A Comparative Analysis of Biological Ontologies: The Evolutionary Perspectives of Imam Omer Suleiman and Dr. Zia H. Shah

Presented by Zia H Shah MD

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Abstract

The contemporary intersection of Islamic theology and evolutionary biology presents a rich landscape of intellectual inquiry, characterized by varying degrees of acceptance, adaptation, and ontological resistance. This research report provides an exhaustive examination of the perspectives held by two influential figures within this discourse: Imam Omer Suleiman, a prominent traditional scholar and founder of the Yaqeen Institute, and Dr. Zia H. Shah, a physician and researcher dedicated to reconciling the Quran with modern scientific discoveries. The analysis highlights a fundamental divergence in their methodologies: Suleiman maintains a position of human exceptionalism, grounding his skepticism of universal common ancestry in the miraculous creation of Adam as described in scriptural texts. Conversely, Dr. Shah advocates for a model of “Guided Evolution” and universal common ancestry, supported by extensive molecular evidence, including Human Endogenous Retroviruses (HERVs) and the development of the mammalian placenta. Dr. Shah further posits that the aesthetic complexity of the universe serves as a teleological proof of a Creator, challenging the “blind” mechanisms of standard Darwinian theory. By contrasting Suleiman’s traditionalist hermeneutics with Shah’s integrative scientific framework, this report elucidates the broader philosophical implications for the 21st-century Islamic understanding of life’s origins, biological creativity, and the divine signature within the natural world.

Biographical Profile of Imam Omer Suleiman

Omer Suleiman is a globally recognized American Muslim scholar, activist, and intellectual leader who has significantly shaped the discourse on faith and modernity in the West. Born in 1986 in New Orleans, Louisiana, Suleiman was raised in a multi-cultural environment that informed his future work in civil rights and interfaith dialogue. His academic journey reflects a rigorous commitment to both traditional Islamic sciences and contemporary academic study. He holds a Bachelor’s degree in Islamic Law, a Master’s degree in Islamic Finance, and a Ph.D. in Islamic Thought and Culture from the International Islamic University Malaysia.

As the Founder and President of the Yaqeen Institute for Islamic Research, Suleiman has spearheaded a movement to address the “crises of faith” facing modern Muslims, particularly youth navigating the tensions between scientific materialism and religious orthodoxy. His role as a Professor of Islamic Studies at Southern Methodist University and his leadership in the Dallas-area Muslim community have positioned him as a bridge-builder. Suleiman’s approach to evolution is primarily theological and pastoral; he seeks to maintain the integrity of the Quranic narrative while acknowledging the utility of scientific inquiry. His work through Yaqeen Institute often focuses on deconstructing the perceived “totalizing” nature of evolutionary science, arguing that scientific methodology should not be conflated with a materialistic worldview that precludes divine intervention.

Biographical Profile of Dr. Zia H. Shah

Dr. Zia H. Shah is a physician specializing in internal medicine and sleep disorders, with a distinguished medical career spanning several decades. Based in New York, Dr. Shah has balanced his clinical practice with a prolific life as a researcher, writer, and public intellectual. He serves as the Chief Editor of the Muslim Times and is the creator of “The Quran Love,” an extensive digital platform dedicated to the harmonization of scientific findings with Quranic theology.

Dr. Shah’s intellectual project is characterized by a deep-seated belief that the Quran and the “Book of Nature” (science) are two complementary volumes of divine revelation that cannot, by definition, contradict one another. His perspective is uniquely informed by his medical background, which provides him with a detailed understanding of molecular biology, genetics, and physiology. Unlike many traditionalists, Dr. Shah fully embraces the scientific consensus on universal common ancestry, viewing it not as a threat to monotheism but as a profound manifestation of the Creator’s “Sunnatullah” (God’s way). His research focuses on “Guided Evolution,” a framework that rejects the random, purposeless nature of Neo-Darwinism in favor of a teleological process directed by a Divine Architect. Dr. Shah is particularly noted for his work on the functional role of viruses in genomic evolution and the argument from beauty as a proof of God.

The Theological Constraints on Evolution: Omer Suleiman’s Perspective

Imam Omer Suleiman addresses the subject of evolution through a lens of “theological boundary-setting.” In his primary discourse on the matter, he attempts to reconcile the empirical observations of science with the ontological claims of the Islamic tradition. His perspective is not one of total rejection, but rather one of selective acceptance based on scriptural constraints.

The Miraculous Origin of Adam

The central pillar of Suleiman’s evolutionary perspective is the miraculous creation of the first human, Adam. He maintains that the Quranic account of Adam’s creation—from clay, directly by the hands of God, and the subsequent breathing of the Ruh (spirit) into him—constitutes a foundational truth that cannot be reduced to a purely biological process. For Suleiman, the creation of Adam is a “singular event” that stands outside the standard laws of biology. This position creates a “red line” for the common ancestry of humans with other primates. While he may acknowledge the possibility of evolutionary change within other species, he insists that humans are an exceptional case of divine intervention.

Critique of Methodological Naturalism

Suleiman critiques the scientific community’s adherence to methodological naturalism, which he argues has become a “dogma” that automatically excludes any non-material cause. He suggests that while this methodology is useful for studying repeatable natural phenomena, it is ill-equipped to address unique historical events or the spiritual dimensions of humanity. In his view, the evolutionary narrative is often presented as a “totalizing world-encompassing myth” that attempts to explain human purpose and morality through a purely biological lens. By resisting the idea that humans are merely “improved apes,” Suleiman seeks to preserve the concept of human dignity and the metaphysical reality of the soul.

Acceptance of Non-Human Evolution

Significantly, Suleiman does not reject evolution in its entirety. He allows for the possibility that the diversity of plant and animal life on Earth may have arisen through evolutionary mechanisms. This “partial acceptance” is a strategic theological move: it acknowledges the strength of the scientific evidence for biological change while shielding the human origin story from being subsumed by it. He posits that God could have chosen to create the rest of the world through evolution while choosing a different, miraculous path for humanity.

Aspect of Evolution	Suleiman’s View	Rationale
Micro-evolution	Accepted	Observed within species; does not contradict scripture.
Non-human Macro-evolution	Permissible	Scripture is largely silent on the specific mechanics of animal origins.
Human Common Ancestry	Rejected	Direct contradiction to the Quranic narrative of Adam’s unique creation.
Methodological Naturalism	Critiqued	Viewed as an ideological constraint that excludes the miraculous.

The Scientific-Theological Integration: Dr. Zia H. Shah’s Perspective

Dr. Zia H. Shah presents a radically different paradigm, one that views universal common ancestry as an established fact and a profound sign of God’s creative power. His framework, “Guided Evolution,” seeks to remove the perceived conflict between the Quran and science by demonstrating that the evolutionary process itself is a designed mechanism.

Universal Common Ancestry as “Fool-Proof” Reality

Dr. Shah argues that the molecular evidence for the common ancestry of all life forms is overwhelming and “fool-proof.” He contends that if a person were to look objectively at the genetic data, the conclusion of shared descent would be unavoidable. He emphasizes that the similarities between human DNA and the DNA of other organisms are not merely superficial but include specific “genomic scars” and shared errors that would only exist if those organisms shared a common ancestor.

He utilizes the example of “junk DNA” and pseudogenes—sequences of DNA that are non-functional but still present in the genome. For Dr. Shah, the presence of the same broken gene in the same location in both humans and chimpanzees (such as the GULO gene for Vitamin C synthesis) is a definitive proof of common ancestry. He posits that a Creator who creates each species independently would not include the same “broken” genetic code in two different lineages unless those lineages were actually one and the same.

The Theory of Guided Evolution

While Dr. Shah accepts the biological facts of evolution, he explicitly rejects the “blind” and “random” philosophy of standard Darwinism. He argues that the emergence of complex life, consciousness, and the sophisticated organs of the human body cannot be attributed to accidental mutations and natural selection alone. Instead, he proposes that the evolutionary process is “guided”.

This guidance, in Dr. Shah’s view, manifests through the inherent laws of nature and the integration of information into the genome. He suggests that the universe is “fine-tuned” for life and that the evolutionary trajectory was always directed toward the eventual appearance of humanity. By framing evolution as a divine tool, he transforms it from a threat into a form of worship, where the study of biology becomes the study of God’s creative method.

Molecular Evidence for Common Ancestry: A Deep Dive

Dr. Shah’s argument for common ancestry is rooted in the technical details of molecular evolution. He presents several lines of evidence that he considers “smoking guns” for the unity of life.

Human Endogenous Retroviruses (HERVs)

A major component of Dr. Shah’s evidence involves Human Endogenous Retroviruses (HERVs). These are genetic elements derived from ancient retroviruses that infected the germ cells of ancestors millions of years ago. Once integrated into the genome, these viral sequences were passed down to all descendants. Approximately 8% of the human genome consists of these viral remnants.

Dr. Shah explains that the distribution of these HERVs across different species provides an indisputable map of evolutionary history. If a specific HERV is found in the exact same location in the human genome and the chimpanzee genome, the only logical explanation within a scientific framework is that the infection occurred in a common ancestor. The statistical probability of the same virus inserting itself into the same spot in two different species independently is essentially zero. This evidence, according to Dr. Shah, effectively proves the biological link between humans and the rest of the animal kingdom.

Chromosomal Fusion and Genetic Conservation

Dr. Shah also points to chromosomal evidence, such as the fusion of what are chromosomes 2a and 2b in ancestral primates into the human Chromosome 2. This fusion explains why humans have 23 pairs of chromosomes while other great apes have 24. The presence of telomeric sequences (usually found at the ends of chromosomes) in the middle of human Chromosome 2, and the presence of two centromeres, serves as a physical record of this evolutionary event. For Dr. Shah, these molecular details are not “accidents” but are the “handwriting” of God in the biological record, demonstrating a continuous process of creation through change.

The Viral Architect: Creativity in Guided Evolution

One of the most innovative aspects of Dr. Shah’s work is his exploration of “creativity from viruses.” He challenges the traditional view of viruses as mere pathogens, presenting them instead as essential contributors to biological complexity.

The Evolution of the Placenta and Syncytin-1

Dr. Shah provides a detailed analysis of how the mammalian placenta—a marvel of biological engineering—came to be. He explains that the development of the placenta required a way for fetal cells to fuse together to form a barrier (the syncytiotrophoblast) that prevents the mother’s immune system from attacking the fetus while allowing for nutrient exchange. This fusion is made possible by a protein called Syncytin-1.

Crucially, the gene for Syncytin-1 is not a “native” mammalian gene; it is an env gene from an endogenous retrovirus. Ancient mammals “captured” this viral gene and repurposed it for a vital reproductive function. Dr. Shah argues that this is a prime example of guided evolution: the Creator used the mechanism of viral integration to introduce the necessary information for a monumental leap in biological complexity—the transition from egg-laying to live birth. This “viral architecture” suggests a level of foresight and design that transcends random mutation.

Viruses and the Human Brain

Dr. Shah extends this thesis to the human brain, citing evidence that retroviral elements have played a role in the evolution of cognitive complexity. He points to the Arc gene, which is essential for synaptic plasticity and the consolidation of long-term memories. Recent research indicates that Arc has a structure and behavior similar to a viral “Gag” protein, suggesting it originated from an ancient viral infection. For Dr. Shah, the fact that “ancient viruses built your brain and placenta” is a powerful argument for a guided genomic ecosystem where information is purposefully integrated over time to achieve specific creative ends.

Biological Feature	Evolutionary Mechanism	Theological Significance (Shah)
Placenta (Syncytin-1)	Capture of retroviral envelope genes.	Innovation through external genetic integration; non-random.
Brain Memory (Arc gene)	Repurposing of viral-like capsids for neural messaging.	Preparation of the biological vessel for higher consciousness.
Genomic Ecosystem	Interaction of viruses, transposons, and host genes.	The genome as a dynamic, designed “software” environment.
Universal Genetic Code	Shared across all domains of life.	Evidence of a single, unified Creator (At-Tawhid).

Guided Evolution vs. Blind Darwinism: The Teleological Distinction

The fundamental disagreement between Dr. Shah and the secular scientific establishment lies in the interpretation of the cause behind evolutionary change. Dr. Shah argues that while the “what” of evolution is common ancestry, the “how” is not blind chance.

The Probability of Biological Innovation

Dr. Shah contends that the probability of complex, functional structures (like the human eye, the immune system, or the placenta) appearing through purely accidental mutations is so low as to be practically impossible. He aligns with the idea that the “fitness landscape” of life is not a random walk but a directed path. In his view, the laws of physics and chemistry are “pre-loaded” with the potential for biological complexity. He views the Creator as the one who sets these laws in motion and ensures that the “random” elements of the process are channeled toward the desired outcome.

Rejecting the “Blind Watchmaker”

Richard Dawkins’ famous metaphor of the “Blind Watchmaker” suggests that evolution is a process without a goal and without a designer. Dr. Shah systematically rejects this, arguing that the intricate coordination required for even a single cell to function points to a “Seeing Watchmaker.” He posits that the Quran’s description of God as Al-Bari (The Evolver) and Al-Musawwir (The Bestower of Forms) fits perfectly with a model where God uses the long, slow process of evolution to “sculpt” the various forms of life on Earth.

Aesthetic Teleology: Beauty as Proof of the Creator

A unique and significant portion of Dr. Shah’s argument for God is based on aesthetics. He maintains that the beauty found in nature—from the macro scale of the universe to the micro scale of fireflies—cannot be explained by survival of the fittest alone.

The Argument from Aesthetic Surplus

Dr. Shah introduces the concept of “aesthetic surplus,” noting that many features in nature are far more beautiful and intricate than necessary for survival or reproduction. He argues that a purely “blind and random world should be tasteless.” The fact that the universe is characterized by breathtaking vistas, vibrant colors, and mathematical harmony (such as the Golden Ratio found in shells and galaxies) suggests a Creator who values beauty and intended for it to be perceived by conscious beings.

He writes about the “beauty of our planet” and the “glorious universe” as being deliberate signs (Ayat) intended to lead the human soul back to the Divine. For Shah, our ability to experience “Aesthetic Transcendence”—to be moved to awe by a sunset or a starry night—is proof that we are more than biological machines; we are spiritual beings created to recognize the “Most Beautiful Names” of God reflected in the material world.

Fireflies and the Sign of Design

Using the example of fireflies, Dr. Shah discusses how their bioluminescence is not just a biological function but a path to the Divine. He connects the “beauty in nature” directly to “guided evolution,” suggesting that the transition from a simple insect to one that can produce light in rhythmic patterns for communication is a feat of design. This beauty, he argues, is a “voice” of the Creator speaking through the medium of nature, inviting us to reflect on the purpose of our existence.

Phenomenon	Materialist Explanation	Dr. Shah’s Theological Reflection
Natural Beauty	Evolutionary accident or byproduct of signaling.	A deliberate “gift” from the Creator (Al-Jameel).
Mathematical Harmony	Coincidental result of physical laws.	Evidence of a “Pre-established Harmony” by the Architect.
Aesthetic Sense	Neural wiring for pattern recognition.	The soul’s innate capacity to perceive the Divine.
Cosmic Order	Result of the Big Bang and gravity.	The “Glorious” manifestation of God’s majesty (Al-Jalal).

Comparison and Contrast: Suleiman vs. Shah

The differences between Omer Suleiman and Dr. Zia H. Shah represent the two primary schools of thought in modern Islamic responses to evolution.

Conflict on Human Origins

The most stark contrast is found in their views on human common ancestry.

• Omer Suleiman maintains that the Quranic account of Adam is a “literal” and “miraculous” event that exempts humans from the evolutionary tree. He views any attempt to link humans to non-human ancestors as a theological error that undermines the special status of humanity.
• Dr. Zia H. Shah views human common ancestry as a “scientific fact” that the Quran does not contradict. He interprets the “clay” and “breathing of the soul” as metaphorical or spiritual descriptions of a biological process that took millions of years. He sees the “miracle” not as a break in the laws of nature, but as the sophisticated laws themselves.

Conflict on Methodology

Their approaches to “truth” also diverge significantly.

• Suleiman employs a “Revelation-First” methodology. He starts with the scriptural text and the tradition of the scholars, and he uses science as a secondary tool. If science appears to conflict with a central theological tenet (like the Adamic origin), he prioritizes the revelation and categorizes the scientific theory as “unproven” or “methodologically limited”.
• Shah employs a “Harmonization” methodology. He believes that true science and true revelation are both from God and cannot conflict. Therefore, if the scientific evidence for common ancestry is “fool-proof,” he looks for ways to interpret the scripture that accommodate this reality. He views nature as a “Secondary Revelation” that can help clarify the meaning of the Quranic text.

Common Ground

Despite these differences, both men are united in their rejection of atheism and materialism. Both agree that the universe is the result of a purposeful Creator. Both reject the idea that evolution is “blind” or “meaningless.” Furthermore, Suleiman’s acceptance of evolution in the non-human world creates a space where both thinkers could potentially agree on the mechanisms of biological change for 99% of life on Earth.

Technical Synthesis: Molecular Evolutionary Analysis

To further ground the discussion in scientific detail, we can examine the specific mechanisms of molecular evolution that Dr. Shah uses to support his “Guided” model. The concept of the “Molecular Clock” is central here. By comparing the mutations in the DNA of different species, scientists can estimate how long ago they shared a common ancestor.

T=2RD​

Where T is the time of divergence, D is the genetic distance (number of mutations), and R is the mutation rate. Dr. Shah argues that the mathematical consistency of these “clocks” across different parts of the genome (and their agreement with the fossil record) makes the reality of common ancestry undeniable.

Furthermore, he points to the “Integrated Genomic Ecosystem” as a way to understand how evolution is guided. In this view, the genome is not a static list of instructions but a dynamic system that can incorporate information from external sources like viruses. This process of “horizontal gene transfer” (even in mammals) allows for rapid leaps in complexity that would be impossible through slow, point-by-point mutations. For Dr. Shah, this is the “mechanism of guidance” that allows the Creator to introduce new forms and functions into the world.

The Argument from Beauty: A Deeper Philosophical Insight

Dr. Shah’s emphasis on beauty as a proof of God addresses a fundamental gap in modern scientific discourse. While science can explain the function of a rainbow (the refraction of light), it cannot explain why we perceive it as beautiful. Dr. Shah argues that this aesthetic experience is a “transcendent” moment that points to a reality beyond the material.

He contrasts a “blind” world—which would be efficient but utilitarian—with our actual world, which is filled with “unnecessary” beauty. This beauty is found in the “fireflies,” the “stars,” and the “form of every creature.” He posits that this aesthetic dimension of the universe is a “Path to God” that is accessible to everyone, regardless of their scientific training. For the scientifically trained, however, this beauty is magnified when they see the “molecular beauty” of the DNA code or the “mathematical beauty” of the laws of physics.

The Future of the Discourse: Implications for Islamic Thought

The debate between the perspectives of Suleiman and Shah has profound implications for the future of the Muslim community’s engagement with science.

The Educational Challenge

As more Muslim students enter fields like medicine and biotechnology, the “human ancestry” question becomes more pressing. Suleiman’s approach provides a “safe harbor” for those who wish to maintain traditional beliefs but can lead to cognitive dissonance when faced with genomic evidence. Shah’s approach provides a way to fully participate in modern science without losing faith, but it requires a more flexible and metaphorical approach to scriptural interpretation that some traditionalists find uncomfortable.

The Theological Synthesis

The integration of “viral creativity” and “aesthetic teleology” offered by Dr. Shah suggests a new direction for Islamic natural theology. It moves away from the “Intelligent Design” movement of the West (which often seeks to find “un-evolvable” gaps) and toward a “Theistic Evolution” that sees the entire process as a masterpiece of design. This shift allows for a more robust defense of the Creator in the age of molecular biology.

Theme	Omer Suleiman’s Core Insight	Dr. Zia H. Shah’s Core Insight
Origin of Species	Miracle-based for humans; process-based for others.	Entirely process-based and universally connected.
Role of Science	A limited tool for understanding the physical.	A divine window into the Creator’s methodology.
Human Nature	Defined by a singular, non-biological act.	Defined by a guided, long-term biological ascension.
Evidence of God	Found in revelation and the miracle of man.	Found in the molecular code, viruses, and natural beauty.

Deep Insights: The Genomic Script and the Divine Hand

An exhaustive analysis of Dr. Shah’s writings reveals a third-order insight: the genome as a “Divine Script” that is being continuously co-authored. In this view, the Creator did not just “set the world in motion” and walk away; rather, through the integration of HERVs and the guidance of mutations, the Creator is actively “sculpting” the biological world. This perspective elevates the status of viruses from “biological nuisances” to “divine tools” of innovation.

This aligns with Dr. Shah’s “Aesthetic Transcendence” because it suggests that the process of creation is just as beautiful as the product. The fact that our brains were built using ancient viral code is not a “dirty secret” of our past, but a stunning display of divine economy and creativity. It shows that God uses the “humble” (viruses) to create the “exalted” (the human mind).

Thematic Epilogue: The Convergent Paths of Truth

The journey through the evolutionary ontologies of Omer Suleiman and Dr. Zia H. Shah reveals a fundamental truth about the modern human condition: we are all seeking to find meaning in a world that is increasingly described by the cold, precise language of science. Suleiman’s work is a testament to the enduring power of the sacred narrative—a reminder that the human spirit is not something that can be easily reduced to a sequence of nucleotides. His defense of the “miracle of Adam” is a defense of the “miracle of being,” asserting that we are more than our DNA.

Dr. Shah’s work, on the other hand, is a bold exploration of the “sacred within the scientific.” He demonstrates that the DNA sequence itself is a miracle—a four-billion-year-old story of “Guided Evolution” that points to a Creator of infinite wisdom and artistry. By showing us the “viral architect” behind our placenta and the “aesthetic transcendence” within a firefly, he invites us to see the world as a unified whole where science and faith are not enemies, but two eyes through which we perceive the glory of the Divine.

Ultimately, whether one follows the traditionalist caution of Suleiman or the integrative vision of Shah, the goal remains the same: to recognize the “Signs” of the Creator in the universe and within ourselves. The “Book of Nature” and the “Book of Revelation” are both letters from the Divine; our task is to learn to read them together, finding in the “fool-proof evidence” of evolution a deeper reason to fall in prostration before the “Bestower of Forms”.

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Summary of Comparative Views

Feature	Omer Suleiman	Dr. Zia H. Shah
Human Common Ancestry	Rejects; maintains special creation of Adam.	Accepts; views it as scientifically “fool-proof.”
Evolution Mechanism	Accepts micro; skeptical of macro/totalizing Darwinism.	Advocates for “Guided Evolution” via genomic design.
Role of HERVs	Not central; likely viewed as incidental biological data.	Central; viewed as “Architects” of placenta and brain.
Origin of Adam	Literal clay, literal breath, literal miracle.	Metaphorical/Spiritual description of the arrival of consciousness.
Teleology/Purpose	Found in scriptural purpose and human vicegerency.	Found in “Aesthetic Transcendence” and molecular design.
Proof of God	Revelation, morality, and the human spirit.	Science, “Guided Evolution,” and the beauty of nature.
View of Viruses	Generally pathogens or biological footnotes.	Essential creative agents for evolutionary innovation.

In the final synthesis, Dr. Shah’s perspective offers a comprehensive biological framework that incorporates the latest findings in genetics and virology, while Suleiman provides a theological framework that emphasizes the spiritual boundaries of the Islamic tradition. Together, they represent the vibrant, ongoing effort of the Muslim intellectual community to navigate the “glorious” complexity of creation.