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H. Allen Orr on DNA as information


From H. Allen Orr in “DNA: ‘The Power of the Beautiful Experiment,’” in a review of Matthew Cobb’s Life’s Greatest Secret: The Race to Crack the Genetic Code (Basic Books)New York Review of Books:

The “information” that is “encoded” in DNA gets “read” by cells. You likely didn’t notice because this is now a nearly reflexive way of talking about DNA, even in popular culture. It’s just obvious to us that DNA stores information—for curly hair or blue eyes—and it’s natural to think of it as an information storage device much like the hard disk of a computer. Yet one of Cobb’s main points is that this is a remarkably recent way of thinking about biology.

True Then it gets interesting.

In the early 1960s, mathematicians confidently declared that “it will be interesting to see how much of the final solution [to the coding problem] will be proposed by mathematicians before the experimentalists find it.” As Cobb concludes, the “answer…was simple: not one single part of it.”

The interesting question is why theory failed here. Part of the answer, as Cobb emphasizes, is related to Crick’s idea of the frozen accident. The genetic code seems at least partly arbitrary. It represents a half-decent arrangement arrived at by the imperfect, tinkering process of evolution by natural selection and, once settled on, it couldn’t be “improved,” or made somehow more systematic. In such a situation theory is likely useless.

I suspect there’s another, related, reason that theory contributed so little to cracking the code. There was, at bottom, a mismatch between the nature of the problem and the nature of much biological theory. Successful theory in biology typically plays a different part than does successful theory in, say, physics. Theory in biology often guides thought, or trains intuition, or points to patterns that might hold approximately in nature. Only rarely does biological theory provide the essentially exact results that physicists are accustomed to. (And in biology approximate results, or even rules of thumb, are often more useful than exact results.) This kind of broad-stroke theory doesn’t provide much help with a problem as specific as the coding question. More.

The actual problem is that biology, as a Darwinian like Orr understands it, does not really account for information.

See also: New Scientist astounds: Information is physical The last time this idea whistled through, couple years back, the alleged substance was called perceptronium.


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as to:
The genetic code seems at least partly arbitrary. It represents a half-decent arrangement arrived at by the imperfect, tinkering process of evolution by natural selection and, once settled on, it couldn’t be “improved,,,
Actually, far from 'half decent, the code is near optimal if not optimal,
“Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature.” (Fazale Rana, -The Cell's Design - 2008 - page 177) “The genetic code’s error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature.” Fazale Rana - From page 175; 'The Cell’s Design' http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code Get Out of Jail Free: Playing Games in an RNA World - September 23, 2013 Excerpt: "The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and near-immutable. In addition, the code is also near-optimal in terms of error minimization," http://www.evolutionnews.org/2013/09/you_cant_get_th077021.html 'Snooze Button' On Biological Clocks Improves Cell Adaptability - Feb. 17, 2013 Excerpt: Like many written languages, the genetic code is filled with synonyms: differently spelled "words" that have the same or very similar meanings. For a long time, biologists thought that these synonyms, called synonymous codons, were in fact interchangeable. Recently, they have realized that this is not the case and that differences in synonymous codon usage have a significant impact on cellular processes,, http://www.sciencedaily.com/releases/2013/02/130217134246.htm
As well there was an ‘optimality’ found for the 20 amino acid set used in the 'standard' Genetic code when the set was compared to 1 million randomly generated alternative amino acid sets:
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 Paper Reports that Amino Acids Used by Life Are Finely Tuned to Explore "Chemistry Space" - Casey Luskin - June 5, 2015 Excerpt: We drew 108 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 108 possibilities tested. That's quite striking: out of 100 million different sets of twenty amino acids that they measured, only six are better able to explore "chemistry space" than the twenty amino acids that life uses. That suggests that life's set of amino acids is finely tuned to one part in 16 million. Of course they only looked at three factors -- size, charge, and hydrophobicity. When we consider other properties of amino acids, perhaps our set will turn out to be the best: (read more here) http://www.evolutionnews.org/2015/06/paper_reports_t096581.html Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement – 2009 Excerpt: A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. http://pre.aps.org/abstract/PRE/v79/i6/e060901
supplemental note:
Complex grammar of the genomic language - November 9, 2015 Excerpt: The 'grammar' of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher --,,, ,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to. Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words. http://www.sciencedaily.com/releases/2015/11/151109140252.htm
as to:
"In the early 1960s, mathematicians confidently declared that “it will be interesting to see how much of the final solution [to the coding problem] will be proposed by mathematicians before the experimentalists find it.” As Cobb concludes, the “answer…was simple: not one single part of it.”"
Actually mathematicians in the 1960s found a 'solution' to the 'coding problem' way before experimentalists did. Yet Darwinists ignored what the mathematicians were telling them since the 'solution' to the 'coding problem' that they had found refuted Darwinian claims that unguided material processes could generate functional information.
50 Years of Scientific Challenges to Evolution: Remembering The Wistar Symposium - video https://www.youtube.com/watch?v=VQy12X_Sm2k HISTORY OF EVOLUTIONARY THEORY - WISTAR DESTROYS EVOLUTION Excerpt: A number of mathematicians, familiar with the biological problems, spoke at that 1966 Wistar Institute,, For example, Murray Eden showed that it would be impossible for even a single ordered pair of genes to be produced by DNA mutations in the bacteria, E. coli,—with 5 billion years in which to produce it! His estimate was based on 5 trillion tons of the bacteria covering the planet to a depth of nearly an inch during that 5 billion years. He then explained that the genes of E. coli contain over a trillion (10^12) bits of data. That is the number 10 followed by 12 zeros. *Eden then showed the mathematical impossibility of protein forming by chance. http://www.pathlights.com/ce_encyclopedia/Encyclopedia/20hist12.htm
Ultimately, mathematicians found that Darwinian evolution can have no real 'solution' to the 'coding problem' since it has no known physical laws to appeal to as other overarching theories of physical science have:
“It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
In fact, Pauli recognized this crushing inadequacy within Darwinian theory way back in 1955
"In discussions with biologists I met large difficulties when they apply the concept of 'natural selection' in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely 'scientific' and 'rational,' they become actually very irrational, particularly because they use the word 'chance', not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word 'miracle.'" Wolfgang Pauli (pp. 27-28) - Letter by Pauli to Bohr - February 15, 1955 http://citeseerx.ist.psu.edu/viewdoc/download?doi=
And without a rigid mathematical basis to test against in order to potentially falsify it, Darwinian evolution does not even qualify as a real science in the first place but is more properly classified as a unfalsifiable pseudo-science
Darwinian Evolution is a Pseudo-Science - Mathematics – video (2016) https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater "In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge
And that, my friends, is why evolution is a FACT and not a "theory." Mung

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