Micro Molecules and Macro Evolution

1
II Peter 33-5 3 Knowing this first, that there
shall come in the last days scoffers, walking
after their own lusts, 4 And saying, Where is the
promise of his coming? For since the fathers fell
asleep, all things continue as they were from the
beginning of the creation. 5 For this they
willingly are ignorant of, that by the word of
God the heavens were of old, and the earth
standing out of the water and in the water
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Theories OnThe Origin Of Life

• Timothy G. Standish, Ph. D.

3
What Does Evolution Mean?

• Evolution has at least three (3) distinct
  meanings
• The fact of evolution - Organisms were different
  in the past than they are today
• Fossil record
• Biblical record - Gods curse on Adam
• Genesis 318 Thorns also and thistles shall it
  bring forth to thee and thou shalt eat the herb
  of the field
• The theory of evolution - Natural selection
• At least partially supported by population
  genetics accounting for changes in allelic
  frequencies within populations
• The doctrine of evolution - All that we see can
  be accounted for by natural random events and
  thus a Designer is not necessary.

4
Arguments for a Designer

• Organisms look designed for at least three (3)
  reasons
• Redundancy - A Designer can engineer redundancy
  into a system, but chance is unlikely to do this.
  An example of this is the presence of degeneracy
  in the genetic code and other features that
  minimize or negate the effects of many point
  mutations.
• Excess potential - Organisms have potential that
  may never be used. For example, Wallace,
  co-discoverer of natural selection, pointed out
  that primitive people have the capacity to do
  calculus when trained. Natural selection is
  unlikely to select for capacity that is not used.
• Complexity - Life is so complex that it is
  improbable it came about by chance.

5
The Likely and the Unlikely

• In general arguments for a designer are arguments
  against the alternative. This does not mean
  these are just arguments against evolutionary
  theory. All arguments, by definition, are
  characterized by taking one side while arguing
  against another side.
• Arguments against a theory are about eliminating
  possible explanations. There is nothing inferior
  about this, in fact, it is deductive reasoning
  which is used by scientists all the time in their
  quest for truth.
• Arguments for a Designer generally revolve around
  probability. Meaningful complexity is unlikely
  to result from random events. Organisms are
  meaningfully complex. Some claim that natural
  selection overcomes much of this problem as,
  while change may be random, selection is not.
• Science is about predicting what is likely and
  what is unlikely. Everyone is in agreement that
  the events leading to production of living
  organisms are unlikely.

6
What This Talk Is Actually About

• In this talk we will look at the mechanisms
  proposed for the origin of living systems in the
  absence of a designer.
• We will then look at one of the many biochemical
  systems that must be in place in all organisms.
• Finally we will compare the information we have
  on organisms at the molecular level, and see
  whether it is best explained as the result of
  natural selection or design.

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In a Long Time and Big Universe

• It has been argued that given massive lengths of
  time and a universe to work in, the unlikely
  becomes likely
• Given infinite time, or infinite opportunities,
  anything is possible. The large numbers
  proverbially furnished by astronomy, and the
  large time spans characteristic of geology,
  combine to turn topsy-turvy our everyday
  estimates of what is expected and what is
  miraculous.
• Richard Dawkins (1989) The Blind Watchmaker Why
  the evidence of evolution reveals a universe
  without design. W. W. Norton and Co. New York.
  p139.

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Understanding Complexity Allows Better Estimates
of Probability

• At Darwins time, his explanation for the origin
  of organisms seemed reasonable as their
  complexity was not understood fully.
• First simple monera are formed by spontaneous
  generation, and from these arise unicellular
  protists . . .
• The Riddle of the Universe at the close of the
  Nineteenth Century by Ernst Haeckel, 1900.

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Little or Big Changes?

• Not all changes improve fitness, they may
• Improve the fitness of an organism (very
  unlikely)
• Be neutral, having no effect on fitness
• Be detrimental, decreasing an organisms fitness
  (most likely)
• The bigger the change the more likely it is to be
  significantly detrimental
• Darwin argued that evolution is the accumulation
  of many small changes that improve fitness, big
  changes are unlikely to result in improved
  fitness.
• Many large groups of facts are intelligible only
  on the principle that species have been evolved
  by very small steps.
• The Origin of Species Chapter VII under Reasons
  for disbelieving in great and abrupt
  modifications

10
Behes Insight

• Michael Behe contends that when we look at the
  protein machines that run cells, there is a point
  at which no parts can be removed and still have a
  functioning machine. He called these machines
  irreducibly complex.
• We encounter irreducibly complex devices in
  everyday life. A simple mouse trap is an example
  of an irreducibly complex device

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Irreducibly Complex Protein Machines

• Cells are full of irreducibly complex devices -
  Little protein machines that will only work if
  all the parts (proteins) are present and arranged
  together correctly.
• Natural selection does not provide a plausible
  mechanism to get from nothing to the collection
  of parts necessary to run a number of irreducibly
  complex protein machines needed to have a living
  cell
• Evolution of these protein machines must occur in
  single steps, not gradually, as to be selected a
  protein must be functional in some way. Each
  protein machine is fairly complex, thus evolution
  in a single step seems unlikely.

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How Can Irreducibly Complex Protein Machines be
Made?

• The evolution model suggests two mechanisms
• Mechanism 1
• Random events produce proteins with some minimal
  function
• These minimally functional proteins mutate and
  less functional variants are removed by natural
  selection
• Some of these proteins cooperate together to do
  tasks
• From this, emergent properties of the system come
  about, these only occur when all the components
  are present
• This mechanism only works if each protein
  involved has individual properties conferring
  added fitness

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What If Proteins Have No Independent Function?

• Evolutionary Mechanism 2
• If the function of each protein in an irreducibly
  complex protein machine is completely dependant
  on the other proteins, then the only way to
  select them would be if the machine was already
  functional.
• Getting a functional machine would require that
  all the components come together by chance
• This would be a big step and seems unlikely

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The Creation Model

• The creation model postulates a Designer who
  first designed each component of the protein
  machine, then created them at the same moment in
  such a way that the machine could start working
• Getting a functional machine in this model does
  not require that all the components come together
  by chance, but does require the existence of a
  Designer

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Chemical Evolution
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Four Postulated Stages of Chemical Evolution

• Chemical evolution is the spontaneous production
  of the molecular components of cells that had to
  be produced prior to evolution of the first cell
• 1) Abiotic synthesis of organic monomers
• 2) Abiotic synthesis of organic polymers
• 3) Self assembly of protobionts
• 4) Evolution of a genetic system
• We will concentrate on the first two steps

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Step 1 Abiotic Synthesis of Organic Monomers

• The monomers that make up polymers in living
  cells are reduced carbon compounds
• Cant happen in modern world due to oxidizing
  atmosphere
• 1920s A. I. Oparin (Russia) and J. B. S. Haldane
  (Great Britain) postulated that as spontaneous
  synthesis of reduced organic molecules is
  impossible in an oxidizing environment, the earth
  must have had a reducing atmosphere
• 1953 Miller and Urey designed a device to test
  the hypothesis that given the right conditions,
  organic monomers could be produced

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JBS Haldane

• While Haldane was one of the founders of
  population genetics, it is worth mentioning that
  he was a screwball of the first order
• Just before the 1925 signing of the Geneva
  protocol banning chemical weapons, Haldane came
  out as an advocate of chemical warfare
• He was a racist who believed blacks were immune
  to chemical weapons and thus should be used as
  the frontline troops in wars (with white officers
  to lead them of course)
• As England had access to black troops from the
  colonies, this would give them an advantage over
  Germany in future chemical wars

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The Miller-Urey Device
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Products of Miller and Ureys Device

• After several days of operation, the Miller-Urey
  device produced a brown organic substance in
  which, either in this experiment or subsequent
  variations, was found many of the basic building
  blocks of
• Proteins (amino acids)
• Nucleic acids (ribose, purines and pyrimidines)
• Polysaccharides (sugars)
• Fats (fatty acids and glycerol)
• Note that it was the building blocks that were
  found, not the actual macromolecules
• Along with these building blocks, there were many
  other molecules not found in organisms

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Did Miller and Urey Prove Chemical Evolution?

• Six reasons that it does not prove chemical
  evolution
• Oparins reducing conditions were postulated
  because they are conditions allowing reduced
  organic molecule production, not because of
  compelling evidence these conditions ever existed
  on earth.
• Reduced organic products were not the result of
  random chance, but of a device that had been
  carefully designed and constructed.
• Products were not enriched in the chemicals that
  make up organisms. This is a particular problem
  when it comes to stereoisomers.
• No organisms were actually made.
• Even if organisms were made in this way, this
  would not prove it to be how things actually
  happened, it only shows it to be one possible
  way.
• Accumulation of organic monomers is only the
  first step in chemical evolution.

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Step 2 Abiotic Synthesis of Organic Polymers

• It has been postulated that the monomer building
  blocks produced under conditions resembling those
  in the Miller-Urey experiment were joined
  together to make polymers
• Experiments have been done that demonstrate this
  is possible in the absence of living cells or
  cell products like enzymes
• The sequence in which monomers are joined
  together to make polymers is vital to the
  function of polymers like DNA and proteins.
• No mechanism has been proposed for joining
  monomers in meaningful sequences, thus
  abiotically synthesized organic polymers are
  assumed to have been random in sequence.

23
A Polymerization ExperimentImai et al, 1999
Science 283831-883

• Imai et als device simulated the pressure and
  temperature conditions of the hydrothermal
  circulation of water
• However, there were still some large differences
  from real hydrothermal vents, for instance, in
  pH, CO2, Na and Cl contents.
• 100 mM glycine in pure water was circulated in
  the system alternating temperature and pressure
  with each circuit
• 2 mM diketopiperazine, 1mM triglycine and 0.4 mM
  diglycine resulted once close to steady state
  condtions were reached
• In the presence of Cu and low pH, small 0.001
  mM concentrations of up to hexaglycine were
  produced

24
Imai et als Device
Cooling
Heating
Depressurization
Sample removal
Pressurization
25
Random Sequences are Unlikely to be Meaningful or
Useful

• Random sequences of amino acids are analogous to
  random sequences of letters
• ldjfire vireahdftrfd
• grvcnlkertpoildrirti
• ugcrtrrtadhk jjkvhvf
• jmvcbkvbkjhcguvdrttr
• k jfvukvfkhjfvkhj he
• Random sequences are unlikely to be meaningful

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Meaningful Sequences are Unlikely

• Even a short meaningful phrase is a very unlikely
  sequence of letters
• For example, In the beginning God is only 20
  letters long, but is very unlikely to be produced
  by random typing of letters
• Ignoring capitalization, and assuming each letter
  is equally probable, the probability that the
  first character will be I is 1/27 (26 letters
  in the alphabet plus the space makes 27)
• The probability that the correct letter will be
  at each position is

• This is 0.0000000000000000000000000000236
• Or about 1 chance in 50,000 trillion trillion

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Is this a Fair Estimate of Probability?

• No!
• There are a number of ways in which this phrase
  can have the same meaning
• God, in the beginning
• In the beginning was the Word
• Before everything God
• The same is true for proteins, in some areas of
  most proteins, there can be a small amount of
  variability, in other areas, there can be no
  change in the sequence of amino acid monomers

28
Does this Make Production of Functional Proteins
Likely?

• No!
• Lets look at an example, the enzyme
  Glyceraldehyde-3-phosphate dehydrogenase
• The Mycoplasma genitalium G-3-P dehydrogenase
  protein sequence
• MAAKNRTIKV AINGFGRIGR LVFRSLLSKA NVEVVAINDL
  TQPEVLAHLL KYDSAHGELK RKITVKQNIL QIDRKKVYVF
  SEKDPQNLPW DEHDIDVVIE STGRFVSEEG ASLHLKAGAK
  RVIISAPAKE KTIRTVVYNV NHKTISSDDK IISAASCTTN
  CLAPLVHVLE KNFGIVYGTM LTVHAYTADQ RLQDAPHNDL
  RRARAAAVNI VPTTTGAAKA IGLVVPEANG KLNGMSLRVP
  VLTGSIVELS VVLEKSPSVE QVNQAMKRFA SASFKYCEDP
  IVSSDVVSSE YGSIFDSKLT NIVEVDGMKL YKVYAWYDNE
  SSYVHQLVRV VSYCAKL

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Why Random Production of Glyceraldehyde-3-Phosphat
e Dehydrogenase is Improbable

• There are 337 amino acids strung together to make
  the Mycoplasma genitalium G-3-P dehydrogenase
  protein
• At each position in the string there could be any
  one of 20 amino acids
• Probability of making this protein using random
  synthesis is (1/20)337 3.5 x 10-439 or 1 chance
  in 2.9 x 10-438
• Even if there are a trillion trillion ways of
  making G-3-P dehydrogenase, that only lowers the
  probability of making a functional protein to 3.5
  x 10-415

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3.5 x 10-439 Is A Very Small Number

• 0.000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  00000000000000000000000000000000000000000000000000
  000000000000000000000000000000000000000035

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Where G-3-P Dehdrogenase Fits Into the Scheme of
Life

• All cells contain a biochemical pathway that
  converts sugar to energy
• The first part of this pathway is called the
  glycolytic (sugar splitting) pathway
• Sugar is taken in at the start of the pathway and
  the products are energy in the form of ATP, a
  chemical called pyruvate and another chemical
  called NADH.
• Glyceraldehyde-3-phosphate dehdrogenase is one of
  the enzymes in the glycolytic pathway.

32
The Glycolytic Pathway

• Each step in the pathway represents a small
  change in the sugar molecule
• As these small changes are made, the sugar is
  slowly turned into something different
• Glyceraldehyde-3-phosphate dehydrogenase is found
  at step 6 in the glycolytic pathway

33
What Actually Happens At Step 6

• By the time step 6 is reached, the 6 carbon sugar
  molecule has been split into two three carbon
  molecules called glyceraldehyde-3-phosphate

• In step 6 of glycolysis, glyceraldehyde-3-phospate
  is converted to 1,3-bisphosphoglycerate and
  oxidized nicotinomide adenine dinucleotide
  phosphate (NAD) is reduced

34
From G-3-P to 1,3-BPG In Four Easy Steps
NADH
NAD
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Summary

• To convert G-3-P to 1,3-bisphosphoglycerate all
  of the following components must be present
• The enzyme - Glyceraldehyde-3-phosphate
  dehydrogenase
• NAD- Oxidized Nicotinamide Adenine Dinucleotide
• Phosphate
• Glyceraldehyde-3-phosphate
• This reaction would be pointless in the absence
  of the next step in the glycolytic pathway, the
  production of ATP catalyzed by phosphoglycerokinas
  e
• A separate set of reactions is necessary to
  regenerate the NAD from NADH

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NAD
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What Does This Mean?

• The glycolytic pathway is central to life
• The components needed for step 6 are unlikely to
  have all come about via chemical evolution
  (random processes) particularly
  glyceraldehyde-3-phosphate dehydrogenase
• Natural selection could not work on the enzyme
  glyceraldehyde-3-phosphate dehydrogenase in the
  absence of the other enzymes in the glycolytic
  pathway as this reaction is pointless without the
  subsequent reactions
• Chemical evolution combined with natural
  selection does not provide a convincing mechanism
  for the production of components needed for step
  6 in the glycolytic pathway
• The same could be said for the other 9 steps in
  the glycolytic pathway

38
Yes, It Is Unlikely . . . But

• The argument is not that the origin of life was
  an unlikely event, but that given sufficient time
  and resources chance events could produce the
  first organism that could then be acted on by the
  guiding hand of natural selection
• So what are the resources available for the
  production of the first/simplest organism? Is it
  really the universe?
• The Monera (for instance, chromacea and
  bacteria), which consist only of this primitive
  protoplasm, and which arise by spontaneous
  generation from these inorganic nitrocarbonates,
  may thus have entered upon the same course of
  evolution on many other planets . . .
• The Riddle of the Universe at the close of the
  Nineteenth Century by Haeckel.

39
Space and Time

• The conditions necessary to produce reduced
  carbon compounds like those produced in the
  Miller-Urey experiment have not, so far, been
  found elsewhere in the universe
• In reality, the conditions needed for life seem
  to only be present in a tiny fraction of the
  universe and we happen to be living on it.
• Time is the other element needed, and this is a
  real problem
• Even if the conventional interpretation of the
  fossil record is used, life seems to have
  appeared very soon (a few million, not billions
  of years) after water appeared on earth

40
Conventional History Of The Earth
-First multicellular animal fossils
-First eukaryotic fossils
-Atmospheric Oxygen accumulation (from
cyanobacteria)
-First fossil prokaryotes
-Crust forms
-Formation of the earth
41
When Was The Earth Sterile?

• Recent explorations of the oldest known rocks of
  marine sedimentary origin from the southwestern
  coast of Greenland suggest that they preserve a
  biogeochemical record of early life. On the basis
  of the age of these rocks, the emergence of the
  biosphere appears to overlap with a period of
  intense global bombardment. This finding could
  also be consistent with evidence from molecular
  biology that places the ancestry of primitive
  bacteria living in extreme thermal environments
  near the last common ancestor of all known life.
• Stephen J. Mojzsis, T. Mark Harrison. Vestiges of
  a Beginning Clues to the Emergent Biosphere
  Recorded in the Oldest Known Sedimentary Rocks.
  GSA Today, April 2000, 10(4), 1-??

42
Newer Ideas

• Mars may have served as lifes incubator as it
  cooled before earth and had a moist environment.
• Life, in the form of bacteria or bluegreen algae,
  was transferred to earth when chunks of Mars
  knocked off by collisions with comets etc. fell
  to earth.
• This general idea is not new. Francis Crick
  called it panspermia in Life Itself where he
  says the earth was seeded with life from space
  (Hoyle may also have published something similar)
• None of this makes explanations simpler, just
  more complex (should Ockhams Razor be invoked?)

43
But Theres MoreA Lot More

• The organism Mycoplasma genitalium from which
  the G-3-P dehydrogenase we looked at came from is
  the simplest known free living organism
  (although it is a parasite)
• M. genitalium has a genome of 580,070 bp (humans
  have about 3,000,000,000)
• The calculated number of proteins (genes) in this
  the simplest known organism, is 470
• The average size of M. genitalium proteins is
  about 350 amino acids (in the ball park of G-3-P
  dehydrogenase)
• Even if enough time and space existed to generate
  a minimally functional G-3-P dehydrogenase, this
  is just the tip of the ice burg M. genitalium
  has to be close to irreducibly complex.
• Conditions under which a less complex organism
  could exist are just about as improbable as
  generating the organism in the first place and
  present a host of other problems

44
Conclusions

• Life is far more complicated than was anticipated
  by the originators and early defenders of natural
  selection as a mechanism for lifes origin
  independent of a Creator
• Natural selection does not provide a convincing
  mechanism for the origin of biochemical pathways
  and other molecular machines basic to life
• Claims that almost infinite amounts of time and
  space could account for the improbable origin of
  life seem less convincing in light of current
  exploration of space and understanding of the
  fossil record
• Creationists can accept change over time and
  natural selection as a mechanism for small
  changes, but, in light of current knowledge faith
  in a Creator of life remains well founded

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Psalms 83-6 3 When I consider thy heavens, the
work of thy fingers, the moon and the stars,
which thou hast ordained 4 What is man, that
thou art mindful of him? and the son of man, that
thou visitest him? 5 For thou hast made him a
little lower than the angels, and hast crowned
him with glory and honour. 6 Thou madest him to
have dominion over the works of thy hands thou
hast put all things under his feet
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The Information Catch 22

• With only poor copying fidelity, a primitive
  system could carry little genetic information
  without L the mutation rate becoming unbearably
  large, and how a primitive system could then
  improve its fidelity and also evolve into a
  sexual system with crossover beggars the
  imagination."
• Hoyle F., "Mathematics of Evolution", 1987,
  Acorn Enterprises Memphis TN, 1999, p20

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Evolution . . . So 20th Century

• "In the realm of science, scholars such as
  William Dembski and Michael Behe have been
  demonstrating how the order in the universe is
  evidence that it has been intelligently designed.
  'No!' say the Darwinists. 'Everything has to be
  random!' But the evolutionists are the ones who
  sound so outdated, so 20th century.
• Veith, Gene E. Reality makes a comeback. World
  Magazine Feb. 12, 2000 Volume 15 Number 6

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49
RNA World

• The 'RNA world' scenario hinges on some rather
  far-fetched assumptions about the catalytic
  ability of RNA. For example, RNA polymerase
  ribozymes must have been responsible for
  replicating the ribozymes of the RNA world,
  including themselves (via their complementary
  sequences). RNA replication is a very
  challenging set of reactions -- far more
  challenging than those yet known to be catalyzed
  by RNA.
• David P. Bartel and Peter J. Unrau, "Constructing
  an RNA World." Trends in Biochemical Sciences 24
  (1999)M9-M13.