fundamental level of existence in Buddhism

The description of science given is that of the Newtonian understanding of physics and chemistry. Scientists like Einstein, Bohr, Schrodinger, Feynman overturned this "mechanical" perspective.

For example, the "sequencing" of which you speak does not apply to the quantum level, where effects can precede cause. On the other side of the scale, in cosmology, time itself is not an independent entity, and past, present & future are completely dependent on the location and velocity of the observer and the observed (General theory of relativity).

Science does not "contain controversies". There are many questions that science currently does not have a theory for, primarily because we lack observational data. In this case, scientists will have no problem saying "we don't know (yet)". There is no shame or controversy in this.

As for the interchangeability of mass and energy, you must realize the amount of energy required to create matter is staggering and beyond human capacity to even imagine.

Science has made great strides in the field of neurology in the last decades. Quantum brain dynamics (QBD) is a recent hypothesis to explain the function of the brain within the framework of quantum field theory. Since quantum theory is the most fundamental theory of matter that is currently available, it is a legitimate question to ask whether quantum theory can help us to understand consciousness. Observations have identified quanta of long-range coherent waves within and between brain cells, and showed a possible mechanism of memory storage and retrieval in terms of Nambu–Goldstone bosons.

The implication is that subjective experiences of all kinds, including experiences of subtle energies, are secondary to, and derivative of, objective, physical processes.

Where science is based on objective observation, Buddhism is experiential. Vīrya (Sanskrit; Pāli: viriya) is a Buddhist term commonly translated as "energy", but it has nothing to do with the concept of energy in physics. To discuss the relation between the concept of energy in Buddhism versus physics, we must differentiate:

1. energy as a primary attribute of the objective, physical world,
2. energy as a secondary attribute of the subjective, sensory world, and
3. a nondual contemplative view of energy in the world of experience.

Many contemplative traditions of the world, including Buddhism, have sought to understand a unified world of experience, which includes a spectrum of subjective and objective phenomena, with no absolute division within this spectrum. Within this world of experience emerged the Greek concept of pneuma, Indian prana, Tibetan loong, Chinese qi, Japanese ki, and Native American mana in their respective medical traditions, all of which are supposedly present in the body and the environment at large.

In Buddhism, the energies coursing through the human body are investigated from a first-person perspective by first honing the attention by means of sophisticated contemplative training. Therefore, the Buddhist view has no objective, quantitative means of examining energy. And since we know that the quantum level very likely plays a role in the brain, the uncertainty principle & the observer effect virtually make it impossible for a contemplative discipline to make 100% accurate predictions and assertions.

The Buddha's focus was empirical and soteriological, not ontological or metaphysical, as evidenced by the following sutta quotes.

The Buddha was only interested in what would end suffering permanently.

The Parable of the Poisoned Arrow from Cula-Malunkyovada Sutta:

"It's just as if a man were wounded with an arrow thickly smeared with poison. His friends & companions, kinsmen & relatives would provide him with a surgeon, and the man would say, 'I won't have this arrow removed until I know whether the man who wounded me was a noble warrior, a brahman, a merchant, or a worker.' He would say, 'I won't have this arrow removed until I know the given name & clan name of the man who wounded me... until I know whether he was tall, medium, or short... until I know whether he was dark, ruddy-brown, or golden-colored... until I know his home village, town, or city... until I know whether the bow with which I was wounded was a long bow or a crossbow... until I know whether the bowstring with which I was wounded was fiber, bamboo threads, sinew, hemp, or bark... until I know whether the shaft with which I was wounded was wild or cultivated... until I know whether the feathers of the shaft with which I was wounded were those of a vulture, a stork, a hawk, a peac**k, or another bird... until I know whether the shaft with which I was wounded was bound with the sinew of an ox, a water buffalo, a langur, or a monkey.' He would say, 'I won't have this arrow removed until I know whether the shaft with which I was wounded was that of a common arrow, a curved arrow, a barbed, a calf-toothed, or an oleander arrow.' The man would die and those things would still remain unknown to him.

"In the same way, if anyone were to say, 'I won't live the holy life under the Blessed One as long as he does not declare to me that 'The cosmos is eternal,'... or that 'After death a Tathagata neither exists nor does not exist,' the man would die and those things would still remain undeclared by the Tathagata.

From Acintita Sutta:

"Conjecture about [the origin, etc., of] the world is an unconjecturable that is not to be conjectured about, that would bring madness & vexation to anyone who conjectured about it.

From Sabba Sutta:

The Blessed One said, "What is the All? Simply the eye & forms, ear & sounds, nose & aromas, tongue & flavors, body & tactile sensations, intellect & ideas. This, monks, is called the All. Anyone who would say, 'Repudiating this All, I will describe another,' if questioned on what exactly might be the grounds for his statement, would be unable to explain, and furthermore, would be put to grief. Why? Because it lies beyond range."

Well, lets try to see how much suffering there's to get this mental view "molecules, atoms, sub particles then energy.", how much suffering it costs to keep it, how much far you can go with it, how you can prove it to yourself the usefulness of it, what's the life span is (i.e., when this view dies). The only reason for this answer is to reduce suffering. Every word I write has this goal in mind. For this it is important to pay attention and analyze the issue. A few useful concepts pop out, interestingly enough the same stuff what Buddha was telling us. Does it make him a sort of a God who knows, and us sort of ghosts injured and hurt wondering around without a goal? I’d say yes. But let’s the question is not about ghosts, so lets focus on the question.

Having molecules, atoms (sub particles to some extend) are useful. On a practical level this creates all kinds of machines from agriculture to iphones. Those machines increase efficiency substantially, one can gather and preprocess more food, transport and reach more people, allowed more and more people be less and less concerned how to fill their stomachs with food. Do we have less suffering in the world? Definitely. Our problems got a lot more complicated though. Now you’ve got at least 4 hours a day (typically we work 8 hours per day compared to 12 hours a century ago) for anything we want. What do we do with it? Take drugs, alcohol, do sports to shut up all the annoying voices in our heads and hide our misery.

Getting this (wrong) view is essential to keep improving our technology and make even better agricultural machines as well as iphones. The way our society does it is through suffering as well: if one learns it at school then this is through force, repetitive memorization, and addictive presentation of the content in discovery, natural geographic channels. How long did you celebrate your high school diploma? How long did you celebrate your college/university degree? Once you got your diploma did you have an inner happiness for a day or two, or did it involve drinking lots of alcohol to “forget” the stress of “fundamentals” you’ve received, that allegedly will help you repay your depts and give some financial stability?

Buddha talks about light in many sutras, e.g. sn56.11 (https://suttacentral.net/sn56.11/en/bodhi). I have a feeling however that this is something different to your concept of “energy”. I have a feeling that what you mean by energy is the famous equation from Einstein E=mc2. If you’ll talk to scientists thought, they’ll tell you that they see this “theory” more like a material that evolves over time, with some ideas taking a birth, enjoying some sort of development (maturing, bringing us to additional knowledge) and eventually dying out. Those scientists will also tell that with every “fundamental knowledge” they introduce “fundamental problems” as well. Examples are indefinability of key mathematical objects like sets (https://en.wikipedia.org/wiki/Russell%27s_paradox) and what we can compute and we cannot (https://en.wikipedia.org/wiki/Halting_problem) We tried to patch those theories the way we tried to this all the time. This created even more complex theories and problems that require even more suffering to understand and learn.

Advances in other sciences are not helping much to reduce suffering as well. Looking at medical sciences, we have no clue why taking any bitter pill (placebo) is better than well designed drug. Even in covid-19 test studies we give 50% of test people a placebo pill, i.e., a pill that should have no effect whatsoever. Impressive enough, this has quite an impressive effect.

The fundamental level of existence is that there’s suffering, there’s an origin of suffering, there’s the cessation of suffering, and there’s a path leading towards cessation of suffering.