Atheism is Incoherent and Filled with Errors

Dennis Bonnette is a philosopher who has undertaken a rigorous critique of atheism and materialiam. The results of this critique have recently been published, and we are happy to bring you an excerpt from the first volume of this extensive critique, entitled, Atheistic Materialism’s Unseen Errors: A Catholic Philosopher Exposes Naturalism’s Incoherent Worldview.

Read excerpts from Book 2, Book 3, Book 4, Book 5 and Book 6.


Following Vatican Council II, most of the previously orthodox Catholic colleges and universities slowly abandoned their firm commitment to the Catholic intellectual heritage, especially by decreasing both the number and traditional content of required theology and philosophy courses—and even by changing theology courses into what they called “religious studies.” This tendency was especially evident in their failure to continue to teach the Thomistic philosophical sciences, such as Aristotelian logic, philosophical psychology, metaphysics, natural theology, and natural law ethics. Such courses were routinely replaced by far fewer ones, which were then taught using an historical method inherently inimical to the truth status of competing historical positions. This, in turn, has led to generations of otherwise educated Catholic college graduates who have little or no real understanding of the Church’s intellectual heritage, and especially, its unequalled contributions offered by the philosophy of St. Thomas Aquinas.

In 2022, my book, Rational Responses to Skepticism, a rather large volume (569 pages), was published—offering robust rational defenses of the philosophical foundations of authentic divine revelation, specifically as seen in Catholic doctrine. It also contains defenses of certain central revealed truths, such as the genuine scientific possibility of a literal Adam and Eve.

This present book, Atheistic Materialism’s Unseen Errors, is the first of a series of publications containing shorter portions of the much larger volume—each with themes coherent in themselves as subjects of independent investigation, and yet, still subordinate to the overall message of Rational Responses to Skepticism.

Atheistic Materialism’s Unseen Errors itself contains four chapters. Each was itself originally published online as an independent essay—making it easier for the reader to make complete sense of its content without reading the other three chapters or the entire large volume from which it came.

This shorter book shows many of the fundamental errors found in the widespread worldview known as scientific or atheistic materialism, a philosophical perspective that claims that nothing but physical things exist. It denies the existence of such a supernatural immaterial entity as the God of classical theism and reduces all matter to tiny particles or waves extended in space/time. It is often identified with philosophical naturalism.

This book will show with forceful logic many basic errors of materialism. For example, it will demonstrate that natural science itself assumes an observational method which contradicts its own conclusions—if you take materialism seriously. It also refutes the materialistic belief that animal sense experience can be explained in purely physical terms—since seeing sense objects as “wholes” simply does not comport with that model. It will also show that materialism, which assumes that all things are composed of tiny atoms, grossly violates our own experience of being one, single, existentially-unified thing. It will show that materialists use metaphysical first principles in an absolute way that contradicts their own assumption that such universal knowledge cannot exist.

Once certain basic errors of materialism are exposed, even the cherished doctrine of biological evolution turns out to be impossible in purely material terms. I speak here not from the perspective of some kind of religious fundamentalism, but rather in purely rational terms of how reality actually is constituted in ways that materialism fails to grasp.

Even many anti-evolutionists do not understand the distinction between the inadequate biological species concept and the philosophical natural species concept. This leads them often to attack evolution by trying to deny adaptive changes which actually have taken place. Solely a proper understanding of the philosophical natural species concept will permit us to understand that a genuine hierarchy of abilities distinguishes lower life forms from higher ones. When grasped, a proper understanding of how the organization of matter can be explained solely by new and higher life principles becomes evident. This explanation, which depends on seeing that truly existentially unified things exist above the atomic level, gives due credit to the higher principles of such unity that cannot be explained by the previous less perfect organization of matter in lower forms of life or even non-life. This analysis requires philosophical tools which are explained in depth within this chapter on evolution.

One can hardly overstate the importance of this explanation as to why purely materialistic evolution theories simply do not work. They are philosophically impossible. And, what is philosophically impossible is simply impossible. This means that the evolutionary theory of natural science is also impossible, since what is truly impossible is universally so.

Therefore, one of the most important chapters of this book is a full explanation of the impossibility of purely naturalistic biological evolution—an explanation originally presented by Australian philosopher and theologian Austin M. Woodbury. Readers of this book will then have access to this critically important information relatively unknown even to most philosophers, not to mention natural scientists.

There are many other areas where materialism—usually identified with naturalism—simply fails to describe the actual world in which we live. This book, Atheistic Materialism’s Unseen Errors, will give the reader a thorough grasp of the many rational inadequacies entailed within a purely physicalist or materialist philosophical worldview.

Atheistic Materialism’s Unseen Errors: A Catholic Philosopher Exposes Naturalism’s Incoherent Worldview

Assuming that vision is a purely material process, this causal chain of events necessarily implies that what we know, in the last analysis, is not the external object, but rather changes in the occipital lobe deep inside the brain. The immanent logic of scientific materialism forces the conclusion that what we actually know by empirical verification is not the external world at all, but some sort of presumed image or neural representation of it inside our heads.

Empirical verification presupposes epistemological realism—meaning that through sensation we know directly the exterior physical world around us. Natural science proclaims that it discovers the nature of the real physical cosmos, external to our brains or subjective selves. Yet, when we trace the optics and physiology of the sense of sight, we find ourselves entrapped in epistemological idealism–meaning that we do not know external reality, but rather merely some change within our brains that we hope to be an accurate representation of the external world.

Worse yet, naturalists tell us that modern science has discovered myriad ways in which the brain adjusts, fixes, completes, smooths, and modifies the incoming neural data so as to make the subjective sensation potentially quite different in content and meaning from that which the “raw data” of the external senses provide.

If we accept the foregoing depiction of visual sensation as correct, what does this imply for the “empirical verification” principle so dear to the hearts of naturalists? Specifically, how do we know that we have a head, a brain, an occipital lobe, light waves, or even an external physical world at all? The only way we have developed this scientific worldview of how sight works is by using our eyes to observe the component parts of the physiological/physical process entailed in vision. Someone had to use his eyes to view the brain of a cadaver and draw the pictures of a brain found in Gray’s Anatomy, or to verify that instrument readings are accurate. Yet, empirical observation using senses or instruments presupposes the validity of epistemological realism. Scientific findings about the visual chain of events, from external object to internal brain, drive the objective scientist into subjective idealism: we don’t directly sense the external world at all.

At this point, the naturalist likely resorts to defending epistemological realism by means of pragmatic verification: It works. Science has made massive progress through direct sense observation and repeatedly validates its theories through predictions that are empirically verified. Still, you simply cannot prove that the senses are reliable by using them in order to prove that they are reliable.

To verify scientific claims about the reliability of the senses, one must already trust them to apprehend external objects with sufficient accuracy so as to “empirically verify” the initial assumption that the senses apprehend external reality—the real physical world that natural science studies. Such circular reasoning proves nothing.

Another Materialist Fiasco: No Substantial Forms

As explained elsewhere on Strange Notions, scientific materialism’s “twin sister,” atomism (the claim that all reality is nothing but tiny physical particles) fails to explain a reality that few want to give up, namely, their own existence as living substantial unities. In a video on atheistic materialism, I showed that, according to the logic inherent in their own basic claims, atomists, such as Richard Dawkins, do not really exist. Atomism exists as a philosophy, but atomists don’t!

Combine oxygen and hydrogen and you get water. But are water molecules substantial unities, or not? Are they single things, distinct from everything else–or, are they still just oxygen and hydrogen atoms, temporarily sharing outer orbit electrons? If you say they are still separate atoms–just sharing electrons, that is what atomism implies.

Atomism maintains that nothing really exists above the atomic level (whatever ultimate physical particles these “atoms” may really be). That means that no macroscopic, substantially-unified things exist–not cockroaches, not kangaroos, not horses, and not human beings (including Dr. Dawkins). There may be amazingly-complex chemical bonding found in dynamic functional unities based on DNA rules (organisms), but none of it constitutes a substantial unity–a real being distinct from other things: just countless infinitesimal particles doing a cosmic dance with different sets of temporary partners.

But what if those hydrogen and oxygen atoms really form an existential bond creating a single substantial unity? What if sequoias and zebras and Dr. Dawkins really do exist? Then, what makes them one being?

Here Aristotle’s hylemorphism rescues materialists from the irrational consequences of their doctrine.

Hylemorphism recognizes the necessity of some unifying principle in macroscopic things. This necessary principle is called “substantial form”–an immaterial co-principle of material beings that makes them substantially one, puts them into a species, and accounts for how they act. Being one substance means that every bodily part shares the same substantial form. For human beings, the form of one’s stomach is not “stomach-ness,” but “human-ness.” The form of one’s big toe is not “big toe-ness,” but “human-ness.” The human substantial form, or soul (life principle), makes us one being by pervading every iota of our being that is truly “us.”

Some “parts” are not us, such as one’s intestinal flora or the hydrochloric acid in our stomachs. But, if one excluded every part of us reductively, there would be no “us” left to be human. So, whatever in us that is human shares the same immaterial substantial form (soul). If we lose a hand or foot, we are not less human, but there is a little less of us (quantitatively) to be human. Thus, form is present everywhere, and yet, physically is nowhere, since it is immaterial. Substantial form acts throughout the whole substance to make it be one single being of the same nature throughout its whole reality.

This brings up the question, if evolution means transforming from one species to another species, what is a “species?” Darwin was utterly confused by the question, since he desperately needed the concept of species to support his claimed “origin of species,” but conceived of evolution in terms of endless mere variations in accidental qualities–thereby undercutting the essential differences needed to render species distinct (Evolution and Other Fairy Tales, 168-72). His more recent disciples do no better. While some still insist on the extra-mental reality of species, the logical default position of mainstream evolutionists is nominalism, according to which “species” do not really exist, but are merely names we give to describe mid-ranges of ever-blending series of unique individuals.

Even the “punctuated equilibrium” hypothesis advocated by Niles Eldredge and Steven J. Gould does not embrace Goldschmidt’s “hopeful monster‘s” instant formation, but merely accelerates the transformation process by reducing it to thousands or even hundreds of years–far too rapid to be observed in the fossil record, but still gradualistic in nature.

Whether expressed in terms of cladistics, morphology, or reproductive isolation, the modern biological species concepts all share the same essential defect: they fail to detect essential differences between individuals in diverse “species.” All differences are expressed in terms of sensible accidents, such as configuration of spines, presence or absence of a backbone, ability to reproduce and produce fertile offspring, and so forth. Biological species concepts fail to express essential differences between species–thus undercutting the whole notion of true evolution from one species to another really distinct species.

Highly-respected biologist Ernst Mayr maintains that it is necessary to get past empirical terms, such as “phenotypic, morphological, genetic, phylogenetic, or biological” in order to get to the “underlying philosophical concepts” (The Species Problem, 1957, 17). The philosophical natural species concept is based on the reality of a metaphysical essence which is undetectable by modern biologists. Penetrating beyond sensible accidents, the philosophical natural species expresses essential properties (per se accidents), which are either present or absent. Living things are different from non-living, not merely in degree, but in kind. Animals possess sentient powers absent in vegetables. Human beings possess intellect and will lacking in merely sentient organisms. Since their essential properties differ, human beings, brute animals, and plants differ according to natural species and specific essence (Origin of the Human Species, 27-39).

Evolutionists and anti-evolutionists alike accept intra-specific evolution or micro-evolution, such as the bacteria that grow resistant to antibiotics or the English peppered moths that changed colors during the industrial revolution. But anti-evolutionists absolutely deny that inter-specific evolution or macro-evolution occurs, such as the fishes evolving into land animals. (Origin of the Human Species, 6-7.)

What confuses the issue is that these same anti-evolutionists usually adopt biological species concepts. This leads them to fight the battle in terms of attacking what might be merely variations within the same philosophical natural species. People do not easily conceive that a dog and an elephant actually belong to the same philosophical natural species because they share the same sentient powers even though their biological organization appears markedly diverse.

Darwinian evolution’s real test rests in its claim to climb the ladder of natural perfections through interaction of unaided matter. That is to say, can matter give rise to life, then to vegetative life, then to sentient life, and then to intellective life–all by itself? Does unaided evolution possess this self-perfecting capability? Or, does this process violate the basic metaphysical principle that the lower cannot give rise to the higher?

In Origin of the Human Species, I suggest that unaided material evolution might be possible, at least up to the appearance of true man, whose spiritual intellective soul demands creative intervention by God (Origin of the Human Species, 41-63,107-10). Now, I propose to show that even the initial stages of evolution from lower to higher natural philosophical species cannot be explained adequately merely in terms of purely physical agents. (I include the transition from non-life to life in the broad notion of “evolution,” since materialists presume this process, called “abiogenesis,” also happens naturalistically.)


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