Evolution-1 Chapter 9. Evolution: A Theory in Crisis* Did life evolve through unguided, materialistic processes from simple chemicals into single cell organisms and then through a process of random genetic mutation acted upon by natural selection into the plants and animals we see today? Or, was life designed by an amazingly competent, perhaps supernatural agent with an end in mind? These are foundational questions. If we are here because of random materialistic processes, then it is hard to argue that our existence has a purpose, but if we are here through the agency of a supernatural creator with an end in mind, then we have value and a purpose defined by our creator. Having previously established my credentials as a Christian heretic to some, I will also establish my credentials as a scientific heretic to others. I believe that Darwin’s theory of evolution, or its neo-Darwinian version, is an elegant theory and worthy of investigation. Darwin was a keen observer of small changes in species, and he tied these small changes to the large changes seen in the fossil record with a plausible theory of accumulated variation operated on by natural selection. However, I believe that Darwin’s theory is a failed theory. But first, we have to define what evolution and Darwin’s theory are. Evolution (or general evolution), according to most biology text books, is simply change over time, or an inheritable change in the characteristics within a population from one generation to the next, or the change in the gene pool of a population over time. Defined in this way, evolution is a well substantiated fact. The fossil record, observed small changes in species over time, and drug resistant strains of bacteria all testify that life has changed over time. Darwinian evolution is the theory that all organisms developed from one or maybe a few original one-celled organisms 1 . This theory is often called common descent. Darwin observed the fossil record and small changes in varieties of animals, such as pigeons, produced by selective breeding. He postulated that small changes could naturally produce large changes such as seen in the fossil record given enough time. The mechanism for change that Darwin suggested was variation operated on by natural selection. A variation was a small change from one generation in a species to the next, and if that change allowed the organism to survive or reproduce better, nature would select it and preserve it. At the time, the source of variation was not known. Darwin believed that change occurred gradually, step-by-small step, over a long period of time. Neo-Darwinian evolution is the theory that common descent is true and that random genetic mutation to DNA operated on by natural selection is the mechanism for change. It is the same as Darwinian evolution except that variation is explained in terms of genetic mutation. Microevolution describes small changes in organisms due to random mutations and genetic variability. We know this is true from bacterial resistance to antibiotics and from changes in animal and plant species over time. _____________________________________ * I borrowed this title from Michael Denton’s 1986 book. Darwinian Evolution is still a theory in Crisis.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Evolution-1
Chapter 9. Evolution: A Theory in Crisis*
Did life evolve through unguided, materialistic processes from simple chemicals into single cell
organisms and then through a process of random genetic mutation acted upon by natural
selection into the plants and animals we see today? Or, was life designed by an amazingly
competent, perhaps supernatural agent with an end in mind? These are foundational questions.
If we are here because of random materialistic processes, then it is hard to argue that our
existence has a purpose, but if we are here through the agency of a supernatural creator with an
end in mind, then we have value and a purpose defined by our creator.
Having previously established my credentials as a Christian heretic to some, I will also establish
my credentials as a scientific heretic to others. I believe that Darwin’s theory of evolution, or its
neo-Darwinian version, is an elegant theory and worthy of investigation. Darwin was a keen
observer of small changes in species, and he tied these small changes to the large changes seen in
the fossil record with a plausible theory of accumulated variation operated on by natural
selection. However, I believe that Darwin’s theory is a failed theory. But first, we have to
define what evolution and Darwin’s theory are.
Evolution (or general evolution), according to most biology text books, is simply change over
time, or an inheritable change in the characteristics within a population from one generation to
the next, or the change in the gene pool of a population over time. Defined in this way, evolution
is a well substantiated fact. The fossil record, observed small changes in species over time, and
drug resistant strains of bacteria all testify that life has changed over time.
Darwinian evolution is the theory that all organisms developed from one or maybe a few
original one-celled organisms 1. This theory is often called common descent. Darwin observed
the fossil record and small changes in varieties of animals, such as pigeons, produced by
selective breeding. He postulated that small changes could naturally produce large changes such
as seen in the fossil record given enough time. The mechanism for change that Darwin
suggested was variation operated on by natural selection. A variation was a small change from
one generation in a species to the next, and if that change allowed the organism to survive or
reproduce better, nature would select it and preserve it. At the time, the source of variation was
not known. Darwin believed that change occurred gradually, step-by-small step, over a long
period of time.
Neo-Darwinian evolution is the theory that common descent is true and that random genetic
mutation to DNA operated on by natural selection is the mechanism for change. It is the same as
Darwinian evolution except that variation is explained in terms of genetic mutation.
Microevolution describes small changes in organisms due to random mutations and genetic
variability. We know this is true from bacterial resistance to antibiotics and from changes in
animal and plant species over time.
_____________________________________ * I borrowed this title from Michael Denton’s 1986 book. Darwinian Evolution is still a theory in Crisis.
Evolution-2
Macroevolution is the Darwinian or Neo-Darwinian theory of evolution. It implies that
successive microevolutionary steps lead to large changes in organisms.
Chemical Evolution is the hypothesis that the origin of life is explained by chemicals combining
through random natural interactions to form the molecules of life and then these molecules
organizing into one-celled organisms by natural processes.
General evolution is quite often treated as an umbrella for Darwinian, neo-Darwinian, and
chemical evolution. That is, general evolution being true implies that Darwinian, neo-
Darwinian, and chemical evolution are also true, but this is faulty logic. Observed change over
time does not imply that Darwinian mechanisms are the cause.
In this chapter, we will explore chemical evolution, neo-Darwinian evolution, common descent
and design, but first we will discuss some basic biochemistry, which is the foundation for all
these subjects.
Modern Understanding of the Cell and Basic Biochemistry
In Darwin’s time, and until the early 20th century, the cell was thought to be a very simple bag of
protoplasm--unstructured organic material. Discoveries of modern science have proved this
concept to be in error. Even the simplest cell is now compared in complexity to an industrial city
with roads, factories, and libraries. The human cell is constructed of roughly 120,000 proteins,
many of which are integrated to form complicated molecular machines that conduct the cell’s
processes. Different compartments in the cell allow the assembly of molecules which require
unique environments. In fact, an environment that is benign to one molecule may be hostile to
another. The cell’s compartments have doors or windows that open automatically when the right
molecule approaches but stay closed when others approach. Molecular haulers transport
materials along highways that connect different parts of the cell. Molecular machines, with the
help of cables, ropes, and pulleys, unzip, read, and duplicate DNA which is a very long molecule
that stores information. The information in DNA is equivalent to many printed volumes and
specifies how to construct and regulate proteins.
Life’s Building Blocks Atoms--the building blocks of matter
(hydrogen, oxygen, carbon, and others)
Molecules--combination of atoms bound together by electrical forces (water, sugar, salt,
amino acids, and many others)
Amino Acids--molecules that are the building blocks of proteins
Proteins--folded chains of amino acids that form the structural building blocks and
machinery in cells
Cells--the building blocks of living organisms
DNA--a long, ladder-like molecule, found in a cell’s nucleus, that stores the information
(code or directions) for building proteins (deoxyribonucleic acid)
Mutation--an error in the DNA code
Evolution-3
Genetic information is stored as chromosomes. We have 23 pairs of chromosomes (apes have
24, mice have 20, corn has10, dogs have 39, but flowering plants have the most). One
chromosome in a pair comes from our mother and the other from our father. A chromosome is
composed of a “ladder” of nucleotides, twisted into a helix. Chromosomes are copied during
reproduction but no new genetic information is created except by an error (mutation). Nearly all
mutations are detrimental, and the cell has mechanisms to correct all but a very few.
it was thought to serve little or no useful purpose,
consisting of repetitive sequences and discarded,
damaged genes. Between 1990 and 2003
information from the Genome Project suggested
that we have between 25,000 and 40,000 genes in
total that code for roughly 120,000 proteins
implying that genes must code for more than one
protein. Between 2005 and 2011 the ENCODE research project indicated that at least 90% of
the genome, previously called “junk” DNA, plays a coordinating, control, and regulatory
function and is not junk at all 3.
Proteins form the building blocks, energy converters, and machinery of cells. Our cells use
roughly 120,000 proteins. Twenty different amino acids are used to construct proteins, and a
typical protein comprises a sequence of hundreds to over one-thousand amino acids. Amino
acids are assembled into a properly sequenced chain by a molecular machine called a ribosome
and folded by other molecular machines to form a functioning protein. The figure below shows
four amino acids and how they are assembled using peptide bonds to form a possible protein
segment.
We say chromosomes hold the
genetic code because they contain
information that specifies the design
and regulation of proteins. The
information stored in a chromosome
by bases is analogous to the
information stored on a computer
disk as binary bits, or to the
information stored in a decimal
number as digits, or to the
information stored on a printed page
as letters and punctuation. The
information stored in one typical
human gene is roughly equivalent to
that stored on one-fourth of an
encyclopedia-type page (1300 letters).
The total information content of the
human genome is roughly equivalent
to 300 encyclopedia volumes (See the note at the end of this chapter). Each set of three bases (a
base triplet is called a codon) within a gene is a code that defines an amino acid by the sequence
of bases in the triplet. The sequence of base triplets in a gene defines the sequence of amino
Amino Acids combine to form a Protein Segment
From Darwin’s Black Box 4
DNA model
Evolution-5
acids in a protein. The genetic code for amino acids is shown in the following table. Most
amino acids can be specified by more than one codon (base triplet).*
Genetic Code for Amino Acids 5
The directions in DNA are read by a molecular machine called RNA polymerase and copied in
the form of mRNA (messenger RNA). This process is called transcription. The mRNA is
transferred to a molecular manufacturing machine called a ribosome. Using the directions in the
mRNA molecule, the ribosome assembles an amino acid chain from amino acids brought to the
ribosome by tRNA or transfer RNA. After assembly, another molecular machine helps the
amino acid chain fold into a protein. Proteins are assembled into the cell’s building blocks and
molecular machines.
Genetic mutations are changes to the sequences of bases. There are different kinds of mutations.
A point mutation replaces one of the bases in a sequence with another base. There are also
deletions, insertions, and transpositions which may change many bases. These changes may
change the amino acid specified in a protein chain which could cause the protein to malfunction,
they could have no effect at all, or they could conceivably improve the protein’s function or
specify a new, functional protein.
To summarize, DNA is a code that has a purpose. Its purpose is to specify the construction and
regulation of proteins through an elaborate process that requires an integrated system of
specialized molecules and molecular machines. DNA replication, necessary for reproduction,
requires the operation of molecular machines that unzip, read, and copy DNA, and molecular
machines require DNA to specify their assembly. DNA and proteins form an interdependent
system, which is necessary for life and reproduction.
______________________________________ * The multiplicity in codons for a single amino acid gives the code a sophistication that goes far beyond what will be
discussed here.
T T T T T
T T A A G
T C A G A
T T C C C C C C
T T T T T T A A
A G T C A G T C
A A A C C
T T T A A
T C A A G
A A A
T A A
G T C
G G G A A
T T T A A
T C G A G
G G G
C A A
A T C
T T T T A A G G
C C C C G G A A
T C A G T C A G
C C C C T T
C C C C G G
T C A G T C
A A A A T
C C C C G
T C A G G
G G G G C C C C A A
C C C C G G G G G G
T C A G T C A G A G
T T G G G G
A A G G G G
T C T C A G
Phenylalanine
Leucine
Isoleucine
Methionine/Start
Valine
Valine/Start
Serine
Proline
Threonine
Alanine
Thyrosine
Stop
Histidine
Glutamine
Asparagine
Lysine
Aspartic acid
Glutamic acid
Cysteine
Tryptophan
Arginine
Glycine
Evolution-6
Chemical Evolution
Darwin’s theory of evolution did not explain how life got started, but the theory of chemical
evolution attempted to fill in this very important
gap. Chemical evolution is the theory (or
hypothesis) that life started when chemicals
combined through random natural processes to
form the molecules of life. According to the
theory, gases in the earth’s early atmosphere, with
the help of lightning, combined to form amino
acids, sugars, phosphates, bases, and other
molecules. These were washed into lakes and
ponds where the amino acids linked into chains to
make proteins. Sugars, phosphates and bases
combined to form RNA and DNA, and lipid
molecules organized to form membranes.
Ultimately, the proteins, RNA or DNA and membranes
“cooperated” to form the first, living one-celled
organisms.
In 1953, the Miller-Urey experiment synthesized some amino acids (the building blocks of
proteins) from atmospheric gases--methane, ammonia, and hydrogen--that were thought to have
been the main gases in the atmosphere at the time life began. Since then, other amino acids and
molecules used in proteins, DNA and RNA have been synthesized in similar experiments. At the
time, the Miller-Urey results seemed to be strong evidence for the theory of chemical evolution
since it demonstrated that amino acids, the building blocks of proteins, which are the building
blocks of life, can be produced by natural processes. Following this success, it was believed that
amino acids could then assemble into functional proteins by natural processes. To date, this has
not been demonstrated. While amino acid strings have been synthesized under very careful
conditions in the lab, they have not been found to assemble into functional proteins in simulated
natural environments outside the cell. In addition, there are some rather serious problems with
the chemical evolution theory.
Problem 1: The Miller and subsequent experiments used an “atmosphere” consisting of
methane, ammonia, and hydrogen but no oxygen. Oxygen would disrupt the formation of amino
acids and other molecules needed for life. Today, scientists believe that methane, ammonia, and
hydrogen were not primary constituents of the early atmosphere, and some believe the
atmosphere may have contained small amounts of oxygen from the photo-dissociation of water
vapor 6.
Problem 2: Amino acids link to each other by peptide bonds, but these bonds do not form
spontaneously. In a neutral environment, peptide bonds require the addition of energy and a
mechanism for using the energy to assemble the molecules 7. In a living cell, amino acids are
linked together by a molecular machine called a ribosome using an RNA transcript and ATP as
an energy source. The peptide bond reaction liberates water and requires a drying environment.
At the same time, a wet environment loaded with amino acids is required to bring different
amino acids together.
Miller Urey Experiment from
answersingenesis.org
Evolution-7
Problem 3: The processes that form amino acids and other basic life molecules also form
contaminants including amino acids that are not used in proteins. There are about 500 different
amino acids, but only 20 are used in proteins. If a non-protein amino acid or other contaminant
links with an amino acid chain, the chain will be useless as a protein.
Problem 4: Nineteen of the twenty amino acids used in proteins come in both left- and right-
handed symmetries. Roughly equal numbers of each are produced in origin-of-life experiments,
but proteins can use only left-handed amino acids. If a right-handed amino acid is included in
the amino acid chain, the chain will be useless as a protein. This is called the chirality problem.
The probability of assembling a short chain of amino acids (400 amino acids long) with all
left-handed amino acids is infinitesimally small (roughly one chance in 5x1061). This
probability is computed in the Chirality Problem breakout below.
The computation assumes the following:
All the carbon in Earth’s crust is used to assemble a reservoir of amino acids;
Amino acids are randomly drawn from the reservoir of half left-handed and half right-
handed amino acids to form strings of 400-amino acids until all amino acids are used;
Every second for 500 million years the chains formed are disassembled to restore the
reservoir and the assembly process is repeated; and
The probability that one of those strings formed every second for 500 million years
contains all left-handed amino acids is calculated.
Problem 5: Not all amino acid strings, even if there are all left-handed amino acids in the string,
will fold into a functioning protein. Doug Axe estimates 1 in 1077 amino acid chains will fold to
produce a functioning protein for amino acid chains that are 150 amino acids long 8.
Problem 6: The simplest living, reproducing cell requires at least 100 (and probably 200 to 400)
average sized proteins 9. Proteins consist of between 50 and 3000 amino acids, and the median
length for bacterial proteins is roughly 400 amino acids 10. If the probability of assembling a
single functioning protein using random, natural processes is infinitesimally small, assembling
100 proteins that work together is far beyond the reach of natural processes. Mathematician and
Astronomer Fred Hoyle calculated the probability of randomly producing the proteins necessary
for a living cell to be 1 in 1040,000 11.
Problem 7: The first living, reproducing cell would also require DNA and RNA to specify
proteins and a cell wall to protect the cell. This cell would require DNA with at least 120,000
base pairs 12. The problems associated with assembling sugars, phosphates and bases into DNA
or RNA is a more difficult problem than assembling amino acids into proteins.
Evolution-8
Note: Large and Small Numbers
In this Chapter I use scientific notation as a shorthand to represent very large or very small
numbers. These numbers are written like 103 or 106 or 10-3. We call them ten to the third
power, ten to the sixth power, and ten to the negative third power respectively. 103 means
10 used as a multiplying factor three times or 10x10x10, which is equal to 1000 or one-
thousand. 106 means 10x10x10x10x10x10, which is 1,000,000 or one million. 10-3
means 1 divided by 103 or 1/(10x10x10), which is one one-thousandth, 1/1000, or 0.001.
109 is one-billion (1,000,000,000), and 1012 is one-trillion (1,000,000,000,000). 10100 is 1
followed by 100 zeros, and 10-100 is a decimal point followed by 99 zeros and a one. The
following examples will give a rough idea of how large or small a number is.
A typical worker in the U.S. earns 4x104 (4 times 104 or 40,000) dollars a year.
There are about 3x108 (300 million) people in the U.S.
The U.S. national debt is about 2x1013 (20 trillion) dollars.
There are roughly 7x1013 cells in the human body (70,000,000,000,000).
There are about 4x1025 atoms in a cubic meter of air
(40,000,000,000,000,000,000,000,000).
There are roughly 1x1011 (one-hundred billion, 100,000,000,000) stars in the Milky Way
Galaxy.
There are toughly 1x1011 galaxies in the known universe.
There are about 1x1057 atoms of hydrogen in our sun.
There are roughly 1x1080 atoms in the known universe.
Human hair ranges from 2x10-5 (.00002) to 2x10-4 (.0002) meters in diameter.
A micron is 1x10-6 meters across (.000001).
An atom is roughly 2x10-10 meters in diameter (.0000000002).
Evolution-9
The Chirality Problem
A simple bacterium needs a few hundred proteins to live and reproduce. The average
bacterial protein is 400 amino acids long. Amino acids from Miller-Urey type experiments
come in equal numbers of left- and right-handed symmetries—chirality. Only left-handed
amino acids are used in proteins. What is the probability that a random, natural process
could have assembled a single 400 amino acid string using all left-handed amino acids?
It is estimated (on the high side) that there are 1020 kg of carbon in the earth’s crust,
oceans, and atmosphere—that is 5x1045 carbon atoms. An average amino acid uses
roughly 4 carbon atoms, so, using all the Earth’s carbon, 1.25x1045 amino acids can
theoretically be made. We assume that these amino acids go into a reservoir from which
amino acids are drawn to assemble amino acid strings. From this reservoir, we will
assemble amino acid strings of 400 amino acids to make 1.25x1045 /400 = 3.1x1042 strings.
To make a string of amino acids we randomly draw amino acids from the reservoir
containing half left-handed and half right-handed amino acids. The probability that the
first amino acid we draw from the reservoir is left-handed is ½ since half are left-handed.
The probability that the second is left-handed is also ½. The probability that both are left-
handed is ½ x ½ = ¼ since there are four possible outcomes with only one of them getting
left-handed amino acids on both draws: RR, RL, LR, LL. If we draw three amino acids,
the probability that all three are left-handed is ½ x ½ x ½ = 1/8. There are eight
possibilities with only one being all left-handed: RRR, RRL, RLR, LRR, RLL, LRL, LLR,
LLL. We use ½ as a multiplying factor each time we draw a new amino acid to calculate
the probability that we get all left-handed amino acids. The probability that we will get
400 left-handed amino acids is (1/2)400 = 3.8 x 10-121 or 1 chance in 2.6 x 10120. This is for
the first try, but we can assemble 3.1 x 1042 strings (see above) using all the amino acids
made from all of Earth’s carbon. With all these amino acid strings, the probability of
getting one string with all left-handed amino acids is 3.8x10-121 x 3.1x1042 = 1.2x10-78.
But we have lots of time so we can disassemble and randomly reassemble that many
strings. We assume we can do that every second in the 500 million years between the time
the earth cooled sufficiently for life to exist and the first living cells are seen in the fossil
record. 1.6 x 1016 is the number of seconds in 500 million years. I use one second as the
assembly time even though it takes a ribosome about a minute to assemble a small protein.
The probability of getting one string with all left-handed amino acids is 1.2x10-78 x
1.6x1016 = 1.9x10-62.
This is the probability of getting one 400 amino acid string with all left-handed amino
acids using all of Earth’s carbon and all of the time available. This probability is: