# Programming of Life

### Donald E. Johnson

Don Johnson is a Ph D Chemist with also a PhD in Computer and Information Sciences. He writes in compact fashion, the kind of style you might expect from a scientist. My second impression was that the book is a goldmine of quotes - he has really read a lot of stuff, and has compact collections of relevent quotes, sort of like "data bursts" of quotes.

Johnson carefully lays out the process of communicating by a code. The code has to have a definite syntax, definite semantics (meanings of the symbol combinations) and the receiver of the code has to have the ability to use the coded message to accomplish something functional. The code, essentially by definition, must be independent of chemistry and physics. So it is difficult to see how the combination of chance and necessity can build a code system to accomplish a purpose or function.

Introduction

pviii "life contains a multitude of complex programming algorithms whose origin by physical interactions cannot be explained using information science"

pviii "the claim that 'we don't have a natural explanation yet, but we will someday' is not a scientific statement. It amounts to a 'naturalism of the gaps' dogma."

1. Math Basics: Probability and Large or Small Numbers

p2 "chance has no causative effect. Chance expresses liklihood, not cause - nothing is 'caused by chance'"

p 3 Calculation of the number of trials to make winning the lottery probable, i.e. to make the probability >0.5

p5 Borel's guideline 10-50 to be called negligible probability.

p6 List of probabilities under UPP (Universal Plausibility Principle). 10-70 for any process on Earth.

p6 Criticism of the use of "it is possible that".

2. Information Basics: Data and Information Types

p7 "The question 'How did life originate?' which interests us all, is inseparably linked to the question 'Where did the information come from?' Since the findings of James D. Watson and Francis H. C. Crick, it was increasingly realized by contemporary researchers that the information residing in cells is of crucial importance for the existence of life. Anybody who wants to make meaningful statements about the origin of life would be forced to explain how the information originated." Werner Gitt "In the Beginning Was Information", 1997. Werner has written articles for AIG, particularly in opposition to evolution.

p7 DNA is an information system which is digital and of base 4.

p7 Information: Shannon, functional, prescriptive "Information always involves contingency that rules out other possibilities."

p8 Comparisons of information. Example of the three types of information.

p11 "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." Richard Dawkins, River Out of Eden, 1995, p17.

p11 Longer definitions of functional, prescriptive and Shannon information.

3. Evolution of Computer Hardware and Software

p13 "Turing-complete" defined. This chapter is a neat brief history of computing.

4. Life Basics

p17 Good condensed introduction to terms - reread with my biology section in mind.

p18 Neat operational definition of an enzyme

p18 "Life's enzyme catalyzed reactions take place in the millisecond time-frame." Points out that there can be a time range of 1019

p18 Good quote of Wolfenden's 03 paper describing a trillion year reaction

p20 "Nobody knows how it happened but, somehow, without violating the laws of physics and chemistry, a molecule arose that just happened to have the property of self-copying - a replicator" Richard Dawkins, Climbing Mount Improbable, p282-3.

p20 More good origin of life quotes.

p21 Discusses "RNA world" and calls it "currently the most widely accepted scenario". The 89 Nobel Prize was given for the demonstration of ribozymes, RNA functioning as an enzyme. Could have inorganic templates, but no resolution of the question about where the information came from. Should compare with his RNA World discussion on pg 37ff of PNNP where he quotes from Orgel, communicating more some of the optimistic view of the RNA World. Here he quotes more from Abel who is more pessimistic about it.

p22 "since life obviously exists and the only allowable mechanism is physicality, it must have occurred that way, despite the improbability" This is a tautology since "life exists" is obviously true so this statement is using the proposition "life can only be the result of purely physical sources" to prove itself.

p22 From Nobel Prize winner Ilya Prigogine "The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero." Prigogine, I., Gregair, N. and Babbyabtz, A. "Thermodynamics of Evolution", Physics Today:25, 1972, p23-28.

p23 Discussion of helicases, the enzyme proteins that form molecular motors that use ATP to break hydrogen bonds and unwind the DNA double helix into single strands, an essential part of cellular reproduction.

p24 From Jerry Bergman Scale up DNA by a factor of one million to equivalent of two 125-mile long strands of fisherman's monofilament line, wrapped together to form a double-helix structure, neatly folded and packed into a basketball-sized cell nucleus. The entire length must be split apart and duplicated to form two identical sets and packed into two new basketballs. There are about 25 million spools around which the DNA is wrapped, and the initiator protein must find the beginning point so that the helicase "unzipper" can unwind the strands at about 8000 rpm. The process involves over 30 specific functional proteins.

p25 Discusses the base-4 digital code, ACGT, 64 codons, genetic code.

p26 Discusses overlapping genes. Human genome of some 31,000 genes can code for 100,000 to 200,000 distinct proteins because of overlapping genes.

p27 sub-coded information - "three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain"

p27 Epigenetics

p27 Discusses idea of codes within codes, when even direct codes have not been explained by reference to any non-intelligent source.

p28 Dawkins' "appearance of design" quote

p28 Assertion that the DNA alphabet is optimum, "the best of all possible codes" according to Freeland et al., "Early Fixation of an Optimal Genetic Code", Molecular Biology and Evolution: 17, 2000, p511-518.

p28 Cites MacDonaill on a chemical structural parity-bit "error-coding approach is coupled with chemical constraints, the natural alphabet of A, C, G, and T emerges as the optimal solution for nucleotides."

p29 The improvement of error correction from the redundancy of the genetic code is addressed by Hubert Yockey in his "Information Theory, Evolution and the Origin of Life" and the conclusion is that error correction and repair make mutations very rare.

p29 "If genomic DNA is the cell's planning authority, then the ribosome is its factory, churning out the proteins of life. It's a huge complex of protein and RNA with a practical and life-affirming purpose - catalyzing protein synthesis. Bacterial cells typically contain tens of thousands of ribosomes, and eukaryotic cells can contain hundreds of thousands or even a few million of them" Stu Borman, "Protein Factory Reveals Its Secrets", Chem & Eng News: 85(8) 2/19/2007, p13-16.

p29-30 Nice quote from Kim on epigenetics as affecting gene expression.

p30 Data on brain. 100 billion neuron cells, each linked to as many as 10,000 other neurons, 1015 total synaptic connections, 1016 operations per second which exceeds all the computers in the world put together. "This means that the most powerful "electrical" computer system in the world resides in the top of your head."

p30-31 Eloquent couple of pages on the brain and its operation.

p31 Discusses the genome and includes a quote from Dawkins, The Information Challenge. Wonderful quote to show the complexity of the genome. Also discusses monarch butterfly.

5. Shannon Information in Life

p33 Good quote of George Williams on the separate domains of matter and information.

p33 Several nice quotes reinforcing the idea that the implementation of the genetic code in DNA is as a true code, unconstrained by the physics and chemistry of attachment.

p33 "There are no chemical bonds between the bases. Thus, there are no chemical rules to determine the order in which the bases will be attached to the background." Davis, Jimmy and Harry Poe, Designer Universe, 2002.

p33 "One cell division lasts from 20 to 80 minutes, and during this time the entire molecular library, equivalent to one thousand books, is copied correctly." Werner Gitt, In the Beginning was Information, 2002

p33 "DNA is a neutral carrier of information, independent of its chemistry and physics .." George Gilder, "Evolution and Me", National Review, 7/17/06.

p33 This chapter summarizes the nature of Shannon information and asserts that whatever code was present in the origin of life must have been at least as complex as the current code, since by mathematical proof it cannot go from less complex to more complex.

p38 Reiterates fact that random data has the highest Shannon information, though it has no functionality. Also called Shannon entropy.

6. Prescriptive Programming Information in Life

p39 Interesting long quote including "no paper has provided a plausible mechanism for natural-process algorithm-writing.." Trevors, J.T. and Abel, D. L., "Chance and Necessity Do Not Explain the Origin of Life", Cell Biology International: 28, 2004, p729-739. David Abel has a lot of papers in peer reviewed journals dealing with this subject.

p39 "Formal algorithmic prescriptive information (PI) is the key to any successful computer program, including the programs within life." This chapter is a very compressed set of reiterations of that theme.

p39 "The essence of prescription itself is choice contingency. Purposeful intent is required at each successive decision node in order to choose configurable switch-settings (or equivalent) and to steer events toward functional results. "

p39 Prescriptive information "instructs or directly produces nontrivial function.."

p39 "PI involves formal choices at decision points that cannot be generated by randomness or law(necessity)."

p40 "information in life is fundamentally formal, not just physical" This is the introduction to a detailed discussion of what "formal" means and implies.

p40 "For prescription to be realized, the destination of any message must have knowledge of the source's alphabet, rules and cipher. The destination must also possess the ability to use the cipher." (Abel, David, "The Biosemiosis of Prescriptive Information", Semiotica, 1/4/2009 p1-19.) "A cipher is an algorithm to perform encryptation or decryptaton." He gives the example of the message "Ju xpslt", which is meaningless unless you know that the cipher is to replace each letter by the one immediately preceeding it in the alphabet so that you can understand the message "It works".

p40 Lots of information science vocabulary in this chapter, like "cybernetics" - the study of control systems with feedback. Requires the three categories syntax (grammar rules), semantics (message meaning) and pragmatics (message function). Semiotics refers to symbols and their meaning, and biosemiotics when it applies to living systems.

p40 Abel does get his back up about this rejection of "formalism" in life's systems: "But when it comes to life's syntax, semantics and pragmatics, we fanatically insist for metaphysical reasons that the system is purely physical. No empirical, rational, or prediction-fulfillment support exists for this dogma." Abel, op cit.

p41 Another long quote from Abel.

p41 "Formalism" is a key word in this chapter and a strong assertion that there are types of non-material prescriptive information that cannot be arrived at by either chance or necessity nor a combination of the two.

p41 "Because of metaphysical beliefs, many scientists recognize only chance and necessity, and dismiss out-of-hand any non-material reality."

p41"Biological information is not a substance ... biological information is not identical to genes or to DNA (any more than the words on this page are identical to the printers ink visible to the eye of the reader). Information, whether biological or cultural, is not a part of the world of substance." Hoffmeyer and Emmeche, 2005

p41 More vocabulary for three qualitative kinds of sequence complexity: random(RSC), ordered (OSC) and functional (FSC). Only in FSC can you have algorithmic instruction. Shannon information theory applicable only to RSC and OSC, cannot measure FSC.

p42 "No empirical evidence exists of either RSC or OSC ever having produced a single instance of sophisticated biological organization."

p43 Abel waxes eloquent about the brilliance of the algorithms in Mycoplasmas, the simplest known organism with the smallest genome. Then asks "How was its genome and other living organisms' genomes programmed?"

p44 Abel again "No empirical support or rational plausibility exists for blindly believing in a relentless natural-process ascent ... toward mountain peaks of formal functionality."

p44-45 Discusses the \$1 Million OOL prize. The wording of the OOL challenge specificically excludes anything supernatural, and its requirements are clearly far beyond anything which has to date been accomplished.

p45 Discussion of "traversing The Cybernetic Cut" "Crossing the Cybernetic Cut requires the ability to purposefully steer through successive bifurcation points down a path toward a desired goal..."

p46 "What exactly is the missing ingredient that renders life unique from inanimate physics and chemistry? The answer lies in the fact that life, unlike inanimacy, crosses the Cybernetic Cut." Abel, David 2008.

p46 "No feasible source of life's prescriptive algorithms has been proposed to date. The speculations proposed thus far are 'dreams', based on the belief that physicality is the only reality, and therefore 'must have' produced life's cybernetic complexity. Information science, by contrast, recognizes non-material formalism as the only reality capable of producing PI."

7. Combining Life's Information Types

p47 Uses programming a remote control for a DVD player as an example of the way different types of information are combined - and asserts that the same kind of combination of elements are used in the cell.

p48 Laws for information: Must have code, code determined by rules and not constrained by necessity, have a sender (agency), must have formal source.

p49 "chance and necessity cannot explain sign systems, meaning, purpose and goals." Sign systems here refers to codes and the rules for sharing information via the codes.

p49 Example of an hypothetical architects plan of a house, which if thrown in the garden, will build the house. From Wilder-Smith, A.E., The Scientific Alternative to Neo-Darwinian Evolutionary Theory, 1987, p73.

p51 "One of many problems with metaphysical materialism is that it acknowledges only two subsets of reality: chance and necessity. Neither can write operating system rules or application software. Neither can generate hardware or any other kind of sophisticated machinery, including molecular machines (the most sophisticated machinery known)." Abel, David, 2007.

p51 Refers to at least 20 different natural information codes discovered in life, such as protein address codes, acetylation codes, etc. This is totally new to me.

p52-53 Description of the explosion of complication in RNA, transcription factors,

p54 "All the known laws, theorems and principles of information science indicate that codes, complex functional information, and prescriptive algorithmic information cannot arise from physicality."

p54 "In examining any complex functional information where the source of the information is known, it invariably (no known exceptions) resulted from a formal source, as opposed to chance and/or necessity."

8. Programming Increasing Complexity in Life

p55 Starts with two quotes from Dawkins' Blind Watchmaker and one classic quote from Darwin.

p55 "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would completely break down." Origin of Species p154

p57 Quote from Dawkins on "increasing Shannon information" shows that Dawkins is dealing with some of these ideas.

p57 Computer simulations, cites Dawkins' "Methinks it is like a weasel" simulation.

p58 Describes Avida

p61 Dawkins and Sagan on junk DNA

p62 Some challenges to idea that junk DNA is just chance driven

p62 Section on reassessing the view of junk DNA. Ref to App F.

p64-65 A number of quotes that target evolution in general. Several along the line that mutations decrease the amount of Shannon information. Dawkins does speak to that objection, admitting the loss of information but saying that the diminishing of the gene pool by natural selection leaves us with a net increase of information. Johnson replies on pg 57 that "This seems like the shop-keeper who lost a little on each sale, but made up for it in volume." Clever, but not entirely convincing - Dawkins has a point - it would seem to be possible that the amount of useful information toward the goal of survival might be increased by the combination of mutation and natural selection.

p65 But Abel certainly doesn't think so. He says "Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information... the amount of coding in DNA actually decreases with evolution... No increase in Shannon or Prescriptive information occurs in duplication." Abel 2009.

p65 From evolutionary geneticist H. Orr "We conclude - unexpectedly- that there is little evidence for the neo-Darwinian view: its theoretical foundations and the experimental evidence supporting it are weak" In "The Genetics of Adaptation: a Reassessment", Am Nat, 1992, p726.

p65 Biologist Lynn Margulis also comes down pretty hard on evolutionary evidence: "natural selection is of critical importance to the evolutionary process. But this Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric." Lynn Margulis and Dorian Sagan, "Acquiring Genomes: A Theory of the Origins of the Species", 2003, p29.

p66-68 Discussion of the fossil record and the problems posed by the Cambrian explosion.

p67 Cambrian quote from Dawkins' "Blind Watchmaker".

p67 Discussion of the development of eyes. Quote from R. L. Gregory, "Eye and Brain: The Psychology of Seeing, 2nd Ed.", 1972 p25 that summarizes the difficulties that eyes pose to the evolutionary model.

pp68 The story of the trilobite eye is particularly fascinating. It is an aspherical, aplanatic doublet made of calcite such that it corrects for spherical aberration - it would be a credit to a modern optical designer. It precisely aligns the optical axis of the calcite to eliminate double images from the doubly refracting nature of calcite. The comment of R Levi-Setti, author of "Trilobites: A Photographic Atlas" was "The design of the trilobite's eye lens could well qualify for a patent disclosure." Since the lenses are mineral, we have examples of them to study. A real problem for the Darwinian model. "Since no immediate precursors of trilobites have been found, Darwnists are without any evidence as to how an organism with an eye as complex as a trilobite could have arisen, especially in such a relatively short time in the lowest multi-cellular fossil-bearing stratum, near the very beginning of life." More detail in App F.

p70 Irreducible complexity, with a quote from Behe's "Darwin's Black Box".

p70-72 The bacterial flagellum - detailed description with some quotes from other authors. Rather thorough overview of the discussion of the bacterial flagellum.

p73 Irreducible complexity in the system of DNA/RNA/enzymes

p73 The mystery of sexual reproduction.

p74 Venter's manufactured genome.

p76 More quotes from biologists blasting strict neo-Darwinism.

9.Unresolved Differences of Life's Information Requirements

p79 Half dozen nice quotes to reiterate the conclusions of the previous chapters.

p80 Comments on Dean Kenyon's "Biochemical Predestination"

p80 A couple of Dawkins' quotes to set up the discussion of beliefs that are often presented as science.

p81 List of Jonathan Wells' 10 "icons of evolution"

Appendix C: Life Details and Origin Speculations

p106 More details on amino acids, peptide bonds, DNA, RNA

p107 More on RNA world

Appendix F: What Happened to Darwinism

p116 More details on junk DNA, different roles for RNA

p117 An excellent section on the trilobite eye including a number of quotes. Look at as an optics example.

Appendix H: Philosophical Hindrances to Scientific Truth

p121 Quote of Dawkins from "The Necessity of Darwinism".

p125 "Undirected physical processes as an absolute belief may have unintended impacts on society in addition to promoting unsubstantiated speculations as science."

p125 Quotes Ruse to the effect that there is no real basis for ethics.