God, Evolution and Darwinism

“It is beyond doubt that the Darwin was right! Evolution created us – not God.” exclaims the speaker. The packed lecture theatre nods in agreement. “Only ignorant people deny these scientific proofs!” as he concludes his full day presentation on Darwin’s theory of evolution. You have just been shown evidence from anatomy, fossils, embryology, genetics, bioinformatics and biogeography. Supposedly, these proofs are enough to undermine any faith that a rational person had in a creator.  

How would you react to this? 

Most would simply accept what they are told and just follow the crowd. No one wants to be the odd one out. The idea that Darwin’s theory is an unquestionable fact and that God doesn’t exist because of the discovery of evolution are popular. You will find these ideas repeated on social media, documentaries, best selling science books and even some well known celebrities pushing this narrative. All people, religious or not, should agree that accepting something without critically analyzing it is blind following, and that is not a good thing. 

By reading this article you will learn that there is a big difference between the public and academic understanding of the following three areas:

  1. Science leads to certainty 
  2. Darwin’s theory of Evolution is indisputable 
  3. Darwin’s theory of Evolution leads to Atheism

Popularly the statements above are true, however from a purely academic point of view these are false. We will deal with each one of these below. 

Claim 1: Science leads to certainty

Although there is a lot of philosophical discussion on what Science is, there is no clear agreement on a precise definition. Nonetheless a basic understanding is that scientists follow the steps below:

Identifying a problem 
Construct a hypothesis 
Testing the hypothesis by observation and experiment 
If the hypothesis fails, go back and amend the hypothesis or discard it and come up with a new hypothesis 
If it is successful, publish findings and get other scientists to test it (this is known as peer review)
If the peer review is successful the hypothesis is elevated to the status of a theory 

The end product of this scientific process is a theory, this is the highest level of certainty that science can achieve. A common misconception is that a scientific facts or laws are weightier than a theory, but that simply is not the case. 

Scientific theories include observations, facts, laws and sometimes mathematical proofs but it is theories that are the real end result of the scientific method. There is obviously more to science than what we have discussed so far, but this is enough to understand the basic elements of the scientific method. 

Scientific theories, no matter how successful, can still change because there can always be a new observation that can go against the previous conclusion. Consider a scientist who is trying to figure out what colour swans are and they spend 20 years travelling across the world and document thousands of swans all of which are white. They therefore make the conclusion ‘all swans are white’. One day they see a black swan. Their theory that all swans are white is therefore shown to be false. This Black Swan problem (formally known as the problem of induction) is well known within the philosophy of Science and it is the reason why philosophers accept that Science can not give us eternal truths. At any given moment the amount of knowledge scientists have is finite and there is an endless number of things they do not know. Believing this does not make one anti-science, it is just the way things are.

 Imagine how much progress we would make if scientists were not allowed to challenge past conclusions: there would be none. Science is not a collection of eternal truths and was never meant to be. Although the general public links Science to truth, philosophers of science do not. This is why many philosophy of Science books give people such warnings:

“Science is revisable. Hence, to talk of scientific ‘proof’ is dangerous, because the term fosters the idea of conclusions that are graven in stone.”

Philosophy of science

Someone may argue not all science changes as we know that fossils of dinosaurs exist, stars exist, water is H20, DNA is a code, and no future observation can undermine these hard facts. These facts are observations but they aren’t science or scientific facts. Something can be considered Science only when through the process of the scientific method observations are used to construct and test hypothesis and theories. Observations in off themselves are not Science, they are just simply, observations. Observations can be used to construct Science, but they can also be used to construct  pseudoscience.  For example the existence of stars can be used within the legitimate scientific field of astronomy.  It can also be used by ‘holy men’ to make predictions within the field of astrology. Science is much more than just observations. Therefore to claim observations are science would be a category mistake.  

Another way it can be claimed that we know Science is giving us truth is because it works. Many philosophers have worked hard to point out that it does not logically follow that just because something works, it is true. The phlogiston theory is an apt example to prove this point. Early chemists postulated the theory that within all combustible objects was a substance called phlogiston. When a combustible object burned, it would release phlogiston. The more combustible a material was, the more phlogiston it contained. The theory worked so well that in 1772 Dan Rutherford used it to explain the discovery of nitrogen. However, phlogiston was later found to be a false theory; phlogiston as a substance did not exist. Another example we get at the beginning of the 20th century, physics looked neat and tidy with its Newtonian model of the universe. No one had challenged it for over 200 years as it was working well and producing fantastic results. However, quantum mechanics and General Relativity shattered the Newtonian view of the world. Newtonian mechanics assumed time and space to be fixed entities, but Albert Einstein showed these were relative and dynamic. Eventually, after a period of upheaval General Relativity replaced the classical Newtonian model of the universe.  

These are some of many examples to show that a theory can work and produce astonishing results, and yet later to be found to be false. History of Science is littered with false theories that were once thought to be true because of their predictive success, interestingly as philosophers point out there are cases in which wrong aspects of wrong theories are responsible for novel predictive success. The lesson is obvious: just because something works, it does not mean it is true. This fact has been long recognised by philosophers and historians of Science:

Historically, there are many cases of theories that we now believe to be false but that were empirically quite successful.

History of science

Scientific U-turns do not care about who is sitting in the passenger seat. Even things which seemed obvious, undeniable and taken for granted can be overturned. Every aspect of science, and even the subtheories that make up the bigger theories in every field can revise their conclusions. The history of science has shown us this trend, so to speak of ‘scientific facts’ as immutable is not accurate. It is also impractical. All scientific theories are ‘work in progress’ and ‘approximate models’. If someone claims there is such a thing as absolute scientific truths, then how would they explain the fact that ‘quantum mechanics’ and ‘general relativity’, which are both accepted by physicists, contradict each other at a fundamental level? They both cannot be true in an absolute sense. Knowing this, physicists assume both to be working models and give neither the label of being absolutely true. The idea that ‘scientific facts’ are final is therefore misleading, impractical and dangerous for scientific progress. Historians and philosophers of science have been vocal in their opposition to use of such language.                                  

Some atheists mock religious scripture for its inability to represent the supposed ‘hard truths’ of Science. There are many online and offline discussions on science versus religious orthodoxy. However, in light of the discussion above, we have created a false dichotomy of religion versus science. It is not as simple as accepting one over the other. Science is the application of reason to the natural world. It seeks to understand how the world works. The Qur’an also refers to natural phenomena, and inevitably there have been times of convergence and conflicts between the Qur’an and Science. When a conflict does arise, there is no reason to claim the Quran is wrong. To do so would be to assume that scientific conclusions are true in an absolute sense and will not change; this is patently false. History has shown that science revises its conclusions, philosophy shows why it does so. Science does not give us truth rather it gifts us instrumentally useful theories.  

If Science conflicts with the Qur’an (after attempting to reconcile the two) it does not mean the Qur’an is wrong and nor does it mean that we should reject the Science. There are good independent arguments to justify the Qur’an’s claim of being God’s word (see the book The Eternal Challenge). So Muslims have reasons to believe what the Quran says is true. Muslims can accept the science that conflicts with the Quran (such as aspects of Darwinian evolution) as the current best-working model, but understand that it is not true in literal sense. Muslims can accept all prevailing scientific theories as working models and at the same time accept the Quran as being true. It is important to note that scientific knowledge and Divine revelation have two different sources. One is from the human limited mind, the other is from God. God has the picture, we have just a pixel of knowledge. Muslims can accept both Science and the Quran as sources of knowledge, however they would not give Science a heavier weight in terms of knowledge than the Quran when a conflict does arise because they have reasons to trust the Quran, and, they know that any scientific theory can be revised. 

Interestingly in the last century there was direct contradiction between the Qur’an and Science, and the Science changed to be in line with the Qur’an. Until the 1950s, all physicists, including Einstein, believed that the universe was eternal; all the data supported this, and this belief conflicted with the Qur’an. The Qur’an explicitly states that the universe had a beginning. Those who think science gives us eternal truth may have used this situation to say the Qur’an is wrong and therefore it can’t be God’s word. However, new observations using powerful advanced telescopes made physicists drop the ‘steady state’ model (eternal universe) and replace that with the Big Bang Model (universe with a beginning). So, science came into line with the Qur’an. Yet this does not mean that the Qur’an is a book of science nor has it ever claimed to be. It’s a book of signs. The Qur’an does not give any details concerning natural phenomena. Most of the things it refers to can be understood and verified with the naked eye. The main objective of the verses that point towards the natural world is to highlight God’s power, majesty and wisdom. Their role does not include elucidating scientific details. Science can change over time; however, the fact that natural phenomena have a power and wisdom behind them is a timeless reality. The upshot of all this is that the false dichotomy between the Qur’an and Science that some atheists posit does not work. Quran is not undermined by Science and neither do Muslims undermine Science even if it as times conflicts with their beliefs.

Claim 2: Darwin’s theory of Evolution is a fact

The image above of a line of ape like creatures progressively evolving into a human being is one of the most iconic images in the world, it is universally recognized and doesn’t even need any captions or translations, if you don’t know anything about evolution chances are you have seen this image on an advert and this is probably the way you believe evolution works. Popular as this image is, it is false! This is not the way evolution works, this is actually a misrepresentation of how the theory works. Biologists have long complained about how this popular view of evolutionary progress is simply wrong. Nature is the oldest and most prestigious science journal in the world. Henry Gee is a paleontologist, evolutionary biologist and the senior editor of the Nature. This is what he had to say about this iconic image: The idea of human evolution as a tale of inevitable progress is, however, a travesty, and has nothing much to do with Darwin. The bastardized view of evolution that’s become so much a part of the general consciousness – so much so that it’s so much low-hanging fruit for admen- owes much to Ernst Haeckel, Darwin’s number one fan in Germany.

How does it make it feel that something that most people believe about evolution is wrong? For one you may be feeling a bit curious about what else you thought you knew about evolution that is wrong. That’s good because that’s what this booklet is about,the aim is give you a paradigm shift in thinking about those things you took for granted. When you are done reading you will learn the significant difference between the way Darwinian Evolution is perceived by the public and the way it is actually understood by academics. On a public level Darwinian Evolution is as true as the fact that the earth goes round the Sun. However academically no biologist or philosopher of science would say this because there are no absolute truths in science. Rather they see it as a valid scientific theory which sits within a probabilistic framework, it has multiple assumptions and there still exists disputes about its core ideas. This isn’t the view of a few fringe biologists, all biologists and philosophers of Science would not deny that.      

It is important to note at this point that when you hear  the arguments like ‘97%  of scientists believe in evolution so it must be true ’, this is simply misleading. It’s true that they believe it, but we need to make clear what this belief is and what it is based upon. It does not mean they believe it to be absolutely true, it means they accept it as a valid scientific theory, that’s all. Even the most famous proponent of Darwinian Evolution today, Professor Richard Dawkins does not believe it to be absolutely true:

Darwin may be triumphant at the end of the twentieth century, but we must acknowledge the possibility that new facts may come to light which will force our successors of the twenty-first century to abandon Darwinism or modify it beyond recognition.

Professor Richard Dawkins

The academics referenced below are mainstream secular biologists and philosophers of Science. None of them believes in creationism, intelligent design or anything like that. It is important to highlight this as the impression that many people have is that only religious people criticize evolutionary theory. 

Evolution and Darwinism 

First thing we need to do is to make a distinction between evolution and Darwin’s theory of evolution also known as Darwinism or Neo Darwinism. On a public level these terms are thought to be the same, however academically they are not. So what is the difference? Evolution as a general concept means ‘biological change over time’. On the other hand Darwinian evolution has two parts, the history of life being represented by a tree, where all the organisms that have ever lived go back to one common origin and secondly that natural selection is the primary driving mechanism behind all this biological change.  

Evolution is a basic observation in nature, we can see it before our very eyes. This basic type of evolution is simply true, it is happening all around us, butterfly populations change biologically over time, bacteria evolve resistance to medicine, fish lose traits that are detrimental over time etc. No one disagrees with this type of biological evolution being ubiquitous and this was well known before Darwin. Even the most primitive human being who has had no interaction with the civilized world would agree that this evolution is an undeniable observation. Darwinian Evolution is way more than this basic observable evolution it claims that all of life evolved from a single cell and all the biological change happened primarily due to natural selection.   

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.  

Darwinian evolution is based on a probabilistic framework which has assumptions and importantly there are ongoing disputes and doubts about its central claims. 

Probabilistic Framework:

Working out the history of life on earth is a difficult task for two simple reasons. Firstly, we are talking about something that happened a very long time ago. Secondly, there is a worryingly 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. So whatever picture of the history of life and evolutionary developments that biologists try to make is going to involve probabilities, simplifications and speculations. To get a feel for this problem consider an analogy given in the prestigious scientific journal, Science. It compares working out the evolutionary history of human life to working out the plot of Leo Tolstoy’s War and Peace with thirteen randomly selected pages!  Tolstoy’s book is one of the largest literary pieces in the world. If you were given a copy with all the pages blank and only thirteen with writing on it, do you really think that you would be able to come up with an accurate rendition  of the major story details, let alone any semblance of details!  One can look at the possible evolutionary history of life on earth and come up with a number of  differing interpretations such as single origin of life or multiple origins of life, universal common ancestor or multiple common ancestors, gradualism or rapid biological changes, hedge of life or tree of life or bush of life or web of life, whatever interpretation you make can be challenged by another alternative one. Working out the history and development of life is an arduous task. It is impossible to give a definitive answer regarding this. Whatever answer is given today by biologists is at best still probabilistic but they can’t say for sure what happened and how it happened. 

The Tree of Life is a well recognized symbol of Darwinism. Darwin assumed all of all 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. You can’t open up any book on biology except that the famous Tree of Life is mentioned. Again on a popular level the tree of life is given to be true, yet within academia it is known as just a model. The tree of life is based on the idea of homology. Homology is the assumption that similarities between genes, anatomy and other traits are due to common descent. Once again in public perception homology is thought to be an indisputable conclusion whereas in fact it is only an assumption. 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. Homology as an assumption is challenged by homoplasy, homoplasy is the observation of similarities in genetic data and anatomy that can not be due to common descent. In other words, even when one builds a tree of life based on the assumption of homology, some similarities can never be due to common descent.   

Whether we look at the tree of life as a whole or two branches of species that are supposed to have a common ancestor, we are still dealing with probabilities based on assumptions not hard facts. In the Cambridge university publication ‘Evidence and Evolution, the logic behind the Science’ it explains:

Both of the following thoughts are therefore naive: humans and chimps must share a common ancestor because they are so similar and humans and mushrooms must have arisen independently because they are so different. There is no must within a probabilistic framework.

Evidence and Evolution, the logic behind the Science

Next we are going to look at some of the many assumptions that the probabilistic framework of Darwinism actually holds. 


There are a number of assumptions that Darwinian evolution is based on upon and many of these are being challenged by new evidence and new interpretations. Below we will cover three assumptions and how they are being challenged. 


Darwin assumed evolution takes place in small slight steps: ‘steady, slow, and continuous’. This assumption of gradualism is an essential part of Darwin’s theory. In fact Darwin made this a as a ‘falsification’ condition to his entire framework: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case”. Unbeknownst to the general public gradualism has always been controversial among paleontologists yet only in the last couple of decades did some of them come out in the open and express their doubts. Paleontologist Stephen J Gould explains the problem with this assumption: “The history of life is more adequately represented by a picture of ‘punctuated equilibria’ than by the notion of phyletic gradualism. The history of evolution is not one of stately unfolding, but a story of homeostatic equilibria, disturbed only ‘rarely’ (i.e. rather often in the fullness of time) by rapid and episodic events of speciation.” What Gould is saying here is that while we expect to see slow steady gradual changes in species, the fossil record shows the opposite, rapid changes in biological features. Gould was probably the most vocal public critic of gradualism, but since he came out many more biologists have challenged gradualism. 

Horizontal Gene Transfer 

Darwinism assumes that genes are only transmitted vertically meaning from parent to offspring. This assumption came under enormous pressure in recent years with the discovery of a process known as Horizontal Gene Transfer (HGT). This is when genes are passed horizontally between species. Initially HGT was assumed to be a minor component of the overall story, transferring only “optional extra” functions such as antibiotic resistance, core biological functions such as DNA replication and protein synthesis were still thought to be passed on vertically. Surprisingly this view was shown to be wrong, HGT was happening everywhere and is complicating the neat picture Darwinism was trying to paint. Commenting on the way process like HGT have strained the traditional simplistic view of Darwinism, Evolutionary Biologist Michael Rose comments: “The complexity of biology is comparable to quantum mechanics.” HGT caught the biological community off guard with some trying to desperately understand it within the Darwinian framework while others just realising that it’s not gonna work and we need a new approach. 


Darwinism assumes that the only reason for our existence is to selfishly care about our own ‘survival and reproduction’. This is the standard Darwinian view of Darwinists today and the first contemporaries of Darwin. Thomas Huxley (known infamously as Darwin’s bulldog) argued in Evolution and Ethics (1893) that “Life was a continual free fight’’ for ‘survival of the fittest’. Dawkins in a similar vein writes about our selfish genes: “They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence.” 

The obvious problem with this view that Huxley and those after him subscribed to is that human beings are ‘hopelessly addicted to altruism’. We care about others for their own sake and don’t always act in a selfish way. To try and fix this problem of ‘altruism’ two theories were put forward; Kin Selection and Reciprocal Altruism. Kin Selection is the evolutionary strategy that favours the reproductive success of an organism’s relatives, even at a cost to the organism’s own survival and reproduction. The reason for this is that our kin carry our genes, and it is our genes that we want to pass on even at the cost of our own life. The closer the kin, the more genes we share. Biologist J.B.S Haldane put it this way ‘’I would lay down my life for two brothers or eight cousins . Kin selection doesn’t explain why we care for non-kin.  Darwinists have tried to develop an answer for this too. The theory of ‘Reciprocal Altruism’ is invoked to explain why we care for others. This theory purports that we are beneficial to others because we know they will return the favor, you scratch my back and I’ll scratch yours. In other words as the Evolutionary Biologist George Williams puts it, morality is ‘’an accidental capability produced, in its boundless stupidity, by a biological process that is normally opposed to the expression of such a capability.’’ The problem with reciprocal altruism is that it doesn’t explain why many people give charity anonymously, why we have governments that collect taxes for hospitals to help the ‘survival of the unfittest’, why people care about animals, ancient buildings and are willing to die for their values and ideals. Philosopher of Science David Strove in his book Darwinian Fairytales challenges these darwinian explanations and argues that they are fundamentally at odds with our nature: ‘If you have made that uncomfortable bed, you will just have to lie in it. And one of its minor discomforts is this: that you will have to reconcile yourself to performing, all your life, that evasive trick of which Hume rightly complained. That is, of calling certain facts – namely the facts of human altruism – a ‘’problem’’ or a ‘’difficulty’’ for your theory, when anyone not utterly blinded by Darwinism can see that these facts are actually a demonstration of the falsity of your theory.’ Although the vast majority of biologists accept the selfish gene view, nonetheless selfishness as an assumption is being challenged by some biologists and philosophers because it contradicts our moral instincts. 

These are some of the assumptions that are being challenged by new evidence or new interpretations. The point of mentioning these assumptions and how they are being challenged is to show the changing nature of scientific ideas and that there is a live discussion going on. Although most biologists accept Darwinism assumptions, others are more critical like the Oxford biologist Denis Noble. He claims:

All the central assumptions of Neo-Darwinism have been disproven.

Denis Noble Oxford biologist

Noble’s view is rare amongst Biologists but the important point to takeaway is that academic criticism of darwinism exists. And this is what one would expect because in science nothing is set in stone. 


Another major issue against the idea that Darwinism is true is the existence of disputes within the theory at a conceptual and a philosophical level. 

Darwin’s central idea was that natural selection is the driving mechanism behind evolution. This was the main thesis of the origin of species. Natural Selection as a creative force is again one of those things the general public thinks of as an indisputable fact. It might come as quite a shock then, that it is not accepted as an immutable truth by all biologists.  It is in fact being disputed and challenged. 

Award winning Evolutionary Biologist Lynn Margulis explains: “This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.” Margulis  is one of many biologists who in recent years have been critical of the power of natural selection. In 2016 the oldest and most prestigious science society, the Royal Society of London, gathered influential evolutionary biologists from across the world to discuss this very problem. The biologists were split into two camps. One believed natural selection was, as Darwin said, the driving force of evolution. The other camp strongly disagreed. They went as far as to proposing alternatives that solved problems that Darwinism could not. Here are three of them:

Evolution by Natural Genetic Engineering (ENGS)

According to the standard darwinian theory the randomness of mutations is the clay that natural selection shapes into all sorts of novel species. Though this has been taught and retold in numerous popular publications and documentaries, some evolutionary theorists claim there is lack of evidence that random mutations can make anything useful. James Shapiro is one of the innovative biologists who is challenging this central pillar of Darwinism. Shapiro is using contemporary research in mutations to make a completely new evolutionary paradigm. In Evolution: A View from the 21st Century Shapiro explains why Evolution by Natural Genetic Engineering can be a  better model than Darwinian Evolution.   

Neo Lamarckian Evolution

Although Lamarck was ignored for a long time, in the last couple of years some biologists have started to look back at his ideas and have developed a revised theory known as Neo Lamarckian evolution. Darwinism assumes acquired characteristics can’t be inherited, the only thing that is inherited from the parents is their DNA which is fixed and any changes in their children is due to random mutations. So under this assumption if someone has a poor diet this doesn’t affect their DNA or their children. Proponents of Neo Lamarckism argue against this. They believe that one’s lifestyle does affect the expression of the DNA and their children directly. Neo Lamarckists cite recent studies to support their view. They propose not only that acquired characteristics can be inherited, but also that these drive some major evolutionary changes. 

Mutation Driven Evolution (Mutationism, neo Mutationism)

Mutationism assumes evolution is driven by large mutations not small incremental steps. This mechanism challenges the idea of Darwinian gradualism and natural selection as the main driving force behind evolutionary change. Although Mutationism was discarded decades ago, in recent years   

Evolutionary Biologist Masatoshi Nei proposes a rehashed version of Mutationism. Nei is a well known, respected and award winning scientist whose work is widely used in population genetics. His book Mutation Driven Evolution shows how developments in molecular biology are challenging the Darwinian predictions and how a new alternative can work. Nei vocally opposes Darwinian hegemony and the unquestionable faith that is placed in it: “Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant. But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books. You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.

It’s simply false to assume that all biologists agree with Darwinian evolution, the popular notion that only religiously scientists challenge darwinism is unfounded. In fact there is project set up by academics called ‘Third Way of Evolution’ in which biologists make it clear that they neither subscribe to Darwinism nor a religiously motivated alternative: “The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis. Many scientists today see the need for a deeper and more complete exploration of all aspects of the evolutionary process.Academics on the ‘Third Way of Evolution’ include biologists and philosophers from prestigious universities like Oxford, Cambridge, Princeton, MIT, Harvard amongst others. 

Clearly there is a valid disagreement in the biological community about the most fundamental parts of Darwin’s theory. This does not mean Darwinism is invalid or unscientific It is still the main scientific theory to explain biological change, and also the majority of biologists subscribe to it. Mentioning the disagreements above is done solely to show that Darwinism is not an eternal truth set in stone. Understanding the history and philosophy of science makes these disputes unsurprising. Indeed, difference of opinion is exactly what one would expect from Scientists as they are not supposed to take anything for granted.      

Darwinism has two main parts, a history of evolution (Tree of life) and a mechanism of evolution (Natural Selection). Both of these are interdependent. If the mechanism is inadequate, the history is directly challenged. Interestingly although on a public level the mechanism of natural selection is thought of as an immutable truth, academically it is well known that there major issues with it, as the biologist Gerd B. Müller explains: “A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution, indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike.” 

Darwinism may be perceived by the public to be true but this is indefensible academically. It is based on a probabilistic framework which has assumptions and there are disputes about its core ideas. Although it is a valid scientific theory, the claim that Darwinian evolution is absolutely true is patently false.                

Claim 3: Darwin’s theory of Evolution leads to Atheism

In The Blind watchmaker, which is one of the most popular evolutionary books, the Oxford Professor Richard Dawkins explains: Although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist. In another popular book ‘The God Delusion’ he similarly argues: “Darwin and his successors have shown how living creatures, with their spectacular statistical improbability and appearance of design, have evolved by slow, gradual degrees from simple beginnings. We can now safely say that the illusion of design in living creatures is just that – an illusion.” When an average person with no training in biology or philosophy reads these kinds of statements coming from a well known academic, they are likely to simply accept them. As social creatures we like to unquestionably accept what is given to us by those in authority.  Dawkins firmly links atheism and darwinism and he is not alone. Millions of people today believe that one leads to the other. Again there is a big gap between the public and the academic understanding of evolutionary science. Dawkins here is stating his personal views on evolution. These aren’t the findings of biology but his atheism coloring the biology. Most people mistake statements coming from scientists as scientific statements. This is of course not true.  A scientist may hold atheism, theism, agnosticism or any other worldview, and they should be careful not to mix their beliefs with science when talking to the public. There is nothing in Darwin’s theory that entails atheism or proves design is an illusion. Dawkins statements are a mixture of oil and water, good biology with bad theology. Philosopher of Biology Elliott Sober, although he is an atheist, gives the correct understanding between the intersection of God and Darwinism: “Theistic evolutionists can of course be deists, holding that God starts the universe in motion and then forever after declines to intervene. But there is no contradiction in their embracing a more active God whose postCreation interventions fly under the radar of evolutionary biology. Divine intervention isn‟t part of science, but the theory of evolution does not entail that none occur. This shouldn’t be a surprise if one understands how Science works. Science uses observations to create and test hypothesis and theories. God by definition is a Being who is unseen. Therefore, any direct observation of Him is impossible. Anyone that claims that God is disproven by anything in Science, whether it’s darwinian evolution or quantum mechanics is clearly mistaken. As Hugh Gauch, Philosopher of Science, explains that the idea that “science supports atheism is to get high marks for enthusiasm but low marks for logic.” Perhaps one of the reasons that people think that Science leads to atheism is because when scientists give explanations for phenomena, they don’t include God as a cause or an active agent, but this does not mean that God doesn’t exist. Mechanics can tell you how your car works. they can explain everything including fuel consumption, electrics, gearing system, braking mechanics, air conditioning and so on. While they are giving natural explanations of how the car works. Their explanation does not entail there is no designer of the car. Likewise Scientists only use natural explanations when they set out to give us accounts of how the world works. This is known as methodological naturalism. All scientists are methodological naturalists. This means they only refer to natural causes and natural effects. God is not allowed to be invoked in Science as per the rule of methodological naturalism. but that does not mean God does not exist. Evolutionary biologist Scott Todd highlights this point: ‘‘Even if all the data point to an intelligent designer, such an hypothesis is excluded from science because it is not naturalistic. Of course the scientist, as an individual, is free to embrace a reality that transcends naturalism.” On the other hand Philosophical naturalism is that idea that nature is all that exists and God does not exist. Methodological naturalism is not the same as Philosophical naturalism. The former does not entail the latter.  The confusion is when these two types of naturalism are conflated. People imagine that since scientists do not refer to God, God does not exist, which is a fallacious thinking. Philosopher of Science Massimo Pigliucci, although he is a proponent of atheism, explains this difference: “The fallacy lies in the fact that most people—including, alas, prominent science popularizers such as Richard Dawkins—do not make the subtle but crucial distinction between methodological and philosophical naturalism.” Pigliucci like other philosophers of Science conclude that Science does not demand any commitment to atheism. 

Although popularizers like Dawkins promote the idea that Darwinism somehow disproves God Darwin himself would have strongly disagreed! Darwin was never an atheist and it would come as a surprise to him that his theory is being used as an argument for God’s non existence, he wrote: “It seems to me absurd to doubt that a man may be an ardent Theist & an evolutionist.” Darwin began off as a Christian and then left that to become a deist. Deists hold that God exists but they don’t believe in any religion, miracles or life after death. Darwin remained a deist while he was writing his theory and even after he published the Origin of species he was a firm believer in God. In fact in his own autobiography he wrote that not only was it possible to accept fully evolution by natural selection and the existence of God, he also said explicitly that this was the position that he himself held. Later on in life he moved away from belief in God and became agnostic. This change was because of the problem of evil, an issue that always made him uncomfortable. He went through a lot of personal tragedies including the death of his beloved children. Nonetheless he still maintained that his theory did not undermine God. The connection between atheism and Darwin’s theory is a missing link, although popular its not something that can be academically justified. 

One of the arguments that some atheists try and make is that Darwin was actually an atheist (while pretending to be an agnostic) and he did believe that his theory lead to atheism. They argue that he softened his stance towards God and the implications of his theory due to public pressure. There are three problems with this argument. Firstly there is no evidence that he was an atheist, so this speculation is baseless. Darwin had already renounced Christianity publically and had argued that a literal reading of the Bible could not be correct.  So if he took these bold steps why would he hide his atheism? Since he already challenged a conservative victorian society, he had nothing to lose. In fact he publicly disagreed with those people who did use his theory to support atheism,. Secondly, even if he was an atheist and believed his theory leads to atheism, he would be wrong. The reason is that Science as mentioned before only deals with observables, so how can a theory based on observations of the natural world disprove the unobservable creator. 

Lastly, what we find in Darwin’s own personal writings is quite the opposite to what we should expect if he was an atheist. In a letter to his John Fordyce in 1879, just 3 years before his death he wrote: ‘’What my own views may be is a question of no consequence to any one except myself.— But as you ask, I may state that my judgment often fluctuates. Moreover whether a man deserves to be called a theist depends on the definition of the term: which is much too large a subject for a note. In my most extreme fluctuations I have never been an atheist in the sense of denying the existence of a God.— I think that generally (& more and more so as I grow older) but not always, that an agnostic would be the most correct description of my state of mind.’’

The upshot is that belief in God is not undermined by Darwinian evolution or any other theory in Science. Science itself does not have the capacity to challenge God. This statement is not anti scientific it is simply a matter of fact. In today’s world we benefit enormously from scientific achievements. Science has helped us live longer, more comfortably and enriched us with knowledge unknown to previous generations, so science and scientists are often venerated. However they should not be venerated to an extent that we subscribe to Scientism (excessive belief in the power of scientific knowledge). Science is great tool but it has limits and can not do everything. Science is based on upon mathematics and logic, these can not be proven by science as it depends on them to function. a2 + b2 = c2 is used in Scientific theories but Science can not tell us why this mathematical formula is the way it is, Science uses inductive and deductive logic but it can not explain how it is that logic works the way it does. Science can not tell us if giving charity is good or if kicking an animal is bad. Science can’t tell us anything about moral facts, aesthetic judgements, metaphysical truths, if historical figures existed or even what to do with scientific knowledge and if it is good to pursue science in the first place! Science also can not tell us why science works, you need philosophy for that. 

If we understand Science, how it works, its philosophy, it’s history we won’t fall into the mistake of thinking that science or any product of science such as darwinism can oust God. Understanding of the philosophy of science and of darwinian evolution shows us that the theory is not literally true, although it may be the best naturalistic  scientific account that we have at this time. 


There is a  difference between the academic and public understanding of Science in general and evolution specifically. The public might imagine that Science gives us truth, yet an academic understanding shows us that nothing in science is “set in stone.” Darwinian evolution as a product of science is not therefore, and never could be some sort of eternal truth. Philosophy of Science teaches us that we can always get a new novel observation which can challenge our previous theories and the history of science shows us that many successful theories turned out to be false. Darwin’s theory of evolution is a working model; a valid scientific theory, not a fact in the sense of being absolute, certain and unchangeable. Darwin’s theory is based on a probabilistic framework, which has assumptions and there are disputes about it’s core ideas. The popular idea that evolution undermines the existence of God is simply wrong. Science only deals with observable phenomena, God by definition is unobservable. Understanding  the philosophical foundations of Science is very important because that is how we get a clearer picture of what Science in fact can and can’t do. 

Atheists and agnostics should recognise that science does not and cannot negate God.  Not only does science not lead to atheism, atheism does not necessarily lead to Science. If someone is an atheist they may choose to or not to pursue scientific knowledge about the natural world. The Islamic tradition has historically been very open to scientific enquiry and for many was and still is a path the leads one closer to God which is rooted in the prime source of Islam, the Quran:

The revelation of this Book is from God—the Almighty, All-Wise. Surely in ˹the creation of˺ the heavens and the earth are signs for the believers. And in your own creation, and whatever living beings He dispersed, are signs for people of sure faith. And ˹in˺ the alternation of the day and the night, the provision sent down from the skies by God—reviving the earth after its death—and the shifting of the winds, are signs for people of understanding. These are God’s revelations which We recite to you in truth. So what message will they believe in after ˹denying˺ God and His revelations? The Quran 45:2-6

The purpose of life in Islam is to know God and through that knowing glorify, love and gladly accept the wisdom of Divine guidance into one’s life. Through deep thinking about God’s creation and studying it to benefit humanity one embarks upon a path of deep insights and profound understandings that engender a sense of gratitude, wonder and awe of the Creator that leaves the one immersed in it complete and filled with noble purpose.


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