Uncommon Descent Serving The Intelligent Design Community

Evolutionists Misrepresent Genetic Code


It would be a full time job to track down, monitor and document the scientific misrepresentations in the evolution literature. From textbooks and articles to websites, videos, popular books and the rest, the evolution literature is a continual stream of exaggerations and misrepresentations of the scientific evidence. Here is an example regarding the genetic code from the Public Broadcasting Service website:  Read more

That doesn’t mean there is no evidence of evolution.
Intelligent Design is NOT anti- evolution: As Dembski/ Wells said Intelligent design only has an issue with materialistic evolution — the idea that all organisms have descended from common ancestors solely through unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms. (Also known as the blind watchmaker thesis.) Intelligent Design is OK with all individuals in a population generally having the same number and types of genes and that those genes give rise to an array of traits and characteristics that characterize that population. It is OK with mutations that may result in two or more slightly different molecular forms of a gene- alleles- that influence a trait in different ways and that individuals of a population vary in the details of a trait when they inherit different combinations of alleles. ID is OK with any allele that may become more or less common in the population relative to other kinds at a gene locus, or it may disappear. And ID is OK with allele frequencies changing as a result of mutation, gene flow, genetic drift, natural and artificial selection, that mutation alone produces new alleles and gene flow, genetic drift, natural and artificial selection shuffle existing alleles into, through, or out of populations. IOW ID is OK with biological evolution. As Dr Behe et al., make very clear, it just argues about the mechanisms- basically design/ telic vs spontaneous/ stochastic. (Yes, design is a mechanism.) Joe
It certainly provides legitimate evidence for universal common descent.
Not really as there isn't any known mechanisms that can account for the transformations required. For example unguided evolution can't even get beyond populations of prokaryotes and that is given populations of prokaryotes to start with. Intelligent design is the only possible explanation for the genetic code. The code is arbitrary and not reducible to physics and chemistry. If science is all about appearance, it appears that unguided evolution is dead in the face of the genetic code. Joe
CH @14
But back to the main point, I’m glad to see you agree that the origin of the genetic code remains mysterious. Thus, it can hardly serve as such powerful evidence for evolution.
It certainly provides legitimate evidence for universal common descent. As to selection, pre-Code organisms have left no non-coding descendants. This may be due to never having existed, but there are some pretty obvious alternative explanations. Such as the evolutionary process: extinction by superior competitors, subsequent to the origination of protein catalysis. If monotony of coding is not powerful evidence for evolution, would this mean you'd find it strengthened by any wider variation? If the modern world was also furnished with a variety of organisms that made no use of a Genetic Code, or possessed a wide variety of uncorrelated codes, would that be better or worse for evolution? Hangonasec
Cornelius Hunter: “That doesn’t mean there is no evidence of evolution” which, while an obvious and trivial truism, Not sure it's a truism on this blog, but true nonetheless. Zachriel
Zach (16): "It’s not a secret that RNA World is either wrong or incomplete in some fundamental way. That doesn’t mean there is no evidence of evolution." Agreed. This is where a historical perspective can help. Historians understand that when there is, over time, a switching between radically different hypotheses, then we can conclude the problem is not converging to a solution. Scientists are doing the best that they can, within the paradigm they are in, but we're not seeing a healthy convergence, where over time the unresolved problem becomes increasingly smaller. This is reflected in your statement: "That doesn’t mean there is no evidence of evolution" which, while an obvious and trivial truism, is quite a step back from the insistence that the genetic code is powerful evidence for evolution. How far the mighty have fallen. Cornelius Hunter
tjguy: I’m wondering how you can really know that the code is not the best possible code, or, for that matter, that it is the best possible code? It is observed that the canonical code is robust to translation error. The question, then, is how does it compare to other codes. tjguy: Science is about much more than appearance. Actually, science is all about appearance. It's called hypothetico-deduction. A confirmation supports, but doesn't prove a claim. tjguy: I want to see them actually create a superior code and show us that it is superior before I believe their claim. Novozhilov et al. tested many possible codes to determine the landscape with regards to translation error, and where the canonical code lies on that landscape. Zachriel
Cornelius Hunter: The paper also rejects the standard RNA world type hypotheses as “unrealistic and incapable of withstanding severity of test.” It's not a secret that RNA World is either wrong or incomplete in some fundamental way. That doesn't mean there is no evidence of evolution. Zachriel
Zachriel @ 2
“In other words, the code is not the best possible code, but highly optimized in a way consistent with selection reaching a local maximum.”
Zachriel, I’m wondering how you can really know that the code is not the best possible code, or, for that matter, that it is the best possible code? It seems like you would have to be almost omniscient to be able to make a statement like that. I think it is easy to know that it is highly optimized because that much can be seen and tested. You believe the code evolved by chance so your view is that the optimization of the code is “consistent with selection reaching a local maximum.” That too seems to be a difficult thing to really test.
“There’s a more recent result: ….“the standard genetic code APPEARS to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak. The fitness landscape of code evolution APPEARS to be extremely rugged, containing numerous peaks with a broad distribution of heights, and the standard code is relatively unremarkable, being located on the slope of a moderate-height peak.”
The key word here is “APPEARS”. Science is about much more than appearance. As we all know appearances can be deceiving. That is why we use the scientific method to test our hypotheses, hypotheses like this one. Without an actual test, how can we really know? In fact, I would love to see these guys create a code they feel is at the summit of the local peak and then find a way to test it to see if their ideas are really accurate. Can they create a code that is better than the actual code? Talk is cheap. I want to see them actually create a superior code and show us that it is superior before I believe their claim. So, show us you can do it – you know, like real scientists do! tjguy
Zach (12): It is good to see that you agree explaining how the genetic code evolved is still largely mysterious. In fact the paper you cite focuses on the aminoacyl tRNA synthetases. Though the paper does not mention this, those enzymes do not at all fit the expected common descent pattern. They are highly incongruent. The paper also rejects the standard RNA world type hypotheses as "unrealistic and incapable of withstanding severity of test." So, no, this is not a case of a good explanation that is gradually refining the details. This is, as usual, an example of failed ideas replaced by yet more speculative, unsupported, ideas. But back to the main point, I'm glad to see you agree that the origin of the genetic code remains mysterious. Thus, it can hardly serve as such powerful evidence for evolution. Cornelius Hunter
Cornelius Hunter: The evolutionary hypothesis, which you spell out Actually, what we pointed out was that the code is not the best possible code, but is "located on the slope of a moderate-height peak" of the fitness landscape. Zachriel
bornagain77: so your evidence for the evolution of what is empirically measured to be a ‘optimal code’ is a ‘toy model’ that is ‘not necessarily realistic’??? The model isn't realistic, but the analysis of the landscape is. Cornelius Hunter: Under this hypothesis we must believe that the genetic code undergoes extensive evolutionary change. There's been quite a bit of work on the origin of the genetic code. While it's still largely mysterious, we do have some evidence of such a history. Caetano-Anollés et al., Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Evolutionary Impact of Protein Flexibility, PLOS ONE 2013: "Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins." Zachriel
Zach (2): "In other words, the code is not the best possible code, but highly optimized in a way consistent with selection reaching a local maximum." The evolutionary hypothesis, which you spell out, contradicts the science. Under this hypothesis we must believe that the genetic code undergoes extensive evolutionary change. It would be an enormous search to find today's code. There is no scientific evidence the code can undergo such change, and there is substantial scientific evidence against any such possibility. We would have to believe there were some other kind of life forms where such change was somehow possible, yet we have no evidence for any such life forms. Furthermore, the design features that would have had to have evolved are subtle. There is no immediate benefit from many of them, and they require nuanced DNA sequence encodings to take advantage of the code features. The benefit of some of these features would come with eukaryotes. This means there would be no selective advantage when they first evolved. Cornelius Hunter
Zachriel, so your evidence for the evolution of what is empirically measured to be a 'optimal code' is a 'toy model' that is 'not necessarily realistic’??? I thought we were talking science not imagination? Where is your empirical evidence that a coding system that surpasses anything man has ever devised can be generated from a primordial soup?
The genetic code is nearly optimal for allowing additional information within protein-coding sequences - Shalev Itzkovitz and Uri Alon - 2006 Excerpt: Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes. http://genome.cshlp.org/content/17/4/405.full Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection - Casey Luskin - December 20, 2013 Excerpt: In fact, one commentator observed that on the same analysis, codons may have more than two uses: "By this logic one could coin the term "trion" by pointing out that histone binding is also independently affected by A-C-T-G letter frequencies within protein-coding stretches of DNA." But this isn't the first time that scientists have discovered multiple codes in biology. Earlier this year I discussed research that found an analog code in the DNA that helps regulate gene expression, in addition to the digital code that encodes primary protein sequence. In other cases, multiple proteins are encoded by the same gene! And then of course there's the splicing code, which helps control how RNAs transcribed from genes are spliced together in different ways to construct different proteins (see here and here). It boggles the mind to think about how such "codes within codes" could evolve by random mutation and natural selection. But now it turns out that evidence of different functions for synonymous codons could threaten many standard methods used to infer selection in the first place,,, http://www.evolutionnews.org/2013/12/codes_within_co080381.html 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
At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years:
Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637
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
bornagain77: I guess you can excuse me for not taking their results as being ‘necessarily realistic’ since they themselves don’t take their results as being ‘necessarily realistic’? But they do take it as a valid determination of the place of the standard code in the code space. Zachriel
Common Creator is universal, Common Descent not so much. Common Descent is limited in scope and full of holes. Common Creation excuisitly fine tuned, Common Descent an incredible kluge. ppolish
Zach, I guess this caveat in your paper missed your notice? Discussion and Conclusion "Of course, one has to realize that the model of code's evolution considered here is not necessarily realistic and, technically, should be viewed as a "toy" model." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211284/ I guess you can excuse me for not taking their results as being 'necessarily realistic' since they themselves don't take their results as being 'necessarily realistic'? As to what the real world tells us: "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.) The coding system used for living beings is optimal from an engineering standpoint. Werner Gitt - In The Beginning Was Information - p. 95 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 Of related note as to how far DNA outclasses anything man has ever made for storing information: DNA: The Ultimate Hard Drive - Science Magazine, August-16-2012 Excerpt: "When it comes to storing information, hard drives don't hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare." http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html bornagain77
Zachriel and Hangonasec: Freeland and Hurst's study is from 1998. That's a long time ago. Just recently they have shown that codons coded by more than one triplet of nucleotides has 'information' which causes the speeding up, or the slowing down, of transcription. That study is simply outdated. PaV
bornagain77: Fazale Rana – From page 175; ‘The Cell’s Design’ Here's a more recent result: Novozhilov et al., Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biology Direct 2007: "the standard genetic code appears to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak. The fitness landscape of code evolution appears to be extremely rugged, containing numerous peaks with a broad distribution of heights, and the standard code is relatively unremarkable, being located on the slope of a moderate-height peak." Zachriel
as to this claim of Zach's "In other words, the code is not the best possible code, but highly optimized in a way consistent with selection reaching a local maximum" Actually, as usual, Zach is wrong. As far as we can tell the genetic code is 'near-optimal in terms of error minimization'
“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' 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 Biological Information - The Fine-Tuned Genetic Code 2-14-2015 by Paul Giem https://www.youtube.com/watch?v=gZB6heP10tw&index=16&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ 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 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 Researchers find hidden meaning and 'speed limits' within genetic code - March 12, 2015 Excerpt: "Our discovery is that the genetic code is more complex than we knew," said senior researcher Jeff Coller, PhD,,, The most significant breakthrough in the Case Western Reserve work is that all of the words, or codons, in the genetic code are deciphered at different rates; some are deciphered rapidly while others are deciphered slowly. The speed of how mRNA decodes its information is the sum of all the codons it contains. This imposed speed limit then ultimately affects the amount of protein produced. Sometimes faster is better to express a high level of protein. Sometimes slower is better to limit the amount protein. Importantly, codons are redundant—many of these words mean the same thing. Coller and colleagues found that each of the codons is recognized differently by a ribosome. Some codons are recognized faster than others, but these differences in speed are tiny. Over the entire span of an mRNA, however, each tiny difference in speed is powerfully additive. "Many codons mean the same thing, but they influence decoding rate differently.",,, http://phys.org/news/2015-03-hidden-limits-genetic-code.html
Moreover, contrary to Zach's claim that codes can easily evolve to reach a 'local maximum', the fact of the matter is that, because of 'shannon channel capacity', it is impossible for a code to 'evolve' once it is put in place:
Shannon Information - Channel Capacity - Perry Marshall - video https://vimeo.com/106430965 “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 reason why codes cannot evolve once they are in place is best summed up by Richard Dawkins himself:
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
Of humorous note, Dawkins just about has a cow in the following video when Venter informs him that the genetic code is not universal:
Dr. Craig Venter, American Biologist involved in sequencing the human genome http://www.youtube.com/watch?v=MXrYhINutuI
Of related note:
A glimpse into nature's looking glass -- to find the genetic code is reassigned: Stop codon varies widely - May 22, 2014 Excerpt: While a few examples of organisms deviating from this canonical code had been serendipitously discovered before, these were widely thought of as very rare evolutionary oddities, absent from most places on Earth and representing a tiny fraction of species. Now, this paradigm has been challenged by the discovery of large numbers of exceptions from the canonical genetic code,,, Approximately 99% of all microbial species on Earth fall in this category, defying culture in the laboratory but profoundly influencing the most significant environmental processes from plant growth and health, to the carbon and other nutrient cycles on land and sea, and even climate processes.,,, "We were surprised to find that an unprecedented number of bacteria in the wild possess these codon reassignments, from "stop" to amino-acid encoding "sense," up to 10 percent of the time in some environments," said Rubin. Another observation the researchers made was that beyond bacteria, these reassignments were also happening in phage, viruses that attack bacterial cells.,,, The punch line, Rubin said, is that the dogma is wrong. "Phage apparently don't really 'care' about the codon usage of the host. http://www.sciencedaily.com/releases/2014/05/140522141422.htm
Freeland & Hurst's result is also accessible without any competition required between variant codes and preservation of those with better error-tolerance, a frequent 'adaptationist' interpretation. Property conservatism is favoured in genome-wide reallocation of a gross codon usage, which would give error tolerance in single positions as an incidental matter of course, where like-property codon groups descend from ancestrally degenerate ones. Hangonasec
Freeland & Hurst, The genetic code is one in a million, Journal of Molecular Evolution 1998: "if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection." In other words, the code is not the best possible code, but highly optimized in a way consistent with selection reaching a local maximum. Zachriel
The genetic code is not universeal. There are 25 genetic codes described here. http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi The Standard Code 2. The Vertebrate Mitochondrial Code 3. The Yeast Mitochondrial Code 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code 5. The Invertebrate Mitochondrial Code 6. The Ciliate, Dasycladacean and Hexamita Nuclear Code 9. The Echinoderm and Flatworm Mitochondrial Code 10. The Euplotid Nuclear Code 11. The Bacterial, Archaeal and Plant Plastid Code 12. The Alternative Yeast Nuclear Code 13. The Ascidian Mitochondrial Code 14. The Alternative Flatworm Mitochondrial Code 16. Chlorophycean Mitochondrial Code 21. Trematode Mitochondrial Code 22. Scenedesmus obliquus Mitochondrial Code 23. Thraustochytrium Mitochondrial Code 24. Pterobranchia Mitochondrial Code 25. Candidate Division SR1 and Gracilibacteria Code Jim Smith

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