Zubiri’s philosophical thought integrates twelve major elements:

• The panorama of the entire Western philosophical tradition from the Presocratics through Heidegger, Logical Positivism, and to some extent, the 20th century English schools of thought. Like Aristotle, Zubiri is constantly in dialogue with his predecessors.
• Aristotle and the tradition of classical philosophy (though subject to relentless critical analysis and rethinking). The gravity of Aristotle, as well as his encyclopedic vision and his understanding of the position of philosophy in the context of human knowledge, are particularly important in Zubiri’s thought.
• Insights from the work of the Phenomenologists in the 20th century. Though ultimately superseding them, Zubiri believes that there is a kernel of truth in their analysis of human experience which is essential to formulating a philosophy which takes account both of our undeniable perception of the world as real, our understanding of it through science, and the limitations of our intelligence.
• The overwhelming force of our direct perception of reality. For Zubiri, this is the salient characteristic of human intelligence and must be the starting point for any firmly grounded theory of the intelligence and any epistemology. Though not specifically discussed by Zubiri, the tradition of the great Spanish mystics and the characteristics of their knowledge, akin in some ways to direct experience of the world, must have been in the back of his mind.
• Scientific knowledge, and especially the insight science has given us into the structure of the natural world and our ability to know that world. Zubiri evinces a particularly keen interest in quantum mechanics and the revolution in physics which occurred in the early decades of this century. His interest extends to all the sciences, and he believes that the cracking of the genetic code has provided insights in the biological realm which are in some ways analogous to those achieved in physics.
• Modern logic and mathematics, especially Gödel’s theorem, and the new insights about mathematical truths and mathematical realities these developments have yielded.
• Nonscientific knowledge, specifically, the need to establish a foundation for it in a comprehensive philosophical system, and recognize its great and continuing contribution to the totality of knowledge. In what sense is a novel, a poem, or a painting about reality? Why do we say that an artist has "perceived essential truths"? Why does an artist create his works rather than just discourse about his subject?
• The relation of God to the physical world and to science and scientific knowledge, especially physics. Again, not explicitly discussed here, but dealt with at length in earlier works.
• Insights from Eastern philosophical/religious traditions, especially the Vedanta. Zubiri regards this as particularly important for understanding how philosophy began and why it emerged as different in the Western tradition.
• The fundamentally different reality of the person, as compared to ordinary physical realities.
• Results and insights from philology, especially Indo-European philology. Zubiri believes that those who first created our language and our words had a freshness and clarity of vision with respect to certain basic human experiences that later generations could not replicate.
• The Christian theological tradition, with equal emphasis on Eastern (Greek) and Western Fathers and theologians

In Naturaleza, Historia, Dios (first edition, 1942, ninth edition, 1987; English translation, 1981), Zubiri began to explore some of the ideas which later developed into his mature thought. These include: the idea of personhood as a unique type of reality; the relationship of God, nature, and scientific laws; and the notion of Logos as the form of explanation of things.

In a remarkable essay, "The Idea of Nature: the New Physics", written shortly after the development of quantum mechanics by Heisenberg and Schrödinger, Zubiri analyzes what this extremely radical break with classical physics truly signifies; in particular, he is interested in the meaning of the Uncertainty Principle and the emergence of purely statistical laws with respect to causality. He points out that the "classical" assumption, viz. that determinism is intimately linked with causality, if not indeed synonymous with it, and which has roots at least as early as Aristotle, is wrong. Rather, determinism is a type of causality, but not the only type. Physical laws are not about deterministic connections between events; rather, the laws are functional in form, and that functionality may be statistical. Does this have negative philosophical implications? No, according to Zubiri, because God is not some sort of superphysicist who created and regulates the universe by means of physical laws; these laws rather have an entirely human meaning. God, on the other hand, sees the universe in a creative vision. Moreover, for God, not only is there no physics, there is no nature in our sense, either.

In On Essence, Zubiri expounds his view of the importance and true nature of essences. Always in a dialogue with the history of philosophy, Zubiri begins by analyzing and criticizing the views of essence held by major figures in the past, including Aristotle, Leibniz, Hegel, Husserl and Heidegger. Because the notion of essence is particularly associated with Aristotle and the later traditions built upon him, especially Scholasticism, as well as the fact that Zubiri’s own ideas are best understood when contrasted with Aristotle’s, some discussion of them is in order.

Zubiri greatly broadened and deepened our understanding of essence, both in the logical as well as the physical sense. He reviews old concepts of essence, and rejects them all as insufficient, before proposing his own, founded upon the notion of system:

For Zubiri, it is the interrelationship of the notes making up essence which is important; each constitutive note is present by virtue of its place in constituting the whole. The notes are mutually dependent, and often lose their individual identity in the constituted system. Every reality is thus a systematic unity. This general discussion is in agreement with the modern scientific concept of things as dynamic systems, in which the interrelationship of the components makes the thing what it is, with its own behavior, different than that of its constituents and often obscuring them.

In light of Zubiri's discussion, it is apparent that old concepts of essence are not congruent with modern-day knowledge, in particular science, because they are what may be termed "flat", i.e., they assume that there is an absolute character of everything that can be captured by some act of the mind, usually unaided, on the basis of which we then "know" the thing. The primary example, of course, is the classical definition in terms of genus and species, as in "man is a rational animal"; though Hegel and Husserl immediately come to mind as well. Zubiri points out that all such concepts of essence are inadequate because they fail to capture its key physical property, that of structural complexity, from which emerge all of a thing’s properties or notes, including its dynamics. Behavior, such as we now understand it, from biological evolution to chaos, is of an entirely different, more subtle order than that envisioned by the creators of the old concepts of essence; and it involves layers of structure which point to a far richer and more complex reality than those concepts are capable of expressing. Indeed, it is unclear that essences can be adequately expressed at all in normal language.

The probing activity of science, through sketching of possibilities and use of experiment, may be the principal route to knowledge of essences, even though essence appears logically in primordial apprehension. Zubiri’s concept of essence is thus much more profound, but also much more difficult to achieve, than earlier conceptions of it. He notes,

This is true with respect to inanimate physical objects as well as biological organisms, where structure ultimately depends upon genotype:

With respect to Zubiri’s concept of essence and modern science, there are three key points: (a) the increasing focus on systems, hierarchically organized, as the object of scientific inquiry; (b) recognition of the exceeding complexity of nature and the complexity of behavior which things in it can exhibit; and (c) the recognition that there is no need to postulate ultimate realities "beyond" what is observed.

(a) Zubiri’s notion of essence concentrates on its system aspect, which is increasingly the focus of science as well, in part as a result of the recognition, at least in practical terms, of the impossibility of reductionism, and the corresponding recognition that knowledge about reality must proceed in different ways and with different methods and assumptions at different hierarchical levels. For example, the biologist or evolutionist use different assumptions and different boundary conditions than the particle physicist. Moreover, things higher in the hierarchy may possess entirely new properties, and because of the dynamics of the new composite systems, the properties of their component subsystems in isolation may fade or become invisible; as Zubiri has pointed out:

(b) There is also an implicit recognition of the great complexity of reality, built up of systems of systems of systems ... which does not permit anything to be captured, in isolation, in a curt formula or vision. Indeed, as we have learned over the past few decades, even simple dynamical systems can give rise to extremely complex behavior. Our awareness of the structural and behavioral complexity of biological organisms and higher levels of organization, such as ecosystems, is steadily increasing. Much has especially been learned from man-made complex systems, such as telecommunications systems. The architecture of such systems comprises a set of hierarchically organized layers, from electronic impulses at the bottom or "physical layer", though "bytes", "packets", "frames", "messages", up to applications such as electronic mail. An observer of such a system would see, depending upon his point of view, electronic impulses, or bits, or bytes, or packets, or frames, or complete electronic mail messages. And no such observer would be wrong; all of these entities are indeed present. The classical-type definitions of essence look at the highest layer only, even though the system comprises all layers; and while the system can be used without knowledge of the entire structure, it cannot be understood without that knowledge. Zubiri’s notion of essence is quite capable of dealing with this situation; earlier concepts, such as the correlate of a definition in terms of genus and species, are not.

(c) Finally, science does not look for some reality beyond the systems it examines; they are the reality at each level. For example, a society is a complex system with certain characteristics, some of which can be modeled mathematically. There is no "real" society lurking behind the system and giving rise to the observed properties. On the philosophical side, Zubiri has said the same:

Zubiri's concept of essence, then, is one which makes sense from both a philosophical and a scientific viewpoint. The task of the philosopher is not to try an end-run around science, and short-circuit the investigation of reality by propounding "true" essences obtained unaided through sheer intuition; rather, it is to understand how all of the diverse forms of knowledge fit together in an integrated whole, based in reality. If one likes, it is to deal with reality in the transcendental order, as opposed to the talitative order (bearing in mind that these two are not disjoint). There is no problem of two types of knowledge of reality, one through philosophical essence and another through scientific "essence", disconnected from it and based on entirely different principles, possibly leading to some new "dual truth" crisis such as arose in the Middle Ages. As Diego Gracia explains,

Zubiri also makes a critical distinction between natural things (e.g. a piece of wood) and meaning things (e.g. the same piece of wood functioning as a table). Natural things interact with us and the rest of the world through natural laws, e.g., gravity; but meaning things refer to the use we make of them.

A brief review of the major insights and innovations in Sentient Intelligence should help the reader understand just how radical is Zubiri’s rethinking of the major themes of philosophy:

• Recognizes the inseparability of the sensible and intellective aspects of human knowledge, the seat of which he terms sentient intelligence. The distinction between sensing and intellective knowing is not something immediately given in human apprehension, but belongs to the rational order.
• Creates a new definition of human intellection: "... mere actualization of the real in the sentient intelligence".
• Distinguishes the formality of reality (i.e., the aspect of reality delivered to us in an impression) from the content of reality of a thing.
• Establishes three stages or levels of human knowledge: reality, logos, and reason or ratio. Truth is ultimately grounded in the first, not the second and third, as has traditionally been assumed (this, in effect, is Zubiri’s "Copernican Revolution").
• Expands our conception of reality to encompass both reity (reality delivered in sensible apprehension, i.e., formality actualized in apprehension) and reality (reality "beyond" apprehension; traditionally the only meaning of the term). The latter is ultimately founded upon the former.
• Recognizes that while the senses (of which he identifies 11 rather than the usual 5) differ in content, it is with respect to their formality, i.e., the way in which they deliver reality to us, that the difference is most important. This implies that there are as many forms of actualization of reality as there are senses; but because the sentient intellection is indivisible, they correspond to different modes of intellective presentation of reality.
• Truth, in the most fundamental or primordial sense, is imposed upon us, through the force of reality, rather than being something we conquer (that applies rather to the derivative sense of truth in rational knowledge).
• A new definition of intelligence: not capability to process information, but actualizing things as de suyo.
• Recognition of human intelligence as something which is not flawed, but rather limited, and therefore subject to error while yet quite capable of apprehending reality and of truth.
• Distinguishes what he terms the talitative and transcendental orders within reality, the former having to do with the content of things (primarily the focus of science), and the latter their formality of reality (primarily the focus of metaphysics).

There is a sense in which the wellspring of this work is Zubiri’s deep reflection on the limitations of human knowledge, as disclosed in our daily experience, as well as through the scientific and mathematical discoveries of the 20th century. He wishes to make sense of the fact that reality is delivered to us not just in sensible apprehension, but through a wide range of sources with roots in the third or rational stage of intellection: history, art, literature, poetry, theology, as well as science and mathematics. His insight is that while human intelligence is not fundamentally flawed, and therefore is capable of truth, it is fundamentally limited, in ways not realized prior to this century because the pretensions of what he terms ‘rational knowledge’ were not recognized.

Of course, the fact that the human mind is finite has been recognized since classical times; but there is a subtle but important distinction between finite and limited, with respect to knowledge. Traditionally, ‘finite’ has been taken to mean some type of scaled-down version. This has contributed significantly to a belief in the exact determinism of nature, for example, because it has been assumed that we perceive the world in some way analogous to the way in which God perceives it, and thus any indeterminism in that world would imply that God is not omniscient. For Zubiri, this is an example of what he terms "logification of intellection". And in fact, it has led to a serious of unresolvable problems, from the famous paradox, "Can God make a stone so heavy that he cannot lift it?", to the collision of determinism and free will; and even within science itself to difficulties with infinite values for physical quantities such as entropy. It has also led to a variety of other problems with classical metaphysics that are discussed below.

In their own ways, both science and mathematics were compelled to abandon this belief in the twentieth century: science through the development of quantum mechanics and the Uncertainty Principle, which affirmed that exact measurement of sets of physical quantities is impossible; and mathematics through the work of Gödel, which demonstrated that all of mathematics cannot be viewed as strict logical deduction from a small number of self-evident axioms which, presumably, corresponded to eternal verities in the Divine mind.

Zubiri also seems to have been impressed by how knowledge changes for one person over the course of that person’s life. We are all familiar with how our own perception of the world evolved, from youngster to adolescent, and through the stages of adulthood. Just as remarkable is how particular experiences can change our perception and understanding, often leading to "paradigm shifts" which elevate us to a new plane of understanding. Even larger changes have occurred over historical time intervals: our perception of the world is considerably different from that of Renaissance, and radically different from that of the Bronze Age, for example.

Of perhaps even greater interest to Zubiri is the fact that our perception is intimately linked to our physical structures. He uses the example of the crab, which apparently does not perceive "rock" and "prey" and then "prey on rock", but just "rock-prey". Zubiri believes that our own perception of the world, though incomparably richer, is still limited in an analogous way, and is fundamentally different than the way God perceives the world.

He also acknowledges, of course, that the senses can at times do strange things. A well-known example is our perception of the sun’s disc: it appears much larger when near the horizon than at the meridian, even though the angular size subtended on the retina is the same in both cases. Sorting out the complexities of this problem, without falling into skepticism, requires an extremely sophisticated analysis of intelligence, such as that provided by Zubiri. The fact that the senses are capable of error does not mean that they are incapable of truth. To understand this, however, requires a careful distinction between primordial apprehension and the ulterior modes of intellection. That subject is discussed below.

Zubiri seeks to radically reestablish the basis for human knowledge. This task goes far beyond any type of Kantian critique—something which Zubiri believes can only come after we have analyzed what human knowledge is. The fundamental nature of human intellection, according to Zubiri, can be stated quite simply: "actualization of the real in the sentient intellection". If the act of "human apprehension", at once sentient and intellective, is referred to as nous, then in accordance with tradition three moments may be distinguished in it:

Intellection or noetic

Reality or noematic

Force of imposition of actualization (religation) or noergic

Zubiri reconceptualizes these moments, however, and they appear as affection, otherness, and force of imposition, respectively. But understanding their full meaning and that of Zubiri’s formula, and consequently the way in which this analysis reestablishes the basis of human knowledge, is a difficult task.

The first step is to analyze human intelligence in its fullness. This inevitably involves a concept of reality:

Zubiri’s point of departure is the immediacy and sense of direct contact with reality that we experience in our perception of the world; the things we perceive: colors, sounds, sights, are real in some extremely fundamental sense that cannot be overridden by subsequent reasoning or analysis. That is, there is associated with perception an overwhelming impression of its veracity, a type of "guarantee" which accompanies it, that says to us, "What you apprehend is reality, not a cinema, not a dream." Implied here two separate aspects of perception: first, what the apprehension is of, e.g. a tree or a piece of green paper, and second, its self-guaranteeing characteristic of reality. Zubiri terms these content and formality of reality, respectively.

Zubiri begins his analysis by dividing human intelligence into three modes or phases:

• Primordial apprehension of reality (or basic, direct installation in reality, giving us pure and simple reality)
• Logos (explanation of what something is vis à vis other things, or what the real of primordial apprehension is in reality)
• Reason (or ratio, methodological explanation of what things are and why they are, as in done in science, for example)

This process, whose three phases unfold logically if not chronologically in sequence, is mediated by what Zubiri calls the ‘field’ of reality. The reality field concept is loosely based on the field concept from physics, such as the gravitational field, where a body exists "by itself", so to speak; but also by virtue of its existence, creates a field around itself through which it interacts with other bodies. Thus in the field of reality, a thing has an individual moment and a field moment. The individual moment Zubiri refers to as the thing existing "by itself" or "of itself"; de suyo is the technical term he employs. The "field moment" is called just that.

Roughly speaking, primordial apprehension installs us in reality and delivers things to us in their individual and field moments; logos deals with things in the field, how they relate to each other; and reason tells us what they are in the sense of methodological explanation. This is illustrated in Figure 1.

Knowing, in the logos stage of intellection, is primarily concerned with relating what a thing, apprehended as real in primordial intellection, is in relation to other things. This is in the sense of knowing that a certain perceived color is "green", or that a perceived object is a "tree" and not a bush or a man. As Zubiri puts it, the logos is what enables us to know what a thing, apprehended as real in sentient intellection, is in reality (a technical term, meaning what something is in relation to one’s other knowledge). This intellection has three characteristics:

• Intellectively knowing what a real thing is in reality, based upon another thing or things apprehended by stepping back (or at a distance).
• Intellectively knowing what a real thing is in reality by going from the real thing to other things of the field. This is the first phase of the dynamic movement of intellection.
• Intellectively knowing, in a movement of reversion or intentum from "the" field toward a thing, not what it "might be" but what it "is" in reality, i.e., affirmation. This is the second phase of the dynamic movement of intellection.

Truth in logos is referred to as "dual truth", to contrast it with the real or simple truth of primordial apprehension. The process of understanding through logos is summarized diagrammatically in Figure 3.

The third level of intellection, ratio or reason—with the broad acceptation of explanation—encompasses far more than what is usually associated with this word in English-speaking countries, viz. knowledge. In particular, knowledge is not just science, nor even principally science. There are other modes of knowledge, for example poetic knowledge and religious knowledge, which fall under the scope of reason as Zubiri understands it. Correlatively, there are realities which are not things in the sense of objects of science; for example, there is the reality of the person. The distinction between the mode of intellection associated with logos and that associated with reason is straightforward:

Zubiri’s ideas here are perhaps born of the 20th century realization that empirical science as an enterprise has limits not dreamt of in the 18th or 19th centuries. As John Templeton puts it,

The limits in question we know as a result of the development of quantum mechanics early in the century and later chaos theory. What these developments tell us is that while unaided reason has hard limits in respect to how far it can penetrate the secrets of the world (in contrast to what classical philosophy and the Continental Rationalists thought), the new language of mathematics used by modern science, though capable of penetrating much further, also has fundamental limits. As mentioned earlier, science is ultimately a human form of knowing, and not the way God understands the universe. There is, indeed, no need for recourse to a "God of the gaps" in scientific knowledge. The limitations to what we can know about the universe, through science, are a reflection of our finite nature. Other types of intellection are possible and can tell us other things. Science and philosophy are, however, the primary sources of our knowledge of the world "beyond".

Reason, for Zubiri, does not consist in going to reality, but in going from field reality toward worldly reality, toward field reality in depth. If one likes, the field is the system of the sensed real, and the world, the object of reason, is the system of the real as a form of reality. That is, the whole world of the rationally intellectively known is the unique and true explanation of field reality.

In Zubiri’s word’s, reason is "measurant intellection of the real in depth". There are two moments of reason to be distinguished here: (1) intellection in depth, e.g., in the example cited above, electromagnetic theory is intellection in depth of color; (2) its character as measuring, in the most general sense, akin to the notion of measure in advanced mathematics (functional analysis). For example, prior to the twentieth century, material things were assimilated to the notion of "body"; that was the measure of all material things. But with the development of quantum mechanics, a new conception of material things was forced upon science, one which is different than the traditional notion of "body". The canon of real things was thus enlarged, so that the measure of something is no longer necesarily that of "body". (Zubiri himself will go on to enlarge it further, pointing out that personhood is another type of reality distinct from "body" or other material things). There is, in addition, a third moment, reason as intellectus quaerens, which means that reason, with is dynamic, directional, and provisional structure, is only able to conquer things in a provisional manner. But provisional only in the sense that our intellection cannot conquer all of reality, or all of any given thing; reality is too rich for our finite minds. This situation is there positive in a radical way: "Reason is the intellection in which in-depth reality is actualized in a problematic way, which therefore sends us forth to inquire about the real in the deepest way, with respect to principles and canon."

There are, for Zubiri, three modes of the moment of reality in impression, which correspond to the modes of intellection we possess:

• Primary and radical: in primordial apprehension, we have reality as mere otherness of what is sensed as de suyo; this is reality as formality.
• Moment of the "toward": In logos, reality is a medium in which we intellectively know what is of the field. This is not formality, but mediality.
• Transfield moment: In reason, reality is not just a medium of intellection, but an in-depth fundament which mediates the simple reality of the real. It is not formality or mediality, but measure.

Reason, as ultimately based on primordial apprehension and logos, is sentient. It can be defined as the measuring modulation of the impression of reality. There is a parallel between field intellection, where each real thing is intellectively known based on others, and rational intellection, where each explanation is intellectively known based on others. The excedence of reason is illustrated in Figure 5.

Openness is a key concept in the book, since Zubiri believes that reality is fundamentally open, and therefore not capturable in any human formula. This openness is intimately related to transcendentality:

For Zubiri, the fundamental or constitutive openness of reality means that the search for it is a never-ending quest; he believes that the development of quantum mechanics in the 20th century has been an example of how our concept of reality has broadened. The same is true with respect to the concept of person:

Zubiri’s views on the reality of mathematical objects and what happens in the process of doing mathematics may help to clarify his thought and at the same time the radical nature of his approach. As is well known, a great deal of mathematics involves assuming or postulating the existence of objects, for example pi, e, the solution of a differential equation meeting existence and uniqueness criteria, Hilbert spaces, Banach spaces, optimal solutions, and so forth. In many cases, the objects so postulated or assumed cannot be explicitly constructed. Most mathematicians, however, regard the postulated objects as real, and talk about them as if they were. For example, they postulate that the square roots of negative numbers exist, and call . Then, for example, the mathematicians demonstrate that .

For Zubiri, this act of postulation is the key operation in mathematics. The objects of mathematics are real, i.e. are objects in reality, the same reality as rocks and stars. This is because reality is formality, and objects of mathematics have it. What is different is the content of the objects. In the case of rocks, there is reality in and by itself, with content fully given. In the case of mathematical objects, the content is freely postulated, so the objects are postulatedly constrained in their content:

To describe the nature of the real by postulation, Zubiri distinguishes the real, the irreal, and the areal. The areal is what has no reality whatsoever. The irreal comes about when the content of reality is left suspended, or is postulated. This is what happens in the case of mathematical objects as well as in literature, when one speaks of a literary character such as Don Juan. Works of fiction arise from distancing and disrealizing, followed by recombination of notes.

Zubiri believes that Gödel’s theorem has a direct bearing on the reality of mathematical objects. Gödel’s famous result, on the incompleteness of formal systems, together with the development of quantum mechanics, represent two of the most significant intellectual developments of the twentieth century. Both of them have been carefully integrated by Zubiri into his thought and philosophy, which accordingly reflect the insights they bear. Zubiri’s interpretation of Gödel is that the content of postulated systems or postulated reality is richer than the original postulation. Or in other words, when reality is postulated in mathematics, the full reality of what is postulated exceeds the postulates in the sense that everything true about the postulated reality cannot be deduced logically from the postulates:

The relationship of normal and postulated reality is shown in Figure 6.

From Zubiri’s standpoint, however, the situation is entirely different:

This logification has led to quite erroneous ideas about reason. According to Zubiri, they are three: reason as organ of evidence about being, of speculative dialectic, and of total organization of experience. He remarks:

In light of the foregoing, Zubiri’s position vis-à-vis classical thought can be put into focus through an enumeration of some key problems of that tradition and his resolution of them. For convenience, the problems may be divided into philosophy of nature, metaphysics, and epistemology, although there is some overlap.

Philosophy of nature. (1) Natural place theory of motion: things move toward their "natural" place, e.g., stones toward the earth. We now know, of course, that things do not have a "natural place" in this sense, and that the idea was a pre-scientific way of explaining behavior such as gravitational attraction. Zubiri would say that motion of things is the result of forces acting which need to be analyzed scientifically. (2) Nature of motion: category of accident for substances. Zubiri points out that motion is relative to an observer, and therefore not a property of a thing in isolation. Moreover, there are some things for which motion is an essential part of their nature, and so cannot be considered "accidental", e.g., subatomic particles. (3) Structure of things: comprised of substantial form and matter. There are two points to Zubiri’s critique of this notion. First, things are made up of many variations (genetic in the case of living things) which can be quite significant, so one cannot speak of a "single" form, but only of stable structures. Second, real things usually have a layered architecture, indicating a structure much more complex than the substantial form theory suggests.

Metaphysics. (1) Reality as entities, or the identification of thing (res) with entity (ens), what Zubiri calls the "entification of reality". Zubiri believes that this causes serious problems because there are many things which are not entities in this sense, e.g. energy, entropy, and psychic realities such as colors and feelings. It also leads to theological problems when knowledge of God is assumed to proceed by analogy from finite things. (2) Substantial change: things lose their form, revert to prime matter, from which new substances arise, as in case of fire burning wood. Zubiri does not directly address this problem, but would argue that this whole paradigm is wrong: we now know that change does not occur in this manner—things may break down into primitive components such as amino acids, molecules, atoms, or even subatomic particles; but always something definite, unlike prime matter. Furthermore, in order to understand this situation, it is necessary to distinguish substantivity (a closed structure of notes) from substance. (3) Cause of motion: motion always requires a contiguous efficient cause. Scientifically, this is known to be incorrect; and Zubiri argues that motion is a characteristic of things in reality which may require a functional explanation (e.g. in terms of a scientific law), but not necessarily a metaphysical one. (4) Essence as what makes things be what they are. This was discussed at length above; Zubiri believes that classical thought was insufficiently radical on this point. (5) Causality implies determinism. This notion, stemming from Aristotle’s Posterior Analytics, is an example of what Zubiri terms "logification of intelligence": a logical notion, that of necessary connection between premises and conclusion of an argument, was applied to physical explanation, where its validity needed to be established empirically. In fact, determinism is a type of causality; but by no means the only type, as science was forced to acknowledge and deal with in the 20th century. Fortunately, the mathematical means to do so were at hand, in the form of probability theory and statistics.

Epistemology. (1) Essence as correlate of the definition. This is related to the previous point, and was also discussed above. Zubiri points out that the assumption that every essence can be defined in genus-species form, or even defined in words at all, is entirely gratuitous. With the exception of "Man is a rational animal", no such definitions were forthcoming from classical philosophy. (2) Knowledge through essences: no knowledge of singular things. Again, Zubiri argues that a radical interpretation of essence, as that which makes a thing what it is, means that the question of knowledge of species versus singular things is entirely irrelevant. (3) Causality as the basis of knowlege. Causality, defined as the "real productive influence of one thing on another", is never directly perceived by humans, and therefore cannot be the basis of knowledge. In practice, it is functionality rather than causality which is used as that basis.

The concept of being and the relationship of being and reality also Zubiri’s concept of deserves some comment. His concept of being is radically different than that of classical philosophy, or later European tradition. Since for him reality is the primary concept, being must be understood with reference to reality, rather than the other way around. Thus, being is actuality (not actuity) of the real in the world; a physical moment of actuality. Specifically, a real thing considered not as formally and constitutively real, but as actual reality in the world. This means that being is posterior to reality, since actuality is posterior to actuity. There is no esse real, only realitas in essendo.

Being does not pertain to reality as a formal moment, but to the real. When we intellectively know the real in and by itself, we know that it is being by being real. Being is an ulterior moment of primordial intellection, i.e., reality is sensed directly, but being is ulteriorly, indirectly sensed or co-sensed. The transcendental openness of the impression of reality which implies an impressive sensing of the real means that we should be sensing that it is being in the world, sensed being (obliqueness).

Being has the three structural moments explained above: actuality, ulteriority, and obliqueness. There are several subsidiary concepts. First is being of the affirmed, which is actuality of the real in the intellective world, in the world of the in reality. This expresses, in an oblique mode, that a realization is intellectively known, what a thing is in reality. It is actuality of the in reality in respectivity to the intellective world. Actuality is here affirmed with respect to what a real thing is as reality. The being of the affirmed is what is obliquely expressed with respect to what a thing is in reality; cf. being of the substantive, which is what is expressed in the primordial apprehension of being. Being of the affirmed is the site of the not-being, thus the answer to the classical problem of the being of not-being.

Second is being of the substantive. This is field and worldly actuality of the real, i.e., actuality of the real in the field and in the world (stemming from the actuality of something real in impressive intellection). The real apprehended in impression sends us to what is ulterior to it, to its being. It is ex-pression of what is in the im-pression of reality. This is the radical form of being.

Being is "of" the real, but is not the real itself. Being of the substantive is not substantial reality, but being of real substantivity. The being of the affirmed is not identical with the copulative "is", because not every affirmation is predication.

Zubiri stresses that intellective knowing is always of reality, not being:

With this background, it is natural that in Zubiri truth will have a different meaning than in classical (or any other) philosophy. The priority of reality is paramount; for Zubiri, truth is intellective actualization of the real qua intellective, in the sense that a thing is really that in accordance with which it has been actualized. He elaborates on the relationship between truth and reality:

Such an approach clearly shows the problems with two of the most famous theories of the past, those of Descartes and Kant:

Knowledge is more of a searching process than an accomplishment; but seen in the light of Zubiri’s breakdown of intellection, this takes on a new meaning. He remarks:

The notion of "judgment" is naturally different in Zubiri than in previous philosophy, due to the differences in Zubiri’s concepts of intelligence: