The Principle of Recursive Genome Function - Supplementary Material

Archieved Free Full Text
"The Principle of Recursive Genome Function", Pellionisz, A. (2008),
The Cerebellum (Springer, New York & Heidelberg), Online before print, DOI 10.1007/s12311-008-0035-y
[recommended citation]

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PRWeb Press Release (on their website)

PubMed Abstract

An Obituary of the misnomer "Junk DNA" (R.I.P., lived 35 years)

The paper "Principle of Recursive Genome Function" introduces the discipline of "HoloGenomics"

Ample background on the misnomer "Junk DNA" is found here.

Figures and Multimedia Supplement

Fig. 1. Nascence of the "Central Dogma of Molecular Biology"; the original concept diagram by Francis Crick in 1956
(not known to have been published, but acknowledged by Crick FHC. (1956, Unpublished but acknowledged by Crick in 1958)

Fig. 2. Watson's simplified rendering of Crick's central dogma states what is certainly a fact
and strips the dogma of its controversial prohibitions

Fig. 3. Gene Paradigm for Forward Growth as of 2003. The left diagram of the double helix with a "genic" region
highlighted is modified from the cover of Scientific American (April, 2003).
Diagram on the right side is a brain cell. The diagram depicts the oversimplification as if 1.3% of the DNA could determine,
in a forward-growth manner, not only the Purkinje neuron shown but, given enough genes, all phenotypes resulting from separate genotypes.
The 98.7% of junk DNA is a no man's land to which there is no recursion.

[Color version of the figure, not in the paper, is below]

Fig. 4. PRGF breaks through the Double Lock of central dogma and junk DNA barriers (shown in A by triple lines),
to yield PRGF (shown in B by checkered circle). The background figures in both A and B is from Fig. 2. from Crick, 1970,
see in this paper as right side of Fig. 5) permits only a "forward growth" from DNA that dead-ends in proteins.
By removal of both the central dogma that arbitrarily forbids information feedback from proteins to
DNA as well as disposing the "Junk DNA" conjecture that claimed that (even if there was a path back to DNA),
zero information would be found in the "Junk DNA", a main recursive path (PRGF, checkered circle and arrows)
is not only available in principle - but it is the principle of recursive genome function.

[Color version of the figure, not in the paper, is below]

Fig. 5. (From Figs. 1. and 2. of Crick 1970). Left side permits an infinite number of possible recursive paths.
Right side arbitrarily prohibits the main path of recursion by "dead-ending" proteins.
The DNA>RNA>PROTEIN>DNA recursion is just a single obvious recursive path,
and the fractal approach already elaborated to some extent is just one of the possible recursive algorithms.

Fig. 6. Sketch of recursive genomic government of the growth of Purkinje neuron.
Starting from a primary information packet highlighted, a Y-shaped protein template is built by the "forward growth" process in accordance with the
simplified (Watson) picture through transcription of DNA to RNA and, in turn, RNA building nucleic acids that form a structural protein.
During the construction of the Y-shaped template, the primary gene is in a "turned on" condition. Thus, the most primitive primary part of the process retains
Watson's simplified scheme. In other words, the postulated process does not contradict to the process of "DNA makes RNA that makes proteins",
but goes beyond it, by violating both the forbidden feedback mechanisms and the notion of junk DNA.
In each recursive stepthe perused auxiliary information packet (formerly "junk DNA" or "regulatory DNA") is cancelled (methylated) upon perusal.

[Color version of the figure, not in the paper, is below]

Fig. 7. An example of a recursive-looking organism (Cauliflower Romanesca).
It is possibly grown by a Lindenmayer L-string replacement recursive algorithm, e.g. governed by the
DNA>RNA >PROTEIN>DNA ... recursion, a massively parallel process executed repeatedly.

[Color version of the figure, not in the paper, is below]


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