“Brain as a Computer” Metaphor Rebooted
While the brain is certainly more
and other than a computer,
it is also not less than one.
The Brain Is Not a Computer, and That’s Not the Real Problem
by John D. Wise, PhD
In a recent book review titled How to breathe life back into brain theory (Nature, 25 May 2026), Àlex Gómez-Marín evaluates Romain Brette’s The Brain, In Theory (Princeton University Press, April 2026). The review reveals a growing insurgency within neuroscience,[1] one in which the discipline is beginning to turn on its most cherished analogy: the brain as a computer. Gómez-Marín notes that
engineering metaphors can be useful but… they are often vague, incoherent and misleading.
More sharply, Brette’s book argues that brains:
are not programmable machines… because neurons do not follow fixed rules or commands, cannot be modified to function arbitrarily and don’t implement computations as such. Nor is neural activity a code, in which one variable is mapped directly to another… In other words, although scientists can infer links between brain activity and external variables, this does not mean that the organism that they are studying is doing that as well.
The critique cuts deeper still, targeting the pervasive claim that the brain is an information-processing system. As the review observes,
information indicates the level of uncertainty… but that tells us little about how the brain works out a signal’s meaning.
In the technical Shannon sense, information measures statistical uncertainty, not semantic understanding. The language of ‘information processing’ thus risks explaining cognition in terms that systematically exclude the very thing it seeks to explain:[2] intentional significance.
Having rejected the machine analogy, Brette reaches for a different vocabulary, asserting that
Neurons are not mechanical components but living units that belong to the whole body.
To salvage an explanation for behavior, Brette and Gómez-Marín are forced to borrow heavily from phenomenological psychology. They speak of “embodied information” and “virtual action” – describing a brain that does not abstractly categorize objects, but rather perceives a world of what are elsewhere referred to as affordances, anticipating the movements required to interact with its environment.
This is a genuine insight, but it reveals a profound historical irony. Decades ago, the astrophysicist Robert Jastrow famously noted that the scientist who relies entirely on the power of empirical reason climbs the mountains of ignorance only to pull himself over the final rock and find “a band of theologians who have been sitting there for centuries.” Neuroscience is treating “interaction” and “embodiment” as cutting-edge frontiers, yet they are merely arriving at the insights that phenomenology and natural philosophy have defended for generations.
If we are looking for a flawed metaphor, the computer is the least of our worries. The one doing much greater damage is materialism itself, a blindfold that restricts scientific vision from seeing what is actually there. Banishing the capacity to see design and infer intelligent agency does not advance our understanding; it simply cripples our ability to describe reality.
Gómez-Marín exposes the boundary, challenging Brette’s total silence on consciousness and extraordinary human experience. Yet Brette retreats behind Methodological Naturalism, eager to wrest biology from the engineers, but terrified of surrendering it to metaphysics.
But science has never operated on any other ground.
Furthermore, we must be careful not to swing the pendulum too far. While the brain is certainly more and other than a computer, it is also not less than one. The computational analogy retains its stubborn usefulness because the brain does exhibit rule-bound fidelity, functional processing, and systematic mechanics. The machine metaphor fails not because it is entirely false, but because it has been treated as exhaustive, as the Whole rather than a functional part.
The essay closes with a strikingly contradictory instruction: we must “study brains as they are, and not through misplaced metaphors.”
Yet there is no observing things as they are without an interpretive lens. Abandoning explicit metaphors does not eliminate them; it merely blinds us to the ones that continue to govern our assumptions. What emerges here is a systemic pattern across modern science. In physics, the timeless fixity of laws is being questioned; in cosmology, the universe is described in organismal terms; now in neuroscience, the computer metaphor is fracturing under the weight of its own data.
Each shift moves closer to a view of reality characterized by process, unity, and dynamic organization. So, set the computational machine metaphor aside, if you like. So long as you retain the most highly-distorting filter of all, methodological naturalism, you’re not likely to find a better one to replace it. Trading a computational lens for an ecological one may reveal some previously unseen nuances within your field of view, but it still hides the full spectrum of what is there.
Because the real problem is not what you’re missing in your visible field; it is that your lenses are polarized. Methodological naturalism systematically filters out the vertical axis of reality, and this is the real reason Brette cannot acknowledge design, purpose, and consciousness. The full spectrum is not revealed by rotating a restricted lens. It is only when the polarizing filter is traded for a lens open to unrestricted illumination that the brain can finally be seen for what it is, and in its true glory.
Footnotes
[1] Led by figures including Matthew Cobb and György Buzsáki, in addition to Brette.
[2] Or, more accurately, to explain away. Methodological Naturalism demands that all intentional, conscious phenomena be reduced to blind physical mechanism, ensuring that the discipline must systematically dissolve the very reality it claims to illuminate.
John Wise received his PhD in philosophy from the University of CA, Irvine in 2004. His dissertation was titled Sartre’s Phenomenological Ontology and the German Idealist Tradition. His area of specialization is 19th to early 20th century continental philosophy.
He tells the story of his 25-year odyssey from atheism to Christianity in the book, Through the Looking Glass: The Imploding of an Atheist Professor’s Worldview (available on Amazon). Since his return to Christ, his research interests include developing a Christian (YEC) philosophy of science and the integration of all human knowledge with God’s word.
He has taught philosophy for the University of CA, Irvine, East Stroudsburg University of PA, Grand Canyon University, American Intercontinental University, and Ashford University. He currently teaches online for the University of Arizona, Global Campus, and is a member of the Heterodox Academy. He and his wife Jenny are known online as The Christian Atheist with a podcast of that name, in addition to a YouTube channel: John and Jenny Wise.