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
\ /
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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,