Molecular homology has been acclaimed as the field
of study that saved the house of evolution from collapsing by
serving as an independent check that confirms evolution to be
a fact.¹ What is molecular homology? Is it an independent
confirmation of evolution? Can it "clock" the course
of evolution?

To answer these questions, let's consider first
the techniques involved in molecular homology. Basic to the
method is the fact that the structure and function of all living
organisms depends on biologic molecules called proteins. These
proteins are in turn made up of carbon-based molecules called
amino acids. Amino acids are the links; proteins are the chains
forged from these links. The specific sequencing of amino acids
determines the exact nature and function of the protein. For
instance, a protein with one specific arrangement of amino acids
will serve to digest fat in our stomachs while another sequence
specifies that the molecule will carry oxygen.

Except for some mutations (which are virtually
always deleterious), the same amino acid sequence for one particular
kind of protein is present in all organisms of the same species.
Between species, however, the amino acid sequence for a protein
such as alpha-hemoglobin, for example, can and usually does
vary. Comparing these differences between two or more species
and drawing inferences from these comparisons is the field of
molecular homology.

Scientists now possess the technology to extract
and, with a fair amount of accuracy, determine the amino acid
sequences of various proteins. For example, the hemoglobin sequences
for man, mouse and horse can be determined. When the sequence
of the man's hemoglobin is then lined up with the sequences
of the mouse and horse, the total number of amino acid differences
between these three species is determined by simply doing a
pairwise comparison of each amino acid at every position along
the entire length of the molecule.² Considering a
hypothetical example, the total number of differences between
man and mouse might be five and for the man and horse seven;
then, from the evolutionist's point of view, the man must be
more closely related to the mouse than to the horse.

Although evolutionary relationship is hardly the
only logical inference from amino acid sequence comparisons,
at least it is a potentially reasonable interpretation of the
data. However, when this pairwise comparison is strictly followed
to produce a phylogenetic (evolutionary) tree, many results
embarrassing for evolutionists are obtained. Perhaps the most
widely pictured evolutionary tree is based on cytochrome c;
yet it shows the turtle is more closely related to the birds
that to its fellow reptile, the snake. Furthermore, the chicken
is grouped with the penguin rather than the duck, and man and
ape separate from the main mammalian branch before the supposedly
less advanced marsupial mammal, the kangaroo.³

The cytochrome c tree pictured in books and magazines
is only one of forty trees generated by computer analysis of
the data—the tree "corrected" for closest fit
to the "known phylogeny" (i.e., the presumed evolutionary
history).⁴ Certainly such a tree cannot be claimed
as independent confirmation of evolution.

Amino acid sequence data are actually heavily
"massaged" even before they are used to construct
these evolutionary trees. Since it is mutational changes in
DNA that are presumed to produce, ultimately, the differences
in amino acid sequences, estimates of silent mutations, one
vs. two step changes in codons, several changes at one position,
and estimates for other such corrections must be made. When
the raw data are actually antigen-antibody tests or DNA hybridization,
as often is the case, uncertainty regarding even amino acid
differences, let alone amino acid changes, becomes
considerable.⁵ The computer must be told in advance
to generate only ancestral sequences that allow for further
ancestral sequences,⁶ otherwise, as we observed in
some of our analyses, intermediate sequences are generated that
break the presumed evolutionary chain.

In spite of all these problems, an ever-hopeful
evolutionist predicted that a more accurate molecular phylogenetic
tree for species would be obtained when "additional proteins
and nucleic acids have been determined."⁷ Quite
the opposite has taken place since he made that prediction.
The more protein sequences determined, the less likely the combined
tree represents the accepted classical evolutionary tree. Workers
with sequences for LH (luteinizing hormones) were "forced"
to postulate that amphibians evolved directly into mammals,
instead, of first into reptiles.⁸ Vincent Demoulin
said that the composite tree including data from many different
kinds of cytochromes simply "encompasses all the weaknesses
of the individual trees."⁹ Reviewing recent
data before a prestigious group at the American Museum Nov.
5, 1981, Colin Patterson, himself an evolutionist, stated that
if only the data of molecular homology were considered, then
descent from common ancestry, the foundational concept of evolution,
was "precisely falsified."¹⁰

In view of the failure of data from molecular
homology even to support evolution, it is surprising that molecular
homology has also been used as an "evolutionary clock,"
i.e., to try to determine rates at which mutations became fixed
in populations. This is done in two basic steps. Step one is
to construct a phylogenetic evolutionary tree based on protein
homologies. Step two is to determine, from the fossil evidence,
when the species diverged from each other. Suppose that the
man and mouse in our previous example shared a common ancestor
twenty million years ago by evolutionary reckoning. That would
be five amino acid differences in twenty million years, or one
amino acid changing "accepted point mutation" (PAM)
per four million years. If that rate is relatively constant
for most proteins, then the calculation can be "reversed"
to determine times of divergence from measured (and "massaged")
amino acid sequence differences.

Like tree construction, molecular clocking seems
an invitingly simple and straightforward use of protein differences,
but, like tree construction, the clocking procedure is plagued
with a plethora of problems. First, the "ticking"
of the clock is invisible—it is presumed "accepted
point mutations" or PAMS, which have never been observed,
not measured mutation rates. Second, the assumption that rates
of evolution should be approximately the same for most proteins
is considered absurd and even anti-evolutionary by the classic
school of evolutionary thought, the selectionists, and the extreme
variability of estimated rates seem to bear out their concern.
Speaking of an average rate is somewhat like saying that on
the average all animals have the same temperature, a statistical
deception that communicates what Patterson might call "anti-knowledge."
Third, we have already seen how imperfect are the evolutionary
trees constructed on the basis of molecular homology. Finally,
evolutionists have at last been forced to admit publicly that
fossil evidence contains virtually no transitional forms and
that, instead, it often suggests the simultaneous, explosive
appearance of diverse types. Therefore, it is at least nonsense
to try to determine when species diverged from each other, and
it may be worse, since types widely different from each other
seem to have diverged at essentially the same time (from unknown
ancestors).

In view of all these difficulties, it is not surprising
that, in a major review of molecular clocks, Walter Fitch dismissed
discussion of the clock dependent on paleontological dates,
since, as he put it, any discrepancy could easily be due to
an error in the dating. He then turned to a "calibration-free"
test of the clock, but had to admit that no satisfactory statistical
test of the clock had yet been done.

All these problems in principle crystallize as
problems in practice when the clock is applied to the snake/bird/turtle
example. Fitch points out, that a relative clock distance of
55 between snake and turtle and only 11 between bird and turtle
(making the two reptiles much less related than the bird/turtle
pair) is, of course, a considerable distortion of our current
biological viewpoint."¹¹ Fitch's explanation
for this conflict between fact and evolutionary theory should
jolt evolutionists and scientists alike: " … the truth
really is that either one or more of the sequences is incorrect,
that our current view of amniote phylogeny [land animal evolution]
is incorrect, or both." Earlier, Fitch had pointed out
a third general source of error: the divergence times could
be in error. Sadly, Fitch does not acknowledge a fourth source
of error, namely, failure of the molecular clock itself. Presenting
evidence that would impress a skeptic only as an "escape
from reason," Fitch clings to the clock hypothesis, even
after showing that the springs and cogs of the mechanism are
scattered and broken.

There is so much "slop" in both the
data and its processing in the field of molecular homology that
Colin Patterson, senior paleontologist at the British Museum,
spoke of it as "anti-knowledge" generating "anti-theory,"
apparently meaning a false assessment of the facts inducing
the false concept that evolutionary common ancestry offers some
sort of explanation for the data (which, as he points out, has
already been "massaged with evolutionary theory").¹²
In fact, after pointing out that the current evolutionary explanation
for molecular homology was "precisely falsified,"
he went on to consider a creationist explanation for the data.

Lest evolutionists try to divert attention from
weaknesses in their view by ridiculing another view (Macbeth's
"best-in-field fallacy"¹³)—Let us
content ourselves first to establish the demise of one theory
and the need for another. After all, good scientists who know
that neither genetics nor paleontology suggest evolution have
been seduced into believing that the rickety edifice of evolution
has somehow been shored up by the enthusiastic—but entirely
baseless—claims of the self-seduced molecular evolutionists.

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