EVOLUTION
& DARWINISM
Flipping the Tree of Life:
Evolution as a Pathway to the Creator
DR. SALWA ELMAHDY
PROFESSOR OF PEDIATRICS
PREFACE
As a paediatrician, I’ve spent my career deeply engaged with the science of human development, and at the heart of that lies the study of genetics—a subject that constantly reveals the elegance, complexity, and precision of life. Day after day, I witness how the tiniest mutations in DNA can lead to profound effects on a child’s development. These experiences have never strengthened my belief in Darwin’s theory of evolution as a complete and adequate explanation for the origin of life—instead, they have compelled me to critically examine its assumptions and limitations. The mechanisms proposed by Darwin—primarily random mutation and natural selection—seem insufficient to account for the intricate, information-rich systems encoded within our genetic material.
Moreover, as a Muslim, my reflections go beyond scientific critique. Through deep contemplation of the Qur’an, I find that the creation and development of human beings is not left to chance or blind processes, but is described with profound clarity and purpose. The Qur’an presents a vision of life where every stage of creation is guided by divine wisdom, not randomness—where human beings are not mere accidents of evolution, but intentional creations with meaning and responsibility.
This booklet aims to clarify the distinction between “evolution” as an observable process within species, and “Darwinism” as a philosophical framework that attempts to explain the origin and diversification of all life without invoking purpose or design. Much confusion arises because these two meanings are often blurred in education and public discourse. As a result, Darwinian theory is often accepted as unquestionable fact, rather than the limited, materialistic hypothesis it truly is—especially in explaining the origin of complex biological structures or the unique nature of human consciousness.
In this work, I will explore the scientific limitations of Darwinism, and discuss how this theory contradicts the Islamic understanding of human origin. The Qur’an provides an alternative narrative—one that is not in conflict with genuine scientific inquiry, but rather calls the human mind to reflect on creation as a sign of the Creator.
My intention is not to reject science, but to free it from the confines of materialism, and to invite readers—both scientifically and spiritually inclined—to consider that the profound order, information, and beauty in life points beyond itself. It points to a Creator who brought it all into existence with purpose.
Let us, then, embark on this journey together: to examine the claims of Darwinism, to distinguish fact from philosophy, and to rediscover the harmony between reason, science, and revelation.
DEFINITION OF EVOLUTION:
Evolution as a general concept means ‘biological change over time.
Therefore, evolution is a process that results in changes in the genetic material of a population over time. Evolution reflects the adaptations of organisms to their changing environments and can result in altered genes and novel traits within the same species.
IS EVOLUTION A FACT?
According to the previous definition, yes. Evolution is a proven and observable fact.
Evolution occurred since the first life forms arose on Earth several billion years ago and is still occurring.
WHAT ARE THE EXAMPLES OF FACTUAL EVOLUTION?
There are many examples of factual evolution:
1- Bacteria developing antibiotic resistance: Antibiotic resistance occurs when bacteria evolve to evade the effect of antibiotics through multiple different mechanisms. As such, dissemination of antibiotic resistance genes is an ecological and public health concern. Other examples similar to antibiotic resistant bacteria include:
• Mosquitoes evolving resistance to DDT.
• Whiteflies evolving resistance to pesticide.
2- Finch birds: On various islands, finch species have famously evolved to have different beaks which are suited to different food types such as large seeds and invertebrates, allowing them to occupy different niches.
3- Selective breeding: People have been artificially selecting plants and animals for thousands of years. These activities have amounted to large, long-term, practical experiments that clearly demonstrate that species can evolve dramatically through selective breeding.
Selective breeding, also known as artificial selection, significantly affects the evolution of dogs. Breeders choose specific dogs with desired traits to reproduce, ensuring that these traits are passed on to the next generation. This process can lead to the development of new breeds over time.
Note in the previous examples that evolution occur within the same species (intraspecies). Bacteria, birds and dogs change some of their biological features but continue to be bacteria, birds and dogs respectively and do not change into different species.
4- Examples in human: Human traits that emerged recently include the ability to free-dive for long periods of time, adaptations for living in high altitudes where oxygen concentrations are low, resistance to contagious diseases (such as malaria), light skin, blue eyes,…etc.
Does this mean that Darwinism is a theory and a proven fact?
No. We need to make a distinction between Evolution as a fact, and Darwin’s theory of evolution, also known as Darwinism or Neo Darwinism.
So, what is the difference between factual evolution and Darwinism?
Darwinian evolution has two parts:
1- Tree of life: the history of life being represented by a tree, where all the organisms that have ever lived go back to one common origin, it claims that all of life evolved from a single cell.
2- Natural selection: As the primary driving mechanism behind all this biological change.
Neo-Darwinism is also known as the Modern Synthetic theory of evolution and is generally used to describe any integration of Charles Darwin's theory of evolution by natural selection with Gregor Mendel's theory of genetics. It states that evolution through natural selection acts on genetic variation such as DNA mutation and recombination.
Darwin defined evolution as "descent with modification," the idea that species change over time, give rise to new species, and share a common ancestor. The mechanism that Darwin proposed for evolution is natural selection. e.g.
• Fish → amphibian
• Reptile → bird
• Ape-like ancestor → human
Has this been proven? NO
Limitations of Darwin's Theory:
Under the weight of modern scientific evidence, Darwin’s theory of evolution is struggling.
Not directly observed: No one has ever witnessed or reproduced the transformation of one species into a completely different one in real time. Darwinian evolution is based on a probabilistic framework, which has assumptions, which have never been proved to be true.
Fossil record is incomplete:
Transitional forms are rare and often debated. There is a large set of data that is missing. Life has been around for about 4 billion years. 99.999 % of all things that ever lived are estimated to be extinct and undiscovered. No one was around billions of years ago to watch how one species lead to another distant one. Since we only have observed 0.0001% of life on earth any “tree” that is made to show genealogical relationships is tentative at best
Genetic limits: Many scientists argue that random mutations are insufficient to build entirely new biological systems.
Irreducible complexity of the cell: The cell is the functional unit of any living being. Actually the cell has a very complex structure.The adult human body is estimated to contain about 30 to 40 trillion (4×1013) human cells, every cell holds 42 million protein molecules, all its components must exit together at the same time for life to begin or exist, scientists reveal.
This means that the cells can't be built gradually, therefore there is nothing for the natural selection to select.
Although Darwin’s theory gained great acceptance throughout the scientific community but there was one area that Darwin did not even attempt to provide any kind of plausible explanation for – the origin of the first replicating cell. This was, and is, a very important piece of the puzzle; for if natural selection is to act, there must first be some type of replicating organism that natural selection can act upon.
The three major limitations of Darwin's theory concern the origin of DNA, the irreducible complexity of the cell, and the paucity of transitional species.
So, while variation within species is scientifically uncontroversial and Qur’ān-compatible, the idea that humans evolved from lower animals without divine intervention contradicts both revelation and reason.
To embrace the idea that all forms of life, great and small, plant and animal, primate and nonprimate, were derived from a common primordial cell or organism requires a scientific perspective. Rather than that, it remains a suspect theory for >150 years after the publication of The Origin of Species by Darwin (1859). The various religions, typically elevate humans above other forms of life. Most Homo sapiens believe that the different species on planet earth were created independently by a God, with the Homo sapiens inherently superior, thus, the resistance to the concept of evolution.
Summary table of factual (intraspecies) evolution versus Darwin's (Interspecies)
Type of Evolution Description Status Quranic Compatibility
Intraspecies (micro evolution) Small changes within a species
Observed
Compatible
Interspecies (macro evolution)
Darwinism Transformation from one species to another
Not observed
Contradicts Quranic view
Human from ape Key Darwinian claim
Refuted philo-sophically and theologically
Strongly incompatible
Is this confusion between the two kinds of evolution intentional?
Some confusion is innocent:
In schools and media: Evolution is often presented without distinction between the observable factual evolution and Darwin theory. Textbooks of biology and the media use evidence and examples of the first kind of evolution to speak about Darwin's theory as an indisputable fact, although the two forms of evolution are clearly very different.
Many people trust authority and assume that science is settled, so they adopt a simplified view. Although it is absolutely clear that there is a difference between evolution and Darwinism, the public thinks they are one and the same. This confusion is not inconsequential. This is because people conflate this apparent observable evolution with Darwinian Evolution. They think evidence for the former is evidence for the latter and this is simply not true. Darwinian evolution has the twin thesis of the tree of life and natural selection and these require evidence other than the basic observation of evolution itself. Clarifying this distinction is important. So one who claims they are the same and uses this to argue for the truth of Darwinian evolution is actually committing a fallacy of equivocation.
In this case, the confusion may be unintentional, caused by lack of deeper education or curiosity.
Confusion May Be Deliberate
Certain secularist thinkers (e.g. Richard Dawkins) use Darwinian Theory as a tool to argue that God is unnecessary. The theory is presented not just as science, but as a philosophical worldview—one that replaces belief in a Creator with naturalism.
This deliberate confusion can easily be found in many scientific journals and websites, as well as in the encyclopaedia and Wikipedia.
You can check the following links as examples:
1. https://en.wikipedia.org/wiki/Evolution_as_fact_and_theory: Evolution as fact and theory
2. https://www.livescience.com/474-controversy-evolution-works.html: What is Darwin's Theory of Evolution?
3. https://new.smm.org/evolution: Science museum of Minnesota, statement on evolution.
4. https://ncse.ngo/evolution-fact-and-theory: National center for science education, Evolution: Fact and Theory.
5. https://pmc.ncbi.nlm.nih.gov/articles/PMC6428117/#:~:text=Evolution%20is%20both%20a%20fact,as%20they%20change%20over%20time. National library of medicine, Science and evolution.
6. https://education.nationalgeographic.org/resource/theory-of-evolution/: National Geographic: Theory of Evolution
7. https://www.youtube.com/watch?v=Ya-JbO5Pgxi: Expelled:
No Intelligence Allowed: This is a documentary hosted by Ben Stein. It explores the claim that scientists and educators who support or are open to Intelligent Design (ID) face discrimination and censorship within academic and scientific institutions, especially in the U.S. The film argues that the scientific community has unfairly silenced any questioning of Darwinian evolution, and that this suppression limits academic freedom.
Stein interviews scientists, professors, and commentators—both supporters of ID and staunch evolutionists—and tries to link the dominance of Darwinian thinking to broader philosophical and even moral consequences.
What is the Impact on Public Understanding? The result is:
• Many people believe that “science has disproved God.”
• They think accepting evolution = rejecting creation,
When in fact:
• Belief in divine design does not deny natural mechanisms—it questions their origin and purpose.
• The Qur’an allows for stages and processes in creation.
So yes, the confusion helps promote a materialistic worldview, whether intentionally or not.
How to debunk Darwin theory of evolution?
That is simple!
Darwin assumed all of life came from one cell sometime in the remote past. Slowly and gradually there was branching out of different species in a tree like pattern through the process of natural selection.
His theory is based on the observation of similarities among living organisms, whereas the basic functional unit in all living organisms is the cell, with its structural components including the DNA, RNA, and proteins.
This observation is called Homology.
Darwin’s theory eventually gained great acceptance throughout the scientific community but there was one area that Darwin did not even attempt to provide any kind of plausible explanation for – the origin of the first replicating cell. This was, and is, a very important piece of the puzzle; for if natural selection is to act, there must first be some type of replicating organism that natural selection can act upon.
By flipping the conclusion taken from the observation of homology:
Similarities in the structure of the cell in all living organisms (e.g. genes, anatomy and other traits) are NOT due to common descent, BUT RATHER DUE TO ONE CREATOR
The very unity and hierarchical complexity seen in this tree may also suggest design, not randomness and blind natural selection.
Rather than disprove a Creator, perhaps the Tree of Life — with its underlying cellular and informational unity — can be reinterpreted as evidence of intelligent causation, and ultimately, a divine source.
The structure of the cell is a scientific proof of the existence and oneness of the Creator:
The Cell: A Universal Signature
At the molecular level, all life on Earth shares a striking commonality. Every organism — from bacteria to elephants and redwoods — is composed of cells built from the same set of molecules: DNA, RNA, proteins, lipids, and carbohydrates. The genetic code is nearly universal. Core processes such as transcription, translation, ATP production, and membrane transport are consistent across species.
Michael Denton, a biologist and author of Evolution:A theory in crisis, 1985 wrote: This high degree of unity in the architecture of life hints at design — not merely common ancestry. Rather than being evidence of accidental divergence, it may be seen as a signature of a Creator who employed a singular, elegant blueprint.
DNA is not just a molecule; it is a storage medium for complex instructions — akin to digital code. The informational content of the cell, points decisively back to an intelligent cause” (Intelligence in Biology, Stephen Meyer, 2009).
In this framework, the Tree of Life can be seen not as a chaotic result of random mutations, but as the outworking of a designed, information-rich system.
Purpose, Beauty, and Meaning in Life’s Design
Finally, a Creator-based interpretation of evolution restores meaning to biology. .” By reinterpreting the Tree of Life as the unfolding of a Creator’s logic, we do not discard science — we deepen its meaning.
The modern understanding of biology — with its deep cellular unity, information-rich systems, and elegant branching forms — may be one of the most compelling arguments for divine design. Evolution and the Tree of Life, when “flipped” philosophically, reveal not a purposeless process but a meaningful, intelligent unfolding of life. The Creator’s signature is not absent in nature; it is written into every cell, every strand of DNA, and every branch of the tree of life.
What does the Quraan tell us about human evolution?
The Qur'an repeatedly reminds us of the origin of human beings from soil or earth, a humble yet profound beginning. This motif is not merely symbolic—it offers a deeply reflective argument for the existence of a Creator.
“And among His signs is that He created you from dust; then, behold, you are human beings dispersing [throughout the earth].” (Ar-Rum 30: 20)
“Indeed, We created man from an extract of clay.” (Al-Mu’minun 23:12)
'And We did certainly create man out of clay from an altered black mud'. (Al-Hijr 15:26)
These verses point to a transformation that cannot be explained by randomness. From inanimate matter—dust, clay, soil—emerges a living, conscious, rational human being. This transformation is not just physical; it is metaphysical. How does non-living matter give rise to self-awareness, speech, moral understanding, creativity, and free will?
To claim this happened without design is like saying a library full of books wrote itself. The Qur’an invites us to reflect: How can something so complex, ordered, and intelligent emerge from something so base, without the intervention of a Supreme Intelligence?
From Earth to Human: A Journey of Purposeful Evolution
Discussion Prompt: Why does the Qur’an emphasize our earthly origin so often? What message does this convey about our identity and purpose?
Death and the Return to Earth: A Cycle with Meaning
“From it (the earth) We created you, and into it We will return you, and from it We will bring you forth once more.” (Taha 20: 55)
This cycle—creation from earth, dissolution back into it, and resurrection—mirrors the natural cycles we observe in life (seeds growing into trees and returning to dust), but applied to the miracle of human life. It points to a deliberate, cyclical system, a process under control, not chaos. It gives weight to the concept of purpose in our creation—not chance.
Do we have a scientific proof that humans were created from earth?
It’s true that science does not “prove” metaphysical claims like divine creation. However, science can point toward meaningful consistencies with such claims.
The Qur’an says humans were created from clay, soil, or dust—all forms of earth. Now here’s what we know scientifically:
The human body is made up of oxygen, carbon, hydrogen, nitrogen, calcium, phosphorus, potassium, sulphur, sodium, magnesium, and trace metals. These elements are abundant in the earth’s crust and soil.
Conclusion:
From a chemical perspective, the Qur’anic statement is scientifically sound: the building blocks of the human body are literally found in the earth.
When we die, do we literally turn back into soil?
Yes—biologically and chemically, we do. After death, the body decomposes through bacterial and enzymatic activity. Complex organic molecules break down into simpler compounds—carbon dioxide, water, ammonia, nitrogen, phosphorus.
These are reabsorbed into the soil, enriching it, and completing the cycle. The Qur’an says: “From it We created you, and into it We shall return you…” (20: 55) And that is exactly what happens.
👉 Literal return to the earth happens through decomposition. It’s not poetic—it’s a scientific reality. Science confirms that our bodies are made from the same ingredients as the earth, and that in death, we rejoin the earth.
The Qur’an revealed this over 1,400 years ago. But more profoundly, the Qur’an asks us to reflect on this cycle not just chemically, but existentially: Who designed this cycle? Who brought life from dust and made it speak, think, and love?
While science can analyse the ingredients, only philosophy and revelation can address the purpose. That’s where the Qur’anic message invites deeper contemplation—not just about how we were made, but why.
By reflecting on our emergence from soil, our life of consciousness, and our return to earth, the Qur’an leads us to the inescapable realization: There must be a Creator—One who began it all with wisdom, sustains it with knowledge, and will recreate it with power.
From Atoms to Galaxies: A Patterned Universe Points to a Creator
Striking similarities: The Atom and the Solar System
Feature Atom Solar system
Central core Nucleus (protons+neutrons) Sun/ Black hole
Orbiting bodies Electrons Planets/ Stars
Governed by laws Electromagnetic and quantum forces Gravity and relativity
Order and harmony Quantized, stable energy levels Predictable orbits and cosmic cycles
Despite the vast difference in scale, there’s a mirrored structure: Smallest matter unit (the atom), Largest observable system (galaxies) Both show motion around a central force — order, not chaos.
Why Does This Point to a Creator?
This patterned harmony across scales suggests:
Unity in design: The same principles repeat in micro and macro scales. Quran does not only give us clues to the origin of humans, but also to the whole universe, something that cannot be explained by the tree of life, whereas unity in design gives a proof of the unity of the creator.
Intelligence behind the laws: Why do particles and planets obey such precise motion?
No randomness: Chaos does not produce order unless guided by intention.
Qur’anic Connection:
The Creator of All Realms “He is the Creator of the heavens and the earth... Everything in the heavens and the earth glorifies Him.” (Qur’an 59:24)
“And He created everything and determined it with precise measurement.” (Qur’an 25:2)
“You do not see any disparity in the creation of Al-Rahman. So return your vision—do you see any flaw?” (Qur’an 67:3) The Qur’an calls us to observe the harmony, then ask: Who created this system? Who sustains it?
