Darwin's Doubt

1. Darwin's Doubt: The Cambrian Explosion as a Challenge

The abrupt manner in which whole groups of species suddenly appear in certain formations has been urged by several paleontologists—for instance, by Agassiz, Pictet, and Sedgwick—as a fatal objection to the belief in the transmutation of species.

Darwin's dilemma. Charles Darwin recognized a significant problem for his theory of gradual evolution: the Cambrian explosion. This event, marked by the sudden appearance of diverse and complex animal forms in the fossil record, lacked the expected transitional fossils in preceding layers. This absence challenged the core tenet of gradualism, suggesting a more abrupt origin of life than Darwin's theory readily accommodated.

Agassiz's opposition. Renowned paleontologist Louis Agassiz challenged Darwin, arguing that the fossil record, particularly the Cambrian explosion, contradicted gradual evolution. Agassiz emphasized the abrupt appearance of complex designs like trilobites and brachiopods, questioning the absence of simpler ancestral forms. This debate highlighted the tension between Darwin's theoretical expectations and the empirical evidence from paleontology.

An enduring mystery. Darwin hoped future fossil discoveries would resolve this anomaly, but the Cambrian explosion remains a significant point of contention. The lack of transitional forms and the sudden appearance of diverse body plans continue to fuel scientific debate, questioning the completeness of the fossil record and the mechanisms driving evolutionary change.

2. The Burgess Shale: A Window into Cambrian Diversity

Here was a great treasure—wholly strange Crustacea of Middle Cambrian time—but where in the mountain was the mother rock from which the slab had come?

Walcott's discovery. Charles Doolittle Walcott's discovery of the Burgess Shale in 1909 unveiled an extraordinary trove of Middle Cambrian fossils. This site revealed a menagerie of previously unknown animal forms, preserved in exquisite detail, showcasing a greater diversity of biological architecture than previously imagined. The Burgess Shale became a focal point for understanding the Cambrian explosion.

A bestiary of bizarre forms. The Burgess Shale contained creatures like Marrella (the "lace crab") and Hallucigenia, so peculiar that paleontologists struggled to classify them. These fossils highlighted the unique body plans and anatomical structures that characterized the Cambrian fauna, challenging existing taxonomic frameworks. The Burgess Shale underscored the sudden appearance of diverse animal forms.

Disparity before diversity. The Burgess Shale revealed a pattern in which radical differences in form (disparity) arose before the diversification of species within those forms (diversity). This "top-down" pattern contradicted the Darwinian expectation of gradual change accumulating over time, further complicating the Cambrian mystery.

3. The Chengjiang Fauna: Soft Bodies and a Sharper Explosion

The remains of hard tissues, such as the shells of brachiopods or the carapaces of trilobites, are well represented in the Chengjiang fauna, but less robust tissues, which are usually lost through decomposition, are also beautifully preserved.

China's treasure trove. The discovery of the Chengjiang fauna in southern China provided an even older and more detailed glimpse into the Cambrian explosion. These fossils, dating back to the early Cambrian, showcased an even greater variety of soft-bodied organisms, challenging the notion that the Cambrian explosion was merely an artifact of hard-part preservation.

Soft-bodied preservation. The Chengjiang fossils demonstrated that sedimentary rocks could preserve soft tissues in exquisite detail, disproving the idea that the absence of Precambrian ancestors was due to the fossil record's inability to preserve soft-bodied organisms. This discovery intensified the mystery of the Cambrian explosion, as it highlighted the absence of ancestral forms even in conditions conducive to soft-tissue preservation.

Turning Darwin upside down. The Chengjiang fauna further emphasized the "top-down" pattern of appearance, with representatives of separate phyla appearing first, followed by lower-level diversification. This pattern, along with the geologically abrupt appearance of the Cambrian fauna, challenged Darwin's picture of gradual evolutionary change.

4. The Artifact Hypothesis: Explaining Away the Missing Fossils

I fully realize that the conclusions above outlined are based primarily on the absence of a marine fauna in Algonkian [Precambrian] rocks, but until such is discovered I know of no more probable explanation of the abrupt appearance of the Cambrian fauna than that I have presented.

Darwin's initial response. Darwin proposed that the absence of Precambrian fossils was due to the incompleteness of the fossil record. He suggested that the ancestral forms of the Cambrian animals were either not fossilized or had not yet been found. This "artifact hypothesis" became a common explanation for the Cambrian mystery.

Walcott's Lipalian interval. Charles Walcott refined the artifact hypothesis, suggesting that the ancestors of the Cambrian animals evolved offshore during a period of low sea levels, making their fossils inaccessible. He termed this period the "Lipalian interval," a time of rapid evolution in a "lost" location.

The demise of Walcott's hypothesis. With the development of offshore drilling technology and the theory of plate tectonics, Walcott's hypothesis was discredited. The discovery of Precambrian sponge embryos and the understanding that oceanic crust is recycled through subduction further undermined the idea that the missing fossils were simply waiting to be found in inaccessible locations.

5. Ediacaran Enigmas: Not the Ancestors We Expected

Both with Darwin and his followers, a great part of the argument is purely negative.

The Ediacaran fauna. The discovery of the Ediacaran fauna, a group of soft-bodied organisms from the late Precambrian, raised hopes that the missing ancestors of the Cambrian animals had finally been found. These fossils, dating back to 570-543 million years ago, represented a diverse array of forms, including Dickinsonia, Spriggina, and Charnia.

Uncertain affinities. Despite initial enthusiasm, most paleontologists now doubt that the Ediacaran fauna represent direct ancestors of the Cambrian animals. The body plans of these organisms bear little resemblance to those of the Cambrian fauna, and their classification remains hotly debated. The Ediacaran organisms may represent a separate experiment in multicellular life, unrelated to the Cambrian animals.

A Precambrian pow. The Ediacaran fauna do represent a significant increase in biological complexity compared to earlier life forms. However, this "Precambrian pow" only deepens the mystery of the Cambrian explosion, as it highlights another period of rapid innovation without clear evolutionary precursors.

6. Molecular Clocks: Genes Tell Conflicting Stories

Now we have a powerful, new, and independent way to establish ancestry: we can look directly at the genes themselves.

The promise of molecular clocks. With the rise of molecular biology, scientists turned to the genes of living organisms to reconstruct the history of life. The "molecular clock" hypothesis suggested that the rate of mutation in certain genes could be used to estimate the time of divergence between different species.

Deep divergence. Molecular clock studies initially pointed to a "deep divergence" of the animal phyla, with the common ancestor of all animals living as far back as 1.2 billion years ago. This hypothesis suggested a long period of cryptic evolution in the Precambrian, hidden from the fossil record.

Conflicting signals. However, different molecular clock studies have yielded widely divergent results, with estimates for the origin of the animal ancestor ranging from 100 million to 1.5 billion years ago. These conflicting signals cast doubt on the reliability of molecular clocks and the deep-divergence hypothesis.

7. The Tree of Life: A Tangled Web of Relationships

What had been distinct species within one genus become, in the fullness of time, distinct genera within one family. Later, families will be found to have diverged to the point where taxonomists (specialists in classification) prefer to call them orders, then classes, then phyla.

The Darwinian tree. Darwin's theory of evolution envisioned a branching tree of life, with all organisms descending from a single common ancestor. This tree implied a gradual accumulation of differences over time, with small-scale variations eventually leading to large-scale morphological disparity.

Molecular vs. anatomical trees. To test the Darwinian tree, scientists compared phylogenetic trees based on anatomical characteristics with those based on molecular data. However, these comparisons often revealed conflicting relationships, challenging the idea of a single, coherent tree of life.

The artifact of assumption. The assumption of universal common descent, inherent in phylogenetic methods, may create an artificial appearance of treelike relationships. The conflicting results from different molecular and anatomical studies suggest that the history of animal life may be more complex than a simple branching tree.

8. Punctuated Equilibrium: A Theory of Rapid Bursts

Stasis . . . was by far the most important pattern to emerge from all my staring at Phacops specimens.

Taking the fossil record at face value. Niles Eldredge and Stephen Jay Gould proposed the theory of punctuated equilibrium to reconcile evolutionary theory with the discontinuous pattern of the fossil record. They argued that evolution occurs in rapid bursts of speciation, followed by long periods of stasis, or little change.

Allopatric speciation and species selection. Punctuated equilibrium invoked allopatric speciation (rapid speciation in small, isolated populations) and species selection (selection acting on whole species) to explain the rapid bursts of change. This theory deemphasized the role of gradual change within lineages.

Inconsistent with Cambrian pattern. Punctuated equilibrium, however, does not fully explain the Cambrian explosion. The top-down pattern of appearance, with disparity preceding diversity, contradicts the theory's expectation of small-scale changes accumulating over time. Moreover, the theory does not account for the origin of the new traits and body plans that characterize the Cambrian animals.

9. The Information Explosion: Building Animals Requires Code

Scientists now know that building a living organism requires information, and building a fundamentally new form of life from a simpler form of life requires an immense amount of new information.

Information is essential. Building a new form of life requires new information, akin to the code needed for a computer to acquire a new function. The Cambrian explosion represents not only an explosion of new animal forms but also an explosion of information.

Measuring complexity. One way to estimate the amount of new information is to measure the number of cell types in different organisms. More complex animals, like trilobites, require more cell types and, therefore, more genetic information than simpler organisms, like sponges.

The digital code of life. DNA stores genetic information in the form of a four-character digital code. The precise arrangement of nucleotide bases in DNA conveys instructions for building proteins, the building blocks of cells and tissues. The Cambrian explosion required a vast increase in this functional, specified information.

10. Combinatorial Inflation: The Improbability of New Genes

No currently existing formal language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed.

The challenge of specificity. The need for specificity in the arrangement of DNA bases makes it extremely improbable that random mutations would generate new functional genes or proteins. Random changes in a code or language system typically degrade function or meaning.

Combinatorial inflation. The number of possible amino-acid sequences for even a modestly sized protein is astronomically large. This "combinatorial inflation" makes it difficult for random mutations to "search" the vast space of possibilities and stumble upon a functional sequence.

The rarity of proteins. Mutagenesis experiments have shown that functional proteins are exceedingly rare within sequence space. This rarity poses a significant challenge to the neo-Darwinian mechanism, which relies on random mutations to generate the raw material for natural selection.

11. The Limits of Mutation and Selection: A Numbers Game

The observation that such fossils are absent in Precambrian strata proves that these phyla arose in the Cambrian.

The neo-Darwinian math. The neo-Darwinian mechanism depends on natural selection acting on random mutations. The equations of population genetics are used to estimate the amount of evolutionary change that can occur in a given period of time, based on mutation rates, population sizes, and generation times.

The waiting time problem. These calculations reveal a "waiting time problem": the time required to generate even a single new gene or protein by random mutation and selection may be far longer than the age of the earth. This problem is exacerbated by the need for multiple coordinated mutations to produce complex adaptations.

The edge of evolution. Michael Behe's work on chloroquine resistance in malaria demonstrates the limits of Darwinian evolution. He shows that even relatively simple adaptations can require multiple mutations, making the evolution of more complex features highly improbable.

12. Intelligent Design: A Different Kind of Cause

The creation of information is habitually associated with conscious activity.

Beyond materialism. The failure of materialistic evolutionary theories to explain the origin of biological information and form raises the possibility of an alternative explanation: intelligent design. This theory proposes that certain features of living systems are best explained by the action of a designing intelligence.

Detecting design. Intelligent design is not based on religious belief but on evidence-based reasoning. It identifies features of living systems, such as specified complexity and irreducible complexity, that are known from experience to be produced by intelligent causes.

A vera causa. Intelligent design meets the key requirement of a good historical scientific explanation: it cites a cause that is known to have the power to produce the effects in question. Intelligent agents have repeatedly demonstrated the capacity to generate functional information and complex integrated systems.

Last updated: February 22, 2025