Prepared May, 2010


       

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

PART II:
Creation of Living Species

Chapter 5
Creation of the First Life

UNDER CONSTRUCTION


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

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

Evidence of life appears in the most ancient geological records, as soon as the Earth had formed and cooled to the point that it could host life, about 3.9 billion years ago (3.9 Ba). This does not prove that life could not have been present earlier, but there is no direct evidence for it. The conclusion from this fact is that life appeared in the oldest rock formations 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, 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 early Earth was a formidable and hostile place for life to begin. In fact complex 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. We will explore some of what this means in the next chapter.

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, the first thing discussed in this chapter. 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.

NOTE: The material of this and the next few chapters is the subject of the lecture
A Fit Place to Live.


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Condition of the Early Earth
. As remarked in an earlier 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 time[FOOTNOTE: See http://www.scotese.com/climate.htm -- + other sources???].

The Earth atmosphere was reducing with very little free oxygen, composed mostly of nitrogen, carbon dioxide and water vapor[FOOTNOTE: 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. 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]. Note that carbon dioxide and water vapor are greenhouse gasses, which may have helped to maintain the surface temperature at a time when the Sun's radiant energy was about 25% lower than it is today.

The ocean at this time was very salty, more salty than it is today. Both the ocean and the crust were reducing. The oceans, in particular, included many mineral salts that were not fully oxidized. This will prove important later on in Earth's history. ???The crust was mildly radioactive -- about the level of radioactivity of the fuel rods used in nuclear power plants[CHECK!!]???.

The Moon was in a close orbit [[CHECK!!] ??? miles at 3.9 Ba, receding to 206,000 miles at 2.45 Ba (compared with 238,600 miles today)[FOOTNOTE: 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. 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.].  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[FOOTNOTE: The dark marias on the nearside are basalt flows (indication of crustal heating), which are virtually absent on the farside].

Clemtine-nearside Clemtine-farside.jpg
Figure 1a
Lunar Albedo nearside
Figure 1b
Lunar Albedo nearside
Source: U.S. Navy Clementine Mission (1994),


Violent volcano activity, partly caused by very high 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 Landscape
Credit: Artwork copyright 2006 Don Dixon/cosmographica.com
NOTE: MAYBE USE HARTMAN PIC?


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.

We will argue that the creation of life by purely natural processes is an incredibly low probability event according to any conceivable method of calculation, even over the 14 billion years since the Big Bang. 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 Bang[FOOTNOTE: Cite authors who argue that life cannot arise in empty space.].

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 deposits.

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. This finding will be discussed further 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. 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 scientists[FOOTNOTE: 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 see 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, thes extremophiles are in fact dependent on the Sun.] assume that because life appeared on earth at the earliest possible moment, life can originate many times throughout the universe. Ward and Brownlee[FOOTNOTE: Op. Cit.], for example, distinguish between primitive life (common and widely distributed in the Universe) and "complex life"  -- advanced animal life (rare in the universe).

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 imagine.

 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 (using their term) from a single first living species. Present species of life did not arise from multiple independent first ancestors.


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The "central dogma" of life

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 dogma[FOOTNOTE: The word was originally used as an ironic epithet by Francis Crick] because every living cell follows the same (give or take a few minor variations) plan. 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.

The following are features of the central dogma.

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 195?[ADD DETAILS].

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 gene.

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  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 4) 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 [CHECK]. 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 t-RNA, further described below. Genes to produce these molecules must be part of the genetic code recorded in the DNA [CHECK].

* 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.

Ribosome.gif
Figure 6
Ribosome
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 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 life."

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 position[FOOTNOTE: 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).].

* 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.


The folding appears to occasionally involve molecular chaperones [COMPLETE]

ProteinFolding.gif
Figure 7
Protein Folding

From Wikipedia

* 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 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 this involves around 200 separate genes (about 200,000 base pairs) -- not including genes to form the amino acids -- 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. 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 1966[FOOTNOTE: Paul Moorhead and *Martin Kaplan (ed.), Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, Wistar Institute Monograph No. 5 (hardcover, 1967).]. 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.

There is no known incremental procedure that would work up to produce the central dogma.


 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.

[COMPLETE THIS]

This problem is more insoluble than the density and smoothness problem of the primordial universe just after the cosmic expansion. So both the universe and life begin with apparently insoluble dilemmas.



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Complex 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. The use of several such motors and complex molecules have been implied in the description of the Central Dogma. For example:
• 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.
• 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.
• 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.
• In the background to all of this activity is a molecular energy "battery" (ATP = adenosine tri-phosphate) which interacts with these molecules many times to provide small increments of energy as needed (approximately 7.3 kCal/mole in releasing a single phosphate to form ADP). All living species appear to use ATP. As far as is known, it is always formed using a molecular motor called
atp synthase (ATPase). This is actually a rotary motor as distinct from the linear motors such as RNA polymerase. ATPase always resides in a membrane that separates media of different acidity [CHECK].
• Also in the background to all of this is the requirement to duplicate the DNA as part of cell reproduction (DNA polymerase or DNA reverse transcriptase -- two different ways to accomplish this). These are also linear motor molecules similar to RNA polymerase.
• Also in the background is the production of sugars for the DNA backbone and nucleotides. Nothing further will be said here, but we will return to sugar production in the next chapter.

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.

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.

ATP synthase. ATP synthase (Figure 8) is a rotary motor that is powered by protons (H+) rather than electrons as in modern electric motors. 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[FOOTNOTE: 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], a parasitic bacterium with one of the smallest known genomes[FOOTNOTE: 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.]. Its DNA includes the 8 ATPase genes designated atpA through atpH. The motor is very complex, and appears to be universal. [MAYBE LINK TO MY TABLES OF THE GENES]

The Universality of ATP Synthase

'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

"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


ATP-Synthase.gif
Figure 8
ATP Synthase
From Wikipedia


RNA Polymerase. Unlike the energy storage via ATP, the RNA polymerase (or rather the polymerases) that conducts transcription of 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 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 assumed 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 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. 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. [ADD MORE ?? ] [MAYBE LINK TO LIST OF GENES in M. gentalium]

t-RNA Synthases. As noted above, the t-RNA synthases (T-RNASase) assign specific amino acids to particular codons. {MORE]

In M. genitalium, there are separate genes to form 21 synthases, each assigning a codon to a separate amino acid. For this species, each amino acid has only one T-RNASase assigned, which means that a single t-RNA serves for all assignments to that amino acid (or the t-RNA is modified to accommodate additional codon assignments). [MAYBE LINK TO LISTS OF THE GENES]


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Size Limits of Very Small Microorganisms

An interesting question to ponder is the genome size of the very first living species. Figure 10 compares the DNA size of species today. If "living" means the ability to engage in the necessary tasks of life such as reproduce and metabolize, then the viruses do not qualify as living. The smallest DNA sizes of the other kingdoms are (from Figure 10):

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.

GenomeSize.gif
Figure 10
Comparison of Genome Size (base pairs)



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.

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[FOOTNOTE: This is my own summary of Schopf's position: I believe it is accurate in essential details. dcb].

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.

This discussion does not consider the problem of nitrogen fixing, which will is considered in the next chapter.


• Viruses are NOT alive
. The simplest biological "species" are the viruses. Many viruses have very small amounts of genetic material. For example, the smallest viral DNA has about 3,200 base pairs [Spherical hepatitis B Virus (HBV)], coding for four genes.

The genetic code in viruses does not include any coding for the Central Dogma, because the virus takes over the host cell's own genetic processes and uses that cell's implementation of the central dogma to reproduce itself.

An autotroph -- a living species that can live exclusively on inorganic food -- must include DNA coding to manufacture the nucleotides and amino acids, because these buildingblocks of life do not occur naturally in significant amounts. Most living species are not strict autotrophs, and so they require organic food -- food derived from other species -- to survive. Clearly the first living species had to be autotrophs, unless there is a natural source of nucleotides and amino acids. [CHECK THIS STATEMENT]




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NOTES


Sharp Point          The First Living Species -- Fixed Nitrogen

The Miller-Urey 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 ammonia.  **CHECK** 

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.

Nitrogen 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.

Complexity of the nitrogenase molecule.  Still don't know how it works.






Sharp Point          The Inadequacy of the Early Earth Environment

1. Very little free oxygen. The first living species were anoxic. Oxygen is needed by all higher organisms.

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 nitrogen compounds.
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.
 
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REFERENCES

Wallace S. Broecker, How to Build a Habitable Planet (1985)
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
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)


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Prepared May, 2010