Thanks for this very nice blog and for sharing it with us! It is always a pleasure to read about particle physics from non-particle-physicist authors.

To rephrase a bit what you wrote, protons are indeed not “simply” made of three quarks. Protons are dynamic objects in which we have continuous interactions between quarks, antiquarks and gluons. Quarks can emit gluons, and gluons can convert themselves in a quark-antiquark pair (of any flavour) or into a pair of gluons. The proton’s content is thus much richer than what we could naively think about, and the dynamic behaviour moreover depends on the energy (accelerated protons in the LHC do not behave as protons at rest).

If you remember the tasks of the second episode of our citizen science project, the proton was defined in MG5aMC as

  p = u d s c u~ d~ s~ c~ g
 

This means that we have up quarks, down quarks, strange quarks, charm quarks, all corresponding antiquarks and gluons inside the proton. We then have parton distribution functions indicating us how to relate the proton itself to its content. This is a bit what I mentioned here.

Finally, I will object one of the points raised in your blog:

In fact, detecting just one is difficult because they are never seen alone. The more quarks scientists try to separate, the more energy they must expend to tear them apart. They finally expend enough energy to create the mass of two new quarks, which can then be bound to the original two.

This is incorrect. The top quark (that is special by virtue of its large mass) has been detected alone (although through its decay products). Yeah, the top quark is a weird beast ;)

Cheers!

PS: you may be interested in this older blog of mine on quark-antiquark bound states.