An Apologetic for Metaphysics in Science

An Apologetic for Metaphysics in Science

Modern science often presents itself as neutral, value-free, and independent of metaphysics. This is a convenient story—but it is not a true one.

Science does not begin with experiments. It begins with axioms. And axioms are not scientific.

Before a single measurement is taken, the scientist must already believe that:

  • Truth exists
  • Reality is intelligible
  • The human mind can understand that reality
  • Understanding the truth is good
  • Reality is ordered rather than arbitrary or deceptive

None of these claims can be proven scientifically. They are metaphysical commitments. Science rests on them, but cannot justify them.

This matters more than most people realise.

The Quiet Removal of the Root

Historically, many of the founders of modern science were explicit about the metaphysical foundation of their work. The universe was intelligible because it was created. The human mind could grasp truth because it was made to know. Inquiry was good because truth itself was good.

In other words, God was not an optional add-on. He was the root of the ontological tree.

What has happened in modernity is not simply the removal of God from scientific method, but the removal of God from ontology—while quietly retaining conclusions that only made sense with that root in place.

This is not neutrality. It is ontological editing after the fact.

The work of earlier thinkers is often reframed as if their metaphysical commitments were irrelevant, or merely cultural decoration. But removing the root while keeping the fruit is not historical honesty—it is misrepresentation.

From Bracketing to Enforcement

Earlier scientists could temporarily bracket theology while keeping metaphysics open. Today, that openness has largely vanished.

Belief in God is no longer merely excluded from science—it is actively stigmatised. The charge is familiar: unscientific, irrational, regressive. This is not passive secularism. It is enforcement.

Ironically, this enforcement only works because the very metaphysical assumptions it denies are smuggled back in through the back door. Truth, meaning, moral obligation, and epistemic trust are all assumed—just never acknowledged.

At that point, science ceases to be a discipline of inquiry and begins to resemble a creed with sanctions.

Mathematics Is Not Ontology

One symptom of this metaphysical vacuum is the elevation of mathematics beyond its proper role.

Mathematics is a language. A map. A powerful one—but still a representation. When mathematics is allowed to replace ontology rather than describe it, science drifts into abstraction unmoored from reality.

“The math works” becomes sufficient. Explanation quietly gives way to prediction. Models become metaphors, metaphors become stories, and stories are repeated until familiarity replaces understanding.

Nowhere is this more visible than in cosmology—but the pattern appears elsewhere too. When ontology is weak, narrative and marketing step in to do the stabilising work.

That is not progress. It is compensation.

Metaphysics as a Guardrail

Metaphysics is not an enemy of science. It is its guardrail.

Good metaphysics limits speculation, disciplines imagination, and keeps inquiry tethered to reality. When those guardrails are removed, science does not become freer—it becomes more prone to fantasy, embarrassment, and wasted effort at enormous scale.

Billions, perhaps trillions, have been spent chasing ontological dead ends that were incoherent from the outset—not because scientists were foolish, but because foundational questions were ruled out as “unscientific”.

Naming the Root

Restoring metaphysics to science does not mean forcing theology into experiments. It means doing something far more modest and far more honest:

Acknowledging that science depends on metaphysical assumptions—and naming them openly.

Whether one ultimately grounds those assumptions in God or elsewhere, pretending they do not exist is no longer tenable. A tree cannot float. If the root is cut, something else will take its place—usually unexamined, unstable, and enforced by social pressure rather than reason.

Science flourishes best when it is humble about its foundations.

And humility, paradoxically, is what keeps inquiry honest.

​

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