In Celebration of Psalm
God's handiwork in Creation
7: A Fit Place For Life:
of the Earth for Advanced Life01
NOTE: Ba (Ma) = Billions (Millions) of
years before the present time. By (My) = years of lapsed time.
Chapters 5 and 6
the state of the
around 3.9 Ba, when it first became able to support a
primitive sort of
life. Very quickly, bacterial life appeared in all of its essential
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 changes. These changes are the subject of this
prepared the earth for the next great innovation: the
"proper" nucleated (eukaryotic)
cell, which is the basic building block for all advanced life -- the
plants and animals.
The preparation involved these things:
• The gradual change from a
reducing to an oxidizing atmosphere. At the start, the
atmosphere had very little free oxygen; at the end, the atmosphere had
about 20-25% oxygen content, and has remained at that level since. Essentially
all of the
oxygen in the atmosphere originated as a "waste" product of the
• The corresponding change from an
ocean and outer surface crust of reduced to oxidized minerals and salts.
the start, "raw" or partially oxidized metals and minerals
dominated (iron, for example), but at the end fully oxidized
minerals dominated (iron and uranium oxides, for example).
Advanced life, particularly
multicellular life, requires the
abundant availability of oxygen: there is no alternative to this. In
practice this meant that the reducing environment of the early earth
had to be transformed to an oxidizing environment. This took a
protracted period of time because the oxygen produced as a waste
product of early bacteria was immediately used
to oxidize nearby
early life was limited to single-celled bacteria which could thrive in
a non-oxygen atmosphere, and this condition continued until the
dissolved minerals in the ocean and on the surface of the earth's crust
were largely oxidized, after which oxygen could finally build
up in the atmosphere. At this point oxidizing bacteria and advanced
eukaryotic life could (and did) form and flourish.
• The global distribution of
biological material and wastes. At the start, no organic
material existed (of course); at the end, biological material abounded
throughout the earth's oceans and outer surface crust. In particular
this material included "fixed"
(biologically available) nitrogen, usually in the form of organic
molecules. Although fixed nitrogen may be inorganic when in the form of
nitrates or ammonia, the early Earth had very little of it, and so
virtually all of the fixed nitrogen was produced from
atmospheric nitrogen by specialized anoxic bacteria in a slow and
process of biological nitrogen fixing. Once fixed and incorporated into
biological molecules, it became available as food for subsequent
generations of life. The protracted preparation of abundant fixed
nitrogen worldwide, required most of the long timespan of this two
billion year era.
• The creation of permanent dry land.
The early earth was covered with a global
ocean -- hundreds
of feet deep -- so the first life lived in a water medium, and since
the ocean was global, life and its products diffused throughout the
oceans 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 due
to violent tides and weather so that for many millions of years there
was nothing resembling permanent dry land. 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. These shallow
tidal zones became the home of photosynthetic life which derived its
metabolic energy from the Sun.
Eventually, dry land (the continents) arose out of the global ocean as
result of tectonic plate movements. Tidal forces of the
nearby moon provided the energy for these tectonic movements.
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 rock older than 3.5 Ga exists, and even
fewer locations where such ancient rock has been preserved in a way
that might preserve fossils. A small amount
of such rock exists in Western Australia, Eastern South Africa near
Swaziland, and in the western margin of Greenland.
Without actual fossil evidence it is (probably) not possible to
identify the very earliest bacterial life. However, living matter
leaves evidence in rocks that show a greater than normal amount of the
carbon isotope C-12 relative to the isotope C-13. This preference for
C-12 is traced to the selective bias of the molecule RuBisCO (perhaps the
most abundant protein on earth), which fixes atmospheric CO2
as part of the sugar production cycle in living matter02.
evidence for life goes back as far as
actual fossils are closely dated to 3.465 Ba ± 5 Ma, discovered
by J. William Schopf03.
This close dating
is possible because the fossils
are sandwiched between lava flows containing zircon crystals that can
be precisely dated.
These early fossils appear in chains as depicted in Figure 104.
Sketch of earliest fossil (3.465 Ba)
appear to be chains of
called blue-green algae. A
typical modern example is Anabaena, see Figure 205.
Photograph of Anabaena,
a modern Cyanobacteria06
Sketch of a
The First Fossils.
Preservation of the earliest
fossils through almost 3.5 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. 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.
species that live in
bathed in light, such as in shallow bodies of water. They are the only
bacteria that produce oxygen as a waste product07
-- which is an important task of this early life. They are
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
to remain attached (Figure 2b). They secrete a kind of mucilage or
to form characteristic multi-layered dome-like structures called
that grow in highly saline tidal basins -- shallow water between high
and low tide. Living
exist today in only a few locations worldwide, one being Hamelin Pool
Western Australia (Figure 3).
Location of stromatolytes
Stromatolytes at Hamelin Pool
Photo by Martin W.
used by permission
these fossils are cyanobacteria (or closely related ancestors), 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 species08.
bacteria and not
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
there are some good reasons to doubt that archaea could "be fruitful
multiply and fill the earth" [Gen. 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
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 -- oxygen-producing cyanobacteria (or close ancestors) -- and
as a matter of fact, these were the first fossils
preserved in the fossil record.
From the point of view that the main task of early life was to form a
fit place for later life, it is significant that no known archaea
species conduct photosynthesis or have oxygen as a waste product, and
so they would be unable to convert the initial reducing environment to
an oxidizing environment, required for advanced life.
Regarding the appearance of
the first life, Alexandre Meinesz, How Life Began: Evolution's Three Geneses
refers to "the strange fact that the ancestral bacteria were already
highly diversified" when the first fossil evidence was found. He then
currently popular idea that life probably arose in warm subsurface
waters along a mid-ocean ridge, the kind of environment where a great
variety of heat-resisting bacteria thrive today, is a hypothesis
without any scientific basis." p.30. Meinesz also cites the syposium Size Limits of Very Small Microorganisms
mentioned in Chapter 6.
Why does animal life
Plants don't require oxygen???
the mitochondria in (most?) animals uses oxygen to form ATP, the major
energy molecule in all cells. Anoxic cyanobacteria (as well as green
plants) derive energy from the Sun by photosynthesis to form ATP
(producing oxygen as a waste product).
life was doomed to remain quite simple; each cell was forced to be
chemically self-sufficient. Only when O2
became available was there a means of transporting chemical energy to
specialized cells. O2 and organic molecules
travel together through blood vessels to the site where energy is
needed. Here an enzyme triggers combustion. Given an atmosphere with O2,
animal life took off, evolving everything from mosquitoes to dinosaurs!"
for advanced life.
The rapid multiplication of the early species of life was needed to
prepare the earth for more advanced species. Almost two billion years
separate the first bacterial fossils and the first eukaryotic fossils
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 animal life cannot take the time or energy to be
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 combustion08.1.
- In particular, this food provides fixed nitrogen, which is essential
for all of life -- including so-called "autotrophic"
plants. Its manufacture from atmospheric nitrogen is a
difficult, energy-consuming and slow process. No eukaryotic
species (plant or animal) is able to manufacture nitrogen (except that
some plants -- the legumes for example -- have a symbiotic relationship
with nitrogen-fixing bacteria). In fact, very few bacteria
species are able to manufacture all of its own requirements for
nitrogen, and even these require cell specialization.
The nitrogen may be either organic or inorganic (in the form of
nitrates or ammonia gas) but the sources of inorganic nitrogen (prior
to the Haber
process, first used by Germany during
WWI to produce ammonia on an
industrial scale) are not sufficient to support abundant life.
These tasks took almost two billion years to achieve, with the aid of
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.
the first living species. Cyanobacteria
are the only known bacteria that produce oxygen by photosynthesis. They
were apparently the bacteria of choice in the task of oxidizing the
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
in such ancient species is something that evolutionary
theory would not have predicted.
using solar energy to energize life processes -- involves interactions
between many individually complex molecules, some of which are not
fully understood today.
the use of a membrane that encloses an acidic interior
(excess H+) to drive the production of ATP -- the universal
energy storage "battery" in all living species. The chlorophyll and ATP
synthase molecules are embedded in this membrane09.
Overview of Photosynthesis
Shown in a plant chloroplast.
In cyanobacteria the same process
is embedded in the thylakoid
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 expected result of random processes.
According to an
analysis of the cyanobacterial genome (Haselkorn and
) 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 design09a
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 (see footnote 4)
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
two parts: the light process
process. In the light
process, chlorophyll uses the energy of
sunlight to produce ATP and NADPH. Each of these
complex molecules: ATPsynthase (a molecular motor described in Chapter 6) and NADP
reductase. Protons are fed into a closed
membrane by splitting a water molecule (using a light photon for
energy) into two protons and oxygen, which is a waste product. This is
called Photosynthesis-II (PS-II). A separate process, involving two
pumps protons from the
membrane exterior to its interior (see Figure 3a). The
ATP Synthase motor molecule is embedded in the membrane and a proton
flow from the interior rotates the molecule, producing ATP from ADP. A
second photon-energized process called Photosynthesis-I (PS-I) uses an
enzyme ferredoxin-NADP Reductase to form NADPH which carries the excess
H to the dark process.
process, also called the Calvin cycle then
uses both ATP and NADPH 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.
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. See the Light
Photosynthesis: Dark Process
5 of 6 triose sugar-phosphates
re-used in the cycle. All cyanobacteria use the Calvin cycle.
chlorophyll molecule of
species captures light
energy using a special ring structure that has a magnesium atom
suspended between four nitrogen atoms. When light hits this structure,
it emits a high energy electron that initiates the
The photosystems PSII and PSI have slightly different chlorophylls, P680 and P700 which are "tuned" to
peak response at slightly different light wavelengths -- 680nm (yellow)
and 700nm (orange) respectively.
Both chlorophylls have the same ring structure centered around a
Magnesium atom. The structural difference between these two
chlorophylls is in the tail, producing (when stimulated by light) the
strongest biological oxidizer (P680) and strongest biological reducer
The hydrophobic tail is embedded in a membrane.
The magnesium complex captures light.
|The Myth and the Reality of "Horizontal Gene Transfer"
|The concept of "horizontal
gene transfer" (HGT) is frequently invoked in explaining the
appearance of highly conserved genes and gene packages in widely
diverse bacterial (and even eukaryotic) species.
HGT is a well-known phenomenon and is a common way in which genes are
transferred between bacteria of widely diverse species, and indeed on
occasion between bacteria and eukaryotes. This mechanism has been
observed in the laboratory and appears to be regularly used, for
example, to propagate immunity of various types between bacteria. The
specific types of HGT include the incorporation of genetic material
from ingested food, transfer through a viral intermediate, and transfer
by bacterial conjugation.
Horizontal Gene Transfer by Conjugation
This is a way to explain why the same genes show up in widely diverse
species. To a person who accepts the reality of a divine Creator, this
mechanism may be one way that God re-uses previously created gene
packages in the creation of new species. Or, God may simply repeat a
successful gene package by fiat. There is probably no easy way to rule
one way or the other.
One reason to postulate lateral gene transfer is to note the low
probability that the genes could have arisen independently by chance.
The lower this probability, the more likely that gene transfer of some
sort occurred, according to evolutionary thinking. So,
invoking the mechanism is a way to get around the low probability of
the genes arising repeatedly by chance. This natural mechanism does not
explain how the gene packages came about in the first place, a
vanishingly low probability chance event.
Carbon and Nitrogen Fixing. One
of the first problems that had to be solved by life was carbon and
nitrogen fixation. This means that the carbon atom, C, and the nitrogen
atom, N, had to be converted from the inorganic gases carbon dioxide
and nitrogen, and incorporated into an organic molecule. In the case of
nitrogen, this conversion usually involves the formation of ammonia (NH3)
gas or a nitrate such as sodium or potassium nitrate, which are not
found in adequate or reliable amounts in the early reduced
environment. Once reduced and placed into an organic molecule,
atoms can be passed on as food for future use. The problem is to
fix the carbon and nitrogen in the first instance.
The solution to the problem of carbon and
nitrogen fixation is two
complex molecules. Carbon is fixed using RuBisCO, a large and
complex catalyst -- incorporated into the sugar-formation Calvin Cycle
of photosynthesis -- that is the most common protein on earth: it is
estimated that RuBisCO accounts for about 50% of all the protein on
Nitrogen is fixed using Nitrogenase, also
a large and complex catalyst -- a molecular motor -- that is perhaps
the rarest of the essential molecules for life: one author estimates
that "The entire world's
supply of nitrogenase could fit into a single large
beaker or bucket."13
carbon and nitrogen fixation are very slow
processes, in comparison with the rate of most life processes. RuBisCO
converts only 2-3 carbon atoms per second, and Nitrogenase is even
slower: 1.2 seconds per fixed nitrogen molecule. Because of its
abundance, the speed of RuBisCO is not a critical factor in the
survival of life, but the rarity of nitrogenase combined with its slow
speed is another matter: the yearly production of fixed nitrogen
accounts for no more than 10-20% of the annual requirement (op. cit. p84) -- hence the need for
a large reserve of organic food to supply the deficit.
Carbon Fixing with RuBisCO. The
RuBisCO molecule is a
large and complex molecule that catalyzes carbon fixation
-- the extraction of C from
atmospheric CO2 -- and adds it to enlarge a
carbon chain as
part of the formation of a sugar-phosphate (trios-phosphate - G3P)
molecule. The enzyme aldolase
then combines two G3P molecules to form fructose sugar - C6H12O6.
Sugar molecules are the
basic "food" for the formation of
many carbon chains in
numerous cell processes.
The RuBisCO molecule
The RuBisCO enzyme
is a protein consisting of
two subunits: the
smaller is made up of 123 amino acids, and the larger has 475 amino
acids. The precise mechanism by which the enzyme works is not fully
understood. RuBisCO is certainly one of the oldest enzymes, and it is
the most abundant. It is responsible for the preferrence of living
material for C-12 over C-14. This relative abundance marker is the
earliest evidence of life on earth -- appearing around 3.9 Ga.
Nitrogen Fixing with
Nitrogenase. Microbes that fix nitrogen are called diazotrophs14.
nitrogen made up about 80% of the ancient earth's atmosphere, it was
not "available" to living species. 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."15
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.
a "Design Flaw" of Evolution?
|In 1999 a classroom
handout titled Improving RuBisCO in Photosynthesis
argued that RuBisCO is "the most inefficient enzyme known to man" with
the implication that this is another example of a suboptimal product of
evolution. The alleged problem is that RuBisCO is slow and
indiscriminately wastes energy: "the reaction leaves a great deal of
free energy," concluding that
|"RuBisCO has the
potential of becoming a more efficient enzyme in
the process of photosynthesis. If researchers are able to find
improve the abilities of the enzyme, then plants can grow faster and
increase the amount of food available. It will only be a matter
time before RuBisCO is engineered to be more efficient and the whole
world will reap its benefits."
The commercial value of a more efficient RuBisCO is evident: if its
efficiency could be increased, crops would be much more productive.
What has happened in the 12 years since 1999? very little. Subsequent
papers remain hopeful, but always project improvements into the future,
and cite little in the way of actual results. In 2010, Biofuels
|Slow, dim-witted RuBisCO. Though
abundant, it is a slow, dim-witted enzyme if ever there was one. So
slow that it fixes just three carbon molecules per second, and so
dim-witted that it has trouble distinguishing between oxygen and CO2.
Under many conditions, it will fix oxygen instead of CO2, in
a process called plant respiration which causes carbon loss and robs
the plant of growth opportunity."
One of the "defects" of RuBisCO is that it will process O2
as readily as it processes CO2 in a
process called photorespiration13.1.
It detracts from the carbon fixing task because it uses energy
unproductively and leads to a net loss of carbon and nitrogen. It would
seem that reducing the tendency of RuBisCO to fix oxygen would improve
plant efficiency, but this appears not to be the case (see Wiki
article). "[P]hotorespiration drains
away as much as 50% of the carbon fixed by the Calvin cycle. If
photorespiration could be reduced in certain plant species, without
affecting photosynthetic productivity, crop yields and food supplies
would increase." [ibid. -
But evidently no solution has been found after over
three decades of
intense research -- and not for lack of biofuels and other research
funding. As a
Creationist, I am tempted to predict that no solution will ever be
found, because RuBisCO is already close to maximally efficient. I won't
make that prediction, however, because I don't know God's reasons for
having things as they are.
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
molecule, which is made up of two giant proteins, must physically
and rejoin eight times, and this takes about 1.2 seconds. Today,
nitrogen fixing worldwide only supplies 10-20% of life's annual
consumption (Wolfe, op. cit.,
p. 84). The rest must come from
recycled organic food (or, in the
past century, from commercial inorganic nitrogen).
molecule, illustrated in Figure 7 has
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.
[Figure 7: Nitrogenase Molecule]
The nominal formula for nitrogen fixing by the nitrogenase molecule
+ 8 H+
+ 8 e− + 16 ATP → 2 NH3 + H2 + 16 ADP
+ 16 Pi,
Pi denotes inorganic phosphorous. This is a formal
equation: 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,
and so cannot be duplicated in the biological world.
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 (2011) the procedure
that it uses is not fully understood. In any case the process is very
slow (taking 1.2 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.
molecule is poisoned by the presence of oxygen. Thus special care must
be made to isolate nitrogen fixing from oxygen. In cyanobacteria, this
is done by the use of specialized
cells called heterocysts to fix
nitrogen. These heterocysts have thick walls and cannot perform some of
the normal tasks of the regular cyanobacteria cell; in particular they
do not have PSII photosynthesis.
is dependent on adjacent cells for a supply of food and energy (ATP),
which it needs in
abundance. In a typical low-nitrogen medium, about one in 15 cells
in a (modern) cyanobacteria chain is a heterocyst (Figure 8).
Frequently the immediate neighbor to a heterocyst is another another
specialized cell called an akinete, which can
survive under harsh conditions -- freezing,
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.
By permission of David Webb
TWO BILLION YEARS
The record of the next two billion years is literally
written in the
rocks. It is evident from ancient
rocks that the earth had a
radical change at around 1.9 Ba. This was the time that the oxygen
content of the atmosphere reached a stable level (20-25%). It also
marks the start of the eukaryotic life (the Third Genesis, the subject
of Chapter 8).
Prior to 1.9 Ba the oceans cycled
between times with large amounts of reduced iron in solution (which
implies that the oceans were acidic) and times in which the ocean
acidity dropped, resulting in the precipitation of this iron in the
form of iron oxides. These cycles resulted in the banded iron
formations in which iron oxides alternate with silicates. The
concentration of iron oxides in these bands can reach as high as
40-50%. After this time, about 1.9 Ba, these cycles gradually ended and
the ocean acidity reached a steady level. For the next billion years,
the iron "red beds"
formed from precipitation of the remaining iron
solutes, but without the characteristic banded formation, and the
concentration of iron oxides in the sediment dropped significantly:
after 1.9 Ba no further high concentration iron ores appear in the
At 1.9 Ba the
oceans and the top portions
of the Earth's crust became oxidized. Even today, the
oxidizing conditions are confined to a thin outer skin of the crust; at
no place is this skin more than a kilometer or so thick, and most
commonly it is much less than that. Below this thin skin, the crust
consists of reduced minerals. Overall, except for the atmosphere,
oceans and this thin skin, the earth is highly reduced, reflecting the
overwhelming abundance of hydrogen since primordial times17.
Life's Early Boom and
The Uranium and Banded Iron Ore Deposits. Because the
earth was starved for free oxygen, the ocean held large amounts of
reduced salts in solution, particularly iron. The "waste" 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
The Banded Iron Formations are a good example of the Silent Speech.
Through them it is possible to reconstruct the gradual build-up of
oxygen in the early atmosphere, and the change of the earth surface
from a reduced to an oxidized condition.
As oxygen content increases, the
ocean becomes less acidic. The solubility of many minerals,
including iron, silicon and uranium oxides varies with the ocean
acidity. As the acidity decreases (oxygen increases) the oxides become
insoluble and precipitate out of the water. When the acidity increases
(oxygen decreases) some of these precipitates again become soluble.
Since the solubility of the oxides are known, it is therefore possible
to infer the acidity of the water (hence the oxygen level) at the time
that they precipitated out. Thus the successive layers of mineral
deposits provide a chronological record of the rise and fall of
oxygen content of the water (and by inference the atmosphere).
The early oceans experienced (local)
changes in acidity that reflected
the changing fortunes of the
oxygen-producing cyanobacteria. When
thrived they produced an over-supply of oxygen which poisoned the
environment and caused the bacteria to falter. This over-supply of
oxygen oxidized the reduced minerals in the local ocean. If the
oxidized minerals were insoluble, they precipitated out onto the ocean
floor and removed the dissolved oxygen waste. If not interrupted, this
process would gradually lead to increased acidity, which also affected
the ocean's solubility. Eventually the reduction of oxygen ended the
bust cycle and led to a recovery of the bacteria. They again thrived,
leading to a new boom cycle.
These repeated boom and bust cycles raised and lowered the oxygen
content (acidity) of the oceans and amosphere until most of the reduced
salts and minerals in the oceans and crust surface had fully oxidized.
At that point the oxygen content of the atmosphere reached a
steady level of 20-25%.
Uranium salts were among the first to precipitate. Under
reduced conditions uranium is insoluble and stable as
uraninite (UO2). As the cyanobacteria build up oxygen waste,
acidity decreases. Under this condition, soluble uranium (U6+) from
volcanic activity, ocean vents and surface runoff enters the ocean
water. When the cyanobacteria become poisoned by excess oxygen waste,
the acidity increases and uranium oxide precipitates out to form
uranium deposits, reaching pitchblende (U3O8)
concentrations as high as 20% to 50% 18.
This continued for about a billion
years, until most of the uranium salts were fully oxidized.
billion years, silicon and iron soaked up the excess oxygen,
and the great banded iron iron ore deposits (Figure 10). The
precipitation of silicon and
iron is sensitive to the acidity
of the environment. As cyanobacterial activity produces waste
oxygen,the ocean acidity lowers. Iron oxide precipitates first, and
when acidity lowers further, the
precipitate out. Eventually the growth of oxygen in the ocean
poisons the cyanobacteria, and then the oxygen level decreases, with a
corresponding increase in the ocean acidity. These boom and bust cycles
can be seen in the banded iron formations. Immediately
a potential problem arose:
oxygen is generally
poisonous to the bacteria that are the only life on earth. As long as
were minerals to draw off the excess oxygen, things could go on. But
the earth's crust is fully oxidized. What is going to keep the oxygen
growing to the point where life hits a stagnant and unfruitful plateau?
Banded Iron Formation
iron oxide (Fe2O3) = dark
and silica (SiO2) = light.
About the same time that the The
banded iron formations
ended and most of the reduced elements in the ocean and
exposed crust are
oxidized, the next great biological invention -- eukaryotes --
appeared on the scene (the subject of the next chapter). The eukaryotes
(and some oxygen metabolizing bacteria) took over the role previously
held by the reduced elements, and used the excess oxygen that was being
generated. A stable equilibrium occurred at about this time, and
the oxygen level rose to a fairly stable
20-25% level in
atmosphere, where it has remained ever since. The stability is the
result of an ecological balance between oxygen-consuming and
carbon dioxide-consuming species of life.
Appearance of Dry Land.
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 stratified (Figure 11). Gravity tended to place the heaviest
material to the core and ligher materials in concentric shells with the
lightest material on top. The core is heavy nickel-iron core mixed
hot) with some heavy radioactive metals and their daughter
products. Layers below the crust are in a plastic or semi-liquid state,
maintained by pressure and radioactive heat19.
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
techniques used in medical imaging) to reconstruct the form of the
interior heat in combination with the tidal
forces of a nearby moon resulted in convection currents in the Earth's
Mantle, energized by the heat emitted by the (semi-solid) core (Figure
12a). These currents carry along the earth's crust, which fractures at
collision and separation points.
Mantle Convection Currents
Present Day Currents
crust broke up into a number of large plates that were carried along by
the convection currents in the mantle (Figure 13), which collided,
one plate to
pass under an adjacent plate. Most of the world's volcanoes lie along
the edges of these plates.
When plates collide, one plate rides over its neighbor and the neighbor
is forced down into the mantle, a process called subduction. The edges
the subducted plates are
carried along by the mantle currents deep into the mantle itself. As
this happens, the leading edges of the subducted plates melt from the
with a lower melting point melts first. This also has
a lower density, and as it melts, it rises through cracks, leaving
denser matter behind. Over time the lighter material forms the
continents which, because of their lower density, literally float atop
the mantle and crust.
continental mass builds up, it rises above the ocean
surface and the result is permanent dry land. This process is called plate tectonics20.
Volcanic activity tends to follow the plate boundaries.
An example of subduction is along the
western coast of South America (Figure 14), forming over
the South American continent and the Andes mountains.
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, both Atlantic and Pacific,
and is denser
than continental rock.
Dry Land and Land Plants
THE GENESIS ACCOUNT
Creation Day 3
Genesis 1:9-13 (ESV)
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
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.
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
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
The tectonic forces that create the
continents also lead naturally to the formation of mountain ranges
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.
Reactions (at 300°K)
of the third phosphate group by hydrolysis: ATP + H2O → ADP
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
-> 2 H+
-> 2 O+
reactions that break down Oxygen take less energy than indicated here
because they exchange the oxygen bond for other bonds.
-> 2 N+
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).
(mid-infrared) Thermal energy (300°K)
Wikipedia Article, Bond
dissociation energy (Bond Strength);
Handbook of Physics and Chemistry, (60th Ed 1980)
of diatomic molecules, table 1, pg F-220ff.
* Morowitz, Table 12.
Note: 23.065 Kc/Mole = 1.000 ev.
|Archaeobacteria are more advanced than
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,
TODO: Compare the ribosome construction and function.
Natural Nitrogen Cycle
contribution of lightning and volcanic activity to the
natural nitrogen cycle is not shown in Figure 15 because it contributes
very little to the cycle.
| The First Living
Species -- Fixed Nitrogen
experiment (1952) showed that some amino acids could be produced in
a strongly reducing atmosphere containing hydrogen (H2),
methane (CH4), ammonia (NH3) and water with
lightning providing the energy source. Since that time, the consensus
in science is that the primordial environment included only traces of
Nitrogen is an essential component of all life
molecules -- indeed all
nucleotides and amino acids contain nitrogen atoms, so life can't even
build its most basic parts -- genes and proteins -- without an
abundance of available
nitrogen. Nitrogen gas (N2) is not available for use by living
cells because the bond that holds together the nitrogen atoms into the
molecule cannot be broken by any normal cellular processes.
From the very start, living cells had to include
specialized cells that
could fix nitrogen, because a reliable supply of available nitrogen was
simply not present in the environment. In archeal times, lightening did
not produce nitrates (one of the major nitrogen products of lightening
today) because of the lack of oxygen in the early atmosphere.
fixing is the name of the process used to break up the nitrogen gas
molecules into ammonia which then is available for use by living cells.
Nitrogen fixing is a very energy-intense process, and there is only one
way to do it in a living cell: using a process that involves a very
complex molecule, nitrogenase.
This process is so intensive that nitrogen-fixing cells are specialized
to do just this one task, and must receive food produced by other cells
in order to do the work. These cells also have to be isolated from
other cellular processes because the nitrogen fixing process can be
poisoned by the waste products of other cellular activity --
particularly by the presence of oxygen. At the heart of the nitrogenase
molecule is a molybdenum atom, which is an example of a rare element
heavier than iron (Atomic number 42) that is essential to life.
of the Early Earth Environment
1. Very little free oxygen.
The first living species were anoxic. Oxygen is needed by all higher
2. Very little available nitrogen.
The first living species had to fix nitrogen from atmospheric nitrogen
gas because there was no reliable supply of ammonia (NH3) or
3. No organic food. The first
living species were autotrophs. The vast majority of species require
parts of their diet to be organic -- these are the molecules that the
species cannot prepare themselves. A major component of this organic
food includes amino acids, sugars, and other compounds that contain
free nitrogen. All advanced species require this food because their
energy budget is not extensive enough to prepare all of their needs
from scratch in a timely manner. True autotrophs -- species capable of
living on purely inorganic matter -- necessarily use excessive energy
in making food, and they do this slowly and laboriously, leaving
nothing over for more advanced tasks.
4. No stable dry land.
Why I Cannot Accept Undirected Natural
Evolutionists in the trandition of Charles Darwin
universally claim that evolution of all living species came about by
purely natural causes. Some Christian scholars accept a (slightly)
modified version of this, usually called Theistic Evolution, which
accepts the general Darwinian Thesis but adds God as a sort of
prime-mover who fixed the parameters of nature in the beginning, but
then let things evolve naturally from that point on. These "Theistic"
evolutionists join the secular evolutionists in loud condemnations of
"Intelligent Design" or any other means by which God may inject himself
into the unfolding of natural Evolution.
I find it difficult to
accept this concept of undirected natural evolution, for the following
reasons, both theological and scientific:
1. The Bible clearly portrays a God who constantly
"interferes" with his creation. Jesus constantly asserts that God
actively cares for his creatures, and the very essence of his Salvation
plan involves deliberate and directed arrangement of human affairs to
bring about the culmination -- the death and resurrection of Jesus
Christ as our redeamer and Messiah. It is impossible to read the Bible
in any way that would imply that God is a "hands off" creator.
2. I question whether it is possible for some of the essential steps in
the creation of modern complex life to be done by natural means. What
evolutionists accept as "proof" of evolution is to present some "just
so" stories about how things occur. What is lacking is laboratory
The lecture A Fit
Place to Live
relates to this chapter. See also the
and highly readable book by J. William Schopf, Cradle of Life (1999).
The biological classifications used in this and following chapters
follow the nomenclature established by
Margulis in Kingdoms
and Domains (2009).
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.
I call eukaryotes "proper cells" which will be the subject of the next
chapter. Kingdom Archaea consists of bacteria-like species that
have a number of special features and are further discussed here.
^n02 Even the earliest living species had to
manufacture sugars, because they are part of the DNA spiral backbone.
RuBisCO is involved in virtually (??)
all known sugar production
in cells. Q: Does the early evidence for RuBisCO imply that
photosynthesis was equally early?
Ibid., Fig. 3.4 for
Robert Haselkorn states, based on
sequencing of cyanobacteria, that "We propose that the first
phototrophs were anaerobic ancestors of
cyanobacteria (“procyanobacteria”) that conducted anoxygenic
photosynthesis using a photosystem I-like reaction center, somewhat
similar to the heterocysts of modern filamentous cyanobacteria. From
procyanobacteria, photosynthesis spread to other phyla by way of
lateral gene transfer." -- Abstract to Robert Haselkorn, et
Cyanobacterial genome core and the origin of photosynthesis
(PNAS, 2006). This tends to support the identity of cyanobacteria as
the earliest photosynthetic bacteria. The remark on "lateral gene
transfer" implies that the genes for photosynthesis were likely created
only one time, at the very earliest stages of life on earth, and then
were re-used by other photosynthetic bacteria. A further remark in the
body of this paper states, "Cyanobacteria are usually not considered
explicitly as a lineage in which photosynthesis could have emerged
because of the far greater complexity of their photosynthetic
machinery. This fact, however, can be interpreted both ways. Indeed,
the total number of genes involved in photosynthesis in cyanobacteria
is much greater than that in any of the other prokaryotic phototrophs
(Table 1). Only cyanobacteria possess photosynthetic reaction centers
of both types, RC1 and RC2, and, in addition to chlorophyll- and
phycobilin-containing light-harvesting systems, have
chlorophyll-binding proteins whose function is believed to be
dissipation of light energy to prevent photodamage (HLIPs; see Table
1). Thus, the majority of
photosynthetic genes must have first appeared in the cyanobacterial
lineage anyway [emphasis added -- dcb]."
by permission. For discussion of Anabaena Cyanobacteria see Lynn
and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to
Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The most
recent edition of this work has been renamed Kingdoms and Domains (2009).
op. cit. "Cyanobacteria are
the earliest branching groups of organisms on this planet. They are the
only known prokaryotes to carry out oxygenic photosynthesis, and there
is little doubt that they played a key role in the formation of
atmospheric oxygen ≈2.3 Gyr ago."
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."
^n08.1 William H. Schlesinger, Biogeochemistry: An Analysis of Global
Change 2nd Ed, (1997), p. 36, "[I]t is interesting to note the
significance of an atmosphere with 21% O2.
Lovelock (1979) points out that with <15% O2
fires would not burn, and at >25% O2
even wet organic matter would burn freely (Watson et al. 1978)."
[MAYBE add chart of Evolution of the Atmosphere: Cumulative history of
O2 by photosynthesis over geologic time. Cf
chart is very small!]
Manfred Schidlowski, A 3,800-million-year isotopic record of
life from carbon in sedimentary rocks, Nature 333:313-318
(1988). Abstract: "An increased ratio of 12C to 13C, an indicator of
the principal carbon-fixing reaction of photosynthesis, is found in
sedimentary organic matter dating back to almost four thousand million
years ago—a sign of prolific microbial life not long after the Earth's
formation. Partial biological control of the terrestrial carbon cycle
must have been established very early and was in full operation when
the oldest sediments were formed."
the box on Motor Molecules
(Chapter 6) for an illustration and discussion of ATP Synthase. A
simplified cartoon of the molecule is shown in Figure ??. View an
animation of ATP Synthase by Donald Nicholson (Leeds University) here,
and the John Walker (Cambridge) animations here.
ATP Synthase Molecule
^n09a Proceedings of the National
Academy of Scientists: "According to an analysis of the cyanobacterial
genome (Haselkorn 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." Cyanobacterial genome core and the Origin
of Photosynthesis (2006).
^n10 From Virtual Cell Animation
Collection which has a number of animations of cellular processes.
Oxidized P680 (P680+) is "the strongest biological oxidizing agent
known", which makes it possible to oxidize water in photosynthesis (Wiki). P700 with a
photon-excited electron is "the strongest biological reducing agent"(Wiki).
^n11 For further
information about photosynthesis
in cyanobacteria, Haselkorn, op. cit,
and the Arizona State University photoweb.
^n12 Wikipedia article on RuBisCo. See also the
Sharepoint article, Improving RuBisCO in Photosynthesis,
abstract: "RuBisCO is the most abundant protein on Earth that triggers
reactions to make carbohydrates, proteins and fats used to sustain all
forms of life. ...RuBisCO is the most inefficient enzyme known to man
because it has an extremely slow reaction rate [2-3 reactions per
W. Wolfe, Tales
from the Underground: A Natural History of Subterranean Life, Perseus,
2001, p.78. "Nitrogenase is
composed of two giant
proteins that physically separate and come back together eight times
over the course of 1.2 seconds, to convert one molecule of N2
to one [sic.] molecule of
Origin of the Organic Soup,
photorespiration is called a "design flaw in photosynthesis." "Since
plants first moved onto land about 425 million years ago, they have
been adapting to the problems of terrestrial life, particularly the
problem of dehydration. The solutions often involve tradeoffs. An
important example is the compromise between photosynthesis and the
prevention of excessive water loss from the plant. The CO2
needed for photosynthesis enters a leaf via microscopic pores called
stomata. However, the stomata are also the main avenues of
transpiration, the evaporation of water from leaves. On hot, dry days,
most plants close their stomata in order to conserve water. This
response limits access to CO2,
thereby reducing photosynthetic yield. Under these conditions, CO2
concentrations in the air spaces within the
leaf begin to decrease and the concentration of oxygen released from
photosynthesis begins to increase. This favors what appears to be a
wasteful process within the leaf called photorespiration."
Wiki definition of a diazotroph
appears to be technically wrong: "A diazotroph is an
organism that is able to grow without external sources of fixed
nitrogen." In fact no organism can grow without external sources of
fixed nitrogen. In my understanding, a diazotroph (for example
a cyanobacterial heterocyst) cannot manufacture enough nitrogen to meet
its own needs. In fact, it expels fixed nitrogen as a waste product
(for use by other cells) and gets its food (including fixed nitrogen)
from other cells. See Wolfe, op. cit.
4, "Out of Thin Air" (
is a fascinating discussion of
W. Wolfe, Out
of Thin Air - nitrogen fixers, Natural History, Sept. 2001.
Note that he suggested a source of nitrogen from lightning forming
Nitrate, but this is not possible because the early atmosphere was
almost entirely oxygen-free. See 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."
^n16 Discussions of this period can be
Peter D. Ward and Donald Brownlee, Rare
Earth: Why Complex life is Uncommon in the Universe. (2000),
Wallace S. Broecker, How to Build a
Habitable Planet. (1985) p. 233ff., William H. Schlesinger Biogeochemistry: An Analysis of Global
Change (2nd Ed. 1997). Schlesinger has a figure similar to
Figure 9 on p. 37 and states "The release of O2 by
photosynthesis is perhaps the single most significant effect of life on
the geochemistry of the Earth's surface." (p.36).
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. Rutherford suggested in 1906 that radioactivity had
a potential for geological time-keeping. See the excellent review of
this in the Wikipedia article "Invention of
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)
S. Broecker, How to Build a
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
Robert Haselkorn, et
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
(Proceedings of the National Academy of Sciences, 2006)
and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to
Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The Fourth
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,
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)
Any comments or suggestions are welcome. Please email: firstname.lastname@example.org
Posted dd Mmmm 201?