Problems with Neo-Darwinian Evolution

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Problems with Neo-Darwinian Evolution
Can chemical evolution create the first living
cell? Can Neo-Darwinian evolution explain all the
organisms we see today?
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Biological OriginsThe Controversy
It is absolutely safe to say that if you meet
somebody who claims not to believe in evolution,
that person is ignorant, stupid, or insane (or
wicked, but Id rather not consider that).
Richard Dawkins (Professor of Zoology at Oxford
University), New York Times, 1989.
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Review of Biochemistry
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 cells nucleus,
that stores the information (code or directions)
for building proteins, cells, and organisms
(deoxyribonucleic acid) Mutation--an error in the
DNA code
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The Chemical Evolution Hypothesis
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Darwinian Evolution Starts With a Living Organism
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Beware of Definitions for Evolution
A. Evolution--Change over time or a heritable
change in the characteristics within a population
from one generation to the next. B. Darwinian
Evolution--The common descent of all organisms
from single celled organisms by the mechanism of
variation operated on by natural selection. C.
Neo-Darwinian Evolution--Darwinian Evolution with
random genetic mutation as the variation
mechanism. D. Micro-Evolution--Small changes in
organisms due to random mutations, genetic
variability, and natural selection. E.
Macro-Evolution--Darwinian or Neo-Darwinian
evolution. F. Chemical Evolution--Chemicals
forming the molecules of life then organizing to
form the first cells by random, natural
processes. A or D being true do not imply that B,
C, E, or F are true.
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How Does Neo-Darwinian Evolution Work?
1. Chemicals combine to form DNA, proteins, and
the first living, reproducing cell.
2. Genes in DNA duplicate, making them free to
mutate without destroying original function.
3. Random mutation creates new genes, and new
genes code for new proteins.
7. The fossil record shows intermediate body
plans and common descent.
6. Accumulated innovations produce new body
plans.
5. Advantageous innovations spread throughout a
population by natural selection.
4. New proteins and interactions among new
proteins provide innovations.
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Can Chemical Evolution Create the First Living
Cell?
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Lifes Basic Molecules Have Been Formed, But
Chemical Evolution Stops There
The Miller-Urey experiment in 1953 and others
synthesized amino acids (the building
blocks of proteins), and heterocyclic bases
(the building blocks of DNA) from the gases
assumed to compose the early atmosphere.
But there are serious problems 1. Oxygen in the
early atmosphere. 2. Contaminants. 3. Chirality
both left and right handed amino acids are
formed. 4. Amino acids and bases have never
assembled naturally into proteins and DNA outside
the cell.
Thaxton, Bradley, Olsen The Mystery of Lifes
Origin Philosophical Library, NY, 1984. Wells
Icons of Evolution Regnery, 2000.
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Proteins are a String of Amino Acids
Amino acids are molecules. There are 20 different
amino acids used in proteins. There are hundreds
to thousands of amino acids in a protein
string. Proteins use only left handed amino
acids. In 19 of the 20 amino acids, both left
and right handed are naturally formed in equal
numbers.
From Darwins Black Box
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Randomly Assembling a Protein is Extremely
Improbable

• A reproducing cell requires at least 100 proteins
  with a median length of 400 amino acids.
• If a right handed amino acid is included in the
  amino acid chain, the chain cannot function as a
  protein.
• Randomly synthesizing a chain of 400 left-handed
  amino acids
• with 1080 tries (number of atoms in the
  universe)
• every micro-second since the beginning of
  time (15 billion years)
• is less likely than 1 in 10 billion.
• There are not enough atoms and time in the
  universe to randomly assemble 400 left-handed
  amino acids into a chain.
• In addition, the right type of bond between amino
  acids is required.
• Even with proper bonds and chirality, very few
  amino acid strings will fold into functioning
  proteins.
• And, there is no known natural means of
  assembling amino acids into strings outside the
  cell.

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Grasping at Straws The RNA World
Since the assembly of DNA and proteins are both
highly improbable, perhaps life started with a
self-replicating RNA molecule. Some RNA molecules
(ribozymes) have catalytic capabilities like
proteins and store information like
DNA. Response Their catalytic properties are
insufficient for the integrated, coordinated
function required for reproduction. To date, no
sugar, phosphate, and base molecules have
self-assembled under natural conditions outside
the cell. RNA has the same chirality problem as
proteins. Without reproduction, RNAs cannot
advance to a reproductive system.
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Crick (co-discovered DNA structure in 1953), Life
Itself, 1988 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.
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How Does Neo-Darwinian Evolution Work?
X
1. Chemicals combine to form DNA, proteins, and
the first living, reproducing cell.
2. Genes in DNA duplicate, making them free to
mutate without destroying original function.
3. Random mutation creates new genes, and new
genes code for new proteins.
7. The fossil record shows intermediate body
plans and common descent.
6. Accumulated innovations produce new body
plans.
5. Advantageous innovations spread throughout a
population by natural selection.
4. New proteins and interactions among new
proteins provide innovations.
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Can Genes Duplicate in DNA?
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The Evidence for Gene Duplication is Declining
There is some evidence for gene
duplication Polyploids (extra chromosomes) in
some plants, Pseudogenes thought to be damaged
duplicates. Gene duplication was thought to be
the source of junk DNA, 97-98 of human
DNA. The ENCODE project is showing that at least
90 of junk DNA is not
junk. Current research is showing at least some
pseudogenes have function. If
there are no junk DNA or pseudogenes, there is
no duplicated DNA to
support neo-Darwinian
evolution.
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How Does Neo-Darwinian Evolution Work?
X
X
1. Chemicals combine to form DNA, proteins, and
the first living, reproducing cell.
2. Genes in DNA duplicate, making them free to
mutate without destroying original function.
3. Random mutation creates new genes, and new
genes code for new proteins.
7. The fossil record shows intermediate body
plans and common descent.
6. Accumulated innovations produce new body
plans.
5. Advantageous innovations spread throughout a
population by natural selection.
4. New proteins and interactions among new
proteins provide innovations.
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Can Neo-Darwinian Evolution Design Innovations?
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A Mutation is a Copy Error in the DNA Base Pair
Sequence
A point mutation gets a single base pair
wrong. There are also deletions, insertions,
transpositions, and etc. Mutations are
infrequent but real. Most mutations destroy
protein function and are detrimental. Some
mutations are neutral. A very few may be
beneficial to the organism under some conditions
and spread throughout a population in future
generations. Human sickle-cell
anemia--resistance to malaria. Antibiotic
resistance of bacteria. A new variety of
bacteria that eats oil or plastic.
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Evolution From a Single Cell to Modern Organisms
Requires Thousands of Innovations Sight
Nervous systems Respiratory
systems Circulatory systems Skeletal
systems Immune systems Molecular
machines Bacterial Flagellum Innovations require
new proteins with binding sites (shapes and
charges) that allow new inter-protein
interactions. Proteins work in multi-protein
complexes, usually 6 or more.
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The Bacterial Flagellum is an Innovation
Requiring 40 Interacting Proteins
For a simple bacterium to develop a flagellum,
roughly 40 new proteins that fit together must be
produced by mutations. The flagellum, like other
innovations, is irreducibly complex, which means
the flagellum is useless unless all proteins are
present. Useless protein interactions and
associated mutations do not spread in a
population, and even die out because of their
energy cost. All 40 interacting proteins would
have to be present at the same time to give an
advantage, which is improbable. combination
lock analogy
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New Binding Sites For More than Three Proteins
are Out of Reach for Neo-Darwinian Processes
According to Michael Behe No new advantageous
inter-protein binding sites have been seen in
1020 malaria, 1020 HIV, and 1013 E. Coli
cells. Generously, assume that one new binding
site between two proteins is possible in 1020
cells. We might expect to see two coordinated
binding sites among three proteins in 1040
cells. Only 1040 bacterial cells have lived
since life began therefore, interactions among
more than three proteins are out of
reach. combination lock analogy
Michael Behe The Edge of Evolution Free Press,
2007.
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Evolutionists Argue
There is a stepwise evolutionary path to every
innovation where each step, requiring new
proteins and binding sites, is beneficial--signifi
cantly increasing innovation probability.
(combination lock analogy) Response Since the
bacterial flagellum needs all 40 proteins, each
protein had to serve some other beneficial
function until all were present. If so, we would
expect to find each protein used in another
beneficial function in the cell, but we dont. We
would also expect to find proteins for assembly,
repair, regulation, and control that came
together, but we dont. Such a pathway has never
been demonstrated for any innovation. And, each
step may be implausible.
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Can a Functional Protein Develop a New Function
Through Mutation?
Doug Axe Ann Gauger experimented with proteins
that have the most similar structures but have
different functions. They found that at least 7,
and probably more coordinated mutations are
required to change the function from one to the
other. Using a population-genetics model, they
found that such a change would require far longer
than 15 billion years. The Neo-Darwinian
mechanism (mutation natural selection) for
developing new functions is not
plausible. Gauger Axe The Evolutionary
Accessibility of New Enzyme Functions A Case
Study from the Biotin Pathway
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Orphan Genes
Orphan genes code for proteins that have a unique
sequence and structure. All organisms have a
significant number of orphan genes. They are so
different from other genes that they are
unexplainable by a neo-Darwinian process of
random mutation and natural selection.
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How Does Neo-Darwinian Evolution Work?
X
X
1. Chemicals combine to form DNA, proteins, and
the first living, reproducing cell.
2. Genes in DNA duplicate, making them free to
mutate without destroying original function.
X
3. Random mutation creates new genes, and new
genes code for new proteins.
7. The fossil record shows intermediate body
plans and common descent.
6. Accumulated innovations produce new body
plans.
X
5. Advantageous innovations spread throughout a
population by natural selection.
4. New proteins and interactions among new
proteins provide innovations.
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Can Neo-Darwinian Evolution Design New Body Plans?
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DNA Does Not Determine Body Plans Thus,
Mutations Cannot Lead to New Body Plans
Recent research indicates that DNA does not
determine an organisms architecture (body
plan)1,2. Something in the egg besides DNA
(centrosomes and membrane patterns) is involved
with determining architecture. This is called
epigenetic information. Embryos develop according
to the egg species plan (until death) when its
DNA is replaced by that from another
species.3 1. See the Epilogue of Stephen Myers
Signature in the Cell. 2. See Chapter 14 of
Myers Darwins Doubt. 3. Jonathan Wells lecture
given in Albuquerque, NM on January 20th, 2009
DNA Does Not Control Embryo Development.
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How Does Neo-Darwinian Evolution Work?
X
X
1. Chemicals combine to form DNA, proteins, and
the first living, reproducing cell.
2. Genes in DNA duplicate, making them free to
mutate without destroying original function.
X
X
3. Random mutation creates new genes, and new
genes code for new proteins.
7. The fossil record shows intermediate body
plans and common descent.
6. Accumulated innovations produce new body
plans.
X
5. Advantageous innovations spread throughout a
population by natural selection.
4. New proteins and interactions among new
proteins provide innovations.
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What About Common Descent?
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Does The Fossil Record Show Common Descent? The
fossil record shows a progression from single
celled organisms to complex multi-celled
organisms over time. Organism Asserted
Age 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 Complex, multi-celled
animals 530-520 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? It
also shows major animal classes and phyla
appearing abruptly, fully formed, and living
unchanged for millions of years. During the
Cambrian Explosion, most phyla (main groups)
appeared without intermediate forms over a few
million years.
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Cambrian Explosion Video
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Famous Intermediates
The fossil record contains few if any
intermediate links, and all are controversial.
Are they intermediate or independent with
intermediate characteristics? Archaeopteryx
Paleontologists now agree that Archaeopteryx is
not the ancestor of modern birds1. WhalesA 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, deerlike animal is the
whales closest land relative. TiktaalikA 2006
article in Nature calls this fish with limb-like
front fins the intermediate between fish and
amphibians. A 2010 Nature article tells of
finding tetrapod footprints, with toes, dated at
20 million years before Tiktaalik. 1. Wells,
Icons of Evolution
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Are We Related to Chimpanzees?
mtDNA estimates a chimpanzee-human common
ancestor about 10 Mypb, but this is based on
assumptions common descent, mutation rates are
known, and all differences in DNA are due to
mutations. Base pair sequences of protein coding
genes for chimps and man may be 98-99 the same,
but total DNA may be only 70-76 the
same. Humans and chimpanzees have the same
broken copy of a vitamin C gene that may
indicate a common ancestor. Similar
pseudo-genes are found to have an important
function, implying that common descent may not be
the only explanation. Richard Buggs as quoted by
Casey Luskin Critically Analyzing the Argument
from Human/Chimpanzee Genetic Similarity
evolutionnews.org, 9/2011.
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Is there an Evolutionary Tree?
Contradictory trees are derived from different
protein and gene sequence comparisons. Contradicto
ry trees are derived from embryonic development
patterns. These imply that the tree model is
wrong. See Myers Chapter 6, Darwins Doubt.
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How Does Neo-Darwinian Evolution Work?
X
X
1. Chemicals combine to form DNA, proteins, and
the first living, reproducing cell.
2. Genes in DNA duplicate, making them free to
mutate without destroying original function.
X
X
3. Random mutation creates new genes, and new
genes code for new proteins.
7. The fossil record shows intermediate body
plans and common descent.
6. Accumulated innovations produce new body
plans.
X
5. Advantageous innovations spread throughout a
population by natural selection.
4. New proteins and interactions among new
proteins provide innovations.
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Conclusion
The Neo-Darwinian mechanism of mutation and
natural selection is a theory in crisis. Evidence
for common descent is declining.
Genesis 1 In the beginning, God created the
heavens and the earth and every living thing
according to its kind.
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How Do The Darwinists Respond?
All critiques of Darwinian evolution are
religiously motivated. Intelligent Design
Creationism is creationism in disguise, not
science. Darwinian evolution is a fact and is the
best supported of all scientific theories. Nearly
all biologists believe in Darwinian
evolution. People who doubt Darwinian Evolution
just dont understand. Imperfections in
biological designs demonstrate that the designs
were not created by an intelligent
cause. Substantive responses are infrequent.
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Reading
The Mystery of Lifes Origin Thaxton, Bradley,
Olson, 1984 Evolution A Theory in Crisis
Michael Denton, 1986 Darwin on Trial Phillip
Johnson, 1993 Darwins Black Box Michael Behe,
1996 Natures Destiny Michael Denton,
1998 Intelligent Design William Dembski,
1999 Icons of Evolution Jonathan Wells, 2000 The
Edge of Evolution Michael Behe, 2007 Signature
in the Cell Stephen C. Meyer, 2009 The Myth of
Junk DNA Jonathan Wells, 2011 Darwins Doubt
Stephen Meyer, 2013
Internet
Discovery.org IntelligentDesignNetwork.org NMIDnet
.org ARN.org
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Probability of Randomly Assembling a Protein-1
Consider an average protein that is 400 amino
acids long. 19 of 20 amino acids are naturally
produced in both left and right handed
molecules Assume amino acids are randomly
attached into a string (polymer). The
probability of getting a polymer made of all
left handed amino acids is 1/2380 4 x
10-115. Assume that we get 1080 tries (very
generous) at building this protein every
micro-second since the beginning of time (very
generous). 1080 is roughly the number of atoms
in the universe. The number of micro-seconds
since the beginning of time is 15x109 yr x 8760
hr/yr x 3600 sec/hr x 106 micro-sec/sec 4.7 x
1023 micro-seconds We get 1080 x 4.7 x 1023 4.7
x 10103 tries.
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Probability of Randomly Assembling a Protein-2
The probability of getting one success over all
these tries is, 4.7 x 10103 x 4 x 10-115 1.9 x
10-11 which is less than 1 in 10
billion. This is almost impossible odds, and we
have been very generous. A reproducing cell
requires at least 100 proteins. The probability
of getting the right bond is ½ for each amino
acid. Other kinds of amino acids will poison the
process. Very few left-handed amino acid polymers
will fold into functional proteins. An estimate
is 1 in 1077 for 150 amino acids. There is no
known natural mechanism for assembling amino
acids into polymers outside the cell.