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Large numbers of exceptions to the canonical genetic code


From ScienceDaily:

the Lewis Carroll classic, Through the Looking Glass, Humpty Dumpty states, “When I use a word, it means just what I choose it to mean — neither more nor less.” In turn, Alice (of Wonderland fame) says, “The question is, whether you can make words mean so many different things.” All organisms on Earth use a genetic code, which is the language in which the building plans for proteins are specified in their DNA. It has long been assumed that there is only one such “canonical” code, so each word means the same thing to every organism. 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, published by a team of researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) in the May 23, 2014 edition of the journal Science.

It has been 60 years since the discovery of the structure of DNA and the emergence of the central dogma of molecular biology, wherein DNA serves as a template for RNA and these nucleotides form triplets of letters called codons. There are 64 codons, and all but three of these triplets encode actual amino acids — the building blocks of protein. The remaining three are “stop codons,” that bring the molecular machinery to a halt, terminating the translation of RNA into protein. Each has a given name: Amber, Opal and Ochre. When an organism’s machinery reads the instructions in the DNA, builds a protein composed of amino acids, and reaches Amber, Opal or Ochre, this triplet would signal that they have arrived at the end of a protein.

“This is sort of a ‘stop sign,'” Rubin said. “But what we saw in the study was that in certain organisms, the stop sign was not interpreted as stop, rather it signaled to continue adding amino acids and expand the protein.”

Why does this remind some of us of human languages?

In some bilingual places, if you are offered something at dinner, Thanks! means yes, but the same word in French, merci, means no.

And if it turns out to be like human languages, well, …

See also: New theory of physics attempts to incorporate information’s “central role” in nature

Genome map shows comb jellies had separate course of evolution

" 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.” Dawkins. Or maybe it could spell Creation? Boom a bird:) ppolish
Thanks BA77. Just realized you had already posted it in this thread i must have missed it. sixthbook
If Darwinian Theory is to survive, it must adapt. Will have to realize "appearance of design" is really true design. This is key to it's survival. Acceptance of Design. Will take the Theory to the next level. The Theory will need to be guided to this realization. Prodded a bit. It won't just happen by chance lol. ppolish
Darwinian Theory would predict it's adherents would have to struggle to survive. Dog eat dog. Most likely end up extinct. Darwinian Theory gets the basic stuff correct:) ppolish
sixthbook: "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." Richard Dawkins - The Greatest Show On Earth (2009, p. 409-10) http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html bornagain77
So a universal genetic code is proof of evolution, except when it's not? I think I see how this works… Related: I read a quote from Dawkins before where he says that if a codon changed what it coded for in an organism in its evolutionary history it would be deadly to the organism. Or something along those lines. If someone could help me find this i would be very appreciative. sixthbook
The genetic code, as the Richard Dawkins' quote in post 2 made clear, is far more inflexible than Darwinists would presuppose prior to investigation. Here are a few more notes that make that 'inflexible' point of the genetic code clear: Though the DNA code is found to be optimal from a error minimization standpoint, it is also now found that the fidelity of the genetic code, of how a specific amino acid is spelled, 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 '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 Synonymous (“Silent”) Mutations in Health, Disease, and Personalized Medicine: Review - 2012 Excerpt: In contrast, a synonymous mutation does not delete or substitute one amino acid for another; thus the protein produced by both the normal gene and the mutant have the identical amino acid sequence. However, it can reduce the amount of a specific protein the cell makes or cause the structure of the protein to be distorted in a manner that disrupts its functioning in the body.,,, The CBER authors compiled a list of synonymous mutations that are linked to almost fifty diseases, including diabetes, a blood clotting disorder called hemophilia B, cervical cancer, and cystic fibrosis. http://www.fda.gov/BiologicsBloodVaccines/ScienceResearch/ucm271385.htm Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. – Jan 2013 Excerpt: Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides.,,, Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. http://www.ncbi.nlm.nih.gov/pubmed/23293005 A hidden genetic code: Researchers identify key differences in seemingly synonymous parts of the structure - January 21, 2013 Excerpt: (In the Genetic Code) there are 64 possible ways to combine four bases into groups of three, called codons, the translation process uses only 20 amino acids. To account for the difference, multiple codons translate to the same amino acid. Leucine, for example, can be encoded in six ways. Scientists, however, have long speculated whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Harvard researchers have deciphered that second code,,, Under some stressful conditions, the researchers found, certain sequences manufacture proteins efficiently, while others—which are ostensibly identical—produce almost none. "It's really quite remarkable, because it's a very simple mechanism," Subramaniam said. "Many researchers have tried to determine whether using different codons affects protein levels, but no one had thought that maybe you need to look at it under the right conditions to see this.",,, While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological failsafe, allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources. http://phys.org/news/2013-01-hidden-genetic-code-key-differences.html bornagain77
I don’t know why this would be so surprising. We have long known that how and when genes are expressed is strongly influenced by the environment the chemistry is exposed to.
Perhaps I misinterpreted the referent. I thought you were referring to the title of the OP. Was I wrong? Mung
There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature. Consider how evolutionists would react if there were in fact multiple codes in nature. What if plants, animals, and bacteria all had different codes? Such a finding would not falsify evolution; rather, it would be incorporated into the theory. For if the code is arbitrary, why should there be just one? The blind process of evolution would explain why there are multiple codes. In fact, in 1979 certain minor variations in the code were found, and evolutionists believe, not surprisingly, that the variations were caused by the continuing evolution of the universal genetic code. Of course, it would not be a problem for such an explanation to be extended if it were the case that there were multiple codes. There is nothing wrong with a theory that is comfortable with different outcomes, but there is something wrong when one of those outcomes is then claimed as supporting evidence. If a theory can predict both A and not-A, then neither A nor not-A can be used as evidence for the theory. When it comes to the genetic code, evolution can accommodate a range of findings, but it cannot then use one of those findings as supporting evidence. (Hunter, 38.) http://www.trueorigin.org/theobald1b.asp
@Mung: "Acartia_bogart, it’s surprising because it wasn’t predicted by evolutionary theory." Really? How so? Darwin didn't know about genetics, let alone DNA, RNA and protein synthesis. Yet his theory did predict that there must be a mechanism for inheritance if traits. In fact, there are theories that suggest that DNA wasn't the original information storage system, just the one that was most successful. Acartia_bogart
bogart The supposed ‘expanded genetic code’ was not mapped to the production of amino acids for proteins, and thus their claim that it represents an expansion of the genetic code is ‘not even wrong’. i.e. just as sticking a few letters on the end of an existing alphabet does not represent a new alphabet by any stretch of the imagination until words are incorporated. Moreover, their speculation that the expansion could lead to the production of ‘custom-built proteins as novel drugs, vaccines and antibiotics’ is nothing but pure hallucination! Because even using the existing code, with existing proteins for comparison, much less a foreign code that the rest of life does not even recognize, extreme effort goes into finding proteins to perform a function that are not even as good as those already found in life: https://uncommondesc.wpengine.com/junk-dna/junk-rna-helps-regulate-metabolism/#comment-499434 bornagain77
Semi related: Some codes are 'species specific', such as the alternative splicing code and the bioelectric code,,, Researchers Crack 'Splicing Code,' Solve a Mystery Underlying Biological Complexity - May 2010 Excerpt: "Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group," http://www.sciencedaily.com/releases/2010/05/100505133252.htm Breakthrough: Second Genetic Code Revealed - May 2010 Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,,, http://crev.info/content/breakthrough_second_genetic_code_revealed Evolution by Splicing - Comparing gene transcripts from different species reveals surprising splicing diversity. - Ruth Williams - December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation – January 2013 Excerpt: A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes. http://www.ncbi.nlm.nih.gov/pubmed/23802040 Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html The (Electric) Face of a Frog – video https://www.youtube.com/watch?v=0VULjzX__OM bornagain77
Acartia_bogart, it's surprising because it wasn't predicted by evolutionary theory. What good is a theory that can't produce predictions? Or, as Q points out, what good is a theory that predicts both a thing and it's opposite? A theory that is so malleable such as to allow any observation to be "consistent" with the theory isn't much of a theory. Mung
Whether there's a canonical genetic code or not, it once again proves Evolution. You just have to look at it the right way. 1. The Canonical Genetic Code proves that all life originated from a single common ancestor, and 2. The variation in the Canonical Genetic Code proves that the code evolved, but either (a) not at the same rate, or (b) it musta evolved or drifted away from the Canonical Genetic Code in some organisms, or (c) both. 3. Absolutely *anything* can happen in billions of years, which can easily be explained with just a little imagination. ;-) -Q Querius
as to:
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,,, http://www.sciencedaily.com/releases/2014/05/140522141422.htm
This, though more devastating, reminds me of this previous exchange between Venter and Dawkins:
Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! - video Quote: "I think the tree of life is an artifact of some early scientific studies that aren't really holding up.,, So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of, now we have about 60 million different unique gene sets, we found 12 that look like a very, very deep branching—perhaps fourth domain of life. " - Dr. Craig Venter, American Biologist involved in sequencing the human genome http://www.youtube.com/watch?v=MXrYhINutuI
the primary reason why different canonical codes are so devastating to neo-Darwinian (bottom up) evolution is best understood by taking a look at what Richard Dawkins has said about what would happen if one were to 'randomly' change part of the genetic code once it is in place:
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) http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html
Further notes:
“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 Shannon Information - Channel Capacity - Perry Marshall - video http://www.metacafe.com/watch/5457552/
Moreover, not only are there different canonical codes operating throughout life, there are also overlapping codes operating within a single organism, many times overlapping within a single sequence of DNA:
"In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010 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
A few more notes:
"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 origins of codes are as well established as the laws of gravity. Scientific experimentation has established a causal relationship between intelligence and codes. The law of information applies universally and predicts that natural mechanisms will only create sequences of order or random complexity, and only intelligence is capable of creating sequences of specified complexity having purpose and intent. This empirical law of science can be refuted or falsified by a single example to the contrary. "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).) “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.” Fazale Rana - From page 175; 'The Cell’s Design'
I don't know why this would be so surprising. We have long known that how and when genes are expressed is strongly influenced by the environment the chemistry is exposed to. Most genetically linked diseases are not an absolute thing. There are some (e.g., Huntington's) that will always result in the disease being expressed if you have that genes. But far more simply increase your probability to develop the disease. There has also been research into actually using base pairs other than A, G, C and T. Researches have been able to incorporate a completely different base pair into the genome of E. coli and have it reproduce and retain the added base pairs. Acartia_bogart

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