Atoms and elements of the Voynichese alphabet

[Jorge_Stolfi]

The parallel frequency distributions of "ir"/"iir"/"iiir" and "iin"/"iiin"/"iiiin" are real but they don't require scribal error as explanation. Similar word endings behave similarly throughout the VMS. The same parallel distribution exists for every pair of similar suffixes — "-ol"/"-or"/"-al"/"-ar", "-edy"/"-eedy"/"-ey"/"-eey",

No, sorry, the pattern in the frequencies of the -ir/-iin endings is not similar to that seen for other endings.  Take for example the words

    chdy            151     chy            183
  chedy    522  chey    369
  cheedy    61  cheey   188
  cheeedy    0  cheeey   10
  cheeeedy   0  cheeeey   0

(Counts are from my working transcription file; your mileage may vary.) Assuming for the moment that 1 = 3, that is a simple proportionality pattern: the insertion of a specific character (d) in a specific context (between the che^x and y) of a series of similar words gives another series of words with similar relative frequencies.  But in the -i^xr series and the -i^yn series the correspondence is one off: the transformation that "preserves" relative ratios is the replacement of in by r (a distance-2 edit).

That is what I take as evidence that dair is somehow analogous to daiin (not to dain), and daiir is analogous to daiiin.  

And the Scribe misreading sloppy in as r is a simple an plausible explanation  for that pattern. Moreover, if all ir endings are actually iin, the structure of the words becomes significantly simpler.  And other things work better too.
  

The same parallel distribution exists for ... "-ain"/"-aiin"/"-air"/"-aiir".

No, the distributions for these two series of words are off by one, like those of the suffixes -i^xr and -i^yn:

  air    98  ain   150
  aiir   41  aiin  606
  aiiir   0  aiiin  50
  aiiiir  0  aiiiin  0

The ratio chedy : shedy (1.2) differs from lchedy : lshedy (2.8) — but the direction is overall that "sh" forms are less frequent than corresponding "ch" forms.

But the ratios are not constant, and they are often reversed:

  chy  185  shy  90
  cho   91  sho 138

So the proper description of the situation is rather the opposite: the frequencies of similar (distance-1) words are generally not proportional.

The self-citation method is the most compact description of all the properties we can observe in the Voynich text.

This claim is trivially and grossly false.  The observable properties of the VMS text include "word #1 is fachys", "word #2 is ykal", "word #3 is ar", and so on.   The text generated by your method may satisfy at most a couple hundred of these properties, just by chance. (Unless the seed text is the whole VMS and the reset and mutate probabilities are set to zero.) 

What you may be able to claim is that a few bulk statistical properties of the output of your method -- like word frequencies, word-word correlations, etc. -- match those of the VMS text.   But surely you can adapt your method so that those statistics of the output match those of Hamlet.  If not, one can always develop a different random text generator algorithm with that property.  Should we take that as evidence that Hamlet may have been created by such method?

I have seen you or some other "gibberish" advocate justify why your method does not produce certain features of the VMS (like the local deviations from Heaps's law in certain sections but not in others, just found by @bi3mw) by saying that the Author was not an automaton, and those special features could be produced by your method if the random choices made by him were not computer-random but merely human-random.  However, with this "modification", your method could also generate Hamlet...

All the best, --stolfi