metaphysics of science

The idea that science can provide a true and complete description of reality, including the nature of mind and consciousness, is deeply engrained in contemporary Western thought. According to this view, philosophical perspectives and spiritual traditions have little or no role to play in our understanding of reality. But can science truly offer a complete account of the cosmos, including the vast and mysterious dimensions of consciousness? Is there a grand, central order—something that meaningfully accommodates consciousness—and, if so, can science adequately describe or explain it? Can science offer meaningful insights into purpose, meaning, or subjective experience, or is it ultimately limited to arbitrating only that which can be measured?

For the last 150 years, science has largely set aside metaphysical questions under the widespread presumption that doctrines such as materialism, reductionism, and positivism are not only sufficient but ultimately the only valid means of accounting for reality. This perspective—often labeled scientism—is understandable, given the predictive power of science and the unprecedented expansion of knowledge and technology it has made possible. See physicalism in this project for a brief summary of this belief system.

However, discoveries over the past several decades, particularly in quantum physics—such as the non-locality of entangled particles and the observer-dependent nature of measurement—have challenged this presumption. For some contemporary physicists and philosophers, these developments point to the need for a new metaphysical foundation, one that can accommodate the profound realities of modern physics and the immense breadth and depth of consciousness. While such a new framework is only beginning to take shape, it tends to align with holism, the integration of scientific and metaphysical perspectives, and an appreciation for the fundamental nature of mind or consciousness.

The term metaphysics refers to matters of first principle—the underlying nature of being. Webster’s defines metaphysics as: “the first branch of philosophy that deals with first principles and seeks to explain the nature of being or reality (ontology) and of the origin and structure of the world (cosmology)… popularly, any very subtle, perplexing, or difficult reasoning.” In the Aristotelian tradition, the term implies “beyond the physical”—a theory of ultimate reality that lies beneath or beyond appearances. One could, of course, deny the existence of anything beyond what the senses perceive, but such a denial is itself a metaphysical stance.

Before the seventeenth century, metaphysics was integral to both physiologia (the rational account of nature) and philosophia naturalis (the philosophy of nature)—distinct but complementary approaches to understanding the world. Aristotle’s conception of the study of nature included both philosophical inquiry and the mathematics of mechanics. For more than a millennium, our understanding of nature was shaped by a synthesis of empirical observation and philosophical reflection.

This unity began to fracture in the seventeenth century. Thinkers such as Francis Bacon, Galileo Galilei, and René Descartes introduced a new perspective on philosophia naturalis that fundamentally reshaped Aristotle’s metaphysics. A key element of Descartes’ view was his skepticism toward the senses. He argued that mathematical ideas were the only trustworthy basis for knowledge, as they reflected God’s design—a design accessible to the human mind. Descartes’ metaphysical framework treated physical laws as revelations of divine rationality, forming what some scholars have called the “hidden ontology” of classical science. The Non-Local Universe, p. 8. See also Nadeau and Kafatos on Descartes’ lasting influence on Western thought.

A few decades later, Isaac Newton published Philosophiae Naturalis Principia Mathematica, often credited as the foundational text of modern science. Newton’s work articulated a mechanical view of nature based on atomistic bodies and mathematical laws. But although remembered today as the father of classical physics, Newton dedicated the vast majority of his writing and intellectual labor to theological speculation and alchemical experimentation, which he regarded as key to uncovering the deeper, divine order of the universe. From Science Wars, The Great Courses, Lecture by Steven L. Goldman.

Yet over time, the predictive success of Newtonian mechanics led to the philosophical dimensions of his work being sidelined. By the late eighteenth century, the distinction between science and philosophy became more pronounced. Mathematicians like Pierre-Simon Laplace proposed that the universe was entirely describable in terms of mechanical laws. Laplace even rejected the need for metaphysical assumptions, famously asserting that the hypothesis of God was unnecessary to explain the workings of nature.

Laplace’s methodological stance also contributed to this shift. He emphasized the importance of induction—drawing general laws from observed data—and discouraged the use of untestable hypotheses. Moreover, he insisted that the true nature of concepts like mass, force, or cause was irrelevant: only their measurable aspects mattered. This outlook was quickly absorbed into the dominant paradigm, and philosophical or metaphysical inquiry was increasingly dismissed as irrelevant. Ivor Leclerc, from Kitchener, p. 26.

Science thereby became increasingly identified with positivism—the doctrine that only empirical observation provides legitimate knowledge. According to this view, there is a direct, one-to-one correspondence between physical theory and reality. Concepts not amenable to quantification, such as meaning or consciousness, were excluded from the domain of legitimate inquiry. This historical perspective is elaborated in Leclerc, from Kitchener, p. 28.

Modern science, still largely grounded in Newtonian mechanics, has thus come to divide the world into measurable, objective phenomena and unmeasurable, subjective experience. The human realm of perception, purpose, and consciousness has been marginalized in favor of the supposedly more real world of quantifiable data. See Koyré in The Non-Local Universe, p. 7.

In the twentieth century, this division deepened. Science and technology became tightly coupled, and science came to be regarded as the ultimate arbiter of truth about nature. Subjective experience was relegated to the sidelines—treated as personal, private, and ultimately irrelevant to objective understanding.

The materialist foundation of modern science has hardened into a widely accepted truth claim. Many prominent scientists assert that biological evolution and neuroscience can, in principle, explain all aspects of life, including consciousness. While this claim might be true, it remains a metaphysical assumption—a belief about the nature of reality that cannot itself be empirically verified. While the materialist position may ultimately be correct, intellectual humility requires that we acknowledge its unprovable status. The central claim of this project, however, is that materialism fails to account for the full spectrum of reality—including consciousness, meaning, and subjective experience.

Today, however, signs of a fundamental shift are appearing. The metaphysical foundations of science are being reevaluated in light of modern developments in physics—particularly quantum theory—and systems biology. Increasingly, these developments challenge the mechanistic, reductionist worldview and suggest a more holistic, relational, and perhaps consciousness-inclusive understanding of the cosmos. Ironically, the evolving picture of nature emerging from contemporary science appears more consistent with many of the insights found in traditional philosophical and spiritual worldviews than with the mechanistic assumptions on which modern science was built.