By Zia H Shah MD, Chief Editor of the Muslim Times

This may be boring, but it is absolutely essential for any discussion with atheists and to distinguish good correlation between the Glorious Quran and science versus what would be invalid or overly zealous.

The distinction between methodological naturalism and metaphysical naturalism represents one of the most significant conceptual frameworks in contemporary philosophy of science, with profound implications for how we understand scientific practice, religious belief, and the nature of reality itself. Methodological naturalism (MN) functions as a procedural constraint within scientific practice, requiring natural explanations for natural phenomena without making ontological commitments about ultimate reality. Metaphysical or philosophical naturalism (PN), by contrast, makes the substantive claim that only natural entities and processes exist, explicitly rejecting supernatural phenomena. This distinction, though formally coined only in 1983 by philosopher Paul de Vries, has become central to debates about science education, the relationship between science and religion, and the philosophical foundations of scientific inquiry.

As a physician and scientist, I am all for MN and forcibly deny PN as that will simply make me an atheist, while I am a devout believer in Islam and the Glorious Quran. This sentence alone should highlight the extreme importance of this article.

The philosophical architecture of two naturalisms

The Stanford Encyclopedia of Philosophy provides the authoritative framework for understanding these concepts. Methodological naturalism operates as “a view about philosophical practice” where philosophy and science pursue similar ends using similar methods, specifically through “a posteriori investigation” to establish “synthetic knowledge about the natural world.” Paul Kurtz’s foundational definition clarifies that MN commits to a methodological principle: “all hypotheses and events are to be explained and tested by reference to natural causes and events.” Barbara Forrest, whose 2000 paper “Methodological Naturalism and Philosophical Naturalism: Clarifying the Connection” remains the seminal work on this distinction, characterizes MN as an epistemology and procedural protocol rather than a metaphysical position—a working assumption that operates within science without making ontological commitments.

Metaphysical naturalism, in contrast, makes substantive claims about reality itself. The Stanford Encyclopedia describes it as asserting that “reality has no place for ‘supernatural’ or other ‘spooky’ kinds of entity,” with all spatiotemporal entities being “identical to or metaphysically constituted by physical entities.” Carl Sagan captured this worldview memorably: “The Cosmos is all that is or ever was or ever will be.” This ontological position goes beyond methodology to claim that natural elements, principles, and relations studied by the sciences exhaust reality.

The fundamental distinction lies in their categorical difference: MN is procedural and epistemological while PN is ontological and metaphysical. MN concerns how we investigate; PN concerns what exists. This allows MN to function as a method-neutral approach compatible with various worldviews, including theism, while PN explicitly excludes traditional religious beliefs about supernatural entities or divine action.

Ancient roots and modern emergence

While the explicit distinction between methodological and metaphysical naturalism emerged only in the late 20th century, naturalistic thinking has ancient origins. The pre-Socratic philosophers of 6th-5th century BCE Greece—Thales, Anaximander, Democritus—were labeled “physikoi” (natural philosophers) for investigating natural causes rather than mythological explanations. Thales of Miletus, considered the first naturalist, proposed that everything was composed of water, seeking natural rather than divine explanations for phenomena.

After Christianity’s dominance made metaphysical naturalism heretical during the Middle Ages, the Renaissance revival of Greek texts contributed to the Scientific Revolution. Francis Bacon (1561-1626) established what would later be recognized as methodological naturalism by developing the scientific method emphasizing empirical observation and arguing that natural philosophy should proceed through controlled experimentation focusing on natural explanations.

The modern distinction crystallized through several pivotal developments. The Vienna Circle of the 1920s-1930s, including Moritz Schlick, Rudolf Carnap, and Otto Neurath, promoted logical positivism with its verifiability principle and physicalist program. W.V.O. Quine’s 1969 “Epistemology Naturalized” marked a crucial development by arguing that epistemology should become “a chapter of psychology,” advocating for continuity between philosophy and science while remaining agnostic about ultimate metaphysical questions.

The formal distinction emerged from 1970s-1980s philosophy of religion debates about whether science necessarily entails atheism. Paul de Vries coined “methodological naturalism” in 1983 to distinguish between naturalism as “a disciplinary method that says nothing about God’s existence” and metaphysical naturalism “which denies the existence of a transcendent God.” This distinction became strategically important in creation-evolution controversies, allowing evolution to be taught without necessarily endorsing atheistic worldviews.

Key advocates reveal the philosophical divide

The debate’s contours become clear through examining major advocates on each side. Supporting methodological naturalism while rejecting metaphysical naturalism, Francis Collins, former NIH Director and evangelical Christian, argues: “Science explores the natural, and God is outside the natural. So there is going to be no substitute for making a decision to believe.” He sees MN as revealing “God’s creation” rather than disproving God. Kenneth Miller, Catholic biologist at Brown University, contends that “Evolution is constantly being equated to PHILOSOPHICAL NATURALISM (rather than naturalism in METHODOLOGY), and to atheism,” arguing one can fully accept evolutionary science while maintaining religious belief.

Pierre Duhem (1861-1916), the French Catholic physicist, provided influential historical precedent: “I have denied metaphysical doctrines the right to testify for or against any physical theory… Whatever I have said of the method by which physics proceeds… does not in any way prejudice either the metaphysical doctrines or religious beliefs of anyone who accepts my words.” His “Duhemian science” allows physicists to collaborate regardless of metaphysical commitments.

Advocates of metaphysical naturalism argue differently. Barbara Forrest contends that while MN doesn’t logically entail PN, “the relationship between methodological naturalism and philosophical naturalism, although not that of logical entailment, is not such that philosophical naturalism is a mere logical possibility.” She sees PN as “the well grounded a posteriori result” of MN’s success, “the only reasonable metaphysical conclusion” given the demonstrated success of methodological naturalism combined with the lack of methodology for knowing the supernatural.

Richard Dawkins argues more stridently: “The big war is not between evolution and creationism, but between naturalism and supernaturalism.” William Provine (1942-2015) drew explicit atheistic conclusions: “Let me summarize my views on what modern evolutionary biology tells us loud and clear… There are no gods, no purposes, and no goal-directed forces of any kind.”

Contemporary academic battlegrounds

Recent scholarship reveals sophisticated ongoing debates. In the Journal for General Philosophy of Science (2020), Zargar, Azadegan, and Nabavi argue that MN necessarily presupposes ontological assumptions including “causal closure of the physical” and epistemological commitments like “evidentialism,” concluding these lead inevitably to metaphysical naturalism—a stronger connection than Forrest’s a posteriori link.

The “new demarcation problem” identified by Holman and Wilholt (2022) focuses on which values may legitimately influence science, connecting to traditional naturalism debates because questions of legitimate values parallel MN/PN distinctions. Contemporary philosophy of science increasingly rejects strict value-neutrality, complicating MN’s claimed procedural neutrality.

Alvin Plantinga’s sustained critique argues MN is not religiously neutral, challenging the “actual practice and content of science.” His Evolutionary Argument Against Naturalism suggests combining evolution and naturalism is self-defeating regarding reliable cognitive faculties. In response, contemporary supporters like Hans Halvorson (2016) argue MN can be justified pragmatically without metaphysical commitments, while critics like the intelligent design movement contend MN artificially constrains scientific inquiry.

Scientific practice and religious reconciliation

How religious scientists navigate methodological naturalism reveals practical implications of these philosophical distinctions. Survey data shows approximately 40-45% of American scientists describe themselves as theistic evolutionists or hold religious beliefs while practicing methodological naturalism. They justify this through various strategies: viewing natural laws as secondary causes through which God operates, embracing “fully gifted creation” where God designed a universe operating through natural processes, and compartmentalizing science and religion as addressing different questions.

Different religious traditions respond variably. Christianity shows diverse approaches: mainline Protestants generally support MN, evangelicals are mixed, and Catholics largely follow Duhem’s tradition. Islam presents historical precedent in classical scientists like Ibn al-Haytham who insisted on natural explanations, though contemporary views vary between theological schools about God’s relationship to natural causation.

The Intelligent Design movement critiques MN fundamentally. William Dembski argues MN renders design “empirically undetectable” by definition. Michael Behe contends MN prevents legitimate detection of irreducible complexity. Defenders respond that MN is methodologically neutral, based on evidential success rather than philosophical bias, and that design arguments haven’t produced successful research programs.

The philosophical verdict remains contested

Contemporary scholarship suggests the relationship between methodological and metaphysical naturalism remains genuinely unresolved. While broad agreement exists that strict logical entailment doesn’t hold, significant debates continue over the strength of evidential connections, whether MN can be genuinely metaphysically neutral, and the coherence of natural/supernatural distinctions.

Barbara Forrest’s position—that MN provides strong evidential support for PN without logical entailment—represents a middle ground many find compelling. The massive success of naturalistic explanations in science, combined with the absence of successful supernatural methodologies, creates what she calls “the only reasonable metaphysical conclusion” for many philosophers. Yet prominent scientists like Francis Collins and Kenneth Miller demonstrate that methodological naturalism can be practiced effectively while maintaining religious commitments, suggesting the philosophical connection remains looser than critics claim.

The distinction matters profoundly for science education, where maintaining MN’s procedural focus allows scientific investigation without requiring metaphysical commitments. For philosophy of science, it highlights questions about the relationship between method and worldview. For science-religion dialogue, it provides conceptual space for religious scientists to participate fully in scientific practice while maintaining their faith. As debates over consciousness, quantum mechanics, and cosmic fine-tuning continue to challenge our understanding of nature’s boundaries, the distinction between investigating nature through naturalistic methods and claiming nature exhausts reality remains both philosophically subtle and culturally significant.

Methodological versus metaphysical naturalism: A comprehensive analysis

The distinction between methodological naturalism and metaphysical naturalism represents one of the most significant conceptual frameworks in contemporary philosophy of science, with profound implications for how we understand scientific practice, religious belief, and the nature of reality itself. Methodological naturalism (MN) functions as a procedural constraint within scientific practice, requiring natural explanations for natural phenomena without making ontological commitments about ultimate reality. Metaphysical or philosophical naturalism (PN), by contrast, makes the substantive claim that only natural entities and processes exist, explicitly rejecting supernatural phenomena. This distinction, though formally coined only in 1983 by philosopher Paul de Vries, has become central to debates about science education, the relationship between science and religion, and the philosophical foundations of scientific inquiry.

The philosophical architecture of two naturalisms

The Stanford Encyclopedia of Philosophy provides the authoritative framework for understanding these concepts. Methodological naturalism operates as “a view about philosophical practice” where philosophy and science pursue similar ends using similar methods, specifically through “a posteriori investigation” to establish “synthetic knowledge about the natural world.” Paul Kurtz’s foundational definition clarifies that MN commits to a methodological principle: “all hypotheses and events are to be explained and tested by reference to natural causes and events.” Barbara Forrest, whose 2000 paper “Methodological Naturalism and Philosophical Naturalism: Clarifying the Connection” remains the seminal work on this distinction, characterizes MN as an epistemology and procedural protocol rather than a metaphysical position—a working assumption that operates within science without making ontological commitments.

Metaphysical naturalism, in contrast, makes substantive claims about reality itself. The Stanford Encyclopedia describes it as asserting that “reality has no place for ‘supernatural’ or other ‘spooky’ kinds of entity,” with all spatiotemporal entities being “identical to or metaphysically constituted by physical entities.” Carl Sagan captured this worldview memorably: “The Cosmos is all that is or ever was or ever will be.” This ontological position goes beyond methodology to claim that natural elements, principles, and relations studied by the sciences exhaust reality.

The fundamental distinction lies in their categorical difference: MN is procedural and epistemological while PN is ontological and metaphysical. MN concerns how we investigate; PN concerns what exists. This allows MN to function as a method-neutral approach compatible with various worldviews, including theism, while PN explicitly excludes traditional religious beliefs about supernatural entities or divine action.

Ancient roots and modern emergence

While the explicit distinction between methodological and metaphysical naturalism emerged only in the late 20th century, naturalistic thinking has ancient origins. The pre-Socratic philosophers of 6th-5th century BCE Greece—Thales, Anaximander, Democritus—were labeled “physikoi” (natural philosophers) for investigating natural causes rather than mythological explanations. Thales of Miletus, considered the first naturalist, proposed that everything was composed of water, seeking natural rather than divine explanations for phenomena.

After Christianity’s dominance made metaphysical naturalism heretical during the Middle Ages, the Renaissance revival of Greek texts contributed to the Scientific Revolution. Francis Bacon (1561-1626) established what would later be recognized as methodological naturalism by developing the scientific method emphasizing empirical observation and arguing that natural philosophy should proceed through controlled experimentation focusing on natural explanations.

The modern distinction crystallized through several pivotal developments. The Vienna Circle of the 1920s-1930s, including Moritz Schlick, Rudolf Carnap, and Otto Neurath, promoted logical positivism with its verifiability principle and physicalist program. W.V.O. Quine’s 1969 “Epistemology Naturalized” marked a crucial development by arguing that epistemology should become “a chapter of psychology,” advocating for continuity between philosophy and science while remaining agnostic about ultimate metaphysical questions.

The formal distinction emerged from 1970s-1980s philosophy of religion debates about whether science necessarily entails atheism. Paul de Vries coined “methodological naturalism” in 1983 to distinguish between naturalism as “a disciplinary method that says nothing about God’s existence” and metaphysical naturalism “which denies the existence of a transcendent God.” This distinction became strategically important in creation-evolution controversies, allowing evolution to be taught without necessarily endorsing atheistic worldviews.

Key advocates reveal the philosophical divide

The debate’s contours become clear through examining major advocates on each side. Supporting methodological naturalism while rejecting metaphysical naturalism, Francis Collins, former NIH Director and evangelical Christian, argues: “Science explores the natural, and God is outside the natural. So there is going to be no substitute for making a decision to believe.” He sees MN as revealing “God’s creation” rather than disproving God. Kenneth Miller, Catholic biologist at Brown University, contends that “Evolution is constantly being equated to PHILOSOPHICAL NATURALISM (rather than naturalism in METHODOLOGY), and to atheism,” arguing one can fully accept evolutionary science while maintaining religious belief.

Pierre Duhem (1861-1916), the French Catholic physicist, provided influential historical precedent: “I have denied metaphysical doctrines the right to testify for or against any physical theory… Whatever I have said of the method by which physics proceeds… does not in any way prejudice either the metaphysical doctrines or religious beliefs of anyone who accepts my words.” His “Duhemian science” allows physicists to collaborate regardless of metaphysical commitments.

Advocates of metaphysical naturalism argue differently. Barbara Forrest contends that while MN doesn’t logically entail PN, “the relationship between methodological naturalism and philosophical naturalism, although not that of logical entailment, is not such that philosophical naturalism is a mere logical possibility.” She sees PN as “the well grounded a posteriori result” of MN’s success, “the only reasonable metaphysical conclusion” given the demonstrated success of methodological naturalism combined with the lack of methodology for knowing the supernatural.

Richard Dawkins argues more stridently: “The big war is not between evolution and creationism, but between naturalism and supernaturalism.” William Provine (1942-2015) drew explicit atheistic conclusions: “Let me summarize my views on what modern evolutionary biology tells us loud and clear… There are no gods, no purposes, and no goal-directed forces of any kind.”

Contemporary academic battlegrounds

Recent scholarship reveals sophisticated ongoing debates. In the Journal for General Philosophy of Science (2020), Zargar, Azadegan, and Nabavi argue that MN necessarily presupposes ontological assumptions including “causal closure of the physical” and epistemological commitments like “evidentialism,” concluding these lead inevitably to metaphysical naturalism—a stronger connection than Forrest’s a posteriori link.

The “new demarcation problem” identified by Holman and Wilholt (2022) focuses on which values may legitimately influence science, connecting to traditional naturalism debates because questions of legitimate values parallel MN/PN distinctions. Contemporary philosophy of science increasingly rejects strict value-neutrality, complicating MN’s claimed procedural neutrality.

Alvin Plantinga’s sustained critique argues MN is not religiously neutral, challenging the “actual practice and content of science.” His Evolutionary Argument Against Naturalism suggests combining evolution and naturalism is self-defeating regarding reliable cognitive faculties. In response, contemporary supporters like Hans Halvorson (2016) argue MN can be justified pragmatically without metaphysical commitments, while critics like the intelligent design movement contend MN artificially constrains scientific inquiry.

Scientific practice and religious reconciliation

How religious scientists navigate methodological naturalism reveals practical implications of these philosophical distinctions. Survey data shows approximately 40-45% of American scientists describe themselves as theistic evolutionists or hold religious beliefs while practicing methodological naturalism. They justify this through various strategies: viewing natural laws as secondary causes through which God operates, embracing “fully gifted creation” where God designed a universe operating through natural processes, and compartmentalizing science and religion as addressing different questions.

Different religious traditions respond variably. Christianity shows diverse approaches: mainline Protestants generally support MN, evangelicals are mixed, and Catholics largely follow Duhem’s tradition. Islam presents historical precedent in classical scientists like Ibn al-Haytham who insisted on natural explanations, though contemporary views vary between theological schools about God’s relationship to natural causation.

The Intelligent Design movement critiques MN fundamentally. William Dembski argues MN renders design “empirically undetectable” by definition. Michael Behe contends MN prevents legitimate detection of irreducible complexity. Defenders respond that MN is methodologically neutral, based on evidential success rather than philosophical bias, and that design arguments haven’t produced successful research programs.

The philosophical verdict remains contested

Contemporary scholarship suggests the relationship between methodological and metaphysical naturalism remains genuinely unresolved. While broad agreement exists that strict logical entailment doesn’t hold, significant debates continue over the strength of evidential connections, whether MN can be genuinely metaphysically neutral, and the coherence of natural/supernatural distinctions.

Barbara Forrest’s position—that MN provides strong evidential support for PN without logical entailment—represents a middle ground many find compelling. The massive success of naturalistic explanations in science, combined with the absence of successful supernatural methodologies, creates what she calls “the only reasonable metaphysical conclusion” for many philosophers. Yet prominent scientists like Francis Collins and Kenneth Miller demonstrate that methodological naturalism can be practiced effectively while maintaining religious commitments, suggesting the philosophical connection remains looser than critics claim.

All discussions on the limitations of science also underscore the total metaphysics that MN should not be equated with PN. It may be part of the agenda for the atheists, but it is not philosophically or theologically true.

The distinction matters profoundly for science education, where maintaining MN’s procedural focus allows scientific investigation without requiring metaphysical commitments. For philosophy of science, it highlights questions about the relationship between method and worldview. For science-religion dialogue, it provides conceptual space for religious scientists to participate fully in scientific practice while maintaining their faith. As debates over consciousness, quantum mechanics, and cosmic fine-tuning continue to challenge our understanding of nature’s boundaries, the distinction between investigating nature through naturalistic methods and claiming nature exhausts reality remains both philosophically subtle and culturally significant.

Additional reading

Atheist Philosophers and Scientists Possessed by Laplace’s Demon

Video: Does Consciousness Defeat Materialism?

Why Should a Dead Universe Give Rise to Consciousness: Richard Swinburne’s Argument for God from Consciousness?

Why Should a Dead Universe Give Rise to Consciousness: JP Moreland’s Argument for God from Consciousness