Spin problem: explain what the various spins of the universe have to do with each other, i.e. what the milky way spin (200 million years/cycle), has to do with the spin of the earth about the sun (365 days/cycle), the earth on its axis (24 hours/cycle) and with human spin in its daily orbitals (one day/cycle) and what this has to do with electron spin and what all of this has to do with the movement of fundamental particles and forces in relation to evolution, the Lewis inequality, and the arrow of time?
In puzzles, intellectual puzzles refers the greatest problems of all time, some solved, some unsolved, some partially solved, referring to the famous intellectual puzzles worked on by the greatest minds of history.

Queries, similar to Newton's queries (1718), listed below are of the type that take decades to solve and many of which, as of yet, have no known solution, some culled from the various ‘greatest unsolved mysteries' of modern times types of books. [1] Many of these problems come from the problems perused in the minds of the people at the top of the IQ=200+ list, the first of which is the "elective affinity problem" worked on by at least three individuals in the IQ=225+ range (Goethe, Sidis, and Hirata) and the one which Goethe, the deemed smartest person ever, considered his "greatest work" or "best book".

Classical
Nature abhors a vacuum (yes/no) (semi-open)

Great problem of natural philosophy (solved by Libb Thims in 2009)

Blue sky problem (solved by John Strutt in 1899)

The blue sky puzzle, prior to its complete solution in 1899 by English physicist John Strutt (IQ=190), the vacuum debate aside, was the longest-standing unsolved puzzle in science, worked on by the biggest thinkers of all time: Aristotle (IQ=190), Da Vinci (IQ=205), Newton (IQ=215), Goethe (IQ=230), Clausius (IQ=205), Maxwell (IQ=210)—in fact every single genius in the IQ=205+ range (see: genius IQs) worked on the blue sky problem, prior to its solution by Strutt.

Hardest
The hardest intellectual genius puzzle of them all is the "elective affinity" problem (see modern queries): namely to explain human passions and experience via the chemical affinities or free energies. The elective affinities problem is the only puzzle common to geniuses cited in the IQ=225+ range, namely: Goethe (1796) (IQCit=225; IQ=230), who called his solution to this problem his greatest work (see: best book), of all his 142+ collected works publications; Einstein (IQCit=225; IQ=220), who commented on the problem in perplexment: “gravitation cannot be responsible for people falling in love” and “how on earth are you ever going to explain in terms of chemistry and physics so important a biological phenomenon as first love?”; Thims (1995) (IQCit=225; IQ=190), who was led into the problem, similar to Goethe, via a mixture of the "love thought experiment" and the "reverse engineering puzzle", and Hirata (2000) (IQCit=225; IQ=190), who called his solution a "fun compilation of worthless applications of physics and mathematics to relationships"; even the great child prodigy William Sidis (IQCit=250-300; IQ=195) attempted solution, in a round-about-way, via his theories on animate matter and entropy.
 A playboy style depiction of the "elective affinities problem", namely how to explain passions of existence in terms of Bergman's 1775 chemical affinities theories (Goethe's day) or in terms of Gibbs' 1876 free energies (modern day).

Elective affinity problem (aka the "attraction Newton left out", Stoppard (1993)) explain human existence in terms of the forces of chemical affinity, starting with the Lewis inequality (ΔG < 0) (see: inequality) (Goethe: Elective Affinities, 1809) (Hirata, 2000).
Reverse engineering puzzle
Love thought experiment

Thick
The following is a significant glass wall problem:

● Human chemical bond problem: explain the nature and operation of the human chemical bond, such as when two people A and B, form a couple:

$A + B \rightarrow AB \,$

in terms of pure physics and chemistry, in the same sense as that in which two hydrogen atoms form a chemical bond:

$H + H \rightarrow H_2 \,$

in this case, the bond going by the name "covalent", in terms of bond categories.

Difficult
Morality problem: explain morality in a modern scientific sense (Goethe: moral symbols; John Stuart Mill: utilitarianism, 1861)
Purpose problem: what is the purpose of one's existence?
Death problem: explain the nature of what happens when one ceases to exist in the context of the overall movement and purpose (if there is one?) of the universe (although, to note, this question is bound to both the morality problem and the purpose problem, via the large and deep ingrainment of the basic principles of Ra theology in the corpus of the world's minds, regarding right or wrong behavior (Freud: death instinct, 1920). [4]

Famous tricky goose-chase questions
● Can Clausius and Darwin both be right? (Roger Caillois, 1973)

● Thermodynamic equilibrium may be characterized by the minimum of the Helmholtz free energy, F = E – TS. Are most types of ‘organizations’ around us, e.g. in a town, in a living system, of this nature? (Prigogine asked this question during his 1977 Nobel Lecture)

● What does Shannon entropy have to do with Clausius entropy? (Myron Tribus was asked this question during his 1948 examination for his PhD at UCLA, after which he spent over ten years trying to solve this query, still having he question on his mind 50-years later).

Semi-difficult
Evolution vs. second law problem: explain the so-called paradoxical trend toward order seen in the case of civilization as contrasted with the trend toward disorder often depicted in the second law (Ubbelohde, 1946) (Prigogine, 1977).

Unsolved
Gravity problem: what is gravity? (Newton, 1686, Einstein, 1912); what does gravity have to do with the electromagnetic force.

Double slits experiment (Young, 1804): explain what is going on in the process of one particle, going through, supposedly, two slits, and thus interfering with itself past the slits to make interference effects?

Spin problem: explain how all the spins of the universe are connected or coupled, from the subatomic spins to human molecular spin to galactic spin to supergalactic spin, in connection to right hand rule (Faraday, 1831; Maxwell, 1873, Haramein, 2003)

Satellite problem (pioneer puzzle or pioneer anomaly): a problem, supposedly, first noted by NASA scientist John Anderson in 1998, which find that the now-powered out Pioneer 10 and Pioneer 11 space probes (launched in the 1970s), which are currently near the edge of the solar system, are decelerating (or accelerating) at a rate that cannot be accounted for current models of gravity. [4]

Dark matter problem: explain where the missing matter of the universe is?

Unification problem: developed a unified theory to explain the total system of the fundamental forces and fundamental particles of the universe.

Coherence problem (Einstein, 1935): explain quantum entanglement, e.g. why photons that had at one point been in contact supposedly remain ‘aware’ of each other even when separated by great distances (John Bell, 1964); or why, as determined by experiments by researchers in Geneva (c.1995), photons sent in opposite directions along fiber optic cables showed ‘nonlocality’, i.e. the two photons acted like one particle even when they were more than 6.2-miles apart. [2]

Semi-solved/semi-open problems
Heat problem: what is heat? (Aristotle: fire, 350BC; Geber: sulphur principle, 790; Paracelsus: sulphur combustion, 1524; Johann Becher: terra pinguis, 1669; Georg Stahl: phlogiston, Lavoisier: caloric, 1789; Clausius: entropy, 1865)
Vacuum problem: does nature abhor a vacuum? (Parmenides, 485; Plato; Aristotle; Galileo; Galileo, 1630); supposedly, the search for the Higgs boson has something to do with this problem.

Solved
● What happens if you attempt to run alongside a beam of light? | Solution: relativity + E = mc² (Einstein, 1905)
Color puzzle (Newton, Goethe, Young): how does light produce color?
Affinity problem: what is affinity, chemical affinity, or elective affinity? | Solution: a force quantified by free energy (Helmholtz, 1882; Nernst, c.1900; Lewis, 1923)
● Aether problem: does aether exist? | Solution: No (Einstein, c. 1905)
What is life? | Solution: defunct theory of life (Tesla, 1925; Thims, 2009)
Free will problem | Solution: the choice of elective affinity by mediated by forces external to the system (Goethe; 1796; Thims, 2007)