ProgramminggoffLife (Has ranked Amazon #1 in category) Printable description (see below for Free or bulk copies) Purchase options
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 
Professional video Highlights Presentation Excerpts
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
Minor typos removed 11/15/10 (including page 51 references [Bar08B] & [Far07])
Recommended sequence: video Presentation Book
The PoL DVD is available with packaged combinations of the "Programming of Life" book(s).
1) To order a single copy of each book and DVD, see purchase options
2) To order multiple copies of the book, and a DVD for non-profit educational use (such as a class), email don@scienceintegrity.net with details of the proposed use, statement that materials will not be sold (cost reimbursement is acceptable), and number of book copies needed. The reply will detail payment details. These royalty-free materials reimburse for costs, with the lowest costs being a full case (under $2/book, including media mail shipping to a US address).
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.
Pertinent Quotes from ProgramminggoffLife (these will make sense after reading PoL)
(vii) This book presents the basis for bioinformatics, which is the study of the information in life... By the time you finish this book, you will have a fairly good understanding of basic bioinformatics, as well as two important subsets, biosemiotics and biocybernetics... Biosemiotics is the characterization of the symbolic representations within life, which is filled with digitally-coded symbolic messages. Biocybernetics involves self-sustaining systems that integrate different levels of information and its processing, including controls and feedback, within biological systems. This is where "programminggofflife" fits in.
(37) Since life involves information, it must follow the rules of information theory, including that of transferring information... whatever the source of life (which is scientifically unknowable), the alphabet involved with the origin of life, by the necessary conditions of information theory, had to be at least as symbolically complex as the current codon alphabet.
(53) For functional communication (including controls) to occur, both sender and receiver of each communication step must know the communication protocol and how to handle the message. In each cell, there are multiple operating systems, multiple programming languages, specialized communications systems, encoding/decoding hardware and software, error detection and correction mechanisms, specialized input/output channels for organelle control and feedback, and a variety of specialized "devices" to accomplish the tasks of life... The challenge for a purely physical origin of such a cybernetic complex interacting computer system is the need to demonstrate that the rules, laws, and theories that govern electronic computing systems and information don't apply to the even more complex digital information systems that are in living organisms.
(83-84) 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.
Interesting quotes by others concerning information
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)
“Life is basically the result of an information process, a software process. Our genetic code is our software.” (Venter 2010 Guardian interview)
While money set aside lasts, a FREE copy will be sent to lending libraries, Have your librarian make the request via email to don@scienceintegrity.net, including the multi-line mailing address as text and subject "Free library circulation copy" (additional eligibility information is needed for non-standard libraries, e.g. non-US, junior high, or church-based).
Interviews: Cell as Computer System PoL Reviews UD EN
ISBN: 0-9823554-6-7 Buy from Science Integrity at Amazon ). Main Amazon link (see book/DVD special price above)
Reviews/endorsements: Amazon Average Customer Review: 5.0 out of 5 stars See all reviews (4 customer reviews)
"The Programming goffLife 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
Broaden Your Appreciation for Life's Complexities, March 5, 2011 Amazon review by Professor Donald Mitchell (an Amazon top 10 reviewer)
A few years ago a good friend asked me what the likelihood was of the current version of evolution theory being correct. I had never been asked the question before and didn't have an answer in mind. My response was that I thought that there was some slight possibility that it could be correct, but that possibility was clearly a lot less than 10 percent. I noted at the time that much of the evidence that evolutionists cite appears to have mistaken the ability of genetic code sequences to be turned on and off by environmental influences for creating new species. Studies, for instance, of Darwin's finches have shown that what Darwin observed in the Galapagos were not new species being formed by trial and error over the eons, but rather genetic potential being turned on and off by quick shifts in the weather.
After reading ProgramminggoffLife, I can safely correct my false views. Like many scientists, my views of how complicated life is were wildly oversimplified. Life is often talked about in physical terms, using everyday analogies. When we mentally employ those analogies, we misstate the problem.
Dr. Johnson concisely defines life in terms of its information content, citing many different scientific sources. Viewed from this more complete perspective, there's no chance that the current evolutionary theories are correct.
I found it refreshing to see such an examination be conducted solely from a scientific perspective. Too often, evolution is uncritically praised or challenged in nonscientific ways. For those who like to understand a subject, it's better to use scientific concepts and perspectives to address a scientific theory.
Clearly, a new theory for the origin of species is needed. Who will provide one?
If you would like to get past any misunderstandings you have about how random interactions might have created life, read this book.
I couldn't help but think that high schools, colleges, and universities would be well served to have independent libraries available that specialize in thoughtful resources for understanding ourselves and our world from both the perspectives of thinking (science and logic) and faith (the Gospel). Otherwise, many young people will graduate from whatever school they attend with many incorrect views about the world.
The ProgramminggoffLife book is excellent!, October 2, 2010 Amazon review by "Algorithm"
"The ProgramminggoffLife 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. Sheer brilliance. "
The Rosetta Stone Inscription a Product of Mindless Erosion?, October 21, 2010 Amazon review By Sioux Smith "book it"
The Rosetta Stone Inscription a Product of Mindless Erosion?
After reading ProgramminggoffLife, you will realize that it is far more likely that the Rosetta Stone inscription is really the lucky result of mindless erosion than it is that the astounding functional complexity of a single cell came about mindlessly and accidentally. Far more information than is inscribed on the Rosetta Stone had to be correctly inscribed in the DNA molecule, a biological storage device (analogous to the disk drive in your computer), that contains the digitally encoded instructions required for the assembly of the protein machines that enable the cell's metabolism.
Dr. Johnson makes clear how infeasible the proposition is that prescriptive information, like that in the code for Microsoft Word, or in the instructions in the DNA molecule, came about mindlessly. What completely natural, mindless, accidental scenario could bring about the digitally encoded instructions required for building the necessary nanotechnology for that first life form's metabolism and reproductive ability? As Dr.Johnson puts it, "For abiogenesis, we could consider ... the probability of forming ... the simplest form of living organism known as 10^-340,000,000 [Mor79]. These figures make these scenarios operationally falsified [Abe09U]. There really is no need for them, however, since the probability of a purely physical source of information contained in life is 0 (impossible, according to information science) based on alphabet requirements for information transfer [Sha48, Yoc05p182] and the complex coding and prescriptive cybernetic information processing systems in life."
As one who has been doing computer programming for years, having written telephony software to manage digital switches and created a program language compiler and interpreter, I knew intuitively that digitally encoded instructions creating complex functionality do not and cannot come about mindlessly. Dr. Johnson enables one to transition from intuitive knowledge to exact understanding. This is true especially regarding the light information science sheds on the matter.
If it is unlikely that the Rosetta Stone, which provided the key to modern understanding of Egyptian hieroglyphs, came about mindlessly, it is even more unlikely that the one who created the inscription on it came about mindlessly.
Computer science merges with molecular biology, December 31, 2010 Amazon review By Dave
The book "ProgramminggoffLife " is a welcome resource towards substantiating the significance of computer science as it relates to the biological regulatory processes, information and control structures in the cell. As a controls systems engineer, I find this book illuminates both the algorithmic and computability side of the DNA system as well as the discretization of biological information and its implication on control of cellular processes. This book will prove to be valuable to bioengineering students and those in bioinformatics as it establishes the foundation for a new paradigm of computer like processes, execution and information processing. This work highlights hypothesis's that set the stage for the integration of computer science principles that earn it scientific credibility.
Superbly Reasoned and Presented, December 30, 2010 Amazon review By Gilbert Dodgen
The thesis presented in Don Johnson's book is thoroughly rational and his logic is essentially irrefutable. In fact, anyone with experience in nontrivial computation should be able to figure out that what he presents is easily recognizable. .. My research has been published in the premier international journal concerning games-playing artificial intelligence, the ICGA Journal, and a PDF is available at my website. If you have sufficient bandwidth you can download my 12-gigabyte mega-checkers program for free, including my perfect-play databases, which no one else has computed.
The ultimate foundation of living systems is informational -- not chemical, stochastic, or a combination of the two -- and Don's beautifully articulated and well documented book lays the groundwork for understanding basic information-theoretic concepts (Shannon, functional, prescriptive) and how they relate to biological systems.
Some familiarity with basic mathematics is advised, but this should not be a problem for people with a reasonable high-school education.
I cannot recommend this book highly enough, especially for those with inquisitive minds.
For non-scientists, too, December 30, 2010 Amazon review By J. Nilo A gripping and well-written book on a fascinating subject. I have very little science background, yet here the concepts are thoroughly explained, and are clearly and logically presented. This book deepens my understanding of and appreciation for the complex information systems allowing life as we know it to exist.