Epistemology, our understanding of how we arrive at knowledge about the world, and ontology, our understanding of what the world consists of, are intimately tied together. This is easy to see, and in the introductory part of this essay, I will describe this relationship between ontology and epistemology. If we consider our world to consist of material entities only, then what we need are methods of discovering these entities and making sure we reduce errors and insecurities in describing the nature of these material entities, how they are related, what they consist of, etc., to a minimum. Our scientific model of understanding the world has been very successful if we consider the progress we have made in understanding our natural world around us. This is partly due to the fact that this scientific model has originally restricted itself to understanding the material world. In order to arrive at reliable knowledge, the scientific epistemological model has started from the assumption that the material world consists of material particles only and has restricted itself to discovering the forces that act on these and the laws that govern these forces. This was, by and large, the success of the approach started by Galileo, Descartes, and Newton (Burtt, 1932; Descartes, 1954; Fischer, 2015; Maxwell, 2017). It operated on idealized material particles in mutual exchange of energy and their movements. The issue became more complicated with the advent of quantum physics, but with some rounding and assumptions, one can derive classical physics from quantum physics and can still use the general approach of classical physics to all macrophenomena, from chemistry to biology and neuroscience (Primas, 1981, 1994b).

This fruitful approach of science is based on observation of the external world and theoretical models of how these observations can be accounted for, as every observation is always dependent on a theoretical model we have of our world and the predictions such a model makes. This is known as the “theory-ladenness” of observations (Hanson, 1969/2018). With the progress of science, such models became ever more abstract and complex, making counterintuitive predictions, such as in quantum physics, defining specified realms of observation. Finally, it is always the observations that are the arbiter on the structure of reality. These observations happen originally through our senses and, in scientific observation, using enhancers such as telescopes of various kinds or microscopes, immunological or biochemical assays. All the same, these subtle enhancers are enhancers of our sense perceptions, mostly seeing, and they are directed toward material objects in the world outside. Since the time of Roger Bacon, i.e., since the 13th century, the experiment as an active manipulation of our objects of interest has been added to the epistemological arsenal (Crombie, 1953; Bacon, 1983, Bacon, 1998; Lindberg, 1992, 1997)¹. While in observation we purely observe, without intervening, natural developments and movement, for instance of stars, or plants and animals, in experimentation, we interfere with their normal dynamics. This is only possible for some of the subject matters of science. We cannot interfere with the movement of stars. But we can interfere with the life cycles of single plants, animals, cells, and meanwhile perhaps even with the evolution of our planet, and we can experiment with chemical substances in biological structures to develop and test pharmaceutical agents, etc. Nevertheless, experimenting is a kind of observation as well, only more directed and purposeful. As Francis Bacon, in the 16th century, said, echoing the tentative steps of his namesake of the 13th century, Roger Bacon (Bacon, 1859, Bacon, 1267/1897): If we direct observation purposefully, we call it experiment, if it happens by accident, we call it experience (Bacon, 1990, I.82).

The ontological assumption behind this is quite clear: What we observe is the material world outside, in contrast to the inner world of our dreams and phantasies. Thus, our observations refer to objects in the world, the nature outside. Therefore, the subject matter of science or the object of interest is nature, the world outside, and its constituents. For a long time, it was quite rational and useful to assume that this is constituted of material objects only or mostly because this is what we can see with our eyes. There might have been invisible things out there as well, such as spirits, ghosts, or suchlike things. But the progress of science and its associated program of ontological reduction has led us to believe that invisible things, if they exist, can always be traced and reduced to material objects or their reverberations (Agazzi (ed.), 1991; Primas, 1991; Dupré and Nicholson, 2018). Electromagnetic radiation would be a pertinent example. We cannot see electromagnetic radiation, except within the small window of visible light. If the wavelength is too long, there is only a small window where we can feel it as infrared radiation or warmth. If the wavelength is too short, we cannot even feel it, let alone see it. We, at most, feel the distant effects, when we suffer from sunburns, or even more distant effects such as genetic deviations that manifest as skin cancer. Other types of electromagnetic radiations, for instance the microwaves from mobile phones, we do neither see nor feel. But we do have a good theoretical model for these kinds of radiation, and this theory tells us that it is carried by minute particles, photons, that can be identified, even though they do not have a mass, by their effects. Their vibration frequency can be measured and various other aspects. Thus, we have succeeded in reducing invisible radiation to material entities. In the same vein, natural science starts from the assumption that everything that is there, worthwhile to discover, is in fact material in essence and hence can be seen, heard, felt, or smelled. Thus, the epistemological mode of science—to discover what is there in the world—is tied to its ontological assumption, which currently is: what is there to discover is in principle material in kind, or, if it is not material prima vista, it can be reduced to material entities.

It might be worthwhile to remind us of the fact that other ontologies lead to different epistemologies. If a society or culture believes, for instance, in the reality and importance of spiritual entities, it normally also develops methods and modes to experience them or, the other way around, develops ontologies in accord with their experiences. Indian shamans, for instance, believe that there are spiritual guides and plant spirits that can be contacted, and have devised rituals to make them experientially available or arrange for their services, for instance in the Ayahuasca ritual (Krippner and Sulla, 2000; Shanon, 2002; Ferrer, 2013, 2018). This is meant to contact plant spirits and other spirit guides to learn about potential healing strategies or other important things. Now, clearly, from our Western scientific point of view, these experiences are considered hallucinatory or imaginary, as we think that there is no outside referent here that can be addressed as a “spirit.” This is so because we start implicitly from the assumption that it is “all in the brain,” or more precisely, we implicitly start from a concept where mental phenomena and experiences are dependent on the brain, and they either have an outside referent, such as in sense experience, or else they are imaginary, as in dreams, or Ayahuasca experiences, for that matter.

Our traditional Western science, we already observed, is mainly directed toward the outside world. This has become a more and more materialistic enterprise, relying mainly on an empiricist model of epistemology trying to unravel those material entities in the outside world and their relationships. Thus, ontology reinforces epistemology, which in turn reinforces the underlying ontology. It will be useful to survey in this paragraph the history and systematic relationship of these two anchors of the modern scientific stance: materialist ontology and empiricist methodology.

At the beginning of University scholarship, in the 13th and 14th century, it was pretty clear that there are both material and spiritual entities in the world. Therefore, two different modes of experience were necessary, one directed to the outside world, experience as we know it, to learn about material entities, and one directed toward the inner world of experience to learn about the spiritual world, what we would today call first-person experience or inner experience. This has changed since. One important watershed was Roger Bacon’s Opus Majus, his sketch how he would envisage a future universal scholarly learning and university model (Bacon, 1267/1897; Power, 2012). He wrote this book at the request of the Pope, whom he knew personally from his previous position as papal legate for his home country, England, and sent it to him in 1267. In it he described how he envisaged a future universal scholarship. Such future scholarship was based, he held, on experience in general and employed mathematics and good knowledge of language, Latin of course as the lingua franca of Western scholarship, but also Hebrew and Greek. Importantly, he saw experience as bimodal². One part of experience, he said, was outward directed, toward the world and the senses and was the source of our general—philosophical, he said—knowledge of the world. The other part was an inner type of experience or spiritual experience. This he identified with the mystical path of inner purification and mystical union, which he had taken over from an earlier writer, Thomas Gallus, who had put together the Franciscan mystical path in a small book (Thomas Gallus, 1243/1503). It was the mode how our patriarchs, prophets, and forefathers had gained knowledge. This, he felt, is necessary to make sense of the other types of experience. It was also necessary for practical purposes of “guidance and political decisions.” Bacon’s Opus Majus existed only in three exemplars. One went to Rome and was buried in the Vatican library. The Pope had received it, but he probably never read it because he died shortly after having received the text. But Bacon’s text was copied from his own copy by some of his friar brethren of the Franciscan study house in Paris, where Bacon wrote it, and so made its way into the world. The Vatican copy was eventually discovered by Pico della Mirandola and made its way out into the world, where the younger Bacon, Francis Bacon, eventually got his ideas from Mandonnet (1910); Newbold (1921). A lot of what Francis Bacon, who was no relative of the older Bacon, teaches—all his teachings about the idols—he found in the older Bacon’s text, and a lot more, for instance the emphasis on experience and experiments.

But what had been lost for good until recently was the older Bacon’s emphasis on the two-pronged approach of experience, one inner and one outer mode. What was kept and nourished was “outer” experience or sense experience. This became the dominant mode of Western science, refined, aided by multiple tools and skills. But it was only half of Bacon’s notion of experience, nevertheless. This was probably a reflection of the rise of an implicit world model that relegated all non-material entities to domains other than science—to private philosophy and mysticism, religion, literature, poetry, and art. By the end of the 17th century, Descartes had paved the way for a separation of cultures. The culture of science was directed toward the outer, material world. The culture of philosophy and religion dealt with the mind, faith, beliefs, and invisible entities like mathematical truths. In the end, after the philosophers of the enlightenment movement had moved science forward as the modern enterprise that would set human minds free from ideological, dogmatic, and political bondage (Dupré, 2004), science and its epistemological mode had only the material world as its object. All other kinds of knowledge acquisition, philosophical reasoning or insight, were no longer considered scientific. After Kant philosophy tried to exercise its critical function, criticizing the cultural dominance of natural science, for instance when Husserl and later Heidegger wrote about the scientistic deviation of natural science, and in their wake, French constructivists and deconstructionists pointed out the social, political, and economic preconceptions that are always present (Heidegger, 1967; Husserl, 1909/1977; Foucault, 1974/1991).

From there, an important tradition arose that took up the strand of inner experience and thus also a different type of ontology, the tradition of phenomenology. It took its origin in the philosophy of Franz Brentano, who had set out explicitly to reform philosophy (Tiefensee, 1998; Binder, 2019). His idea of reform was to adapt the method of science, experience. This, for Brentano, was a systematic way of introspection or inner experience, using the terminology adapted here. Brentano’s most famous student was Edmund Husserl, who inspired the French tradition of phenomenology (Merleau-Ponty, 1966; Zahavi, 2003; Husserl, 1930/2009). This was, eventually, also connected back to neuroscience: Varela was the first to postulate a phenomenology of experience as a complement to neuroscientific methods (Varela et al., 1991). This has inspired a strand of research within neuroscience that calls itself contemplative neuroscience (Shear, 2007; Berkovich-Ohana et al., 2013; Dor-Ziderman et al., 2013; Jo et al., 2013, 2014, 2015; Lutz et al., 2015; Winter et al., 2020). This refers to a scientific model of experience, where neuroscientific methods, such as electroencephalogram (EEG), MRI, magnetoencephalogram (MEG), or others, are used to understand brain states or dynamics—experience of the outer world or third-person types of experience. As a complement, inner phenomenological accounts of the subjective experiences of research volunteers are collected and put into relationship with these brain states. Also inspired by the phenomenology of Husserl and Merleau-Ponty are modern revivals of systematic introspection (Petitmengin and Bitbol, 2009; Bitbol and Petitmengin, 2013). They are being used to understand experience directly, for instance as forerunners of epileptic fits (Petitmengin et al., 2007; Heinen, 2012) or as the direct experiential content of reality as such (Petitmengin, 2006, 2007; Petitmengin and Bitbol, 2009; Weger and Wagemann, 2015). This phenomenological tradition is a very important and rich new movement. It adopts a different epistemology and hence also leads to a different ontology (Varela, 1981a, b, 1984; Ferrer, 2018): There is no split between mental and physical phenomena because each statement about the outside world starts from lived, embodied experience. This, indirectly, illustrates my point: Epistemology and ontology are tied together. However, even phenomenology was unable to break the stride of current science toward rampant materialism, although it added important nuances and caveats.

What had been lost along the way was a viable concept of “mind” or “consciousness” that would be ontologically anchored and thereby support its own epistemological mode (Beckermann, 1989). Descartes’ dualism was philosophically problematic, as philosophers in his immediate temporal vicinity, such as Spinoza and Leibniz, had pointed out. But it was the starting point for exorcizing, ostracizing even, all things mental from the remit of natural science. The program of reduction of all biological things to machines and mechanical workings that Descartes had started with his Traité de l’Homme published posthumously in 1664 (Descartes, 1664/2003) surreptitiously also moved over to the mind when scientists started to consider the brain as the organ that produced the mind or, more radically even, as identical with the mind (Armstrong, 1968; Churchland, 1986, 1988). Even more radical, in modern times, some scientists considered the mind superfluous as an entity and thought it sufficient to understand the workings of the brain (Dennett, 1991). Never mind that this program of neuroreductionism, i.e., the assumption that a thorough neurological understanding of the processes in the brain would give us a full understanding of the workings of the mind, has not produced a satisfactory theory as yet and very likely will not do so for some time to come, and perhaps never (Hasler, 2015). The abstraction that only material things are really important is still very powerful, or put differently, the historical consequence of the process set into motion by Descartes, Newton, the enlightenment philosophers of France and England, and the historical success of the natural sciences has led to an implicit materialist ontology, not only of science itself but also of our whole scientific culture at large. This has spilled over into our popular culture, where rampant materialism in the way we are treating our planet and in the dominance of the capitalist economic model has become the mainstream.

This ontological model of materialism, even though only implicit in many fields, supports, consequently, the epistemological model of empiricism understood as the idea that we only need sense perception to learn about the world. Such scientists Baas van Fraassen has called “naturalistic natives” (van Fraassen, 2002, 2016) because they cannot even imagine that this is a very limited, flawed conception. Yet, it has become the dominant mode (Principe, 2016; Robinson, 2016; Williams and Robinson, 2016). It is associated, ontologically, with the idea that consciousness, or mind, is secondary to, dependent on, derived from, brain activity, or as stated above, only brain activity is necessary to understand the mind.

Conundrums, Paradoxes, and Empirical Anomalies of the Current Model