• Home
  • Site Overview
  • Page Menu
    • The Ultimate Question
    • Physics and Evolution
    • The Origin of 1st Life
    • The Fossil Record
    • Punctuated Equilibria
    • Other Supposed Evidence
    • Molecular Evidence
    • Genetic Evidence
    • Biochemistry & Design
    • Probability Science
    • In Their Own Words
    • Interpretation and Bias
    • Ultimate Origins
    • Reliability of the Bible
    • Archaeology and the Bible
    • Prophecy and the Bible
    • Conclusion
    • The Historicity of Jesus
    • The Dating of the Gospels
    • Jesus' Death/Resurrection
    • Prophecies Fulfilled
  • Jesus
    • The Historicity of Jesus
    • Dating of the Gospels
    • Death and Resurrection
    • Prophecies Fulfilled
  • Appendices
    • I. The Genesis Flood
    • II. Age of the Earth
    • III. Mormonism
  • Contact Us
  • More
    • Home
    • Site Overview
    • Page Menu
      • The Ultimate Question
      • Physics and Evolution
      • The Origin of 1st Life
      • The Fossil Record
      • Punctuated Equilibria
      • Other Supposed Evidence
      • Molecular Evidence
      • Genetic Evidence
      • Biochemistry & Design
      • Probability Science
      • In Their Own Words
      • Interpretation and Bias
      • Ultimate Origins
      • Reliability of the Bible
      • Archaeology and the Bible
      • Prophecy and the Bible
      • Conclusion
      • The Historicity of Jesus
      • The Dating of the Gospels
      • Jesus' Death/Resurrection
      • Prophecies Fulfilled
    • Jesus
      • The Historicity of Jesus
      • Dating of the Gospels
      • Death and Resurrection
      • Prophecies Fulfilled
    • Appendices
      • I. The Genesis Flood
      • II. Age of the Earth
      • III. Mormonism
    • Contact Us
  • Home
  • Site Overview
  • Page Menu
    • The Ultimate Question
    • Physics and Evolution
    • The Origin of 1st Life
    • The Fossil Record
    • Punctuated Equilibria
    • Other Supposed Evidence
    • Molecular Evidence
    • Genetic Evidence
    • Biochemistry & Design
    • Probability Science
    • In Their Own Words
    • Interpretation and Bias
    • Ultimate Origins
    • Reliability of the Bible
    • Archaeology and the Bible
    • Prophecy and the Bible
    • Conclusion
    • The Historicity of Jesus
    • The Dating of the Gospels
    • Jesus' Death/Resurrection
    • Prophecies Fulfilled
  • Jesus
    • The Historicity of Jesus
    • Dating of the Gospels
    • Death and Resurrection
    • Prophecies Fulfilled
  • Appendices
    • I. The Genesis Flood
    • II. Age of the Earth
    • III. Mormonism
  • Contact Us

CLEARING THE PATH

The Molecular Evidence

Can the field of Molecular Biology / Modern Biochemistry save the theory of evolution?

The typological (“types”) model of nature, which can be defined as classification according to general types, was the prevailing view of biologists in the first half of the nineteenth century, before the theory of evolution came into vogue.  In this page we will show that perhaps those biologists were right after all.(1) 


Evidence for evolution exists in nature wherever a group of organisms can be arranged into a lineal or sequential pattern.  Obviously the more perfect the sequence the more convincing it is as evidence for evolution.  However, it was primarily because most groups of organisms seemed so isolated and unlinked by transitional forms that, prior to 1859, most biologists saw the facts of biology as pointing to a model of nature which was diametrically opposed to the notion of organic evolution.  These typologists denied absolutely the existence of any sort of sequential order to the pattern of nature.  Many prominent biologists of the time believed it was only the intellectual appeal of the concept of continuity, and the elimination of the need for a God, which made the interpretation of nature in evolutionary terms so appealing.(2)


According to the typological (types) model of nature all the variation exhibited by the individual members of a particular class was merely variation on an underlying theme or design which itself was fundamentally invariant and immutable.  So each individual member of a class conformed absolutely in all essential details to the theme of its class.  It followed from this that all the members of a class were equally representative and characteristic of their class.  No individual member could be considered, in any fundamental sense, any less characteristic of its class, nor any closer to any member of another class than any of the other members of its class.  In other words, all the members of any defined class are equidistant from the members of other classes as well as being equally representative of their class. 


Such a model of biological classes completely excluded any sort of significant sequential order to the pattern of nature, as evolution requires.  Because no member of any defined class could stray beyond the confines of its type in terms of its basic characteristics, then no class could be led up to gradually or linked to another class through a sequence of intermediates.  Further, within one class, because all the members conform absolutely to the same underlying design and are equidistant in terms of their fundamental characteristics from all other classes, it is impossible to arrange them into a sequence leading in any significant sense towards another class.  Where the representative of one class happens to resemble the representative of another class, the resemblance is only superficial and not indicative of any sort of profound relationship.


Typologists acknowledged the existence of biological variation but denied that it could ever be radical or directional.  It was fundamental to typology that variation was always conservative and limited, always intra-type, and never inter-type as is required by evolution.  Nearly all the great biologists and naturalists of the late eighteenth and early nineteenth centuries who founded the modern disciplines of comparative anatomy, taxonomy and paleontology adhered strictly to a discontinuous typological model of nature. 


There has always been massive empirical evidence for the typological model of nature.  It must be noted, however, that the axioms of typology have been shown to be inapplicable at the level of the species,* which is the smallest division in nature.  Species can and do “evolve” and many can be linked to other species through clear sequences of intermediate subspecies. 

*    The primary divisions (called taxons, which means "using the principles of taxonomy") of the animal and plant kingdom are:       Species --> Genus --> Families --> Orders --> Class --> Phyla --> Kingdom  

For example, humans are of the: 

species=sapien - genus=homo – family=hominadae – order=primata – class=mammalia – phyla= chordata – kingdom=animalia 

However, this "evolution" at the species level is only microevolution. (as explained on "Ultimate Question" page)   Creationists do not doubt that this type of “evolution” takes place.  After all, who would doubt that creatures have the ability to adapt to their environment in order to better survive.  However, it is always within well demarcated boundaries.  Consequently, distinct demarcations cannot be drawn at the lowest taxonomic level of species*.  But, at all levels above the species, the typological model holds universally.  


The macroevolutionary claims of evolutionists, that these higher levels can be bridged, are completely without merit.  Darwin’s central problem in the Origin lay in the fact that he had absolutely no direct empirical evidence, in the existence of clear-cut intermediates, that evolution on a major scale had ever occurred and that any of the major divisions of nature had been crossed gradually through a sequence of transitional forms.  


The isolation and distinctness of different types of organisms and the existence of clear discontinuities in nature have been self-evident for centuries, even to non-biologists.  No bird is any less a bird than any other bird, nor is any cat any less a cat or any closer to any non-cat species than any other cat.  Although evolutionists have frequently claimed that typologists’ views were derived from religious preconceptions which were prevalent at the time of Darwin, the fact is they simply saw no evidence for a sequential order to the pattern of nature. 

DOES MODERN BIOCHEMISTRY SUPPORT TYPOLOGY OR EVOLUTION?

As stated, the pattern of nature seems to correspond very well with the old nineteenth-century typological model, which is mostly based on structure (morphology).  Nearly all known groups appear to be isolated and well defined.  Clear sequential patterns whereby one class is linked to another through transitional forms, as evolution would require, are virtually unknown. 


However, no matter how much the diversity of nature may appear to conform to the theory of types at a morphological (= structural) level, there is no way of quantifying such conclusions. Judging relationships in terms of morphological characteristics is bound to involve an element of subjectivity.  It was not until the advances in molecular biology that we were finally able to quantitatively describe the relationship between different organisms at a biochemical level. 


In the late 1950s it was found that the sequence of a particular protein, hemoglobin for example, was not fixed but varied considerably from species to species.  The amino acid sequence of a protein from two different organisms can be readily compared by aligning the two sequences and counting the number of positions where the chains differ.  The differences between two proteins can be quantified exactly and the results of these measurements can provide an entirely novel approach to measuring the differences between species.


As work continued in this field, it became clear that each particular protein had a slightly different sequence in different species and that closely related species had closely related sequences.  When the hemoglobin sequences in different mammals, such as man and dog, were compared, the sequential divergence was about twenty percent.  When the hemoglobin in two dissimilar species such as man and carp were compared, the sequential divergence was found to be about fifty percent.


These results showed that not only did organisms vary at a morphological level in terms of their gross anatomy, but that they also varied at a molecular level as well.  It became increasingly apparent as more and more sequences accumulated that the differences between organisms at a molecular level corresponded to a large extent with their differences at a morphological level. 


Armed with this new technique, biology at last possessed a strictly quantitative means of measuring the distance between two species and of determining the patterns of biological relationships.  If it is true, as typology implied, that all the members of one type always conform exactly to the basics of their type, all possessing equally all the defining character traits of their type and all standing equidistant from the members of other types, then these molecular studies should bear that out. 


Conversely, this new molecular approach could potentially have provided very strong, if not irrefutable, evidence supporting evolutionary claims.  All that was necessary to demonstrate an evolutionary relationship was to examine the proteins in the species concerned and show that the sequence could be arranged into an evolutionary series.  


The prospects were very exciting to evolutionary biologists.  Where the fossils had failed and morphological considerations were at best only ambiguous, perhaps this new field of comparative biochemistry might at last provide objective evidence of sequence and of the connecting links which these evolutionary biologists had long sought. 


Unfortunately for the evolutionist, as more protein sequences began to accumulate during the 1960s, it became increasingly apparent that the molecules were not going to provide any evidence of sequential arrangements in nature.  Instead, they reaffirmed the typological view.  In fact, the divisions turned out to be more mathematically perfect than even the most die-hard typologists would have predicted !


In his book, Evolution: A Theory in Crisis, (1), Michael Denton used data from the Dayhoff Atlas of Protein Structure and Function (3),  which compiles and compares various amino acid sequences for hundreds of species.  The data is presented in the form of a percent sequence difference.  Upon examination, it was found that the groups correspond precisely to the groups arrived at on traditional morphological grounds. (4) 


It also became apparent that the sequential divergence becomes greater as the taxonomic distance between organisms increases, as typologists would have predicted.  For example, one would expect the divergence to be greater between a horse and a fruit fly (two animals) than between a horse and a dog (two mammals), and this is exactly what was found. 


The most striking feature is that each identifiable subclass is isolated and distinct.  Every sequence can be unambiguously assigned to a particular subclass.  No sequence or group of sequences can be designated as intermediate with respect to other groups.  All the sequences of each subclass are equally isolated from the members of other groups.  Transitional or intermediate classes are completely absent. (5)


For example, Denton provides a chart showing the percent of sequence divergence of a specific cytochrome C protein between a bacteria and a wide variety of eukaryotic organisms (organisms whose cells possess a nucleus). (6)   Bacteria do not possess a nucleus, whereas all other organisms have a nucleus, hence they are two fundamentally different types of organisms.

CHART: The Percentage of Molecular Difference between these Eukaryotic Organisms and Bacteria*(6). So, for example, human cytochrome C protein is 65% different than bacteria, monkey 64% different and so on.

*Bacteria do not possess a nucleus, whereas all other organisms have a nucleus, hence they are two fundamentally different types of organisms. 


Upon studying the data, it is found that with the exception of three yeasts, the various eukaryotic cytochromes in the chart exhibit a sequence divergence of between 64 and 67 percent from this particular bacterial cytochrome (those 3 yeasts show divergences of 72, 69, 69).  Considering the enormous variation of eukaryotic species, from unicellular organisms like yeasts to multicellular organisms such as mammals, it is truly amazing that no eukaryotic cytochrome is intermediate between the bacterial cytochrome and any of the other eukaryotic cytochromes.  So, as far as the bacterium is concerned, all eukaryotes are equally distant.  No intermediate type of cytochrome exists to bridge the discontinuity which divides these two fundamental types of life.(7)


Further, when the three eukaryotic subgroups of yeast, plants and animals are compared to each other, no intermediates are observed as well.  Just as there are no intermediates to bridge the gap between bacteria and eukaryotes, there are also no intermediate types between these three basic eukaryotic groups.  Although the distance between the three eukaryotic types is less than between the bacteria and the eukaryotes, the division among these three fundamental types is still clear and unambiguous.  Each type is just as unique and isolated from the others. 


Denton concludes that from the sequential divergence of their cytochromes, it is possible to classify the living kingdom into various divisions.  The primary division is clearly between bacteria and eukaryotes.  The eukaryotes are subdivided into three distinct classes: yeasts, plants and animals.  The animals can be subdivided into two further subclasses: insects and vertebrates.  The vertebrates can further be divided into two fundamental divisions: the jawless cyclostomes (such as the lamprey) and the higher jawed vertebrates—fish, amphibian, reptiles and mammals. 


Each class is isolated and unique.  No classes are intermediate or partially inclusive of other classes.  The isolation of each class becomes greater as the taxonomic hierarchy is ascended, but even relatively closely related classes such as insects and vertebrates are still clearly distinguished.


An interesting finding is the division within the vertebrates of the jawless cyclostomes and the higher jawed vertebrates.  In itself, the existence of this fundamental division is not surprising, as it corresponds exactly with a traditional division based on morphological characteristics.  But the strange thing about the division is the fact that although the proteins in the higher jawed vertebrate groups, (fish, amphibian, reptiles and mammals), diverge greatly when they are compared with those of the jawless cyclostomes, invariably the degree of difference is always the same (chart below).(8) 


For example, the percent sequence difference between the hemoglobin of the lamprey, which is a jawless cyclostomes, when compared to a variety of jawed vertebrates, is relatively large, i.e. 70 percent or more (9).  But the thing is, all the jawed vertebrates show about the same percentage difference from the lamprey.  As Denton comments, the almost mathematical perfection of the isolation of the two fundamental classes at a molecular level is astonishing! (10) 

Percent sequence difference of hemoglobin molecule

                                          ← 75 → carp (fish)

           lamprey                 ← 81 → frog (amphibian)

 (jawless cyclostome)      ← 78 → chicken (bird)

                                          ← 76 → kangaroo (marsupial)

                                          ← 73 → human (mammal)


There is not a trace, at a molecular level of the traditional evolutionary series 

of cyclostome --> fish --> amphibian --> reptile --> mammal.   None is significantly closer to the lamprey than any of the others.  Incredibly, man is as close to lamprey, (a jawless cyclostome), as are fish!  None of the higher jawed vertebrate groups is in any sense intermediate between the jawless vertebrates and other jawed vertebrate groups. 

Molecular Evidence and “Living Fossils”

While most species make only a relatively fleeting appearance in the fossil record, some have persisted almost unchanged from ancient days to modern times.  These can be called the ‘living fossils.’  The lungfish is a classic example.  The modern lungfishes are members of an ancient group which is considered almost directly ancestral to the amphibian.  Lungfish almost identical to those found today in modern Africa are found as fossils in the rocks of the Devonian era (supposedly 350,000,000 years ago).  They are found alongside fossils of the earliest amphibians and the very fish groups from which the amphibian supposedly arose. 


While the tree of evolution supposedly continued to grow in all directions above the lungfish, the lungfish remained the same, so that over the supposed eons of time they were increasingly left behind, increasingly primitive and ancestral with respect to the newer groups.  Yet the protein sequences of lungfish are just as far from lamprey (vertebrate) as any other fish, amphibian or mammalian group! 


The case of lungfish hemoglobin is not unique.  The opossum is another classic living fossil, virtually unchanged morphologically from its ancient ancestors of the late Cretaceous period (supposedly nearly one hundred million years ago).  But when opossum hemoglobin is compared with the hemoglobin of other mammals it is in no way primitive with respect to other mammalian species.  So this mammalian species, considered a living fossil, has hemoglobin as far removed from presumed mammalian ancestors as any of the supposedly recently evolved mammalian types !  


For evolutionists, its easiest to just ignore this evidence.  Some may question the methodology with no real basis to do so.  But that's all it takes for others to just push this evidence aside and ignore it.

Molecular Clock ?

So how can evolution recover and explain away this data.  By far the most challenging aspect of this new biochemical picture as far as evolution is concerned is the incredible orderliness of all the divisions.  The only way to explain this in evolutionary terms is to propose that since all the different lines of a group diverged, each particular protein has continued to evolve in each of the lines at its own characteristic uniform rate.  


This concept is widely known as the ‘molecular clock hypothesis.’  The problem with this explanation, however, is that only if the degree of evolution in a family of molecules had been constrained by some kind of unknown and unimaginable time constant mechanism can the ordered pattern of molecular diversity be explained.  That’s quite a stretch to say the least, with no evidence to back it up.


But there is an additional problem with this clock hypothesis.  Different proteins exhibit different degrees of interspecies variation.  For example, while hemoglobin sequences differ by fifty percent between man and carp, cytochrome C differs by only thirteen percent between the two.  To account for this fact it is necessary in evolutionary terms to presume that the molecular clock has ticked at a faster rate in the case of cytochrome C than in the case of hemoglobin. 


However, as there are hundreds of different families of proteins, each exhibiting its own unique degree of interspecies variation, then it is necessary to propose not just two clocks but one for each of the several hundred protein families, each ticking at its own unique and highly specific rate.  It is beyond comprehension to believe this could have happened.


Despite the fact that no convincing explanation of how random evolutionary processes could have resulted in such an ordered pattern of diversity, the idea of uniform rates of evolution is presented in the literature as if it were an empirical discovery.  The hold of the evolutionary paradigm is so powerful that an idea which is more like a principle of medieval astrology than a serious twentieth-century scientific theory has become a reality for evolutionary biologists.  Yet in the face of these extraordinary discoveries the biological community seems content to offer explanations which are no more than apologetic tautologies. (11)  


And they have the nerve to call Creationists non-scientific !!  After reviewing this data in depth Denton concludes:

There is little doubt that if this molecular evidence had been available one century ago it would have been seized upon with devastating effect by the opponents of evolution theory, and the idea of organic evolution might never have been accepted.  This new era of comparative biology illustrates just how erroneous is the assumption that advances in biological knowledge are continually confirming the traditional evolutionary story. (12)

 

 

 

Next Page -- The Genetic Evidence

REFERENCE NOTES

  1. Denton, M. (1986)  Evolution:  A Theory in Crisis, Adler & Adler, Publishers, Inc. Note that Denton is not a creationist.
  2. ibid. p. 94.
  3. Dayhoff, M.D. (1972)  Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Silver Springs, Maryland. vol. 5.
  4. Dayhoff, M.D. (1972)  Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Silver Springs, Maryland, vol 5, Matrix 1, pD-8. as quoted by Denton p. 278.
  5. Denton, p. 278-280.
  6. Dayhoff, M.D. (1972)  Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Silver Springs, Maryland, vol 5, Matrix 1, pD-8. as quoted by Denton p. 280.
  7. Denton, p. 281.
  8. Dayhoff, M.D. (1972)  Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Silver Springs, Maryland, vol 5, Matrix 7, pD-52. as presented by Denton, p. 284.
  9. Denton, p. 284.
  10. Ibid. 
  11. Denton. p. 306.
  12. Ibid. p. 290-1.


Copyright © 2025 Clearing the Path - All Rights Reserved.

Powered by GoDaddy