Is There a Scientific Conflict Between the Theory of Darwinian Evolution and the Fossil Record?


Charles Darwin proposed his theory of evolution in his 1859 book On the Origins of Species, in which he claimed that biodiversity is due to natural selection favoring individuals that are better suited for the environment. Individuals with genes for superior traits leave more offspring that also have the genes for superior traits. Over time, those individuals out-compete inferior individuals and the entire population now carries the superior traits. This may result in an improved or new species.

Darwin also proposed that all organisms derive from a common ancestor that lived in the distant past. Thus, Darwin’s theory proposes a common origin (ancestor) for all organisms, variations in populations that produce differences in fitness, and natural selection of those traits in the struggle for survival. These processes entail gradual, slow change over a long period of time with multiple intermediate stages in morphology and complexity of the organisms as they evolved.

For his theory, Darwin collected data from both the living organisms and fossils. Early in his career he went around the world on a scientific survey cruise that lasted almost five years.[1] Of special importance were his notes and specimens taken in South America and in the Galapagos Islands. Back in England, he also queried farmers about the way they obtained new breeds of animals, and studied how breeds of fancy pigeons were developed by looking for slight variations and accentuating them through selective mating. This he called artificial selection, which was widely applied in England and other countries to obtain desirable traits in animals and plants. After reading Essay on the Principle of Population, by the economist Thomas Malthus,[2] Darwin began to see similarity between the way breeders obtained new variations and his observations of variants in the Galapagos Islands and other places. Malthus argued that human population growth outruns the food supply, triggering a struggle for resources. This exposed the poorer, lower social classes to hardship, famine and disease to a greater degree than affluent people. Observing the process of artificial selection by farmers, Darwin began to think that variations could spontaneously occur in nature and that the struggle for survival was a constant feature in the natural world, as depicted in human populations by Malthus. Individuals with advantageous traits would be favored over those weak or less fit in the competition for resources. The ensuing competition would weed out the unfit. Thus natural selection would play the role of the breeder, gradually selecting the better fit individuals and eventually eliminating the weak or less fit ones, all of this happening slowly, gradually, over a very long time. Natural selection would lead to the rise of new species and the extinction of others. All organisms, from the humble earthworms to the majestic African lions, from the fishes in Galapagos to the British noblemen, came from a common ancestor in the distant past that evolved through variations and natural selection in a world rife with struggle.

Darwin and the Fossil Record

Darwin saw evolution as a slow and steady process with species gradually transforming into new species over long time. He thought that the fossil record should provide evidence for his theory of evolution.[3] In South America he had collected bones of extinct animals, and had seen layers of shells up in the Chilean mountains that seemed to support Charles Lyell’s claim that the Earth was slowly, gradually changing. The story of life recorded in the rocks would be the confirmation of his theory.

The fossil record, though, proved not to be the strong evidence for his theory. Darwin recognized the problem, and was well aware that his opponents would use this evidence against his theory. Although he could account for the minor changes observed in the Galapagos finches, Darwin knew that his theory would be challenged to explain the origin of the major phyla with the disparity of characters observed both in the fossil record and present time, from mollusks to mammals, and from moss to maple trees. For his theory to be well supported, he had to show that fossils told a story of gradual change over millions of years and that the record included forms with transitional morphologies and showed the gradual appearance of species, families and various groups of organisms. However, the needed evidence proved to be elusive, and Darwin knew that strife was inevitable because his theory was in conflict with some important features of earth’s natural history.


Gogia is an echinoderm from Cambrian layers. Echinoderms appear abruptly in Lower Cambrian sediments in great diversity and complexity, without trace of evolutionary ancestors or intermediates with other forms of life.

A Record of Abrupt Appearance

First, Darwin’s theory is in conflict with the fossil record with respect to the origin of major groups of organisms. The fossil record does not show this as a gradual process at all. For example, Darwin reflects on the abrupt appearance of ‘higher plants’ (angiosperms) in the fossil record. The very earliest fossils of those plants were from the middle of the Cretaceous period, and they came in a bewildering wide variety of sizes and forms. This was like a bloom of plants instead of the gradual appearance that his theory proposed. Darwin described this abrupt appearance of diverse higher plants as an “abominable mystery,” and as “a most perplexing phenomenon.”[4] Although there have been scattered reports of putative angiosperms from Triassic and Jurassic layers, critical evaluation of these reports shows that, so far, none provide unequivocal evidence of pre-Cretaceous angiosperms.[5]

Darwin was also perplexed by the sudden appearance of the Cambrian fossils (now called the ‘Cambrian Explosion’ of life): “To the question of why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer.”[6] To this date, paleontologists have not given a satisfactory answer to the question of why so many life forms appear suddenly in the Cambrian layers. But the same problem occurs in other rock layers above the Cambrian, where various groups of animals and plants appear without ancestors in lower layers.

Our knowledge of the fossil record has immensely increased in the last 160 years, but the problems Darwin recognized have not been resolved. Many scientists acknowledge this issue, though few dare to state it publicly. One exception is T. S. Kemp, who in 1999 asserted that “The observed fossil pattern is invariably not compatible with a gradualistic evolutionary process.”[7] The fossil record is not compatible with Darwin’s idea that evolution is gradual. Darwin knew that, and modern paleontologists quietly recognize it too.

Absence of Intermediate Forms

The second conflict of Darwin’s theory of evolution with the fossil record is also related to the pattern of appearances of new types of organisms. Darwin suggested that old species gradually transform into new species with significant differences accumulating over intense spans of time. If variations in species occur and morphological change is gradual, then we would expect to see “infinitely numerous intermediate forms”[8] in the fossil record, that is, animals and plants with intermediate anatomical traits showing the transition to new body plans. Also, there should be intermediate forms of their internal organs, especially in those animals that supposedly evolved from a water to a land environment or the opposite. Although the intermediate internal traits would not be expected to be recorded in the rocks because they pertain to soft tissue, the rocks should have many fossils with intermediate anatomical traits. There should be millions of them owing to the alleged long time available for evolution on earth.

Darwin was a strict adherent to gradualism and so convinced of it that he even challenged his readers to contest his theory by asserting:

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous successive slight modifications, my theory would absolutely break down.[9]

Yet Darwin knew that his view of life faced a major stumbling block: the fossil record. In the chapter titled “On the imperfection of the geological record” he honestly admits:

…the number of intermediate varieties, which have formerly existed, [must] be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links. Geology assuredly does not reveal any such finely-graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against the theory.[10]

Despite the serious problems the fossil record presented, Darwin believed that more discoveries would reveal the numerous transitional forms that his theory required. However, such is not the case and several paleontologists have openly acknowledged it. David Paul, former curator of geology at the Chicago’s Field Museum of Natural History, wrote in 1979,

Well, we are now about 120 years after Darwin and knowledge of the fossil record has been greatly expanded…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…[11]

Evidence of transitional forms between higher taxonomic levels of order, class and phylum is either disputed or non-existent. Unquestionably, current knowledge is that no pervasive pattern of gradualism exists in the fossil record. This is remarkable true for the higher taxa like families, orders and classes, which appear abruptly in the fossil record and have no transitional forms between them. This was acknowledged several decades ago by paleontologist George Gaylord Simpson asserting that,

[The] regular absence of transitional forms is not confined to mammals, but is an almost universal phenomenon, as has long been noted by paleontologists. It is true of almost all classes of animals, both vertebrate and invertebrate…it is true of the classes, and of the major animal phyla, and it is apparently also true of analogous categories of plants.[12]

More recently, other researchers have confirmed the nature of the fossil record of higher taxa. For example, commenting on the sudden appearance of multiple phyla in the Precambrian/Cambrian sedimentary transition and the absence of intermediate species or taxa between those and the hypothetical ancestors, Valentine et al. assert,

This situation is in fact true of most invertebrate orders during the remaining Phanerozoic as well. There are no chains of taxa leading gradually from an ancestral condition to the new ordinal body type. Orders appear as rather distinctive subdivision of classes rather than as being segments in some sort of morphological continuum.[13]

What are Valentine et al. saying here? They say that even lower taxonomic ranks like classes and orders, where the fossil record should show a rich content of intermediates, lack the morphological continuum. At all taxonomic levels, the fossil record does not conform to the Darwinian postulate of gradual transformation of species. The rock record does not provide the transitional forms that evolution theory requires. That was the most serious objection to the theory when it was presented in his book On the Origin of Species, and despite occasional claims of fossil intermediates the fact is that the gap between theory and data not only remains, but it has grown wider as many more fossils have been discovered. Fossils do not show the gradual transition in morphology and complexity that the theory requires. In the fossil record, the major groups (higher taxa of families, orders, classes, etc.) of organisms arise suddenly and fully formed, highly complex, and diversified, many of them with wide geographic distribution and well adapted to the environment. That is opposite of what the theory of evolution predicts. Darwin hoped that the absence of fossil intermediates (incompleteness of the fossil record) was due to the lack of knowledge—so little was known at his time, and many areas of the world remained unexplored for fossils. However, this hope has vanished among paleontologists who now recognize that the lack of transitional fossils is real, not at artifact. In the words of Arthur L. Battson III, “Darwinian evolution predicts the regular presence of transitional forms. The fossil record reveals their regular absence.”[14]


Paradoxides gracilis is one of the many species of trilobites that appear abruptly in the Paleozoic layers, from Cambrian sediments upwards. Trilobites are highly complex organisms, with an articulated body and sensory organs. The rocks only preserve the outer skeleton of the body but we can infer that the internal structure and physiology was just as complex as those of modern arthropods, and they show up in the fossil record without a record of gradual appearance. There is great variety of morphological forms from the very first appearance, but they do not seem to have evolved over the alleged millions of years during which they populated the oceans. Thus, besides being an example of sudden appearance, they illustrate stasis, remaining unchanged for long geological time until they went extinct, leaving no intermediate successors.

Stasis: No Change after Initial Appearance

The third conflict between Darwinism and the fossil record is the phenomenon of stasis. Once fossil species appear in a sedimentary layer they remain almost unchanged for the remaining of the record. Stasis in the fossil record is expressed as the invariability and permanence of traits over what are interpreted as large periods of time between the sudden appearance of a species and its extinction or the present. The core of Darwinian evolution is constant change. Yet stability, rather than gradual transformation into substantially different body plans, is the norm. Even evolutionist icon Stephen Jay Gould, the late professor of geology and paleontology at Harvard University, admitted that the history of most fossil species include two features particularly inconsistent with gradualism: stasis and sudden appearance:

“The history of most fossil species includes two features particularly inconsistent with gradualism: 1) Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking pretty much the same as when they disappear, morphological change is usually limited and directionless; 2) Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and fully formed.”[15]

Both sudden appearance of fossil forms and stasis are significant problems for the theory of evolution because the theory presupposes the opposite in the fossil record. Exceptions to the general pattern of stasis are known at lower taxonomic levels (species, genera), yet stasis, not gradual transformation, is the norm throughout the geological record of life. This is extremely problematic for a theory whose backbone is regular, gradual change. For 160 years, scientists working within the Darwinian paradigm have attempted to develop models and theories for data that do not exist. One of the reasons for their failure to produce a good model for the origin of the major taxa is that scientists have refused to address the pattern of stasis in the fossil record.

Scientists need to examine this fact with open minds and consider the possibility that there may be a biological mechanism preventing the degree of change needed to produce higher taxa. This stability suggests that there are natural processes that prevent major evolutionary change from happening at all. This has been demonstrated in the lab by thousands of experiments of experimentally induced mutations in fruit flies and other organisms. No matter how much or how often the DNA is altered, these organisms remain what they are without developing new structures although they may produce deleterious traits. Organisms have a built-in resistance to genetic change that prevents them from jumping into major transformations, and even small changes are buffered. Stasis is the norm. Darwinian evolution is based on random genetic variation and natural selection, but to this date scientists have not been able to show how those mechanisms can create new body plans, structures, complexity and diversity. It seems that the norm is stability, not gradual change, and that’s what we see in the fossil record.

Diversity of Species and Morphological Disparity

The fourth conflict refers to the prevalent pattern of paleontological succession of life forms. Darwinian theory predicts that the gradual accumulation of minor changes (genetic variations) should produce significant differences among organisms, originating new body plans and higher taxa. Species diversity represents the number of species present in an ecosystem. Disparity, on the other hand, is how morphologically different they are from one another. For example, a marine ecosystem consisting of a species of crab, a species of seagrass, a species of sea urchin and a species of shark would have very low diversity, but very high disparity—the body plans (morphology) of the species present are very different from each other.

What we see in the fossil record in the Lower Cambrian layers, which is where an “explosion” of life is recorded, are many new forms (body plans) with relatively few species of each represented. In other words, diversity should precede disparity, but the fossil record shows that disparity precedes diversity—the opposite to what Darwinian evolution predicts. Almost every metazoan[16] phylum with hard parts, and many that lack hard parts, appear in the Cambrian layers. The only modern phylum with an adequate fossil record to appear in rocks above the Cambrian was the phylum Bryozoa.[17] The major body plans or themes appear suddenly in the rocks, followed by only minor variations of the pre-existing themes. This pattern is pervasive in the fossil record even in lower taxonomic ranks like orders and families.

Insects are a good example. They are commonly considered a class (Insecta) within the Arthropoda phylum. With the exception of a few fossil insects (such as Collembola) in Devonian layers, the record consists of sudden appearance of multiple forms in upper Carboniferous and Permian layers. As recorded in the rock record, a burst of different shapes (disparity) of insects precedes the increase in species number (diversity).[18] Darwinian theory postulates that the fossil record should record the opposite: a large number of species arising gradually (diversification) followed eventually by multiple disparate body plans. Almost every group of animal and plant follows this pattern of low diversity and high disparity when they first appear in the sedimentary record. Thus, the fossil record of sudden appearance of multiple morphologies does not follow the expected Darwinian gradual, step-by-step appearance.

Darwin’s Illusion

As explained above, Darwin’s theory focuses on selection of favorable or positive traits in organisms with minor variations. His theory of evolution by natural selection was based on inferences from artificial selection of characters in pigeons, sheep, horses and other animals. Darwin saw that farmers and breeders could produce sheep with thicker wool, dogs with larger, skinny legs for running, and faster horses by controlling the breeding process in order to bring about the desired characters and form an ‘improved’ population. Darwin thought that those variations were continuously happening on a larger scale in the natural populations, and the step-by-step changes would gradually create new body plans. However, the evidence was contrary to his postulates. Had Darwin developed a theory to explain the actual data observed in the natural world, he should have arrived at the opposite conclusion. Instead of proposing a theory to explain how species and body themes arise from gradual variations, he should have developed a theory to explain how species do not change in a step-by-step fashion. The evidence for stasis and stability of the major body plans was there in the fossil record and in the living forms for Darwin to consider, but he chose to ignore it.


Darwin’s theory of evolution presupposes variations in organisms that are passed on to the next generation. These variations are naturally selected, the best fitted survive and leave more and more fit descendants. In time, gradual variations will accumulate, producing new organs, new structures and new morphologies. The evidence for gradual change should be observed in the natural world and also in the fossil record. However, the natural world does not show gradualism among the different groups of organisms and the fossil record lacks the features that the theory demands.

The theory postulates gradual appearance of different body plans with increasing diversity in species over long time. Instead, the Cambrian strata, where most of the body plans first appear, shows sudden appearance of many different body plans (high disparity) and low numbers of species (diversity), the opposite of what the theory requires. The body plans that arise and the species that characterize them then stay stable throughout the record, with only minor changes, if any, over alleged millions of years of history. This phenomenon of stasis is also the opposite of what the theory requires, which is gradual modifications in morphology and physiology.  These gradual changes should be observable as multitudes of intermediate forms or transitional morphologies in the fossil record, yet they are absent, with minor exceptions which are contested by many paleontologists.

Darwinian evolution is thus challenged by its own assumptions. The challenges derive from the very biological mechanisms that are supposed to generate gradual change. To this date, most scientists stay faithful to the Darwinian theory of gradual change despite the fact that the fossil evidence does not support it. After 160 years of Darwinism, science needs a better theory to explain how diversity arises and a theory to explain why species remain unchanged without gradually evolving into something significantly different.

By Raúl Esperante, PhD
Geoscience Research Institute


[1] This voyage was a circumnavigation of the globe between 1831 and 1836. Darwin was 22 years old when he embarked in the HMS Beagle.

[2] Thomas Malthus (1766-1834) was a British scholar and influential economist.

[3] Darwin did not use the word “evolution” until the last edition of his book the Origin of Species in 1872.

[4] Darwin expressed this concern in a letter in 1879 to his friend Joseph Hooker, Director of the Royal Botanical Gardens Kew. Darwin F., Seward, A. C., Darwin, C. 1903. More Letters from Charles Darwin, eds. Darwin F., Seward, A. C. Appleton: New York. It is debatable whether Darwin referred to angiosperms in general or to a limited group of them. Richard Buggs, after researching the sources for the meaning of “higher plants” in the late 19th century comes to the conclusion that “In [this] context… therefore, Darwin seemed to be referring to the sudden appearance of diverse dicotyledons—rather than all angiosperms—in the fossil record as the “abominable mystery”” Darwin’s abominable mystery. 24 May 2017., accessed 10 April 2020.

[5] Herendeen, P. S., Friis, E. M., Petersen, K. R., Crane, P. R. 2017. Palaeobotanical redux: revisiting the age of the angiosperms. Nature Plants 3:17015.

[6] Origin of Species. 1872 edition, p. 308. Available at John van Wyhe, editor. 2002-. The Complete Work of Charles Darwin Online (, accessed 10 April 2020.

[7] Fossils and Evolution. Oxford: Oxford University Press, p. 16.

[8] Darwin, Charles (Darwin, Francis ed.). 1909. The Foundations of The Origin of Species. Two Essays Written in 1842 and 1844. Cambridge: Cambridge University Press, p. 136.

[9] Darwin, Charles. 1859, 1979. On the Origin of Species (Reprint of the first edition). New York: Avenel Books, Crown Publishers, 219.

[10] Darwin, Charles. 1872, 1958. On the Origin of Species (Reprint of the sixth edition). New York: Mentor Books, 287.

[11] Raup, David. 1979. Conflicts between Darwin and paleontology. Field Museum of Natural History Bulletin 50(1):24,25.

[12] Simpson, George Gaylord. 1944. Tempo and Mode in Evolution. New York: Columbia University Press, 107.

[13] Valentine, J. W., Awramik, S. M., Signor, P. W., Sadler, P. M. 1991. The biological explosion at the Precambrian-Cambrian boundary. Evolutionary Biology 25.

[14] Battson, A. L. 1994. On the origin of stasis by means of natural processes. Perspectives on Science and Christian Faith 46(4):232.

[15] Gould, S. J. 1977. Evolution’s erratic pace. Natural History 86 (May); Gould, S. J. 1980. The panda’s thumb. New York: W. W. Norton, 182.

[16] Metazoan refers to animals that are multicellular and have cells with a true nucleus and mitochondria. Metazoan encompasses all animals with differentiated tissues, including muscles and nerves.

[17] Marshall, Charles R. 2006. Explaining the Cambrian “explosion” of animals. Annual Review of Earth and Planetary Sciences 34(1):335-384.

[18] Hoy, M. A. 2008. Fossil Record of Insects. In: Capinera J.L. (ed.) Encyclopedia of Entomology. Dordrecht: Springer.