Posted dd Mmmm 201?, Revised December, 2010

       

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

PART III

THE CREATION OF LIFE ITSELF

Chapter 6

The Second Genesis:
   
Creation of Bacterial Life*

 
"The chemist puts his mind at rest regarding the existence of life, just as the physicist calms his regarding the existence of matter, simply by turning his back on the problem. Thereby he suffers nothing in his practical task as a man of science01."
Lawrence J. Henderson, The Fitness of the Environment (1913) p310.

NOTE: Ba (Ma) = Billions (Millions) of years before the present time.
The material of this and the next few chapters is the subject of the lecture A Fit Place to Live.


Introduction. This chapter marks the beginning of the third part of the Creation Narrative, the creation of life and all living species.

The surprising fact is that e
vidence of life appears in the most ancient geological records. This evidence appears at the first opportunity, as soon as the Earth had formed and cooled to the point that it could host life, as early as 3.9 billion years ago (3.9 Ba). Evidence of life is present in the oldest rock formations on Earth that have (providentially) survived to the present time. This is a very limited and fragmentary record: only a few places on earth have rocks that old and these places are all small -- small portions of Western Australia, Western Greenland and South Africa.  From this point onward, the Earth's temperature has always been moderate enough to maintain life, and life has always been present, and it has expanded globally over the next billions of years to produce the vast array of living species we see today.

The earliest evidence for life is chemical evidence (discussed below), but the earliest fossil evidence came soon (in geological terms) thereafter, and that fossil evidence gives graphic evidence that the first fossil life was advanced, not primitive.

The early Earth was a formidable and hostile place for life to begin. In fact more advanced life could not live there. So the first life on earth faced formidable challenges. For one thing, there was (of course) no organic food, so the first life had to make food from inorganic matter -- it was autotrophic in the fullest sense. For another thing, the first life had to have available nitrogen, a rare and unreliable commodity on the early earth.

To get a sense of how complex even "simple" life is, this chapter looks at the most general things that all living species, however simple or complex, have to do. This includes the machinery to metabolize and to reproduce. Only features shared by all living species are considered here; later chapters consider more specialized features.

At the root of all metabolism is the genetic machinery that builds and controls the tools for metabolism. This is life's so-called Central Dogma. This leads naturally to discussion of some of the biological molecular machines that carry out metabolism -- those shared by all species.

The point of this discussion is to note the vast complexity required for even the simplest of life, a complexity that displays the glory and handiwork of God; a complexity that has only been understood and described in the past few decades.

Condition of the Early Earth
. As remarked in the last chapter, the Earth and other planets in the Solar System formed out of debris orbiting the Sun. Shortly after formation, a Mars-sized object collided with the Earth and the debris that orbited the Earth after this collision eventually formed the Moon.


Between 4.5 and 3.9 Ba many meteorites and comets bombarded the Earth and Moon causing the Earth's crust to melt and re-solidify several times. The craters on the Moon date back to and witness the intensity of this bombardment.

At about 3.9 Ba the bombardment ceased and the Earth surface temperature dropped below the boiling point of water, forming a (relatively) smooth crust under a global ocean about 800 ft. deep. The Earth's surface temperature cooled to an average of 10-25°C, where it has remained since that time02.

As the earth gradually cooled from a molten state, virtually all minerals began in reduced form because it was too hot for the chemical bonds of the oxidized forms to hold. Most of the oxygen existed in the form of water. As the earth cooled further to the point where oxidized forms could exist, any available free oxygen was quickly taken up by the reduced minerals.

In the end (3.9 Ba), the cooled earth ended up with a crust made up of reduced minerals, a very salty ocean made up of water and reduced salts, and a reducing atmosphere that had very little free oxygen. The atmosphere was composed mostly of nitrogen. water vapor and carbon dioxide
03. The crust was mildly radioactive -- about the level of radioactivity of the fuel rods used in nuclear power plants (including 3% uranium and proportionate amounts of other long-lived radioactive materials)04.


The Moon at this time was in a close orbit -- ??? miles at 3.9 Ba, receding to 206,000 miles at 2.45 Ba (compared with 238,600 miles today)05.  It is apparent that the moon became tidally locked to the Earth quite early because the opposing sides of the Moon have very different cratering as indicated in Figure 1.

Clemtine-nearside Clemtine-farside.jpg
Figure 1a
Lunar Albedo nearside

Figure 1b
Lunar Albedo farside
Source: U.S. Navy Clementine Mission (1994)06,


Violent volcano activity on the Earth, partly caused by very strong tidal effects from the nearby moon, and partly due to the continued cooling and fracturing of the crust, filled the Earth's atmosphere with a dense cloud of volcanic debris and gases. As volcanic cones broke through the ocean surface, they quickly eroded away to tidal waters (shallow ocean waters) because of the severe tides and violent storms. The tidal waters would later become the locus of early life.

All in all, the Earth at 3.9 Ba was a barren and unpleasant place (Figure 2)!

   
Figure 2
Early Earth Landscap
e
Credit: Artwork copyright 2006 Don Dixon/cosmographica.com


Evidence for the First Life. Almost immediately as soon as the Earth had cooled there is evidence that life was present. Since life certainly could not have been present while the Earth was significantly above the temperature of boiling water, this fact presents only two possibilities. Either life must have been put on Earth from an outside agency (arrived from space or by a creative act of God), or else life arose very quickly on earth itself from non-living matter.

The creation of life either on earth or in outer space by purely natural processes is an incredibly low probability event according to any conceivable method of calculation, even over the 13.7 billion years since the Big Bang, even if ours is only one of a myriad of universes. Although bacterial spores can survive in empty space, anything as complex as living matter cannot be created in space: it would require an earth-like environment somewhere in our galaxy to host the first living matter, and go through its entire life cycle before the creation of the Solar System, which itself formed at about the earliest possible time after the Big Bang08.

The earliest evidence for life on Earth comes from ancient rocks that have an overabundance of the carbon isotope C-12. These rocks appear as early as 3.9 Ba in Greenland and Western Australia. The ratio of C-12:C-13 is an indicator of biological activity because cell metabolism preferentially selects the lighter isotope of carbon when it forms biological material, thus concentrating this isotope in biological carbon deposits09.

The first fossil evidence for life on Earth is chains of cells found in Western Australia and dated to 3.65 Ba by J. William Schopf. We will discuss this evidence in the next chapter.

 Sharp Point
Life Appeared on Earth at the Earliest Possible Moment
As soon as the conditions on Earth cooled to the point that life could exist, there is evidence that life was present. This is the first instance of an often repeated refrain throughout the whole creation process of life on Earth. It indicates that, unlike the long preparation of the elements and the Solar System over nearly 10 billion years,  the vastly more complex creation of life occurred in a mere blink of time.


The Unity of Life. Life was created only once (see box). This is the conclusion of biologists who take into account both the phenomenal complexity of even the simplest life forms, and the fact that all of life exhibits the same complex genetic make-up, and appears to solve many complex issues in the same, apparently arbitrary, way: biologist Stephen Jay Gould called these contingent solutions.

Some less cautious scientists10 assume that because life appeared on earth at the earliest possible moment, life can originate many times throughout the universe. Ward and Brownlee10a, for example, distinguish between primitive life (common and widely distributed in the Universe) and "complex life"  -- advanced animal life (rare in the universe). This distinction overlooks the vast complexity of even the simplest of living species, as we will note below.

Evolutionary biologists would very much like to find some evidence of pre-cursors to this full-fledged life -- or even to show that a much simpler sort of "life" might be possible -- but there is none to be found. All life is the same, and exceedingly complex; there are no precursors, and even the nature or form of such precursors is hard to imagine11.

 Sharp Point
Life on Earth Was Created Only Once
There is only one basic life-form on Earth. That life-form has many contingent features that are shared by all living species. An independent creation of life would have different contingent features, and therefore most knowledgable biologists recognize that all living species descended from a single first living species. Present species of life did not arise from multiple independent first ancestors.
fractal

The Complexity of "Simple" life -- the Central Dogma
"DNA makes RNA makes Protein"

Every species of life on earth, from the simplest to most complex, carries out the so-called Central Dogma of molecular biology. This "dogma" is the detailed plan for how a living cell stores genetic information, how it copies that information, and how it interprets the information to form the molecules that build the cell and carry out its tasks. This plan is called a dogma12 because every living cell follows the same plan, give or take a few minor variations. The remarkable thing is that the plan is very detailed and that many of the specific ways that it performs its various tasks seem to be quite arbitrary (what Gould would call "contingent") in the sense that they might (one imagines) have been done in quite different ways. This is a major reason for the belief that life on earth arose only once.

 Sharp Point
Components of the Central Dogma
Every species of life on earth, from the simplest to most complex, carries out the so-called central dogma of molecular biology. This "dogma" is the detailed plan for how a living cell stores genetic information, how it copies that information, and how it interprets the information to form the molecules that build the cell and carry out its tasks.
The components of the central dogma are as follows:

DNA and RNA molecules record and process the genetic information in all living species. The molecules consist of a backbone built up of sugars with the genetic information attached to the backbone. The first understanding of the genetic role of DNA and RNA was discovered in the 1940s. Watson and Crick first described the structure of these molecules in 1953.

All genetic information is recorded in digital form. Every living species does this in the same way.

* The information in a DNA molecule is organized in base pairs, codons, and genes.

+ The basic information is recorded as one of four specific molecules called nucleotides. They are designated A (adenine), C (cytosine), G (guanine), and T (thymine). In DNA, the nucleotides always appear as base pairs: A pairs with T, and G pairs with C. In RNA, T is replaced by U (uracil) (see Figure 3). The structure of the nucleotides and the DNA backbone are modeled and described here.
+ A codon is a triplet of nucleotides recorded in successive positions in the DNA.
+ A gene is a sequence of codons that code for a protein. Special start and stop codons mark the beginning and end of the gene13.

DNA-Ladder.gif
Figure 3
Portion of DNA

From Wikipedia


* The DNA molecule is a long sequence of nucleotide base pairs attached to a double-helix backbone.  The pairs are placed in the DNA like rungs in a ladder with two long right-handed spirals forming the sides. In the pairs, the nucleotides on the right (in the direction of transcription) define the gene codons.

dna-structure.gif
Figure 4
DNA Helix


* The DNA molecule codons specify for amino acids which are the building blocks of proteins.

There are about 20 amino acids used in all living species, and all are left-handed (with rare exceptions). This is somewhat unexpected since natural (inorganic) processes produce left- and right-handed amino acids in equal numbers. Since it appears that life based on right-handed amino acids would work just as well, this seems to be another example of contingency, and again argues for a single original creation of life on earth.

* Each codon corresponds indirectly to an amino acids that will be used to form proteins as described below. The correspondence is summarized in a table (figure 5) which is part of the central dogma. All living species incorporate this table (with a very few species using minor variations) which appears to be quite contingent in Gould's sense of the word. There does not appear to be any deterministic or chemical basis for these particular associations between nucleotide triplets and the selected amino acids. Therefore one would assume that an independent generation of life would develop a different codon table, even if it would come up with a similar coding scheme for genetic information. This is a strong argument for the conclusion that all life on earth arose from a single life-forming event.

CodonTable.gif
Figure 5
RNA Codon Table
(Replace U with T for the DNA Codons)


* Special molecules associate each codon used in the DNA to an amino acid. These are the transfer RNA, t-RNA, further described below. Genes to produce these t-RNA molecules must be part of the genetic code recorded in the DNA. Thus the codon table is built into the DNA and is the same for all species of life.

* Complex linear motor molecules called RNA polymerases read the DNA codons for a gene, and form a messenger RNA molecule, m-RNA. This process is called transcription.

* The m-RNA molecule then moves away from the DNA and attaches to another complex molecule, the ribosome, which controls the codon translation. This is another linear motor molecule.

Ribosome.gif
Figure 6
Ribosomes and Peptide Synthesis
From Wikipedia

The ribosome is in itself an exceedingly complex compound molecule consisting of an upper and a lower part. The ribosome is the place where the codons of the m-RNA are translated into a sequence of amino acids and form a protein chain. Each codon is processed by the ribosome and adds a single amino acid to the protein chain.

The general function of the ribosomes is the same across all species, although the specific ribosome configuration varies somewhat. For an interesting description of how ribosomes work, see The Smartest Living Nanomachine. Here is one quote from the article:

"Ribosomes are found in practically identical form in every living cell on Earth, whether it be the single-celled archaea in the thermal vents of the ocean floor, the bacteria on the surface of the planet, or the cells in the human body. ... ribosomes are believed to be among the most-ancient molecular machines of life13.1."

A cell builds ribosomes from Ribosomal DNA genes. In Eukaryotes (proper cells), the nucleolus is the building site. About 150 genes are involved in the construction of ribosomes. A typical ribosome contains about 250,000 atoms. Of course ribosomes have to be constructed without the benefit of ribosomes (used to construct most other molecules in a cell). This requires additional genes, many of which do not appear in the final product. A typical cell has thousands of ribosomes.

* Translation in the ribosome requires the presence of transfer RNA molecules, t-RNA, designed for each amino acid. One end of the t-RNA has a codon from the codon table, the opposite end has the corresponding amino acid attached. The ribosome reads the codons on the m-RNA one at a time, matches the codon to a corresponding t-RNA molecule, detaches the amino acid from the t-RNA, and adds it to a building chain of amino acids that will form a protein when the chain is complete. The t-RNA molecules are released to capture another amino acid for future use.

t-RNA molecules are small -- about 74-95 nucleotides. A cell requires a minimum of 31 t-RNA types to translate all of the 64 possible codons. The lower number is possible because many codon translations are in effect defined by only 2 nucleotides: for example, from the codon table above it is evident that CUx is the amino acid leucine, regardless of which nucleotide is in the x position14.

* On completion of a protein chain, the protein folds into its final form. There is some mystery (see, for example, the waffling in the Wikipedia article) as to how this is done, since the specific folding can be critical. In general a given protein chain could be folded in many ways, but without proper folding, which occurs after the entire protein chain has been completed, the protein will not function properly.

Associated to the question of folding is the Levinthal paradox, which asserts that the "best" protein folding cannot come from any process of sampling even a small fraction of the possible folding configurations, because such an approach would be far too slow.

"Computational approaches to protein structure prediction have sought to identify and simulate the mechanism of protein folding, however these have been largely unsuccessful." -- Wikipedia.


ProteinFolding.gif
Figure 7
Protein Folding



* Gene expression depends critically on gene regulation: the methods used to determine when (or if) specific genes are to be read. Hovering over the entire information content of the DNA is an entire separate layer of this regulatory information, involving many specialized molecules and procedures to control gene blocking and gene expression.

For example, in higher species, development genes determine how an embryo evolves from the initial fertilized egg to maturity. Incorrect sequencing of events here is a recipe for disaster. Even the simplest single-celled species must follow specific sequential gene expression. To put it simply, not every gene can be expressed all the time, as rapidly as possible. There must be some imposed order provided by a mechanism for gene regulation.

In the view of some, the complexity and information content involved in gene regulation (particularly in eukaryotes) is potentially greater than the information content of the DNA itself.

The central dogma encompasses this entire sequence, which is the same (with rare minor variations) for all living cells. The genetic coding required to build and carry out the central dogma involves around 200 separate genes (about 200,000 base pairs) -- not including genes to form the amino acids
15 -- that the DNA for every species of life must include.

There is no known sequence of steps that could lead naturally to a plan as complex as the central dogma (See the box). The central dogma involves so many inter-related factors that it defies any attempt to explain how it could have been constructed by natural, undirected steps. It appears to require numerous independent complex events to occur in a tightly synchronized manner and in a single brief span of time.

Even production of a single specified gene of average size by random sampling, even one time in the entire universe since the Big Bang, is easily shown to be such a low probability event that it is impossible for all practical purposes. This is the conclusion to a symposium held by the Wistar Institute in Philadelphia in April 196616. Since that time, such combinatoric arguments for the random appearance of genes have generally been abandoned as unproductive, and no consistent alternative solution to the problem of how life appeared has gained general acceptance in the scientific community.

 Sharp Point
Even the Simplest Life on Earth is Vastly Complex
NO known natural procedure can produce such complexity.

Every species of life has the full machinery of the Central Dogma. It seems impossible to imagine how any form of self-sustaining life could exist without the whole of this complex, inter-connected machinery already in place.

The problem of how the Central Dogma could be created by purely natural processes, seems as insoluble as the question of how the density and smoothness of the primordial universe came to have its precise and essential values just after the cosmic expansion (see Chapter 3). So both the universe and life begin with apparently insoluble issues for evolution by purely natural means.

Undoubtedly future research will show how isolated  parts of the vast enterprise can be achieved naturally: for example, there may be experimental verification that a reduced codon table suffices to specify for protein amino acids in a viable life form, or that a simplified method of peptide synthesis exists. But there are two paradoxes that stand in the way of any comprehensive natural solution to this complexity. These are called Eigen's Paradox and Levinthal's Paradox. Eigen's paradox states, in effect, that functional protein changes over 100 amino acids in length cannot be produced by random natural processes. Levinthau's paradox states that complex protein folding cannot be arrived at by natural processes 17.

One can reasonably conclude that if the vast complexity of the genetic processes had been known in Darwin's day, any attempts to extend his theory to the origin of life by purely natural processes would never have been taken seriously.

Sharp Point     Error Correction Coding -- Eigen's Paradox

Eigen's Paradox is based on the observation that any naturally formed protein with a length of over about 100 amino acids must employ error correction. However (and this is the paradox) any effective error correction of a protein requires (in effect) another protein of even greater length.

Wikipedia states this as follows:
  * Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs.
  * For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."


The conclusion is:


 "Primitive organisms would not have had the ability to manufacture complicated error-correction enzymes. However without the ability to correct errors at all, early organisms would have been very limited to in the amount of information they could carry without suffering from an error catastrophe." 

Only crystal growth processes have been able to apply error correction techniques of a comparable level of complexity. "No other high-fidelity information copying process - or error correction process - outside of the products of modern biological systems - has ever been demonstrated or observed." [ibid.]

Wikipedia concludes,
"Eigen's paradox is one of the most intractable puzzles in the study of the origins of life. It is thought that the error threshold concept described above limits the size of self replicating molecules to perhaps a few hundred digits, yet almost all life on earth requires much longer molecules to encode their genetic information. This problem is handled in living cells by enzymes that repair mutations, allowing the encoding molecules to reach sizes on the order of millions of base pairs. These large molecules must, of course, encode the very enzymes that repair them, and herein lies Eigen's paradox."

One other source concludes from these observations that "Darwinism is Dead:"

"All of the above speculative notions arose because the scientific complexity of the cell was nothing Darwinism predicted or could explain. The scientific consensus is that there is no way chance could produce something so complex. There had to be, therefore, additional naturalistic answers. There just had to be. They've looked for forty years; so far, nothing. ...If random processes cannot produce even a single cell, how much more impossible is it that they produced a daffodil, a dolphin, or a man? Darwinism is dead."


Sharp Point          Protein Folding -- Levinthal's Paradox

On completion of a protein chain, the protein folds into its final form. There is some mystery (see, for example, the waffling in the Wikipedia article) as to how this is done, since the specific folding can be critical. In general a given protein chain could be folded in many ways, but without proper folding, which occurs after the entire protein chain has been completed, the protein will not function properly.

Associated to the question of folding is the Levinthal paradox, which asserts that the "best" folding cannot come from any process of sampling even a small fraction of the possible folding configurations, because such an approach would be far too slow.

"Computational approaches to protein structure prediction have sought to identify and simulate the mechanism of protein folding, however these have been largely unsuccessful." -- Wikipedia.

ProteinFolding.gif
Figure 7
Protein Folding





fractal

Complex Molecules found in all living species

Since these specialized molecules seem to be absolutely essential for the dogma to work, it seems worth noting some of them here. As far as can be determined, all of these motors (or unimagined equivalents) must be present in the very first living species.

 Sharp Point
Motor Molecules found in All Living Species

One of the amazing facts discovered in the past few decades is the extent to which a living cell uses molecular motors and other complex molecules to do even the most basic tasks.

ATP synthase. We mention ATPase first because this is a molecular motor that is used throughout the implementation of the Central Dogma, and so, to that extent, it is even more basic to all living species than the Central Dogma itself! The next chapter has further remarks on the ways that a cell uses the energy "battery", ATP.

ATP synthase (Figure 8) is a rotary motor that is powered by protons (H+) rather than electrons as in modern electric motors.

ATP-Synthase.gif
Figure 8
ATP Synthase
From Wikipedia

The proton flow arises because the atp synthase is embedded in a membrane which is more acidic on one side than the other.  A number of genes (typically 8, labeled "a" to "h") specify the various parts of the synthase: for example, M. genitalium, a parasitic bacterium with one of the smallest known genomes. Its DNA includes the eight ATPase genes designated atpA through atpH. The motor is very complex, and appears to be universal (see the box)18.

The Universality of ATP Synthase (ATpase)

"Among the questions evolutionists must answer include the following, 'How did life exist before ATP?' 'How could life survive without ATP since no form of life we know of today can do that?' and 'How could ATP evolve and where are the many transitional forms required to evolve the complex ATP molecule?' No feasible candidates exist and none can exist because only a perfect ATP molecule can properly carry out its role in the cell... In bacteria, the ATPase and the electron transport chain are located inside the cytoplasmic membrane between the hydrophobic tails of the phospholipid membrane inner and outer walls. Breakdown of sugar and other food causes the positively charged protons on the outside of the membrane to accumulate to a much higher concentration than they are on the membrane inside. This creates an excess positive charge on the outside of the membrane and a relatively negative charge on the inside [which drives the rotary ATPase motor -- dcb]."
Jerry Bergman, ATP: The Perfect Energy Currency for the Cell
in ATP Synthase: A brief Introduction.
See also John W.Kimball's on-line Biology Text, Biology Page on ATP


From the viewpoint of evolution, "The ATP synthase enzymes have been remarkably conserved through evolution. The bacterial enzymes are essentially the same in structure and function as those from mitochondria of animals, plants and fungi, and the chloroplasts of plants."
Crofts Laboratory, University of Illinois at Urbana, Lecture 10, ATP Synthase

The following molecular motors are found in all species because they are required to carry out the Central Dogma:


RNA Polymerase (RNApase). The formation of m-RNA implies the presence of a linear motor (RNA polymerase (RNAPase)) that moves along the DNA. It moves to a base pair, separates the pair, retrieves a matching nucleotide from the surrounding medium, attaches it to the m-RNA chain, and then re-connects the DNA pair as it advances ahead one base pair.

Unlike ATPase and the ATP molecule itself, the RNA polymerase that transcribes DNA has a variety of forms in a cell and varies considerably over the domain of living species. However all function as linear motors, and their functions are correspondingly complex. Life cannot exist without these complex motor molecules.

One curious fact is that archaea, the domain of bacteria that includes the so-called extremophiles as well as many autotrophs, has an RNAPase that is closer to that of eukaryotes, living species that are much more advanced than bacteria. This poses a problem of classification because the archaea are generally thought to be more ancient than bacteria (as the name implies), but their RNAPase appears to be more advanced. We will return to this at the appropriate point in the following chapters.

In advanced species the RNAPase uses a number of "add-on" auxiliary molecules that perform a number of functions such as transcription error checking and correction. As remarked in the Wikipedia article, "the activity of [RNAPase] is both long and complex and highly regulated."

In a typical transcription, multiple copies of RNAPase operate simultaneously on a single DNA gene, as shown in Figure 9, viewed on a scanning electron microscope.

GeneTranscription.jpg
Figure 9
Gene Transcription
Note the multiple copies of the growing RNA along the gene. Each copy grows from an RNAPase that moves along the gene.
Source: Wikipedia


Ribosome. The translation of m-RNA to form a protein implies another linear motor (the ribosome). It attaches to the m-RNA, reading it one codon at a time, matches that codon to the appropriate t-RNA, detaches the amino acid from the t-RNA, adds it to the growing protein chain, releases the t-RNA and then advances along the m-RNA to the next codon.
 
We noted above the complexity of the ribosomes. Many genes are encoded in the DNA to form the ribosome, which has a large upper part and a smaller lower part. In M. genitalium, mentioned above, the genome includes about 33 genes to form the upper part, and about 20 genes to form the lower part.

t-RNA Synthases. The t-RNA loads itself with the proper amino acid using the assistance of another molecule (t-RNA synthetase -- a separate synthetase exists for most distinct codons), and then cooperates with the ribosome to release the amino acid. Some authors describe the t-RNA as a motor molecule in its own right because of the way it changes configuration as it gains entry into the ribosome.

DNA duplication. Duplication of the DNA is an essential part of cell reproduction. There are two different ways that this is done -- all living species have to use one or the other: DNA polymerase or DNA reverse transcriptase. These are also linear motor molecules similar to RNA polymerase.

Production of Sugars in the DNA backbone. This will be discussed in the next chapter. This process includes the molecule
RuBisCO (see footnote 9) which appears to be necessary to fix carbon from atmospheric CO2.


Life processes depend on very subtle chemical interactions between molecules. Small changes in temperature, acidity, and electrical forces can make or break these interactions. Often these small changes involve creating local pockets where the changes can be made -- small but important changes in electrical potential, focussed application of energy, local changes in acidity (e.g. introducing available H+), etc. Likewise the advancement of the motors (along a molecule in the case of linear motors, and rotary motion in the case of rotary motors) also involves these subtle forces -- literally behaving much as rotors and stators do in conventional electric motors.

Molecular motors carry out these small changes repeatedly and systematically as they perform their tasks. It is difficult to see how the tasks such as reading the DNA or RNA could be done otherwise.



fractal

ENDNOTES



 
fractal

FOOTNOTES

* The background is cyanobacteria (Anabaena), descendents of the oldest fossils discovered to date. These bacteria formed matted structures called stromatolytes (Figure ??). The bulbous cells that appear periodically in the cyanobacteria chain are heterocysts, which specialize in fixing Nitrogen gas.

Anabaena Cyanobacteria
Figure ??
Anabaena Cyanobacteria


^n01 This willful disregard for the metaphysical aspects of science is justifiable if the purpose is to concentrate on the factual aspects of science. For example, if Isaac Newton (and scientists in general) had obsessed over the physical explanation of action at a distance, the powerful implications of the inverse-square law for gravity, and its application to the laws of planetary motion might have suffered as a result. Today, scientists do not fret over much about what force, mass, quantum energy and so on, "really are" but over the physical laws that faithfully describe outworking of these things in nature.

The problem arises if this disregard becomes part of an attempt to suppress "inconvenient" implications in favor of a divine Creator. Lydia Miller, wife of the great popularizer of geology, Hugh Miller, complained of this in 1869, a decade after Darwinian evolution swept the world:
“I must confess that I was at first startled and alarmed by rumours of changes and discoveries which, I was told, were to overturn at once the science of geology as hitherto received, and all the evidences which had been drawn from it in favour of revealed religion. Though well persuaded that at all times, and by the most unexpected methods, the Most High is able to assert Himself, the proneness of man to make use of every unoccupied position in order to maintain his independence of his Maker seemed about to gain new vigour by acquiring a fresh vantage-ground. The old cry of the eternity of matter, and the 'all things remain as they were from the beginning until now,' rung in my ears. God with us, in the world of science henceforth to be no more! The very evidences of His being seemed about to be removed into a more distant and dimmer region, and a dreary swamp of infidelity spread onwards and backwards throughout the past eternity.”
Lydia Miller, preface to Hugh Miller,  Sketchbook of Popular Geology, 4th Ed. 1869, p. xxx.
She argued that there was an attempt to remove inconvenient facts into a "distant and dimmer region" so that an atheistic (or at least Creator-less) agenda could advance without impediment. The facts are still there, but are pushed away, out of view. Biologists who believe in evolutionary change by purely natural processes (i.e. without a divine Creator) may be vulnerable to this charge regarding the origin of life. Their a-priori assumptions conflict with the observed data, so the data must be removed from view. This is the opposite of what Johannes Kepler did when his data on the movements of the planet Mars conflicted with theory -- see the Box on Kepler.

The "Inconvenient Data" of Johannes Kepler.
Kepler's three laws of planetary motion, are still used today. Arthur Koestler in The Sleepwalkers (1959) stated: "For the first time since antiquity, an attempt was made not only to describe heavenly motions in geometrical terms, but to assign them a physical cause." (p. 258). These laws came about because Kepler realized that the astronomical model predictions of Ptolemy and Copernicus "were only accurate within a margin of ten minutes" (p. 322) when compared with Tycho Brahe's precisely measured observations of the planet Mars, accurate to about 1 minute. Earlier astronomers such as Copernicus and Ptolemy would have "corrected" the geometry by adding epiycles, but Kepler concluded that the assumed orbital model was wrong, and  sought to correct the model. His success marked the start of modern science.
Whitehead (quoted in Koestler's book, p. 322) described the essence modern science: "All the world over and at all times there have been practical men, absorbed in 'irreducible and stubborn facts': philosophic temperaments who have been absorbed in the weaving of general principles. It is this union of passionate interest in the detailed facts with equal devotion to abstract generalization which forms the novelty in our present society." The novelty is not that scientists sought generalizations (such as that planets move at constant speed over circular orbits, with superimposed epicycles) but that the generalizations must relate to a physical cause that must agree in detail with observed facts.

^n02  See the Paleomar Project on climate at http://www.scotese.com/climate.htm.

^n03 From the very early formation of the Solar System, there was a shortage of free oxygen because it would combine with the abundant hydrogen to form water (not hydrogen peroxide -- see American Scientific article). As a result, all of the Sun's planets, including the Earth, are reducing, taken as a whole. The fact that the Earth presently has an oxidizing atmosphere (abundant free oxygen available) is an anomaly -- the result of biological activity, as we will note in future chapters. See Broecker, p.231ff. Without this biological activity the Earth would have a reducing atmosphere today (and advanced life could not exist). For the composition of early Earth atmospheres, see the Wikipedia article on paleoclimatology

^n04  [GET REFERENCES FOR THE LEVEL OF RADIOACTIVITY IN THE EARLY EARTH -- 3.9 Ba].

^n05  See Pre-cambrian History of Earth's Rotation and the Moon's Orbit by George E. Williams (2000), Table 1. Rhythmite measurements indicates at 2.45 Ba the Lunar semimajor axis was (from 2 sites) 51.9±3.3 Re/54.6±1.8 Re (514±33/466±15 solar days/year) compared with 60.27 Re today (Re = Earth radius). It is important to note that the rate of recession (presently about 4 cm/yr) changed over the years; for example it was less than 2 cm/yr at 2.45 Ba. The rate is a complex function of the tectonic plate movements as well as the size and depth of the ocean. The current rate of recession is unusually high.]

^n06  The dark marias on the nearside are basalt flows (indication of crustal heating), which are virtually absent on the farside.

07   ^n07 [CITE THE HEIGHTS AND VIOLENCE OF THE EARLY TIDES DUE TO NEARBY MOON] up to 200 ft? globally? Don't seem to be much on web.

^n08  It is difficult to find rational discussions about the development of life in outer space, and so not much more can be said here. Virtually all such commentary is of the "enthusiast" variety and ignores the vast complexity of the project. Most "scientific" discussions note the discovery of certain life molecules, such as the amino acids and then jump from that to speculation about the "likelihood" that life may exist in space, even though the presence of such molecules is fairly predictable, but is of vanishing triviality in comparison with the complexity required to support even the simplest conceivable life forms. In my view the suggestion of life on earth coming from outer space is incredibly facile and begs the question: no answer at all.

^n09  The discrimination against the isotope C-13 is primarily due to one protein, RuBisCO. This is an enzyme that assists in the use of atmospheric carbon dioxide to form sugars. It is said to be the most abundant protein on earth, and also must be one of the oldest, in view of the evidence for its activity in the C-13/C-12 ratio of ancient rocks. The enzymic activity of RuBisCO is very slow -- 3 to 10 CO2 molecules per second per enzyme molecule. See Calvin Cycle.  See also Carbon Isotope Abundance and Discrimination in Plant Studies (2004).

^n10 Peter D. Ward and Donald Brownlee, Rare Earth: Why Complex Life is Uncommon in the Universe, Chapter 1 "Why Life might Be Widespread in the Universe", quoting Robert Ballard, Explorations "The fact that this chain of life existed in the black cold of the deep sea and was utterly independent of sunlight -- previously thought to be the font of all Earth's life -- has startling ramifications. If life could flourish there, nurtured by a complex chemical process based on geothermal heat, then life could exist under similar conditions on planets far removed from the nurturing light of our parent star, the Sun." As we will point out here and in later chapters there are several fallacies in this facile statement. For one thing, so-called extremophiles (Archaeans) are not examples of the first living species since their genetics are relatively advanced; for another, these extremophiles are in fact dependent on the Sun.

^n11  See the National Research Council Symposium held in 1998, published in 2000: Size Limits of Very Small Microorganisms. See the following box on this subject.

Size Limits of Very Small Microorganisms.
A symposium was held in 1998 by the National Academy of Sciences on the subject, Size Limits of Very Small Microorganisms. The proceedings of the symposium was published in 2000 and is available online. The purpose of the symposium was to estimate the smallest possible size for a self-sufficient microorganism. The question arose to address whether the "Martian fossils" discovered in the early 1990s might be the remains of a living microorganism. The symposium concluded that these "fossils" were too small to contain the minimum number of molecules required to carry out life processes of any conceivable kind of living organism.
Sizes of Existing Species. Figure ?? compares the DNA size of species today. Note that the genome size only weakly correlates with the complexity of the species: for example, the dna of humans is only of middling size when compared with other mammals, and many plants have dna that is orders of magnitude larger than the human dna.

Viruses have the smallest genomes, but since viruses cannot carry out the essential cell functions of metabolism and reproduction, they cannot carry out the
necessary tasks of life without co-opting the dna of bacteria; thus if "living" means the ability to engage in these functions, viruses do not qualify as "alive." The smallest viral DNA has about 3,200 base pairs [Spherical hepatitis B Virus (HBV)], coding for four genes.

GenomeSize.gif
Figure ??
Comparison of Genome Size (base pairs)


The smallest DNA sizes of the kingdoms are (from this Figure):

Bacteria DNA are over 400,000 base pairs (bp);
• Fungi DNA are over 10,000,000 bp;
• Plant DNA are over 65,000,000 bp; and
• Animal DNA are over 400,000,000 bp

Still the question arises: how small could the DNA of a living species possibly be, and still be able to metabolize and reproduce? Perhaps all species today are much larger than the minimum size possible.

 Carbonaceous-Foliage
Figure ??
Cell Size Scale
Note relative size of Mars "fossils"


This very question was the topic of a 1998 symposium conducted by the National Research Council of the National Academy of Sciences. The proceedings are published in the symposium Proceedings,
Size Limits of Very Small Microorganisms, published in September, 1999. Invited participants included J. William Schopf, author of Cradle of Life, who will figure prominently in the next chapter.

A major factor that led to this symposium was the alleged discovery of Mars fossils in meteorites retrieved from Antartica and announced in 1996 by NASA scientists. A number of scientists, Schopf in particular, questioned whether they were genuine fossils, and the resulting controversy within the scientific community was a factor leading to this symposium. The question was not whether there could be remnants of life on Mars, but whether these particular specimens could possibly be fossils (whatever their origin). Schopf contended that the "fossils" were too small to contain enough biological material to support a living cell. He argued that the fossils were about 1000x too small to support any kind of life and therefore they were artifacts of the meteorites and not fossils at all.

The symposium cited "the recent report of evidence for life in a martian meteorite
" as it posed the question (citing the Summary), "How small can a free-living organism be?" They sought an answer based on a "a fundamental understanding of the chemistry and ecology of cellular life." The concensus of the symposium was that  "Free-living organisms require a minimum of 250 to 450 proteins along with the genes and ribosomes necessary for their synthesis. A sphere capable of holding this minimal molecular complement would be 250 to 300 nm in diameter." This is far larger than the alleged Martian fossils.

A statement of the minimum genome size varies among the participants. One participant suggested 320,000 bp coding for 256 proteins (p.43), but without asserting that this size could be free-living. A "cell that
synthesizes all of its cellular material from CO2 [an autotroph, which the first life must be -- dcb] requires... closer to 750 genes." For comparison the symposium estimated that the smallest actual modern autotroph has about 1500 genes. [pp 77-78]. Using 1000 bp as the size of an average gene, the minumum genome size for an autotroph must be at least 750,000 bp.

The symposium noted that the bacterium Mycoplasma genitalium, one of the smallest living species on earth, is (at 582,970 bp) close to the limit of smallest possible size, but that this bacterium is not fully self-sufficient because it depends on the availability of organic food and enzymes provided by its host, which a fully self-sufficient organism would have to manufacture. In 2002, a smaller bacterium was discovered, but it too is incapable of independent existence.

Among modern bacteria on earth, the smallest autotroph -- able to manufacture all of its own food and enzymes from inorganic sources -- requires over 1 million bp. Such a bacterium must include
DNA coding to manufacture the nucleotides and amino acids, because these buildingblocks of life do not occur naturally in significant amounts. Even this size assumes the availability of fixed nitrogen.

^n12  The word "dogma" was originally used as an ironic epithet by Francis Crick in 1956. See his aticle, Central Dogma of Molecular Biology (1970). 

^n13  In some bacteria the genes may overlap, and in other bacteria, some genes may be read backwards -- with the reverse direction genes overlapping the forward direction genes. Bacterial dna occurs in a closed loop, and does not have "junk dna" which is a characteristic feature of non-bacterial life (the Eukaryotes -- plants and animals) which typically has dna contained in non-looping chromosomes. The gap between bacterial and eukaryotic life is so profound, that eukaryotic life amounts to a new creation of life (see Chapter 8).

^n13.1 The Smartest Living Nanomachine, 1663: Los Alamos Science and technology Magazine, August 2008.


^n14 This redundancy has led to the conjecture that an early version of the codon table may have been based on nucleotide pairs rather than triplets (4x4 = 16 amino acids coded for). However, there is no known species that has such a codon table.

^n15  Many (most?) living species rely on food to provide at least some of the amino acids that they require to carry out their life functions. These species either lack the genes to make all of the needed amino acids, or else they "prefer" not to have to make certain amino acids from scratch because of the effort required. Of course the very first living species on earth had to make all of their needed amino acids because they lack a reliable inorganic source. Incidentally, viruses in general do not have coding to manufacture amino acids.

^n16  Paul Moorhead and Martin Kaplan (ed.), Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, Wistar Institute Monograph No. 5 (1967). I suspect that some explanations of how complex biological systems are built are based on the fallacy of those who devise gambling schemes. The fact is that there are no winning strategies that can avoid the combinatoric complexities of large randomly constructed systems. If a given (apparently) random combination of amino acids is required and there is no evident regularity in the combination, then no scheme will have a higher probability of attaining that combination than any other.

^n17 Eigen's Paradox was noted by Manfred Eigen in 1971: "Selforganization of matter and evolution of biological Macromolecules". Naturwissenschaften 58 (10): 465. Levinthau's  Paradox was noted by Cyrus Levinthal in 1969: "Are there pathways for protein folding?" Journal de Chimie Physique et de Physico-Chimie Biologique 65: 44–45. 

^n18  This species is parasitic, which means it carries out its own metabolism but it does not manufacture some of its food needs. In particular it does not manufacture amino acids, relying on its host to provide them. "They do however possess the genes necessary for DNA replication, transcription, and translation, but even these contain a minimal set of rRNA and tRNA genes." -- MicrobeWiki. M. genitalium was one of the first genomes to be sequenced by the "shotgun" technique pioneered by J. Craig Venter. See The Minimal Gene Complement of Mycoplasma genitalium Claire M. Fraser et. al. Science Vol. 270, 20 October 1995.

19   ^n19  n

20   ^n20  n


21   ^n21  n


22   ^n22  n


23   ^n23  n


24   ^n24  n


25   ^n25  n


26   ^n26  n


27   ^n27  n


28   ^n28  n


29   ^n29  n


30   ^n30  n



fractal.gif

REFERENCES

Wallace S. Broecker, How to Build a Habitable Planet (1998)

National Research Council Symposium Size Limits of Very Small Microorganisms (2000)



Wallace S. Broecker, How to Build a Habitable Planet (1985)
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
Alexander Meinesz, How Life Began: Evolution's Three Geneses (2008)
Peter D. Ward &  Donald Brownlee, Rare Earth: Why Complex Life is Uncommon in the Universe. (2000)
J. Willliam Schopf, Cradle of Life: The Discovery of Earth's Earliest Fossils (1999).
David C. Bossard, A Fit Place to Live. (2003)


mailbox Any comments or suggestions are welcome. Please email: webmaster@19thpsalm.org



fractal.gif


       


Posted dd Mmmm 201?