Releasing the Truth

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Debunking the “29 evidences for macroevolution” part 1

From: Trueorigins



n “29 Evidences for Macroevolution,” Douglas Theobald sets forth the evidence that he believes proves scientifically that all living organisms descended from “one original living species.”  He does so by listing what he claims are 29 potentially falsifiable predictions of the hypothesis of universal common ancestry and presenting the evidence that he believes confirms each of those predictions.

Dr. Theobald does not address the origin of the first living thing or the mechanism by which that first organism diverged into every life form that has ever existed.  His thesis is expressly restricted to the affirmation of universal common ancestry.  In other words, he argues that, without knowing anything about how the first life arose or how it diversified, one can still be certain that all living things descended from the same ancestor.  He states in the introduction (emphasis supplied):

In this treatise, I consider only macroevolution [which he labels a “virtual synonym” for universal common descent].  I do not consider microevolutionary theories, such as natural selection, genetic drift, sexual selection, theories of speciation, etc., which biologists use as mechanistic theories to explain macroevolution.  Neither do I consider abiogenesis; I take it as axiomatic that an original self-replicating life form existed in the distant past.

In the conclusion, he says (emphasis supplied):

These previous points are all proofs of macroevolution alone; the evidences and the conclusion are independent of any explanatory mechanism.  This is why scientists call macroevolution the “fact of evolution.”  None of the 29 predictions directly address how macroevolution has occurred; nevertheless, the validity of the macroevolutionary conclusion does not depend on whether Darwinism, Lamarckism, or something else is the true mechanism of evolutionary change or not.  The macroevolutionary conclusion still stands, regardless.

Dr. Theobald understandably seeks to free the claim of universal common ancestry from the debate about the sufficiency of evolutionary mechanisms, particularly the debate about Neo-Darwinism.  It should not go unnoticed, however, that a bare claim of universal common ancestry is compatible with allmechanisms of common descent, including divine direction.  So if God chose to have a reptile give birth to a bird, for example, that would be consistent with an “amechanistic” argument for universal common ancestry.[1]

The fact that Dr. Theobald leaves the mechanism of descent completely open does not make his claim trivial.  On the contrary, the claim of universal common ancestry is incompatible with the belief that God separately created more than one living thing.  It therefore challenges the convictions of biblical creationists, progressive creationists, and all who believe that mankind was created separately from animals.

I address Dr. Theobald’s predictions in the order in which he presented them.  The italicized paragraphs following the predictions are quotations from his article.  I quote only the prediction portion (or what I deem the relevant parts of it), not the alleged confirmations and potential falsifications.  That would require me to duplicate the entire article.  The accuracy of my references to the alleged confirmations or potential falsifications can be verified by consulting Dr. Theobald’s article.

I appreciate the civility with which Dr. Theobald argued his case and hope that my response is in kind.  I also appreciate his candor in acknowledging that “science can never establish ‘truth’ or ‘fact’ in the sense that a scientific statement can be made that is formally beyond question.”  (That may seem obvious to those attuned to the philosophy of science, but I suspect it will come as a surprise to many.)  So however much weight one assigns to the evidences adduced by Dr. Theobald, they cannot “prove” universal common ancestry in the sense of rendering its rejection illogical.[2]  That being said, the focus of this response is on the weight to which the evidences are entitled.

I include here for convenient reference Dr. Theobald’s Figure 1, which he labels “The standard phylogenetic tree.”


According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past.  In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) information flow in continuity of kind, (3) catalysis, and (4) energy utilization (metabolism).  At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.

If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions.  Most importantly, they should have inherited the structures that perform these functions.  The genealogical relatedness of all life predicts that organisms should be very similar in the particular mechanisms and structures that execute these basic life processes.

The alleged prediction and fulfillment are:

  1. If universal common ancestry is true, then all organisms will have one or more traits in common.
  2. All organisms have one or more traits in common.

Unless one inserts an additional premise imposing a limit on the degree to which descendants can vary (which would require specification of a mechanism of descent), the claim of common ancestry does not require that all of the descendants share one or more traits.  There is no logical reason why completely novel organisms could not arise in one or more lineages.  Absent specification of a mechanism of descent, which Dr. Theobald purposefully avoids, there is no way to tether the traits of the descendants to those of the common ancestor.

The belief that evolution predicts biologic universals is “one of evolution’s major illusions.” (ReMine, 92.)  As Walter ReMine says:

First, evolution does not predict that life would arise precisely once on this planet.  If there were two or more unrelated systems of life, then evolutionary theory would effortlessly accommodate that situation.[3]

Second, even if life originated precisely once, then evolutionary theory would still not predict biologic universals.  Shortly after life’s origin, nothing prevented life from branching and leading separate lineages to higher life forms entirely lacking the known biologic universals.

Third, evolutionary loss and replacement processes could prevent biologic universals.  If one organism is a distant ancestor to another, then nothing in evolution predicts the two must share similarities.  If evolution were true, then distant ancestors and descendants (as well as sister groups) can be totally different.

Evolution never did predict biologic universals, it merely accommodated them.  (ReMine, 92-93.)

Biophysicist Cornelius G. Hunter concurs.  He writes:

There is yet another reason that the universality of the genetic code is not strong evidence for evolution.  Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all).  In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature.

Consider how evolutionists would react if there were in fact multiple codes in nature.  What if plants, animals, and bacteria all had different codes?  Such a finding would not falsify evolution; rather, it would be incorporated into the theory.  For if the code is arbitrary, why should there be just one?  The blind process of evolution would explain why there are multiple codes.  In fact, in 1979 certain minor variations in the code were found, and evolutionists believe, not surprisingly, that the variations were caused by the continuing evolution of the universal genetic code.  Of course, it would not be a problem for such an explanation to be extended if it were the case that there were multiple codes.  There is nothing wrong with a theory that is comfortable with different outcomes, but there is something wrong when one of those outcomes is then claimed as supporting evidence.  If a theory can predict both A and not-A, then neither A nor not-A can be used as evidence for the theory.  When it comes to the genetic code, evolution can accommodate a range of findings, but it cannot then use one of those findings as supporting evidence.  (Hunter, 38.)

The fact that some leading evolutionists believe early life forms were biochemically distinct from modern forms confirms that evolution does not predict biologic universals.  Robert Shapiro, for example, entertains the possibility of finding living relics of an original protein-based life form that lacked DNA and RNA. (Shapiro, 293-295.)  Likewise, A. G. Cairns-Smith thinks that descendants of ancient crystalline clay organisms may be all around us.  He states: “Evolution did not start with the organic molecules that have now become universal to life:  indeed I doubt whether the first organisms, even the first evolved organisms, had any organic molecules in them at all.” (Cairns-Smith, 107.)

On the other hand, ReMine argues that biologic universals are a prediction of his message theory of creation, which “says all life was constructed to look like the unified work of a single designer.” (ReMine, 94.)  So evolution does not predict the unity of living things, but at least one theory of creation does.

Of course, the biochemical similarity of living things fits easily within a creation framework.  As biochemist Duane Gish explains:

A creationist would also expect many biochemical similarities in all living organisms.  We all drink the same water, breathe the same air, and eat the same food.  Supposing, on the other hand, God had made plants with a certain type of amino acids, sugars, purines, pyrimidines, etc.; then made animals with a different type of amino acids, sugars, purines, pyrimidines, etc.; and, finally, made man with a third type of amino acids, sugars, etc.  What could we eat?  We couldn’t eat plants; we couldn’t eat animals; all we could eat would be each other!  Obviously, that wouldn’t work.  All the key molecules in plants, animals, and man had to be the same.  The metabolism of plants, animals, and man, based on the same biochemical principles, had to be similar, and therefore key metabolic pathways would employ similar macromolecules, modified to fit the particular internal environment of the organism or cell in which it must function.  (Gish, 277.)

As for the alleged fulfillment, I do not doubt that all living things have carried out the basic functions of life in similar ways, but there are many organisms, past and present, about which we know nothing.  It is impossible to be certain that none of these organisms is (or was) biochemically unique (witness the speculations of Shapiro and Cairns-Smith).  The claim that all organisms have one or more traits in common is true in the sense that all living things necessarily have the traits by which life is defined, but that is simply a tautology—living things all have the traits of living things.



As you can see from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as “groups within groups.”  This nested hierarchical organization of species contrasts sharply with the continuum of “the great chain of being” and the continuum predicted by Lamarck’s theory of organic progression.  Few other natural processes would predict a nested hierarchical classification.  Real world examples that cannot be classified as such are elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.  That certain organisms merely are similar to each other is not enough to support macroevolution; the nested classification pattern that satisfies the macroevolutionary process is very specific.

The alleged prediction and fulfillment are:

  1. If universal common ancestry is true, then organisms will be classifiable in a nested hierarchy.
  2. Organisms are classifiable in a nested hierarchy.

It is not a corollary of the hypothesis of common descent that organisms will have features by which they can be classified as groups within groups.  Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it.  There are mechanisms of descent from a common ancestor that would yield a different pattern.  If common descent can yield either nested hierarchy or something else, then the presence of nested hierarchy does not count as evidence of common descent.

Hunter puts it this way:

It has been known since Aristotle that species tend to cluster in a hierarchical pattern, and in the eighteenth century Linnaeus saw it as a reflection of the Creator’s divine plan.  Obviously this pattern does not force one to embrace evolution.  Also, Darwin’s law of natural selection does not predict this pattern.  He had to devise a special explanation—his principle of divergence—to fit this striking pattern into his overall theory.  To be sure, evolution can accommodate this hierarchical pattern, but the pattern is not necessarily implied by evolution.  (Hunter, 108.)

Even a mechanism of descent that includes branching events does not ensure a nested pattern.  As ReMine explains:

The pattern of descent depends on the extent that evolved characters are later lost.  Suppose losses are significant, and characters are replaced at a high rate.  Then there is no reason to expect a nested pattern.  Descendants could be totally different from their distant ancestors and sister groups, with little or no semblance of nested similarities linking them.  (ReMine, 343.)

Evolution does not predict a hierarchical pattern.  Simple processes of loss, replacement, anagenesis, transposition, unmasking, or multiple biogenesis would prohibit such a pattern.  Since hierarchical patterns (such as cladograms or phenograms) are not predicted by evolution they are not evidence for evolution.  (ReMine, 444.)

In fact, nested hierarchy raises some difficult issues within a Neo-Darwinian framework.  As Michael Denton observes:

In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed.  There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process.  If the hierarchy suggests any model of nature it is typology[4] and not evolution.  How much easier it would be to argue the case for evolution if all nature’s divisions were blurred and indistinct, if thesystema naturalae was largely made up of overlapping classes indicative of sequence and continuity.  (Denton 1986, 136-137.)

The notion that the nested hierarchy of organisms is incompatible with creation is based, not on science, but on the unprovable theological assumption that if God created life he would do it in some other way.  As biologist Leonard Brand explains:

The hierarchical arrangement of life illustrated in Fig. 9.6 has been used by Futuyma (1983) and others as evidence that life must have evolved.  They believe that if life were created, the characteristics of different organisms would be arranged chaotically or in a continuum, not in the hierarchy of nested groups evident in nature.  If we think of that concept as a hypothesis, how could it be tested?  Actually, to state how a Creator would do things and then show that nature is or is not designed that way is an empty argument.  Such conjecture depends on the unlikely assumption that we can decide what the Creator would be like and how he would function. (Brand, 155.)

It may be that the nested hierarchy of living things simply is a reflection of divine orderliness.  It also may be, as Walter ReMine suggests, that nested hierarchy is an integral part of a message woven by the Creator into the patterns of biology.  (See, e.g., ReMine, 367-368, 465-467.)  The point is that the hierarchical nature of life can be accommodated by creation theory as readily as by evolution.  Accordingly, “[i]t is not evidence for or against either theory.” (Brand, 155.)

Dr. Theobald’s claim that “specially designed objects like buildings, furniture, cars, etc.” cannot be classified in a nested hierarchy requires elaboration.  In terms of mere classification, it is incorrect.  Buildings and vehicles have both been used as examples of nesting (Ridley 1993, 52-54; Fastovsky and Weishampel, 51-53; Brand, 165-166).  According to Mark Ridley:

Any set of objects, whether or not they originated in an evolutionary process, can be classified hierarchically.  Chairs, for instance, are independently created; they are not generated by an evolutionary process: but any given list of chairs could be classified hierarchically, perhaps by dividing them first according to whether or not they were made of wood, then according to their colour, by date of manufacture, and so on.  The fact that life can be classified hierarchically is not, in itself, an argument for evolution. (Ridley 1985, 8.)


If there is one true historical phylogenetic tree, all separate lines of evidence should converge on the same tree, our standard phylogenetic tree.

The alleged prediction and fulfillment are:

  1. If universal common ancestry is true, then phylogenies constructed from any comparisons of organisms will “converge” on the standard phylogenetic tree.
  2. Phylogenies constructed from comparisons of certain biological molecules in organisms “converge” on the standard phylogenetic tree.

There is an obvious disconnect between the alleged prediction and fulfillment.  The fulfillment refers to only one basis of comparison (biological molecules), not all bases of comparison, and it refers to only some comparisons on the selected basis (some biological molecules), not all comparisons.

The alleged prediction could, of course, be amended to conform to the statement of fulfillment.  The important point is that it is not a prediction of the hypothesis of common ancestry that phylogenies[5] constructed from comparisons of biological molecules will match phylogenies constructed from comparisons of morphology.  This is obvious from the fact molecular and morphological phylogenies often are inconsistent, and yet the hypothesis of common descent is not considered falsified.  The discordant data are simply accommodated by the theory.

The conflict between molecular and morphological phylogenies is a notorious problem in systematics.  In fact, it was the focus of a recent article in Nature, subtitled:  “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.  Can the two ever be reconciled, asks Trisha Gura.” (Gura, 230.)  Ms. Gura states in the article:

When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents.  But the phrase could also be applied to a debate that is raging within systematics.  On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics.  On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. . . .

Battles between molecules and morphology are being fought across the entire tree of life.  Perhaps the most intense are in vertebrate systematics, where molecular biologists are challenging a tradition that relies on studies of fossil skeletons and the bones and soft tissue of living species. . . .

So can the disparities between molecular and morphological trees ever be resolved?  Some proponents of the molecular approach claim there is no need.  The solution, they say, is to throw out morphology, and accept their version of the truth.  “Our method provides the final conclusion about phylogeny,” claims Okada.  Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent.  But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date.  (Gura, 230, 232.)

These conflicts have long been recognized.  In 1986, biochemist Christopher Schwabe wrote:

Molecular evolution is about to be accepted as a method superior to paleontology for the discovery of evolutionary relationships.  As a molecular evolutionist I should be elated.  Instead it seems disconcerting that many exceptions exist to the orderly progression of species as determined by molecular homologies; so many, in fact, that I think the exception, the quirks, may carry the more important message.  (Schwabe, 280.)

The incongruities of the molecular evidence led Schwabe to conclude that there were multiple evolutionary trees stemming from many separate origin-of-life events.  In other words, he thought the evidence favored the existence of different genealogies instead of a unique one, i.e., polyphyletic evolution rather the traditional view of monophyletic evolution (universal common ancestry).  He opined, “The quirks that will not submit to the neo-darwinian hypothesis are telling us that life had countless origins and that the chemistry of the origins of life has produced the diversity that has become a substrate for the evolution of biological complexity.” (Schwabe, 282.)

Two years earlier, Schwabe and Gregory Warr were equally blunt in their criticism of molecular phylogenies.  They saw the field of molecular evolution as being mired in subjectivity driven by an a priori commitment to universal common ancestry.  They wrote:

We believe that it is possible to draw up a list of basic rules that underlie existing molecular evolutionary models:

  1. All theories are monophyletic, meaning that they all start with the Urgene and the Urzelle which have given rise to all proteins and all species, respectively.
  2. Complexity evolves mainly through duplications and mutations in structural and control genes.
  3. Genes can mutate or remain stable, migrate laterally from species to species, spread through a population by mechanisms whose operation is not fully understood, evolve coordinately, splice, stay silent, and exist as pseudogenes.
  4. Ad hoc arguments can be invented (such as insect vectors or viruses) that can transport a gene into places where no monophyletic logic could otherwise explain its presence.

This liberal spread of rules, each of which can be observed in use by scientists, does not just sound facetious but also, in our opinion, robs monophyletic evolution of its vulnerability to disproof, and thereby its entitlement to the status of a scientific theory.

The absolute, explicit and implicit, adherence to all the monophyletic principle and consequently the decision to interpret all observations in the light of this principle is the major cause of incongruities as well as for the invention of all the genetic sidestepping rules cited above.  (Schwabe and Warr, 467.)

In 1993, Patterson, Williams, and Humphries scientists with the British Museum, reached the following conclusion in their review of the congruence between molecular and morphological phylogenies:

As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened.  Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology. . . .

Partly because of morphology’s long history, congruence between morphological phylogenies is the exception rather than the rule.  With molecular phylogenies, all generated within the last couple of decades, the situation is little better.  Many cases of incongruence between molecular phylogenies are documented above; and when a consensus of all trees within 1% of the shortest in a parsimony analysis is published (e.g. 132, 152, 170), structure or resolution tends to evaporate. (Patterson and others, 180.)

Citing many recent examples, Laura Maley and Charles Marshall wrote in 1998:  “Animal relationships derived from the new molecular data sometimes are very different from those implied by older, classical evaluations of morphology.  Reconciling these differences is a central challenge for evolutionary biologists at present.” (Maley and Marshall, 505.) An important issue is the nature of the assumptions under which this reconciliation will be pursued.

The following year, biologist Carl Woese, an early pioneer in constructing rRNA-based phylogenetic trees, wrote:  “No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced.  Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.” (Woese, 6854.)

It should be noted that molecular phylogenies are constructed on the basis of certain evolutionary assumptions.  The tree that is presented is chosen from a forest of alternatives, typically on the assumption of maximum parsimony.  That is, the tree that is selected is the one that reflects the least amount of presumed evolutionary change.  But if the assumption of maximum parsimony fails to fit the data, it can be jettisoned in favor of another. (Hunter, 40-41.)[6]  The availability of such ad hoc adjustments for resolving incongruities makes the claim of falsifiability an illusion.  Any result can be accommodated by the theory by revising one or more of the underlying assumptions.

Even if a morphological phylogeny was matched closely by multiple molecular phylogenies, that would not prove that the groups in question descended from a common ancestor.[7]  The molecular differences could be linked to the morphological differences for some other reason.  Hunter illustrates the point this way:

Penny[8] obtained his trees by culling those that were most parsimonious—that is, he selected the trees that showed the least amount of evolutionary change to represent the history of life.  The first problem is that Penny’s method works perfectly fine on things we know did not come about via Darwinian evolution.  For example, Penny’s method would also claim that automobiles evolved from one another.  Consider a group of vehicles, beginning with a small economy car and increasing in size to larger cars and to minivans and large-sized vans.  One could quantify several aspects of the vehicle designs, such as tire size, steering mechanism, engine size, number of seats and so forth.  Presupposing the evolutionary paradigm and searching for parsimonious relationships, we would find that most of the design measures suggest the same relationship.  The smaller vehicles have smaller tires, manual steering, smaller engines, and fewer seats.  The larger vehicles have larger tires, power steering, larger engines, and more seats.  In other words, the groupings suggested by the different design measures (tire size, steering mechanism, engine size, etc.) tend to be similar.  But of course, the family of automobiles did not evolve from one another via random mutations.  The groupings of the design measures are a natural result of engineering and have nothing to do with Darwinian evolution.  How then can Penny’s results provide “strong support” for evolution? (Hunter, 40.)

As Gish explains, it would not be surprising from a creation perspective to find that biochemical similarities increase in relation to other similarities of the creatures being compared.  He writes:

We know, for instance, that man is more similar to a chimpanzee than he is to a bat; that he is more similar to either a chimpanzee or a bat than he is to a crocodile or a flea.  Man, chimpanzee, and the bat are mammals.  The creationist would expect, therefore, that his protein, DNA, and RNA molecules, those macromolecules that are among the most important molecules in metabolism, would be more similar to those of the chimpanzee and to those of the bat than to those of the crocodile or the flea. . . . Creationists believe that all normal genes, the genes that account for the normal, healthy differences in plants and animals, were created.  Each basic type of plant and animal was created with a sufficient genetic potential or variability (or gene pool, as geneticists say) to permit sufficient variability within the circumscribed boundaries of each kind, in order to adapt to various environments and conditions.  (Gish, 277-278.)

Biologist Leonard Brand concurs.  “Anatomy is not independent of biochemistry.  Creatures similar anatomically are likely to be similar physiologically.  Those similar in physiology are, in general, likely to be similar in biochemistry, whether they evolved or were designed.” (Brand, 156.)  He makes the same point with specific reference to phylogenies based on cytochrome c.

An alternate, interventionist hypothesis is that the cytochrome c molecules in various groups of organisms are different (and always have been different) for functional reasons.  Not enough mutations have occurred in these molecules to blur the distinct grouping evident in Fig. 10.1 [the cytochromes percentage of sequence difference matrix]. . . .  If we do not base our conclusions on the a prioriassumption of megaevolution, all the data really tell us is that the organisms fall into nested groups without any indication of intermediates or overlapping of groups, and without indicating ancestor/descendant relationships.  The evidence can be explained by a separate creation for each group of organisms represented in the cytochrome c data.  (Brand, 158-159.)

Of course, failure to discern a relationship between morphology and a particular biological molecule does not prove the nonexistence of such a relationship.  It may mean simply that the relationship is beyond our present understanding.  The possibility of our ignorance is obvious, but even if it was not, earlier proclamations that most DNA is functionless “junk” illustrate the point.  “Recent research has begun to show that many of these useless-looking sequences do have a function.” (Walkup, 19.)

The cytochrome c data on which Dr. Theobald relies present some puzzles from a Neo-Darwinian perspective.  First, the cytochromes of all the higher organisms (yeasts, plants, insects, fish, amphibians, reptiles, birds, and mammals) exhibit an almost equal degree of sequence divergence from the cytochrome of the bacteria Rhodospirillum.  In other words, the degree of divergence does not increase as one moves up the scale of evolution but remains essentially uniform.  The cytochrome c of other organisms, such as yeast and the silkworm moth, likewise exhibits an essentially uniform degree of divergence from organisms as dissimilar as wheat, lamprey, tuna, bullfrog, snapping turtle, penguin, kangaroo, horse, and human.  (See matrices in Brand, 157 and Davis and Kenyon, 37.)

Why would the sequence divergence of cytochrome c between bacteria and horses be the same as the divergence between bacteria and insects?  The presumed evolutionary lineage from the ancestral cell to a modern bacterium differs radically from the presumed evolutionary lineage from the ancestral cell to a modern horse, both of which differ radically from the presumed evolutionary lineage from the ancestral cell to a modern insect.  How could a uniform rate of divergence have been maintained through such radically different pathways?  According to Michael Denton, a molecular biology researcher, “At present, there is no consensus as to how this curious phenomenon can be explained.” (Denton 1998, 291.)

Moreover, the notion that the rates of divergence remain uniform regardless of evolutionary pathway does not fit all of the cytochrome c data.  For example, referring to Dr. Theobald’s Figure 1 (reproduced above), lampreys, carp, and bullfrogs allegedly shared a common ancestor above the node labeled “vertebra.”  Since that time, the branch leading to carp and bullfrogs evolved independently of the branch leading to lampreys.  If the rates of cytochrome c divergence remain uniform regardless of evolutionary pathway, then the degree of sequence variance between the cytochrome c of lampreys and carp would be essentially the same as the degree of variance between the cytochrome c of lampreys and bullfrogs.  That is not the case.  The variance between the cytochrome c of lampreys and carp is 12%, whereas the variance between lampreys and bullfrogs is 20%.  (See matrix in Davis and Kenyon, 37.)

Second, the sequences of cytochrome c sometimes differ inversely to the presumed evolutionary proximity of the organisms being compared.  For example, turtles and rattlesnakes, both being reptiles, are presumed to have shared a common ancestor with each other more recently than they shared a common ancestor with humans.  So the evolutionist would expect the cytochrome c of a rattlesnake to be more similar to that of a turtle than to that of a human.  That, however, is not the case.  The cytochrome c of the rattlesnake varies in 22 places from that of the turtle but only in 14 places from that of a human.  (See matrix in Brand, 134.)

Humans and horses, both being placental mammals, are presumed to have shared a common ancestor with each other more recently than they shared a common ancestor with a kangaroo (a marsupial).  So the evolutionist would expect the cytochrome c of a human to be more similar to that of a horse than to that of a kangaroo.  Yet, the cytochrome c of the human varies in 12 places from that of a horse but only in 10 places from that of a kangaroo.  (See matrix in Brand, 134.)

Such discrepancies between traditional phylogenies and those based on cytochrome c are well known.  Even Ayala could only bring himself to say that “[t]he overall relations agree fairly well with those inferred from the fossil record and other sources” (emphasis supplied). (Ayala, 68.)  He then acknowledged:

The cytochrome c phylogeny disagrees with the traditional one in several instances, including the following: the chicken appears to be related more closely to the penguin than to ducks and pigeons; the turtle, a reptile, appears to be related more closely to birds than to the rattlesnake, and man and monkeys diverge from the mammals before the marsupial kangaroo separates from the placental mammals.  (Ayala, 68.)



Any fossilized animals found should conform to the standard phylogenetic tree.  Every node shared between two branches represents a predicted common ancestor; thus there are ~30 common ancestors predicted from the tree shown in Figure 1.  Our standard tree shows that the bird grouping is most closely related to the reptilian grouping, with a node linking the two (A in Figure 1); thus we predict the possibility of finding fossil intermediates between birds and reptiles.  The same reasoning applies to mammals and reptiles (B in Figure 1). However, we predict that we should never find fossil intermediates between birds and mammals.

The alleged prediction and fulfillment are:

  1. If universal common ancestry is true, then all fossilized animals will “conform”[9] to the standard phylogenetic tree.
  2. All fossilized animals “conform” to the standard phylogenetic tree.

Universal common ancestry affirms only that all creatures descended from the same ancestor.  There is nothing about that affirmation that requires conformity to the standard phylogenetic tree.  A phylogenetic tree is merely a diagram that reflects current evolutionary thinking about the relationships of the taxa included.  Branches are arranged on the tree on the assumption of evolution and according to perceived similarities in selected traits.[10]  The relationships of some branches are viewed more dogmatically than the relationships of others, but none of the branches are set in stone.

Since phylogenies are by nature provisional, the suggestion that the hypothesis of common descent would be falsified by “[a]ny finding of mammal/bird intermediates” is mistaken.  Should a strikingly birdlike mammal be discovered, the standard tree simply would be modified to accommodate the new creature, after wrangling over its placement in the schema.

The ease with which this precise adjustment could occur was illustrated two decades ago, when “[t]he reality of the ‘mammal-bird,’ a hypothetical common ancestor of birds and mammals, [was] a contentious issue in modern systematics.” (Mike Benton, 18.)  Brian Gardiner’s cladistic analysis indicated that birds were most closely related to mammals, which relationship was supported by two Cambridge scientists’ analysis of molecular data.  That view was readily accepted by some, even to the point that one French paleontologist “published a restoration of the hypothetical common ancestor between birds and mammals—a sort of warm-blooded, hairy/feathery climbing insect eater!” (Mike Benton, 18.)  Branches can be rearranged, even between mammals and birds, without skipping a beat in terms of commitment to common ancestry.

Of course, the discovery of a strikingly birdlike mammal would not necessarily force a shift in thinking about the relationship of mammals and birds (a placing of their branches next to each other).  The birdlike features could be attributed to convergent evolution.  Many organisms are believed by evolutionists to have evolved similar traits independently.  (In fact, some experts believe that the birdlike features of dromaeosaurids, the dinosaurs considered by most experts to be the sister group to birds, arose independently rather than by inheritance from the ancestor of birds.)  If the mammal’s birdlike traits were judged to be the result of convergent evolution, the species would be shown on the phylogenetic tree as a subset or side branch of mammals that was unrelated to birds.

The shift in thinking over the last 30 years about the relationship of dinosaurs and birds is an example of a generally accepted phylogenetic adjustment, albeit at a lower taxonomic level.  From the publication of Gerhard Heilmann’s The Origin of Birds in 1926, it was a matter of textbook orthodoxy that birds were more closely related to thecodonts (an order of reptiles) than to theropods (a suborder of a different order of reptiles).  Thus, the discovery in 1964 of the birdlike theropod Deinonychus was contrary to phylogenetic expectations.  Today, however, the standard phylogeny shows birds more closely related to theropods than to thecodonts.

The assertion that all fossilized animals conform to the standard phylogenetic tree is unprovable, because one can never be sure that all fossilized animals have been discovered.  But more importantly, the premise turns out to be merely a restatement of the claim of nested hierarchy.  It adds nothing to the case for common ancestry.

Conformity and nonconformity to the standard phylogenetic tree are defined in the article in terms of “intermediates.”  It is stated that, given the standard phylogeny, one would expect “intermediates” between reptiles and birds and between reptiles and mammals (because these pairs are shown as sharing hypothetical common ancestors, A and B in Figure 1), but one would not expect “intermediates” between mammals and birds.  It is then alleged that the fossils conform to this expectation, and thus “conform to the standard phylogenetic tree,” in that “intermediates” have been found between reptiles and birds (citing mainly dromaeosaurids) and between reptiles and mammals (citing synapsids) but not between mammals and birds.

But according to the definition of “intermediate” given in the article, dromaeosaurids are not reptile-bird intermediates and synapsids are not reptile-mammal intermediates.  An “intermediate form” is defined as “[a] fossil or modern species that displays characters definitive of two or more different taxa” (emphasis supplied).  Dromaeosaurids do not display characters that aredefinitive of both reptiles and birds (which is why they are not considered birds), and synapsids do not display characters that are definitive of both reptiles and mammals (which is why they are not considered mammals).

On the other hand, under the given definition, all taxa qualify as “intermediates” between themselves and the taxa in which they are shown as nested.[11]  For example, all mammal species, including all monotremes and marsupials, are reptile-mammal “intermediates” because they all possess the traits that are definitive of both Reptilia and Mammalia.[12]  That is, they are all amniotes with the definitive traits of Mammalia. (Reptilia is defined simply as amniotes that are not birds or mammals [Carroll, 193].)  Likewise, all bird species, including the Kiwi (called an “honorary mammal”), are reptile-bird “intermediates” because they all possess the traits that are definitive of both Reptilia and Aves.

But if taxa are intermediate by virtue of being nested, the existence of intermediates is not a separate argument for common ancestry.  It is the argument of nested hierarchy under a different label.  And if there are no intermediates between non-nested taxa, that means only that nested hierarchy is a pattern to which there are no known exceptions.  As previously explained, that result could be accommodated by the theory of common descent, but it is not evidence for it.

In citing dromaeosaurids as reptile-bird intermediates and mammal-like reptiles as reptile-mammal intermediates, Dr. Theobald is apparently defining “intermediates” as organisms that are morphologically between alleged ancestors and descendants (rather than using the specified definition of organisms that possess the definitive traits of the two relevant taxa).  But if intermediates can occur by definition only between alleged ancestors and descendants, then they can occur by definition only in conformity to the phylogenetic tree.

Consider the striking similarities between some marsupials and placentals.  If the consensus were that a marsupial wolf evolved into a placental wolf, then the marsupial wolf would qualify as an intermediate under the definition being considered.  That is, it would be morphologically between its alleged ancestor (an earlier marsupial) and descendant (the placental wolf).  But since the consensus (which is reflected in the standard phylogeny) is that marsupial wolves and placental wolves arose independently, the marsupial wolf cannot qualify as a marsupial-placental intermediate, whatever its morphology.  Conformity with the standard phylogeny is guaranteed by the definition.

The assertions that there are “no morphological gaps” in the alleged dinosaur-to-bird transition and that there is an “exquisitely complete series of fossils” for the alleged reptile-to-mammal transition are debatable, to say the least.  I have elsewhere tried to point out some of the limitations of those claims (see, “On the Alleged Dinosaurian Ancestry of Birds” and “Reappraising the Crown Jewel”).

But even if one granted that reptiles evolved into a bird and a mammal, that would not establish that reptiles and all other organisms descended from a common ancestor, which is the proposition being argued.  The difference between a bacterium and a reptile, not to mention the other organisms, is considerably greater than the difference between a reptile and a bird or a reptile and a mammal.  So the fact a reptile could evolve into a bird or a mammal would not mean that a bacterium could evolve into a reptile and everything else.  In fact, granting that reptiles evolved into a bird and a mammal would not even establish that all birds and all mammals descended from a reptile.  That would be an assumption.


Fossilized intermediates should appear in the correct general chronological order based on the standard tree.  Any phylogenetic tree predicts a relative chronological order of hypothetical common ancestors and intermediates between these ancestors.  For instance, in our current example, the reptile/mammal common ancestor (B) [from Figure 1] and intermediates should be older than the reptile/bird common ancestor (A) [from Figure 1] and intermediates.

The alleged prediction and fulfillment are:

  1. If universal common ancestry is true, then fossil intermediates will appear in the “general chronological order” reflected in the standard phylogenetic tree;
  2. Fossil intermediates appear in the “general chronological order” reflected in the standard phylogenetic tree;

As pointed out above, “intermediate” is defined in the article as “[a] fossil or modern species that displays characters definitive of two or more different taxa” (emphasis supplied).  Since, under that definition, a taxon is intermediate by virtue of being nested within another, the alleged prediction is that fossils will appear in the order of nesting reflected in Figure 1.  In other words, a prokaryotic organism would appear first, followed successively (in the fungi/metazoan direction) by organisms with nuclei, multicellularity, organs, nervous and vascular system, and so on up the deuterostomic and protostomic branches.

There is nothing about the hypothesis of universal common ancestry that requires organisms to have descended in the pattern depicted in the standard phylogeny.  Common ancestry does not even require nested hierarchy, let alone any particular pattern of nesting.  A phylogeny is simply a depiction of the order in which evolutionists believe taxa arose, not the order in which they wererequired to arise.  (And even if it was believed that universal common descent could occur in only one way, that is an assertion about the mechanism of descent, a subject Dr. Theobald purposefully excluded from his case.)

Moreover, while ancestral taxa must have existed before any taxa that descended from them, that does not mean the appearance of their fossilized forms must correspond to that order of existence.  However unlikely the claim may be, it remains possible for a proponent of common descent to assert that select taxa appear in the fossil record contrary to the order in which they came into existence.

Witness the fact dromaeosaurids, which are offered by Dr. Theobald as “reptile-bird intermediates,”[13]  first appear in the fossil record some 25 million years after the first fossil bird.  (If one accepts Protoavis, rather thanArchaeopteryx, as the first fossil bird, the gap in appearance increases to about 100 million years.) Rather than disqualifying dromaeosaurids in Dr. Theobald’s eyes as “reptile-bird intermediates,” which he argues must appear in the order suggested by the standard phylogeny, it is simply assumed that dromaeosaurids lived tens of millions of years before there is any evidence of their existence.  (The ambiguity of “general chronological order” prevents such nonconformities from falsifying the claim.)

This same strategy could be employed if dromaeosaurids turned up in strata older/lower than that in which synapsids first appear.  That is, it could be assumed that pelycosaurs and therapsids actually predated dromaeosaurids but for some reason did not appear in the fossil record until later.  So the suggestion that the hypothesis of universal common ancestry would be falsified if dromaeosaurids first appeared in the fossil record before synapsids reptiles is incorrect.

The fact synapsids appear before dromaeosaurids hardly constitutes proof (confirms the “prediction”) that “fossilized intermediates” appear in the general chronological order indicated in the standard phylogeny.  They are only two data points.  But more importantly, one must bear in mind that Figure 1 is of necessity a simplified and fragmentary phylogeny.  The picture changes significantly when the scope of inquiry is broadened.[14]  According to one Harvard-trained paleontologist:


[T]he correspondence between phylogeny and the fossil record is not as strong as it might first seem.  When the order of all kingdoms, phyla and classes is compared with the most reasonable phylogenies, over 95 percent of all the lines are not consistent with the order in the fossil record.  The only statistically significant exceptions are the orders of first appearances of the phyla of plants and the classes of vertebrates and arthropods.  Yet these three lineages also order organismal groups from sea-dwellers to land dwellers.  The land-plant phyla, for example, are in a simple sequence from plants that need standing water to survive (e.g., algae and bryophytes) to those that can survive extreme desiccation (e.g., the cacti).  The vertebrate classes go from sea-dwellers (fish) to land/sea creatures (amphibians) to land creatures (reptiles/mammals), to flying creatures (birds).  The arthropod classes go from sea-dwellers (e.g., trilobites, crustaceans) to land dwellers (e.g., insects).  So it’s not clear that macroevolution is a truly good explanation for the order of fossil first appearances of major groups of life.  Such a radical idea as a global flood, for example, which gradually overcame first the sea and then the land, actually explains the primary order of major groups in the fossil record (sea to land) better than macroevolutionary theory.  (Wise, 225-226.)



Some of the more renowned evidences for evolution are the explanations it provides for nonfunctional or rudimentary vestigial characters, both anatomical and molecular. Throughout macroevolutionary history, functions necessarily have been gained and lost; thus, we predict vestigial structures, which are structural evidence of lost functions. Since there is no apparent reason for their existence, nonfunctional characters of organisms are especially puzzling. So are rudimentary structures, which have different and relatively minor functions compared to the same more developed structures in other organisms. Consequently, evolutionary explanations for vestigial characters are strong proofs.

Explanations are not evidence; they are attempts to explain evidence. So the first and last sentences of the quoted paragraph are at best overstatements. The question is whether the evidence of “vestigial” structures favors the explanation of universal common ancestry, and if so, how strongly.

The alleged prediction and fulfillment are:

If universal common ancestry is true, then some organisms will have structures the function of which was lost or diminished in the course of the organism’s evolutionary history (“vestiges” of the organism’s evolutionary history).

Some organisms have structures the function of which was lost or diminished in the course of the organism’s evolutionary history.

Vestigial structures are not a necessary result of all possible mechanisms of universal common descent. They are understandable within a Neo-Darwinian framework of random mutation and natural selection, but since Dr. Theobald has chosen to argue for common ancestry without regard to any mechanism of descent, he cannot offer as evidence data that can be explained only by particular mechanisms of descent.

Moreover, even Neo-Darwinism does not demand vestigial structures; it simply accommodates them. They can exist or not exist with equal ease under the theory and can appear with any frequency. Any result can be explained by appeal to the randomness of mutation and the uncertainty of the selective pressures that were at work in any given lineage.

In any event, vestigial structures provide no support for the claim of universal common ancestry. A bona fide vestigial structure says only that the organism in which it is found descended from an earlier organism that possessed the structure in fully functional form. It says nothing about how that earlier organism came to exist, whether it descended from a universal common ancestor, descended from one of many independently created organisms, or was itself created independently.[15] Since vestigial structures can arise in unconnected lineages as well as in lineages that are rooted in a common ancestor, they do not count as evidence for universal common ancestry.

Of course, the identification of bona fide vestigial structures is fraught with difficulty. Dr. Theobald defines a vestigial character as “a character that for all intents and purposes has no obvious or important function, yet is structurally similar to functional characters in other species” (emphasis supplied). He elaborates: “If the character appears reduced and rudimentary compared to the same structure in other organisms, and the structure has obvious important functions in the majority of other organisms, then it is considered a vestigial structure.”

The problems are illustrated by Dr. Theobald’s use of the human coccyx (which he describes as “the four fused tail vertebrae of humans”) as an example of a vestigial structure. It has long been known that the coccyx serves as a point of attachment for ligaments and several important muscles. So why think the coccyx was not specially designed by a Creator to fulfill that function?

The answer, from Dr. Theobald’s definition, is twofold. First, the function of the coccyx must be judged “unimportant” (given that the function is obvious). That, however, is a grossly subjective assessment. It is also clearly theological. How does one determine when a function is important enough to make it plausible that a Creator would specially design a structure to fulfill it?

This particular trap is avoided if vestigial structures are defined as those that have no function (rather than those that have no important function). But that definition stumbles over the fact one can never really be certain that an apparently functionless structure is really functionless. It may be that we lack the knowledge necessary to appreciate its function. As S. R. Scadding pointed out 20 years ago:

I would suggest that the entire argument that vestigial organs provide evidence for evolution is invalid on two grounds, one practical, the other more theoretical. The practical problem is that of unambiguously identifying vestigial organs, i.e., those that have no function. The analysis of Wiedersheim’s list of vestigial organs points out the difficulties. . . . Wiedersheim could list about one hundred in humans; recent authors usually list four or five. Even the current short list of vestigial structures in humans is questionable. . . . (Scadding, 173.)[16]
Second, the coccyx must be judged “similar” to a functional structure in another organism. But how similar must the structures be and how is that similarity to be measured? It is a vague concept that can be shaped easily by one’s presuppositions. Moreover, there is no reason why a Creator could not adapt similar designs for different purposes. To conclude that one structure is too similar to another to have been separately designed to fulfill a function requires an assumption about the Creator’s modus operandi. It is, therefore, a theological assessment.

In his recent book, Hunter spotlights the metaphysical nature of such arguments. After citing comments by evolutionists about various alleged vestigial structures, he writes:

Behind this argument about why the patterns in biology prove evolution lurks an enormous metaphysical presupposition about God and creation. If God made the species, then they must fulfill our expectations of uniqueness and good engineering design. We might say that God was supposed to have optimized the design of each species. Evolutionists have no scientific justification for these expectations, for they did not come from science. They are part of a personal religious belief and as such are not amenable to scientific debate. In fact, evolutionists rely on a rather narrow metaphysical target in their attacks on creation. The evolutionist’s notion of God and divine creation is, for many people, just a straw man—an overly simplified metaphysic that conveniently supports their views. (Hunter, 49.)
The suggestion that universal common ancestry would be falsified by finding “vestigial structures” in an organism that were not present in that organism’s alleged ancestors, as depicted in the standard phylogeny, is incorrect (in that it is based on a false premise). To use one of Dr. Theobald’s examples, if a fish species were discovered with a relatively small, nonfunctional leg or pelvis, it would only be labeled a “vestigial structure” if that species was judged to have “evolved back” from a tetrapod (i.e., if its branch on the phylogeny was relocated). Otherwise, it would be hailed as an example of a nascent structure, that is, a structure that is on its way “in” rather than on its way “out.” Rather than being the death knell of common descent, it would be touted as evidence that tetrapods evolved from fish. Dr. Theobald sorely underestimates the flexibility of the theory he is asserting.

In fact, the absence of nascent structures poses a problem for Neo-Darwinian common descent. If, as Dr. Theobald says, “functions necessarily have been gained and lost” throughout evolutionary history, why does one find evidence only of degeneration? As Wise says:

The absence of [nascent] organs would seem to argue that although we have evidence of degeneration from an earlier, more optimal design, we lack evidence of a move toward a new optimal design. It would seem that if an Intelligent Designer created optimal designs in the past and life’s history has been a move away from that optimum, the presence of vestigial organs and the absence of nascent organs would be better explained by intelligent design than by evolutionary theory. (Wise, 223.)


Vestigial characters should also be found at the molecular level. Humans do not have the capability to synthesize ascorbic acid (otherwise known as Vitamin C), and the unfortunate consequence can be the nutritional deficiency called scurvy. However, the predicted ancestors of humans had this function (as do all animals except primates and guinea pigs). Therefore, we predict that humans, primates, and guinea pigs should carry evidence of this lost function as a molecular vestigial character.

Just for the record, it is not true that all animals except primates and guinea pigs have the ability to synthesize ascorbic acid. That ability is lacking in some species of fish, birds, and bats and is present in some species of primates.

The alleged prediction and fulfillment are:

If universal common ancestry is true, then some organisms will have genes the function of which was lost in the course of the organism’s evolutionary history.

Some organisms have genes the function of which was lost in the course of the organism’s evolutionary history.

Since this is the concept of vestigial structure applied to genes, the preceding response is largely applicable. Vestigial genes are not a necessary result of all possible mechanisms of universal common descent, and since Dr. Theobald has chosen to argue for common ancestry without regard to any mechanism of descent, he cannot offer as evidence data that can be explained only by particular mechanisms of descent.

Moreover, even Neo-Darwinism does not demand vestigial genes; it simply accommodates them. If they did not exist, it would mean that an incapacitating mutation never occurred or never occurred in an environment that was selectively neutral in terms of the gene’s function. If they did exist, it would mean the opposite. Any result can be fit within the scheme.

In any event, vestigial genes provide no support for the claim of universal common ancestry. A bona fide vestigial gene says only that the organism in which it is found descended from an earlier organism that possessed the gene in functional form. It says nothing about how that earlier organism came to exist, whether it descended from a universal common ancestor, descended from one of many independently created organisms, or was itself created independently.

Consider Dr. Theobald’s primary example, the L-gulano-g-lactone oxidase gene, which is one of the genes required for the synthesis of vitamin C. Assuming this is a bona fide pseudogene in humans, meaning a nonfunctional version of a gene that was functional at some point in the human lineage, it says nothing about the origin of the ancestor that possessed the functioning gene. That ancestor could have been independently created or could have descended from a creature that had been independently created. So this entire line of argument cannot do what Dr. Theobald needs it to do.

As with other vestigial structures, it is difficult to identify bona fide vestigial genes. We simply do not know enough to be able to declare definitively that any given series of nucleotides has absolutely no function. As molecular biologist Pierre Jerlstrom recently noted:

Pseudogenes are often referred to in the scientific literature as nonfunctional DNA, and are regarded as junk. But more scientists are now conceding that this is far from true for many pseudogenes. Failure to observe pseudogenes coding for a product under experimental conditions is no proof that they never do so inside an organism. It is also impossible to rule out protein expression based solely on sequence information, as DNA messages can be altered by, e.g., editing the transcribed RNA, skipping parts of the sequence, etc. Moreover, the inability to code for a protein useful to an organism hardly exhausts other possible functions pseudogenes may have. (Jerlstrom, 15.)
The possibility of an undiscovered function has become even greater with the recent sequencing of the human genome. Though humans may have as many as 300,000 proteins, it turns out that they have only about 30,000 genes.[17] Thus, the genome is even more complex than previously believed. As J. Craig Venter of Celera Genomics explained in the press conference announcing the sequencing of the human genome:

[O]ur understanding of the human genome has changed in the most fundamental ways. The small number of genes—some 30,000—supports the notion that we are not hard wired. We now know the notion that one gene leads to one protein, and perhaps one disease, is false.

One gene leads to many different protein products that can change dramatically once they are produced. We know that some of the regions that are not genes may be some of the keys to the complexity that we see in ourselves. We now know that the environment acting on our biological steps may be as important in making us what we are as our genetic code. (Bethell, 52.)

When asked immediately after the press conference about Venter’s suggestion that one gene could give rise to ten proteins, James Watson (of DNA fame) said, “Some genes can give rise to 50 different proteins.” (Bethell, 56.) As summed up by the Washington Post, “The way these genes work must therefore be far more complicated than the mechanism long taught.” (Bethell, 52.)

Indeed, the evolutionists’ claim that pseudogenes are still present and recognizable tens of millions of years after they supposedly ceased functioning suggests that they serve some kind of purpose. Otherwise, they should have been removed or altered beyond recognition by the accumulation of mutations. Jerlstrom writes:

The persistence of pseudogenes is in itself evidence for their activity. This is a serious problem for evolution, as it is expected that natural selection would remove this type of DNA if it were useless, since DNA manufactured by the cell is energetically costly. Because of the lack of selective pressure on this neutral DNA, one would expect that ‘old’ pseudogenes would be scrambled beyond recognition as a result of accumulated random mutations. Moreover, a removal mechanism for neutral DNA is now known. (Jerlstrom, 15.)
Granting the possibility that pseudogenes have a function, the claim that they are a vestige of evolutionary history reduces to the notion that a Creator would not fulfill a function in one organism by using a series of nucleotides that are similar to a series of nucleotides that fulfill a different function in another organism. That, however, is a theological argument. Hunter makes the point well:

A pseudogene is a DNA sequence that resembles a gene but appears to be nonfunctional. In evolutionary lore, these are vestigial organs at the molecular level. And just as the vestigial organ argument for evolution relies on the assumption of full knowledge about the organism, so too the pseudogene argument assumes that we can be sure they are not useful. They are assumed to be the byproduct of useless, but not terribly harmful, mutations. Gray writes:

Further analysis shows that this gene is a pseudogene, i.e., it looks like a real gene, but it is not expressed due to a mutation in the gene itself. Now we could argue that in God’s inscrutable purpose he placed that vitamin C synthesis look-alike gene in the guinea pig or human DNA or we could admit the more obvious conclusion, that humans and primates and other mammals share a common ancestor.

Here Gray makes a negative theological argument. He seems comfortable in assuming just what God would have done when it comes to designing the genotype. Gray states unequivocally that the pseudogene is a result of mutation, but this is nothing more than evolutionary speculation. More important, he then claims that God obviously would not have an inscrutable purpose for having the nonstandard gene there. For our purposes the point is not that pseudogenes do or do not have function or that God must have or must not have designed them. The point is simply that, like evolutionists, theistic evolutionists need Darwin’s negative theology. (Hunter, 168-169.)

Even if one could be certain that a gene was functionless (a pseudogene) and had been rendered such by a specific mutation, finding that same gene and mutation in another species would not mean that those species had descended from a common ancestor. The same gene could have been inactivated by the same mutation occurring independently. The evolutionists’ reply that this suggestion is too improbable to take seriously depends on the assumption that the mutation in question occurs randomly. But if there is (or was) a mechanism of mutation that favors certain locations in the gene, the odds against an independent occurrence of the mutation drop according to the strength of that bias.

As in the case of possible functions for pseudogenes, we simply do not know enough to assess definitively the odds against the independent occurrence of inactivating mutations (because we lack complete knowledge of all past and present mechanisms of mutation). So even conclusions about common ancestry that are based on the presence of similar, bona fide pseudogenes must remain tentative.[18]

For example, molecular biologist Michael Brown believes there is evidence for the existence of either viral or enzymatic activity that creates mutations. He writes:

So I think there is a mechanistic process that has produced many of the Pseudogenes that we have, rather than a random process. If the Pseudogene is truly defective and if the mutations are truly found in patterns (not random), then the idea that it’s a common mechanism is possible. Viruses have enzymes that, under the same conditions, do repeatable reactions.

If the DNA in Humans, Chimps, Monkeys, etc., are very similar, then if they are all infected by the same virus, would we expect the virus to do the same thing in the different species? I think so.[19]

The point is not that Brown’s opinion necessarily is correct but that it (or something analogous) may be correct. Our understanding is just too rudimentary to permit us to say with certainty that similar pseudogenes were not caused independently by a nonrandom mechanism.

The fact some pseudogene-derived phylogenies disagree is consistent with the suggestion that something other than common descent is involved in the phenomenon. Phylogenies based on several pseudogene sequences have yielded conflicting results with regard to the human-chimp-gorilla trichotomy. (Woodmorappe 2000, 62-63.) Of course, evolutionists have ways of accommodating these discordant data, but their presence remains noteworthy.

Embryology and developmental biology have provided some fascinating insights into evolutionary pathways. Since the cladistic morphological classification of species is generally based on derived characters of adult organisms, embryology and developmental studies provide a nearly independent body of evidence.

The ideas of Ernst Haeckel greatly influenced the early history of embryology; however, his ideas have been superseded by those of Karl Ernst van Baer, his predecessor. Van Baer suggested that the embryonic stages of an individual should resemble the embryonic stages of its ancestors (rather than resembling its adult ancestors, a la Haeckel). The final adult structure of an organism is the product of numerous cumulative developmental processes; for species to evolve, there necessarily must have been change in these developmental processes. The modern developmental maxim is the inverse of Haeckel’s biogenetic law. “Phylogeny recapitulates Ontogeny,” not the opposite. Walter Garstang stated even more correctly that ontogeny creates phylogeny. What this means is that once given knowledge about an organism’s ontogeny, we can confidently predict certain aspects of the historical pathway that was involved in this organism’s evolution (Gilbert 1997, pp. 912-914). Thus, embryology can provide confirmations and predictions about evolution.

Two different concepts seem to be mixed here. On the one hand, there is the suggestion that descendant ontogenies tend to recapitulate ancestral ontogenies (Garstang’s notion of paleogenesis). This is the claim that all vertebrates, for example, are very similar at an early stage of embryological development, with noticeable differences coming only in later stages. The more closely related the species being compared, the longer their embryos will develop similarly. The more distantly related the species, the sooner their embryos will diverge in appearance.

On the other hand, there is the suggestion that the embryos of organisms develop in ways that exhibit aspects of the organism’s evolutionary history.[20] Thus, Dr. Theobald points to the fact certain reptile jaw bones and marsupial middle ear bones develop from the same embryological structures as evidence that the middle ear bones of mammals evolved from the jaw bones of reptiles.

The alleged prediction and fulfillment under the first concept are:

If universal common ancestry is true, then all ontogenies will begin similarly, and the ontogenies of more closely related species will remain similar longer than will the ontogenies of more distantly related species.

All ontogenies begin similarly, and the ontogenies of more closely related species remain similar longer than do the ontogenies of more distantly related species.

The alleged prediction and fulfillment under the second concept are:

If universal common ancestry is true, then certain aspects of an organism’s evolutionary history will be exhibited in its ontogeny.

Certain aspects of an organism’s evolutionary history are exhibited in its ontogeny.

There is nothing about the hypothesis of universal common ancestry that requires any particular manner of reproduction, let alone one in which embryos either recapitulate the ontogenies of their ancestors or pass through stages representative of their evolutionary history. Common ancestry can accommodate such phenomena, but it certainly does not predict it. And if it does not predict the phenomena, it cannot be falsified by their absence or confirmed by their presence.

Even if one could rightly claim these as predictions of the hypothesis of universal common ancestry, they are too general to be scientifically meaningful. How does one measure objectively the similarities of various ontogenies? What specific aspects of an organism’s evolutionary history will be reflected in its ontogeny and why those aspects and not others?

And even if these ambiguities could be nailed down, views about “closely related species” and “evolutionary history” are tentative. So if all other avenues of accommodating the embryological data should fail, the option of revising phylogenies is always available. Falsifiability is again merely an illusion.

As for the first concept, the claim that ontogenies of organisms begin similarly and then progressively diverge in accordance with their alleged evolutionary proximity is false. Developmental biologist Jonathan Wells explains:

Although it is true that vertebrate embryos are somewhat similar at one stage of their development, at earlier stages they are radically dissimilar. After fertilization, animal embryos first undergo a process called cleavage, in which the fertilized egg divides into hundreds or thousands of separate cells. During cleavage, embryos acquire their major body axes (e.g., anterior-posterior, or head to tail, and dorsal-ventral, or back to front). Each major group of animals follows a distinctive cleavage pattern; among vertebrates, for example, mammals, birds, fishes, and reptiles cleave very differently.

Animal embryos then enter the gastrulation stage, during which their cells move relative to each other, rearranging themselves to generate basic tissue types and establish the general layout of the animal’s body. The consequences of this process are so significant that embryologist Lewis Wolpert has written that “it is not birth, marriage, or death, but gastrulation which is truly the important event in your life” (Wolpert 1991, 12). Like cleavage patterns, gastrulation patterns vary markedly among the major groups of animals, including the different classes of vertebrates (Elinson 1987).

Only after gastrulation do the embryos of mammals, birds, fishes and reptiles begin to resemble each other. In the pharyngula stage, every vertebrate embryo looks vaguely like a tiny fish, with a prominent head and a long tail. (Wells 1998, 59.)

Reviewing the notion that “during their ontogenies the members of twin taxa follow the same course up to the stage where they diverge into separate taxa,” embryologist Wolfgang Dohle wrote:

Everybody who is even slightly acquainted with ontogenetic facts knows that there are hundreds of examples to which this theorem does not apply. In many polychaete and prosobranch genera one species develops through a planktonic larva, whereas another species has direct development. The telolecithal cephalopod eggs cleave in a bilateral manner without any similarity to the spiral cleavage of other related Mollusca. Triclad eggs have a blastomeric anarchy, whereas the adults very closely resemble the polyclads which show spiral cleavage. This list could easily be elongated. (Dohle, 285.)
Wells points out that this ontogenetic pattern of early differences followed by similarities and then differences again “is quite unexpected in the context of Darwinian evolution.” He adds, “Instead of providing support for Darwin’s theory, the embryological evidence presents it with a paradox.” (Wells 2000, 99.) Of course, attempts are being made to explain the paradox by proposing that early development evolves more easily than expected, but as Wells notes, “it is clear that [these proposed explanations] start by assuming Darwinian evolution, then read that back into the embryological evidence.” (Wells 2000, 99.)

Of course, this is the exact opposite of basing evolutionary theory on embryological evidence. If one were to start with the evidence and then follow Darwin’s reasoning about the implications of development for evolution, one would presumably conclude that the various classes of vertebrates are not descended from a common ancestor, but had separate origins. Since this conclusion is unacceptable to people who have already decided that Darwin’s theory is true, they cannot take the embryological evidence at face value, but must re-interpret it to fit the theory. (Wells 2000, 101.)
Even if one ignores the paradoxical hourglass pattern of vertebrate ontogenies (the fact they start out looking very different, converge in appearance midway through development, and then increasingly diverge toward adulthood) and focuses only on the latter half of development, common ancestry is not the only explanation for the gradual divergence of different species. As Brand explains:

[A] home builder builds the foundation first (homes that look very different when complete can have similar foundations) and adds the unique features of the home later. An engineer attempting to design the developmental stages of all these organisms would very possibly find that it is most efficient to follow a basic plan for all and add special features later in the process, as needed for each animal. (Brand, 150.)
In addition, if Dr. Theobald’s assertion that “[t]he final adult structure of an organism is the product of numerous cumulative developmental processes” (emphasis supplied) is correct, then organisms that are thought to be more evolutionarily derived would take longer to develop. But as Wise points out, that is not the case. “[O]rganisms that are thought to be more evolutionarily derived don’t seem to have longer development.” (Wise, 216.)

As for the second concept, the claim that “certain aspects” of an organism’s evolutionary history are exhibited in its ontogeny (such as the alleged evolution of the mammalian middle ear from reptile jaw bones) is nothing more than an opinion. Common descent is not the only explanation for the fact separate structures in adults of different species develop from an analogous embryological structure. It is certainly possible for a designer to fabricate different structures from similar elements. A manufacturer, for example, can make the tops of one kind of footwear and the laces of another from the same nylon.

The notion that God would not employ an ontogeny in which the middle ear bones of mammals develop from the embryological structure that is analogous to that from which reptile jaw bones develop is a theological assessment. Those who reject that assessment are rightly unimpressed by evidence that draws its weight from it.

Moreover, it is unclear in what sense the ontogenetic development of mammalian middle ear bones from a structure analogous to that from which certain reptile jaw bones develop can be said to exhibit the evolution of the mammalian middle ear from the reptile jaw. The evolutionary claim is that the quadrate and articular bones of the reptilian jaw were (on two separate occasions) gradually transformed into ear ossicles through many random steps, each of which provided a significant enough advantage to be established in the population. There is no need, however, for the intermediate stages of an embryo’s development to be progressively advantageous, as they are part of a directed development program that unfolds in a protective environment. The two thus seem quite unrelated.

Because species divergence happens not only in the time dimension, but also in spatial dimensions, common ancestors originate in a particular geographical location. Thus, the spatial and geographical distribution of species should be consistent with their predicted genealogical relationships. The standard phylogenetic tree predicts that new species must originate close to the older species from which they are derived. Closely related contemporary species should be close geographically, regardless of their habitat or specific adaptations. If they are not, there had better be a good explanation, such as extreme mobility (cases like sea animals, birds, human mediated distribution, etc.), continental drift, or extensive time since their divergence. In this sense, the present biogeographical distribution of species should reflect the history of their origination.

A reasonable nonevolutionary prediction is that species should occur wherever their habitat is. However, macroevolution predicts just the opposite—there should be many locations where a given species would thrive yet is not found there, due to geographical barriers (Futuyma 1998, pp. 201-203).

The standard phylogenetic tree does not “predict that new species must originate close to the older species from which they are derived.” A phylogeny is simply a diagram that depicts current evolutionary thinking about the genealogical relationships of the taxa included. It does not address questions of geographical proximity.

It is unclear (at least to me) what is being claimed here. On the one hand, there is the suggestion that the geographical distribution of species should be consistent with their believed (not “predicted”) genealogical relationships. Thus the statement, “Closely related contemporary species should be close geographically, regardless of their habitat or specific adaptations.”

On the other hand, there is the suggestion in the second quoted paragraph that only macroevolution (which Dr. Theobald labels a “virtual synonym” for universal common descent) can explain why some species live only in certain areas, despite the existence of similar habitat elsewhere. This point relates solely to the location of “given species,” not to their distance from “closely related contemporary species.”

It is not spelled out how these two propositions translate into support for the hypothesis of universal common ancestry. Presumably they are to be merged into something like the following: only universal common ancestry can explain the fact groups of similar species are often restricted to a particular geographic region. In that case, the alleged prediction and fulfillment can perhaps best be expressed as:

If universal common ancestry is true, then groups of similar species will often be restricted to a particular geographic region.

Groups of similar species are often restricted to a particular geographic region.

The fact groups of similar species are often restricted to a particular geographic region is not evidence of universal common ancestry. At best, it suggests that the similar species arose in that region from a common ancestor. It says nothing about whether that regional common ancestor descended from a universal common ancestor, descended from one of many independently created organisms, or was itself created independently. It therefore does not do what Dr. Theobald needs it to do.

In fact, the degrees of evolution suggested by biogeography are quite limited. As biologist L. James Gibson notes, “Geographical distributions indicate common ancestry only for lower taxonomic categories. Endemic groups are most common at the Family level or lower. Few Orders are endemic to a particular region. Thus common ancestry is suggested primarily among members of families and genera.”[21]

Wise makes the point this way:

There are two sorts of biogeographical evidences. One type is the claim that very similar species are often found near one another, as if they evolved from one another. This type of biogeography, which I call microbiogeography, has many supporting examples. Microbiogeography is evidence for microevolution (the evolution of populations) and the origin of species, however, not for macroevolution of the origin of major groups. What I call macrobiogeography is the claim that major types of organisms tend to be associated with one another.

There are very few examples of macrobiogeographical evidences for macroevolution, and none of them is very strong. (Wise, 223.)

The best known claim of macrobiogeographical evidence is the one cited by Dr. Theobald—the concentration of marsupials in Australia. But as Wise explains, “there are several reasons that marsupials in Australia are actually a poor example.”

First, all marsupials are not in Australia. The Virginia opossum of North America, for example, is a marsupial. It is thought to have come from South America, not Australia. Thus, not all similar organisms are in the same area. Second, in the fossil record marsupials are known from every continent. Third, marsupials are the oldest fossil mammals known from Africa, Antarctica and Australia—in that order. The fossil record seems to show a migration of marsupials from somewhere around the intersection of the Eurasian and African continents and then a survival in only the continents farthest from their point of origin (South America and Australia). The same major groups of marsupials (opossums) are found in both South America and Australia. Macroevolutionists claim that these major groups of marsupials are together because they evolved from a common ancestor, but the evidence can be at least as well explained as similar organisms (fit for similar environments and with similar capabilities) traveling more or less together to similar environments. (Wise, 223.)
All of Dr. Theobald’s other examples involve endemic groups at lower taxonomic categories (species of lungfishes, ratite birds, leptodactylid frogs, alligators, giant salamanders, magnolias, cacti, and pineapples). Of course, creationists of all stripes accept speciation or diversification within created kinds (understanding that both “species” and “created kinds” are nebulous concepts).

Dr. Theobald acknowledges that species of alligators, giant salamanders, and magnolias occur half a world apart, but he still counts them as “close” species because it is hypothesized that Eastern North America and East Asia were once close together. There are many other seemingly anomalous geographical occurrences of the same or similar species that are explained with speculative hypotheses.[22]

The flexibility of biogeography is well illustrated by the fact it was used as support for evolution prior to the acceptance of plate tectonics and continental drift. As ReMine explains:

One reason for this erosion [in the assessment of the importance of biogeography as evidence for evolution] was the 1960s development of plate tectonics and continental drift. This development radically changed the picture, and forced evolutionists to rapidly restructure biogeographical ideas away from the fixed continents axiom of Darwin and Wallace. The biogeographers tried to reconcile their data with the new concepts of movable paleogeography. The plasticity of evolutionary biogeography was nakedly revealed by its ability to suddenly adapt to the dramatic shift in geologic understanding. (ReMine, 437.)
Though biogeography has from the earliest days of the theory been touted as strong evidence for evolution, Nelson and Platnick wrote in 1981: “We conclude, therefore, that biogeography (or geographical distribution of organisms) has not been shown to be evidence for or against evolution in any sense.” (Nelson and Platnick, 223.) Perhaps that explains why “Mark Ridley has an entire chapter on biogeography in his evolution textbook [see bibliography] but does not use biogeography as one of his evidences for evolution.” (Hunter, 184 n.64.)

The assertion in the second quoted paragraph that under nonmacroevolutionary theories species should exist wherever there is suitable habitat for them is groundless. It not only ignores the room nonmacroevolutionary theories can leave for microevolution and ignores the complexity of factors that can shape the distribution of species, it is apparently based on a theological presupposition. Hunter is again worth quoting on the subject:

And for Michael Ruse, God cannot be reconciled with the facts of biogeography, so we must turn to evolution. He argues, “Given an all-wise God, just why is it that different forms appear in similar climates, whereas the same forms appear in different climates? It is all pointless without evolution.” According to Edward Dodson and Peter Dodson, if God created the species, then they should be distributed uniformly around the globe. They write, “had all species been created in the places where they now exist, then amphibian and terrestrial mammals should be as frequent on oceanic islands as on comparable continental areas. Certainly, terrestrial mammals should have been created on these islands as frequently as bats were.” It is remarkable how often evolutionists feel free to dictate what God should and shouldn’t do. (Hunter, 113.)
Finally, the suggestion that universal common ancestry would be falsified by finding elephants or amphibians on remote islands is incorrect. Their presence would be explained in a way consistent with evolutionary convictions. Ideas of continental drift, land bridges, human involvement, storm rafts, unknown swimming ability, some form of hitchhiking, etc. would be invoked and judged more likely than the alternative. In fact, many amphibians exist on many islands, and their presence is not viewed as a threat to the evolutionary hypothesis.

Past biogeography, as recorded by the fossils that are found, must also conform to the standard phylogenetic tree. As on [sic] example, we conclude that fossils of the hypothetical common ancestors of South American marsupials and Australian marsupials should be found dating from before these two landmasses separated.

The alleged prediction and fulfillment are:

If universal common ancestry is true, then the geographic distribution of fossil species will conform to the standard phylogenetic tree.

The geographic distribution of fossils conforms to the standard phylogenetic tree.

As I have pointed out, it is not a prediction of the hypothesis of universal common ancestry that organisms, past or present, will conform to the standard phylogenetic tree. Rather, the standard phylogenetic tree is a depiction of current evolutionary thinking about the genealogical relationship of the taxa included. Phylogenies are provisional, evolutionary constructs of data, including biogeography. If facts develop that make some aspect of a phylogeny untenable, adjustments will be made within the evolutionary framework and a new orthodoxy will be established.

Judging by the example given, the geographic distribution of fossil species is deemed to conform to the standard phylogenetic tree if the date and location of alleged ancestors do not render impossible the claim of descent. Thus, if Australian marsupials originated on another continent, one would expect to find marsupials on that continent prior to the time Australia is believed to have become geographically isolated.

The presence of similar marsupials in South America, Antarctica, and Australia may be evidence for the claim that the continents were at one time contiguous, but it is not evidence for the hypothesis of universal common ancestry. It is not even evidence for the claim that all Australian marsupials arose from a common ancestor.

“There is no direct evidence to document when marsupials first entered Australia.” (Carroll, 431.) When they first appear in the fossil record of Australia in the late Oligocene, “the major groups had already differentiated,” and “the interrelationships of the various lineages have not been satisfactorily established.” (Carroll, 431, 440.) According to Carroll, marsupials may have entered Australia “at least 40 million years” before there is a record of their presence. (Carroll, 435.)

There is thus no way to tell what marsupials entered Australia or when they did so. If representatives of the major groups of Australian marsupials were included among the immigrants, Australia would at most bear witness to diversification at lower taxonomic levels.

Finding marsupial fossils in Antarctica establishes that there were once marsupials on that continent, but it says nothing about their having evolved from some nonmarsupial stock or even about their having given rise to distinct marsupial suborders. If South America, Antarctica, and Australia were once contiguous and if one hypothesized that marsupials radiated from South America into Australia (or vice versa), then one would predict that marsupials once existed in Antarctica. Finding that to be the case certainly is not “an astounding macroevolutionary confirmation.”

Determining the place of origin and direction of marsupial dispersal is not a simple matter of tracking the date of known fossils (i.e., they arose in North American and migrated to Australia). As Carroll’s statement about the entry of marsupials into Australia makes clear, the absence of fossils is not necessarily evidence of the absence of marsupials.[23] That is why “[t]he place of origin and direction of dispersal of marsupials in the southern continents is subject to continuing debate.” (Carroll, 431.)

The uncertainty surrounding this issue is apparent from the remarks of Clemens, Richardson, and Baverstock:

Against this background of ignorance and uncertainty, no definitive evaluation of the competing hypotheses concerning the time and place of the origin of the marsupials can be presented. Almost every continent on which marsupials have existed has been nominated as an area of origin of the group. . . .

Currently, hypotheses suggesting origin and early radiation of marsupials in the southern continents, particularly Australia, Antarctica and South America are favoured by many workers. (Clemens and others, 542.)

Under the heading “Potential Falsification,” Dr. Theobald writes, “We confidently predict that fossils of recently evolved animals like apes and elephants should never be found on South America, Antarctica, or Australia (excepting, of course, the apes that travel by boat).” But finding fossil apes or elephants on one or more of those continents would not falsify universal common ancestry.

Any such find would, of course, face an extreme standard of proof in terms of both identification and dating (the more recent the date the more readily the explanation of human involvement would be accepted). Assuming the problem could not be avoided by denying the identification or dating, a devotee of common ancestry could revise his theory of continental drift or historical geography, propose temporary land bridges, reconsider when apes or elephants arose, suggest parallel or convergent evolution, etc. However problematic any of these proposals may be, they would be considered more likely than the alternative, i.e., that universal common ancestry is false.

The fact geography does not rule out the possibility that the modern horse descended from Hyracotherium provides no support for the claim of universal common ancestry. Assuming that Equus descended from Hyracotherium, that is merely diversification within the family Equidae. The change from Hyracotherium to Equus is trivial compared to the changes required by the theory of universal common ancestry.

Again, the claim under the heading “Potential Falsification” that it would be “macroevolutionarily devastating” to find an equid in South America before about 12 million years ago underestimates the theory’s flexibility. It has great capacity for accommodating seemingly discordant data. Various hypotheses for fitting the data within an evolutionary framework would circulate, and the issue would be considered “a problem” until a consensus was reached regarding the solution. It would not, however, be judged a threat to (and certainly not a falsification of) the evolutionary paradigm.




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