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.

A nucleotide is made up of one sugar

molecule (deoxyribose), one phosphate

molecule, and one base molecule. Sugar

and phosphate molecules make up the sides

of the “ladder,” and pairs of bases make up

the rungs. There are four kinds of base

molecules: thymine (T), adenine (A),

cytosine (C), or guanine (G). Base

molecules are paired across the rungs of the

“ladder” with A always pairing with T and

C always pairing with G; thus, one side is

the “reverse image” of the other. The sides

of the ladder hold the base-pairs in a

sequence. The sequence of bases makes up

the genetic code. Any base-pair can follow

another in the sequence.

The Cell Separate compartments with unique

chemical environments

Controlled access passages between

compartments

A molecular transportation network to

supply raw materials and distribute finished

products

Molecular machines

Hauling cargo Cables, ropes, pulleys

Switches Energy conversion

Propulsion Manufacturing

Unzipping, reading, and duplicating DNA

A library (chromosomes) containing

information that specifies how to build and

regulate proteins (DNA)

Harris; DDD-V; September 2004 2

© 2001 Sianuer Associates, Inc.

Life: The Science of Biology, 6th edition by

Purves et al (2000) Fig 4.7a.

By Permission of Oxford University Press, USA

www.oup.com

Evolution-4

Humans have a total of roughly 3 billion base-

pairs divided among our 46 chromosomes. Each

chromosome contains base sequences called

genes, which are the code for building proteins

and comprise roughly 2% of our DNA. A typical

gene is composed of 3,000 bases. The remainder

of our DNA has been called “junk” DNA because

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:

0.000000000000000000000000000000000000000000000000000000000000019

Evolution-10

In a living cell, the assembly of a protein requires carefully controlled environments, molecular

machinery, and the information provided by RNA, not just matter, energy, and amino acids.

RNA transcription and DNA replication require the action of protein machines. These form an

integrated, interdependent system in a living cell. Assembly of the first living cell is out of reach

for natural processes. Astrophysicist and mathematician Fred Hoyle compared the probability of

the first living cell being naturally assembled to a tornado going through a junk yard and

assembling a Boeing 747 13.

Since assembly of proteins or DNA by natural processes is extremely improbable (outside a

living cell), it has been conjectured that the path to life started with self-replicating molecules.

One conjectural example is a reproducing strand of RNA called a ribozyme. Some ribozymes

have catalytic capabilities like proteins and store information like DNA. However, their catalytic

properties are insufficient for the integrated, coordinated functions required for reproduction.

Also, ribozymes are fairly long strings of bases, and assembling a functioning ribozyme faces the

same difficulties as assembling proteins or DNA.

To summarize: while the basic molecular building blocks for proteins and DNA have been

synthesized in the lab using a carefully controlled environment, the assembly of these building

blocks into proteins and DNA has never been achieved in the lab using natural conditions. The

probability that they could randomly assemble into functional proteins and DNA, much less a

living cell, even if all the Earth’s material and temporal resources were available, is so

infinitesimally small that the chemical evolution hypothesis should be discarded. Problems with

the origin of life have been acknowledged by some.

Klaus Dose: (Dose is a professor of biochemistry at the Johannes Gutenburg University.) “More

than 30 years of experimentation on the origin of life in the fields of chemical and molecular

evolution have led to a better perception of the immensity of the problem of the origin of life on

Earth rather than to its solution. At present, all discussions on principal theories and experiments

in the field end either in stalemate or in a confession of ignorance” 14.

The Chirality Problem, Continued

Calculating the probability by multiplying the number of tries by the probability of getting

one right is not exactly correct, but it is an accurate approximation for small probabilities,

which is true for this case. [Rigorously: P = 1-(1-p)n where “P” is the probability of getting

at least one left-handed string in “n” tries, and “p” is the probability of getting a left-handed

string in one try.] Thus, the probability of getting a single string of 400 left-handed amino

acids using all the available resources and time on Earth is infinitesimally small, and this

assumes there is a mechanism for assembling amino acids into a string, but there is no

known natural mechanism for assembling amino acids outside the living cell. This

calculation tells us that the chances of getting a single, functioning protein is infinitesimally

small. The probability is actually much smaller than that because we have neglected other

amino acids that do not participate in proteins and contaminants which could poison the

assembly of an amino acid string, and because very few strings of left-handed amino acids

will form a functioning protein.

Evolution-11

Francis Crick (co-discoverer of DNA’s structure in 1953 and an evolutionist) said “An honest

man, armed with all the knowledge available to us now, could only state that in some sense, the

origin of life appears at the moment to be almost a miracle, so many are the conditions which

would have had to have been satisfied to get it going” 15. This statement is still true today. On

the other hand, claiming the death of the chemical evolution hypothesis is premature as seen in

the following statements.

For example, Robert Shapiro stated: “Some future day may yet arrive when all reasonable

chemical experiments run to discover the probable origin of life have failed unequivocally.

Further, new geological evidence may indicate a sudden appearance of life on earth. Finally, we

may have explored the universe and found no trace of life, or processes leading to life,

elsewhere. In such a case, some scientists may choose to turn to religion for an answer. Others,

however, myself included, would attempt to sort out the surviving less probable scientific

explanations in the hope of selecting one that was still more likely than the remainder” 16.

Neo-Darwinian Evolution

Neo-Darwinian Evolution is considered to be a proven fact among many scientists.

Official 1995 Position Statement of the American National Association of Biology

Teachers: “The diversity of life on earth is the outcome of evolution: an unsupervised,

impersonal, unpredictable and natural process of temporal descent with genetic modification that

is affected by natural selection, chance, historical contingencies and changing environments.”

(This statement has since been altered by removing the words “unsupervised” and “impersonal.”)

Julian Huxley, 1959 speech in Chicago: “In the evolutionary pattern of thought there is no

longer either need or room for the supernatural. The earth was not created, it evolved. So did

all the animals and plants that inhabit it, including our human selves, mind and soul as well as

brain and body.”

Although chemical evolution fails to explain how life started, we will presume that life did get

started by some mechanism and consider the possibility that Darwinian processes explain the

evolution of life from single celled organisms to the variety of complex, multi-celled organisms

we see today. Darwin noticed that selective breeding can produce new varieties within a species,

for example in pigeons. He also saw change over time in the fossil record. Darwin theorized

that, if variation and natural selection can produce small beneficial changes over a short time,

then variation and natural selection can produce large beneficial changes over a very long time

and lead to the new biological organisms seen in the fossil record. This is the basis for the theory

of Darwinian Evolution. For the information Darwin had available at the time, this was a

reasonable theory. At the time, Darwin did not know the mechanism for a variation, but when

the structure and role of DNA was discovered in the 20th century, variations were explained by

mutations to DNA and resulting changes to proteins.

The neo-Darwinian mechanism consists of random changes (mutations) to DNA, which

supposedly produce new proteins and protein interactions. Since the sequence of bases in DNA

determines the sequence of amino acids in a protein chain, a change in the DNA base sequence

Evolution-12

can change the amino acid sequence in a protein and theoretically produce a new functioning

protein. If the new protein is beneficial, it will be passed to future generations by natural

selection. If it is detrimental, it will be bred out of the population by natural selection. If it is

neither detrimental nor beneficial, it could persist indefinitely if it does not change the protein’s

function.

Mutations can cause small changes to the offspring of an organism. These small changes are

referred to as microevolution.

Another example of mutations causing changes is seen in parasitic, bacterial, and viral

development of resistance to drugs. Resistance is usually developed by a single point mutation.

Even though mutations can provide resistance to drugs, no bacterium has been observed to

evolve into a new species of bacteria.

Darwinian evolution must explain not just the small changes of microevolution but the large

changes of macroevolution. It must explain the evolution from single celled organisms to the

complex organisms we see today. To evolve from a single celled organism to the organisms we

see today requires the development of many new systems such as nervous systems, circulatory

systems, skeletal systems, digestive systems, and reproductive systems. These new systems

required thousands of new proteins and multi-protein interactions, which required large-scale

changes to the genome by adding new genetic information to chromosomes. Can a process of

random genetic mutation operated on by natural selection produce these new proteins and protein

interactions?

In the next few paragraphs, five arguments against Darwinian evolution are presented.

1. Argument from Irreducible Complexity

In his book, Darwin’s Black Box, Ph.D. microbiologist Michael Behe discusses the evidence

against the neo-Darwinian mechanism offered by irreducibly complex molecular systems 17.

Irreducibly complex systems are systems made up of several parts that will not function unless

all parts are present. To illustrate irreducible complexity, Behe uses the example of a mouse trap

consisting of a platform, a spring, a hammer, a holding bar, and a catch. If any one of these parts

is missing, the mouse trap will not function. Likewise, the formation of a new, microbiological

system requires many new interactive proteins and corresponding mutations to the DNA

sequences which code for the new proteins. If any single protein is missing, the whole system is

useless. All proteins of a microbiological system must be present at the same time for the system

to function and be beneficial. Can the system be built up over time, protein by protein? If a

An example of mutations causing a small change is seen

in a fruit fly where three mutations produce an extra set

of wings, but the fly has no muscles, nerves, or control

system to make them work. Natural selection would

soon remove these fruit flies from the breeding

population because the extra set of wings interferes with

flight.

Evolution-13

protein and its corresponding DNA sequence is not beneficial, it will disappear through the same

mutation process that formed it. Neo-Darwinian evolution does not plan ahead and retain

proteins that may be useful in the future. The probability that mutations can produce a single

new functional protein is very small. The probability of getting all the necessary new proteins

together at the same time to produce a new, functioning system before some are mutated away is

infinitesimally small and cannot explain the large number of these systems that exist. Behe gives

some examples of irreducibly complex protein systems:

Vision: There are 10 proteins in the cascade that turns a photon striking the retina into an

electric impulse in the optic nerve. If any of these 10 is missing, the process does not work at all.

In addition to these 10 proteins are many supporting proteins. Not only do the proteins have to

be there, they have to be constructed in the proper sequence and maintained in proper balance.

Blood clotting: Blood clotting is a complicated and very precise process that requires a cascade

of at least 14 proteins. If any one is missing, blood will not clot or it will clot throughout the

organism.

Immune system antibodies: A first antibody attaches to the surface of an invading cell, and the

cell is destroyed when ten different antibodies (proteins) intricately lock together and blow a hole

in the invading cell’s membrane. Each protein must be present for the system to operate.

Molecular machines perform the processes necessary in a living cell. They are irreducibly

complex, requiring a large number of interacting proteins. If one protein is missing, the machine

will be useless. All of the parts of the machine must be there at the same time for the machine’s

instructions to remain in the genome.

The bacterial flagellum is a good

example of an irreducibly complex

molecular machine. It consists of

parts formed by 40 different

proteins. If any one of the proteins

is absent, the flagellum is useless

and would be eliminated in future

generations of bacteria. Building a

nonfunctioning flagellum requires

significant energy but gives no

benefit. A bacterium with a

useless flagellum would be unable

to compete with bacteria that

require less energy. It would be

eliminated from the population.

Kenneth Miller, in his article “The Flagellum Unspun: The Collapse of ‘Irreducible

Complexity,’” argues that proteins analogous to the motor proteins in the flagellum’s motor are

found in other molecular machines within the bacterium 18. In fact, he suggests that all of the

proteins found in a system might have independently developed in other beneficial systems.

When they are all present in the next generation, they will assemble into a bacterial flagellum. If

this is true, having all the necessary proteins at the same time is much more probable. This

Bacterial Flagellum

(Artist’s reproduction from an electron micrograph)

From the Discovery Institute, discovery.org

Evolution-14

argument is called co-option, and while it sounds like a reasonable theory, it has some serious

problems.

If co-option were true, we would expect to find all analogous bacterial flagellum proteins used in

different beneficial functions in the bacterium, but we don’t. Only some analogous proteins are

found. They are analogous to but not the same as those needed for the new flagellum. They

must undergo at least a few mutations to interact with the other proteins in the system. There

must also be a protein system for the assembly process which builds the flagellum and another

protein system to maintain the flagellum. The machine, its assembly process, and its

maintenance process would have to be present for the flagellum to be built, work, and keep

working. We would expect to find proteins for assembly, repair, regulation, and control of the

flagellum that came together from other systems, but we don’t. The idea that all of the

components of a multi-protein flagellum, its assembly process, and its maintenance process

developed independently and then came together to form a new biological system is

infinitesimally improbable and has never been demonstrated.

2. The Problem with Changing Protein Function

Is it even possible for a protein having one function to evolve by random mutation into an almost

identical protein with a different function? In recent experiments, Gauger & Axe started with

functional proteins that are almost

identical in structure but have different

functions 19. They attempted to mutate

one protein to obtain the function of

the other. They determined that more

than seven mutations were necessary,

ran a population genetics model, and

found that seven mutations would

require far longer than 15 billion years

and is thus out of reach for a random

mutation-natural selection process. This implies that the probability of random mutation and

natural selection developing a new functional protein, even from a nearly identical one is

extremely small. In addition, many systems contain “orphan” genes and proteins. These are

genes and proteins that are unique in structure. The number of mutations needed to develop

these proteins is far beyond the capability of random mutation and natural selection.

3. The Problem with Creating New Protein Binding Sites

Proteins interact with each other through binding sites. Most proteins work together in groups of

six or more. The bacterial flagellum consists of forty interacting proteins. New biological

systems using hundreds of new proteins and their interactions are required for Darwinian

evolution. In The Edge of Evolution, Michael Behe documents laboratory experiments on cell

growth and the development of resistance by parasites, bacteria, and viruses to drugs. P.

falciparum is the parasite that causes malaria by attacking red blood cells. The drug chloroquine

interferes with the parasite’s ability to neutralize the heme molecule of hemoglobin which is

poisonous to the parasite. P. falciparum developed resistance to chloroquine when two amino

acids were changed (with corresponding DNA mutations) in a protein which participates in

pumping chloroquine out of the parasite’s gut. By multiplying the number of people who have

Nearly Identical Proteins

from Bio Complexity 19

Evolution-15

been infected by malaria since chloroquine was introduced times the number of P. falciparum

parasites in an infected person, Behe concluded that the two coordinated mutations occurred at

some point in a population of 1020 parasites. According to Behe, it takes five or six mutations to

produce a new protein binding site that would bind two proteins. He generously assumed that

the mutations needed to produce a new binding site would require the same number of cells

(1020) as the number of parasites required to change two amino acids in P. falciparum. Since

mutations are random, two new coordinated binding sites for a new three-protein interaction

might be possible in 1040 cells. Since 1040 cells is the number of cells that have lived on Earth in

all organisms from the beginning of life, the coordinated interaction of more than three new

proteins is out of range for a Darwinian process 20. New biological systems, like nervous

systems, circulatory systems, skeletal systems, digestive systems, and reproductive systems,

require far more than three new proteins and their interactions and therefore did not arise through

random genetic mutation operated on by natural selection.

4. The Problem of Searching for a Functioning Protein

Genetic mutations may change the amino acids in a protein. Theoretically changing one or more

amino acids in a protein could produce a new functioning protein, but how many functioning

proteins are there among all the possible amino acid strings? In a paper Estimating the

Prevalence of Protein Sequences Adopting Functional Enzyme Folds in the Journal of

Molecular Biology, Doug Axe estimated that only 1 in 1077 amino acid chains will fold to

produce a functioning protein for amino acid chains that are 150 amino acids long 8. Thus,

functioning proteins are very rare among strings of amino acids, and finding one by random

mutation is like finding a needle in a haystack. Since there have been 1040 cells since the

beginning of life, there have not been enough cells to find a functioning protein by random

mutation.

5. The Source of an Organism’s Architecture

Besides the development of new systems, Darwinian evolution requires he development of new

body architectures. A body architecture is the way the body is put together, for example, worms,

fish, and birds all have different body architectures. Until recently it was believed that DNA

determined the architecture of an organism. In 2009, Jonathan Wells, a Ph.D. in biology

specializing in embryological development, gave a lecture on research indicating that DNA may

have little to do with an organism’s architecture 21. The design for an organism’s body comes

from something in the egg or ovum (for animals). In this research, experiments with various

animal species replaced the DNA in the egg or ovum of one species with the DNA of another

species. The embryo developed with the architecture of the egg’s species then died, presumably

because the DNA did not produce the proteins necessary for the egg species’ architecture. It

appears that DNA plays a very limited role in the architecture of a species other than supplying

and regulating the building materials, which are proteins. This implies that the neo-Darwinian

process of random mutation, which alters DNA, and natural selection is not the mechanism for

changing body architecture 22,23. I hate mentioning this because I really enjoyed the movie

Jurassic Park.

Each of these five arguments show that the neo-Darwinian mechanism of random mutation and

natural selection is inadequate to produce the biological systems required for evolution from a

bacterium into a complex vertebrate. The mechanism of random mutation and natural selection

Evolution-16

is incapable of producing the life we see today. So, what is capable of producing the life we see

today? We will get to that in a minute.

The neo-Darwinian theory of evolution is not going to die easily, but cracks are forming.

James Shapiro, who is a professor of biochemistry and molecular biology at the University of

Chicago, wrote: “The past five decades of research in genetics and molecular biology have

brought us revolutionary discoveries. Rather than confirm the oversimplified views of cellular

organization and function held at mid-century, the molecular revolution has revealed an

unanticipated realm of complexity and interaction more consistent with computer technology

than with the mechanical viewpoint, which dominated when the neo-Darwinian Modern

Synthesis was formulated. The conceptual changes in biology are comparable in magnitude to

the transition from classical physics to relativistic and quantum physics. … The point of this

discussion is that our current knowledge of genetic change is fundamentally at variance with

postulates held by neo-Darwinists” 24.

Common Descent

The neo-Darwinian process of random mutation operated on by natural selection is not a viable

explanation for the evolution we see in the fossil record, but could common descent still be true?

Common descent is the theory that all life has evolved from one, or perhaps a very few, single-

celled ancestors. The fossil record appears to support the Theory of Evolution in that life has

changed over time. According to the fossil record, the first multi-cellular organisms came into

existence 570-565 million years ago in the form of sponges, cnidarians, and Ediacaran biota. A

detailed look at the fossil record shows that changes were not gradual. Large numbers of new

species, which were totally unlike previously existing species, suddenly appeared from time to

time, remained unchanged for millions of years, then, in most cases, disappeared. A good

example of this sudden change is the “Cambrian Explosion” 530 million years ago in which

there was a giant step from single celled organisms to complicated, multi-celled organisms.

Between 19 & 35 out of 40 phyla came into existence in only 5 to 10 million years 25,26. The

idea that one phylum gave rise to another in an evolutionary process is not supported by the

fossil record. Fossils representing transitions from one species to another appear in the fossil

record very rarely if at all, and those that have been proposed as transitional have been

challenged.

Stephen J. Gould (Harvard Paleontologist) stated: “The extreme rarity of transitional forms in the

fossil record persists as the trade secret of paleontology. The Evolutionary trees that adorn our

textbooks have data only at the tips and nodes of their branches; the rest is inference, however

reasonable, not the evidence of fossils” 27.

In Robert L. Carroll’s popular textbook, he states: “Progressive increase in knowledge of the

fossil record over the past hundred years emphasizes how wrong Darwin was in extrapolating the

pattern of long-term evolution from that observed within populations and species” 28.

Evolution-17

The Fossil Record

The fossil record contains few if any intermediate links, and all are controversial and often

revised.

Archaeopteryx—Archaeopteryx was proposed as the missing link

between reptiles and birds. “Paleontologists now agree that

Archaeopteryx is not the ancestor of modern birds 29.”

Horses—The presumed horse ancestry changes from time to time.

Pliohippus, once thought to be intermediate between merychippus and

equus, is now thought to be a dead-end side branch.

Whales—A 2001 National Geographic article cited evidence that

hippos are the closest land-dwelling relatives of whales. A 2007

Nature article cited evidence that Indohyus, a small, deer-like animal is

the whale’s closest land relative.

Tiktaalik—A 2006 article in Nature calls this fish with limb-like front fins an intermediate

between fish and amphibians. A 2010 Nature article tells of finding tetrapod (amphibian)

footprints with toes dated at 20 million years before Tiktaalik. Tiktaalik was touted as the

missing link between fish and amphibians until the footprints were found.

Man—Evidence tying modern humans and chimpanzees to a common ancestor is controversial.

Early DNA studies had shown that base pair sequences of protein coding genes for chimps and

humans are 98-99% the same, but more recent studies have shown that total DNA may be only

70-76% the same 30. In addition, Humans have “ORFan” genes dissimilar to any chimpanzee

genes. Possible evidence for common descent is that humans and chimpanzees have the same

“broken copy” of a vitamin C gene. Some animals can synthesize vitamin C, but man and

chimpanzees cannot. If this is truly a broken gene, common ancestry would be the best

explanation. This broken gene is in a class of DNA sequences called “pseudo-genes.” Many

pseudo-genes like the “broken vitamin C gene” have been found to have important functions

implying that common descent may not be the only explanation 31. Skeletal evidence for

anthropoids who lived before Homo Erectus touted them them as missing links between modern

man and a presumed human-chimpanzee common ancestor, but the evidence is fragmentary,

inconsistent, and inconclusive 32.

Archaeopteryx from Wikipedia

Organism Years Ago Blue-green algae in the oceans 3.5 to 1 billion

Blue-green algae and bacteria on land 1.2 billion to 800 million

Single celled animals 1 billion

Invertebrates 600-500 million

Higher plants on land 425-400 million

Fish, amphibians, forests, insects 400-345 million

Reptiles 345-280 million

Dinosaurs, flowering plants 225-65 million

Mammals, birds 65 million

Man 1 million?

Evolution-18

The Original Evolutionary Tree

The original evolutionary tree was constructed using

physical characteristics of organisms to determine

evolutionary connections. Since then, evolutionary trees

have been constructed from the comparison of different

gene and protein sequences and from embryonic

developmental patterns. The relationships shown by one

tree is different than those from other trees. A consistent

tree has not been found. This implies that the

relationships among organisms is far more complicated

than shown by an evolutionary tree and that evolutionary

connections are in doubt 33.

Common descent is by no means a proven fact. The

evidence is inconclusive and molecular and embryonic

evidence challenges the theory of common descent. What

does seem to be true is that change over time, as illustrated in the fossil record, is not gradual.

The general lack of intermediate fossils implies that the Darwinian mechanism of random

mutation and natural selection, being gradual by nature, cannot explain the sudden changes that

are seen in the record. This does not necessarily eliminate common descent, but a non-

Darwinian mechanism for change must have been in operation.

Design in Biology

Richard Dawkins was an Oxford Zoologist and the University of Oxford’s Professor for the

Public Understanding of Science from 1995 to 2008. He is a noted champion for the theory of

evolution. Francis Crick, with Watson, uncovered the structure of DNA. Both Dawkins and

Crick observed that life seems to be designed, but rejected their observations in favor of

materialistic, Darwinian mechanisms.

One of the major problems for the Theory of Evolution is that life is complex, and not only

complex in a random way, but complex in a specified way. By specified, we mean that it has

purpose or meaning, and William Dembski, who has Ph.Ds. in both math and philosophy, calls

this specified complexity 35. In other words, some aspects of life show characteristics of having

been designed for a purpose, with an end in mind.

“Biology is the study of complicated things that give the appearance of

having been designed for a purpose” 34.

(Dawkins, The Blind Watchmaker)

“Biologists must constantly keep in mind that what

they see was not designed, but rather evolved.”

(Crick, What Mad Pursuit, 1988, p.138)

Evolution-19

To state it simply, design is something humans can recognize:

It has a Meaning or Purpose (we call this “specification”),

It is sometimes Complex, and

It is not the product of an Automatic Process.

Quite often design can be recognized in an integrated system of parts that has a function.

Something can be very complex and not be designed, for example the Grand Canyon. The

difference between the Grand Canyon and the carved heads on Mt. Rushmore is that Mt.

Rushmore specifies something, namely faces of known presidents. Specification can refer to a

pattern agreed upon in advance, a prescription that performs a specific function, or a pattern that

has recognizable meaning. It is also possible that something can be designed but not complex,

like a plain glass window; therefore, Dembski’s criteria for specified complexity cannot identify

everything that is designed; but it can infer that something which has specification and is

sufficiently complex is designed. In some cases, things that are the result of an automatic

process, like crystals or snow flakes, may appear to be specified but are not.

A living cell is full of molecular machines that carry out the cell’s processes. Molecular

machines use a system of integrated, interacting parts, they are extremely complex, and they

serve specific functions. Many of them look like machines designed by human engineers. The

best explanation for their existence is that they were designed with a purpose in mind. Three

molecular machines are shown below.

A bacterial flagellum rotates to propel the

bacterial cell. The flagellum is driven by a

molecular motor, which runs on protons

(instead of electrons). The flagellum is made

up of more than six different moving parts

(rotor, stator, drive shaft, bushings, a

universal joint, and a propeller) consisting of

roughly 40 proteins. Not only is the system

complex, but it must be assembled in a

specific sequence by assembly machines.

One might be inclined to say that it looks

like a motor. That would be incorrect

because it is a motor.

F1F0 ATP synthase is a molecular machine embedded

in a mitochondria’s wall that synthesizes ATP from

ADP using the energy from a proton motor. ATP is a

highly energetic molecule used to store, transport, and

provide energy for cell functions. The head of the

machine protrudes into the cell and joins an ADP to a

phosphate molecule making ATP using the spinning

head’s energy. The ATP gives up its phosphate

molecule to power a cell function and then returns to

the ATP synthase to be recharged. Lipidmembrane

b

ab

g

ATP

ADP

H+

H+

ac’s Lipid

membrane

b

ab

g

ATP

ADP

H+

H+

ac’s Lipid

membrane

b

ab

g

ATP

ADP

H+

H+

H+

H+

ac’s

F1F0ATP Synthase

Bacterial Flagellum

(Artist’s reproduction from an electron micrograph)

From the Discovery Institute, discovery.org

Evolution-20

A ribosome (left) is a molecular machine made of 50

proteins that assembles proteins as described earlier in

this chapter. Amino acids are brought to it by tRNA

(transfer RNA). An mRNA (messenger RNA) template

is brought to it from the cell’s nucleus. The mRNA is a

string of base letters (A, C, U, and G) with each three

letters (a codon) in the sequence specifying an amino

acid. The sequence of codons specifies the amino acids

to be connected and the order in which they are to be

connected. The ribosome reads the template and

connects the prescribed amino acids in the prescribed

order to form a protein.

DNA is a complex code that has a purpose, which is to specify how to build and regulate the

proteins that compose molecular machines; thus, it has specified complexity. During

reproduction, the DNA code must replicate, which it does using molecular machines that read the

code and duplicate it. These DNA replication machines are assembled from proteins by other

molecular machines, ribosomes, that use the specifications given by DNA through RNA. Thus,

DNA and molecular machines form an integrated system of interdependent parts whose purpose

is to give life and reproduce. Design, with an end in mind, is the only realistic explanation for

this living, reproducing system.

According to Paul Davies (Davies is a theoretical physicist, visiting professor at Imperial College

and honorary professor at the University of Queensland, Australia.): “The world is already full of

nanomachines: they are called living cells. Each cell is packed with tiny structures that might

have come straight from an engineer's manual. Miniscule tweezers, scissors, pumps, motors,

levers, valves, pipes, chains, and even vehicles abound. But, of course, the cell is more than just

a bag of gadgets. The various components fit together to form a smoothly functioning whole,

like an elaborate factory production line. The miracle of life is not that it is made of nanotools,

but that these tiny diverse parts are integrated in a highly organized way.” “A law of nature of

the sort we know and love will not create biological information or indeed any information at all.

... The secret of life lies, not in its chemical basis, but in the logical and informational rules it

exploits. ... Real progress with the mystery of biogenesis will be made, I believe, not through

exotic chemistry, but from something conceptually new” 36. While Davies described a designed

system, he is not an intelligent design proponent.

William Dembski, in his essay in Debating Design says: “Science is supposed to give the full

range of possible explanations a fair chance to succeed. That’s not to say that anything goes; but

it is to say that anything might go. In particular, science may not, by a priori fiat, rule out logical

possibilities. Evolutionary biology, by limiting itself exclusively to material mechanisms, has

settled in advance the question of which biological explanations are true, apart from any

consideration of empirical evidence. This is armchair philosophy. Intelligent Design may not be

correct. But the only way we could discover that is by admitting design as a real possibility, not

by ruling it out a priori.” He goes on to quote Darwin from The Origin of Species: “A fair result

can be obtained only by fully stating and balancing the facts and arguments on both sides of each

question 37.”

Evolution-21

Conclusion

There is little, if any, evidence that the mechanism of random mutation operated on by natural

selection can do more than fine tune an existing organism, and there is significant evidence that

it is incapable of evolving the systems necessary for complex life. There is even less evidence

that chemicals can organize by natural processes into the molecules of life beyond amino acids,

much less living cells, and there is convincing evidence to the contrary. Even the evidence for

common descent is inconclusive. The most reasonable explanation for the existence of DNA,

molecular machines, and life is both intuitive and mathematically defensible--they were

designed. So, if life did not develop by a neo-Darwinian evolutionary process but was designed,

who designed it?

In the beginning, God created the heavens and the earth. He created vegetation,

living creatures in the water, in the air, and on land according to their kind, and

He created man in His image. (Genesis 1)

While evidence pointing out the weaknesses of the Neo-Darwinian Theory of Evolution has been

growing since the 1950s, most scientists and biology teachers still believe that macroevolution is

a proven fact. Neo-Darwinian Evolution was an elegant and plausible theory before the

discoveries of modern genetics and biochemistry revealed the complex nature of the cell, the

code for proteins in DNA, and the operation of molecular machines. The fossil record was

relatively incomplete in Darwin’s time leaving open the possibility of transitional forms being

discovered, but that has not happened. Even so, there appears to be a commitment to a

naturalistic explanation for the origin of life by many scientists and biology teachers, as is

demonstrated in the statement by Richard Lewontin below.

Richard Lewontin is a Harvard Genetics Professor, and his comment comes from The New York

Review of Books, 2/9/1997: “We take the side of science in spite of the patent absurdity of some

of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and

life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories,

because we have a prior commitment, a commitment to materialism. It is not that the methods

and institutions of science somehow compel us to accept a material explanation of the

phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material

causes to create an apparatus of investigation and a set of concepts that produce material

explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated.

Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door”

(emphasis added). 38

There is a divine foot in the door, and no one has the authority to allow or disallow it, only to

accept that it is there or to ignore it. Since “there is a divine foot in the door,” the resurrection of

Jesus, discussed in Chapter 1, is plausible.

Evolution-22

The Information Content of DNA

To compare the information content of DNA to that of English words, we can use some

basic information theory 35. According to the theory, the information content for a string of

letters is related to the number of permutations (different arrangements) that can be formed

by the string of letters. Imagine an alphabet containing three letters, A, B, and C. If a word

contains 1 letter there are three possible ways to “spell” it: A, B, or C, and we have 3

permutations. If our word in our three-letter alphabet has two letters, there are 9 (which is 3

x 3) ways to spell it: AA, AB, AC, BA, BB, BC, CA, CB, CC, and we have 9 permutations.

If there are three letters in our three letter alphabet word, there are 27 ( which is 3 x 3 x 3)

ways to spell it: AAA, AAB, AAC, ABA, ABB, ABC, ACA, ACB, ACC, BAA, BAB,

BAC, BBA, BBB, BBC, BCA, BCB, BCC, CAA, CAB, CAC, CBA, CBB, CBC, CCA,

CCB, CCC. Do you see the pattern? Each time we add a letter to the word (or sequence)

we multiply by the number of letters in our alphabet. So, the number of permutations is

equal to the number of letters in our alphabet used as a multiplier N times where N is the

number of letters in our word.

Now, consider our 26-letter alphabet but ignore capitalization and punctuation. For a

sequence of 10 letters (for example a 10-letter word) there are 2610 (which is 26 x 26 x 26 x

26 x 26 x 26 x 26 x 26 x 26 x 26) possible combinations or permutations of letters. There

are 26 ways to pick the first letter, 26 ways to pick the second letter, 26 ways to pick the

third letter, and so on 10 times, and we multiply 26 10 times to get the total number of

possible combinations. A specific sequence of 10 letters represents 1 out of 2610

possibilities, and if the sequence has meaning, its uniqueness eliminates a lot of other

possible meanings and it conveys information. If there are more letters in a word, phrase,

sentence paragraph or book, then more information can be conveyed. For our example of a

26-letter alphabet and 10 letters in a sequence, the information content is said to be 2610 and

the specific information is 1 in 2610.

Since there are 3 billion base pairs in human DNA and there are 4 base molecules (4 letters

in DNA’s alphabet), then a measure of the information in our DNA is 43,000,000,000, which is

roughly equivalent to 261,300,000,000. In other words, 3 billion base pairs contain roughly the

same information content as 1.3 billion letters. My encyclopedia set contains roughly 650

pages per volume, 120 lines per page, and 55 letters per line. The number of volumes

needed to hold 1.3 billion letters is 1.3 billion divided by (650 x 120 x 55) ≈ 300. Thus,

our DNA contains roughly the same information content as 300 encyclopedia volumes.

Evolution-23

References

1. Darwin, Charles; The Origen of Species, Modern Library; NY, 1998.

2. Harris, William; Darwin, Design, and Democracy V; Albuquerque, September 2004.

3. Wells, Jonathan; The Myth of Junk DNA; Discovery Institute, 2011.

4. Behe, Michael J.; Darwin’s Black Box; Simon and Schuster, New York, NY, 1996; Page

261.

5. Behe, Michael J.; Darwin’s Black Box; Simon and Schuster, New York, NY, 1996; Page

269.

6. Meyer, Stephen; Signature in the Cell; Harper One, New York, NY, 2009; Page 224.

7. Thaxton, Charles; Bradley, Walter; and Olsen, Roger; The Mystery of Life’s Origin:

Reassessing Current Theories; Philosophical Library, 1984; Page 135.

8. Axe, Doug; Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme

Folds; J. Molecular Biology, 341, 2004.

9. Denton, Michael; Evolution: A Theory in Crisis; Adler & Adler, Bethesda, MD, 1986; Page

264.

10. Behe, Michael J.; Darwin’s Black Box; Simon and Schuster, New York, NY, 1996; Page

262.

11. Meyer, Stephen; Signature in the Cell; Harper One, New York, NY, 2009; Page 213.

12. Denton, Michael; Nature’s Destiny; The Free Press, New York, NY, 1998; Page 309.

13. Meyer, Stephen; Signature in the Cell; Harper One, New York, NY, 2009; Page 257.

14. Dose, Klaus; The Origin of Life: More Questions than Answers, Interdisciplinary Science

Review 13, 1988; Page 348.

15. Crick, Francis; Life Itself, 1988.

16. Shapiro, Robert; Origins: A Skeptic’s Guide to the Creation of Life on Earth; Bantam, 1986.

17. Behe, Michael J.; Darwin’s Black Box; Simon and Schuster, New York, NY, 1996.

18. Dembski, William and Ruse, Michael; Debating Design; Cambridge University Press, 2004.

19. Gauger & Axe; The Evolutionary Accessibility of New Enzyme Functions: A Case Study from

the Biotin Pathway; Bio Complexity 2 no. 1, 2011.

Evolution-24

20. Behe, Michael J; The Edge of Evolution; Free Press (Simon and Schuster), New York, NY,

2007; Page 143.

21. Wells, Jonathan; DNA Does Not Control Embryo Development; Lecture in Albuquerque

NM, January 20th, 2009. See also reference 22 and 23.

22. Meyer, Stephen; Signature in the Cell, Epilogue; Harper One, New York, NY, 2009.

23. Wells, Jonathan; Zombie Science; Discovery Institute, 2017; Chapter 4.

24. Shapiro, James; “Scientific Alternatives to Darwinism: Is there a Role for Cellular

Information Processing in Evolution,” Boston Review, February/March 1997.

25. Wells, Jonathan; Icons of Evolution; Regnery, Washington, DC, 2000; Page 41-42.

26. Meyer, Stephen; Darwin’s Doubt; Harper One, New York, NY, 2013.

27. Gould, Stephen; Natural History; V 86, May 1987.

28. Carroll, Robert; Patterns and Processes of Vertebrate Evolution; Cambridge, 1997.

29. Wells, Jonathan; Icons of Evolution; Regnery, Washington, DC, 2000

30. Buggs, Richard, as quoted by Casey Luskin; Critically Analyzing the Argument from

Human/Chimpanzee Genetic Similarity; evolutionnews.org, 9/2011.

31. Wells, Jonathan; The Myth of Junk DNA; Discovery Institute, 2011; Page 54.

32. Gauger & Axe; The Evolutionary Accessibility of New Enzyme Functions: A Case Study from

the Biotin Pathway; Bio Complexity 2 no. 1, 2011.

33. Meyer, Stephen; Darwin’s Doubt; Harper One, New York, NY, 2013; Chapter 6.

34. Quoted by: Johnson, Phillip E; Darwin on Trial; 2nd edition, Inter Varsity Press (IVP), 1993;

Page 168.

35. Dembski, William; Intelligent Design; Inter Varsity Press, Downers Grove, Ill, 1998.

36. Davies, Paul; The Fifth Miracle; Simon and Schuster, 1999, Page 210-216.

37. Dembski, William and Ruse, Michael; The Logical Underpinnings of Intelligent Design;

Debating Design; Cambridge University Press, 2004.

38. Reproduced from: Johnson, Phillip E; Objection Sustained; IVP, 1998.