Dear Tejinder Singh and Anshu,
Your essay contains a numer of insights. Of course elementary counting, or number sense, is hardwired into the brain, but counting exists at almost every level of reality, from three quarks per baryon to the number of telomeres on chromosomes, and a significant number of lower lifeforms. Our own hardwired structures are extremely high level.
As for "primordial physics", I have employed a robot as a vehicle to eliminate bias and "baggage", while providing pattern recognition, learning algorithms (neural nets, self organizing maps, etc.) and have shown how counting, derived from logical physical structures, is essentially (along with simple arithmetic logic circuitry, silicon or biological) all that is required to go from raw measurement data to feature vectors of the quantum persuasion. This work is summarized in the first two pages of my essay.
It is appropriate to point out that mathematics is "an enterprise of the human mind, and not a universal Platonic truth 'out there'." This mystical misconception is a major problem for many physicist today. As you say, it is an "act of faith" (at best!) Lee Smolin provides an excellent analysis of this in his essay.
Your "three key developments in cognitive science" do bear crucially on the math-physics connection, and your hunter lighting the fire is very akin to my robot physicist, who notes changes and acts on or processes them. Comparison of differences is at the root of it all. Lack of change typically implies something can be ignored, while lack of change in a dynamic situation leads to conservation relations.
Most significant is your endnotes treatment of the 'oddities' of quantum mechanics:
1.) The theory has to rely on its own limits, i.e., classical mechanics.
2.) With initial state known precisely, yet the outcomes are probabilistic.
3.) The "collapse of the wave function" is a mystery, and has problems.
4.) The quantum theory depends on classical time for describing evolution.
You say "we physicists feel reluctant to modify quantum theory" (due to its successes). It may not be necessary to modify QM so much as to simply admit that it is incomplete. My essay describes a local model that accomplishes what Bell proclaims impossible, and analyzes how he correctly applies math to incorrect physical assumptions, leading to a false conclusion. My model should be experimentally verifiable, which, as you say 'reigns supreme in physics'.
I hope that you will find the time to read my essay and to grace me with your comments.
Best regards,
Edwin Eugene Klingman