The different genetic codes

The different genetic codes

https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes

Jonathan Wells, Paul Nelson, Rhetoric and Public Affairs, November 1998: Dobzhansky believed that the common ancestry of all living things could be seen in the universality of the genetic code. This was the basis of his claim that “all organisms, no matter how diverse in other respects, conserve the basic features of the primordial life.” But we now know that the genetic code is not universal. Thomas Fox reported in 1985 that “some ‘real’ exceptions have come to light” in bacteria and single-celled organisms, “and the notion of universality will have to be discarded.” The number of exceptions has grown since then; a 1995 review noted that “a relatively high incidence of non-universal codes has been discovered … widely distributed in various groups of organisms.” The non-universality of the genetic code suggests that living things may well have had multiple origins. –  2

Steve Meyer, Signature in the Cell,  page 201:  The discovery of thirty-three variant genetic codes indicates that the chemical properties of the relevant monomers allow more than a single set of codon–amino acid assignments. The conclusion is straightforward: the chemical properties of amino acids and nucleotides do not determine a single universal genetic code; since there is not just one code, “it” cannot be inevitable. The codon–amino acid relationships that define the code are established and mediated by the catalytic action of some twenty separate proteins, the so-called aminoacyl-tRNA synthetases (one for each tRNA anticodon and amino-acid pair). Each of these proteins recognizes a specific amino acid and the specific tRNA with its corresponding anticodon and helps attach the appropriate amino acid to that tRNA molecule. Thus, instead of the code reducing to a simple set of chemical affinities between a small number of monomers, biochemists have found a functionally interdependent system of highly specific biopolymers, including mRNA, twenty specific tRNAs, and twenty specific synthetase proteins, each of which is itself constructed via information encoded on the very DNA that it helps to decode. This is an integrated complex system. To claim that deterministic chemical affinities made the origin of this system inevitable lacks empirical foundation. Given a pool of the bases necessary to tRNA and mRNA, given all necessary sugars and phosphates and all twenty amino acids used in proteins, would the molecules comprising the current translation system, let alone any particular genetic code, have had to arise? Indeed, would even a single synthetase have had to arise from a pool of all the necessary amino acids? Again, clearly not.

The National Center for Biotechnology Information (NCBI), currently acknowledges nineteen different coding languages for DNA. And i list 31 different ones.

Dawkins: The Greatest Show On Earth (2009, p. 409): 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)
https://www.amazon.com/Greatest-Show-Earth-Evidence-Evolution/dp/1416594795

Dr. Jay L. Wile (2016):However, the eukaryotic cells that eventually evolved into vertebrates must have formed when a cell that used the “universal” code engulfed a cell that used yet another different code. As a result, invertebrates must have evolved from one line of eukaryotic cells, while vertebrates must have evolved from a completely separate line of eukaryotic cells. But this isn’t possible, since evolution depends on vertebrates evolving from invertebrates. Now, of course, this serious problem can be solved by assuming that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work. Along with explaining how nuclear DNA can evolve to produce the new structures needed to change invertebrates into vertebrates, proponents of evolution must also explain how, at the same time, mitochondria can evolve to use a different genetic code! In the end, it seems to me that this wide variation in the genetic code deals a serious blow to the entire hypothesis of common ancestry, at least the way it is currently constructed. Perhaps that’s why I hadn’t heard about it until reading Dr. Rossiter’s excellent book.
http://blog.drwile.com/?p=14280

Bye-bye common ancestry !! 





The basic process by which proteins are made in a cell. (click for credit)
I am still reading Shadow of Oz by Dr. Wayne Rossiter, and I definitely plan to post a review of it when I am finished. However, I wanted to write a separate blog post about one point that he makes in Chapter 6, which is entitled “Biological Evolution.” [url=https://books.google.com/books?id=kuwmCwAAQBAJ&pg=PT108&lpg=PT108&dq="To+date,+the+National+Center+for+Biotechnology+Information+%28NCBI%29,+which+houses+all+published+DNA+sequences"&source=bl&ots=y3djhymXWq&sig=SSjcioRSaQEZcuSGiztSRGYrJIw&hl=en&sa=X&ved=0ahUKEwjelt-frrPKAhWISCYKHSuJD9UQ6AEIHjAA#v=onepage&q="To date%2C the National Center for Biotechnology Information %28NCBI%29%2C which houses all published DNA]He says[/url]:

To date, the National Center for Biotechnology Information (NCBI), which houses all published DNA sequences (as well as RNA and protein sequences), currently acknowledges nineteen different coding languages for DNA…

He then references this page from the NCBI website.
This was a shock to me. As an impressionable young student at the University of Rochester, I was taught quite definitively that there is only one code for DNA, and it is universal. This, of course, is often cited as evidence for evolution. Consider, for example, this statement from The Biology Encyclopedia:

For almost all organisms tested, including humans, flies, yeast, and bacteria, the same codons are used to code for the same amino acids. Therefore, the genetic code is said to be universal. The universality of the genetic code strongly implies a common evolutionary origin to all organisms, even those in which the small differences have evolved. These include a few bacteria and protozoa that have a few variations, usually involving stop codons.

Dr. Rossiter points out that this isn’t anywhere close to correct, and it presents serious problems for the idea that all life descended from a single, common ancestor.
To understand the importance of Dr. Rossiter’s point, you need to know how a cell makes proteins. The basic steps of the process are illustrated in the image at the top of this post. The “recipe” for each protein is stored in DNA, and it is coded by four different nucleotide bases (abbreviated A, T, G, and C). That “recipe” is copied to a different molecule, RNA, in a process called transcription. During that process, the nucleotide base “U” is used instead of “T,” so the copy has A, U, G, and C as its four nucleotide bases. The copy then goes to the place where the proteins are actually made, which is called the ribosome. The ribosome reads the recipe in units called codons. Each codon, which consists of three nucleotide bases, specifies a particular amino acid. When the amino acids are strung together in the order given by the codons, the proper protein is made. The genetic code tells the cell which codon specifies which amino acid. Look, for example, at the illustration at the top of the page. The first codon in the RNA “recipe” is AUG. According to the supposedly universal genetic code, those three nucleotide bases in that order are supposed to code for one specific amino acid:methionine (abbreviated as “Met” in the illustration). The next codon (CCG) is supposed to code for the amino acid proline (abbreviated as Pro). Each possible three-letter sequence (each possible codon) codes for a specific amino acid, and the collection of all those possible codons and what they code for is often called the genetic code.

Now, once again, according to The Biology Encyclopedia (and many, many other sources), the genetic code is nearly universal. Aside from a few minor exceptions, all organisms use the same genetic code, and that points strongly to the idea that all organisms evolved from a common ancestor. However, according to the NCBI, that isn’t even close to correct. There are all sorts of exceptions to this “universal” genetic code, and I would think that some of them result in serious problems for the hypothesis of evolution. Consider, for example, the vertebrate mitochondrial code and the invertebrate mitochondrial code. In case you didn’t know, many cells actually have two sources of DNA. The main source of DNA is in the cell’s nucleus, so it is called nuclear DNA. However, the kinds of cells that make up vertebrates (animals with backbones) and invertebrates (animals without backbones) also have DNA in their mitochondria, small structures that are responsible for making most of the energy the cell uses to survive. The DNA found in mitochondria is called mitochondrial DNA. Now, according to the hypothesis of evolution, the kinds of cells that make up vertebrates and invertebrates (called eukaryotic cells) were not the first to evolve. Instead, the kinds of cells found in bacteria (called prokaryotic cells) supposedly evolved first. Then, at a later time, one prokaryotic cell supposedly engulfed another, but the engulfed cell managed to survive. Over generations, these two cells somehow managed to start working together, and the engulfed cell became the mitochondrion for the cell that engulfed it. This is the hypothesis of endosymbiosis, and despite its many, many problems, it is the standard tale of how prokaryotic cells became eukaryotic cells. However, if the mitochondria in invertebrates use a different genetic code from the mitochondria in vertebrates, and both of those codes are different from the “universal” genetic code, what does that tell us? It means that the eukaryotic cells that eventually evolved into invertebrates must have formed when a cell that used the “universal” code engulfed a cell that used a different code. However, the eukaryotic cells that eventually evolved into vertebrates must have formed when a cell that used the “universal” code engulfed a cell that used yet another different code. As a result, invertebrates must have evolved from one line of eukaryotic cells, while vertebrates must have evolved from a completely separate line of eukaryotic cells. But this isn’t possible, since evolution depends on vertebrates evolving from invertebrates. Now, of course, this serious problem can be solved by assuming that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work. Along with explaining how nuclear DNA can evolve to produce the new structures needed to change invertebrates into vertebrates, proponents of evolution must also explain how, at the same time, mitochondria can evolve to use a different genetic code!
In the end, it seems to me that this wide variation in the genetic code deals a serious blow to the entire hypothesis of common ancestry, at least the way it is currently constructed. Perhaps that’s why I hadn’t heard about it until reading Dr. Rossiter’s excellent book.
http://blog.drwile.com/?p=14280

There are variants of the standard genetic code. These variants are used for instance in the mitochondria of many species, and they consist in the modification of one or several codons of the standard genetic code. 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909233/

Richard Dawkins has claimed that the genetic code is universal across all organisms on earth. This is “near-conclusive proof,” he writes, that every living thing on this planet “descended from a single common ancestor” (1986, p. 270) at the root of Darwin’s universal tree of life. More recently, Dawkins repeated the claim in his bestseller The Greatest Show On Earth (2009, p. 409):

…the genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means ‘start reading here’ or ‘stop reading here,’ is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization).

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)

And now, see here: 

https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

• 1. 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. Rhabdopleuridae Mitochondrial Code
  
• 25. Candidate Division SR1 and Gracilibacteria Code
  
• 26. Pachysolen tannophilus Nuclear Code
  
• 27. Karyorelict Nuclear Code
  
• 28. Condylostoma Nuclear Code
  
• 29. Mesodinium Nuclear Code
  
• 30. Peritrich Nuclear Code
  
• 31. Blastocrithidia Nuclear Code
  
• 33. Cephalodiscidae Mitochondrial UAA-Tyr Code
  

Simple counting question: does “one or two” equal 33? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information (NCBI). By any measure, Dawkins is off by an order of magnitude.



In human cells, the codon UGA codes for “stop,” meaning the end of an open reading frame (i.e., section of DNA coding for a protein). When the ribosome, the molecular machine that constructs proteins, encounters UGA in the messenger RNA of a human cell, it ceases translation. Not so in Mycoplasma, where UGA codes for the amino acid tryptophan. On encountering UGA in an mRNA strand, the Mycoplasma ribosome would insert a tryptophan (in the protein the ribosome is assembling) and keep chugging right along with translation, through the following codons, until it met a Mycoplasma stop codon. Human and Mycoplasma cells do not read their DNA in the same way.

We must bear in mind that most non-canonical codes evolved independently from the others, and so may have evolved through different steps

My comment: It is evident why the authors make that claim. As Dawkins wrote: 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.

And Dr.Wile: Someone can assume that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work.

Even in a genome that has only 30-50 proteins, each protein is very long and uses the same amino acid multiple times. It would have to be shown how it is possible for four codons to go completely out of use. Then, how they can get reassigned in order to go from the “universal” code to the vertebrate mitochondrial code. Also, how did this happened only at the base of the vertebrate tree?

Why alternative genetic codes?
One reason why there are alternative genetic codes is the reduction of the number of tRNA needed. Furthermore, one alternative genetic code (the 'Echinoderm and Flatworm Mitochondrial Code') that seems to be better at reducing mutation and translation loads, and particularly yields better translation load except for very small AT content (approx. 20% AT content or less).

Of course, science literature claims that there was an adaptive advantage and improvement of fitness of these alternative codes, but how the transition could have happened is an open question. 

The implications are significant: If the origin of the universal genetic code is an enigma, imagine another 33 different ones, that had to emerge independently !!!! This is simply evidence that the best explanation is an intelligent designer which created and generated different codes for different life forms separately. And it means, that the tree of life is bunk. 

Since 1985 molecular biologists have discovered 33 different genetic codes in various species. Many of these are significantly different from the standard code. For example, the standard code has three different mRNA stop codons: UGA, UAA, and UAG . (A “stop codon” tells the cell to stop building-the protein is complete.) However, some variant codes have only one stop codon, UGA. The other “universal” stop codons now code for the amino acid glutamine. It’s very hard to see how an organism could have survived a transformation from the standard code to this one. Changing to this new code would cause the cell to produce useless strings of extra amino acids when it should have stopped protein production.
https://uncommondescent.com/evolution/there-are-now-many-variants-of-the-universal-genetic-code/

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes 17 April 2006
If a change in the translation system occurs in an organism such that a codon is reassigned, most of the occurrences of this codon will still be at places where the old amino acid was preferred. We would expect the changes causing the codon reassignment to be strongly disadvantageous and to be eliminated by selection.

My comment: A reassignment means, that the tRNA's amino acid binding site would have to change to reassign a different amino acid. 

The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases 28 July 2020 3
One of the most profound open questions in biology is how the genetic code was established.  The correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.

A glimpse into nature's looking glass -- to find the genetic code is reassigned: Stop codon varies widely 4
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. Phage infect bacteria, injecting their DNA into the cell and exploiting the translational machinery of the cell to create more of themselves, to the point when the bacterial cell explodes, releasing more progeny phage particles to spread to neighboring bacteria and run amok.

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.

It is possible for mutations to cause disappearance of the codon in its original positions and reappearance in positions where the new amino acid is preferred. Mutations throughout the genome are required for it to readjust to the change in the genetic code. The problem is therefore to understand how codon reassignments can become fixed in a population despite being apparently deleterious in the intermediate stage before the genome has time to readjust.

There Are Now Many Variants Of The “Universal” Genetic Code  June 13, 2018
Since 1985 molecular biologists have discovered at least 18 different genetic codes in various species.13 Many of these are significantly different from the standard code.14 For example, the standard code has three different mRNA stop codons: UGA, UAA, and UAG . (A “stop codon” tells the cell to stop building-the protein is complete.) However, some variant codes have only one stop codon, UGA. The other “universal” stop codons now code for the amino acid glutamine. It’s very hard to see how an organism could have survived a transformation from the standard code to this one. Changing to this new code would cause the cell to produce useless strings of extra amino acids when it should have stopped protein production.
https://uncommondescent.com/evolution/there-are-now-many-variants-of-the-universal-genetic-code/

Different genetic codes are strong evidence that they were designed.

Craig Venter vs Richard Dawkins:
It’s instructive to watch a fascinating exchange between Dawkins and genome guru J. Craig Venter, which occurred during a science forum held at Arizona State University. The question for discussion at the forum was “What is life?” Most of the panelists agreed that all organisms on Earth represent a single kind of life — a sample of one — because all organisms have descended from a last universal common ancestor (LUCA). This “sample of one” problem is strong motivation, panelist and NASA scientist Chris McKay argued, for exploring Mars and other planets (or their moons) in our solar system, to try to find a second example of life, unrelated to Earth organisms.
Venter disagreed — in a remarkable way (start at the 9:00 minute mark). “I’m not so sanguine as some of my colleagues here,” he said, “that there’s only one life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn’t call you [Venter said, turning to physicist Paul Davies, on his right] the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it.”
“Well, I’ve got the same genetic code,” said Davies. “We’ll have a common ancestor.”
“You don’t have the same genetic code,” replied Venter. “In fact, the Mycoplasmas [a group of bacteria Venter and his team have used to engineer synthetic chromosomes] use a different genetic code that would not work in your cells. So there are a lot of variations on the theme…”
Here Davies, a bit alarmed, interrupts Venter: “But you’re not saying it [i.e., Mycoplasma] belongs to a different tree of life from me, are you?”
“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.”
Dawkins is Flabbergasted
Fast forward to 11:23, when moderator Roger Bingham turns the microphone over to Dawkins:
“I’m intrigued,” replies Dawkins, “at Craig saying that the tree of life is a fiction. I mean…the DNA code of all creatures that have ever been looked at is all but identical.”
WHOPPER. Venter just told the forum that Mycoplasma read their DNA using a different coding convention than other organisms (for “stop” and tryptophan). But Dawkins is undaunted:
“Surely that means,” he asks Venter, “that they’re all related? Doesn’t it?”
As nearly as we can tell from the video, Venter only smiles.





https://www.sciencedirect.com/science/article/pii/S0960982216309174
2. https://uncommondescent.com/evolution/there-are-now-many-variants-of-the-universal-genetic-code/

https://www.youtube.com/watch?v=xIHMnD2FDeY

1. https://sci-hub.st/https://www.sciencedirect.com/science/article/pii/S0960982216309174
2. https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C
3. https://www.nature.com/articles/s41598-020-69100-0
4. https://www.sciencedaily.com/releases/2014/05/140522141422.htm
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894752/

Tan; Stadler: The Stairway To Life
Biology textbooks like to simplify life by providing a single table of codons for translating DNA to proteins. But in fact, the National Center for Biotechnology Information (NCBI) currently lists thirty-three different genetic code tables for a variety of life-forms. The differences are subtle, but even subtle differences produce fatal incompatibilities between life-forms. For example, if mycoplasmas are ancestors to bacteria or yeast, one must explain how the codon UGA could switch from coding for the amino acid tryptophan to coding for the end of translation without killing the organism. As this coding transition occurred, every protein that contains tryptophan coded by UGA would suddenly be truncated at that point, causing certain death. Furthermore, bacteria, archaea, and eukaryotes each have their own unique way to define and recognize the starting codon and to discriminate the starting codon from other appearances of the same codon. As a result, an organism that operates according to one genetic coding-decoding system cannot survive under a different genetic coding-decoding system. The near impossibility of maintaining life while changing the genetic coding-decoding strategy therefore poses another challenge for the assumed common ancestry of all life.

Codon reassignment and amino acid composition in hemichordate mitochondria 1

The genetic code, once thought to be “universal,” is now known to vary among several groups of organisms (1). There exist two hypotheses that attempt to explain how changes in the code come about. First, according to the “codon capture hypothesis” (1–4), it would be deleterious for an organism if a codon was assigned to two amino acids (or an amino acid and polypeptide chain termination) simultaneously. Thus, the first step in the change of the genetic code is assumed to be the complete disappearance of a codon from a genome. Subsequently, the tRNA (or release factor) assigned to this codon loses its capacity to recognize it, so that the codon becomes unassigned, and another tRNA acquires this capacity, allowing the codon to reappear at new positions in protein-coding genes. Second, in contrast, the “ambiguous intermediate hypothesis” (5, 6) proposes that the reassignment of a codon takes place via an intermediate stage during which the codon is recognized by two tRNAs assigned to different amino acids (or a tRNA and a release factor). This leads to heterogeneity in the encoded proteins that, according to this hypothesis and experimental results (7, , can be tolerated by an organism. Because a change in the assignment of a codon must occur over relatively long evolutionary periods, it should in principle be possible to find organisms that represent intermediate stages in this process and thus to differentiate between the codon capture and ambiguous intermediate hypotheses. Indeed, unassigned codons have been observed in bacterial and mitochondrial genomes (9–11). Most of these cases are associated with a bias in the base composition. However, none of the codons effected are known to change their amino acid assignment in related evolutionary lineages (1).

1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC19900/

It is generally known, that explaining where the information stored in DNA comes from, in special to make the first organism, is a problem not explained by science, and unsolved. While it is true, that mutations provoke change, it is by far not substantiated, that such changes, either single point mutations, or lateral gene transfer, or larger sections like exons, nor genetic shift or gene flow could bring forward the millions of different species on earth. But when we look to the root of the problem, the gigantic problem faced by science to solve the riddle becomes clear. And so, why no naturalistic explanations exist, despite decades of attempts to explain the riddle.
The problem is formidable, and manyfold. First of all, there is no evidence that the atoms required to make DNA were extant in a usable form on the early earth.

The Onset of Information on Earth
Life on earth is the product of information recorded inside the cell. When this information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth. The mystery of life’s origin is therefore equal to the mystery of information. Where did the information come from that organized the very first living cell on earth? Did this information come together as an incredible chance event in chemical history, or was it the result of a deliberate act of design? To organize the first living cell, one set of objects must encode the information in a series of representations, and the other set of objects must specify what is being represented. This is how a "recipe" for the cell can exist in a universe where no object inherently means (represents or specifies) any other object. It requires both a representation and the means to interpret it.

But there is a third requirement. The organization of the system must also preserve the natural discontinuity that exists between the representations and their effects. By doing so, a group of arbitrary relationships are established that otherwise wouldn't exist. That set of relationships is what we now call The Genetic Code. The unique physical conditions described here are the universal requirements of translation. They were proposed in theory, confirmed by experiment, and are not even controversial. They are also something that the living cell shares with every other instance of translated information ever known to exist. 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.

And as a final indication of just how profound the appearance of this system was, an almost impossible observation remains – not only must these objects arise from a non-information (inanimate) environment, but the details of their construction must also be simultaneously encoded in the very information that they make possible. Without these things, life on earth would simply not exist.
https://web.archive.org/web/20170715000000*/http://biosemiosis.org

“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’

Overlapping codes:
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.

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.,,,
https://sci-hub.ren/10.1016/s1672-0229(11)60001-6

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.”
https://www.biologicinstitute.org/post/128798433944/dynamic-genomes-in-bacteria-argue-for-design

Despite their differences, all genetic systems share one significant bias: the vast majority of changes to the code we presently know of involve termination or stop codons being reassigned to encode an amino acid. This may be a true reflection of natural diversity of the code, because stop codons are by definition rare (only one of three possibilities appearing per gene, whereas even rare amino acids are typically found many times) and the fidelity of termination is potentially less critical than other possible changes.

Problems explaining the evolution of the different genetic codes

Tan; Stadler: The Stairway To Life
Biology textbooks like to simplify life by providing a single table of codons for translating DNA to proteins. But in fact, the National Center for Biotechnology Information (NCBI) currently lists thirty-three different genetic code tables for a variety of life-forms. The differences are subtle, but even subtle differences produce fatal incompatibilities between life-forms. For example, if mycoplasmas are ancestors to bacteria or yeast, one must explain how the codon UGA could switch from coding for the amino acid tryptophan to coding for the end of translation without killing the organism. As this coding transition occurred, every protein that contains tryptophan coded by UGA would suddenly be truncated at that point, causing certain death. Furthermore, bacteria, archaea, and eukaryotes each have their own unique way to define and recognize the starting codon and to discriminate the starting codon from other appearances of the same codon. As a result, an organism that operates according to one genetic coding-decoding system cannot survive under a different genetic coding-decoding system. The near impossibility of maintaining life while changing the genetic coding-decoding strategy therefore poses another challenge for the assumed common ancestry of all life.


Jay Wile:
If the mitochondria in invertebrates use a different genetic code from the mitochondria in vertebrates, and both of those codes are different from the “universal” genetic code, what does that tell us? It means that the eukaryotic cells that eventually evolved into invertebrates must have formed when a cell that used the “universal” code engulfed a cell that used a different code. However, the eukaryotic cells that eventually evolved into vertebrates must have formed when a cell that used the “universal” code engulfed a cell that used yet another different code. As a result, invertebrates must have evolved from one line of eukaryotic cells, while vertebrates must have evolved from a completely separate line of eukaryotic cells. But this isn’t possible, since evolution depends on vertebrates evolving from invertebrates. Now, of course, this serious problem can be solved by assuming that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work. Along with explaining how nuclear DNA can evolve to produce the new structures needed to change invertebrates into vertebrates, proponents of evolution must also explain how, at the same time, mitochondria can evolve to use a different genetic code!

Mark Ridley, Evolution 3rd ed.
http://library.lol/main/F0C84F72B8E4C6D45DE7348D599AB035
The original coding relationships were accidental, but once the code had evolved, it would be strongly maintained. Any deviation from the code would be lethal. An individual that read GGC as phenylalanine instead of glycine, for example, would bungle all its proteins, and probably die at the egg stage.

The Genetic Code Part V: It Can't Evolve
https://www.youtube.com/watch?v=cf-pn1nmsOU

i want to show you two papers about the genetic code and what we can conclude from them about evolution okay this is the first paper a 2016 paper that talks about this idea that the code evolved and then must not have evolved it evolved rapidly early in the evolutionary history and then came to a point where it could not evolve at all strict conservation so quote

" The code may have evolved in a series of steps from simpler codes with fewer amino acids so the code was not always thus but once it was established it remained under very powerful selective constraints that kept the code frozen in nearly all genomes that subsequently diversified "

so you have this kind of a picture where early in evolutionary history you have rapid evolution followed by conservation of the code at first no life no genetic code then you reach the standard genetic code that we know today and after that no evolution okay so here's the second paper the title kind of says it all here the genetic code is one in a million

The genetic code is one in a million
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.
http://www.ncbi.nlm.nih.gov/pubmed/9732450

 it's not a random code it is a structured code with error correction and other capabilities you have to search through a lot of codes to find one that's better than the existing code so this paper says it's basically one in a million 

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. 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. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832087/?report=classic

so back to this graph this early evolution phase would have to have selection working to improve the code you have to go through millions of codes it's probably a lot more than one million by the way because the code has other features that have since been discovered since that paper 

The Genetic Code Part I: The Genetic Code Has Error Correction Features
https://www.youtube.com/watch?v=XQ5qPtKFze4

you have to have evolution working away selection working away a lot of change happening to improve the code to get to today's standard code that's the the key here a lot of evolution happening improving the code a lot of evolution happening in this early phase no evolution happening after that okay those are the two papers what can we conclude from that so in terms of evolution the first step you would have to evolve genes a protein synthesis capability and a genetic code after that you could then start mutating the genetic code to do this evolution of the code step now when you do happen to randomly mutate the code once in a while you don't actually test out the error correction capability in order to test that out and have selection working like we just talked about you also have to mutate some genes when some genes mutate that then would be a test of how well did the error correction capability work so that's our next step here randomly mutate some genes you then would get some selection effects some sometimes the new code works better this would have to be done a lot of times so i've drawn this this yellow circle here to indicate searching through a large number of randomly mutated codes to improve your code and get something better finally you arrive at today's standard genetic code and at that point the evolution of the code is frozen any random mutations that change the codewould be selected against because that new code would corrupt the existing genes at the translation step genes that have code for proteins wouldn't work anymore so there's the cycle there's the evolution explanation of how this would work how you would have evolution evolving the code and then become frozen now there are many problems with this so let's go through the the major problems first it's unlikely that random mutations could construct the genes the protein synthesis and the genetic code that you need to get this whole thing going in the first step there's too much complexity and circularity in that system even with a simple genetic code but let's move on assuming you are somehow able to randomly evolve this system what's the next step randomly mutate the genetic code okay you need this step in order to improve the code under selection as we talked about the problem is when you randomly mutate the code you're going to run into the same sorts of problems we just talked about when the code was frozen ultimately in other words here you do have genes you have a protein synthesis system up and running when you mutate the code you're going to create problems for those existing genes you need to mutate the code in order to evolve it but when you do so it will cause problems for those existing genes it will also cause problems for genes that are imported from other organisms this is called horizontal gene transfer or hgt evolutionists have hypothesized that this hgt would be very much needed in the early evolutionary phases when you change the code that's going to be a problem for these imported genes okay now the next step assuming that somehow you can get around these previous problems i just mentioned what about this selection step well the selection here is going to be very weak what we're talking about is one mutation changing one minor element of the genetic code you need to get a bigger change to the genetic code so selection could work okay so let's assume somehow you could do all this and cycle through this millions of times to arrive at a better code what's next now you have finally arrived at what we call today the standard genetic code and there is this big shift that has now happened now you suddenly can no longer evolve the code you were in a regime of high evolution a lot of change happening a better code being evolved to now it's frozen it cannot change this is an unexplained sudden shift and there really is no reason for this dramatic change so you can see there are many problems here now evolutionists have other ideas about how the code could have evolved but they're no better than this one when you have a lot of different ideas that's not always a good sign in science it means that there's not a good idea in this case there isn't now look i don't care whether evolution is true whether evolution is false it makes no difference to me but i do care about the science and the fact is the science contradicts the

2. Alternative Genetic Codes: Variations in the genetic code among organisms

1. Existence of Alternative Genetic Codes: There are multiple versions of the genetic code present among different organisms, varying from the standard genetic code. This indicates that different species or groups of species have distinct codes, suggesting independent origins.
2. Domain-Specific Genetic Codes: Some alternative genetic codes are predominantly found in specific domains of life, like in certain mitochondrial genomes, which further indicates the possibility of separate creation events for each domain.
3. Unique Codon Assignments: Certain organisms possess unique codon assignments that differ from the conventional genetic code. This uniqueness in codon assignments in specific lineages suggests they were endowed with this trait independently.
4. Inconsistent Distribution of Alternative Codes: The alternative genetic codes are not uniformly distributed across the tree of life. Their inconsistent distribution points toward the idea of multiple, separate origin events.
5. Functional Relevance of Alternative Codes: The alternative codes are not merely random deviations but have functional implications in the organisms in which they exist. The presence of functional, alternative codes in specific lineages suggests these organisms were designed with specific purposes in mind.
6. Code Evolution Limitations: The genetic code is highly optimized, and extensive changes can be detrimental to an organism's survival. The presence of distinct, alternative genetic codes in different lineages indicates they were not derived from minor modifications of a universal code but had separate origins.
7. Stop Codon Variability: Some organisms have reassigned stop codons to encode amino acids, a fundamental change to the genetic code. This reassignment in specific lineages suggests these organisms had distinct creation events.

1. Knight, R. D., Freeland, S. J., & Landweber, L. F. (2001). Rewiring the keyboard: evolvability of the genetic code. Nature Reviews Genetics, 2(1), 49-58. Link. (This study delves into the existence of alternative genetic codes and their evolutionary implications.)
2. Sengupta, S., & Higgs, P. G. (2005). A unified model of codon reassignment in alternative genetic codes. Genetics, 170(2), 831-840. Link. (The article focuses on domain-specific genetic codes and offers a model for their origin and evolution.)
3. Behrens, M., Michael, V., Pradella, S., & Päuker, O. (2013). Unique assignment of archaeal Group II intron ORFs with divergent, bacteria-like organization to homologs in Methanosarcina barkeri Fusaro. Mobile Genetic Elements, 3(2), e24783. Link. (This research observes unique codon assignments in certain archaeal organisms.)
4. Jukes, T. H., & Osawa, S. (1993). Evolutionary changes in the genetic code. Comparative Biochemistry and Physiology. B, Comparative Biochemistry, 106(3), 489-494. Link. (This paper analyzes the inconsistent distribution of alternative genetic codes across various organisms.)
5. Schultz, D. W., & Yarus, M. (1994). Transfer RNA mutation and the malleability of the genetic code. Journal of Molecular Biology, 235(5), 1377-1380. Link. (This research delves into the functional relevance of alternative codes, focusing on the adaptability of tRNA.)
6. Freeland, S. J., & Hurst, L. D. (1998). The genetic code is one in a million. Journal of Molecular Evolution, 47(3), 238-248. Link. (The study considers the optimization of the genetic code and the evolutionary implications of its variations.)
7. Santos, M. A., Cheesman, C., Costa, V., Moradas‐Ferreira, P., & Tuite, M. F. (1999). Selective advantages created by codon ambiguity allowed for the evolution of an alternative genetic code in Candida spp. Molecular Microbiology, 31(3), 937-947. Link. (This paper studies the variability in stop codons in Candida species, suggesting a distinct evolutionary path.)





On the Origin of the Codes: The Character and Distribution of Variant Genetic Codes is Better Explained by Common Design than Evolutionary Theory
Winston Ewert

Abstract

The near universality of the genetic code is frequently cited as evidence for universal common ancestry. On the other hand, critics of universal common ancestry frequently point to exceptions to the universal code as evidence against it. However, there has never been a comprehensive investigation into the character and distribution of variant genetic codes and their implications for the debate over universal common ancestry. This paper develops a framework for understanding codes within a common design framework, based crucially on the premise that some genetic code variants are designed and others are the result of mutations to translation machinery. We found that these two sources of variant codes can be distinguished by considering organismal lifestyle, taxonomic rank, evolutionary feasibility, codon rarity and complexity of distribution. These different approaches to distinguishing the codes give highly correlated results, demonstrating impressive explanatory power for our framework. In contrast, we find that evolutionary theory has difficulty explaining the character and distribution of variant genetic codes.

https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2024.1