There is an external world even though this is only believed on faith, whether it is realized or not, by all but a few. It is impossible for basic perceptions to come anywhere near the only logical proof that matter of any sort exists, yet absolute certainty of the existence of an external world is attainable [1], just not when it comes to whether the vast majority of one's sensory experiences pertain to anything beyond one's immaterial consciousness. Even ordinary sensory experiences, however, do not so much as hint at microscopic structures of matter like molecules and atoms, which cannot be observed with the unaided eye and thus are subject to epistemological limitations beyond those affecting almost the whole of sensory experiences. After all, at least one can look around and see buildings and rivers and vegetation, even if the sense of sight proves only that the perceptions exist. One cannot just suddenly look at an object and see its increasingly small particles.
All the same, even if there was no such thing as molecules or atoms or any material unit smaller than them, the entirety of science reduces down to the composition and behavior of physical matter, including how material things interact with immaterial things like consciousness (correlations between the various functions of the body and mental experiences are still somewhat scientific in nature although this transcends physics into broader metaphysics). Physics, in spite of all the limitations that prevent people from knowing whether hearsay or speculation about microscopic particles or even basic everyday sensory experiences are even accurate, can be known with absolute certainty to encompass everything physical. Even biological phenomena concerning the growth or nature of living tissue and cells are within the domain of physics, though this is connected with phenomenology in the case of all conscious but embodied creatures.
The living matter of a body is still a matter of physics and particle physics more specifically, the only core difference being that this matter belongs to a living being. Physics does not stand on other philosophical branches of science; chemistry, biology, geology, astronomy, and so on. No, it is these other branches that stand on physics, for all of them would only deal with various specific manifestations of physical matter. Of course, then there are other metaphysical existents that must exist prior to or more fundamentally than matter for there to even be a universe, great or small. There must be metaphysical space for matter to exist, and if matter is to be perceived, there must be consciousness to experience it, even if its perceptions cannot be proven to be accurate or illusions. More importantly, there is the uncaused cause without which a cosmos could not have existed (the universe having an eternal sequence of events, creating itself, or coming into existence uncaused are all logical impossibilities [2]), and then there are the necessary truths of logic that not only exist in the absence of all things and cannot not exist, but that dictate what is possible, so that it is only possible for a universe have existed at all because there is no logical contradiction in this.
One does not need to hear or think about various particles and organic chemicals, which, like most things in the perceived external world, cannot even be proven to exist beyond perceptions, in order to realize that there are many different logically possible forms for matter to take. When it comes to current scientific paradigms, there is posited to be an increasingly smaller and smaller set of particles, some of which are perhaps the final particles in their metaphysical chain: in other words, they would be fundamental/elementary particles that do not break down into smaller physical components, not that it is verifiable that they would be elementary. All of these fundamental particles, if there is such a thing (and as long as there is a fixed starting point at the macroscopic level, there might be a one-way infinite set of smaller and smaller particle types, much like how there could be a future set of infinite events, just not a past-eternal sequence or else the present moment and its events could never arrive), would be the true "building blocks" of matter, unlike atoms.
Despite the personal awe that the different scales of the universe can provoke, all of which can be triggered or savored by far more philosophically central or weighty things than the nature of particle physics, it is vital to realize that there is nothing particularly foundational about particle physics to the absolute core of reality except as it pertains to the smallest aspects of the external world, which is not the core of all things. It is the necessary truths of logic, the nature of morality (if obligations exist and not just preferences), and other aspects of metaphysics like the uncaused cause that underpin or transcend the material world altogether, and even on an epistemological level, the fact that things like the laws of logic and the uncaused cause are both absolutely certain, unlike the very existence of tables or fellow humans that one casually perceives in daily life. The universe, from the largest celestial objects like stars to the smallest subatomic particle, is incapable of having utter metaphysical and epistemological primacy, and it could not have been any other way.
Setting aside the fact that it is not by pure logical necessity that the universe exists in any form or that it is logically possible for there to be/have been fundamental particles, current scientific paradigms, though ultimately unverifiable, do entail a chain of physical structures and particles that contribute to macroscopic items. Living things with cells only add another level to this chain. Cells are made of proteins, which are themselves made of amino acids, which are composed of molecules, which are formed by atoms--which then reduce to a trio of subatomic particles, with neutrons and protons in a nucleus and electrons in orbit around the nucleus. Of the three particles at the next level below the atomic scale, two of them break down into even more miniscule particles called quarks, though quarks and electrons are seemingly elementary particles that are not divided into still smaller particles. Still, perhaps some sort of indirect evidence will surface suggesting that even particles like these are composed of even more miniscule subatomic particles.
There is already string theory, a proposed form of quantum physics where quarks and electrons are the smallest particles, and yet there are underlying "strings" of energy that these particles are made of. These strings would give rise to every unit of matter above it, literally forming matter out of the immaterial. Strings of energy that do not even have a physical form are indeed a logically possible thing, as paradoxical as it would be for matter to be sustained by quantum energy that itself is not made of matter. If string theory or this rendition of it is true, then not only is it already true by necessity that the laws of logic, the uncaused cause, and metaphysical space must exist apart from and prior to the universe in order for matter to exist, but the universe itself would reduce to the immaterial at the quantum level. The cosmos already relies on the nonphysical by default: if the existence of a universe was not logically possible, it could not have existed, the uncaused cause must create the universe or at least start a causal chain that leads to it, and then without metaphysical space (not the outer space with its stars and planets and nebulas, but the otherwise empty space that holds matter), there is nowhere for matter to exist.
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