Quantum Mechanics is a comprehensive theory of physics at the smallest scales. The Wikipedia article on Particle Physics is a good place to start.
As a whirlwind summary, the Standard Model puts fundamental particles called Fermions into 2 categories Leptons and Quarks with 6 particles in each.
The leptons are further subdivided into 2 subcategories, Electrons and Neutrinos, each with 3 successive generations.
Quarks are not the easiest of things to understand (or pronounce) but the standard theory assigns charges of:
along with a chart which shows which reallife composite particles are made up of which quarks.
Then there are 4 Bosons which are the force carriers:
There are additional theories including:
Together, these theories do a good job of explaining every experimental result so far, at least if we stay within the bounds of particle physics and ignore gravity (which is governed by the separate and incompatible theory General Relativity).
So if the Standard Model does all this, then what's the problem?
If we take a look at Unsolved Problems in Physics, we find a long list, including things like:
The list is too big (around 70) to delve into all of them. Suffice it to say that if the Standard Model was the final answer then we would not expect so many problems.
If we wanted to be critical of the Standard Model, where would we start?
One major concern surrounds the subatomic particle masses. Essentially, the Standard Model does a very poor job of explaining any of their masses, to the extent that they all have to be fed in as parameters in order to get the right answers out at the other end. A preferable theory would have a smaller number of starting parameters and could account for a much larger number of things via logic and calculation.
This line of reasoning is known as Ockham's Razor.
Particle  Mass  Lifetime 

Electron  0.511 MeV/c^{2}  Stable 
Muon  105.7 MeV/c^{2}  2 x 10^{6} s 
Pion^{0}  135.0 MeV/c^{2}  8.4 x 10^{17} s 
Pion^{+/}  139.6 MeV/c^{2}  2.6 x 10^{8} s 
Kaon^{0}  497.7 MeV/c^{2}  Stable 
Kaon^{+/}  493.7 MeV/c^{2}  1.2 x 10^{8} s 
Proton  938.3 MeV/c^{2}  Stable 
Neutron  939.6 MeV/c^{2}  15 mins 
Tau  1776 MeV/c^{2}  2.9 x 10^{13} s 
Some authors including Malcolm MacGregor in The Power of Alpha and Paolo Palazzi in Patterns in the Meson Mass Spectrum have looked at particle masses and lifetimes in detail to deduce some underlying patterns, including a 35 MeV/c^{2} mass quantum.
Is it possible to pick up on these clues and predict the particle masses with any degree of accuracy?
The message from Dark Matter is really just a statement:
We don't understand why galaxies hang together without flying apart in a billion pieces.
Likewise, the message from Dark Energy is really just a statement:
We don't understand why galaxy clusters are flying apart at everincreasing speeds when they should be hanging together more.
So it seems that the universal law of gravitation courtesy of Newton and Einstein is not so universal after all. It works at the level of everyday life on planet Earth, the solar system (including the Sun, the planets and their moons, minor planets, asteroids and comets), star clusters like the Pleides and globular clusters like Omega Centauri, but that is all.
As soon as we go to the next level up with Elliptical and Spiral galaxies then standard gravity starts to fall apart. Even more so at the level of the universe as a whole.
Neutrinos are not well understood at all. We don't know whether they have zero mass or close to zero (which turns out to be a big difference if you add things up at the level of the visible universe). Furthermore, they've been assigned values such as spin1/2 and then classified as "fermions" on this basis.
Are we really sure about that? And at the last count, they were clocked faster than than the speedoflight going through solid rock, which is a surprise to all of us.
Then there are the "pseudoscalar mesons" which we are told all have spin zero. This is necessary in order that the particle spins add up when you look at the decay products. But when you delve deeper, it turns out that experimental measurements of meson spins is not as precise as you might think. In particular, the charged pion is supposed to have spin 0, but the uncertainty in the results would also be consistent with it having spin 1/2.
Could it be that something is really wrong here, and that if we start to pull, various aspects of the Standard Model might fall apart a bit like a house of cards?
If we put a bullet in a gun, sit in a spaceship in orbit around the Sun and then press the trigger, what happens?
Of course firing a gun inside a spaceship is unlikely to be a very good idea because the bullet would pierce the outer skin, causing depressurisation and probable death to all those onboard. Even if we fired a blank, the pressure wave from the blast could easily disrupt the fragile environment in outer space.
Nevertheless, if we disregard such practical concerns for the moment and fire the gun anyway, where would we expect it the bullet to go? For the purposes of this thought experiment, we can assume that the Sun and the bullet are stable, electrically neutral bodies, space is a perfect vacuum and nothing else in the universe exists. The laws of physics tell us that the primary force acting on the bullet will be gravity due to the Sun.
We can simplify the problem a little bit by assuming that we fire the gun at right angles to the Sun, that the Sun is of zero size and that the motion (and gravity) of the spacecraft can be ignored.
There are 2 limiting cases that we can easily understand:
What happens if we fire it with a more realistic intermediate speed?
It turns out that there are 4 more possible cases for the orbit of the bullet around the Sun. These were first investigated by Johannes Kepler in the 1650s and can be deduced from Newton's laws of motion and gravitation.

Cool, job done, so we can relax, right? Certainly Kepler did and his work has been a staple part of physics textbooks ever since. But is this really the end of the story?
If we take another look at the formula y = 1/x, we notice that there are 2 distinct parts to the graph, depending on whether we're looking at positive or negative numbers. Is it possible for the bullet to take one of those paths instead?
Note that the only way to achieve this is if the bullet is repelled by the Sun rather than attracted towards it, an effect known as antigravity and one of science fiction's favourite topics.
As a matter of fact, it is unknown in scientific terms as to whether antimatter falls down or up due to gravity. This may sound surprising, yet there is currently an experiment underway at CERN to measure this for real.
At this point in time, it remains a possibility that if our bullet (and gun and spaceship and inhabitants) were made of antimatter that the bullet would follow the negative part of the hyperbola, flying away from the Sun.
Finally, if we look at the fundamental interactions in particle physics, it includes things like Electron / Positron Annihilation and Pair Production. In these cases, it would seem that "things" are not conserved at all and that particles can spring into and out of existence at whim. Yet in other areas physicists are fanatical about saying that things like Energy must be conserved.
So why are they so happy to accept fundemantal processes that seem to have such big holes in them?
This point was made at length by Donald Hotson in Dirac's Equation and the Sea of Negative Energy.
This has been a very brief discussion of "what's wrong".
In our quest to try and put some of it right, this is enough to be getting on with...
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