Principle of Recursive Genome Function

e-mail: Andras Pellionisz

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Principle of Recursive Genome Function

by Andras Pellionisz

Article in SpringerCerebellum d.d. June 2008

Responding to an open request, the principle of recursive genome function(PRGF) is put forward, effectively reversing two axioms of genomics as we used to know it, prior to the Encyclopedia of DNA Elements Project (ENCODE).

The PRGF is based on the reversal of the interlocking but demonstrably invalid central dogma and “Junk DNA” conjectures that slowed down the advance of sound theory of genome function, as far as information science is concerned, for half a century.

PRGF illustrates the utility of the class of recursive algorithmsas the intrinsic mathematics of post-ENCODE genomics.

A specific recursive algorithmic approach to PRGF governing the growth of the Purkinje neuron is sketched, building the structure in a hierarchical manner, starting from primary genomic information packets and in each recursion using auxiliary genomic information packets, cancelled upon perusal.

The predictive power of the principle and its experimental support are indicated. It is argued that genomics is no longer an exceptional instance of the applicability of recursion throughout
the sciences.

So: the genome function is a fractal function.

Authors - not involved in the study - comment:

"Epigenetics is rapidly revising Darwin and opening whole new realms in medical science and technology. Dr. Andras Pellionisz, who is Director of Genome Informatics at Mitrionics in Silicon Valley, saw it all coming decades ago. A scientific visionary, Pellionisz has made a career of being ahead of his time. His profoundly influential work on the mathematics of brain function inspired generations of leaders in neuroscience, including the Churchlands. This time around, his far-sighted work on fractal mechanisms in genetics has recently been vindicated. Pellionisz drew attention early on to the fractal character of dendritic trees. He then moved on to genetics, where he argued that gene expression is not, as was dogmatically asserted, a one-way street from DNA to organism, but rather a recursive process akin to the generation of fractals. Today, in groundbreaking work on 'nanotrees,' scientists have produced a spiral shape akin to the helical structure of DNA -- an aperiodic crystal. Nanotrees are microscopic structures which result from crystalline 'defects' in nanowires. Although these developments are fast-breaking and the implications have yet to be worked out, it seems clear enough that we have here a direct path from the atomic symmetries of quantum theory thru simple fractal crystals thru DNA and on up the ladder to fractal neurons. What's also clear is that these developments open entire new vistas for R&D on medical diagnosis, therapy and up to cure for a host of diseases and hologenomic risk factors and disorders." [Brian Flanagan, USA]

--- "PRGF of Pellionisz is helping not only his algorithmic recursive approach to the genome (FractoGene), but puts ‘epigenetics’ into the perspective of clearly defined novel axioms. The PostModern Age of Genomics (starting with his PostGenetics), embraces many interpretations and examples of ‘epigenetics’ and is synthesizing haphazard notions into a solid scientific foundation of our era of HoloGenomics". [Alexandre Akoulitchev, Fellow of the Royal Society of Medicine, Oxford University, UK]

--- “Based on Pellionisz' 'Principle of Recursive Genome Function' the puzzling history becomes understandable why the first wave of suspecting fractality of DNA in the late 1980-s and early 1990-s by his own fractal Purkinje neuron model (1989), and efforts by Drs. Buldyrev, Stanley et al (1993), Flam 1994, Mantegna (1994) could not break through. They violated not one, but two prevailing dogmas - and could not provide a replacement for the dogmas of "junk DNA” and “No feedback recursion". Now, with Pellionisz’ Principle, such unifying synthesis is available to greatly facilitate progress. Therefore, an avalanche of recursive algorithms is likely to ensue his breakthrough. Fractals, however, are very computation-intensive, though both an algorithmic approach, and especially the data-compression by fractals are likely to significantly ease the burden of a brute-force approach to cope with the dreaded DNA data-deluge." [Jules Ruis, Director of EU Center of Excellence of Fractal Design, THE NETHERLANDS]

--- “The Principle accounts for and smoothly puts together hitherto ill-fitting pieces in the old puzzle. The different picture, with a new meaning, calls for a new name. With PRGF, the unresolved relationship between mathematical information and biological formation is explained by the repetitive action and consequent feedback of the genome where any incremental DNA information refines a formative protein growth, governed e.g. the algorithmic guidance of fractals. Reading The Principle, Eugene Wigner’s reminder in the year of discovery of Operon regulation (1961) rings loudly in our ears: ‘There is a contradiction between the model of reproduction proposed by Crick and Watson, in which a determined mechanism is transferring the characteristics to the descendants. This model is also based on classic and not quantal concepts ... the particulars of this model are not completely worked out (Eugene Wigner; The Probability of the Existence of a Self-Reproducing Unit, In: The Logic of Personal Knowledge, Routledge and Kenan Paul Ltd, London 1961 p. 231)’” Another early giant, John von Neumann , architect of both serial and parallel computers in the 1940s-1950s would probably look upon this progress with interest as well, since genome computing is likely to bring about a synthesis of both architectures. [The Michael Conrad Group for Bioinformation and Biocomputation Research; E. Perjes, E. Pataki and I. Szentesi, HUNGARY]


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