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The First Gene: An information theory look at the origin of life

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The First Gene: The Birth of Programming, Messaging and Formal Control

Here, edited by David Abel, The First Gene: The Birth of Programming, Messaging and Formal Control :

“The First Gene: The Birth of Programming, Messaging and Formal Control” is a peer-reviewed anthology of papers that focuses, for the first time, entirely on the following difficult scientific questions: *How did physics and chemistry write the first genetic instructions? *How could a prebiotic (pre-life, inanimate) environment consisting of nothing but chance and necessity have programmed logic gates, decision nodes, configurable-switch settings, and prescriptive information using a symbolic system of codons (three nucleotides per unit/block of code)? The codon table is formal, not physical. It has also been shown to be conceptually ideal. *How did primordial nature know how to write in redundancy codes that maximally protect information? *How did mere physics encode and decode linear digital instructions that are not determined by physical interactions? All known life is networked and cybernetic. “Cybernetics” is the study of various means of steering, organizing and controlling objects and events toward producing utility. The constraints of initial conditions and the physical laws themselves are blind and indifferent to functional success. Only controls, not constraints, steer events toward the goal of usefulness (e.g., becoming alive or staying alive). Life-origin science cannot advance until first answering these questions: *1-How does nonphysical programming arise out of physicality to then establish control over that physicality? *2-How did inanimate nature give rise to a formally-directed, linear, digital, symbol-based and cybernetic-rich life? *3-What are the necessary and sufficient conditions for turning physics and chemistry into formal controls, regulation, organization, engineering, and computational feats? “The First Gene” directly addresses these questions.

As we write, it is #2 in biophysics, and the trolls haven’t even got there yet.

Here’s Casey Luskin’s review:

Materialists Beware: The First Gene Defends a Strictly Scientific, Non-Materialist Conception of Biological Origins:

The First Gene investigates a number of different types of information that we find in nature, including prescriptive information, semantic information, and Shannon information. Prescriptive information is what directs our choices, and it is a form of semantic information — which is a type of functional information. In contrast, Shannon information, according to Abel, shouldn’t even be called “information” because it’s really a measure of a reduction in certainty, and by itself cannot do anything to “prescribe or generate formal function.” (p. 11) Making arguments similar to those embodied in Dembski’s law of conservation of information, Abel argues that “Shannon uncertainty cannot progress to becoming [Functional Information] without smuggling in positive information from an external source.” (p. 12) The highest form of information, however, is prescriptive information:

Comments
Petrushka:
I find it interesting that ID advocates accuse the mainstream of reductionism, then proceed to reduce life to some vague notion of information.
Information is just part of a living organism. meaning ID does not attempt to reduce living organisms to just information. Not only that "information" is not a vague notion- civilization could not live without it.
Ignoring that rather obvious fact that emergent phenomena like protein folding are not amenable to prediction by computer, but are accomplished easily by chemistry.
Is that why chaperones are required to properly fold long AA chains?
Chemistry does things that are unpredictable and therefore not reducible to information.
Information is what allows for the atoms that chemistry requires.Joseph
November 19, 2011
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If I grant that DNA is a digital code, explain how one anticipates the utility of changes in the code. Give me a detailed, worked out illustration of how one anticipates the total net utility of a change equivalent to a point mutation, or any of the other couple dozen kinda of mutations and chromosomal rearrangements.Petrushka
November 19, 2011
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Steering toward utility is an interesting concept. Give me an example from the world of biochemistry. A drug, for example, whose utility was determined from first principles without producing thousands or millions of candidates and sieving them. Show me how one anticipates emergent properties.Petrushka
November 19, 2011
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KF: Well, when Petrushka loses all rationality, it's always a good sign (for us) :)gpuccio
November 19, 2011
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YUP!kairosfocus
November 19, 2011
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Petrushka Please read again: Abel et al are arguing here that especially functional prescriptive information and agent cause by choice contingency need to be ADDED to our key categories for analysing the world of life. The opposite of reducitonism. KFkairosfocus
November 19, 2011
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KF, I believe we are going love this book :)gpuccio
November 19, 2011
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I find it interesting that ID advocates accuse the mainstream of reductionism, then proceed to reduce life to some vague notion of information. Ignoring that rather obvious fact that emergent phenomena like protein folding are not amenable to prediction by computer, but are accomplished easily by chemistry. Just about everything in biochemistry fits this pattern. Chemistry does things that are unpredictable and therefore not reducible to information. At least not information as used by engineers when designing.Petrushka
November 19, 2011
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Johnson, too . . .kairosfocus
November 19, 2011
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H'mm: So does Casey Luskin in his review: _____________ >> Formal control is a major theme of this book, where "uncoerced choices" (p. 4) are used to actualize functional goals that fit into abstract categories. This Platonic idea finds support in mathematics, language, and computation, where non-physical entities exist and have meaning apart from their physical form. Thus, Abel explains that "None of these formalisms can be encompassed by a consistently held naturalistic worldview that seeks to reduce all things to physicodynamics." (p. 5) In Abel's view, such "formalisms depend upon choice contingency rather than chance contingency or necessity." (p. 5) Yet life is built upon formalisms. The First Gene investigates a number of different types of information that we find in nature, including prescriptive information, semantic information, and Shannon information. Prescriptive information is what directs our choices, and it is a form of semantic information -- which is a type of functional information. In contrast, Shannon information, according to Abel, shouldn't even be called "information" because it's really a measure of a reduction in certainty, and by itself cannot do anything to "prescribe or generate formal function." (p. 11) Making arguments similar to those embodied in Dembski's law of conservation of information, Abel argues that "Shannon uncertainty cannot progress to becoming [Functional Information] without smuggling in positive information from an external source." (p. 12) The highest form of information, however, is prescriptive information: "Prescriptive Information is much more than intuitive semantic information. PI requires anticipation, "choice with intent," and the diligent pursuit of Aristotle's 'final function' at successive bona fide decision nodes. PI either instructs or directly produces formal function at its destination through the use of controls, not mere constraints. Once again, PI either tells us what choices to make, or it is a recordation of wise choices already made." (p. 15) In Abel's view, if you're going to explain the origin of prescriptive information, then "Choice Contingency (Selection for potential []not yet existing[] function, not just selection of the best already-existing function) must be included among the fundamental categories of reality along with Chance and Necessity." (p. 25) He further argues, "Chance and necessity cannot generate formal controls. Chance and necessity cannot pursue 'usefulness.'" (p. 263) Moreover: "No physical entity can "self-organize" itself into existence. An effect cannot cause itself. Organization is the effect of choice-contingent determinism, not physicodynamic determinism or chance." (p. 264) So how does prescriptive information arise? Abel explains that "Only agents have been known to write or program meaningful and pragmatic linear digital PI" (p. 40) for "We are hard-pressed to provide empirical evidence, rational justification, or references showing how programming can be accomplished without intentional choices of mind (crossing The Cybernetic Cut)." (p. 78) >> >>[Durston and Chui] "The primary feature of FSC that distinguishes it from RSC and OSC, is the imposition of functional controls upon the sequence." (p. 161) They then measure the FSC for various protein families, showing that functional protein sequences are rare. They believe there is "almost infinitesimal size of functional sequence space relative to the size of the entire sequence space for a given number of sites." (p. 175) >> >> Donald E. Johnson, author of Probability's Nature and Nature's Probability, has a chapter looking at the "minimal replication and control information" required for a protocell. He lists many requirements, such as "A robust information structure that can be self-maintained (including error-correction)" (pp. 414-415) or "Controlled chemical metabolic networks are needed that can selectively admit 'fuel' (redox, heat, photons, etc.) into the cell and process the 'fuel' to harness the energy for growth, reproduction, manufacturing of needed components that can't migrate in, and other useful work." (pp. 413-415) Johnson critiques both the RNA world hypothesis and metabolism-first scenarios for the origin of life. The RNA world hypothesis suffers from the "the infeasibility of forming functional RNA by chance" (p. 405), whereas metabolism-first scenarios cannot achieve life-like replication, and complex chemical catalysts are unlikely to be available on the early earth. The problem, Johnson explains, is that "inanimate nature" cannot "write those programs and operating systems" (pp. 407-408) found in life, and "Coded information has never been observed to originate from physicality." (p. 408)>> CL comments: >>From reading The First Gene, a number of minimal theoretical and material requirements for life emerge: *High levels of prescriptive information *Programming *Symbol systems and language *Molecules which can carry this information and programming *Highly unlikely sequences of functional information *Formal function *An "agent" capable of making "intentional choices of mind" which can "choose" between various options, select for future function, and instantiate these requirements for life . . . . Anti-ID conspiracy theorists love to say that those pesky creationists are always changing their terminology to get around the First Amendment. ID's intellectual pedigree refutes that charge, but The First Gene adds more reasons why that charge should not be taken seriously. The book offers highly technical, strictly scientific arguments about the nature of information, information processing, and biological functionality. Even a cursory read of this book shows that its contributors are just thinking about doing good science. And this science leads them to the conclusion that blind and unguided material causes cannot produce the complexity we observe in life. Some agent capable of making choices is required to produce the first life. >> ______________ Pop, pop, pop, pop, POP, pop, pop, POP, POW . . . GEM of TKIkairosfocus
November 19, 2011
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Of related note: it is now found that the fidelity of the genetic code, of how any particular amino acid is 'spelled in a sequence', is far greater than had at first been thought:
Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010 Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,, http://www.creationsafaris.com/crev201009.htm#20100919a
Further notes:
DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video http://www.metacafe.com/watch/4491422 Nick Lane Takes on the Origin of Life and DNA - Jonathan McLatchie - July 2010 Excerpt: It appears then, that the genetic code has been put together in view of minimizing not just the occurrence of amino acid substitution mutations, but also the detrimental effects that would result when amino acid substitution mutations do occur. http://www.evolutionnews.org/2010/07/nick_lane_and_the_ten_great_in036101.html
somewhat related note: On top of the fact that Origin of Life researcher Jack Szostak, and others, failed to generate any biologically relevant proteins, from a library of trillions of randomly generated proteins, proteins have now been shown to have a 'Cruise Control' mechanism, which works to 'self-correct' the integrity of the protein structure from any random mutations imposed on them.
Proteins with cruise control provide new perspective: "A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order." http://www.princeton.edu/main/news/archive/S22/60/95O56/
Cruise Control permeating the whole of the protein structure??? This is an absolutely fascinating discovery. The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent that highly advanced mathematical information must somehow reside 'transcendentally' along the entirety of the protein structure, in order to achieve such control. This fact gives us clear evidence that there is far more functional information residing in proteins than meets the 'reductionist' eye. More clearly put, this ‘oneness’ of cruise control, within the protein structure, can only be achieved through quantum computation/entanglement principles, and is inexplicable to the reductive materialistic approach of neo-Darwinism!
Quantum states in proteins and protein assemblies: The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign. http://www.tony5m17h.net/SHJTQprotein.pdf
For a sample of the equations that must be dealt with, to 'engineer' even a simple process control loop like cruise control for a single protein, please see this following site:
PID controller A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. http://en.wikipedia.org/wiki/PID_controller
It is in realizing the staggering level of engineering that must be dealt with to achieve ‘cruise control’ for each individual protein, along the entirety of the protein structure, that it becomes apparent even Axe’s 1 in 10^77 estimate for rarity of finding specific functional proteins within sequence space is far, far too generous. In fact probabilities over various 'specific' configurations of material particles simply do not even apply, at all, since the 'cause' of the non-local quantum information does not reside within the material particles in the first place (i.e. falsification of local realism; Alain Aspect). =========== Here is a informative comment by gpuccio on rarity of protein folds: https://uncommondescent.com/darwinism/media-mum-about-deranged-darwinist-gunman/comment-page-5/#comment-363452 verse and music:
– 1 Peter 1:24-25 For, “All people are like grass, and all their glory is like the flowers of the field; the grass withers and the flowers fall, but the word of the Lord endures forever.” And this is the word that was preached to you. Marc Antoine Sunland - smooth jazz http://www.youtube.com/watch?v=OAAjpl23pAI
bornagain77
November 19, 2011
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H'mm: Reviewer DM hits a mother-lode in the quotes mine: ____________ >> Dr. Abel seems unafraid to boldly address issues that have been rendered taboo by many in the scientific community. This lack of intimidation is further evident in statements as this on page 28: "Chance and necessity are completely inadequate to describe the most important elements of what we repeatedly observe in intra-cellular life, especially. Science must acknowledge the reality and validity not only of a very indirect, post facto natural selection, but of purposeful selection for potential function as a fundamental category of reality. To disallow purposeful selection renders the practice of mathematics and science impossible." This is an amazing acknowledgement coming from a prominent member of the science community. On page 33 we fine another example of Dr. Abel's bold frankness and piercing insight as he states: "Choice Contingent Causation (CCC) can generate extraordinary degrees of unique functionality that has never been observed to arise from randomness or necessity. Highly pragmatic choice contingency is consistently associated with purposeful steering toward potential utility. The kind of contingency associated with sophisticated cybernetic function is invariably associated with what philosophers of science call "agency." The hallmark of agency is the ability to voluntarily pursue and choose for potential function. Potential means "not yet existent." If anything is repeatedly observable in science, it is abundant evidence of agency's unique ability to exercise formal CCC in generating potential formal functionality. The only exception to human agency's unique ability to do this is life itself, which is of course what produces agency. Life itself is utterly dependent upon cybernetic programming--a phenomenon never observed independent of agency. Thus we are confronted with still another chicken-and-egg dilemma of life-origin science. Whatever the resolution of this riddle, one thing is for certain. We are forced to consider two kinds of contingency, 1) Chance contingency and 2) Choice contingency as fundamental categories of reality along with law-like necessity." On page 307, the end of chapter 8 where Dr. Abel's masterfully examines "The Birth of Protocells", he asks this question: "By what supposedly "natural" process did inanimate nature generate phenomena like 1) A genetic representational sign/symbol/token system? 2) Bona fide decision nodes and logic gates (as opposed to just random "bifurcation points")? 3) Physicodynamically-indeterminate (dynamically inert, incoherent) configurable switch-settings that instantiate functional "choices" into physicality? 4) formal operating system and the hardware on which to run such software? 5) an abstract encoding/decoding system jointly intelligible to both source and destination? 6) many-to-one Hamming "block codes" (triplet-nucleotide codons prescribing each single amino acid) used to reduce the noise pollution in the Shannon channel of genetic messages? 7) the ability to achieve functional computational success in the form of homeostatic metabolism? His conclusion: "All of these attributes of life are nonphysical and formal, not physical and natural. They cannot have a materialistic, naturalistic explanation." >> ____________ The strange repeated popping noise you hear is heads exploding with new ideas. GEM of TKI PS: if you see some very familiar themes in the above tied to necessity vs chance vs choice and to the idea of functionally specific complex organisation and information FSCO/I, it is no coincidence.kairosfocus
November 19, 2011
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F/N: Shannon's metric is a metric of info-carrying capacity. Especially the H-metric, which boils down to being average info-cap per symbol. The underlying Hartley-derived metric, I = - log p, is effectively a stochastically based measure of the likelihood of symbols from an alphabet being used in a given code, estimated from typical samples. The H-metric is closely linked to the reduction in uncertainty about the state of an emitter of the symbols or signals, on receiving the same. This has led to an increasingly accepted informational view of thermodynamics; which is closely related to design theory, cf the discussion in my always linked note, here on. KFkairosfocus
November 19, 2011
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J: The context of the Shannon metric is that information bearing signals are readily distinguishable from noise, so much so that a key measure in the targetted channel capacity theorem is the signal to noise ratio. That is, it is recognised intuitively that noise follows stochastic patterns subject to probability distributions and thermodynamic considerations. These make it maximally unlikely that the special configurations that constitute signals that are meaningful would occur by chance-driven processes rather than intelligent and purposeful choice. That is why I keep saying that design inferences are built into the core of information theory, and that we should not overlook that. This is a part of why I think the explanatory filter approach that characterises the aspects of what is going on in a comms system, is so useful. Nor, should we neglect that once we have a comms system, we have protocols implemented across the system, so that symbols or signals and rules for their manipulation to convey meaning are an underlying framework. This also flags up the irreducible complexity of a sender-receiver system that works to convey those messages or signals. When we detect such a thing, we should take pause,as the only credible, observed and empirically warranted explanation for such, where we can see the causal process directly, is intelligence. A capital example, of course, is that in the heart of the living cell we see the DNA --> mRNA --> Ribosome protein assembly system that uses exactly this sort of technology. (Cf here on, note vids.) GEM of TKIkairosfocus
November 19, 2011
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gpuccio, thanks for taking the time to clear that up!bornagain77
November 19, 2011
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It looks like a wonderful book. Abel, Durston, Chiu... Great team! I have already ordered it.gpuccio
November 19, 2011
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Starbuck: People can already make a protein with only a small set of ancient amino acids. That's not what they have done. Read the paper, please. "As a first attempt, we designed randomized src SH3 gene libraries in which approximately half the residues of the SH3 gene were replaced by randomized codons in the lower or upper half of the table of the genetic code (Fig. 1)." ... "A subset of amino acids that are coded by the lower half of the genetic code are mainly putative primitive amino acids (e.g., Ala and Gly), whereas a subset of amino acids that are coded by the upper half contains many putative new amino acids (e.g., Cys, Phe, Tyr and Trp)." ... "Therefore, we used mRNA display to elucidate and compare the frequency of functional SH3 sequences in randomized SH3 libraries with different sets of amino acids." ... "First, we constructed partially (28 out of 57 amino acids)randomized SH3 gene libraries, SH3(RNN)28 and SH3(YNN)28, with randomized codons RNN (R = A or G; N = T, C, A or G) and YNN (Y = T or C), corresponding to the lower and upper half of the table of the genetic code, respectively (Fig. 1). We also prepared a randomized SH3 gene library SH3(NNN)28 with all 20 amino acids as a control. If particular amino acid residues are essential for a randomized position of the SH3 gene, the frequency of occurrence of functional proteins will be greatly affected. To exclude this possibility, the randomized codons were introduced into 28 out of 57 amino acid residues of the src SH3 domain and not in the highly conserved residues of the SH3 domain." So, just to be clear: a) They did not make any protein at all. They randomly substituted the non conserved codons (about half of the total) in an existing domain. b) Therefore, it is obvious that in no way the resulting proteins were made of "only a small set of ancient amino acids", given that half of the sequence (the conserved codons) was in its original form. It seems to be common practice for darwinists to quote from interesting papers attributing them non existing meanings and unwarranted conclusions, for their propaganda. Sometimes that is done by the authors themselves. More often, as in this case, by "distracted" readers.gpuccio
November 19, 2011
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I suppose I'll need something to read as I travel back to 1990. xpmaterial.infantacy
November 18, 2011
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Information must not be confused with meaning? How confusing is that? It leads to such absurdities as "meaningless information," whatever that is.Mung
November 18, 2011
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lol. Well, the Nature of Nature had been in the works for a while.Mung
November 18, 2011
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No Kindle edition -- aaarrrrgggghhhh!!!!! Add it to the list of books that need to come into the current millennium, along with The Myth Of Junk DNA and The Nature Of Nature.material.infantacy
November 18, 2011
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Shannon Information – Channel Capacity – Perry Marshall – video http://www.metacafe.com/watch/5457552/bornagain77
November 18, 2011
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I have no idea what you mean by shannon channel capacity "dicating" that the original DNA code had to be at least as complex as the current one, it is not even possible to know such a thing without experimentation. And the experimentation I referenced shows you can get a rather versatile sh domain from a limited set of amino acids thought to be very ancient (the first ones). With regard to "changing the code once it's in place" , we see alternative codes in bacteria and mitochondria, so the code isn't frozen in place and can change.Starbuck
November 18, 2011
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Starbuck, not sure what you wrote has anything to do with anything.M. Holcumbrink
November 18, 2011
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Hi Eric, Both you and Joeseph are spot on. The mis-use and associated rhetoric come up all the time. (second paragraph)Upright BiPed
November 18, 2011
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Go David.Upright BiPed
November 18, 2011
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starbuck, Shannon channel capacity dictates that the original DNA code had to be at least as complex as the current 'optimal' one in use today. Thus negating the assertion of the paper you cited that a simpler/smaller set of 'putative ancient' amino acids was previously in use gradually building to the 20 amino acid set in general use today with the DNA code.,,, The two papers cited afterwards shows, 1, the 'optimality' of the amino acid set in the codon code (which begs the question of how did it arrive at optimality if Shannon channel capacity prevents such changes in the DNA code once it is established) and, 2, highlights the catastrophic effects of changing the code once it is in place.bornagain77
November 18, 2011
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Not sure what either of those two have to do with what I wrote.Starbuck
November 18, 2011
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Starbuck, Well besides the study ignoring Shannon channel capacity (among other things) there is this:
Does Life Use a Non-Random Set of Amino Acids? - Jonathan M. - April 2011 Excerpt: The authors compared the coverage of the standard alphabet of 20 amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) drawn randomly from the pool of 50 plausible prebiotic candidates. The results? The authors noted that: "…the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof." http://www.evolutionnews.org/2011/04/does_life_use_a_non-random_set045661.html
as well as this,
Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal: "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10) OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code). Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two. http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html
bornagain77
November 18, 2011
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People can already make a protein with only a small set of ancient amino acids. See Tanaka J et al. PLOS ONE 6, e18034, 2011.Starbuck
November 18, 2011
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