Let’s look at what orthodox science says to us about ourselves and the world we live in.
The Big Bang: It all started with the “Big Bang,” when a virtually infinitely small and virtually infinitely dense particle of some unknown substance exploded for an unknown reason and launched the universe.
What surrounded that primordial particle is unknown. What came before that primordial particle is unknown. Where the universe is headed, as it expands in all directions, is unknown. The expansion does seem to be speeding up, though no one knows why.
Black Holes: The universe is composed, among other things, of billions of galaxies made up of billions of stars. It appears that there is a “Black Hole” (a concentration of gravity so powerful that light can’t escape from it) at the center of each galaxy, but science doesn’t know anything about what is going on inside any of these Black Holes.
Dark Matter and Dark Energy: For the equations of astro-physics to work, scientists have had to postulate that most of the universe is composed of dark matter, an unknown substance that has never been directly experienced in any way, and also of dark energy, another completely unknown substance.
According to the NASA website, “It turns out that roughly 70% of the Universe is dark energy. Dark matter makes up about 25%. The rest – everything on Earth, everything ever observed with all of our instruments – all normal matter adds up to less than 5% of the Universe.”
Quantum Indeterminism: Things are similarly opaque at smallest levels of sub-atomic quantum physics, where the mechanistic/deterministic model of explanation has become the mechanistic/probabilistic model of explanation, which sees the smallest energy units, quanta, as having the characteristics of both waves and particles, with measurement difficulties.
It takes at least a quantum of energy to measure a quantum of energy and the act of measurement changes the system, so all knowledge must become approximate and take into consideration the observer. Some scientists hold the view that all of the possible states of a quantum system exist in a multiverse of many parallel universes. However, why any of this should be so is left unexplained. Are there many universes? If so, why is this so? How many universes are there? Why and how do they interpenetrate each other? These are all questions that have not been answered.
Time: The situation isn’t much better when it comes to time. According to Einstein’s equations, time could just as well flow backward as forward. There is no explanation as to why time flows from past to future. One of the most significant, largely hidden assumptions of orthodox science has been that the future will, in essential respects, be like the past. All of the “laws of science” assume that the future will be the same as the past in respect to these laws (the deterministic aspect of the mechanistic/deterministic model of explanation). Yet there is no explanation for why the future should be essentially like the past.
It’s clear that, in many respects, the future is different from the past. However, the most basic question of why some aspects of the future are different from the past and some aren’t, remains unexplored. For that matter, there is no explanation for why numbers and mathematical equations can describe and predict the behavior of many aspects of the universe/multiverse.
Energy and Matter: Einstein showed that matter can be transformed into energy and that the amount of energy would be the square of the speed of light. The atomic bomb was a dramatic demonstration that Einstein was correct in his assertion, but why is it that, when matter transforms into energy, the amount of energy produced is the amount of matter times the square of the speed of light? Why does light move at the constant speed that Einstein formulated? Can anything move faster than the speed of light? Science doesn’t know.
Life: Life is an emergent property in relation to the agglomerations of chemicals that compose any living system, but science hasn’t been able to produce life from chemicals or to explain either how or why it happens. The 2nd law of thermodynamics posits that all systems tend to degrade into their simpler and simpler components, yet the whole of evolution is the story of increasingly complex systems, with emergent properties that can’t be predicted based on their component parts, building on their predecessors to produce new complexity with different newly emergent properties. This is clearly a huge, unexplained, violation of the 2nd law of thermodynamics.
I could go on, but I think the point is made. The scientific method with its mechanistic/deterministic/probabilistic metaphysics has produced a significant amount of scientific knowledge surrounded by a much vaster amount of ignorance.