Genetic Phylogeny
Sean D. Pitman M.D.
© April 2002

Biologists are not entirely satisfied with the intrinsic subjectivity of classification and have hoped that molecular biology would yield a more quantitative approach. It was hoped that comparisons of the nucleotides of DNA or RNA sequences would yield quantitative numbers that could be used to classify organisms with a high degree of accuracy. However, according to an article in the January 1998 issue of Science:

"Animal relationships derived from these 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. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally   thought. "(1)

The article then discusses a figure that shows that mollusks (scallop) are more closely related to deuterostomes (sea urchin) than arthropods (brine shrimp). This is not too surprising. Intuitively, a scallop seems more like a sea urchin than a shrimp. So, the 82% correlation between the scallop and sea urchin is not surprising. But, what is surprising is that a tarantula has a 92% correlation with the scallop. It does not seem reasonable that a scallop should be more closely related to a hairy, land-dwelling spider than to a sea urchin. This troubling thought led the authors of the Science article to remark:

"The critical question is whether current models of 18S rRNA evolution are sufficiently accurate … current models of DNA substitution usually fit the data poorly." (Ibid)

There are many other interesting little problems concerning commonly used phylogenic tracing genes and proteins. For example, mammalian and amphibian luteinizing hormone — releasing hormone (LHRH) is identical. Birds, reptiles, and certain fish have a different type of LHRH. Are humans therefore more closely related to frogs than to birds? Not according to standard evolutionary phylogeny trees. The theory does not match the data. Cytochrome c is another famous phylogenic marker protein used to determine evolutionary relationships. There is only a single amino acid difference between human and chimp cytochrome c. Because of this, many assume that the evolutionary link is obvious. However, with many other animals, this link is not so obvious. For example, the cytochrome c protein of a turtle is closer to a bird than it is to a snake and a snake is closer to a human (14 variations) than it is to a turtle (22 variations).(5) 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.(5)

The cytochrome c data presents 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.(5,6) According to Michael Denton, a molecular biology researcher, "At present, there is no consensus as to how this curious phenomenon can be explained."(7)

Such discrepancies between traditional phylogenies and those based on cytochrome c are well known. Even Ayala could only bring himself to say that:

"The overall relations agree fairly well with those inferred from the fossil record and other sources. "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." (8)

Calcitonin (lowers blood calcium levels in animals) is yet another famous protein used to determine phylogenies. Humans differ from pigs by 18 of 32 amino acids, but by only 15 of 32 amino acids from the salmon. Are we therefore more closely related to fish than to other mammals like the pig?

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 structure or resolution tends to evaporate."(2)

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." (3)

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." (9)

"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."(4) In other words 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. The molecular differences could be linked to the morphological differences for some other reason. For example, all of the living organisms on this planet live in a relatively similar environment. All use the same water, breathe the same air, and eat the same basic foods for building blocks and energy. Is it not reasonable to assume that a similar environment requires at least some similarities in the creatures that utilize it for survival?

Consider a world were plants utilized a different type of amino acid for protein metabolism than animals. This would mean that animals could not eat plants because the amino acids for one metabolic system would not necessarily work in the other system. The animals in such a world would be left with nothing to eat except for each other. The fact that creatures have many of the same or similar genes and proteins means that they are integrated with their environment. If they were not, they could not survive. Similar proteins and metabolic pathways are needed to utilize similar sources of food and energy. The various parts of organic life on this planet are interchangeable, not because of some random happenstance, but because of necessity… like Lego blocks. Building blocks not made by the Lego company will not "work" with Lego blocks.

Nothing lives to itself. All living things are dependent upon other living things. If they were not molecularly and thus genetically compatible, nothing would survive very long. The "cycle of life" is dependent upon this fact. There would be no cycle if the basic building blocks of the creatures involved were not interchangeable with each other. Considering this need, it seems reasonable to assume that those creatures that share the most similar environments, body plans, and physiology would also have the most similar needs and thus the most similar genetic and molecular machineries. 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… 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. If we do not base our conclusions on the a priori assumption 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.(5)