Prescribed Reading On Prescriptive Information

Description of "Programming of Life." This book highlights the informational aspects of life that are usually overlooked or ignored in chemical and biological evolutionary scenarios. Each cell of an organism has thousands (or millions) of interacting computers reading and processing digital information using algorithmic digital programs and digital codes to communicate information. Life is an intersection of physical science and information science. Both domains are critical for any life to exist, and each must be investigated using that domain's principles. Yet most scientists have been attempting to use physical science to explain life's information domain, a practice which has no scientific justification. 1 Math Basics: Probability and Large or Small Numbers 2 Information Basics: Data and Information Types 3 Evolution of Computer Hardware and Software 4 Life Basics 5 Shannon Information in Life 6 Prescriptive Programming Information in Life 7 Combining Life’s Information Types 8 Programming Increasing Complexity in Life 9 Unresolved Difficulties of Life's Information Requirements References – over 350 from multiple disciplines Eight appendicies for added depth of coverage This book stresses the principles of information science to show that the natural scenarios proposed so far fail to account for life's information and related processing systems. The book doesn't propose any alternative scenario, as that would fall outside science, just as the current scenarios do. After reading PoL, the terms used in these final paragraphs of the book will make sense. Known facts of life include its extreme cybernetic complexity, with millions of interacting co-dependent structures and components. Life is cybernetic in that it generates and controls its components using its components. Life’s control and communication is digitally-based, and can be analyzed as a multi-computer system. Some of the specific problems that require explanation before propagating naturalistic speculations as science include the following. How did nature write the prescriptive programs needed to organize life-sustaining metabolism? Programs are shown by computer science to require a formal solution prior to implementation. How did inanimate nature formally solve these complex problems and write the programs? How did nature develop the operating systems and programming languages to implement the algorithms? How did nature develop Turing machines capable of computational halting? How did nature develop the arbitrary protocols for communication and coordination among the thousands (or millions) of computers in each cell? How did nature develop multiple semiotic coding systems, including the bijective codon-based coding system (for symbolic translation) that involves transcribing, communicating, and translating the symbolic triplet nucleotide block-codes into amino acids of the proteins? How did nature develop alternative generation of such messages using techniques such as overlapping genes, messages within messages, multi-level encryption, and consolidation of dispersed messages? A protein may obtain its consolidated prescriptive construction instructions from multiple genes and/or from the "junk" DNA, sometimes with over a million nucleotides separating the instructions to be combined. How did nature defy computer science principles by avoiding software engineering’s top-down approach required for complex programming systems? How did nature produce complex functional programs without planning by randomly modifying existing algorithms? How did multiple such programs become simultaneously modified to result in the production of irreducibly complex structures? Speculation is important when generating or imagining new scientific theories. Scientists should strive to keep such speculation within the scientific community, however. Since the public tends to view what a scientist expresses as a view or belief as being "truth," it is important not to propagate unsubstantiated speculation as something worthy of consideration by non-scientists. It should be noted that all science is tentative, so new findings may require modification of what is considered "true." The questions raised in this book require scientific answers before promoting as "science" any scenario for the origin of life or the origin of species. Perhaps different avenues of thinking are required in order to find scientific "truth" in these areas. Doggedly insisting that a scenario is true despite the evidence is unscientific. Maybe it’s time to leave the "flat-earth" mentality that views things only from a particular limited perspective, and really examine what science is telling us. Evolutionary biologist George Williams observed, "Evolutionary biologists have failed to realize that they work with two more or less incommensurable domains: that of information and that of matter... These two domains will never be brought together in any kind of the sense usually implied by the term ‘reductionism.'... Information doesn't have mass or charge or length in millimeters. Likewise, matter doesn't have bytes... This dearth of shared descriptors makes matter and information two separate domains of existence, which have to be discussed separately, in their own terms." (A Package of Information," in The Third Culture: Beyond the Scientific Revolution, 1995, p42-43) Richard Dawkins wrote, "The machine code of the genes is uncannily computer-like. Apart from differences in jargon, the pages of a molecular biology journal might be interchanged with those of a computer engineering journal." (River Out of Eden: A Darwinian View of Life, 1995, pg. 17) Carl Sagan wrote: "The information content of a simple cell has been established as around 1012 [a trillion] bits, comparable to about a hundred million pages of the Encyclopaedia Britannica." ( "Life," Encyclopaedia Britannica: 22, 1997, p964-981)tgpeeler

October 14, 2010

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http://scienceintegrity.net/ProgrammingofLife.aspx New book. Reviews/endorsements follow. "The Programming of Life is an excellent freshman level review of the formal programming, coding/decoding, integration, organization, Prescriptive Information (PI), memory, regulation and control required for a physical object to find itself “alive.” Donald E Johnson, with Ph.Ds in Chemistry, Information Theory and Computer Science, is uniquely qualified to unpackage the strong parallels between everyday cybernetic design and engineering and the workings of the cell. I highly recommend this book." David L. Abel, Director, The Gene Emergence Project, Department of ProtoBioCybernetics and ProtoBioSemiotics, The Origin of Life Science Foundation, Inc. "In the pandemonium of forward progress regarding the design of technological systems based on natural science, Dr. Johnson pauses to contemplate the implications of these discoveries and developmental theories of information science as they apply to the current theories of the origin of life and species diversity." Joshua A. Mitchell, Biologist / Regulatory Project Manager, US Army Corps of Engineers "This is currently the best book covering the relationship between genome and computer architectures." Jonathan Bartlett, Director of Technology/Author / Speaker "You have put together an amazing array of quotations from scientist of all persuasions, and given so much information that I think that anyone who wants to dismiss [information]... from the equation of life must be doing so out of some religious zealotry rather than from a hard look at the facts. Jim Pappas, Author/playwright/producer "The Programming of Life by Donald E. Johnson is an excellent presentation of the parallels between the everyday practical cybernetics of computer science and the programming, control and regulation mechanisms of cellular life. The book is easily understandable by non biologists, and seems to be written on a college freshman level. It has good illustrations. It also has extensive citations and quotes from peer-reviewed literature. It's perspective and content are well supported, and should be readily received by a properly skeptical scientific community (of which I am a member). The book is a fun, quick, interesting read of under 150 pages. In my opinion, the book is amazingly underpriced for what it provides. I cannot recommend this book highly enough. It provides a unique education that I have never seen available from any source other than technical scientific literature, but it is wonderfully explained in lay terms. This would be a great mini text for public high school AP Biology classes." Bringing Life Sciences Into the Twenty-First Century, October 2, 2010 Amazon review by Morris Hedge "This book addresses head on an issue which has been retarding understanding of life--failure to adequately consider its information processing aspects. After reading this book it will become clear why this failure must be corrected. One very critical reason is to put medical science on a more sure-footed path, one which more readily corresponds to reality; for example, the author points out that all human organs previously thought to be vestigial are now known to have functions--at the molecular level this means there is no "junk DNA". This book is very readable for anyone with a modest mathematics or science or computer science background to include, of course, computer programming. The light will really shine as the reader comprehends these topics as operating in profound ways at the lowest level of life. It made me wonder how such purposeful, directed information came to be in the very first cell, at the origin of all life. The book is replete with attributed quotes, references, and appendices expanding upon difficult topics introduced in the text. I believe it should be on the shelf of all scientists and mathematicians. " Prescriptive Information Brings Fresh Perspective To The Evolution Debate, October 8, 2010 Amazon review by Robert Deyes "There are some science writers that quite simply have a knack for combining the detail of their subject of expertise with a talent for exposition that a wide audience can easily understand. Donald Johnson is one of them. After carefully defining the various types of information- functional, prescriptive and Shannon- that information theorists have set out in their realm of study, Johnson takes the reader on a tour of cellular gene expression by focusing on the digital code of DNA. Shannon information, which provides a mathematical measure of improbability without regard to functionality does not help us in the description of life since the digital code of DNA is rich in what Johnson terms 'functional prescriptive information'. While initiatives such as the Origin Of Life Prize have encouraged researchers to find non-super-naturalistic processes that might explain the origins of prescriptive information, no offerings to-date have withstood the test of scientific scrutiny. Indeed all known cases of such information invariably point to the work of a mind. Johnson emphasizes the relevance of probability in his espousal of this inference- the simplest form of life was found to be 10exp80,000 times more likely of having a mindful than a non-mindful source. Johnson repeatedly stresses how the information content of DNA is analogous to the information carried on a computer disk drive.Within such a schema, each of the enzymes that decode the information can be seen as individual computers that bring `meaning' to the code through the RNA that is transcribed and the proteins that are translated. 23,000 genes make up the human genome. And the multi-functional nature of these genes in self evident in the way that RNAs are differentially spliced and glued together. Johnson's perspective packs a might punch on the evolutionary edifice. Computer simulations and evolutionary algorithms such as MeThinksItIsLikeAWeasel and AVIDA have failed to show how evolution can generate prescriptive information since pre-specified targets, unrealistic protection of replication instructions and unrealistic energy rewards abound in each of these systems. While the battle over the categorization of junk DNA rages on amongst biologists, Johnson gives us a succinct and well-buttressed view on the subject: "Researchers are discovering that what has been dismissed as evolution's relics are actually vital for life". There is no evidence that new prescriptive information can be built up by genetic rearrangements such as transposition, inversion, duplication or point mutation. We can therefore understand Lynn Margulis' reference to the Darwinian claim as a `half truth' grounded in religious ferocity. This half truth forms the foundation for Johnson's final attack as he considers the merits of irreducible complexity and Craig Venter's recently produced artificial genome. Rather than showing how an organism could arise from scratch, Venter's enterprising achievement revealed the need for careful engineering of existing parts into a form that could be introduced into an existing organism. Johnson's writing style is captivating. The extensive range of resources he draws from only serves to build confidence in the factual accuracy of his case. What a terrific read. Shear brilliance. "tgpeeler

October 14, 2010

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Exactly, Tom, It seems to me the materialist's ball park has two home plates. One is the repeated (and intellectually nauseous) obfuscation over the existence and definition of information. The other is the denial of the self.Upright BiPed

October 11, 2010

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"Johnson repeatedly stresses how the information content of DNA is analogous to the information carried on a computer disk drive." I have tried, with little effect, as far as I know, to make the argument that it is impossible IN PRINCIPLE (really impossible, logically impossible, in other words) for any naturalistic account of information to be true. If methodological naturalism (or materialism or physicalism) entails that "natural causes" can explain everything (ontological naturalism), and it does entail that because that's part of what naturalism means, it's part of the definition, then naturalism must be able to explain information. I believe this argument applies perfectly well to biological information but even if not, surely it is decisive against naturalism itself. Here's why. "Natural causes" means physics. Thus, naturalism claims that all phenomena in the universe (or at least on this planet/solar system/galaxy) can be explained by the laws of physics. That is, nature is causally closed. That is, if one traces back along an antecedent chain of causes, one will never leave the "natural" realm as described by physical laws and enter into the realm of the mind. Since mind does not exist. And if mind does not exist (if mind = brain) then how could anything that does not exist have causal power in nature? I think I've been fair to naturalism here. But here's the problem. Information requires language. We cannot conceive of information apart from language. Language is the tool that allows us to encode abstract thoughts into physical substrates for transmission, reception, and decoding on the other end. All languages, whether human or animal, consist of symbols and rules for the manipulation of those symbols. In English, we call these rules vocabulary, grammar, and syntax. But how to explain the symbols and/or the rules in terms of physics? It's impossible in principle because the laws of physics only have things to say of sub-atomic particles in energy fields, i.e. physical or material or natural things. There is no law of physics that suggests that "dog" means a certain kind of mammal and "god" means a supernatural being of one kind or another. Those are freely agreed upon conventions by, in this case, English speaking people, and nothing in physics has anything to say about it. Another way to look at it is that this merely points out the logical flaw in naturalist thinking which is the denial of the "spooky" world of causal forces outside of nature, whether those be souls or God, i.e. mind/Mind. Naturalism in essence, must say that information does not exist because it cannot explain it. Naturalists deny other things that are self-evident to all sentient and rational beings such as purpose, design, and a moral law. Those things can be denied without self-contradiction so we must weigh the evidence on either side to make our choice. But the REAL existence of information cannot be denied without self-contradiction because to deny information is to communicate information. Game, set, match. Or so I say. I also think this argument can be used to great effect on the evolution front. The only challenges I have received on UD are "Well, what IS information, after all?" Funny that the people communicating information can't seem to grasp the concept of it.tgpeeler

October 11, 2010

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