How do you know what you don't know. This is the crux of basically every line of empirical inquiry and the inevitable unconscionable lie we try desperately to believe.
Take electrons for example.
An electron is a quantized volume of negative electrical charge that has negligible but non-zero mass. Now most amateur physicists (and professionals alike) will nod their heads sagely, and quibble about some finer points of this definition, but this is generally accepted to be true.
But here's the rub, no such thing exists.
Oh we can build things to detect them, our lightbulbs work because of them, and the standard model relies on them. But in reality, they're only a model like Camelot in Monty Python and the Holy Grail. It is a useful prop to describe interactions between things we can perceive. What happens when we can't see something.
We invent dark matter!
What is dark matter? It is something of non-zero mass but is electromagnetically neutral, and it glues all galaxies together. Why? Because we can only see so much mass via electromagnetism, and can calculate the force of gravity by estimating the mass producing those effects, but can't see the electromagnetic radiation produced by visible matter.
If there is an observable phenomena and not enough to account for the observation, we have a known unknown. We put a placeholder variable, call it dark matter, and then move on trying to figure out how to solve it. But what is not acceptable by these rules is proposing an unknown unknown, some extra factor or factors.
Enter the God defence
It amazes me that religious fundamentalists have not latched onto dark matter and energy as the fundamental proof for the existence of God. I mean what could be more obvious than 90%+ of the universe being invisible and unknowable through human experience. It would seem like a giant neon sign saying "if you can see this, I do exist".
But the reason they don't is probably an inescapable truth in itself. It would mean they'd first have to accept a ton of beliefs which would negate most of their mythology, like thermodynamics, evolution, and other seditious concepts like knowing things.
So maybe the more fertile ground for dark energy is UFO conspirators. Let's start with the hypothesis that life is the norm in the universe, not the exception. In fact, it is so common that intelligent life abounds. By pure chance, most worlds in a habital zone with in their geologic lifetime give rise to intelligent life, which ultimately wipes itself out with intelligent machines. Machines who's memories span aeons and never forget short of intergalactic civil war.
Let's also hypothesize that these computers can construct nano-materials so thin and strong that they can effectively capture 99.99% of a solar mass's outbound electro-magnetic radiation. In effect, turning ordinary matter dark. We cans see it only by its effect on radiation not trapped inside this Dyson-Herbert no-sphere via gravitational lensing.
Now what is funny about this hypothesis is:
1.) it is testable
2.) it accounts for 100% of dark matter
3.) it involves no physics outside the standard model
4.) it will get you banned from any serious academic publication
Why? Because super-intelligent alien machines hiding 99.99% of the observable universe seems a little far fetched, and reeks of "God did it". Now it doesn't matter that the background radiation map of the big bang matches closely the observable network of super galactic clusters, and that we can be certain dark matter and normal baryonic matter are cohabiting on a universal scale. Exotic weird exotic subatomic particles are more believable than alien machines.
The stories we tell ourselves about our universe contain mostly historical bias redressed as fact. The validity of an argument invoking alien material vs. alien intelligence does not rest upon whether or not some people once believed in witches and daemons, but our cultural bias against certain types of magical thinking prevent us from seriously considering any idea that reeks of an analogy. A desire to believe in a cold desolate universe where the most common stuff is something we can neither feel nor see but gives structure to all that is, however, is just as magical as a mythical sky daddy made the world in 7 days.
And this is the problem with most modern scientists. They believe their models to be true, and not what they really are: useful approximations of something that could be true. An electron does not really exist. On the quantum level, you can't pin it to a specific point in space time, nor can define its boundaries. It is like a bump in an infinitely large blanket, being made of the same stuff, but only existing in your perception of the topology. Since the blanket exists everywhere at once, bits of it becoming particularly wrinkled don't make them something fundamentally different.
If you look at the macroscopic fundamental forces of electro-magnetism and gravity, what you quickly realize is that they are following an inverse square law, relating distance to the observed amplitude. But what is distance?
Well distance is the inverse square of the amplitude of to masses or charged particles acting upon each other. If you take 3 charges, their relationships to each other will each follow this law and define a plane. Take a four point not on that plane and you'll have a 3D volume. Now if you find a 5th point acting upon each of those, you have a 4D volume.
How could something in the 4th dimension manipulate something at a distance? Look at a Star. The star's electromagnetic oscillations are traveling across space time to oscillate chemicals in your retina hundreds, thousands, or millions of years away. It is as if you dropped a pebble in a reflecting pool, and the eddy washed across the surface of the pool for a million years just to lap at your feet. That photon that strikes your eye is no more real than the electron it "strikes". Both are modeled as localized fluctuations in an infinite field as a smooth curve over 6 dimensions.
What are these other 2 dimensions? Well electromagnetism is itself an oscillation between two different sets of poles: an electrical dipole and a magnetic dipole. Typically we model these two using complex numbers as these oscillations are not strictly independent of time. But what is interesting about these oscillations is that within their specific context, they at regular intervals transfer all of their energy from on dimension to the other. Like two vibrating strings orthogonal and overlapping, this oscillation is what we think of as light.
But this explanation does not truly capture what light is or is not. We know that changes in the electromagnetic field always maintain a fixed rate of change with respect to a 4D reference frame, so much so that the entropy of any system as it approaches this limit decreases. We also know that as one increases the velocity of any object towards this limit, the amount of energy necessary to move it increases as its mass grows. In this model, moving through space time is like swimming through a fluid. As you speed up, the drag on the solid body becomes insurmountable. In effect, you can think of the speed of light as a physical limitation or there's another totally possible reality.
Suppose our universe were in fact a giant computer program. That every update to the position of any unit in space time required some finite amount of computation, to calculate the effect of every field perturbation on every element. Suppose now that the simulation could not calculate everything quickly enough due to a carrying capacity of the underlying computing medium. Effectively, the propagation of information through a medium has a non-zero cost. The computation probably cheats by compressing the representation of empty space, but struggles when the level of detail is set to high (Heisenberg ) or breaks down when the speed exceeds the resolution of its quantized timer. Time does not so much delay, but the programmer traded off calculating particle decay effects to cover the calculations of more gross approximations.
This idea of God the Programmer has intrigued me since college when I worked as a programmer on simulating non-linear systems of Duffings Oscilators. You'd think that a simple 3rd order polynomial would be easy to spot in real world data. It turns out that bounding any sufficiently complex depends highly on your level or resolution. Sure the simulation works in the general case, but it tends to break down at the edges. This behavior is currently seen in our models for general relativity and quantum mechanics. Since we model the universe with a series of equation, in other words a computer, it really should come as no surprise that our simulation breaks down at the edge cases.
And this is the real danger of modeling the universe as a computer, it reeks of deus ex machina. It is like saying the guy on the prop is a god, while the chorus sings about him coming down to build an orderly universe through reason alone. It's like the aliens in the no-spheres, it reeks of the anthropic principle run amok. We can imagine a video game, therefore the universe is a video game.
But the funny thing is, like with all gods, the math does not prove or disprove their existence. It just reinforces the preexisting biases of the scientist looking for an answer to the ending of a story he spends a life time writing, but can never tell.