“Evolution of genetic code” article illustrates fundamental problem

_{Denyse O'Leary

February 4, 2017

Design inference, Evolution, Genetics, News}

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In Biological Theory (2015):

There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids.

The error-minimization theory maintains that in primitive systems the apparatus of protein synthesis was extremely prone to errors, and postulates that the genetic code evolved in order to minimize the deleterious effects of the translation errors. This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity and eventually removed it altogether. This proposal is distinct from the stereochemical and the coevolution theories because they do not contemplate any ambiguity in the genetic code, and it is distinct from the error-minimization theory because ambiguity-reduction is fundamentally different from error-minimization. The concept of ambiguity-reduction has been repeatedly mentioned in the scientific literature, but so far it has remained only an abstract possibility because no model has been proposed for its mechanism. Such a model is described in the present article and may be the first step in a new approach to the study of the evolution of the genetic code. (paywall) – Evolution of the Genetic Code: The Ribosome-Oriented Model Barbieri, M. Biol Theory (2015) 10: 301. doi:10.1007/s13752-015-0225-z More.

The problem is: “This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity and eventually removed it altogether.”

Systematic reduction of ambiguity is called design. Thanks for making it so clear. We had tried but we don’t have this guy’s gift for clear explanation.

See also: Large numbers of exceptions to the canonical genetic code

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Comments

harry @14:
To me, Popper’s “disturbing riddle” is the “Signature in the Cell.”
Well said.Eric Anderson_{February 9, 2017
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Dionosio @13:
As far as I understand it the expression ‘reverse engineering’ applies to ‘engineered’ objects or systems. Is this correct? Can one reverse engineer something that was not engineered? Maybe, not sure.
Yes, but you have to understand the materialist double-speak. Michael Shermer's current tactic, for example, is to argue, in essence, "Of course life is designed. Everyone can see that living systems are wonderfully designed. But they were designed by natural processes such as mutations and natural selection." Shermer's claim is absurd nonsense, and twists the definition to the breaking point. But it is precisely the argument the materialists have to make: you can have design without a designer. I don't know anything about the leanings of the author of the paper you cited. But it is, unfortunately, very possible for a materialist to use the word "designed" and mean "not-designed". So I don't usually get too excited when an evolutionary proponent uses the word "design." However, 76 times is quite a lot! Maybe the author is serious about design after all? That would be great.Eric Anderson_{February 9, 2017
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And how did mindlessness overcome a difficulty Karl Popper feared was insurmountable? Consider his remarks on the information in DNA:
What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code cannot be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code. Thus we may be faced with the possibility that the origin of life (like the origin of physics) becomes an impenetrable barrier to science, and a residue to all attempts to reduce biology to chemistry and physics.
There is a “disturbing riddle” only when an a priori assumption is made that intelligence cannot have been a causal factor in the emergence of the information in DNA. Without such an assumption it becomes obvious that an intelligent agent knew how to construct the machinery by which the cell translates the code without the assembly instructions contained in the DNA memory, and how to place the assembly instructions for that same machinery within DNA memory. Intelligence is a known reality and therefore it is entirely legitimate for science to consider it among the possible causal factors in a given phenomenon coming about. Intelligent agency is currently the only causally adequate explanation for the machinery by which the cell translates DNA code having its assembly instructions also coded in the DNA. To me, Popper's "disturbing riddle" is the "Signature in the Cell."harry_{February 8, 2017
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Eric Anderson, Thank you for commenting on this. Yes, agree that "There is so much to be learned here." On the "gossiping" side the paper seems to shed light on an apparent conflict between traditional (old school) experimental biologists and the systems biology folks. But perhaps it was my mistaken perception. The word 'design' or a variation of it was counted 76 times in this paper. Of those, 37 times it was 'design principle(s)'. Curiously the expression "reverse engineering" seems to appear also 76 times. The word 'reductionism' appears 6 times. The word 'reductionist' is 8 times. As far as I understand it the expression 'reverse engineering' applies to 'engineered' objects or systems. Is this correct? Can one reverse engineer something that was not engineered? Maybe, not sure. The ongoing research is discovering a very complex complexity. :)Dionisio_{February 8, 2017
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Dionosio: Interesting issue discussed in the paper. (BTW, the first thing that jumped out at me from the paper was: Why are there so many typos (typically dropped 'f's)?) I've read only part of the paper, but agree with the general thrust that reverse engineering is still a very fruitful avenue of research and further understanding. The dynamic nature of some biological systems is, indeed, important and critical. And, yes, that means we may not be able to completely pre-define the entire system and all its functions. But it seems to me we should be able to define a great deal of the system. Furthermore, if we are able to ever understand how the dynamic aspects are initiated, that would be a tremendous discovery as well. There is so much to be learned here. We need programmers and systems engineers to focus on these issues at both a deep conceptual and practical level. Hopefully some of the next generation will be able to do so without the blinders of materialistic just-so stories to hamper their progress.Eric Anderson_{February 8, 2017
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Any comments on this paper? https://www.researchgate.net/profile/Sara_Green3/publication/275360137_Can_biological_complexity_be_reverse_engineered/links/557563eb08aeacff1ffcd01b/Can-biological-complexity-be-reverse-engineered.pdfDionisio_{February 7, 2017
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The other, highly problematic elephant in the room, is that you don't get reproduction first and then progress to a code and the coordinated machinery required for accurate reproduction. The evolutionary storyline is fundamentally wrong at that most basic level. It is exactly backwards from everything we understand about systems and engineering. At the risk of tooting one's own horn, this is worth reviewing: https://uncommondescent.com/origin-of-life/thinking-upside-down-the-abiogenesis-paradigm/Eric Anderson_{February 7, 2017
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gpuccio, Glad to hear back from you!
I think your engineering mind would certainly love to speculate about complex life forms that rely on an “apparatus of protein synthesis extremely prone to errors”, or simply definitely “ambiguous”. Think how fascinating the error correction software should be!
While the error-correction software is tested, at least we could have some job security fixing programming bugs. :)
And evolving the code from “chemical affinities and from metabolic relationships between codons and amino acids” that simply do not exist must be a programming challenge too!
Yes, agree, that must be mindboggling, but I'd rather let my boss figure that out for me. :)
[...] “whatever” is certainly the most rigorous solution IMO.
Agree. BTW, there are rumors within the academic community that Cinderella's slippers were not made of glass, but plastic. The original glass slippers were under tremendous negative selective pressure -they couldn't reproduce easily- that eventually eliminated them, leaving only the plastic ones which resulted from beneficial mutations in the selfish slippery gene. The fairies Ran Mut and Nat Sel did it in order to establish a new trendy fashion. That could increase the number of "origin/evolution" theories exponentially! :)Dionisio_{February 5, 2017
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Dionisio: N. 12 is certainly the best. But, while the role of Cinderella is certainly interesting and worth further investigation, I would definitely not include the first 4 theories as plausible! :) I think your engineering mind would certainly love to speculate about complex life forms that rely on an "apparatus of protein synthesis extremely prone to errors", or simply definitely "ambiguous". Think how fascinating the error correction software should be! And evolving the code from "chemical affinities and from metabolic relationships between codons and amino acids" that simply do not exist must be a programming challenge too! So, better go back to Cinderella, even if "whatever" is certainly the most rigorous solution IMO. :)gpuccio_{February 5, 2017
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Articles like this make me sick to my stomach... Who can blame Donald Tuck or others wanting to eradicate funding for nonsense research materialists try to convince the public is "science"? BTW: I've never thought I'd see the day when so much nonsense would be exposed on both sides; materializm and religious. Too me it makes sense if there is a God/Intelligent Designer. Iz 42:8 " I am Yahweh, that is my name; and my glory will I not give to another, neither my praise to engraved images."J-Mac_{February 5, 2017
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All four ideas seem to assume a primitive self-reproducing system that is littered with errors. However it is self-evident that evolution by reproduction cannot be based on a system that cannot produce a (rather) accurate record of itself. Without a high level of self-reproduction accuracy there cannot be an evolving system.
The genetic translation system provides objective physical evidence of the first irreducible organic system on earth, and from it, all other organic systems follow. Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life's capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity. [biosemiosis.org]
Origenes_{February 5, 2017
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As to:
There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory.
And then there is the correct theory which Darwinists completely ignore:
"Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source -- from a mind or personal agent." - Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004). "As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information." - Stephen Meyer "A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107." (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.) “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life “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' Collective evolution and the genetic code - 2006: Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving. http://www.pnas.org/content/103/28/10696.full Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://www.youtube.com/watch?v=fDB3fMCfk0E
In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark):
"Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi-dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Thirty Years of Multiple Sequence Codes - Edward N. Trifonov - 2011 How Many “Second Genetic Codes”? Excerpt: According to the media sympathetic to science and enthusiastic about sensational discoveries, the “Second Genetic Code” as it was called by New York Times (8) was discovered by Ya-Ming Hou and Paul Schimmel and published in Nature in 1988 (9). It was about recognition of tRNAs by respective aminoa- cyl-tRNA synthetases. Thirteen years later New Scientist announced the second Second Genetic Code (13), discovered by Jenuwein and Allis (14) and published in Science. This time it was about histone modifications. Five years later, New York Times, again, reported about “a second code in DNA in addition to the genetic code” (15). This was already the third Second Genetic Code, discovered by Segal et al (16), sug- gesting now nucleosome positioning rules. One, surely, would raise eyebrows having learned that there is also the fourth Second Genetic Code (17)—on in- teraction specificities between proteins and DNA, and the fifth Second Genetic Code, the name given by Nature magazine (18) to the set of rules governing gene splicing(19). Bewildered reader, naturally, would say “I’m done with seconds, can I have a third?” (20) The conclusion from the above is obvious: one has to admit that the genetic sequences carry many different codes. If we are to know what the sequences are about, we have to detect and decipher these codes. The times of surrender to “junk” and “selfish DNA” are over, and “non-coding” becomes a misnomer.,,, http://www.sciencedirect.com/science/article/pii/S1672022911600016 Codon Degeneracy Discredited Again by Jeffrey P. Tomkins, Ph.D. - 2016 Excerpt: One of the main themes of evolution is the belief that certain types of DNA sequences freely mutate and develop new functions that allow for new creatures to evolve. This mostly mythical concept was applied to the protein-coding regions of genes, but in recent years this idea was discredited by the discovery of multiple codes embedded in the same sequence—because the disruption of these codes is typically harmful, mutations are not tolerated. And now another critical embedded code was discovered, further discrediting the idea of pervasive mutable DNA in genes.1,,, We have three different types of codes specified by codons that not only overlap each other, but play key roles in diverse types of cellular function. To sum things up, full codon utility (all three bases, besides specifying which amino acid is produced) controls: 1) transcription factor binding, 2) protein production rate and protein folding, and 3) gene transcription rates and levels. While human generated computer code is linear with only one meaning, the genetic code created by an Omnipotent God has multiple complex meanings and functions—all in the same sequence. The complexity of the genetic code points directly to a Divine Engineer instead of random purposeless evolution. http://www.icr.org/article/codon-degeneracy-discredited-again Dynamic Genomes in Bacteria Argue for Design - By Ann Gauger - 2015 Excerpt:"Codes within codes within codes – highly efficient and highly intelligent systems – don’t happen by accident and/or selection. The cell might begin with one code, which is incredible in itself. To layer another code in the opposite direction is far and away beyond that. Then to add a third layer of structural dynamics is simply awe-inspiring." http://www.biologicinstitute.org/post/128798433944/dynamic-genomes-in-bacteria-argue-for-design
But perhaps the easiest way to see that DNA is designed is to just look at it:
photo - DNA cross-section http://3.bp.blogspot.com/_S1W3JqHGyUQ/Sm9OC4riusI/AAAAAAAAO1A/848Ude_GMvw/s1600/Slide1.JPG
bornagain77_{February 5, 2017
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Actually, there are several major theories on the origin and evolution of the genetic code: 1. the stereochemical theory. 2. the coevolution theory. 3. the error-minimization theory. 4. the ambiguity-elimination theory. 5. Cinderella lost her left glass slipper. 6. Cinderella lost her right glass slipper. 7. Cinderella lost both glass slippers, but the prince found only the left one. 8. Cinderella lost both glass slippers, but the prince found only the right one. 9. Cinderella lost both glass slippers, the prince found both but only the left one was used in the fit test. 10. Cinderella lost both glass slippers, the prince found both but only the right one was used in the fit test. 11. Cinderella lost both glass slippers, the prince found both and they were used in the fit test. 12. Whatever.Dionisio_{February 4, 2017
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Speculation and opinion. Nothing more.Truth Will Set You Free_{February 4, 2017
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What a complete and utter joke. All four ideas. It is remarkable what hogwash one has to swallow in order to maintain the materialistic paradigm. Unbelievable that otherwise intelligent people take this stuff seriously.Eric Anderson_{February 4, 2017
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