen atom and one of the hydrogen atom together make a total sharing of the usual eight valence electrons, but three bonds or pairs of valence electrons with the nitrogen atom. Hydrogen cyanide is a crucial molecule in our story; however, with a slight change, substituting sodium (Na) or potassium (K) for the hydrogen atom (H), it becomes a dangerous and powerful poison to us now.

17
Thus, in summary, if members of atomic dance teams hold two or three hands with a particular partner instead of just one, the resulting double or triple bonds are accordingly stronger than the single covalent bonds. In hydrogen cyanide (HCN), the carbon atom shares three atoms of its valence electrons with the three vacancies of the nitrogen atom, making a very strong triple bond. It shares its fourth valence electron with the hydrogen atom, thus filling out hydrogens single shell (which is full at two electrons). Thus, each bond represents two shared electrons. Second, there are ionic bonds. When atoms are scattered through a solution in which individual atoms can react with and travel among the atoms of the solvent (which is normally liquid, like water), one atom may actually borrow an electron from another, departing from the normal situation in which an atom is electrically neutral. That happens between sodium and chlorine in water. The sodium atom (a metal) gives up its single valence electron, which joins the chlorine atom. The result gives the chlorine (a nonmetal) atom a full valence shell but one more electron than the number of protons. That extra charge of negative electricity (due to the extra electron) gives this atom a net negative charge (-1). This charge allows the atoms to move freely about in the water, interacting with water molecules, especially hydrogen (+1 with the negative Cl-1) or other atoms and molecules that may be dissolved in the water. At the same time, this process leaves the sodium with one less electron than it has protons. That makes it, also, electrically unbalanced, not neutral, but with a +1 electrical charge, giving a similar effect as just described for chlorine (H+1 may interact with the radical -1 OH from the water, etc.). The two formerly electrically neutral atoms, by becoming electrically charges, become ions. The result increases the likelihood of further interactions with other available chemicals, but the resulting opposite charges also tend to keep these two atoms near each other, drawn by the electrical attraction of the opposite electrical charges. Thus, they rejoin if the water evaporates and become table salt once again. Even in solution, these ions make the water taste salty. Another especially strong kind of bond is the aromatic ring or benzene ring bond. Carbons ability to form strings or chains of itself sometimes results in the ends of these chains hooking up into a sort of round dance or molecular team, with six carbon atoms in a twisted circle, or, more properly, a twisted hexagon, each one attached to the next. Each carbon bonding with the next carbon atom uses up two of each atoms valence electrons (one at each end). But what of the other two? One is usually holding a hydrogen or other atom off to the outside of the ring, but the other joins the ring-shared pool. That provides the ring with six more valence electrons (one from each carbon atom) but does not make enough for six normal double bonds. Instead, these extra six electrons circulate through the pool, or circle, moving or acting as if they were distributed around the ring, a sort of extra half-electron bond. It is stronger than if it had only a single bond. It is strange, but occurs in this one kind of structure, originally discovered in the benzene ring, the main part of benzene. Substances of this class usually have a distinctive odor so they are called aromatic hydrocarbon compounds and this special kind of bond is termed aromatic. This kind of bond is ordinarily shown by printing two lines connecting the odd carbon atoms but only single lines connecting even ones (see accompanying diagram). In addition to these common bonds, there are also a number of much weaker influences. One is the hydrogen bond. It arises where hydrogen atoms, bound in a large molecule, are bonded in some other and stronger way (like a covalent bond) to one other atom, but are also held by the structure of the large molecule to keep them near different atoms in the same molecule. This happens particularly in nucleic acid chains.

18
The strength of the stronger bond to another atom may keep the sole electron of a hydrogen atom mainly in the area between the hydrogen proton and the other atom (usually another hydrogen or carbon, nitrogen, or oxygen) to which it is more strongly bonded. That leaves the other side of the hydrogen atom with limited electron coverage resulting in the proton having a small proportion of its electrical charge directed away from its electron. Where two hydrogen atoms, or one hydrogen and another kind of atom, especially a nonmetal, are held near each other in this arrangement by other atoms bonds, this location and the electron orbital distribution may slightly attract the two hydrogen atoms (or the single hydrogen and the other nonmetal atom) to each other. (See accompanying diagrams.) In individual cases, this hydrogen bond attraction between the two atoms is too weak to have much effect. But if, as in nucleic acids, the molecules are in long chains, the total effect of all the attractions of hydrogen to other atoms may tend to hold two complementary chains together, or to shape individual chains to some degree (in a helix). Other similar weak attractions, such as the van der Waals attraction, exist in particular situations. Step 15. General process results. As mentioned in Chapter C, a potential process in general, and, of course, in chemistry particularly, may have several possible outcomes. The potential process may not occur at all where conditions are not suitable: (1) temperature, access of each molecule to others, available energy, other needed elements or property such as acidity, etc., may be lacking, or (2) other atoms or conditions may interfere. The process may be interrupted by intervening events. The process may go on to completion: (1) for example, two kinds of atoms may join into a molecule, immediately and directly or indirectly through several steps, and continue until all of one kind are combined into the molecule. The process then has to stop because no more of one of the constituents remains available. For example, when iron filings buried in sulfur particles are heated in oxygen, nearly all of the iron atoms join sulfur atoms, making ferrous sulfide. The extra sulfur then burns up (combines with oxygen and rises into the air). (2) Even where all of one kind of atom is not really consumed, it may become unavailable in two common ways, leading to the process stopping. First, one of the products may be a gas (like sulfur dioxide, just mentioned), which rises into the air, leaving the site of the reaction. Second, if a process is happening in the Ocean, one of the products may be insoluble. In this case, this product will settle out of the water, sinking to the bottom, and, again, leaving the site of the reaction (which is called precipitating). The process may reach equilibrium. In this common case, the atoms join to form the molecule in question, but the molecule remains soluble and hence dissolves in the Ocean. But at some point, as much of the molecule is formed as can dissolve. If any more molecules are formed, an equal number of molecules will break up into their constituents, keeping the number of molecules the same. More atoms may be available to form more such molecules, but the reverse will also happen, so that progress ends. The process may become circular. On Venus, as mentioned previously, water evaporates into air, but sulfur oxides combine with it to form sulfuric acid, which precipitates back to the planetary surface and the process repeats. Similarly, on Earth, warm water evaporates from the Ocean, rises into the air as water vapor, but later cools, forms droplets, falls to the land, runs down river to the Ocean, and the process repeats endlessly without making any progress.

19
The process may be driven by some outside influence. Our Sun sends light and heat, created in its continuous nuclear fusion reactions, to Earth, providing energy. This energy helps drive the biological process of Earth, in particular (now) pouring sunlight on the leaves of biota which use that energy to convert carbon dioxide and other atoms and molecules into biological molecules and build biological systems and processes. Animals, fungi, and other biota use those plants and other biota or their products as sources of food and energy for themselves, in most cases providing in turn more carbon dioxide and other products needed by the plants, etc. This system has circular aspects (the same atoms on Earth are continually recycled) but also changes over time, making progress rather than just repeating. This is possible only because the energy from the Sun drives the whole system, and that energy comes from fusion reactions of protons or pre-existing atomic nuclei. When these are finally used up in several billion years, the whole process will run down. So major biological processes of Earth are ultimately driven by this Solar energy source. On early Earth when the Sun was much less productive another process seems to have provided the most important driving force for the beginning of biology. That process was plate tectonics. Hot spots in or below the mantle of Earth produce upwelling molten rock (magma) through volcanoes but mostly along the trenches in the deep Ocean where the crust of the Earth is thinnest. That upwelling pushes the continental plates of crust around but the upwelling itself provided, and still provides, great heat and a continuing source of elements not sufficiently available from air or water alone, which was crucial to the earliest Earth biology. Without that beginning, we would not be here. Our bodies still contain aspects of that process, as we shall see. Step 16. Inferred early Earth air. We have already noticed that the continual, cyclic process of plate tectonics, driven by the internal heat of the Earth, continually pushes new molten rock to the surface of the crust (most under the Ocean), which in turn pushes the plates the lightest (continental) crust against and over each other. This part of the process thus drives older continental rock back into the hot, pressured mantle, where it is recycled into new igneous (remelted) rock, no longer containing any fossils or other indicia of what it had been like before. Because of this process, none of the rock found by humans near the surface of the crust directly reveals information about that crust from before about 39 hundred millads ago (3.9 billion years). The earliest Earth crust that has been found, however, shows that free oxygen (meaning oxygen atoms not attached to any other types of atoms, in the air) did not yet exist in any significant amount.24 In addition to rocks in the crust, we have meteorites (rocks falling to Earth from nearby space), our moon rocks (collected by astronauts), and rocks from Mars (arriving as meteorites or detected on Mars on in its thin atmosphere). We also have atmospheric information about Europa and other moons of Jupiter, as well as Titan and other moons of Saturn, collected by space probes. Especially useful has been a type of meteorite called a carbonaceous chondrite. This type contains meaningful amounts of carbon, mostly in various kinds of molecules.
24

According to Wikipedia, the earliest atmosphere on earth was primarily hydrogen, with some compounds of hydrogen with other gases producing water vapor, methane, and ammonia (en.wikipedia.org/wiki/Atmosphere_of_Earth#Earliest_atmosphere). Nitrogen, carbon dioxide, and inert gases came from volcanoes and asteroids that bombarded the Earth. Free oxygen existed in the atmosphere only after about 1.8 billion years ago, as a result of biological processes. For a chart showing

20
relative amounts of atmospheric gases during Earths existence, see www.scotese.com/precamb_chart.htm (citing Brimblecombe, P. and T.D. Davies, The Cambridge Encyclopedia of Earth Sciences, David G. Smith, ed. Cambridge University Press. P. 276, fig. 17.1).

Finally, we have the various experiments with the likely early air of Earth. It turns out that all of these sources lead to the same conclusions. That early air probably contained at first free hydrogen (as the atmospheres of the four gas giant planets still do), the most abundant substance in the Universe (without counting black holes). Most of that was rapidly lost, very early, because of Earths heat, the Suns heat and gravity, numerous collisions of smaller celestial bodies (large meteorites and one Mars-sized planet) with Earth, and hydrogens innate volatility (the tendency of its atoms to escape into outer space). Much of the hydrogen stayed on or near Earth after the earliest period, but only in molecular combination with other atoms. Hydrogen combines particularly with oxygen, raining down on the crust and forming the Ocean and other bodies of standing or flowing water (H2O), with nitrogen (some staying in the air and ultimately making up most of the atmosphere but some being washed out and falling into the Ocean or on land), forming compounds like ammonia (NH3). And hydrogen combines with carbon, forming compounds like methane (CH4), also known as natural or marsh gas. Hydrogen also remains in the air. These four kinds of atoms, light and the most common in the known Universe (except for neon, which mostly did not remain on Earth and need not concern us here), are found on many planets, moons, and some meteorites, largely made up our early air. They formed numerous different kinds of combinations, including hydrocarbons (carbon and hydrogen), with a huge variety of lengths of carbon atoms joined to each other, with their remaining valence electrons, unused in this chaining, holding mostly hydrogen, but sometimes other elements, in short, intermediate, and surprisingly long molecules. The latter precipitated out of the air and became parts of the oldest known rocks. Volcanoes also added carbon monoxide and carbon dioxide (CO and CO2), created by oxygen burning carbon, i.e., combining with it. This early Earth air, with the help of lightning and other energy sources, and the Ocean, created many molecules (or compounds) of which the most important to us were (1) aldehydes, which are chains of carbon atoms with an oxygen atom bonded to a carbon atom second from either end of the chain, e.g., formaldehyde, the simplest, with the following arrangement of atoms:

O || H-C-C-C-H / \ H H Another variety of molecules formed from carbon are called amino acids. The word amino is used because each molecule of this class contains an amino group or amine composed of one nitrogen atom and two hydrogen atoms. This group or part of the molecule therefore may be thought of as a molecule of ammonia without the third hydrogen atom. The structure is as follows: H H \ /

21
N | The vertical line below the N means that nitrogen normally has a third bond, but in this case it is not attached to a third hydrogen atom, but instead to a carbon atom (shown as an outlined C in the diagram below). That carbon atom may also be attached to other carbon or other types of atoms. But to qualify as an amino acid in organic chemistry that carbon atom must also be bonded to another particular carbon atom. That particular carbon atom (shown simply as C) must be doublebonded to one oxygen atom and single-bonded to a second oxygen atom. Finally, that last, single-bond oxygen must use its other bond for a hydrogen atom, which in water becomes a hydrogen ion. This ion is what makes the whole molecule an organic acid and is what we taste when we say something is sour. But that atom will only become an ion in a carbon-containing molecule if the molecule has that carbon atom with its two attached oxygen atoms. The following diagram shows glycine, an amino acid: H H \ / N | H-C-H | H-O-C=O This, now, is the simplest possible amino acid. Amino acids are crucial to modern biology and probably played a role in the beginning of biology. Twenty different kinds of amino acid are common in most cellular biota today, including us. Some amino acids appeared among the products of the first simulated Earth-air experiment (the Miller-Urey experiment), including at least one of the modern kinds. These molecules may not have been in the earliest bions, but appear now in many protobions, while being absent from many others, which are the simplest. We shall see more of them as we proceed. Aldehydes are not usually in bions today, but a slight modification of them is common in us and most cellular biota. That modification has even occurred in outer space, apparently without any biological input, so the early origin of that modification on Earth seems reasonably easy and early. One more type of molecule formed in or from the early air, which seems to have been of crucial importance to the origin of bions, is called hydrogen cyanide. It contains three of the four important early air elements: hydrogen (H), carbon (C), and nitrogen (N). (Cyanide contains just one of each of these atoms.) In the air, the bonds of this molecule are covalent (sharing electrons). The nitrogen atom, having five valence electrons, has vacancies for three more. The carbon atom, having four valence electrons, can therefore easily fill these three vacancies by sharing three of its valence electrons. That makes a very tight bond. It also leaves one extra valence electron for the carbon atom, which there shares it with a hydrogen atom. The outer electron shell of the hydrogen atom then is full, with its own single electron and the remaining one from the carbon atom. We may represent this molecule as follows: HCN

22
Where each bond represents a pair of shared electrons. This molecule is dangerous to us today, especially if a sodium (Na) or potassium (K) atom is substituted for the hydrogen, as happens easily (because these alkali metals have a strong +1 valence, stronger than that of hydrogen). Today we need to avoid the poison cyanide, but, in the beginning, it probably was the kind of building block composing the first organic base, a necessary part of every bion.25
25

Matthews, C.N. 2004. The HCN World: Establishing Protein-Nucleic Acid Life via Hydrogen Cyanide Polymers, in Origins: Genesis, Evolution and Diversity of Life. Cellular Origin and Life in Extreme Habitats and Astrobiology 6. Pp. 121-135. Doi:10.1007/1-4020-2522-X_8.

From this step we see that the main early atoms in our air just before and around the time of the first bions were hydrogen (H), carbon (C), nitrogen (N), and oxygen (O), and these same atoms are among the most common in us today. (Then on Earth, as now, and as on Titan, nitrogen was likely the most abundant in the air, more than three-fourths of the total.) These four early kinds of atoms (H, C, N, O) are fundamental in every bion on Earth and apparently always have been from the beginning. We may therefore say that they were and remain necessary for biology on Earth. But by themselves they are not sufficient. Even the first bions seem to have had at least one more element (or type of atom) within them and indirectly needed access to the influence of others. That one additional kind of atom required was not significantly available in the early air.
[A page is missing here, in which the author states that sulfur was available and used in early biology, as was phosphorus. These two elements are available at geothermal vents in the deep Ocean. Thus, the author concludes that it is at these vents that biology most likely began.]

Biology, though helped by air, probably did not originate there. Nor did it likely begin in calm, segregated puddles separated from the Ocean (though some theorists disagree), because these normally lack enough of the other necessary element, phosphorus (P, atomic number 15, weight 31, with 15 protons in its nucleus, 15 electrons in neutral atoms, and five electrons in its outer, valence electron shell). It is a nonmetal, of course, like nitrogen (but solid at temperatures common on the surface of the Earth). No bion can exist without phosphorus, none has been shown to exist without it, and lack of this element often limits biology in some parts of the Earth today. Farmers often seek out phosphorus from other parts of the Earth and have it shipped to them to provide for (i.e., fertilize) their crops. Because the early Earths atmosphere lacked free oxygen (O2), it is often described as a reducing atmosphere rather than an oxidizing one. Other elements besides oxygen can oxidize but this early air lacked them and could not oxidize in the period covered by this volume. Biology, it seems, cannot begin in an oxidizing atmosphere, but only in a reducing one. So this factor also was crucial to the origin of biology on Earth. Today, of course, our present air is an oxidizing atmosphere, with plenty of oxygen, as rust and multi-celled life witness, and a new biology therefore could not now arise.

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Some Early-Earth Air Initial Chemical Interactions NH3 CH4 H2O Ammonia Methane Water / \ / \ / \ H NH2 H CH3 H OH \ Amine / \ / \ H-CN / \ CH3OH Hydrogen Cyanide Methyl Hydroxide With the amine group, carbon, hydrogen, and oxygen, at a slightly later stage we get a carboxyl group joined to another carbon, which carries an amine group, giving amino acids. For example:

Glycine, an amino acid (from Wikimedia Commons).

Formaldehyde, an aldehyde (from Wikimedia Commons).

Names, Abbreviations, and Structures of the 20 Usual Amino Acids Used in Biology
Those numbered 1-9 have non-polarity (i.e., no electric charge on the side groups, the parts distinguishing them from each other). The next few have neutral polarity.

Name (Abbrev.)

Structure

H O 1. Glycine (Gly) (slightly abbreviated diagram above)| // HCCOH | HNH

2. Alanine (Ala)

H H O | | // HCCCOH / | H NH

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| H Alanine can also be abbreviated CH3CHCOOH | NH2

Alanine in a somewhat abbreviated diagram (from Wikimedia Commons).

3. Valine (Val) (from Wikimedia Commons).

Red numerals indicate positions of carbon atoms; denotes the carboxyl carbon, 4 and 4 methyl carbons.

4. Leucine (Leu) (from Wikimedia Commons).

5. Isoleucine (Ile) (from Wikimedia Commons).

6. Phenylalanine (Phe) (from Wikimedia Commons): A benzene ring or phenyl group attached to alanine. In such ring structures, carbon atoms (and any hydrogen atoms needed to use up the remaining unused carbon bonds) are present at each corner of the hexagon unless shown otherwise).

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7. Methionine (Met) (from Wikimedia Commons) (note the sulfur).

8. Proline (Pro) (from Wikimedia Commons): note that in proline and some others, some of the carbon backbone is in a ring. In these diagrams, each corner of the pentagonal or hexagonal ring represents the location of a carbon atom.

9. Tryptophan (Trp) (from Wikimedia Commons).

10. Serine (Ser) (from Wikimedia Commons).

11. Threonine (Thr) (from Wikimedia Commons).

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12. Tyrosine (Tyr) (from Wikimedia Commons).

13. Asparagine (Asn) (from Wikimedia Commons).

14. Glutamine (Gln) (from Wikimedia Commons).

15. Cysteine (Cys) (from Wikimedia Commons): Note the sulfur atom in the cysteine; otherwise, cysteine is identical to serine. Methionine is the other amino acid that contains sulfur. These two amino acids with sulfur enable some formation of sulfur bonds between different parts of the same protein molecule, helping to control its 3-D shape.

16. Aspartate (Asp) (from Wikimedia Commons): the last five amino acids in this list, beginning with aspartate, have charged polar side groups.

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17. Glutamate (Glu) (from Wikimedia Commons).

18. Arginine (Arg) (from Wikimedia Commons).

19. Lysine (Lys) (from Wikimedia Commons): note the extra amine group, NH2.

20. Histidine (His) (from Wikimedia Commons).

This ends the list of common amino acids currently made and used by bions. Glycine and alanine are the simplest with only one and two chains, not counting the carboxyl ends. The linking amine group is always on the carbon next to the carboxyls. Counting unbroken ring carbons as part of the chain, the longest carbon chains are tryptophan, phenylalanine, tyrosine,

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and lysine. Two amino acids have sulfur methionine and cysteine and two have extra amines. Step 17. Solutions and ions. As mentioned earlier, sometimes hydrogen or a metal may lend its valence electron(s), leaving it as a positively charged ion, while a nonmetal may borrow one or more valence electrons, becoming a negatively charged ion. This process can help such ions to interact with some fluids, keeping the ions floating about in the fluid. That means the ion is in solution. The fluid is the solvent; the ion is the solute. An atom, molecule, or particle which cannot so interact will tend to settle out, either to the bottom or sides of the container, if it is denser than the fluid, or to the top if it is less dense. If it is a gas, it will normally rise to the surface and leave the fluid. Such an atom, molecule, or particle is not in solution, but merely temporarily suspended or mixed in the fluid. A mixture, like a metal alloy, is normally not a solution, even when the metals are melted. Water happens to be a solvent of many elements, which also has proven crucial to the formation of bions. This is because the water molecules themselves split into ions, and are thus able to interact with other ions among them. The water molecule has one oxygen and two hydrogen atoms. But the split or ionization is not between the oxygen on one side and the hydrogen atoms on the other. Rather, it is between one hydrogen atom, which becomes a hydrogen ion, and the remaining two atoms together (an oxygen and a hydrogen atom), which together make a hydroxyl ion. These may be diagrammed as follows: H+ -OH Hydrogen ion Hydroxyl ion

One other kind of situation can also exist. A particle may sometimes be so small that it will not settle out of a heavier fluid even though it is not technically in solution. This is called a colloid particle and the whole system is, in this respect, a suspension. Colloidal suspensions can occur where the colloid particles are so small that random movements of atoms, etc., in the fluid simply keep them moving and not settling out. Step 18. Radicals. A radical is a group of atoms chemically bonded together, which is only part of a larger molecule. (Usually the atoms join by means of covalent bonds). For example, in basic, inorganic chemistry, a sulfur atom (S-2) and four oxygen atoms may join by covalent bonds to form the sulfate radical SO4-2. This radical is fairly stable, so this radical, a single unified radical, may combine with many other elements, mostly metals, into a larger molecule, just as easily as if the whole radical were a single nonmetal atom. Such a molecule would normally be called a sulfate. For example, a magnesium atom, with a valence of positive two, could join a sulfate radical, which has a valence of negative two, to form magnesium sulfate, MgSO4. Similarly, copper sulfate would be CuSO4. Likewise, a carbon atom and three oxygen atoms can form the carbonate radical, CO3-2. As shown by the superscript -2, this radical happens also to have a net valence of negative two. Like sulfate, it could join with a metal that has a valence of +2. Either of these radicals, like an atom with similar valence, could also bond with two atoms each having a positive valence of

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one, such as sodium: sodium carbonate (Na2CO3) or carbonic acid (H2CO). Substituting a sodium atom for one hydrogen atom yields sodium bicarbonate, used as an antacid. Carbonates, sulfates, and many other radicals can be, and in water usually are, ions. When the other ions attracted to such ionic radicals in water are hydrogen ions, then the resulting molecule has an ionic bond, and is an acid (tasting sour and destroying flesh and even metals if strong enough). Sulfuric acid, hydrochloric acid (H2), and nitric acids definitely can be strong enough so do not taste them! Citric and other organic acids are not so strong. Nitric acid is made of one hydrogen atom, one nitrogen atom, and three oxygen atoms (notice how often oxygen turns up in radicals): HNO3. This molecule has only the one hydrogen ion and the rest is the nitrate ion. Besides the sulfate radical, H2SO4, there is also a sulfite radical, with only three oxygen atoms, SO3, which also has a valence of -2. If it joins with hydrogen ions, it makes sulfurous acid. One more example may be helpful. We have noted that hydrogen cyanide played a crucial part in the origin of bions, although today it can kill them (rather like the Genesis Project in the movie Star Trek II: The Wrath of Khan). The strong triple bond (three pairs of shared valence electrons) between the carbon and nitrogen atoms makes up the unified cyanide radical, which has a valence of only -1. The hydrogen atom that is bonded to this radical in the air again becomes an ion in water, making the compound molecule, cyanic acid. Thus, in the Ocean, a sodium or potassium atom (strong alkali metals) could easily replace the hydrogen. One of these two alkali metals (powerfully attracted to nonmetals and negative radicals) is usually present in cyanide intended as poison. So the cyanide radicals probably combined in the air rather than in the Ocean, to make the first cyclic organic bases. Step 19. Monomers and polymers. Instead of two or three atoms bonding into a small molecule, sometimes a larger number of atoms will combine into one molecule, often by stages. For example, we saw earlier that an amino acid may be formed by a chain of carbon atoms, which may have been added one at a time, collecting a couple of oxygen atoms and one more carbon, to make an organic acid, as shown in step 16 above. The crucial hydrogen atom is the lowest H shown in the diagram, which in water becomes an ion and acts as hydrogen ions normally do, to make an acid. In addition, an amino or amine group joins, likely originally from a separate source. When this molecule is complete as an amino acid, it contains at least 11 atoms, usually more. This molecule also has another important property or characteristic, besides being basically (1) a hydrocarbon chain, (2) with an amine group, and (3) an organic acid. It also (4) has the ability to attach itself to another amino acid (of the same kind or any other kind) at both ends of itself, with both atoms oriented in the same direction. This last ability makes this molecule a monomer. If a molecule can join with another of the same general class, at both ends, with both oriented in the same direction, then it can form a long chain of similar atoms. Such a chain is a polymer, and can have remarkable capabilities of size, structure, and function! So a monomer is an amino acid with an ability to join another amino acid at both ends, while a polymer is a set of such monomers. The ability of amino acid monomers to form such polymers lets them form chains or rings of a few or several amino acids, which have special properties important in biology. (Such a polymer of amino acids is called a peptide. Yet polymers originally formed without biology and before it began, even in outer space. A patch of space with significant amounts of cellulose a complex polymer has even been reported, though cellulose on Earth is a product of advanced plants.26)

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26

The Murchison meteorite, which fell in Australia in 1969, was found to contain organic molecules (purines, pyrimidines, polyols, and several amino acids, including some forms not found in earthly proteins). The ALH84001 meteorite, from Mars, also contained organic molecules. In addition to such meteors, evidence comes from astronomers using infrared spectroscopy to identify elements in interstellar space. With this method, they have found further evidence of organic molecules (methane, methanol, formaldehyde, cyanoacetylene, and polycyclic aromatic hydrocarbons). For details, see http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AbioticSynthesis.html#Molecules_from_outer _space? (however, I am uncertain of the precise source of the authors reference. I have found no mention of cellulose specifically).

Step 20. Catalysts. We all are aware that oxygen can combine with iron to produce rust or with wood to produce charcoal or, in a hot fire, to produce just ash. We are also aware that our air now contains free oxygen. But then why does a piece of iron not immediately turn to rust (iron oxide, FeO2 or FeO3) or wood to potash (CO2) as soon as it is exposed to air? Because, although the process can and does happen, it typically does not happen quickly. If a volcano erupts and pours out hot lava, that lava hitting a tree or board will ignite it and it will burn quickly. Or if lightning strikes a tree, it may immediately catch fire. The extra energy pushes the process along. Inner-Earth (geothermal) heat, focused sunlight (as through a magnifying glass), lightning, the help of water on iron to hasten rust all can get the oxidizing process moving sooner and faster. But even without these, over time, oxygen will rust iron and eventually burn a tree or board. Another kind of influence can also hasten a chemical process if that process would ultimately occur anyway, given enough time and no interference. That is the process of catalysis. Catalysis is the influence of one element (type of atom) or compound (type of molecule) on a reaction between other elements and compounds, without the first substance being used up. Ordinarily, it occurs by reducing the energy obstacle to getting the process started. Fire, for example, does not usually occur spontaneously because a high initial heat is needed, though after that an adequately fueled fire will usually maintain its own needed heat of combustion. Catalysis may also reduce the obstacle of needed energy by providing one or more easy, intermediate steps from the existing situation to the desired one. This may involve the particular shape and electron configuration of whatever is causing the catalysis or catalytic process. For example, the catalytic converter which is designed to reduce particles of unburned fuel and carbon polluting the air works on the principle that a bit of platinum (a rare and expensive element) with its one valence electron (usually) influences the hot exhaust gases to continue the burning longer, so unused fuel and unburned particles of carbon will be reduced. It may influence other exhaust materials as well. Platinum is better for this role than are other metals with only one valence electron more grudgingly and less extensively than light metals do. That means it lasts longer and does more good. (Palladium can also function somewhat similarly.) The extra substance that provides this influence is called the catalyst. Most catalysts are metals, generally light ones. These were very likely of crucial importance in the origin of biology. Certainly they are important today. Humans and most cellular life use metals to help in making biological processes in the body move along more easily when needed. That is why we need various metals (most of the so-called minerals required in the average recommended diet). We need salt or sodium chloride (NaCl), potassium (really KCl, potassium chloride), magnesium

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(Mg), calcium (Ca), copper (Cu), and zinc (Zn), as well as smaller amounts of aluminum (Al), chromium (Cr), manganese (Mn), molybdenum (Mo), lithium (Li), etc., and larger amounts of iron (Fe) and cobalt (Co). We could not, for example, use oxygen without having iron in the blood stream. Each catalyst works in a slightly different way from many of the others, so we need not become entangled in the details of each of the chemical processes, but the general pattern is that they ease the start, or conduct, of various necessary or useful chemical processes in the body (or, in some cases, just outside it). But normally they are not used up in the process, in inorganic cases. In us, however, the metal atom may be carried in a coenzyme, an organic compound (i.e., a compound built on carbon) which is also, today, a biological compound (made by a bion). These compounds are often destroyed when done with their job, so the waste material is eliminated from the body and some of the metal catalyst with it. The first biota did not have this capability. They could only use, or at least benefit from, the metals that happened to be present in the right place at the right time. We do not know all the details, but some will be mentioned further on in the story. The first case must have been the movement of partial steps toward biology in early the early atmosphere of the Earth (built here or added by cometary or meteor encounters with Earth) out of the air, driven by rain, etc., into the Ocean, where plenty of sodium, potassium, and other light elements would already have been dissolved. Iron was then plentiful in the Ocean, also fortunate for the beginning, as we shall see later. It would not be adequate for a restart today.

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Chapter F: Steps 21-30 Early Earth Cycles, Beginnings of Chemical Cycles, and Rings
21. Catalyzing the polymerization of amino acids. In chapter E we met the ideas of monomers and polymers, of catalysts (especially metals) and of amino acids, probably formed in the early atmosphere of Earth and sometimes even in outer space. There has also been mentioned of cycles. Let us put these four ideas together to examine their relationships in a particular, crucial step in our development. We have previously touched on the several amino acids found after the original experiment on the simulated conditions of the early Earth and the upper parts of the early Ocean.27 (That Ocean would have had smaller amounts of dissolved atoms and molecules then, before the present amount had been leached out of the continents and washed into the Ocean.)
27

Miller, Stanley L.; Harold C. Urey (July 1959). "Organic Compound Synthesis on the Primitive Earth". Science 130 (3370): 24551. Doi:10.1126/science.130.3370.245

Of course, we must remember that the Miller-Urey experiment was conducted in two flasks in one laboratory by one chemist with a few elements and molecules to start with and lasted only two weeks, while the Ocean had most of the surface of the Earth, nearly all of the water over time, with a wide variety of circumstances and participating atoms and starting molecules, through hundreds of millions of years. The original Earths experiments, therefore, probably produced somewhat more amino acids, as well as other molecules, than the chemists did. We do not know how many early amino acids formed on the early Earth or all of what they were. Doubtless both their variety and the effectiveness for certain influences increased over time, for varying reasons, both before and after the origin of bions. The present number of common amino acids is 20, but some others play a role in some bions and situations. The diagrams of the structures of the common amino acids used in biology appeared in the previous chapter. We have already learned that organic monomers are molecules that can join together in chains or polymers of multiple monomers of the same type, rather like chains of multiple carbon or silicon atoms. (In our analogy of the atomic dance team, this would be a sort of conga line.) We have also noted that polymers are only possible if the individual monomers each can bind to another at two separate points. (Although their valences are compatible, carbon chains and silicon chains are usually separate, because silicon reacts best at the high temperatures (hot enough to melt rock) in the course of Earth formation and later in the deep Earth, while carbon chains usually form later and mainly within two miles of the surface, where temperatures are rarely conducive to extensive rock melting, dissolving, or chemical action. Because of the astonishing variety of carbon compounds and their crucial roles for us, chemists separate the chemistry of carbon compounds, called organic chemistry, from all other chemistry, called inorganic. Organic chemistry is a far larger and more complex subject.) The reason that a monomer must bind to another monomer at two separate points is that a chain is only possible if each link can attach both to the link before it in the series and also to the one after it. In ordinary, literal chains of loops, both ends of each loop usually look alike

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and that is also at least figuratively true of carbon and silicon chains. But in polymer chemistry, it is normally opposite that attract rather than similar connections. For this reason, amino acids have two different parts such that, if they line up in a row facing in the same direction, the acid front of one will bind with the amine group at the rear of the next. Let us examine this a little more closely. Amino acids, in general, have four parts, called functional groups. These are a little like inorganic radicals but are also very different. Usually one or two radicals, composed of very few atoms rather firmly bonded together, can join one or a very few atoms or a molecule, in inorganic chemistry, and commonly they can be ions. Functional groups (a term used only in organic chemistry) may have a larger number of atoms and the whole resulting molecule will feature carbon atoms. The first functional group of an amino acid is the central carbon atom, bonded by a single covalent (sharing) bond to a single hydrogen atom, thus:

H | - |
That carbon atom is also single-bonded with all three of the other functional groups and that is all that holds them all together. The second part (functional group) is the amine group, a nitrogen atom bonded to the carbon (single bond) and to two hydrogen atoms, thus:

H \ N / H

H | -C|

The third group is called the carboxylic acid group. This group consists of one carbon atom bonded in three directions. First, a single bond holds this carboxylic carbon to the central carbon atom. Second, a double bond attaches an oxygen atom to the carboxylic carbon. The one remaining (fourth and single) bond attaches a second oxygen atom, which, in turn, normally uses its other electron vacancy to bond with a hydrogen atom, which tends to become an ion when in water. (The presence of the hydrogen ion, as always in chemistry, makes the monomer molecule into an acid and the presence of the amine group makes this molecule an amino; hence the term amino acid.)

H \ N / H

H | -C-C=O | \ R O-H+1*

Some scholars show this hydrogen (marked with a superscript asterisk above) as pulled off its holding oxygen atom (leaving O-1) and move the last mentioned hydrogen atom to the amino group, which is thereby rendered electrically positive (+). Regardless of which way the

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drawing is made, the effect in the real world is that two amino acid molecules can line up with the carboxyl group of the first molecule, say, next to the amine group of the second molecule. When this happens, the oxygen atom single bonded to the carboxylic carbon of the first molecule, together with its hydrogen atom (no matter where it is pictured), will join another hydrogen atom taken from the amine group of the second molecule, making a new molecule of HOH (water, also written H2O), which separates from the amino acid molecules. At the same time, the (hitherto carboxyl) carbon atom of the first molecule (the monomer) forms a single bond with the nitrogen atom of the amine group in the second molecule (amino acid monomer) (see accompanying diagram). Thus, the amine group and the carboxyl group are both consistently present and characteristic of amino acids monomer molecules; they all have both and any molecule that lacks both is not an amino acid. Separately, such a monomer can bond to or otherwise interact with a wide range of atoms and other molecules. But the formation of the polymer chain of amino acids depends on the presence of both these functional groups and, in the resulting polymer chain (called a peptide) the primary function of these two functional groups is to form the unlike connections necessary for each monomer to join in forming such a polymer. The reader will have noticed that the last diagram of an amino acid shown above also contains the letter R. This represents the fourth functional group in the monomer, as promised, besides the amine and carboxyl groups, all attached to the central carbon atom. This fourth group is the one part of an amino acid which differs from one specific amino acid to another, making the 20 different usual (and a few unusual) amino acids. This variable part is called the side group because it is not one of the standard groups forming the links in the chain. In one sense, it is thus not necessary (a simple hydrogen atom could be substituted, making the amino acid glycine). If nothing more were present, however, there could be only one kind of amino acid. The side groups are crucial for they create the influences which a particular monomer amino acid molecule and the resulting combination of amino acids in a chain (a peptide) has on other atoms and molecules, especially their enzymatic influences. These enzymatic influences are vital to all but the simplest of bions and certainly to us. We urgently need a proper and sufficient balance of enzymes (peptide chains having enzymatic influences) for health and life. The common modern specific side chains or fourth functional groups of each of the 20 main current amino acids can be seen in the accompanying diagram list. (In looking at any diagrams of molecules or functional groups in organic chemistry, it is important to remember that a diagram can only be a flat (two-dimensional) representation of an actual threedimensional object. That means the atoms that appear farthest apart are not spread quite as far away in one dimension/direction; some, instead, are in effect above and others below the plane (i.e., the paper) on which they appear. This fact is meant to be illustrated by the diagram of the simple molecule, methane, which appears before those of the amino acid side chains.) Now, amino acids can (and did) form in space or the early atmosphere of Earth under suitable circumstances without any catalyst (as far as has been discovered) and, under ideal circumstances, usually in water, where they can also link together into a chain or polymer commonly called a peptide. (A protein is merely a very long, specially folded peptide.) A peptide is specifically a string or chain of linked amino acid (monomer) molecules (minus the water molecules removed to make the link this removal of one water molecule at each linkage, mentioned above and shown in an accompany diagram of the peptide link, is called dehydration and is common in many kinds of organic molecular links).

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There is, however, a certain kind of each or clay on our Earth which greatly improves the likelihood of such a chain of peptide linking, making it (1) start more easily, (2) proceed more quickly, and (3) continue farther than it otherwise would. This material occurs naturally on certain surfaces of land and Ocean bottom, and is variously called fullers earth (used by fullers of cloth) and as montmorillonite clay. The structure of this mineral doubtless plays a part in its catalytic effect but the crucial element is aluminum. This catalyst does appear in the deep Ocean along the underwater ridges where recycled magma wells up and pours out onto the solid surface of the Ocean bed, pushing the crustal plates away from each other. The consequent effect seems to be that some early amino acids, mostly formed in the air or the upper Ocean (and perhaps a bit from outer space), managed to circulate through the Ocean and come into contact with this aluminum mineral catalyst in the deep Ocean, causing them to form chains (i.e., peptides). Those chains that became long enough, if not destroyed first by some other process, were flexible enough to be pushed by passing random water movements into various twists, until some peptide chains ends met and also joined one more time, making a closed loop. Such loop peptides are better able to survive because their amine and carboxyl functional groups were all occupied and joined and thus less exposed to attack by other atoms and molecules. The same would be true of the central carbon in each monomer. Even the side groups, though more exposed, might be close enough together to reduce the directions from which attacks could come. Thus these polymer peptides could form by processes specified so far and some could last longer than others. This form of chemical might be called a pre-bion. It could have biological effects as an enzyme (depending on which side groups were present and in what order) and differential degrees of survival of such molecules could be compared to competition for survival. Such a molecule would certainly not yet be a bion because it would lack the ability to reproduce directly, unless one could, through its enzymatic influence, increase the chances of the formation of other peptide molecules containing the same or similar monomers (amino acids) as itself. This is conceivable but no such form has been found and it seems unlikely, because an enzyme or catalyst normally can only influence one or a very few types of reactions. A closedloop peptide might easily induce the formation of another peptide but without control of its detailed composition. But such a peptide may very likely have influenced the occurrence of some other chemical effects on some other kind of molecule that did play a part in the origin of biology, as we shall see further on. Now, it turns out that experiments have confirmed the foregoing (1) formation of amino acids, (2) their linkage, especially in the presence of montmorillonite clay (as a metallic catalyst), into peptides, (3) the linkage of the ends of these peptides into loops, and (4) the biologically enzymatic influences of some such loops so spontaneously formed. These enzymatic influences do not depend on metals as catalysts do, and the peptide loops contain no metals.28 These prebiological enzymes, though not necessarily super-efficient, do appear to have had a significant role in the origin of real biology!
28

The author may be referring to this study: Hanczyc, Martin M., Shelly M. Fujikawa, and Jack W. Szostak. 2003. Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division, in Science 24 (October 24): 618-622. Doi:10.1126/science.1089904.

22. Geocycles.

36
The previous section has reviewed and refined some previous material and brought us to a polymer, in this case a peptide made of amino acid monomers, including a closed-loop peptide, enable or made more common by a natural, mineral catalyst, and the peptide thereafter most likely had a similar influence on other chemical events to be described later. Such a spatial loop is not quite the same thing as a temporal loop or cycle but there are similarities or at least parallels and the two processes tend to influence each other in later steps. In this step, we consider various time cycles characteristic of the Earth itself. We have considered the alternating evaporation-condensation or water, sulfure dioxide, sulfuric acid, and back again on Venus. Mercury has little atmosphere or water to participate in a similar process. But Mars has a very thin atmosphere of carbon dioxide which blows around the planet and some of which freezes out and settles at the poles (unequally), creating polar frozen carbon dioxide, commonly known here as dry ice. There seems to be some water ice, but no convincing sign yet of substantial fluid water, despite the confidence of some astronomers that liquid water is there somewhere, or at least was there four billion plus years ago. Evidence for father objects is less clear on chemistry, though the four big gas giants have huge amounts of hydrogen, some larger moons seem to have nitrogen, methane, and water ice, and comets seem to have ice and other sparse material. a. Time cycles The Earth for both astronomical and geological reasons has a whole series of its own built in time cycles. One is the heat cycle. When the Earth first coalesced into a single (moving) planet from countless atoms, molecules, larger particles, dust, clods, rocks, and perhaps some planetoids, almost all traveling in close and similar orbits around the early Sun, but slightly different paths and at different rates, their collective gravity brought them gradually together, uniting in a single, common location, traveling at a nearly single rate around the Sun and in a nearly single orbit. The process of unifying these motions approximately to a single one created great heat (as relative potential motion among them declined). This energy was not instantly lost but changed to heat. This internal heat has been gradually radiated into space but that process has not fully ended, being delayed by the density of Earth. Also, the process of formation and growth of Earth has not totally ended. A planet estimated to have had roughly the mass of Mars (perhaps dislodged from Mars itself or from the planetoid/asteroid belt between the orbits of Mars and Jupiter) hit the Earth about 4.5 billion years ago.29 The Earth has also been continually bombarded by meteorites of various sizes from its founding to now, although much more so in the first few hundred million years. These impacts also created heat (arrested motion of the in-falling matter) from the forceful collisions and Earth mass has also likely continued to increase slightly.
29

Canup, R. and E. Asphaug. 2001. Origin of the Moon in a giant impact near the end of the Earths formation, in Nature 412 (6848): 708-712. Doi:10.1038/35089010.

Thirdly, as Earth grew larger, the pressure of the outer weight on the deeper parts has increased its temperature. Fourthly, nuclear fission of unstable atomic nuclei steadily creates heat. So, altogether, these influences have created great internal heat for Earth and the internal parts maintain tendencies to increase internal heat further. At the same time, heat radiation from Earth tends to reduce that internal heat (but only very slowly). For small objects like typical meteorites, internal heat has been lost fully, but Earth has a long way to go. The heat is

37
gradually being drawn off, but to some extent also added to. The two processes are probably not equal, so one of them will win out eventually, but at present forces that both add to and subtract from the Earths heat are at work, so the situation at least resembles a cycle of countervailing processes. Also, the Sun adds external heat. This, too, is to some extent reflected (especially off the ice caps) and to some degree radiated back into space. The result is not a continual stalemate, but a variable system of counterbalancing influences. Sometimes the heat rises too high, killing off some bions. Sometimes it falls too low, creating ice ages. And sometimes it is more equable. This aspect of the heat flux seems like a cycle, even so, because the Sun still shines and brings in new heat, while the radiation, on balance in the past, seems usually to have permitted the survival and sometimes even the flourishing and progress of bions. b. Daily spin. When Earth first consolidated, some bits of separately traveling matter caught up with or fell back against other bits, helping to consolidate all, but also perhaps tending to induce a spinning of the result, if the matter falling against or pushing one side exceeded that on the other side, thus presenting all surfaces of Earth to the Suns light in the course of a day-night cycle. In this way the original orbital movement may also have affected the daily spin. The collision that is believed to have created the moon surely must have contributed as well and may have been even more important. At first Earth spun much faster than now. We do not know the exact rate at first, but a couple billion years later, more or less, the Earth spun at least a third faster than now, making the days a third shorter.30 The influence of our relatively large moon, which does not and cannot orbit the Earth as fast as Earth now spins, has gradually slowed that spin. The Ocean (and solid Earth) tides play a role in that effect.
30

On the slowing of Earths rotation and the increase in the moons speed, see Stephenson, F.R. 2002. Harold Jeffreys Lecture 2002: Historical eclipses and Earths rotation, in Astronomy and Geophysics 44: 2.22-2.27. On the measurement of the rate of slowing with atomic clocks, see McCarthy, D.D., C. Hackman, and R.A. Nelson. 2008. The Physical Basis of the Leap Second, in Astronomical Journal 136: 1906-1908. On the effect of tides, see Munk, Walter. 1997. Once again tidal friction, in Progress in Oceanography 40 (1-4): 7-35. I am uncertain of the reference for the Earth spinning a third faster in the early period.

The daily spin tends to give us several effects. One is alternating periods of light (and relative heat) and darkness (and relative cool). The earliest bions could not respond directly to compensate for this, but it likely affected them, and many modern ones now have body chemical processes to help them cope with and take advantage of this daily set of changes. c. Water cycle. Evaporation and precipitation are countervailing processes which cause individual atoms and (more often) molecules to cycle back and forth between these two conditions, rising into the air as vapor and later raining back down again (most often as water) as liquid, maintaining a degree of both balance and replenishment of what has become a crucial resource, so that in many places an adequate balance of fresh water supply is available for biological purposes. This is also a clear but variable time cycle for each molecule. So far, the other three obviously rocky inner planets appear to differ from Earth in this respect.

38

d. Annual cycle. The Earth orbits around the Sun once each year. (A celestial orbit like the trajectory of a cannon ball or other unguided ballistic missile is not strictly a circle, but an ellipse. (An ellipse, instead of having a center like a circle, has two foci. One can draw an ellipse by fastening a string or other non-stretching, closed loop around two pins or tacks inserted into a firm surface at separate points and then place writing instrument pen or pencil within the loop, pressed against the writing surface but also against the loop, pulling it taut. Then, keeping the loop taut with the writing instrument, and keeping the writing instrument vertical, one moves the writing instrument completely around the pins until a closed loop has been drawn.) The orbits of the eight major solar planets, including the Earth, are fairly close to round (to circular), because the imaginary pins or foci are fairly close to each other. The Sun is located at one of them. Many of the smaller planetoids also have fairly round orbits, though actually ellipses, but many are also more complicated because they tend to be more influenced by each other and by the large planets. The two most remote planets have longer ellipsoid orbits whose foci are relatively far apart. Our orbit is round enough (foci close enough together) so that Earths distance from the Sun does not have much effect on Earth biology (it has a little effect), but the spin of Earth is significantly tilted in comparison to its orbit, so that the direction of tilt gives the northern hemisphere more heat from late June to late September, but less from late December to late March. The southern hemisphere experiences the opposite. Advanced biota have managed to acquire adaptations to cope with these seasonal situations, but earlier bions could not survive in many places too severely affected by these seasonal cycles. e. Topographic cycles. Volcanic eruptions and crustal plate tectonics, especially collisions between plates of Earths crust, cause one plate to push up over another and the second to dive under the first. The result is massive mountain building. These mountains are then exposed to wind, rain, sleet, snow, the cracking effect of alternating freezing and melt, running water, wind, and all the other processes that we lump together under the title of erosion. Erosion wears down river beds and valleys between mountains and eventually the mountains themselves. This, too, is a true time cycle, providing us with a variety of habitats. Some biota adapt to particular niches or corners among these various habitats and others do better in other niches. f. Stellar orientation.

Over thousands of years, the orbit and orientation of Earth within the Solar System has a slight wobble with respect to stars outside the Solar System. The wobble is actually a slow, circular change, called precession, returning to its earlier status over a period of time incompatible with compensation by evolutionary adaptation, if any such compensation were needed. For most purposes, this precession does not require meaningful adjustment. What it does do is gradually change the point in the sky that would appear to a human at the North Pole to be directly overhead. Thus, the ancient, pre-classical Egyptians recognized the star Sothis to be the north star, but today we recognize the star Polaris as our north star. Eventually, each of these will again become the North Star. A spinning top or gyroscope shows the same precessional wobble or tilt.

39
This process is a true time cycle, but the only effect is a slight cultural one, to which humans can easily adjust, without even knowing of it. Some archeologists have used it to estimate the ages of early human-made structures intended to be conformed to the apparent celestial structure. g. Geomagnetism. The spinning of the Earth, and particularly of the molten, heavy metal core, with its iron and cobalt, subject to magnetic influences, produces a magnetic field (effect) emanating from the Earth. This magnetic influence affects the magnetic orientation of molten, iron-bearing rock when it solidifies, is used by a few periodically migrating animals, and, much more importantly, strongly influences the path of cosmic rays and objects approaching Earth from outer space, usually protecting Earth biology fairly effectively against many dangers from outer space. At irregular intervals of often tens of thousands of years or more, this magnetic force fades and breaks up into inconsistent, regional patterns, and may finally reverse the poles of the magnetic field. The full reversal phase is probably not especially dangerous to most biota, but the intervening period of inconsistent and inadequate magnetic fields is quite dangerous. This is a true time cycle but the times are very irregular. In summary, these various cycles of Earth itself affect all or many biota and play their parts in our history, although we do not always have enough information on past cycles to see exactly what the effects were. But cycles are crucially important to maintaining supplies of what is needed and these cycles mentioned above have been supplemented (or in some cases obstructed) by biota in ways that, in least in some cases, have led to maintenance of supplies of various resources by various kinds of recycling. This is a lesson of nature for us all. Step 23. Chemical competition, cooperation, and evolution, and time cycles. Chemical evolution. As Chapter D has already outlined, atomic nuclei, other than that of hydrogen (some physicists also assert helium) were formed in the high-energy nuclear fusion reactions of many stars, repeatedly. The atoms then normally do not evolve any further (until processed again by yet another star), except for unstable atomic nuclei, like argon, radium, uranium, etc. The much smaller energies involved in chemical processes cannot influence the identities of atoms. So there is no chemical evolution of atoms. (At least one location on Earth appears to have wound up with such a concentration of uranium atoms that the neutrons ejected from spontaneously deteriorating, unstable uranium atoms actually induced further fission reactions in other surrounding uranium atoms, producing a sort of natural fission reactor! This happened many millions of years ago, however, has ended, and is not known to have played any part in biological evolution. No other example of this is known.) Atoms with the capacity to interact (or react, as chemists say) with other atoms, either like themselves or different, or both, tend to do so, especially in water solution, and even more so in the highly ionic water of the Ocean (because of strong ions like sodium, potassium, chlorine, and many others). They may, as said earlier, join to or part from other atoms, or change partners, as they drift about in the Ocean, forming a wide range of different molecules over time. Some of these molecules are more stable than others, hence last longer, and thus tend to be more numerous than others. This process may be regarded as a kind of competition

40
among the molecules. (Of course, this is not a matter of choice or any other kind of intention; it just depends on the characteristics of the particular atoms and the nature of the environment.) It happens that some chemical interactions actually change a particular molecule, which we will call MA, to another particular molecule, MB, more often than to other kinds of molecules. This would tend to make the second molecule, MB, more common than otherwise. What happens if the second molecule, MB, also tends to change back to the first, MA? In the planetary time cycles of Earth, Mars, and Venus, discussed in step 22, two processes, each producing the ingredient required at the start of the other, make a repeating cycle, but in chemistry and chemical processes in the same body of water, events occur so quickly that the most than can happen ordinarily is that the two processes reach a point of equilibrium (unless one product is continually drawn away to the surface, the sea bed, or some sequestered place, or extra ingredient are continually added). Yet it may be that MA tends to increase the amount of MB, and the latter tends to increase the amount of a third molecule, MC. In that case, we do have a true time cycle, because each process is likely to be influenced by other factors, so that a precise equilibrium is less likely to occur. In a real Ocean, constant changes and interference happen, but here we have a self-reinforcing cycle, which could and most likely did occur, probably leading to increase or maintenance of considerable numbers of a range of different molecules in different cycles. This surely occurred in early, deep Ocean along the mid-Ocean ridges. In those areas, upwelling magma produced, and continues to produce today, continuing plumes of hot gasses and other products, including carbon dioxide (CO2), sulfur dioxide (SO2), and various phosphorus oxides. This steady supply drove a series of interactions leading to formation of a number of pre-biological molecules (helpful to the origin of bions) and probably some of what we might call bio-adjuvant molecules (helpful to the continuance of the earliest actual bions). So here we had a competition among molecules, and, in the last two paragraphs, time cycles from one kind of molecule to another, producing a kind of cooperation (again not a matter of choice) among those molecular participants in each single cycle: true chemical evolution was afoot. This was not yet biology, but it was a prelude, and it has continued and grown vastly in and by biology since then. Step 24. Hydrocarbons: aliphatic and aromatic rings The previous chapter touched on the nature and components of one kind of monomer molecule, the amino acid, with its core, two linking functional groups, and the varied influential side groups; their linkage together into polymer chains, in that case peptides; the tendency of such chains to form closed loops by binding their ends to each other (with the assistance of an aluminum catalyst); and their enzymatic (influential) effects. We have not yet discussed the nature of that influence. That comes later. We have also encountered the idea of both competition and cooperation among molecules for existence and repetition or re-formation, which is really early chemical evolution. In the present step two other kinds of ring appear, which are called organic but not necessarily biologic, which have been mentioned before. An organic ring is simply a chain of carbon atoms which, like pre-biological peptide rings, is formed by the ends of a short carbon chain binding together. Before going into these, remember that on Earth and in the early MillerUrey experiment on the atmosphere of the early Earth most of the carbon atoms formed such chains (usually not bound at the ends), usually with hydrogen atoms bound to the carbons. Such a chain is called a hydrocarbon. A short one would have a structure like this:

41

Hendecane (also called undecane), with 11 carbons (from Wikimedia Commons).

A wide range of these chains formed on the early Earth with different lengths, some with side chains, many with far more carbon atoms than this, and some with other atoms substituted for one or more of the hydrogen atoms, such as the aldehydes mentioned previously, and detailed more fully in the next step. All of these are called saturated aliphatic hydrocarbons because they have as many hydrogen atoms as a chain of that many carbon atoms can possibly have. Some (called unsaturated) hydrocarbons also have double or triple bonds and therefore necessarily fewer hydrogen atoms, because each carbon atom in hydrocarbons have exactly four valence electrons and therefore normally only four covalent (sharing) bonds. For example, ethylene is an unsaturated aliphatic hydrocarbon because its two carbon atoms each share two bonds with the other, leaving only two bonds on each carbon atom to bind to a hydrogen atom, as follows:

Ethylene (from Wikimedia Commons).

Besides the simple and branched aliphatic hydrocarbon chains, such chains of carbon atoms may also form loops by binding their end carbons together. For example, a simple ring hydrocarbon composed of five carbon atoms would be called cyclic pentane. Because the carbons are all joined together, we can abbreviate the structural diagram of such a molecule by merely showing the bonds, and assuming that the reader will understand that end bend in the shape between two bonds is an understood carbon atom and any bond not used to hold another carbon is holding one additional hydrogen atom: / \ |=| Here the bonds are shown not quite meeting. These points of near junction are the carbon atoms. The reader can see that each carbon uses up half its valence electrons to bind with two other carbon atoms, so how many hydrogen atoms will be bound to each carbon atom? Two, giving 10 hydrogen atoms for the whole molecule. Another kind of organic (but not biologic) molecule, which formed at the same time (and therefore perhaps not as a separate step) as the early, geologically formed aliphatic hydrocarbons were formed, is the benzene ring. It is composed of six carbon atoms, each attached to two others. (It is thus logically a hexagon rather than a ring, but it is called a ring.) As described earlier, these molecules have a special kind of valence arrangement, in which each ring-carbon atom in effect shares 1.5 valence electrons with each ring-carbon atom to which it is bound, leaving it with only one extra valence electron to bind with a hydrogen or any other atom. This is presumably accomplished by a circulation of electrons among the electron clouds of all six of the carbon atoms.

42
Such a bond is much stronger than a normal covalent single bond, hence explaining the long survival of these bonds in the Earth, which is not possible with a ring with any other number of carbon atoms than six. It leaves each carbon with only one bond to link to an atom outside the ring, usually hydrogen though not necessarily. In place of one or more hydrogen atoms there may appear a single-valence nonmetal atom like chlorine (Cl) or bromine (Br) or iodine (I) (or a single bond of any other atom where that other atom shares still other bonds with yet other atoms). The structure for such a molecule may be abbreviated as follows: // \ | || \\ / 25. Aldehydes and carbohydrates. As mentioned in the previous step, chains of carbon atoms often have their other valence electrons (those not used to make the chain) binding hydrogen atoms, but sometimes other atoms are substituted for hydrogen. One set of examples is called the aldehydes. An aldehyde is a hydrocarbon chain in which the carbon atom on an end of the chain (either end), instead of being bonded to three hydrogen atoms as in the hendecane molecule shown earlier, has an oxygen atom bound by a double bond, as follows:

Formaldehyde (from Wikimedia Commons).

Acetaldehyde (from Wikimedia Commons).

Butyraldehyde (from Wikimedia Commons).

43
Now it happens that, as with other molecular chains, an aldehyde can also form a closed loop by bonding both ends together, if it has a suitable length (three to eight carbon atoms, besides the oxygen). In that case, that means not two end-carbon atoms but the oxygen atom at one end and the carbon atom of the other end forming a heterocyclic form, i.e., a ring composed of more than one kind of atom: in the last example just above, of four carbon atoms and one oxygen atom. The result is the basic ring of pentose because the ring contains five atoms. The hydrogen atoms attached to the sides of the chain are not part of the chain or ring, even though attached to it. The diagram of this pentose looks like this: H O H \/ \/ HC CH | | HC CH / \ H H
Pentose

We might note three aspects of this aldehyde-to-pentose transformation. The first two are merely side notes at this point, though useful to notice. First, in the linear aldehyde-chain situation, if a hydrogen ion binds to the oxygen atom on the end, it takes up one of the two oxygen bonds, and converts the chain into an alcohol, which always has a hydrogen atom or ion bound to the oxygen atom, which in turn is bound to a carbon, as in the diagram below. This is only one more oxygen atom away from the carboxyl functional group described earlier in the discussion of amino acid structure, making the result an organic acid. See the second diagram below: H H H H | | | | HCCCCOH | | | | H H H H
Butyl alcohol

Butyric acid
31

31

The author uses the name butylic acid, which Wikipedia says does not exist. I include butyric acid (from Wikimedia Commons), on the assumption that the name is a typo. It has the atomic structure depicted by the author.

Third, it is important to be aware that pentose merely means any ring composed of five combined atoms of carbon and oxygen, as shown, but includes more than one variation. The important one that we shall look at more fully soon is ribose, a very specific molecule that lies at the foundation of biology.

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Now, first of all, ribose is a sugar and we have already seen its basic structure. There are also other sugars, one also made with a somewhat similar but slightly different structure, still with a five-atom ring, including both carbon and oxygen. Most other sugars either have a ring of six atoms or a double ring with 12 atoms. Sugars became a major food storage structure in cellular bions, but that will be more important in volume II. A single sugar ring is a monosaccharide. Sugars are also included in the larger category of carbohydrates. Carbohydrates containing more than eight carbon atoms are made by combining shorter units. A carbohydrate composed of two such units is a disaccharide. One with three units of six atoms (i.e., three simple sugars, each made up of a ring of six atoms) is an oligosaccharide (from Greek oligos, few). The basic ring structure of sugars can be combined by a polymerization process into much larger chains to make larger carbohydrates (starches or polysaccharides), which have the same nutritional value per carbon but do not taste as sweet until saliva breaks up the chains into sugar rings. Again, these aspects do not concern us yet but it is still significant that sugar, made on Earth today by bions, has been identified in space, in the still more complex form of cellulose, evidently formed by non-biological processes.32
32

I find references to hydrocarbons in meteorites from Mars, where minerals crystallized from magma on the surface of Mars, trapping carbon inside, and the organic compounds formed inside these mineral casings. Scientists have also detected hydrocarbons in a galaxy 12 million light-years away (www.space.com/1686-life-building-blocks-abundant-space.html). Halite or rock salt crystals have also been found to enclose small amounts of water, including drops that were 250 million years old, in which cellulose fibers were abundant (www.space.com/5677-signs-life-rock-salt.html). This ancient cellulose is on Earth, though, and always was. I have not found references to cellulose in meteorites or in space. The author may have conflated these two findings.

Other carbohydrates are also formed from a kind of chain slightly different from an aldehyde. This form is a ketone. The main difference is that the end carbon bound to the oxygen atom, instead of being also bound to a single short carbon chain, is bound to two chains, which may be alike or different. In the diagrams below, R and R stand for any such carbon chain:

Aldehyde (from Wikimedia Commons).

Ketone (from Wikimedia Commons).

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Now the specific sugar molecule (monomer) ribose, while it has the ring identified earlier as a heterocyclic pentose, also has two modifications of the atoms attached to the ring, known generally as the substituents (as though were substitutes for the basic hydrocarbon chains accompaniment of hydrogen atoms).31 The first of these modifications is the substitution of an OH side group for the hydrogen atoms normally attached to the ring carbons farthest from the oxygen atom in the ring (see diagram).

Beta-D-Ribofuranose (from Wikimedia Commons).

33

33

Again, I am not certain of the authors intent. He appears to diagram w hat Wikipedia identifies as BetaD-Ribofuranose. The term heterocyclic pentose does not appear there. Lacking a background in organic chemistry, I cannot clarify further. In his own diagram, the author does not abbreviate the top portion of the molecule or use the simpler pentagon in the center, instead showing each carbon, oxygen, and hydrogen atom. But he is emphasizing the base, the two OH groups at the bottom, which are clearly marked here.

The reader will probably have noticed that the second modification is also a substitution for one of the hydrogen atoms, in this case bound to a ring carbon adjacent to the ring oxygen (upper left corner of the above diagram, here abbreviated as CH2OH). Here the single bond that in earlier diagrams bound a hydrogen atom on the upper left of the ring now binds a non-ring carbon with its attendant hydrogen atoms and oxygen. That is, two of the remaining three bonds of this non-ring carbon hold hydrogen atoms and the remaining bond binds to another OH group. The oxygen atom has one bond with the carbon and another bond with a hydrogen atom. This, then, is the simplified diagram of ribose, a five-atom sugar ring with one branch in the form of the functional methyl group (a methane molecule modified to bind to something else through its carbon atom). There are also three attached OH groups. A molecule with this many atoms in it has a three-dimensional structure, which we shall see further on. At this point it is important to note (1) that ribose is a ring compound with its special attachments, (2) that its ring structure improves its longevity; and (3) that this molecule was crucial in constituting the first and most basic constituent of the first bions. It was not then used as food but was an integral and necessary part of the first bions and of all biota since then, including us. No evidence yet shows that it arose in the air though this might be possible. More likely it first formed to a meaningful extent in the deep Ocean, exposed to phosphate ions or phosphoric acid. Among those molecules that we have encountered so far in this volume, it is the first one actually to constitute a necessary part of the first ancestor! Remember ribose. Before we proceed to the next ring, also crucially important, let us look at the nature, source, and influence of phosphate. 26. Phosphorus, sulfur, and deep oceanic geothermal plumes

46

Phosphorus (P) is atomic number 15; it therefore has 15 protons and, when neutral, 15 shell electrons, including the standard two in its innermost orbital, a full eight in the next, and five in the outermost shell as valence electrons. That gives it a valence of -3 (three electron vacancies) or three negative bonds, like nitrogen (N). Phosphorus is relatively light, so it is relatively active. Like hydrogen (H), carbon (C), nitrogen (N), and oxygen (O), phosphorus is absolutely necessary for every Earth bion, so true biology could not start before or outside of where phosphorus was plentiful. It was not plentiful in the air or even on many parts of the solid Earth, both on land and under water. Even today it is an important limiting factor in the abundance of life. Many farmers have to get it from great distances in areas where local resources are inadequate. On the prebionic Earth, the most plentiful local source was in geothermal plumes of hot, pressured gases, molecules, and particles pouring out from molten or nearly molten rock under the sea floor, along undersea ridges, where new material pushes up between existing continental plates, driving tectonic plate movements. From this source phosphates and various phosphorus oxides, carbon dioxide, sulfur dioxide, and many other products were emitted, some crucial for any potential biota, as well as new or recycled rock for continent building (and sometimes island building). Geothermal plumes and volcanoes exist above water also, but usually only an intermittent basis, while those in the deep Ocean are relatively continuous. This continuous source of phosphorus and sulfur atoms and molecules, especially oxides, provided and continues to provide an available supply of the crucial element phosphorus, which reacts well with oxygen atoms, producing a range of radicals and compounds, the most for our purposes being the radical PO4-3. Because of its valence (combining power) of negative three (three electron vacancies, like the atom itself but more interactive), it can bind to three hydrogen atoms (H3PO4) or three sodium atoms (Na3PO4) or a combination of three atoms, including each (Na2HPO4). The structural formula or diagram of this phosphate radical is as follows (other phosphates also exist):

Phosphate (from Wikimedia Commons).

In this diagram, the vertical and horizontal lines represent actual or potential bonds between atoms. The five in the middle join the phosphorus (P) atom to the oxygen (O) atoms, while the three on the outside, leading away from the three singly bound oxygen atoms, represent potential bonds in the form of valence electron vacancies which can be filled by other atoms not shown. Sometimes this is shown with a superscript -1 by each of the lower three oxygen symbols. If the radical is floating free as an ion, it may have a hydrogen atom bound to one or two of these oxygen atoms, but any of them can join with other potential dance partners. As a result, such a geochemically produced PO4 ion (i.e., one produced by geologic or Earth

47
processes) can join with one or two others like itself in a short chain. We can therefore consider this radical as a kind of simple monomer (although it is not by itself a carbon compound), capable of joining end-to-end into an oligomer (longer than one monomer but not long enough to be a polymer, having a few instead of many monomers. Also, this tetra-phosphate (or four-oxygen phosphate) is attracted to the five-ring sugar ribose, previously discussed, to which the phosphate radical tends to bind with one of its loose bonds, as follows:

Phosphate group (from Wikimedia Commons).

34

34

The author does not use the abbreviation R shown in the above diagram, ins tead showing the ribose molecule attached at this point.

These two units, the phosphate racial with its four oxygen atoms and three (potential) bonds and the ribose ring of four carbon atoms and one oxygen atom, plus its attached hydrogen atoms and methyl group, are thus merged by excising one of the two oxygen atoms and two hydrogen atoms, again producing another water molecule, a common part of the process of joining large molecules. On the pre-biologic Earth, this was only likely in or near a geothermic plume, where a continuing supply of hot phosphate was available. This step was an absolutely crucial step in the origin of bions on Earth. Still, we are not quite there yet. Such a combination is not a bion able to reproduce by use of a template process. Even so, this much does suggest that biology began in that same environment (near a geothermal plume). Another factor supporting that view is the fact that such plumes (like volcanoes) also spew out sulfur and its compounds, especially sulfur dioxide (SO2). Sulfur has the same valence (-2) as oxygen but is less violent and destructive. It is especially important in providing sulfur bridges binding one part of a peptide back to another part of the same peptide by hooking up two carbon atoms in different parts of the same chain. Two advantages flow from this. First, the whole peptide is therefore made stronger and less fragile, thus lasting longer. Second, this binding can help the peptide to fold and retain that fold in a particularly useful shape, enhancing its enzymatic influence. But one other event had to happen before reaching the final point in the linking discussed in this step. 27. Organic bases While the word base has a number of other meanings in other contexts, in chemistry it normally refers to an atom or molecule that tends to interact with an acid in such a way that both molecules will largely bind together, forming a salt. Acids tend to form hydrogen ions (protons) in water, especially salty water. In simple, inorganic chemistry, acids interact with metals by the metal taking the place of the hydrogen. For example, hydrochloric acid (HCl) acts on sodium (Na), yielding sodium chloride and freeing hydrogen. We abbreviate this sentence as 2Na + 2HCl 2NaCl + H2. The arrow means becomes or yields. The full-sized numeral 2

48
in each case means two atoms two atoms of sodium, two molecules of acid, and two resulting molecules of sodium chloride or table salt. The subscript 2 means two atoms of hydrogen in one molecule. Another example is H2SO4 + Mg MgSO4 + H2. Here, sulfuric acid acts on magnesium to produce magnesium sulfate (and, again, a molecule composed of two hydrogen atoms). Besides mere metals, however, inorganic bases include molecules that have an OH radical in them (a hydroxyl radical). If this kind of base interacts with an acid, the hydroxyl radical from the base binds to the hydrogen ion of the acid, making H2O (water), a separate new molecule that leaves the former acid and base, and the remainder of those two molecules join. The molecule resulting from both the acid-on-metal and acid-on-hydroxyl interactions is a salt. For example, when potassium hydroxide and nitric acid interact, the result is the salt, potassium nitrate, and a water molecule: KOH + HNO3 KNO3 + H2O Turning from inorganic to organic chemistry, the fundamentals are the same but the details differ. The organic acid molecule still puts out a hydrogen ion in a solution of salty water, but only from a carboxyl group that is part of the molecule. We discussed this carboxyl group as one of the functional groups composing the amino acids. If an organic molecule does not contain a carboxyl group, it is not an acid, no matter how many hydrogen atoms it may have. Likewise, organic molecules can contain OH groups that form a separate water molecule when exposed to a hydrogen ion from either an inorganic or organic acid. Such a molecule is called an alcohol. For example, ethane is a hydrocarbon chain with two carbon atoms and, of course, the typical six hydrogen atoms:

Ethane (from Wikimedia Commons).

Alcohol (from Wikimedia Commons).

35

35

The author positions OH of the alcohol in parentheses to the right of the hydrogen on the far right of the ethane diagram.

Adding ethyl alcohol (from the paragraph above, with the R of the alcohol depicted above taken by the ethane molecule) to acetic acid (CH3COOH) results in ethyl acetate and a new water molecule. The resulting molecule, ethyl acetate, in the case of organic compounds, is not called a salt (and is not salty tasting) but rather an ester (not spelled like the homophonous name, Esther). So in organic chemistry, an organic acid and an organic base can make an ester. This is a common event. Even some organic compounds that are not alcohols can also behave in somewhat similar ways under the influence of organic acids. These are therefore also called organic bases.

49
One very important class of the latter, non-alcoholic organic bases, consists of heterocyclic molecules with a few substitutions bound to ring-member atoms. These are well known today, are a crucial part of every bion, and so surely existed more than four billion years ago. A number of these are known now, some more common than others, and five or six are absolutely necessary for biology. It is not known exactly how they first formed. One view is that they arose directly from hydrogen cyanide molecules (HCN).36 The reason for this view seems to be that these cyanide molecules are composed of a single carbon, nitrogen, and hydrogen atoms, as are the pertinent organic bases. It is certainly plausible that another atom could be substituted for the hydrogen atom, including either another carbon or nitrogen of another HCN molecule: NC H + H CN NC CN or CN C
36

Some pyrimidines, including uracil and cytosine, were synthesized in an experiment attempting to replicate possible conditions of early Earth: Menor-Salvan, Cesar, Dra. Marta Ruiz-Bermejo, Marcelo I. Guzman, Susana Osuna-Esteban, and Sabino Veintemillas-Verdaguer. 2009. Synthesis of Pyrimidines and Triazines in Ice: Implications for the Prebiotic Chemistry of Nucleobases, in Chemistry A European Journal 15: 4411-4418. Doi: 10.1002/chem.200802656. Urea solutions in water were subjected to freezethaw cycles for three weeks, under a methane-based atmosphere, also subjected to spark discharges for the first 72 hours, yielded triazines and pyrimidines. A control experiment at room temperature but with the same atmosphere and energy, led to the synthesis of hydantoins but no pyrimidines or triazines.

By this method alone, it is plausible to get two or three cyanide molecules into or attached to a heterocyclic ring of carbon and nitrogen atoms. In the known rings of this type, only two ring nitrogen atoms and, in some cases, one peripheral nitrogen atom appear. More than that seemingly had to happen, but the above steps may well have constituted part of the process of forming the first such organic bases. It is, however, also quite plausible and even necessary, that one bond of the triple bond (binding the nitrogen atom to the carbon atom) would also switch to binding another carbon atom into the ring or even enough substitutions occurred to result in the loss of a nitrogen atom. However it happened, the simplest such heterocyclic organic bases today contain two nitrogen atoms (not adjacent to each other) and four carbon atoms in their rings. Some also have nitrogen atoms attached to the exterior of the ring as a sort of decoration.

Cytosine (from Wikimedia Commons).

50

Uracil (from Wikimedia Commons).

As the reader can see, the only difference between these two is at the top of the diagram, the symbol attached to the carbon ring but outside it. Also note the nitrogen symbol at the bottom of the ring. In describing or referring to such a molecular diagram, that nitrogen atom is numbered one, and other atoms are numbered from that. Counting counterclockwise, atoms 1 and 3 of the ring are nitrogen, while the atoms forming the rest of the ring are carbon. This kind of single-ring, organic base is a pyrimidine. Every bion has at least two kinds of these. We have four or more. Another possibility also exists. In our time, this kind of heterocyclic, organic base is actually built in bions by adding bits of it at a time with the aid of phosphate, presumably originally in or near a geothermal plume. It is therefore possible that the first such pyrimidine was built up by somewhat similar steps. One such step, for example, starts from the amino acid glutamine, whose structure can be abbreviated thus:

Glutamine (from Wikimedia Commons).

Step One: A high energy source (plentiful in geothermal plumes), the glutamine, a carbonate ion, and a phosphate radical interact to produce carbamoyl phosphate:

Carbamoyl phosphate (from Wikimedia Commons).

Step Two: This carbamoyl phosphate then interacts with another amino acid (aspartate), adding it to the carbamoyl in place of the phosphate:

51

Dihydroorotate (from Wikimedia Commons).

Step Three: Through loss of a water molecule and the binding of one amine group with one carboxyl group, a ring is formed, called dihydroorotate, leaving the other carboxyl outside the ring but still attached. Two more steps eliminate that remaining carboxyl group and one hydrogen atom, while another step moves a nitrogen to an oxygen atom in the ring, eliminating a double bond to that oxygen atom. All of this makes the result an early organic base of this group, uracil, depicted earlier. Hence, at least two plausible possibilities exist for the origin of the single-ring pyrimidines, something like the piece by piece assembly and the cyanide-chain ring formation. The current system seems to me a bit complex for a pre-biologic world, but aspects of both ideas may have interacted to bring this crucial step in late pre-bion chemical evolution. Further progress to the double-ring purines may have arisen in the same combination of ways. With one or more of these heterocyclic organic bases, the stage was set for the first bion, out of which all the rest of biology has come! Each of us still depends on about seven kinds of these bases for the origin, continuance, and nature of life. 28. Purine di-heterocyclic organic bases The previous step touched on the origin of the six-atom, pyrimidine, single-ring bases. The other basic category of heterocyclic ring bases contains the purines. The main difference between purines and pyrimidines is the complexity of the molecule. Pyrimidines have a single ring; purines each have a double ring. This also causes the purines to take up more space. As we shall see later, this size difference has an important effect on our history. (To help the reader remember which category is which between these two category names, note that the one with the longer name is the smaller molecule; the one with the larger molecule has the shorter name.) The structure of a purine double ring comprises two rings sharing a common portion, like row houses that share a common wall. The larger ring is essentially like the six-atom pyrimidine ring, with two nitrogen atoms separated by a carbon atom and a total of four carbon atoms altogether in the ring. The smaller ring shares two atoms with the larger ring and has three more atoms, a total of five atoms: three carbons and two nitrogens (each unmarked corner of the pentagon or hexagon the rings represents a carbon atom):

Adenine (from Wikimedia Commons).

52

Guanine (from Wikimedia Commons).

These are the only two common purines. Another one, however, exists in with a specialized set of functions. It is like guanine except that it lacks the amine group shown above on the lower right (NH2). With respect to the origin of purines, some of the same considerations arise as in the case of pyrimidines, which we need not repeat. Here, however, some other considerations arise as well. First, although simpler forms do not invariably arise before more complex ones, this is the normal progression. Because pyrimidines are simpler than purines, they more than likely arose earlier. The earlier molecules could have played a role in the rise of the later ones. Second, besides and before the pyrimidines arose, two other kinds of molecules had already developed that are still simpler: phosphate radicals and simple sugars, in particular the five-carbon sugar ribose. These play a part today and, because they arose early, may always have done so in the development of both pyrimidines and purines. Because the phosphate radicals were and remain most abundant and persistent near geothermal plumes in the deep Ocean, their role most likely occurred in that vicinity. In particular, phosphate radicals are plentiful sources of chemical energy, tend to join together at times, and also bind to other molecules. It appears that some ribose molecules joined with phosphate radicals, forming ribose-5-phosphate. Because we have already learned that the ribose ring has carbon atoms at four corners, we abbreviate the diagram to show only the bonds and oxygen atoms of the ribose ring (from Wikimedia Commons):

Ribose-5-phosphate, so-called because the carbon atom which links the ribose portion to the phosphate portion is counted as atom number five.

With a sufficient energy boost, the molecule above (ribose-5-phosphate) can bine to a combination of two more phosphates (these two together are called pyrophosphate). Such an arrangement may end in the presence of the amino acid glutamine, mentioned before (though perhaps any amino acid would do), with the modified earlier molecule taking an amine group (NH2) from the amino acid with the energy provided by losing the pyrophosphate radical. In pyrimidine formation, the ring forms before binding to its other final partners. But purine is built by small steps, adding parts to the sugar phosphate, at the sugar (ribose) end opposite the phosphate. Thus, a purine starts as the amine group from the amino acid, adding carbon atoms, etc., to the end. The first part built from the original amine group becomes the small, five-atom ring, and from its wall (two carbon atoms bound to each other as well as to the amines

53
nitrogens), separating it from (and joining it to) the potential, larger, six-atom ring as the latter is built, a bit at a time, until it is large enough to close into a ring. This course of events further suggests that the pyrimidine bases formed originally before the purine bases, out of and because of molecules already then existing in the air and Ocean, and probably the purines followed only after the completed pyrimidines had already begun to link to ribose phosphates. We are now ready for a climactic step: the linkage of three molecules which we have examined into something new, with incredible potential. 29. Nucleotides: three musketeers team up To review, once Earth formed and its surface cooled somewhat and hardened, and after the Moon was carved out of it, any hydrogen atoms in the earliest air either teamed up with oxygen to make water, with carbon atoms to make hydrocarbons, with other atoms to form other molecules, or escaped the Earths air. The water (and other heavy molecules) largely rained out of the air and onto the surface of the land, forming the Ocean, rivers, lakes, swamps, and the like, washed salts out of rock, and began its perpetual cycle of evaporation and precipitation. In the course of their perennial dance, various atoms formed various molecules. Some of them, particularly carbon atoms, built larger molecules, including monomers, which strung themselves together to make polymer chains. Sometimes the latter were branched, sometimes they formed rings of a few to several atoms, with accompanying atoms of non-carbon types attached. Particularly important to our story, among all these molecules, were amino acids, carbon dioxide, cyanide, methane and other hydrocarbons, aldehydes, sugars and larger saccharides. But all the myriads of other molecules also formed on Earth. With the help of catalysts, usually metallic, the earliest molecules to form (including enzymatic peptide rings), and the great heat, pressure, and resources continually provided by geothermal plumes in mid-Ocean, many molecules formed, were destroyed, and were reformed. Three molecules most vital to us finally came into existence with the help of those factors and others (and despite the hindrance of many factors as well). Doubtless many factors not mentioned or not known also played a part, some favoring, some hindering, some making no difference. These three vital molecules, as we have seen, are (1) phosphate radicals, ion, and molecules, (2) ribose molecules, and (3) heterocyclic organic bases. Phosphate ions were provided by the geothermal plumes. Phosphate radicals arose from volcanoes on continents and islands, as well as in the Ocean. In the case of the radicals on dry land, rain and the weight of the molecules brings them down again and washes them back into the Ocean. These phosphate ions are a source of high energy and so quite chemically active. They can and do join together into pyrophosphate (two like ions joined together) and triphosphate (three merged ions). They seem even now to take the lead in finding partner molecules to bind to. The five-atom ribose ring (with its external attachments) has two kinds of atoms in its ring, carbon and oxygen. It can stand separately as a single-ring molecule, but it can also join other sugar monomers to make chains or other larger structures, attaching to the mother molecules at various points on its periphery, just as amino acids do. The organic bases like the sugars have rings composed of two kinds of atoms. In this case, they are carbon and nitrogen, in addition to their various external attachments. These bases are divided into pyrimidines, which have rings of six atoms, and purines, two rings of six atoms each joined together plus a ring of five atoms, joined by a common, shared boundary or wall of two atoms. Altogether, there are seven such organic bases that are common, as well as a few other rare ones. They likely did not all come into existence at the same time, but one

54
by one over a period of time. Uracil could have been first, though that is not certain. Thymine was probably last, for reasons to be mentioned later. Every bion contains and many consist of these three very different types of molecules, including the phosphate, ribose, and typically four to seven classes of bases. Yet these all came into existence before there was biology and thus, necessarily, arose in non-biologic ways. But the presence of all three together made biology possible. Still, biology could not arise these three musketeers joined forces. As the fictional French musketeers declared, there is strength in unity, as in their motto, One for all and all for one!37
37

Dumas, Alexandre. 1844. Les Trois Mousquetaires (The Three Musketeers) live by this motto (in French, un pour tous, tous pour un).

The first step in that process was for one or more, probably two, phosphate radicals or ions to appear and bind to one end of a ribose molecule, and another to attach to the other end. This probably happened many times before a further step occurred, which was for an organic base to replace two of the phosphate ions, forming a three-part molecule, with the remaining phosphate at one end, the base at the other end, and the ribose in the middle linking all three together. This new molecule was not merely larger than any of its parts but had a combination of qualities that none of its parts individually could provide. This new and bigger molecule is a nucleotide. The phosphate unit and the ribose unit in every nucleotide molecule were then alike, but, as pointed out previously, several possibilities existed for the role of organic base. Thus, a single, unified molecule, with parts protecting each other to some extent, could still vary enough among individual cases to function in slightly different ways. This was still not quite a bion, but it was only a step or two from it. Such molecules still exist in all of us, busy all the time, often changing by adding an extra phosphate or two to the phosphate end of the this nucleotide, then losing one again, in this wasy providing enough chemical energy to drive another reaction, usually helping to build another molecule, even such as each other. Most of the common nucleotides can perform this energizing function. The nucleotides with the organic bases adenine and guanine seem to perform this function most often. That activity likely did provide some slight increase in the likelihood of a larger quantity of nucleotides being formed, a tendency to reinforce their numbers and their helpfulness to each other. This probably was the last pre-bionic form before bions did form. But before we look into that process and event (the formation of a bion), we need to be aware of one more characteristic of molecules, whether biological or not. 30. Chirality: three dimensions and mirrors One feature of atoms enables us to distinguish between certain made by bions and otherwise identical molecules made by non-biological processes and otherwise identical molecules made by non-biological processes (i.e., geochemical processes). This feature is chirality, which we may think of as a type of handedness. Atoms with more than one electron in their outermost shells (valence electrons), when a shell has less than its maximum number of electrons, can sometimes bind to more than one other atom. If one atom does bind to more than one other atom, ordinarily physical chemists (those who study the physics aspects of chemistry) say the points of directions of such bonds tend to keep the same relationship in a wide range of compounds. A water molecule, for

55
example, is often shown as HO or HOH, but the atoms do not assemble in a straight line; rather, the molecule is shaped as follows:

Water molecule (from Wikimedia Commons).

In this instance, it is possible to turn the molecule around or tilt it in different ways without changing the identity of the molecule depicted. That still lets us show a diagrammatic or structural formula on a flat surface as an essentially flat molecule. This is still true, for most purposes, of some chain compounds, such as the hydrocarbon butane:

Butane molecule (from Wikimedia Commons).

On the other hand, many molecules, even relatively simple ones, especially organic molecules, even if they can be shown flat, actually are not, but have definite three-dimensional shape. For example, the butane molecule could be shown with each carbon atom (C) surrounded above, below, and on its sides by its hydrogen atoms:

Three-dimensional, ball-and-stick depiction of a butane molecule (from Wikimedia Commons).

For a small molecule, it may make no difference whether the depiction is in two or in three dimensions. The molecule may look the same from any angle. But for many larger molecules it does make a difference. The three-dimensional structure of a molecule can result in two molecules with the exact same atoms appear almost identical, but one becomes the other by flipping it over or turning it. To each other, these two versions seem like mirror images. Just as when a person looks in the mirror, the image moves the right hand when the real one moves the left and vice versa. This is true of objects such as books writing viewed in a mirror is backward. It is also true of parts of bodies (right and left hands, right and left feet, etc.) and things worn on them (gloves, shoes, etc.). These pairs all have a matching composition with similar structure and internal relationships, but one is not completely identical to the other. Molecules sometimes have this mirror-image relationship as well. Most geochemistry and human industrial processes do not distinguish between right- and left-handed forms of

56
molecules, nor do they need to. Most non-biological processes produce essentially equal numbers of both forms, mixed indiscriminately. Bions, however, are all so finely detailed in their chemical functions that they cannot make, and usually cannot use, molecules of both forms. All of their molecules must be compatible with each other. Bions exclusively use dextroribose (right-handed ribose, abbreviated D-ribose) and not laevoribose (or levoribose, i.e., left-handed ribose, abbreviated L-ribose). Amino acids, organic bases, and most biological foods, products, and parts have one form and not the other. All bions use the same form of sugar, amino acid, etc.; none use the opposite. These facts tell us at least two things. First, they tell us that all bions have a genetic relationship with each other; we are all one, big family if we look back far enough. Second, they make the distinction clear when we find traces of past bions in rocks, even if those traces are no more than a few molecules. If the molecules all have the biological form (the dextrorotated form), they originated from biology. Other aspects of nature never do that. It is not yet clear why this distinction exists. Do we use and consist of molecules of same handedness or chirality because there is (or was) some inherent advantage to that particular one? Or was it merely the case of one coming first, by chance? I would guess the latter, but no test of that idea has been published. Perhaps something akin to Earths biology functions on some other planet. If we could find 1,000 such planets and test them all, and if we should find that some arose with the opposite orientation (the levorotated form), we could infer that life could arise from either form. But it may be that any process like biology on other planets would make and use totally different molecules so that there could be meaningful comparison on that point. Some simulated, three-dimensional, structural formals are shown in accompanying figures, where structural features that are depicted as larger indicate that they are nearer to the eye, while those depicted smallest are farther away. It is not necessary to memorize the particular chirality of each molecule, only to remember that, for bions, it is only one of two possible forms that matters. Supplemental Diagrams A third pyrimidine molecule, thymine, developed later than the others discussed previously:

Thymine (from Wikimedia Commons).

57

Methionine (from Wikimedia Commons).

Methionine, like glutamine, is an amino acid. Thus, we see that amino acids, which appear to have first formed very early in the Earths atmosphere and in the Ocean (probably by 4.4 billion years ago), or something closely related, seem to have played a crucial role in the somewhat later (100 millads?) formation of early mono- and heterocyclic organic bases, likely at least providing the two extra carbon atoms that might not always come from the linkage with cyanide molecules (see below). Clearly, a short sequence of two cyanide molecules could create half of the pyrimidine ring, plus two more bonds as well, as in the diagram below (cf. thymine ring above): \ NH | C :

| C \

NH The first CN monomer is in bold print. The second monomer comprises the carbon to the left of the first, with the nitrogen at the bottom. These atoms cannot make such a tight ring such as occurs in thymine. Another two carbon atoms may come from more hydrogen cyanide molecules (HCN), losing their nitrogen (N) atoms, or from amino acids or other organics, to create such a ring.