The history and the logic of the arguments of the current leading particle physics theory is not understood by the general public and, I am almost sure, not even by most of the scientists in the field. This allegory demonstrates almost exactly the cultural and historical aspects of an important element of this complex field in physics.
I suggest that you read the whole story without looking in the footnotes. This will enable you to understand the logic which is used in scientific discussions of this field. Later, read the footnotes which explain the exact analogy.
While reading the story you may find that the logic of the scientists is absurd. I promise you that I didn’t make any effort to exaggerate. We simply live in an absurd situation.
The 1960s puzzle
During the 1960s a rather large cave was found in the middle of the Sahara desert. Paintings that were created some 8,000 years ago were all around and showed unclear human figures which look very tall.
This discovery astonished the scientists. It was clear that a new civilization was revealed. However, things didn’t match. Scientists assumed that:
– There was no water resource  near the cave because the cave was found in the middle of the desert.
– The humans in the paintings were very tall, nearly 2 meters . Such tall humans  could not exist without almost unlimited resources of water and food.
This contradiction bothered the scientists at the time. But in 1972 a new idea was presented. Three scientists showed that there is a specific DNA chain which builds humans that are very tall, very intelligent, and do not need any water or food except air. Furthermore, these humans cannot live near a water source. The theory was called Quasi Chain DNA  (QCD).
Although the theory looks fantastic and without any parallel in nature , one of its inventors was a leading scientist in the field, and scientists gave it a chance and tried to see whether the theory is compatible with what they found in this cave.
One of the strange things in these paintings was that the figures were painted quite far from one another. When scientists investigated the Quasi DNA chain they found that humans with such DNA prefer to make sexual interactions while the partners are quite far apart from one another , exactly the opposite of any other known mammals on earth.
This DNA feature, which received the name “sexual freedom” , is considered until today as a crucial proof for the validity of QCD.
Scientists who checked the DNA chain predicted that such humans should prefer to live in family cells. In 1979 new paintings were found showing party events in which the humans were painted in groups which look like two parents and a child. These beautiful paintings, called the “3 dancer events”  are considered as another crucial proof for QCD, although humans with “normal” DNA behave in a similar manner .
Some of the first articles that were found in these caves were tools which look very similar to the tools that were found in other caves in Northern Africa. This similarity  is unexplained until today. In fact, even leading QCD supporters said that this seems to contradict QCD .
In 1974 scientists discovered huge pools  near the cave. Since QCD humans cannot live near water, QCD supporters claimed that these pools didn’t contain water .
It has also been predicted that unlike many other human beings, the QCD humans do not need kings or gods. However, the Explorers of Mountain Caves (EMC) , a group of independent researchers, found in 1983 a big palace  near the Sahara cave. This discovery contradicts the predicted behavior of these humans and it remained unexplained until today. 
In 1987 the EMC group found beds of these humans. The size of the beds clearly indicates that the humans were not so tall – they were around 1.55 meters. This is similar to human height found in other civilizations of that time.  This discovery remained unexplained until today.
During the 1990s signs of single celled organisms were found inside the pool . These findings provided an indication that the pools contained water. At the beginning of the 2000s another group of researchers  found fish bones in pools  near by. This was a clear indication that the pools contained water . These discoveries are unexplained until today, because QCD humans cannot live near water resources.
Many caves were found in that area and scientists were able to perform a very good statistical analysis. It was found that bigger families live in smaller houses. This seems to contradict the “sexual freedom” because it seems that more sexual interactions were done in smaller space, in contrast to the expected sexual freedom of QCD humans.  Another bothering discovery was a series of paintings that show two figures, each from a different family, doing sex together. It seems that the intensity of their sexual interaction was greater when they were closer. This also seems to contradict the expected sexual freedom .
QCD experts have carefully analyzed the specific DNA chain of the Sahara cave people and concluded that their skeleton must be different than that of normal human beings. Based on that analysis they predicted that several new “exotic” bones  will be found. However, in spite of finding many ordinary bones of the QCD people, none of these exotic bones have ever been found.
So what do we have here? First of all, the two assumptions which led to the invention of QCD were:
– There was no water resource near the cave
– The humans were very tall
These two assumptions seem to be wrong.
Furthermore, many of the findings in these caves look very similar to “normal” human behavior. However, these humans are far from being “normal”: their DNA is very different, and the expected behavior of the QCD humans didn’t match the findings.
What do scientists say
By trying to explain the contradictory findings, QCD supporters claim today that it is very difficult to calculate the exact behavior of these humans using their DNA chains, and it is possible that even the fastest computers will not be able to provide a prediction of these properties ever.
Furthermore, they claim that QCD has very good predictions regarding the population expansion ratio of this civilization. Therefore, they believe that QCD must be correct. By the way, there are other models that provide very accurate predictions of population expansion without assuming that QCD is correct and without any underlying theory.
In spite of the many different kinds of failures and contradictions which are described above, all mainstream scientists are very satisfied with QCD, and many of them claim that they will not examine any competing theory ever, even if the unexplained findings will remain unexplained, simply because the DNA chain are so hard to calculate.
This is QCD, in a nutshell.
Does it make sense?
 Scientists thought that the 3 quarks are the only massive elements inside the proton
 They thought that the proton quarks and several other baryon quarks are S-Wave only
 They thought that strong interactions are not like the electromagnetic interactions of known and established particles like atoms because in an electromagnetic-like theory quarks should repel one another and stable baryons, which are made of only 3 quarks, could not exist. Furthermore, they thought that since the quarks are the only massive particles, they must exist in the most inner shell (S-Wave), and this led to a contradiction because the inner shell cannot contain 3 identical quarks with the same spin direction..
 Quantum Chromodynamics
 QCD assume fantastic things which do not have any parallel in nature: forces with 3 colors, particles that cannot exist unless they have the same amount of the 3 colors, etc.
 The force between particles becomes stronger if they are far from one another
 Asymptotic freedom
 Three jet event
 The three jet event is analogous to a well known electromagnetic effect, called bremsstrahlung
 The similarity between the force which acts between noble gas atoms (the van der Waals force) and the force between protons and neutrons (the nuclear force)
 “Ironically, from the perspective of QCD, the foundations of nuclear physics appear distinctly unsound.” Frank Wilczek, Hard-core revelations, Nature, 445 156 (2007)
 That the quarks carry only part of the proton mass
 They claimed that gluons carry the missing mass
 EMC – European Muon Collaboration
 The first EMC effect (http://en.wikipedia.org/wiki/EMC_Effect)
 J. Arrington et al., New Measurements of the EMC Effect in Few-Body Nuclei, J. Phys. Conference Series 69, 012024 (2007). “So while the experimental signature is clear, the interpretation of this effect is, at present, ambiguous.”
 The proton spin crisis (http://en.wikipedia.org/wiki/Proton_spin_crisis) indicates that the quarks are not S-Waves. e.g.: A.W. Thomas (http://arxiv.org/pdf/0803.2775.pdf), Interplay of Spin and Orbital Angular Momentum in the Proton. Physical Review Letters, 101, 102003 (2008). For a proof showing that the state of quarks of the Delta++ baryon is NOT an s-wave, see http://www.tau.ac.il/~elicomay/dpp_new.pdf
 The proton-proton elastic collision takes a non-negligible part of the scattering events, which is an indication that they contain a massive core which can act like billiard ball during hard collisions without breaking the proton structure. BTW, when an energetic electron hits the proton’s quarks it almost always creates an inelastic collision.
 The number of elastic events started to rise.
 This indicates that there are inner quark shells inside the proton.
 An analysis of the form factor proves that quarks tend to be located near the center of the proton, like the electrons tend to be located near the center of the atom. Even the statistical graphs look the same. The distribution of the electrons inside atoms is explained by the electric force which is weaker when the distance is larger.
 The p-p cross section graph shows that the forces between a quark of one proton to the quark of the other proton behave like electromagnetic forces, in contrast to the asymptotic freedom
 Based on QCD pentaquarks, dibaryons, glueballs and strange quark matter should exist.
 All these particles and matter states have never been really found in all experiments that were supposed to detect them.
 Even QCD experts admit that the quarks do not carry all the proton mass and that the quarks are not S-Wave only (see the article of A.W. Thomas, above). These were the assumptions which led to the invention of QCD. See the QCD history section in Wikipedia.
 QCD faces very difficult mathematical problems and for solving them people use supercomputers. Even with supercomputers, calculations are very long and mathematical approximations techniques are necessary for finding approximate results.
 Phenomena like hadron masses and hadron life-time
 Like Gell-Mann—Okubo mass formulae