Darwinism or neo-Darwinism, named after the British naturalist Charles Darwin, has become a foundational pillar of the modern secular worldview.

It offers a naturalistic explanation for the diversity and complexity of life, territory once occupied exclusively by traditional religious cosmologies. By proposing the mechanism of natural selection, Darwinian theory reframed the question of life’s origin and development, shifting it from theological teleology to empirical biology, thus effectively abolishing what I’d describe as the “epistemological dominion” of faith.

To clarify the terminology: Darwinian evolution refers to Charles Darwin’s original theory of evolution by natural selection, where random variations in traits provide differential survival advantages. Neo-Darwinism or “the Modern Synthesis” incorporates later developments in genetics, particularly Mendelian inheritance and molecular biology, combining them with Darwin’s original framework. It explains evolution as the result of random genetic mutations filtered by natural selection over time. I use Darwinism and neo-Darwinism interchangeably as, ultimately, they describe a common paradigm.

Anyway, Darwin’s challenge to religion was not limited to his scientific claims. Darwin was once a theology student himself and directly confronted one of the most enduring theological arguments for the existence of God: William Paley’s watchmaker analogy. Paley had argued that just as a watch found in the desert implies a watchmaker, the intricate design of living organisms implies a divine designer. Darwin’s theory of natural selection fundamentally undermined this reasoning by alleging that complex biological structures could arise gradually, through cumulative, non-teleological processes without the need for a purposeful designer, namely, God.

Thus, Darwinism not only offered a rival account of life’s origins but also eroded the intellectual foundation of natural theology, particularly the assumption that complexity necessarily entails intentional design. This represents a deeper philosophical shift, from a universe governed by divine intention to one shaped by impersonal, observable forces.

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Theistic Arguments & Intelligent Design

Numerous efforts have been made to challenge Darwin’s theory of natural selection, particularly from within the framework of intelligent design (ID). One prominent critique comes from biochemist Michael Behe, who introduced the concept of “irreducible complexity.” According to Behe, certain biological systems, such as the bacterial flagellum, are composed of interdependent parts that could not function if any component were removed and, therefore, could not have evolved through gradual, stepwise processes.

Mathematician and philosopher William Dembski extended this critique by proposing the concept of “specified complexity.” This notion suggests that when a structure is both complex (unlikely to occur by chance) and specified (conforms to an independently given pattern), it is best explained by an intelligent cause rather than by undirected natural processes. Dembski attempted to formalize this through probabilistic reasoning, using tools from information theory to argue that certain biological patterns exceed the threshold of what random mutation and natural selection could plausibly generate.

These arguments form the backbone of the modern intelligent design movement, a school of thought situated within the broader field of Christian apologetics. One of its most visible contemporary proponents is Stephen C. Meyer, who has sought to give intelligent design philosophical and scientific legitimacy, particularly through his writings on the origin of biological information.

Critics, however, contend that these arguments rest on flawed assumptions about biological and molecular systems. Scientists like Denis Alexander, a Christian and a theistic evolutionist, argue that invoking “complexity” as evidence of design is epistemologically weak, since nearly all natural structures appear “complex” at some scale. From this perspective, complexity alone does not necessitate intelligent design, nor does it invalidate evolutionary mechanisms.

“Agnostic” Criticisms

In addition to critiques from religious or explicitly theistic perspectives, there have also been agnostic or non-religious challenges to Darwinism, as I would term them. These critiques often come from individuals who do not publicly adhere to any particular faith tradition but still question the sufficiency of Darwinian explanations. A notable example is Michael Denton, a molecular biologist, whose book Evolution: A Theory in Crisis (1985) offers a detailed scientific critique of neo-Darwinism without appealing to theology.

One of Denton’s key arguments centers on the concept of “molecular equidistance.” By analyzing protein sequences across different species, Denton observed that the molecular differences between simpler and more complex organisms are not always consistent with what would be expected in a straightforward evolutionary tree. For instance, when comparing a protein such as cytochrome c across various species, simpler organisms (like bacteria) appear roughly equidistant, at the molecular level, from multiple more complex organisms (like mammals or birds).

According to Denton, this pattern challenges the assumption that complex organisms evolved “directly” from simpler ones through gradual modification, because the molecular data does not reflect a clear linear progression.

While critics have argued that these observations can be reconciled with evolutionary theory, often by citing neutral mutation rates and molecular clocks, Denton’s work has nonetheless contributed to a broader scientific discussion about the limits of phylogenetic inference and the adequacy of current models in explaining life’s diversity.

His critique stands out precisely because it refrains from invoking intelligent design or divine causality, making it an example of what could be called an “agnostic dissent” from Darwinism.

Another prominent agnostic critic of Darwinian evolution is David Berlinski, a secular Jewish mathematician and philosopher. In his book The Devil’s Delusion: Atheism and Its Scientific Pretensions (2008), Berlinski challenges the explanatory power of natural selection, particularly from the standpoint of mathematical probability. He argues that the emergence of complex biological systems, such as functional proteins, genetic codes, and cellular machinery, through undirected, random mutations filtered by natural selection is statistically implausible.

Berlinski questions whether the vast combinatorial space of possible genetic sequences could realistically be navigated by evolutionary processes within the available time frame of Earth’s history. He emphasizes that even slight functional proteins require precise amino acid arrangements, and the probability of randomly generating such arrangements through mutation is astronomically low. From his perspective, the Darwinian model relies on assumptions that fail to meet the rigor of mathematical scrutiny, especially regarding the likelihood of incremental steps leading to highly ordered biological systems.

While Berlinski, too, does not advocate for a specific religious alternative, his critiques are aimed at exposing what he sees as the metaphysical overreach of scientific materialism and the limitations of natural selection as a comprehensive explanatory framework, essentially a secular criticism of a secularist ideology.

The (Very) Hard Problem of Consciousness

Another notable agnostic critique of Darwinism comes from philosopher Thomas Nagel, who hails from an ethnic Jewish background. Nagel has expressed deep skepticism about the explanatory scope of Darwinian evolution, particularly regarding the emergence of consciousness. In his book Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False (2012), Nagel argues that the prevailing scientific worldview rooted in Darwinian principles fails to account for the subjective and qualitative aspects of the conscious experience.

Nagel contends that even this more advanced, gene-centered view, while successful in explaining the development of physical traits, cannot adequately explain how conscious subjectivity, intentionality, and rational thought could emerge from purely physical processes. He is particularly critical of materialist reductionism, the idea that everything about the mind can be explained by biochemical processes in the brain. For Nagel, consciousness is not an evolutionary afterthought or an emergent epiphenomenon. Rather, it must be treated as a fundamental feature of the universe, possibly requiring a new kind of teleological or non-materialist framework.

What makes Nagel’s critique especially significant is that he is not motivated by religious belief. In fact, he states explicitly that he does not want theism to be true.

His position reflects an internal philosophical tension within secular naturalism, suggesting that it may be insufficient not only empirically but also logically to explain certain profound aspects of human existence.

Even prior to Nagel, beginning in the 1990s, philosopher David Chalmers (widely regarded as one of the leading figures in the philosophy of mind) introduced the concept of the “hard problem of consciousness.” This refers to the difficulty materialist theories face in explaining how and why physical processes in the brain give rise to subjective experience. Chalmers argued that materialist ideologies—including those grounded in Darwinian or neo-Darwinian frameworks—focus on explaining cognitive functions in terms of neural activity but fail to address the qualitative, first-person aspect of consciousness.

More recently, philosopher Philip Goff has extended this line of critique in his book Galileo’s Error: Foundations for a New Science of Consciousness (2019). Goff traces the problem back to the scientific revolution, arguing that Galileo effectively removed consciousness from the domain of science by focusing exclusively on quantifiable, physical properties. He contends that Galileo’s framework established a mechanistic and materialist model of nature that excluded so-called “secondary qualities” such as color, sound, and pain—qualities which are directly tied to conscious experience. In doing so, modern science marginalized the subjective dimension of reality.

This philosophical trajectory can be observed in the work of John Locke, the pioneer of liberalism, who distinguished between primary and secondary qualities, ultimately regarding secondary qualities, such as color, taste, and sound, as mere subjective effects produced in the mind by external objects. This distinction paved the way for further skepticism about the nature of physical reality. George Berkeley took this to a more radical conclusion by rejecting even the existence of primary qualities, such as extension and motion, unless perceived. In Berkeley’s idealist framework, all qualities, primary and secondary, exist only within perception, effectively reducing the external world to individual subjectivity sustained by the continuous perception of God.

To return again now to Goff, he eventually advocates for a revival of panpsychism, i.e., the view that consciousness is a fundamental and ubiquitous feature of the physical world.

While panpsychism poses significant theological and metaphysical challenges from an Islamic perspective, particularly in its tendency to blur the line between Creator and creation, Goff’s critique of the materialist and Darwinian limitations in explaining consciousness nonetheless raises important philosophical concerns from a non-religious perspective.

From an Islamic perspective, consciousness is not a “problem” to be solved but a defining feature of human dignity and moral responsibility. It is through consciousness that we engage in inner deliberation, distinguish between right and wrong; and also take responsibility for our actions. It enables self-reflection, the recognition of error, the capacity for repentance, and the potential for moral and spiritual transformation. In this sense, consciousness is the very seat of the self, engaged in a continuous dialogue with itself.

By contrast, reductive materialist worldviews, such as those underlying much of neo-Darwinian theory, tend to explain consciousness in purely physical terms, as nothing more than the by-product of neural activity or biochemical processes.

This perspective, while methodologically “useful” in scientific inquiry, risks stripping human experience of its depth and meaning, reducing profound moral and existential phenomena to neurochemical trivialities.

Such reductionism fails to account for the inward, subjective dimension of human life that believers see as central to our purpose and accountability before God and without which our lives are, quite literally, meaningless.

Our origin is not traced to a common ancestor with chimpanzees who “diverged” some six million years ago, as proposed by evolutionary biology. Rather, our ancestor is Prophet Adam (peace be upon him), the first human being, who was created with inherent dignity and honored by Allah through the gift of consciousness, moral responsibility, and prophecy.