11.12.2011 The programmer shifts in his seat, loving how much there is to learn about phylogons. There is nothing else for him right now beyond this knowledge.

Appendix A continues:

PKD did not refer to the phylogons in print beyond the paragraphs in The Divine Invasion. However, he does discuss the concept in some of his published letters. The parts of the letters relevant to phylogons are summarized by John Fairchild and reprinted by Ragle Gumm in this blog post.

PKD's letters reveal his struggle for a rational explanation of his visions. The struggle led him to theorize that the visions were projections of a fourth spatial dimension into our more familiar three. When a sphere passes through the plane in E. A. Abbott's Flatland, the residents of the plane see a tiny circle appear, grow, shrink and disappear again. Who is to say that the warping of higher dimensional forms doesn't cast some shadows onto what we see everyday?
Fairchild states, "One of the things [PKD] saw he labeled phylogons. 
This is Phil’s term for the Forms of the macrometasomakosmos that get 
morphologically arranged conceptually. The phylogons are permanent and 
accrete new layers. The phenomenal flux world, the world we normally see, 
is being converted into a conceptually arranged structure, being accreted 
into the macrometasomakosmos, laminating down in successive waves. 
Phil’s term for what gets accreted is ontogons. These are non-permanent.
 
And here he directly quotes PKD's letters:

“The billions of phylogons are crosslinked to form a unitary reality 
which is Pythagoras’ kosmos, ‘the harmonious fitting-together of the 
beautiful,’ a vast structure that is sentient, that assimilates its 
environment selectively, using the … universe as a supply of parts.” (p.13)"
The first thing of note is the introduction of the term 'ontogons'; the accreting layers. Coincidentally, Ontogons are being included as a new feature in the upcoming release of the Phylogon Engine Operating System v2.0, due out fourth quarter 2011.

The second idea of note is PKD's assertion that phylogons are conceptually arranged; that the underlying structure of reality comes from intelligence. To quote his letters...
“I believe that they are conceptually arranged; that is, in terms 
of meaning. They have the same necessary relationship to one 
another that logical truths or mathematical propositions have to one another.” (p.116)
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