The Human Journey: Volume I. Chemical Evolution Chapters DEF

7/28/2019 The Human Journey: Volume I. Chemical Evolution Chapters DEF

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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 itand 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 otherand 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 enoughtogether 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


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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 numberof 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 cloudconsisting of


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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 astar 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 dwarfstar. 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 thatthe 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:


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Hydrogen1

1H

Helium4

2He

Carbon 126C

Oxygen 168O

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 toseveral times more), the star swells up, its surface cools, and it becomes a red giantstar. 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

+1 +2 +3 4 -3 -2 -1 0

0 *

1

1H

1+

4

2He

0

1 *

63Li

1+

84Be

2+

105B

3+*

126C

4*

147N

-3*

168O

-2

189F

-1

2010Ne

0

2 *23

11Na *24

12Mg *27

13Al ?28

14Si *31

15P *32

16S *35

17Cl40

18A

3a *3919K *40

20Ca2+ 4521Sc

4822Ti

4123V

5224Cr *25Mn

3b *56

26Fe *59

27Co59

28Ni

3c *29Cu *65

30Zn70

31Ga73

32Ge ?75

33As *122

51Sb *80

35Br84

36Kr

4 *96

42Mo *127

53I131

54Xe

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.


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

Element Symbol Element Symbol Element Symbol Element Symbol

Hydrogen H Magnesium Mg Calcium Ca Antimony Sb

Lithium Li Aluminum Al Manganese Br Bromine Br

Carbon C Phosphorus P Iron Fe Molybdenum Mo

Nitrogen N Sulfur S Cobalt Co Iodine I

Oxygen O Chlorine Cl Copper Cu

Sodium Na Potassium K Zinc Zn

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 sometime) 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 whichmakes 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 so-

called 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


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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 atomswandering 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, theelectrons 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 cloudchanged. 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.

16The 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).

17See 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 objectdistinct 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 cruston 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.


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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.

19There 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 atomsare 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 skinbecame 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 usbecause 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.Chemistryis 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


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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 informationbecame 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 mostelongated 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


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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.

202003 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

23In 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-formerly-

known-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.
http://www.space.com/1876-solar-system-crazier.htmlhttp://www.space.com/1876-solar-system-crazier.htmlhttp://www.space.com/1876-solar-system-crazier.htmlhttp://www.caltech.edu/content/dwarf-planet-formerly-known-xena-has-officially-been-named-eris-iau-announceshttp://www.caltech.edu/content/dwarf-planet-formerly-known-xena-has-officially-been-named-eris-iau-announceshttp://www.caltech.edu/content/dwarf-planet-formerly-known-xena-has-officially-been-named-eris-iau-announceshttp://www.caltech.edu/content/dwarf-planet-formerly-known-xena-has-officially-been-named-eris-iau-announceshttp://www.caltech.edu/content/dwarf-planet-formerly-known-xena-has-officially-been-named-eris-iau-announceshttp://www.caltech.edu/content/dwarf-planet-formerly-known-xena-has-officially-been-named-eris-iau-announceshttp://www.space.com/1876-solar-system-crazier.html


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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 dancetempo) 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 theattraction 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.


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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 theaccompanying 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


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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, calledbonds, 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 haveeight 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 farapart 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


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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 manyshells 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 life-

like 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.


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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 hasprotons. 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 twistedcircle, 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 calledaromatic

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.


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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. Theextra 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 calledprecipitating).

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.


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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 itselfprovided, 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 thehot, 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.

24According 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


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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 abundantsubstance 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 wordamino 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

\ /
http://www.scotese.com/precamb_chart.htmhttp://www.scotese.com/precamb_chart.htmhttp://www.scotese.com/precamb_chart.htm


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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 acidin organic chemistry that carbon atom must also be bonded to another

particular carbon atom. That particular carbon atom (shown simply as C) must be double-

bonded 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, butappear 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:

H C N


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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

25Matthews, 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 sulfurwas available and used in early biology, as

wasphosphorus. 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, weight31, 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 thisfactor 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

H H O

2. Alanine (Ala) | | //

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;

1 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,

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