Molecular Clock Hypothesis, Part IV

Molecular Clock Hypothesis, Part II

By Jon Covey, B.A., MT(ASCP)
Edited by Anita Millen, M.D., M.P.H., M.A.

(1 Cor 15:39) "All flesh is not the same flesh, but there is one flesh of men, and another flesh of beasts, and another flesh of birds, and another of fish."

Although the Apostle Paul is speaking of bodily resurrection, there are fundamental differences among the major created kinds (also know as the baramin) [Wise]. We can easily see the structural and morphological (shape) differences. We can taste and smell other differences. There are physiological and molecular differences among these creatures.

Perhaps God implied through Paul that He made each major kind different at the DNA level, so that organisms belonging to one kind have sharp, distinct boundaries with no intergrading connection with a different kind. Geneticist Michael Denton discussed both shapes and types as well as the biochemical relationships to type [Denton, pp. 274-307]. He concluded there is no continuum in either realm, although this didn’t make him comfortable. Denton explained to his readers that the morphological or external visible features among living organisms have a pattern reminiscent of the typological model of the nineteenth century dominated by creationist biologists, such as Louis Agassiz. Agassiz believed that each created kind conformed in all essential details with an idealized archtype or general pattern, e.g. fish type. Each group is isolated and well defined with no series of intergrading organisms among living or fossil species linking one to another. On p. 94 of his book he says:

"...all the members of any defined class are equidistant from the members of other classes as well as being equirepresentative of the archetype of their class....Typology implied that intermediates were impossible, that there were complete discontinuities between each type...When the members of one class are compared with the members of another, all are found to be equally isolated in terms of their fundamental characteristics."

Denton showed that the same was true on the genetic level. Each group was equidistant from all other groups. Organisms belonging to the same archtype share a similar genetic code, but when compared to a dissimilar group, they are just as isolated genetically from that group as any other group. Lamprey, pigeon, horse, wheat, silkmoth, tuna, and yeast are all equidistant from a bacterium Rhodospirillum rubrum. The percent differences among the amino acid sequences of these organisms’ cytochrome c are essentially equal. At first glance, one might think this is exactly what we would expect to see with a molecular clock–equidistance from a common ancestor. Biologist William Thwaites argued this point [Thwaites], but he gave no rational explanation why we should expect to see each of these organisms so equally unrelated, especially since most proteins do not exhibit clocklike properties or have clocks that run 5-10 times faster in one group than another. Some of these organisms exhibit exceptional morphological stasis, meaning that there has been little or no change since their first appearance in the fossil record until now, implying that there has also been genetic stasis. A good example of this would be any organism considered a "living fossil." Several studies, using DNA sequences for cytochrome b and other proteins, show that sharks have remained almost unchanged [Martin]. The slow change that was noticed is an artifact of evolutionary assumption because 13 species of shark were compared, and based on the differences in their DNA, the analysts assumed that these differences represent divergence from a common ancestor millions of years ago. Even the tuna, mackerel, and bass seem to have very slow molecular clocks, having about the same rate as the sharks when compared to primates and ungulates (hooved animals) [Cantatore].

Thwaites would prefer the use of cytochrome c to prove his point, but why should we choose cytochrome c as the true clock simply because it is one of the few proteins that seems to exhibit any clocklike tendency? Cytochrome c and hemoglobin seem clocklike, but when compared to each other, one is much faster than the other, depending on the organism being analyzed.

Evolutionary molecular biologists take a leap of faith when they attempt to show evolutionary links from one group to another (e.g., fish to amphibian) by assuming that relatively few DNA differences imply a common ancestor. Despite their arguments, there is no evidence that the DNA of each animal is the product of mutational processes from an ancestral genome. Mutation experiments on fruits flies (Drosophila melanogaster) are legion. They have gone on for many generations without ever producing anything other than fruit flies, albeit sometimes as monstrosities. If after all these years, something else, maybe a rhinoceros beetle or butterfly, arose from a population of irradiated flies, I’d say there is something to their claim.

Let’s look into the world of paleontology, the study of ancient life which can be seen only through the fossils they left behind, to see if the alleged marriage between molecular biology and the fossil record really exists. Are they really in agreement? We have already seen evidence that they are not. Let’s consider Denton’s musings. He considered the impossibility of determining the exact evolutionary distance between two organisms, such as a cat and a dog, or a cat and a mouse based solely on morphological differences. The cat and dog seem much more alike than the cat and the mouse, but can we be sure this is true? Unless we have some more objective way of guiding us, our prejudice may cloud our judgment.

There has been a certain amount of change within the created kinds, but the change never goes beyond what is contained within the gene pool of the common ancestor. The finch evolution Darwin perceived is accommodated within the creationist framework. Evolutionists go astray when they interpret change within morphologically and genetically similar organisms and apply it to their grand scheme from primitive first cell to man.

The advent of molecular biology supposedly brought with it a new, more exact means by which one could judge the genetic distance between these organisms and decide which were more closely related evolutionarily. The promise of delineating evolutionary ancestry by molecular inferences was built on the unproven premise that evolution is true. We have seen that there are many contradictions concerning the molecular clock hypothesis and neutral theory. These ideas are flawed. Some proteins behave as very erratic clocks, such as the superoxide dismutase (SOD) [Ayala]. Others have acceptable clocklike behavior such as cytochrome c or hemoglobin, but as Ayala asked, which mode is more common over broad evolutionary spans–the erratic or the clocklike? Denton noted that cytochrome c varied less between organisms than hemoglobin. He also observed that, generally, organisms that were closely related in terms of their cytochrome sequences were also closely related in the sequences of all other proteins. This is what one might expect if creation is true, but I am not so sure this would fit the evolutionary model. We creationists would expect there to be molecular similarity among closely related organisms because of the good engineering principle of building on fundamental designs.

The same is true of information systems such as computers. Certain subroutines are used over and over again. Certain commands in assembly and BASIC languages point to subroutines or program modules that perform certain functions that are repeated at different times in the program’s run. Rather than design and write a new routine to do the same thing, a programmer will simply design a common subroutine that can be called upon many times. DNA is another form of programmed instruction. Parts of DNA are going to be nearly the same for all organisms because it is coding for functional proteins such as enzymes that must have certain invariable regions in order to interact with target molecules in a relevant way. Some biochemical pathways are going to be similar in a wide range of organisms, e.g. the Krebs cycle or the glycolytic pathway, as S. Conway Morris at the University of Cambridge (Dept. of Earth Sciences) affirms [Morris, 1994]. Many biochemical pathways require 10 or more sequential enzyme-mediated reactions, and each enzyme in the pathway is much the same from organism to organism. Cytochrome c belongs to such a pathway.

Ayala assumes that there are broad evolutionary spans, but are there? Evolutionists commonly assume there have been long ages from the alleged first cell until now. They have chosen physical "clocks" that tend to give them the ages they believe must have passed, e.g., radiometry, rejecting the clocklike behavior of the constantly increasing concentration of salt in the sea which indicates a much shorter earth history, approximately 62 million years at the most [Austin, 1990].

The Cambrian Explosion and the Molecular Data

Evolutionists remain puzzled by what they call the "Cambrian Explosion" that is characterized by the abrupt appearance of a wide variety of multicellular organisms in the fossil record with no hint of ancestors in the earlier sedimentary rocks (Precambrian). What was the ancestral lineage (or lineages) that produced them? Precambrian stromatolites, composed mainly of laminated calcium carbonate structures that allegedly accumulated under the influence of blue-green algae, do not seem proper ancestors of the complex organisms found in Cambrian rocks alleged to be 570 million years old.

Did the Flood produce this seeming explosion by burying these fully developed organisms together in the way that they now appear in the fossil record? Qualified geologists who are creationists think it did. If it did, how did it fairly consistently bury characteristic groups of organisms together (index fossil assemblages belonging to specific geological periods, e.g. Jurassic) throughout the world? John Woodmorappe tried to reconcile what was seen in the fossil record with the events of flooding, volcanism and tectonism during the Flood [Woodmorappe]. In this astounding study, Woodmorappe plotted over 9500 global occurrences of major index fossils on 34 world maps and developed the concept of TABs (Tectonically Associated Biological Provinces). Some fine-tuning of his concept is needed, but this was an impressive study that went a long way toward explaining why we find the biostratigraphical order seen throughout the world in the fossil record as a result of the Flood. It will take geologists and paleontologists many years to work out the details.

Creationists believe that the "Cambrian Explosion" is an artifact and that the Flood created most of the fossil record. Stromatolites are identified as laminated mats produced by blue-green algae according to some geologists, although Austin explains that the only evidence of organic binding of the calcium carbonate laminations is the laminated structure [Austin, 1994]. He says that microscopic examination rarely reveals any trace of microscopic organisms, and that numerous laminated structures are known to form without biological activity. For example, some formations are found in caves where there was no light for algal growth. Magnesium nodules develop on the sea floor as laminated spheres, and certain processes in soil formation produce laminated structures. In other words, Precambrian stromatolites, considered a product of blue-green algae by evolutionists, have other explanations for their origin.

From an evolutionary point of view, the sudden appearance of the wide variety of complex organisms in the Cambrian strata seems like an evolutionary explosion. Creationists see this as clear evidence for the effects of the Flood.

André Adoutte explains that most of the major invertebrate phyla appear in the fossil record during a relatively short time interval (about 20 million years) of the "Cambrian Explosion," 540-520 Myr ago. His group wanted to know if they could trace this "explosion" by molecular phylogeny. Of course, we understand that tracing an explosion that did not happen would be extremely difficult, but with a little tweaking of the figures, almost anything can be made to seem true. However, they discovered that they could only poorly resolve the divergence among the major Cambrian lineages (mollusks, echinoderms, arthropods, chordates, etc.), although they had used complete 18S rRNA (ribosomal RNA) sequences of 69 existing representatives of 15 animal phyla obtained from genetic data banks such as GenBank. They assumed a molecular clock and used paleontological dates to calibrate it, only to discover that they could not "confidently resolve cladogenetic [diverging or branching] events separated by less than about 40 Myr. Thus at the present time, the potential resolution by the paleontological [fossil] approach is higher than by the molecular one [Philippe]." He still enthrones the stones and bones. That 40 Myr is closer to 40 days by Flood reckoning.

Conway Morris explains why molecular biology needs paleontology [Morris, 1993]. He says that the origins of the 30-40 metazoan phyla are an intractable problem. Despite 200 years of enormous research efforts, controversy remains, along with "a plethora of proposals and hypotheses." He makes a noteworthy remark concerning the fossil record:

"The morphological gaps that, by definition, separate phyla, remain inviolate. We remain uninformed both about the now extinct intermediates and the evolutionary processes that would have been responsible for the diversification of early multicellular animals into what we now perceive as distinct phyla, each with its own body plan."

This sounds like what we would expect if creation is true: gaps, separate groups, no intermediates, sudden appearance in the fossil record, and unexplainable, rapid diversification from an unknown common ancestor to great variety. Obviously, not much about evolutionary history is firmly established. Is the coelom (lined body cavity of organisms higher than flatworms) a primitive structure as favored by the German school? What can larval anatomy tell us about the ancestry and relationships among the phyla? Do the brachiopods (fairy shrimp, clam shrimp, water fleas) belong within the deuterostomes (sea stars, sea urchins, arrowworms, acorn worm)? Humorously, Morris says:

"For each and every proposal concerning metazoan relationships, there was almost invariably a counter-suggestion. The existing literature is like the Sargasso Sea of mythology, dotted with hulks of varying decrepitude, each manned by a crazed crew or more likely, ghosts. This morass persisted because whatever phylogenetic scheme was proposed had to rely on a handful of features being chosen as axiomatically suitable for identification...For various reasons, features such as segmentation and type of body cavity came to occupy effectively inviolate positions in terms of phylogenetic reliability, although in their more candid moments most zoologists will admit that there is little a priori evidence that metameric segmentation, for example, could not have evolved independently several times. The net result is that any scheme of metazoan phylogeny will inevitably involve characters that to one set of workers are crystal-clear guides to relationships, but to another group are examples of rampant convergence."

The study of fossils and living organisms didn’t resolve the problems and I suppose that the additional information from molecular biology will not help. For as Morris observes, the molecular methods are not foolproof. Indeed, the molecular data mimics the typology discussed earlier. Morris agrees, saying that further problems arise where the morphological distinctiveness of a group is echoed in its molecular sequence and so it remains phylogenetically isolated. We saw from the dental HIV study that the statistical methods are probably more hype than help. Morris notes other problems with the methods, questioning the suitability of the molecules chosen for establishing phylogenetic relationships and the appropriateness of the statistical methods used for the tree-building creation of the phylogenetic diagrams and their interpretation. Depending on which part of a DNA, RNA or protein sequence we are looking at, different parts evolve at different rates. Evolve? When one assumes evolution is true, the differences in sequences in yeast and fish are seen as the product of random mutations from a common ancestor, and based on this assumption statistical methods are constructed. In other words, the math is tailor-made to fit the assumption. With a few snips and tucks, the calculations can be made to look very tidy. In this same vein, Hickman flatly states that molecular evidences for descent from a common ancestor do not agree well with fossil evidence [Hickman].

Polyploidy and Tetraploidy: an Unreasonable Explanation for the Origin of New Genes

Peter Holland and others [Holland; Monastersky] claim that gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. This is not a new idea, and it is not plausible. We’ve already seen cogent information about pseudogenes and here they are again. Only now, instead of being a runaway train of mutational headaches, pseudogenes become the source of novel genes with entirely new functions. The magic here is for an organism to make an additional gene or genes by accident. This genetic material is taken "off-line," no longer under control of the cell, and begins mutating in new and wonderful ways. Monastersky quotes Nicholas Holland:

"Evolution of the vertebrate body plan is one of the great questions." This means no one has a clue how the transition from the supposed ancestors of amphioxus (a marine lancet 5-8 cm long) to vertebrates happened genetically. Of course, this is one of those unobservable events in the past that must have happened if evolution is true. Peter Holland suggests two major gene duplication events: one for the stage from amphioxus’ ancestor to vertebrates and another for the stage from jawless vertebrates to jawed vertebrates.

A Final Word

I decided to do this short series on molecular biology because of the claims of a paleoanthropologist at Harvard University who feels that the molecular clock hypothesis and the neutral theory provide good evidence for evolution. We had a disagreement about the falsifiability of the theory of evolution. He claimed evolution is falsifiable, and one way falsification could be done is by repudiating the molecular clock hypothesis. I was dubious about this and told him that even if I thoroughly refuted the hypothesis, it would not affect one's faith in evolution. I was certain that I would find difficulties concerning the hypothesis, but I was not prepared for the breadth and depth of ill-founded support and contradictory evidence.

One difficulty with getting evolutionists "to see the light", regardless of their theological position, is their deep commitment to the theory on the basis of faith. Scientific observation is not a requirement for them to accept evolution as scientific. In their minds, circumstantial evidence and inference is perfectly acceptable for establishing evolution as fact. They might recognize that this means evolution may not be completely empirical science, but enough circumstantial evidence is there to remove any "reasonable doubt." The fossil record can have gaps as far as they are concerned, for they would argue that is to be expected. They see the fossil record as a series of periodic snapshots taken during the long history of evolution.

Bibliography

Austin, Steven A., and D. Russell Humphreys, 1990, "The Sea’s Missing Salt: A Dilemma for Evolutionists," Proceedings of the Second International Conference on Creationism 1990, Vol. II, Creation Science Fellowship, Pittsburgh.

Austin, S., Grand Canyon: Monument to Catastrophe, Steve Austin, editor, Institute for Creation Research, Santee, CA 92071, pp. 134-135, 1994. This is an excellent book on Flood geology written by several creationary biologists and geologists. It can be ordered by calling 1-800-999-3777, Master and Visa cards accepted.

Ayala, Francisco J., 1986, "On the virtues and pitfalls of the molecular evolutionary clock," The Journal of Heredity 77:226-235.

Cantatore, P. et al, 1994 "Evolutionary Analysis of Cytochrome b Sequences in Some Perciformes: Evidence for a Slower Rate of Evolution Than in Mammals," J Mol. Evol., 39:589-597.

Denton, Michael, 1985, Evolution: A Theory in Crisis, pp. 274-307.

Hickman, Cleveland P., Jr., Larry S. Roberts, and Frances M. Hickman, 1988, Integrated Principles of Zoology, 8th ed., Times Mirror/Mosby College Publishing, St. Louis, p. 124.

Holland, Peter W.H., Jordi Garcia-Fernàndez, Nic A. Williams, and Arend Sidow, 1994, "Gene Duplications and the Origins of Vertebrate Development," Development, Supplement, pp. 125-133.

Martin, Andrew P., Gavin J.P. Naylor, and Stephen R. Palumbi, "Rates of Mitochondrial DNA Evolution in Sharks are Slow Compared With Mammals, 1992, Nature 352:153-155.

Monastersky, Richard, 1996, "Jump-Start for the Vertebrates: New clues to how our ancestors got a head," Science News, vol. 149, pp. 74-75.

Morris, S. Conway, 1993, "The Fossil Record and the Early Evolution of the Metazoa," Nature 361:219.

Morris, S. Conway, 1994, "Why Molecular Biology Needs Palaeontology," Development 1994 Supplement, p. 9.

Philippe, Hervé, Anne Chenuil and André Adoutte, 1994, "Can the Cambrian Explosion be Inferred through Molecular Phylogeny?" Development Supplement, pp. 15-25.

Thwaites, William, 1990, "Molecular Clocks and Creationism," NCSE Reports, vol. 10(5), p. 14.

Wise, Kurt, 1992, "Practical Baraminology," Creation ex nihilo Technical Journal, 6(2):122-137.