Lack of Identifiable Phylogeny in the Fossil Record

“Darwin arguably was wrong. For most of Life and most of its history, descent with modification is not the simple branching process he envisioned.” (Doolittle, W. Ford, “The Attempt on the Tree of Life: Science, Philosophy and Politics,” Biology and Philosophy 25, 2010, p. 469.)

After reviewing the increased difficulties  in constructing a darwinian Tree of Life and the evidence contradicting a single common ancestor, the molecular biologist Carl Woese declared, “The time has come for biology to go beyond the Doctrine of Common Descent.” (Woese, Carl, “On the Evolution of Cells,” Proceedings of the National Academy of Sciences, 2002, p. 8745.)

“To recall what I said in chapter 1, no fossil is buried with its birth certificate. That, and the scarcity of fossils, means that it is effectively impossible to link fossils into chains of cause and effect in any valid way, whether we are talking about the extinction of the dinosaurs, or chains of ancestry and descent. Everything we think we know about the causal relations of events in Deep Time has been invented by us after the fact. …To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story — amusing, perhaps even instructive, but not scientific.” (Gee, Henry, In Search of Deep Time, 1999, pp. 113,116-117.)

[Concerning the phylogeny leading from fish to amphibians] “Evolutionary relationships of early tetrapod groups remain controversial.” (Hickman, et. al., Integrated Principles of Zoology, 2014, p. 538.)

[Concerning the absence of a fossil ancestor for turtles] “To derive a transformed, newly adapted structure from an ancestral one requires the ancestral structure to be primitive, or generalized, in all aspects relative to the derived structure. Such a totally generalized ancestral structure would, however, not be adapted to any specific mode of life. But every living organism must somehow be adapted to some sort of mode of life. This renders such a generalized, zero-value ancestor that is not adapted to any specific mode of life a biological impossibility.” (Meylan, Peter A., Turtles as Hopeful Monsters, 2017, p. 122.)

“Incongruence among phylogenies estimated from different sets of characters is pervasive. Phylogenetic conflict has become a more acute problem with the advent of genome-scale data sets. These large data sets have confirmed that phylogenetic conflict is common, and frequently the norm rather than the exception (Dávalos, Liliana M., et. al., “Understanding Phylogenetic Incongruence: Lessons from Phyllostomid Bats,” Biological Reviews of the Cambridge Philosophical Society 87, 2012, pp. 991-1024.)

“Of the various transitions that occurred during human evolution, the transition from Australopithecus to Homo was undoubtedly one of the most critical in its magnitude and consequences….the bad news is that many details of this transition are obscure because of the paucity of the fossil and archaeological records.” Lieberman, D.E., Pilbaem, D.R., and Wrangham, R.W., “The Transition from Australopithecus to Homo,” Transitions in Prehistory: Essays in Honor of Ofer Bar-Yosef, p. 1. (John J. Shea and Daniel E. Lieberman eds., Oxbow Books, 2009.)

“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, Carl, “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, 95:6854-9859, June, 1998.)

“The tree-of-life concept was absolutely central to Darwin’s thinking, equal in importance to natural selection, according to biologist W. Ford Doolittle of Dalhousie University in Halifax, Nova Scotia, Canada. Without it the theory of evolution would never have happened… ‘For a long time the holy grail was to build a tree of life,’ says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded.” (Lawton, Graham, “Why Darwin was Wrong about the Tree of Life,” New Scientist, Issue 2692, January 21, 2009. )

“[D]isparities between molecular and morphological trees [lead to] evolution wars [because e]volutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.” (Gura, Trisha, “Bones, Molecules or Both?,” Nature 406, July 20, 2000, 230-233.)

“[T]he mitochondrial cytochrome b gene implied . . . an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.” (Lee, Michael S. Y., “Molecular Phylogenies Become Functional,” Trends in Ecology and Evolution 14, 1999, p. 177.)

“When we view Darwinian gradualism on a geological timescale, we may expect to find in the fossil record a long series of intermediate forms connecting phenotypes of ancestral and descendant populations. This predicted pattern is called phyletic gradualism. Darwin recognized that phyletic gradualism is not often revealed by the fossil record. Studies conducted since Darwin’s time likewise have failed to produce the continuous series of fossils predicted by phyletic gradualism. Is the theory of gradualism therefore refuted? Darwin and others claim that it is not, because the fossil record is too imperfect to preserve transitional series…Others have argued, however, that the abrupt origins and extinctions of species in the fossil record force us to conclude that phyletic gradualism is rare. …A number of contemporary biologists, however, favor various hypotheses of the punctuated equilibrium theory…They base their hypotheses on fossil records which have large “chains” of missing organisms. Although missing-link fossils are occasionally discovered, the record does little to support Darwin’s concept of gradual, long-term change…Others opposed to hypotheses of evolution through sudden change argue that because such a tiny percentage of organisms becomes fossilized…drawing definite conclusions from fossil evidence about evolution through either gradual or sudden change is not warranted.” (Hickman, C.P., Roberts, L.S., and Larson, A. 2000. Animal Diversity. McGraw Hill, NY. pp. 23, 261.)

“The question of the structure and biology of the ancestral angiosperms, and especially their flowers, is an enduring riddle.” (Endress, P.K., Doyle, J.A., “Reconstructing the Ancestral Angiosperm Flower and Its Initial Specializations, American Journal of Botany, 2009 (1), pp. 22-66.)

“One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes.” (Rokas A., et. al., “Genome-scale Approaches to Resolving Incongruence in Molecular Phylogenies,” Nature, Oct 23, 2003, p. 798.)

Michael Syvanen, a biologist at the University of California at Davis studied thousands of genes from various animals hoping to find a tree like pattern. He failed and summarized the results bluntly: “We’ve just annihilated the tree of life. It’s not a tree anymore, it’s a different topology [pattern of history] entirely. What would Darwin have made of that?” (Syvanen, as quoted in Lawton, Graham, “Why Darwin was Wrong About the Tree of Life,” New Scientist, January 21, 2009).

“A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome.” ( Degnan, James H., Rosenberg, Noah A., “Gene Tree Discordance, Phylogenetic Inference and the Multispecies Coalescent,” Trends in Ecology and Evolution 24, 2009, pp. 332-340.)

“From 1860 onward the more distant fossil record became a big issue, and over the next two decades discoveries were made that at first seemed to give support to the theory particularly the claimed discovery of a well-ordered sequence of fossil horse’ dating back about 45 million years. Successes like this continue to be emphasized both to students and the public, but usually without the greater failures being mentioned. Horses according to the theory should be connected to other orders of mammals, which common mammalian stock should be connected to reptiles, and so on backward through the record. Horses should thus be connected to monkeys and apes, to whales and dolphins, rabbits, bears. …But such connections have not been found. Each mammalian order can be traced backward for about 60 million years and then, with only one exception the orders vanish without connections to anything at all. The exception is an order of small insect-eating mammal that has been traced backward more than 65 million years…” (Hoyle, Fred, Mathematics of Evolution, [1987], 1999, p.107.)

“Fossil discoveries can muddle over attempts to construct simple evolutionary trees–fossils from key periods are often not intermediates, but rather hode podges of defining features of many different groups… Generally, it seems that major groups are not assembled in a simple linear or progressive manner–new features are often “cut and pasted” on different groups at different times.” (Shubin, Neil, “Evolutionary Cut and Paste,” Nature, vol. 349, 1998, p. 39.)

“Our lives would be greatly simplified if we could just draw lines on a time chart to join up earlier fossils with later ones in a progressive sequence. Unfortunately, we can’t. …Descendants there are, and ancestors there must have been. The problem is, how do we recognize them?” (Eldredge, N., and Tattersall, I., The Myths of Human Evolution, 1982, p. 127.)

“It is a mistake to believe that even one fossil species or fossil ‘group’ can be demonstrated to have been ancestral to another. The ancestor-descendant relationship may only be assumed to have existed in the absence of evidence indicating otherwise . . . The history of comparative biology teaches us that the search for ancestors is doomed to ultimate failure, thus, with respect to its principal objective, this search is an exercise in futility. Increased knowledge of suggested ‘ancestors’ usually shows them to be too specialized to have been direct ancestors of anything else . . . In contrast to what is usually stated, therefore, a more complete sample of the fossil record in itself would only complicate the problem of assessing the interrelationship of the fossil species.” (Nelson, Gareth V., “Origin and Diversification of Teleostean Fishes,” Annals of the New York Academy of Sciences, 1971, pp. 22-23.)

“Fossil discoveries can muddle over attempts to construct simple evolutionary trees–fossils from key periods are often not intermediates, but rather hode podges of defining features of many different groups… Generally, it seems that major groups are not assembled in a simple linear or progressive manner–new features are often “cut and pasted” on different groups at different times.” (Shubin, Neil, “Evolutionary Cut and Paste,” Nature, vol. 349, 1998, p. 39.)

“The fossil record of evolutionary change within single evolutionary lineages is very poor. If evolution is true, species originate through changes of ancestral species: one might expect to be able to see this in the fossil record. In fact it can rarely be seen. In 1859 Darwin could not cite a single example.” (Ridley, Mark, The Problems of Evolution, 1985, p. 11.)

“[T]here are no fossils leading to primitive chordates or linking them with the vertebrates to which they must have given rise. The latter showed up possessing such advances as a brain case, specialized sense organs, and calcified bones.” (Wesson, Robert, Beyond Natural Selection, 1993, p. 41.)

“If we were to expect to find ancestors to or intermediates between higher taxa, it would be the rocks of the late Precambrian to Ordivician times, when the bulk of the world’s higher animal taxa evolved. Yet traditional alliances are unknown or unconfirmed for any of the phyla or classes appearing then.” (Valentine & Erwin, Development As An Evolutionary Process, 1987, p.84.)

“Well, we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is still surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than we had in Darwin’s time. By this I mean that some of the classic cases of Darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information…” (Raup, David M., “Conflicts Between Darwin and Paleontology,” Field Museum of Natural History Bulletin, vol. 50, 1979, p. 25.)

“The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nods of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record.” (Gould, Stephen J. The Panda’s Thumb, 1980, p. 181.)

“The main problem with such phyletic gradualism is that the fossil record provides so little evidence for it. Very rarely can we trace the gradual transformation of one entire species into another through a finely graded sequence of intermediary forms.” (Gould, S.J. Luria, S.E. & Singer, S., A View of Life, 1981, p. 641.)

“The Eldredge-Gould concept of punctuated equilibria has gained wide acceptance among paleontologists. it attempts to account for the following paradox: Within continuously sampled lineages, one rarely finds the gradual morphological trends predicted by Darwinian evolution; rather, change occurs with the sudden appearance of new, well-differentiated species. Eldredge and Gould equate such appearances with speciation, although the details of these events are not preserved. …The punctuated equilibrium model has been widely accepted, not because it has a compelling theoretical basis but because it appears to resolve a dilemma. Apart from the obvious sampling problems inherent to the observations that stimulated the model, and apart from its intrinsic circularity (one could argue that speciation can occur only when phyletic change is rapid, not vice versa), the model is more ad hoc explanation than theory, and it rests on shaky ground.” (Ricklefs, Robert E., “Paleontologists Confronting Macroevolution,” Science, vol. 199, 1978, p.59.)

“…if this diversification has taken place through the multiplication of species through speciation, then the fossil history of life is something that cannot be directly discovered. …Our lives would be greatly simplified if we could just draw lines on a time chart to join up earlier fossils with later ones in a progressive sequence. Unfortunately, we can’t.” (Eldredge, N. and Tattersall J., The Myths of Human Evolution, 1982, p. 127.)

“Many ‘trends’ singled out by evolutionary biologists are ex post facto rendering of phylogenetic history: biologists may simply pick out species at different points in geological time that seem to fit on some line of directional modification through time. Many trends, in other words, may exist more in the minds of the analysts than in phylogenetic history. This is particularly so in situations, especially common prior to about 1970, in which analysis of the phylogenetic relationships among species was incompletely or poorly done.” (Eldredge, Niles, Macro-Evolutionary Dynamics: Species, Niches, and Adaptive Peaks, 1989, p. 134.)

“Few paleontologists have, I think ever supposed that fossils, by themselves, provide grounds for the conclusion that evolution has occurred. An examination of the work of those paleontologists who have been particularly concerned with the relationship between paleontology and evolutionary theory, for example that of G. G. Simpson and S. J. Gould, reveals a mindfulness of the fact that the record of evolution, like any other historical record, must be construed within a complex of particular and general preconceptions not the least of which is the hypothesis that evolution has occurred. …The fossil record doesn’t even provide any evidence in support of Darwinian theory except in the weak sense that the fossil record is compatible with it, just as it is compatible with other evolutionary theories, and revolutionary theories and special creationist theories and even ahistorical theories.” (Kitts, David B., “Search for the Holy Transformation,” review of Evolution of Living Organisms, by Pierre-P. Grassé, Paleobiology, vol. 5, 1979, pp. 353-354.)

“I agree …that ancestral-descendant relationships cannot be objectively recognized in the fossil record.” (Schoch, R.M., “Evolution Debate,” Science, April 22, 1983, p. 360.)

“One of the most pervasive myths in all of paleontology…is the myth that the evolutionary histories of living beings are essentially a matter of discovery. Uncertainties in our interpretations of the fossil record are ascribed to the incompleteness of that record. Find enough fossils, it is believed, and the course of evolution will somehow be revealed. But if this were really so, one could confidently expect that as more hominid fossils were found the story of human evolution would become clearer. Whereas if anything, the opposite has occurred.” (Eldredge, N. and Tattersall, I., The Myths of Human Evolution, 1982, p. 127.)

“One thing which has struck me very forcibly through they years is that most of the classic evolutionary lineages of my student days, such as Ostrea-Gryphaea and Zaphrentis delanouei, have long since lost their scientific respectability, and in spite of the plethora of palaeontological information we now have available, there seems to be very little to put in their place. In twenty years’ work on the Mesozoic Brachiopoda, I have found plenty of relationships, but few if any evolving lineages.” (Ager, D., The Nature of the Stratigraphical Record, 1981, p. 20.)

“The origin of no innovation of large evolutionary significance is known.” (Wesson, R., Beyond Natural Selection, 1991, p. 45.)

“Some of the classic cases of darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information – what appeared to be a nice simple progression when relatively few data were available now appears to be much more complex and much less gradualistic.” (Raup as cited in Godfrey L. R., “Scientific Creationism: The Art of Distortion – Where is the Science in Scientific Creationism,” 1984, p. 177.)

“Many fossils have been collected since 1859, tons of them, yet the impact they have had on our understanding of the relationships between living organisms is barely perceptible. …In fact, I do not think it unfair to say that fossils, or at least the traditional interpretation of fossils, have clouded rather than clarified our attempts to reconstruct phylogeny.” (Fortey, P. L., “Neontological Analysis Versus Palaeontological Stores,” 1982, p. 120-121.)

“With the benefit of hindsight, it is amazing that palaeontlogists could have accepted gradual evolution as a universal pattern on the basis of a handful of supposedly well-documented lineages (e.g.GryphaeaMicrasterZaphrentis) none of which actually withstands close scrutiny.” (Paul, C.R.C., “Patterns of Evolution and Extinction in Invertebrates,” 1989, p. 105.)

“But it is the pattern that interests us most here. And if the fossil record tells us anything about evolutionary pattern, it is that some episodes of diversification can happen so rapidly that no detailed, stratified record showing the gradual development from primitive to advanced is ever formed.” (Eldredge, Niles, The Monkey Business: A Scientist Looks at Creationism, 1982, p. 47.)

“Non-paleontologists readers…should be aware of several common occurrences within the professional paleontologic literature which could conceivable be confusing. …For instructional purposes, some authors illustrate a series of fossils which show a progression in morphology, but which are not chronologically successive. These therefore are not evolutionary sequences, even though they resemble such.” (Cuffey, R. J., “Paleontologic Evidence and Organic Evolution,” 1984, p. 264.)

“There is no central direction, no preferred exit to the maze – just a series of indirect pathways to every twig that ever graced the periphery of the bush.” (Gould, Stephen J., “Life’s Little Joke,”Natural History, 1987, p. 21.)

“The proper metaphor of a bush also helps us to understand why the search for a ‘missing link’ between advanced ape and incipient human – that musty but persistent hope of chimera of popular writing – is so meaningless. A continuous chain may lack a crucial connection, but a branching bush bears no single link at a crucial threshold between no and yes. …No branch point can have special status as the missing link – and all represent lateral relationships of diversification, not vertical sequences of transformation. (Gould, Stephen J., “Empire of the Apes,” Natural History, 1987, p. 20.)

“No matter how high we tune the power of our microscope, we cannot escape an evolutionary topology of branching and bushiness. …The metaphor of the bush (and the falsity of the ladder) permeates evolution at all genealogical scales, from the history of a species to the unfolding of life’s entire tree. Bushiness is a pattern of self-similarity that emerges whenever we magnify successively smaller segments of life’s tree. …life’s tree is a fractal, and tiny parts, when magnified, look much like the whole.” (Gould, Stephen J., “Bushes All the Way Down,” Natural History, 1987, p. 19.)

“Even when all evidence is used, there are often several alternate phylogenies that are equally plausible. This is especially true for taxa in higher categories, such as phyla or classes.” (Ayala F.J., and Valentine, J.W., Evolving: The Theory and Processes of Organic Evolution, 1978, p. 244-245.)

“Large evolutionary innovations are not well understood. None has ever been observed, and we have no idea whether any may be in progress. There is no good fossil record of any.” (Wesson, R., Beyond Natural Selection, 1991, p. 206.)

“Undeniably, the fossil record has provided disappointingly few gradual series. The origins of many groups are still not documented at all.” (Futuyma, D., Science on Trial: The Case for Evolution, 1983, p. 190-191.)

“Most groups of organisms are best visualized as highly complex phylogenetic bushes …In large parts of the natural system it is impossible to demonstrate that one particular taxonomic sequence is superior to other alternatives.” (Mayr, E. The Growth of Biological Thought: Diversity, Evolution and Inheritance, 1982, p. 242.)

“Species, or taxa generally, which can be placed in a higher taxon, but whose relationships are otherwise obscure, are commonplace.” (Nelson G., and Platnick, N., Systematics and Biogeography: Cladistics and Vicariance, 1981, p. 263.)

“Indeed, it is the chief frustration of the fossil record that we do not have empirical evidence for sustained trends in the evolution of most complex morphological adaptations.” (Gould, Stephen J. and Eldredge, Niles, “Species Selection: Its Range and Power,” 1988, p. 19.)

“It should come as no surprise that it would be extremely difficult to find a specific fossil species that is both intermediate in morphology between two other taxa and is also in the appropriate stratigraphic position.” (Cracraft, J., Systematics, Comparative Biology, and the Case Against Creationism, 1983, p. 180.)

“We must learn to accept the fossil record at face value and construct our theories around it, not the other way round. Too often we have endeavored to force it into a particular mold or to ignore awkward facts contained in it. …We still have a long way to go before we look at the fossil record for what it is and not for what we would like it to be. Historically, from Lyell and Darwin onwards, people have looked at the fossil record with a particular pattern in mind. They have failed to find the pattern they sought and have appealed to the incompleteness of the fossil record to explain way this anomaly. We are still doing this…” (Paul, C.R.C., “The Adequacy of the Fossil Record,” 1982, p. 115-116.)

“Species that were once thought to have turned into others have been found to overlap in time with these alleged descendants. In fact, the fossil record does not convincingly document a single transition from one species to another.” (Stanley, S.M., The New Evolutionary Timetable: Fossils, Genes, and the Origin of Species, 1981, p. 95.)

“A large number of well-trained scientists outside of evolutionary biology and paleontology have unfortunately gotten the idea that the fossil record is far more Darwinian than it is. This probably comes from the oversimplification inevitable in secondary sources: low-level textbooks, semipopular articles, and so on. Also, there is probably some wishful thinking involved. In the years after Darwin, his advocates hoped to find predictable progressions. In general, these have not been found – yet the optimism has died hard, and some pure fantasy has crept into textbooks.” (Raup, D. M., “Evolution and the Fossil Record,” Science, 1981, p. 289.)

“A persistent problem in evolutionary biology has been the absence of intermediate forms in the fossil record. Long term gradual transformations of single lineages are rare and generally involve simple size increase or trivial phenotypic effects. Typically, the record consists of successive ancestor-descendant lineages, morphologically invariant through time and unconnected by intermediates.” (Williamson, P.G., “Palaeontological Documentation of Speciation in Cenozoic Molluscs from Turkana Basin,” Nature 293, 1982, p. 440.)

“At the higher level of evolutionary transition between basic morpological designs, gradualism has always been in trouble, though it remains the ‘official’ position of most Western evolutionists. Smooth intermediates between Baupläne are almost impossible to construct, even in thought experiments; there is certainly no evidence for them in the fossil record (curious mosaics like Archaeopteryx do not count).” (Gould, S.J. and Eldredge, N., “Punctuated Equilibria: the Tempo and Mode of Evolution Reconsidered.” Paleobiology 3, 1977, p. 147.)

“The known fossil record fails to document a single example of phyletic evolution accomplishing a major morphologic transition.” (Stanley, Steven M., Macroevolution: Pattern and Process, 1979 p. 39.)

“The exact sister group relationship of arthropods is, however, still debated.” (Giribet and Edgecombe, “Reevaluating the Arthropod Tree of Life,” Annual Review of Entomology 57, 2012, p. 662.)

“The evolutionary relationships among the echinoderms are not clear. Numerous fossils date into the Cambrian period, but no interpretation of the evolutionary relationships among living and extinct echinoderms is definitive.” (Miller and Harley, Zoology, 2010, p. 156.)