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Table of Contents
• Things Change
• Gregor Mendel
• Richard Dawkins - to the Rescue?
• How Does Natural Selection - Select?
• Real Evolution - In Action
• The Non-Beneficial Gap Problem
• A Little Math
• Armadillo vs. Armada
• A Few Skeptics
• More Than a Theory?
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Things Change
The observation that things in nature change has been considered and theories
proposed as explanations throughout recorded history. Plato, Socrates, Aristotle, etc. all
However, not until Charles Darwin (1809-1882) published his On the Origin of Species
in 1859, with the proposed mechanism of "natural selection", did a purely non-deliberate
naturalistic process become generally accepted by the scientific community as the true
origin of all living as well as non-living things. Finally, a logical, apparently rational,
evidence-based theory had been proposed that seemed to clearly explain most, if not
all, of the observed changes in the natural world without the need to appeal to a God or
changes; to the point of evolution between species. He in fact proposed that all living
things, including humans, evolved from a single common ancestor and that all life
continues to evolve. The proposed process of evolution suggested that very slight
This very slight advantage translates into better survival and reproductive fitness. These
advantages are passed on to the favored offspring, who in turn survive better and are
more reproductive. More and more traits are added (or subtracted) in each generation
until, over the course of millions of years, the incredible diversity of living things that we
in the size and shape of finch beaks etc. However, Darwin never did see a finch turn
into an iguana or visa versa (or any other such major change). The small changes are
testable, but the larger changes are not because they are theorized to take many
thousands or even millions of years to occur. This is far too long to be observed or
tested for, even in many lifetimes. Can it then be said that large-scale evolution is not
observable or directly testable and therefore not a true science? Well, not quite.
Science convincingly proposes a great many things that cannot be or at least have not
been directly observed based on what has been observed and tested. However, lets
take a look at what has been observed and see if Darwin's conclusions really stand up
Darwin did observe very clear changes in creatures, no doubt. These changes are
the candid mind. In fact, it seems like the only reason that it was not accepted without
any qualms whatsoever is because it clashed with the prevailing understanding of
origins in the religious communities of the day. However, just because truth might be
distasteful, does not change the fact that it is true. Those with strong religious
convictions seemed unable to explain the obvious evidence in existence before their
own eyes. The reaction of the religious community in general was not calm and
because no effective challenge could be given during Darwin’s day does not mean that
a theory should not continue to be tested and questioned. Only by testing and retesting
do theories grow and improve. We are now in the age of genetics where the small
cellular/molecular level.
Gregor Mendel
Darwin’s time, no one knew about DNA or genes or exactly how traits
were passed on from parents to offspring. It was generally known that certain traits
could be selected for since this was commonly done with the breeding of animals such
as dogs, cats, cows and horses etc. But, until Mendel, no good explanation for the
specific characteristics of various plants in his garden as he bred them in specific ways.
He observed that certain “traits” were predictably “dominant” in expression over other
So, what does this prove? Mendel’s experiments proved that not all observed
changes are random, but are based on predictable rules of inheritance. A certain degree
of potential variation is programmed into the “genetic pools” of many creatures giving
offspring.2
Acid). We know that this language is written using an alphabet of four chemical letters
DNA has also been decoded. We know that this language only recognizes three letter
words or “codons.” A three-letter codon in turn is “transcribed and translated” into one of
twenty different amino acid "residues". Amino acid residues are also letters in another
code-like language of proteins. Specific orders and lengths of the twenty different
residues make different proteins with specific functions - much like different letter
sequences make words with different functions. Not every series of amino acids is
recognized by an individual cell, but only those that have a recognized function within
that particular cell (Just as not every series of letters in the alphabet is recognized by an
English speaking
person as having
meaning).
Proteins perform
order to have
make proteins. In
order to make proteins, a cell must have DNA that tells it exactly how and when to make
each protein as well as how to use each protein. DNA is the “blueprint” for the
cell/creature. DNA contains all the instructions for the building and function of every part
change in DNA. Therefore, if evolution occurs, it will be occurring in DNA since the
traits “dominant” while others are “recessive?” The dominance and recessiveness of
genes is made possible because of sex. Creatures that have the ability to reproduce
sexually have some pretty interesting DNA. Half of that creature’s DNA came from its
mother and half from its father. This creature is able to make specialized cells called
“gametes.” As this cell develops during a very complex process called “meiosis,” the
DNA that came from one parent mixes with the DNA that came from the other parent in
a very specific and yet random way called “genetic recombination.” If all goes according
Genetic recombination does not involve any mutational changes in the genes, and yet it
allows for a huge variety in expression of these genes. A gamete that is produced by the
“mother” is then joined with a gamete that is produced by the “father” and they fuse into
a single cell and combine their DNA. During its life, the creature expresses only those
traits that it received from its parents via their combined DNA. Because of genetic
recombination, the expression of traits is always unique and yet predictable. The
likelihood of having two identical offspring from the same set of parents at different
times is, for all practical purposes, zero.3,13 For example, I have light skin, light brown
hair and blue-green eyes. My brother by the same parents has very dark skin, dark
brown hair, and dark green eyes. We do have similarities, but we do not look exactly like
each other, or even our parents. These differences are not the result of any evolutionary
changes, but are simply the result of genetic recombination of pre-existing options in our
impossible to breed beyond certain limits. For example, in dog breeding there is a limit
to the maximum or minimum size that can be bred for. No matter how much selection
pressure is applied, a Great Dane is about as big as a dog can get, and a Chihuahua is
probably at the limit of doggy smallness. There is definitely a very wide range for size,
color, temperament et cetera that can be bred for, but there are limits to the expression
of each of these traits. This applies to all creatures that multiply using sexual
reproduction. Likewise, the variation in groups of finch beaks that Darwin noted is easily
explained using genetic recombination. The same can be said for the famous color
changes in England’s peppered moth. The major variations between the different
human races are also easily explained using genetic recombination. Therefore, these
"examples" are not examples of evolution at all - at least not when it comes to producing
any new types of functions within the pool of options which were not already there.
excluded.”4
Darwin had no idea since he was not capable of understanding the genetics
involved, so he can be excused for assuming some sort of evolutionary process here.
However, for us in this modern age of increased enlightenment we can no longer use
evolution in action. Why? Because in none of these examples has anything that is
The Theory of Evolution claims not only that life has evolved in the past, but that it
continues to evolve. If these claims are to be born up scientifically, then this theory is
going to have to be subjected to tests that give evidence to present evolutionary activity.
demonstrated, but the extent to which these changes can add up must be tested. For
a cat or a monkey into a man regardless of the selection pressure applied. Different
gene pools are involved and some similar genes work together in different ways in
explain the “missing links” between unique, functionally different genes and gene
combinations.
problem despite much effort by many great minds to explain it away. One
computer would, over time, generate the line from Hamlet, “METHINKS IT IS LIKE A
WEASEL.” This line has 28 characters (including spaces), so the computer was
programmed to make 28 selections using the 26 letters of the alphabet plus a space for
probability of picking the “correct” sequence can be made, as well as how long it would
take, on average, to find this "correct" sequence. Dawkins's own calculations suggested
that it would take his computer a million million million million million million years (or a
Well, this is clearly way too long for the current theory. So, how could evolution
possibly take place? Dawkins now put some “natural selection” into the computer
program to simulate “real life” more closely. The computer made multiple copies of
“errors” (mutations) into the copies. The computer then examined all the mutated
“offspring” and selected the one that had the closest match to, “METHINKS IT IS LIKE A
WEASEL.” This selection by the computer (nature) was now used to make new copies
and random mutations (in a “new generation”), from which the best copy was selected
again… and so on. By ten “generations” the sequence had “evolved” to read something
and zillions of years this time, the computer came up with the “fittest” phrase in about 40
generations.5 Of course, Dawkins made a disclaimer noting that this experiment was
not intended to show how real evolution works, but that it does illustrate the advantages
ways. One of these is that, in each generation of selective 'breeding', the mutant
criterion for selection, although human vanity cherishes the absurd notion that our
species is the final goal of evolution. In real life, the criterion for selection is always
Now, if Dawkins's illustration does not show how real evolution is supposed to work,
what's the point? Clearly a selection mechanism can work in certain cases like this, but
can biosystem functions evolve in any remotely similar way? Therein lies the problem.
Dawkins's computer did not make its selection based on phrase function, but on phrase
problem? After all, its just an illustration. Perhaps it is an illustration, but it is not
illustrating anything even close to what natural selection is capable of achieving when it
comes to many types of functional biosystems. The theory of evolution is based on the
fantastic powers of "Natural Selection". The problem is, natural selection, in real life,
If two genetic sequences are both non-functional or if they both have the same
function, then natural selection cannot select between them. In other words, nature is
blind to their genetic sequence differences if they both have the same function. If
Dawkins had wished to mirror the type of selection proposed by the theory of evolution,
he would have based his computer model on functional phrase selection. The problem
here is that "MDLDMNLS ITJISWHRQEZ MECS P" doesn't mean anything. This
phrase has no language function. A selection mechanism that only recognized changes
in function would look at this phrase and compare its function to the function of a
phrase like, "SDLDMNLS ITJISWHRQEZ MECS P" where an M was mutated into an S
and throw up its hands and say, "I can't tell the difference". Why? Because, both
phrases have the same non-functional function. A selection mechanism that is based
on function will not be able to tell the difference between them. Therefore, one
sequence will not be selected over the other for "survival" in the next generation. In
short, there will be no "directed" evolutionary change toward some sort of improvement
or new function. At this point, nature is basically blind to such changes; it cannot act as
Another problem with Dawkins's illustration is that the computer already had the
The evolution of something that is already there is not the evolution of anything new at
all. If nature already has what it wants or needs, then it does not need to “evolve" it.
Mindless nature does not “see” the actual letters of words (in DNA or Protein). All
that a mindless nature can see is what function results. Since function is arbitrarily
definition, a gradual change in the letters of the words themselves is not necessarily
recognized word or phrase will most likely destroy its original meaning well before any
Richard Dawkins will admit that without natural selection to guide evolution, evolution is
statistically impossible.
Yes, blind evolution might result in change to the "spelling" of genetic sequences, but
functional change since both words remain, well, nonfunctional or non-beneficial to the
same degree. Two nonfunctional words both have the same nonfunctional function.
You see, although natural selection is a real force of nature, it acts as a stabilizing force;
it does not promote speciation. It is not the creative force that many people have
suggested.16
occurred. There are assertions that such evolution occurred, but absolutely none are
the unique functions that result have their limits. Often such
function. The reason for this is that each functional sequence is surrounded by a vast
very few mutations are all that are needed to change a functional sequence into a
particular sequence into the surrounding ocean of the potential of sequence space. A
huge number of evolutionary paths lead from function to nonfunction. Any one of these
paths will do. So, this type of evolution is simple and happens all the time. Remember
good ol' Humpty Dumpty? It was much easier to break Humpty Dumpty than it was to
put him back together again. Why? Because there were a lot more ways for Humpty
Dumpty to be broken than there were ways for him to be fixed. But, there are actually a
Well, yes there are. The actual gain of new genetic or biosystem functions, new
functions that are not based on the loss or disruption of some other functional system,
have in fact been demonstrated with experiments that include the evolution of the
lactase enzyme in E. coli bacteria performed by Professor Barry Hall,23 and the
evolution of the nylonase enzyme demonstrated by Kinoshita, et. al., 24,25 - to name just
two of many such examples. However, all such examples of the evolution of novel
functions occur as the result of one or two point mutations. No gaps of neutral or
ever been crossed. Statistically, as the size of the gaps increase in a linear fashion, the
exponentially - to the point were increasing the population size simply cannot keep up.
As Richard Dawkins noted himself, "However many ways there may be of being
alive, it is certain that there are vastly more ways of being dead." 5
So, do these non-beneficial gaps really increase in real life? And, if they do
functional systems that have a greater and greater minimum threshold structural
requirement. What this basically means is that those types of biosystem functions that
require a greater minimum number of amino acid residues all working together at the
same time in specific orientation relative to each other are more and more isolated from
each other in the potential of sequence space. The odds that anything that exists in a
gene pool will be just one or two mutations away from any potentially beneficial
sequence that does not yet exist start to drop with each increase in the minimum
structural threshold requirements - by more than 2 fold for each single character
sequence position (out of 20 total character options). Pretty soon trillions upon trillions
of years are required to cross apparently small non-beneficial gaps between anything
that exists within a gene pool and anything that might exist at a higher-level of functional
complexity. In real life, this problem translates into a complete lack of evolution "in
action" beyond those types of functions that require more than one or two thousand
fairly specified residues working together at the same time. There isn't a single example
they work. In a living cell, proteins work like locks and keys called enzymes and
substrates. Like other locks and keys, proteins are very specific molecules. All proteins
have certain amino acids or protein “letters” in their makeup that cannot change without
a loss of protein function. These amino acids are called “invariant” and are generally the
hemoglobin protein consists of four amino acid residue chains (of two different types)
adding up to a total of 574 amino acids. Richard Dawkins claims that 190 (33%) of
these are “invariant.”5 Much more of the molecule is “nonpolar” and can only change
within a group of eight nonpolar amino acids (partially variant).7 Of course, this means
that the hemoglobin "function" requires a fairly high degree of "specificity" of amino acid
arrangement before its function can be realized to a beneficial degree. In short, only a
very tiny fraction of the huge number of potential arrangements of 574 amino acid
residues (~1e746) will actually work to produce the hemoglobin function (a ratio of less
than 1e-500). Given these odds, one would have a far far greater chance of finding one
differences, the various cytochrome c sequences are basically the same, having
essentially the "same 3D topology." Furthermore, in vitro studies have shown that the
cytochrome c sequences from any species can integrate themselves correctly with the
other elements of the oxidation processes of all other creatures using cytochrome c. In
other words, all the varieties are interchangeable because they are basically identical in
3D structure and function. In order to maintain this specificity, other studies that
compared sequences of 40 species have shown that "at least 35 of the 104 amino acids
are invariant. . . Furthermore, at another 40 sites, only 2 or 3 amino acids occur, and at
each of those sites, the pairs of triplets are always very similar in chemical character -
i.e., they are either hydrophilic, hydrophobic, or neutral with respect to water. At only a
very few sites can radically different amino acids occur. Why might this be?
Presumably, mutations occur at all sites. However, changes at some sites destroy the
function of the molecule, whereas at other sites, some change is tolerable, and at a few
sites, major changes don't seem to be of much consequence. Subsequent detailed
studies of molecular structure confirmed these premises. Many of the invariant sites are
critical in causing the molecule to fold itself properly--changes at these sites would
With these thoughts in mind, lets do a few calculations and see if we cannot make
the situation a little more clear. Let's take a protein sequences of 100 amino acid
residues. How many different 100aa protein sequences are possible? There are just
over 1e130 different possible amino acid arrangements in a 100aa protein (20100). That
is a huge number. It is estimated that there are only 1e80 particles of matter (electrons,
proteins, neutrons) in the entire universe. The question is, of these 1e130 different
sequences, how many of them would have the cytochrome c function? If we say that
35aa of the 100aa are invariant and that another 40aa can only change between two
amino acids, and perhaps another 20aa can change between 5 or so amino acids and
the five that are left over can change between all 20 amino acids . . . how many
variations will still have the cytochrome c function? These numbers add up to around
1e40. Of course, 1e40 is the tiniest of tiniest tidbits when compared to a number like
1e130. However, there are some who suggest that there are actually several more
"variant" amino acids in cytochrome c and that even certain amino acids that are
"invariant" between many different groups of animals can in fact be changed without a
complete loss of cytochrome c function. They suggest that a more reasonable number
of amino acid sequences with potential cytochrome c function would be on the order of
1e60. Certainly 1e60 is a great deal larger than 1e40, but this is still nothing compared
with a number like 1e130. In comparison, each one of the functional 1e60 sequences
would be surrounded by 1e70 sequences that would have absolutely no cytochrome c
function. This is an absolutely huge sea of protein sequences that would not have even
a small bit of cytochrome c function. Finding even one of the 1e60 functional
What one has to ask is what are the odds that the any of the correct sequences, at
this level, will be within striking distance of anything that already exists within any
genome?
To help visualize
nonfunctional gaps,
the English language system. However, lets say that the next closest understood word
in the English language is "armada." Obviously no single letter change is going to get
the new function of "armada" all function is going to be lost. For example, what does
"armadallo" mean? If we are allowed to only select between words that have meaning,
we cannot select armadallo over, say, "brmadillo" simply because "armadallo" is closer
to our desired goal of "armada." Why? Because, as with natural selection, we can only
are equally nonfunctional or functionally "neutral" when compared with each other. So,
there is no basis for non-random selection between them. Without selection ability, it is
quite obvious that random chance alone will take a very long time, on average, to cross
the functional gap between armadillo and armada - if we use one letter change at a
time. Remember how long Dawkins said it would take to evolve, "Methinks it it is like a
weasel" without the benefits of a selection mechanism?. . . zillions of years? So, you
see, the gap problem is really a tough one for evolution to explain since the mindless
No intuition, creativity, or intelligence is allowed in the door to help out the process.
But, what about multicharacter mutations? What if we can change many characters
at the same time or import pre-formed commonly used character sequences from
somewhere else within the gene pool? Such mutations are called "indels" or "genetic
duplication" mutations. The problem is, as the gaps between higher-level systems
become wider, the odds that any sequence that could fill the gap exists preformed
anywhere within the gene pool drop dramatically - exponentially in fact. Also, the odds
that a longer sequence will get copied and pasted into the new position properly also
A Few Skeptics
Problems such as this have caused many well-educated scientists
words, “driven by logic” to conclude that there "must be a Creator." Both of them
admitted that this was a tough conclusion for them to admit and that their conclusions
now find myself in. But there is no logical way out of it. I now
way in which we can understand the precise ordering of the chemicals of life except to
invoke the creations on a cosmic scale. . . We were hoping as scientists that there
promotes the idea of “irreducible complexity” in the natural world as giving evidence of
intelligent design.6
There are many more scientists, famous and non-famous, who are leaving the
theory of evolution behind, often reluctantly, because of the overwhelming “logical” flaws
in the theory. So why does it continue to be so popular with most modern scientists?
Evolution is rarely questioned in the public school system, but instead is taught as
the gospel truth; as "more than a theory." Textbooks never question it but instead refer
debated in the public school system, but no one ever challenges the fundamental "truth"
that all living things have descended from a common ancestor life form and that this life
form arose from the non-living prehistoric ocean chemistry. Perhaps then Dr.
experts and professors? No one seems to know exactly how evolution works, but most
conclude that many scientists and technologists pay lip-service to Darwinian theory only
phenomena, and not because it has been paradigmatic in establishing the canons of
The idea of an intelligent Creator or “God” seems to bother a lot of people. For
some, God might create meaning in life, and therefore personal responsibility. Many
might have a desire to be free from any such personal restraint. Others might have a
painful image of God, or associate the idea of God with dogmatic superstition and
ignorance.
wants to do, or why his friends should not seize political power and govern in the way
that they find most advantageous to themselves. … For myself, the philosophy of
I find it very interesting that what is supposed to be a completely rational science can
be so influenced by personal feelings and philosophy. It seems like even scientists are
human. We cannot avoid our personal biases but we can at least be aware of them and
how they influence our perception of “truth.” However, if there is a “truth” it will be true
regardless of how we might feel about it. An honest seeker for truth will search for it and
So, how does one search and sort out truth from error in a non-passionate manner?
It seems that the subjective human mind cannot know truth absolutely, but can know
error. The scientific method does not prove theories to be absolutely true, but it can
prove them to be false. Theories that are beyond the realm of human investigation
cannot be proven false and so remain beyond the reach of the scientific method. Such
concerning the past are not directly covered here, but are its claims concerning the
present and the future testable? If so, they have yet to be demonstrated or even
theorized in a testable way. If this particular part of evolutionary theory is in fact non-
testable, then it is not a science. It therefore remains strictly a theory based in historical
demonstrate the “Designer of life at work.” However, without the ability for evolutionary
theories to demonstrate or even theorize genetic evolution in any meaningful way, the
obvious complexity of living things does historically match with the complexity seen in
other complex objects/machines, all of which were designed outside of any naturalistic
process with the use of intelligence. For historical studies, correlation seems to be very
important. Design Theory does have the ability to correlate the complexity of living
things with the complexity of intelligently designed machines and not with any other
like evolutionary theories have had ample time to prove themselves. “Darwin's theory of
natural selection has never had any proof, yet it has been universally accepted.”18 If
significant evolution could happen in just a few generations as Dawkins indicates, then
why is it not being observed in life forms like bacteria that have very short generation
times? Over the past 50+ years, greater than one million generations of E. coli have
been observed, radiated, drugged, burned, frozen, dissected, mutated, selected and
manipulated in every conceivable manner (talk about selection pressure), yet E. coli are
still E. coli. This seems especially strange when one considers that humans supposedly
evolved from apes in less than 200,000 generations using a much lower mutation rate
(on the order of one mutation per gene per 100,000 generations).19, 20
A similar case can be made for the fruit fly. Fruit flies are still fruit flies. Why is this?
Gordon Taylor observes, “In all
certain highly complex bacterial functions when he states, “…one can only marvel at the
intricacy in a simple bacterium, of the total motor and sensory system which has been
the subject of this review and remark that our concept of evolution by selective
example, from a "preflagellum" (meaning a subset of its components), and yet what is
becomes advantageous?”21
The fact is that scientists are speaking beyond their ability to really know. They are
so cock sure of themselves and the theory of evolution, and yet they really do not have
a very good idea about how DNA really works. They have some idea, but when it really
comes down to it, DNA and the information it contains is far more complicated than
scientists have even begun to realize. For example, for many years it was thought that
humans had between 60,000 to 100,000 genes. But, a surprising discovery was made
by those working on the human genome project. When they finished the project in
2001, they estimated a that the actual gene count was somewhere between 35,000 to
40,000 genes. What is even more surprising is that the estimates for the genes needed
to make a mouse were only about 500 or so different from the absolute number needed
to make a human. 14 These new estimates were short lived however. In February of
2002, at the annual meeting of the American Association for the Advancement of
Science (publisher of Science), one of the presenters, Victor Velculescu, suggested that
the real number of genes in the human genome may actually be closer to 70,000 genes
after all. He and his colleagues, at Johns Hopkins University in Baltimore, Maryland,
have gone back to the lab to look for genes that the computer programs may have
missed. Their technique, called serial analysis of gene expression (SAGE), works by
tracking RNA molecules back to their DNA sources. After isolating RNA from various
human tissues, the researchers copy it into DNA, from which they cut out a kind of
genetic bar code of 10 to 20 base pairs. The vast majority of these tags are unique to a
single gene. The tags can then be compared to the human genome to find out if they
match up with genes discovered by the computer algorithms. Velculescu said that only
roughly half of the tags match the genes identified earlier. For him, this is evidence that
the human inventory of genes had been underestimated by about half. The reason for
the disparity may be that the standard computer programs were largely developed for
the genomes of simple (prokaryotic) organisms, not for the more complex sequences
found in the genomes of humans and other eukaryotes. "We're still not very good at
predicting genes in eukaryotes," said Claire Fraser of The Institute for Genomic
Research in Rockville, Maryland. It's entirely possible that there could be more than
32,000 genes, and SAGE is an important approach to finding them. She adds, "You
absolutely have to go back into the lab and get away from the computer terminal." 26
Even more recently it seems that what used to be known as non-coding "junk DNA", the
remnants of evolutionary discards, may actually be more informationally rich than the
If we still do not really know how many genes we have in our genome, even after
having sequenced the entire human genome, how can we be so sure that our genes
evolved from lower organisms? And, if even so-called junk-DNA isn't really junk
anymore, how do we anyone "know" that humans are between 94% and 99% the same
as chimps? And, even if we are, who is to say that our similarities were clearly the
result of common descent over some other possibility? The similarities are easily
explained by common descent, but what about the functional differences that exist
between many different living things? The differences are the real question here. How
the theory of evolution, well and good. However, there seem to be many differences
between various genes and biosystem functions that cannot be explained as a result of
common descent. The problem is that these “small” differences might turn out to be
rather huge. Even a single gene difference can be gigantic depending on how isolated it
is in functional sequencing from the available genetic real estate of a given gene pool.
“...An intelligible communication via radio signal from some distant galaxy would be
widely hailed as evidence of an intelligent source. Why then doesn't the message
sequence on the DNA molecule also constitute prima facie evidence for an intelligent
source? After all, DNA information is not just analogous to a message sequence such
Has Design Theory come full circle? Many, even among the most respected of
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