Prepared May, 2010


In Celebration of Psalm Nineteen:
God's handiwork in Creation

Chapter 6
Preparation of the Ecosystem
and Formation of Dry Land
3.9 to 1.8 Ba


NOTE: Ba (Ma) = Billions (Millions) of years before the present time.

NOTE 1: see the lecture A Fit Place to Live for a synopsis of Chapters 5-??. The excellent and highly readable book by J. William Schopf,  Cradle of Life treats the material of this chapter in greater depth.

NOTE 2: This website follows the nomenclature established by Lynn Margulis, Five Kingdoms. Some biological systematists use the term "domain" where Margulis uses the term "kingdom." Furthermore, we use the term "bacteria" for the more formal term "prokaryotes" (kingdom prokaryota or eubacteria), meaning single-celled species that lack a nucleus. Nucleated species are eukaryotes, kingdom eukaryota[See Margulis, Kingdoms and Domains, p.9ff.]. I call eukaryotes "proper cells" which will be the subject of the next chapter.


The last chapter described the state of the Earth around 3.9 Ba, when it first became able to support a primitive sort of life. Immediately bacterial life appeared in all of its essential complexity.

The earliest actual fossils that have survived undamaged come from some 400 million years later, about 3.5 Ba. For the next 2 billion years (to about 1.8 Ba), bacterial life dominated the world and caused major transformations of the earth's surface and atmosphere. These changes prepared the earth for the next great innovation: the "proper" nucleated cell -- the kingdom of Eukaryotes, the subject of the next chapter.

The Primordial Environment and the Necessary Changes to Foster Advanced Life.

The first living material had to be strictly autotrophic, that is, (obviously) all of its food and energy had to come from inorganic material. In modern usage the term "autotrophic" is used in a much looser sense. often including plants and bacteria that utilize carbon dioxide or sulphur rather than oxygen.

Just as importantly, the first living material had to have a source for fixed nitrogen, which is a major component of organic food. The early atmosphere was mostly nitrogen gas. The two nitrogen atoms in the gas are very energetically bound. It takes a very large amount of energy to separate ("fix") the atoms so they can be used biologically, usually as ammonia, NH3 or the salt NH4OH. In the inorganic world, these necessary products are rare and occur mostly as transient byproducts of chance events such as lightning or volcanic activity -- not a stable or abundant source of nitrogen needed for the necessary rapid proliferation of life worldwide.

The early earth was strongly reducing, which means that free oxygen was not reliably available -- it would be sucked up in oxidizing nearby minerals. Advanced life, particularly multicellular life, requires the abundant availability of oxygen: there is no alternative to this. Thus early life was limited to single-celled bacteria which could thrive in a non-oxygen atmosphere.

Advanced life is too busy with other activities to make its own food from scratch. Therefore a major requirement for a global environment that supports advanced life is that pre-processed organic food must be readily available worldwide, together with a vast global distribution of bacteria to produce it and break it down. This requires in particular, that fixed nitrogen must be prepared in advance and readily available. In a word, Advanced life cannot be autotrophic in the strict sense.

The early earth was covered with a global ocean -- hundreds of feet deep -- so the first life thrived in a water medium. The water distributed life and its products worldwide. The tidal effects of a nearby moon and the continued cooling of the earth's crust resulted in many large volcanoes whose debris often penetrated the ocean surface to form volcanic cones, but these quickly eroded by the violent tides and weather so that for many millions of years there was nothing resembling permanent dry land.  Eventually the volcanic activity resulted in extensive, reasonably stable, shallow-water tidal zones -- areas that were washed by the ocean and tides but reliably remained within reach of sunlight.

Bacteria dominated the scene for over two billion years. In this time (as we will see) it transformed the atmosphere from a reducing, oxygen-free atmosphere, to an oxidizing one that has oxygen gas as a major component. Towards the end of this period, the earth also began to form permanent dry land, the ancestors of the continents that exist today.

The Earliest Fossil Species.
Fossils, of course, exist in rocks that must be at least as old as the fossils, and that must have been preserved intact without being deformed or subjected to extreme heat or pressure. There are very few locations on the earth where such ancient rocks exist. A small amount of such rock exists in Western Australia, and another place is portions of Eastern South Africa near Swaziland.

Although there is evidence of life as far back as 3.9 Ba, the earliest actual fossils are closely dated to 3.465 Ba ± 5 Ma, disovered by J. William Schopf. This close dating is possible because the fossils are sandwiched between lava flows containing zircon crystals that can be precisely dated[FOOTNOTE: Schopf, Fig. 3.4 p.77; "The Apex fossils are preserved in a chert bed sandwiched between two massive lavas of the Pilbara sequence." p. 88.].

These early fossils appear in chains as depicted in the Figure 1[FOOTNOTE: See Op. Cit. Fig. 3.4 for photographic images].

Figure 1
Sketch of earliest fossil (3.465 Ba)

They appear to be chains of dessicated cyanobacteria, also called blue-green algae. A typical modern example is Anabaena, see Figure 2.

Figure 2a
Photograph of Anabaena, a modern Cyanobacteria

Figure 2b
Sketch of a Cyanobacteria chain.
[FOOTNOTE Used by permission. For discussion of Anabaena Cyanobacteria see Lynn Margulis and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The most recent edition of this work has been renamed Kingdoms and Domains (2009)].

The First Fossils

Preservation of the first fossils through almost 4.5 billion years of chaotic upheaval of the earth's crust is practically a miracle. Almost all of the rock on earth has been melted, compressed, distorted or otherwise changed in ways that would destroy fragile fossil evidence. Schopf's book gives a vivid description of what has to happen for these ancient fossils to survive to the present day[FOOTNOTE: Get reference]. The result is that such fossils are found in only a few small location worldwide: small areas in South Africa (Swaziland formation) and in Western Australia. Indeed it is remarkable that there are any fossils remaining from these ancient times.

In the example of Schopf's fossils they had to avoid being "cooked" by lava flows both below and above the actual fossils -- a rare event indeed -- but without this lava and the risk of overheating, the fossils could not be dated.

I believe this is an example of the silent speech that God preserves in his creation to declare his glory and handiwork.

Cyanobacteria are moss-like species that live in oxygen-poor environments bathed in light, such as in shallow bodies of water. They are exceedingly complex, far from what one would think to call primitive. They grow in long chains because when the cells reproduce they divide in half and tend to remain attached. They secrete a kind of mucilage or slime which solidifies to form characteristic multi-layered dome-like structures called stromatolytes that grow in shallow water between high and low tide. Living stromatolytes exist today in only a few locations worldwide, one being Hamelin Pool in Western Australia.

Location of stromatolytes

The fossils appear to be a type of bacteria that formed stromatolytes, which are found in ancient rocks worldwide. Stromatolytes grow  in highly saline tidal basins and are relatively rare today. An example of modern living stromatolyte formations is found at Hamelin pool, a tidal flat in Western Australia.

Stromatolites-HamelinPool.jpg Martin Peters
Figure 2
Stromatolytes at Hamelin Pool
Western Australia
Photo by Martin W. Peters,
Landmark Solutions
used by permission

If the identification of these fossils as cyanobacteria is correct (the assumption here), then it immediately poses a problem because -- as we will see -- cyanobacteia are advanced bacteria, not what one would assume to be representative of the earliest living species[FOOTNOTE: Schopf, ibid, p.78 "It seems to me likely that several of the Apex species are cyanobacteria, a fairly advanced group of microorganisms that until this find was not guessed to be present so early in Earth history.].

Why bacteria and not archaea? Some paleo-biologists insist that the earliest life was from the kingdom Archaea (indeed the name implies that they are the most ancient bacteria), based on the ability of archaea to manage in very hostile environments (which the early earth certainly was), and the claimed advantages of survival near deep water thermal vents.

It is not the purpose here to confirm or deny this possibility, but there are some good reasons to doubt that archaea could "be fruit and multiply and fill the earth"[FOOTNOTE: Genesis 1:22] to the degree required at this point in the earth's history: Archaea are too limited and specialized to fill that role. In addition, the genetic make-up of the archaea appears to be more advanced than that of bacteria, more akin to eukaryotes, and therefore (one would assume) a later development. In the final analysis, though, it does not really matter whether the first living species were archaea; the first practical living species had to be bacteria, and as a matter of fact, bacteria were the first fossils preserved in the fossil record.

Preparation for advanced life. The rapid multiplication of the early species of life was needed to prepare the earth for more advanced species. Almost three billion years separate the first fossils and the first eukaryotic fossils -- the first step towards complex, multicellular life.

Looking ahead, the main tasks for the early bacteria were:

• Distribute abundant amounts of organic food worldwide.
- This task is needed because advanced life cannot take the time or energy to be self-sufficient (autotrophic).
- In particular, this food provides fixed nitrogen, which is essential for all of life. Its manufacture from atmospheric nitrogen is a difficult, energy-consuming slow process (see below). No eukaryotic species is able to manufacture nitrogen. In fact, very few bacteria species are able to manufacture all of its own requirements for nitrogen. The nitrogen may be either organic or inorganic (in the form of nitrates or ammonia gas).

• Convert the earth's atmosphere and the oceans from reducing to oxidizing. The atmosphere must have around 20-25% oxygen content. Complex life requires at least the lower limit of abundance, and the upper bound is needed to avoid spontaneous combustion.

It appears that the limiting requirement was the oxygen supply, which took the full three billion years to achieve, with the aid of oxygen-producing bacteria. The global distribution of the food supply, fixed nitrogen, and the formation of vast mineral deposits that are so essential to the modern technological age were by-products of this push to develop the oxygen supply.
Complexity of the first living species. Cyanobacteria are apparently the bacteria of choice in this task because they produce oxygen as a "waste" byproduct of photosynthesis. One problem is that cyanobacteria are complex -- in Margulis' classification they are phylum B-6, about half-way up the ladder of bacterial complexity. This complexity in such ancient species is something that evolutionary theory would not have predicted.

Photosynthesis. Photosynthesis -- using solar energy to energize life processes -- involves interactions between many individually complex molecules. Photosynthesis requires the use of a closed membrane that can enclose an acidic interior (excess H+) to drive ATP production. The chlorophyll and ATP synthase molecules are embedded in this membrane.

The similarities between all photosynthetic systems and its complexity is such that evolutionists such as Stephen Jay Gould assert that it could only have evolved once, which means (in his lingo) that it is a very low probability result of random processes.[FOOTNOTE: CITE].

The Creation of Photosynthesis

According to an analysis of the cyanobacterial genome (Hasselkorn and Johnston (PNAS)) the earliest cyanobacteria already had the light & Calvin processes for photosynthesis in place. These are two very complex and subtly linked processes and involve many specialized molecules working together. These are such complex biological processes, that the complexity and early appearance on earth seems to indicate planning and design.

Biologists universally (as far as I am aware) point to the complexity and the similarity of photosynthesis among all species to imply that the process evolved only once in earth's history[FOOTNOTE: for example, Schopf p. ???; other references] -- the chance events that had to occur for photosynthesis to arise even once by natural processes are vanishingly low probability, so that assuming the same system would arise more than once defies even an evolutionist's credulity.

Photosynthesis divides into two parts: the light process and the dark process. In the light process, chlorophyll uses the energy of sunlight to produce ATP and NADPH. Each of these processes involves complex molecules: ATPsynthase (a molecular motor described in the last chapter) and NADP reductase. The  dark process, also called the Calvin cycle then uses these products to form triose sugar (C3H6O3) with the help of another complex molecule (RuBisCo). The triose sugar is used to form starch, amino acids and sugars.

Wiki-lightProcess.gif Wikipedia Photosynthesis Wiki-CalvinCycle.gif Wikipedia Photosynthesis
Figure 3A
Photosynthesis: Light Process
ATP provides energy to the dark process and to the cell generally
NADP is an H carrieer enzyme used in the dark process.
In cyanobacteria photosynthesis occurs in a thylokoid membrane.
Light Process Animation [FOOTNOTE: From Virtual Cell Animation Collection]
Figure 3B
Photosynthesis: Dark Process (Calvin Cycle)
5 of 6 triose sugars are re-used in the cycle.
All cyanobacteria use the Calvin cycle.
[FOOTNOTE: Hasselkorn, Johnston].
Calvin Cycle Animation

The chlorophyll molecule of all photosynthetic species captures light energy using a special ring structure that has a magnesium atom suspended between four nitrogen atoms. When light hits this structure, a high energy electron is emitted and its energy initiates the photosynthetic activities.

photo-chlor.gif NASA/JPL-CalTech
Figure 4
Chlorophyll "Antenna"
The hydrophobic tail is embedded in a membrane.
The magnesium complex captures light.

TODO: Discuss the special molecules and the genetic machinery to construct them. See The Cyanobacterial genome core and the origin of photosynthesis (Proceedings of the National Academy of Sciences, 2006).

Nitrogen Fixation. Although nitrogen made up about 80% of the ancient earth's atmosphere, it cannot be used to fill every living cell's need for nitrogen. As one author remarked, "No animal, plant, fungus, or protist has mastered the chemical art of converting the abundant gaseous form of nitrogen into a biologically useful one."[FOOTNOTE: David W. Wolfe, Out of Thin Air - nitrogen fixers, Natural History, Sept. 2001. Note that he suggested a source of nitrogen from lightening forming Nitrate, but this is not possible because the early atmosphere was almost entirely oxygen-free. See Schopf, p. 153]

Ancient life had to fix nitrogen; that is, convert atmospheric nitrogen to amonia; otherwise life could not flourish. There was no other effective way to get the nitrogen needed[FOOTNOTE: SCHOPF p 153 "Today, large amounts of nitrate are made when oxygen and nitrogen combine during lightening storms, but this could not happen in the early oxygen-deficient atmosphere.... The scarcity of ammonia and nitrate posed a major problem to life." Also see NAS studies].

Only one way to fix nitrogen exists in nature, and that is with the use of the complex nitrogenase motor molecule. Nitrogen fixing is a very slow process. To convert a single molecule of nitrogen gas to ammonia, the nitrogenase molecule, which is made up of two giant proteins, must physically separate and rejoin eight times, and this takes about 1.2 seconds. Today, nitrogen fixing worldwide only supplies 10-20% of life's annual consumption. The rest must come from recycled organic food (or, in the past century, from commercial inorganic nitrogen).

Nitrogenase molecule, illustrated in Figure 5  has 24,190 atoms and is composed of two proteins involving a molybdenum and magnesium atoms, called MoFe (dinitrogenase) and FeMo-co (MoFe cofactor). MoFe is produced by the genes nifD and nifK. All told some 22 genes are involved in producing and regulating the molecule. A full explanation of how nitrogen fixation works is still unresolved.

The formula for nitrogen fixing by the nitrogenase molecule is:

N2 + 8 H+ + 8 e + 16 ATP → 2 NH3 + H2 + 16 ADP + 16 Pi

where Pi denotes an inorganic phosphorous compound. This is a formal equation only: other than with the use of the nitrogenase molecule as a catalyst, there is no known way to execute the equation at normal ambient temperature and pressure in any chemistry laboratory. The formula indicates that 16 ATP molecules are reduced to ADP to supply the energy to produce 2 ammonia atoms. This is very expensive energy-wise, as well as very slow.

The only commercial way to fix nitrogen is by using the Haber process, which operates at high temperature and pressure[FOOTNOTE: pressure 2250-4000 psi. and temperature 300-550°C.], and so cannot be duplicated in the biological world.

A cell that fixes nitrogen is called a diazotroph. The irony is that such a cell that fixes nitrogen cannot produce enough nitrogen to meet its own needs. Typically, the fixed nitrogen is released from the diazotroph as a waste product rather than used directly for its own needs. In exchange, the cell receives the bulk of its own nitrogen needs from food which it receives from its surroundings. So the typical nitrogen-fixing bacteria live in a symbiotic relationship with a normal cell and exchange food for fixed nitrogen. [QUESTION: TRUE? HOW MANY NITROGENASE "FACTORIES" ARE IN OPERATION IN A TYPICAL FIXING CELL AND WHAT THROUGHPUT? ANSWER THIS: A CELL NEEDS ABOUT ??? NITROGEN ATOMS AND PRODUCES ABOUT ??? FIXED NITROGEN ATOMS PER UNIT OF TIME.]

Nitrogen Fixing and Nitrogenase

A method to fix nitrogen was absolutely critical for the early species to fluorish on the early earth; otherwise life at best could only falter along using the scarce fixed nitrogen found naturally. A major task of this early life was to spread fixed nitrogen as food worldwide so that it could be used by more advanced life, and so it had to have an abundant supply.

There appears to be only one way to fix nitrogen naturally, and that is with the use of the complex nitrogenase molecule.
The nitrogenase molecule is so complex that to date (2010) the procedure that it uses is not fully understood. In any case the process is very slow (taking 1.3 seconds to fix a single nitrogen molecule), and requires not only a very complex molecular process, but it also requires a specialized cell in which oxygen is excluded.

How is such a molecule to be developed by purely natural, undirected processes? As with photosynthesis, the molecule is so complex and unique that it is inconceivable that the molecule could have arisen naturally more than one time in the history of life -- and I would argue that it stretches credulity to think that it could have arisen even one time without a creator's hand.

Nitrogenase is also very scarce. All the world's supply of nitrogenase could be carried in a single bucket[FOOTNOTE: David W. Wolfe, Tales from the Underground: A Natural History of Subterranean Life, Perseus, 2001, p. 78; Huxtable, Reflections: Fritz Haber (regarding the Haber process whish is the only inorganic way to fix nitrogen).]. It's not surprising that nitrogen-fixing bacteria had to work for billions of years to make enough nitrogen available for higher plants and animals to thrive. It was a vital task for the early cyanobacteria, along with building the earth's supply of atmospheric oxygen.

There is an irony here: It was vital that cyanobacteria produce oxygen, but oxygen is lethal to the nitrogen-fixing process[FOOTNOTE: Schopf, p153, "The ferredoxin-driven [nitrogenase] complex dates from early in Earth history when the environment was all but oxygen-free... [It] is brought to a standstill by trace amounts of molecular oxygen. N2-fixation happens only if O2 is shut out, even in oxygen-producing cyanobacteria....".]. The solution is that the cyanobacteria had to conduct nitrogen-fixing in a specialized cell, called a heterocyst, that was isolated from the photosynthetic activity. The heterocyst has a thick wall to isolate its contents, and it is dependent on other cells for food and energy, which it needs in abundance. In a typical nitrogen-starved medium, about one in 15 cells in a (modern) cyanobacteria chain is a heterocyst (Figure 6).

Figure 6
Cyanobacteria showing Heterocysts and Akinetes.
By permission of David Webb

SHARP POINT: Nitrogenase molecule

Preservation. Cyanobacteria also produce another specialized cell called an akinete, which can survive under harsh conditions -- freezing, starvation and dehydration -- for long periods of time. Since the early earth was constantly changing with no permanent dry land or shorelines, the ability to survive and resume growth in another locality or time was important. In addition the ability to go into a kind of suspended existence also allowed the cyanobacteria to drift with the ocean currents and distribute life and nutrients worldwide.

Stromatolyte Colonies. TODO - describe the form/interdependence of the colonies.  Multiple layers, etc.


Life's Early Boom and Bust Cycles: Formation of Uranium and Iron Ore Deposits. Because the early earth was starved for oxygen, the ocean held abundant amounts of reduced salts in solution. The oxygen produced by the early cyanobacteria combined with these reduced salts. If the product was (relatively) insoluble, it precipitated out, forming over time vast ore deposits.

Uranium salts were among the first to oxidize because [Explain chemical reason]. The product, UO2 (pitchblende) is virtually insoluble and so as the salts oxidized the product precipitated out, forming the uranium ore deposits. This continued for about a billion years, until most of the uranium salts were fully oxidized.

For the next billion years, silicon and iron soaked up the excess oxygen, forming sand and the great iron ore deposits.  The precipitation of silicon and iron is sensitive to the acidity of the environment. When acidity is high, silicates remain dissolved in the ocean water, but iron oxide precipitates. When acidity drops, the silicates precipitate out. These boom and bust cycles can be seen in a geological record known as the banded iron formations.

The banded iron formations end at about 1.5 Ba, when most of these elements in the ocean and exposed crust are oxidized, and the next great biological invention -- eukaryotes -- appears on the scene. Afterwards, the oxygen rose to a fairly stable 20-25% level in the atmosphere, where it has remained ever since. The stability is the result (???CHECK) of an ecological balance between oxygen-consuming and carbon dioxide-consuming species.

You may immediately see a potential problem: oxygen is generally poisonous to the bacteria that are the only life on earth. As long as there were minerals to draw off the excess oxygen, things could go on. But now, the earth's crust is fully oxidized. What is going to keep the oxygen from growing to the point where life hits a stagnant and unfruitful plateau? We will see the answer next.

The changes in acidity reflect the changing fortunes of the oxygen-producing biological material in the oceans. When the bacteria thrive they produce an over-supply of oxygen which poisons the environment and causes the bacteria to die out. When the over-supply is absorbed by reduced salts, the bacteria recover and once again over-produce oxygen. Ultimately the problem is that there is not enough oxygen-consuming biological material to provide a biological balance: the arrival of eukaryotes will resolve the imbalance. This is the subject of the next chapter.

Figure 7
Banded Iron Formation
iron oxide (Fe2O3) = dark
and silica (SiO2) = light.

The Appearance of Dry Land. For the first two billion years, the earth had no permanent dry land. Frequent volcanoes caused ashes and debris to form volcanic cones that would penetrate the ocean surface, but these cones were not permanent because storms and tidal activity eroded them over time. The final result of these temporary penetrations of the ocean surface was the formation of extensive shallow tidal areas that became homes for extensive shallow-water species including the cyanobacteria and other bacteria that formed extensive beds containing stromatolytes.

When the earth cooled from a molten state, its interior formed strata (Figure 8), with a heavy nickel-iron core mixed (and kept hot) with a low concentration of other heavy radioactive metals and their daughter products. Layers below the crust are in a plastic or semi-liquid state, maintained by pressure and radioactive heat[FOOTNOTE: Without radioactive heating, the Earth's interior would have cooled because of radiation to space, over a time on the order of a hundred million years. This realization was a great puzzle to scientists until the discovery of the heating potential radioactive decay in the early 1900s. See Lord Kelvin [GET REFERENCE]]. The layered structure of the earth has been confirmed by analysis of global acoustic sound transmission (seismology) conducted over many years. The most recent analyses use a form of tomography (similar to the techniques used in medical imaging) to reconstruct the form of the interior.

Figure 8
Earth Layers
Source: Wikipedia

The interior heat gives rise to convection currents in the Earth's Mantle, energized by the heat emitted by the (semi-solid) core (Figure 9a). These currents carry along the earth's crust, which fractures at collision and separation points.

MantleConvection.gif tectonic-currents
Figure 9A
Mantle Convection Currents
Figure 9B
Present Day Currents

The earth's crust broke up into a number of large plates that were carried along by subduction currents in the mantle (Figure 10). These collided, causing one plate to pass under an adjacent plate. This is called subduction. The edges of the plates that end up underneath in the collision are carried along by the mantle currents deep into the mantle itself. As this happens, the sinking edges of the plates melt from the heat. Material with a lower melting point melts first. This also happens to have a lower density, and as it melts, it rises through cracks, leaving heavier, denser matter behind. Over time the lighter material forms the continents which, because of their lower density, literally float atop the mantle. As the continental mass builds up, it rises above the ocean surface and the result is permanent dry land. This process is called plate tectonics[FOOTNOTE: For an interesting account of plate tectonics, see "Plate Tectonics in a Nutshell" by the U. S Geological Survey.].

An example of this subduction is along the western coast of South America, forming over time the South American continent and the Andes mountains.

Figure 10
Source: USGS

Figure 11 shows a map of the tectonic plates at the present time. Volcanic activity tends to follow the plate boundaries.

Figure 11
Present Day Tectonic Plates
Showing Active Volcanic Zones
From itsyourexperiment08
Where mantle currents diverge, the crust separates, causing newly formed crust to form under the oceans. The mid-Atlantic ridge is an example of such a divergence. The newly formed material is basalt. Recently formed material (within the past 600 Ma) 
underlays most of the ocean floor. It is denser than continental rock.


CREATION DAY THREE: Dry Land and Land Plants
Creation Day 3
Genesis 1:9-13 (ESV)


9 And God said, “Let the waters under the heavens be gathered together into one place, and let the dry land appear.” And it was so. 10 God called the dry land Earth, and the waters that were gathered together he called Seas. And God saw that it was good.

11 And God said, “Let the earth sprout vegetation, plants yielding seed, and fruit trees bearing fruit in which is their seed, each according to its kind, on the earth.” And it was so. 12 The earth brought forth vegetation, plants yielding seed according to their own kinds, and trees bearing fruit in which is their seed, each according to its kind. And God saw that it was good. 13 And there was evening and there was morning, the third day.

DAY THREE.  The geological record shows that the creation of dry land began around 2 Ga. with the formation of what would become the continents. The geological record agrees completely with the Genesis account in the fact that the earth was initially covered with water and that the dry land was made to appear out of the waters. This happened by forming the continents of less dense granites and other materials by the process of fractionation that is described above. Both the less dense continental rocks and the denser magma that forms ocean floor and underlays the continents float together on the fluid mantle with the result that the continents rise above the ocean surface much as icebergs float on the oceans. This is a physically stable and permanent arrangement. The opposing tendencies of weather and water erosion and dry land formation achieved an equilibrium by about 600 Ma, and then the  tectonic plate movements gradually moved the continents to the present configurations forming the seas, all of which connect with each other into a single watermass.

The tectonic forces that create the continents also lead naturally to the formation of mountain ranges along the collision lines of the plates (and abyssal depressions where they separate). The mountain ranges have a beneficial effect in climate control since the prevailing westerly winds precipitate rain as they rise over the mountains.

The "earth sprouting vegetation" -- creation of seed plants, fruit trees, etc., was a long process that started with microscopic life but the full-fledged creation of air-breathing plants: grasses (a more literal translation of "vegetation"), and eventually fruit trees, required one major innovation, namely the ozone layer in the high atmosphere, to shield exposed plants from damaging cosmic rays. This layer began to form once the oxygen content of the atmosphere stabilized at around 20%, but it took until about 300 Ma to develop fully. Thus the second half of the creation recorded in Day Three really took off by around 300 Ma, and overlaps with the creation of sea animals in Day Five.



Energies for Biological Reactions (at 300°K)
~7.3 Kc/Mole
Removal of the third phosphate group by hydrolysis: ATP + H2O → ADP + Pi
This is the standard source of energy for most bioloical activity. Pi denotes an inorganic phosphate (-PO4). The exact energy depends on the particular reaction. See Alberts et al. Essential Cell Biology, Ch. 3 p.96ff.

H2 -> 2 H+

O2 -> 2 O+
Most reactions that break down Oxygen take less energy than indicated here because they exchange the oxygen bond for other bonds.

N2 -> 2 N+ 225.94
Nitrogen has one of the highest bond strengths. As a result, nitrogen fixing is a very energy-intensive process. The usual end product of nitrogen fixing is ammonia (NH3).
N2 -> 2NH3 420
(Source: WIKI)

room temp
10 μm (mid-infrared) Thermal energy (300°K)

Space UV
100 nm
visible light

Source: Wikipedia Article,  Bond dissociation energy (Bond Strength); Handbook of Physics and Chemistry,  (60th Ed 1980) Bond Strength of diatomic molecules, table 1, pg F-220ff.
* Morowitz, Table 12.
Note: 23.065 Kc/Mole = 1.000 ev.

Archaeobacteria are more advanced than Bacteria.

One argument against the view that archaeobacteria were the first form of life is that archaeobacteria appear to be more advanced than other bacteria. For example, the ribosomes of archaeobacteria look like eukaryotic ribosomes and they differ considerably from bacterial ribosomes, as shown in the following sketch[FOOTNOTE: Source: Margulis, Kingdoms and Domains, p59].

RibosomeShape.gif NASA/JPL-CalTech

TODO: Compare the ribosome construction and function.



Bruce Alberts, et al. Essential Cell Biology: An Introduction to the Molecular Biology of the Cell (1998),
David C. Bossard, A Fit Place to Live. (2003)
Wallace S. Broecker, How to Build a Habitable Planet (1985)
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
Robert Hasselkorn, The Cyanobacterial genome core and the origin of photosynthesis (Proceedings of the National Academy of Sciences, 2006)
D. T. Johnston et al, Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age (Proceedings of the National Academy of Sciences, 2006)
Lynn Margulis and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The most recent edition of this work has been renamed Kingdoms and Domains (2009) by Lynn Margulis and Michael J. Chapman.
Harold J. Morowitz, Beginnings of cellular Life, Yale University Press, (1992).
J. Willliam Schopf, Cradle of Life: The Discovery of Earth's Earliest Fossils (1999).
Peter D. Ward &  Donald Brownlee, Rare Earth: Why Complex Life is Uncommon in the Universe. (2000)


mailbox Any comments or suggestions are welcome. Please email:


Prepared May, 2010