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Donald E. Johnson Bibliography
Dr. Johnson's website:
Science Integrity - Exposing Unsubstantiated Science Claims
Cells Are Like Robust Computational Systems, - June 2009
Excerpt: "We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail."
Nanoelectronic Transistor Combined With Biological Machine Could Lead To Better Electronics: - Aug. 2009
Excerpt: While modern communication devices rely on electric fields and currents to carry the flow of information, biological systems are much more complex. They use an arsenal of membrane receptors, channels and pumps to control signal transduction that is unmatched by even the most powerful computers. http://www.sciencedaily.com/releases/2009/08/090811091834.htm
Ben Stein - EXPELLED - The Complexity of the Cell - video
The Capabilities of Chaos and Complexity - David L. Abel - 2009
Excerpt: "A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes.
The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy
John Sanford, a leading expert in Genetics, comments on some of the stunning poly-functional complexity found in the genome:
"There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). (Dr. John Sanford; Genetic Entropy 2005)
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. - 2009
Excerpt: We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
Here is a site that gives a clear example of what Dr. Sanford means by Poly-Functional equals Poly-Contrained:
Poly-Functional Complexity equals Poly-Constrained Complexity
Intelligent Design - The Anthropic Hypothesis