Intelligent Design

Amino Acid Frequency Correlates With the Number of Codons

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One of the powerful evidences for evolution is the DNA code, at least according to evolutionists. The DNA code is essentially the same across all of life and, evolutionists explain, there is no reason for such universality. The code is ubiquitous across all life, but it is not special or unique. It is a mundane code, like any other, which just happened to evolve early in evolutionary history. But once in place it could not evolve, so it has been preserved ever since. In other words, the DNA code is the result of contingency, not law. As usual the evolutionary reasoning makes no sense. There is no credible, scientific, explanation for how a code could arise spontaneously in some primitive cell. And if it could not evolve once it was in place, then how could it evolve in the first place? Beyond all this, it certainly is not just another code. For instance, consider Morse code shown below:  Read more

4 Replies to “Amino Acid Frequency Correlates With the Number of Codons

  1. 1
    Axel says:

    They are always like children playing on an adults’ soccer field, because of their refusal to discard their secular fundamentalist assumptions.

  2. 2
    bornagain77 says:

    as to the claim that:

    “The DNA code is essentially the same across all of life”

    Actually, as you have mentioned previously Dr. Hunter in one of your other articles, that validity of that claim was at the heart of a disagreement between Dawkins and Venter:

    Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! – video

    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.

    Moreover, the deviations from the canonical code are not merely ‘evolutionary oddities’:

    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.

    The reason why a code cannot change once it is in place is also clearly seen by what is termed ‘shannon channel capacity’:

    Shannon Information – Channel Capacity – Perry Marshall – video

    “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

    Also of related note:

    ‘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,,

    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.”,,,

    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.

    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.”

    Biological Information – The Fine-Tuned Genetic Code 2-14-2015 by Paul Giem

    “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’

  3. 3
    harry says:

    The coding regions of DNA contain massive quantities of functionally complex, digitally stored, tokenized, extremely precise information:

    Functionally complex information in that it is essentially the assembly instructions for intricate protein machines used by the cell for metabolism and reproduction.

    Digitally stored information as in computer memory, only in DNA memory base four is used instead of binary. One of four nucleotide bases (abbreviated A, C, G and T) is contained in each unit of memory, as opposed to a “zero” or “one” in computer memory. Base four allows for very densely packed information. For example, in binary, 16 units of memory can contain 65,536 possible values. In base four, 16 units of memory can contain 4,294,967,296 possible values.

    Tokenized information in that just as in computer memory where each letter of the English alphabet is represented (in ASCII) by a unique series of seven 0 and 1 memory unit values, DNA uses a twenty character amino acid alphabet where each “letter” is represented by a series of three A,C,G and T values (a codon). Of course, there is also punctuation; there are codons for “stop.”

    Extremely precise information in that just as with the English alphabet, there are a virtually infinite number of ways to arrange the “letters” of the amino acid alphabet that will be meaningless gibberish, and relative to that an infinitesimally small number of ways to arrange those “letters” such that they are a coherent composition, i.e., the assembly instructions to construct functional protein machines. Just assuming that such an arrangement was arrived at mindlessly and accidentally is like assuming encyclopedias are arrived at by randomly generating letters of the alphabet.

    It is entirely reasonable to conclude that massive quantities of digital information in the coding regions of DNA, consisting of extremely precise assembly instructions for nanotechnology the functional complexity of which is light years beyond that which the best minds of modern science know how to build from scratch, did not come about mindlessly and accidentally. Such a conclusion is a “no brainer” for the same reason it was entirely reasonable to conclude that a mind was the source of the information inscribed on the Rosetta Stone, which, by the way, is much less information and far less complex. If it would be silly to assume the inscription on the Rosetta Stone was the mindless, accidental, albeit peculiar product of erosion, then it is absolutely ridiculous to refuse to admit even the possibility that the source of the information in the coding regions of DNA was an intellect. A mind is the only known source of functionally complex, tokenized, digitally stored, extremely precise information.

    And how did mindlessness overcome a difficulty Karl Popper feared was insurmountable? Consider his remarks on the information in DNA:

    What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code cannot be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code. Thus we may be faced with the possibility that the origin of life (like the origin of physics) becomes an impenetrable barrier to science, and a residue to all attempts to reduce biology to chemistry and physics.

    There is a “disturbing riddle” only when an a priori assumption is made that intelligence cannot have been a causal factor in the emergence of the information in DNA. Without such an assumption it becomes obvious that an intelligent agent knew how to construct the machinery by which the cell translates the code without the assembly instructions contained in the DNA memory, and how to place the assembly instructions for that same machinery within DNA memory.

    Intelligence is a known reality and therefore it is entirely legitimate for science to consider it among the possible causal factors in a given phenomenon coming about. Intelligent agency is the only causally adequate explanation for the coding regions of the DNA molecule being correctly populated with encyclopedic amounts of functionally complex, digitally stored, tokenized, extremely precise information.

    If atheism were the result of a physical defect in the brain, it might then become more understandable, but it would be no less irrational.

  4. 4
    awstar says:

    Dr. Hunter makes this assessment at the end of his post.

    When evolutionists say the DNA code is powerful evidence for evolution they are manipulating science to support their preconceived truth.

    I would like to hear what evolutionists have to say about how this functionality in the body came into existance.

    Body’s ‘serial killers’ captured on film destroying cancer cells

    One would think the children of disobedience would just give up by now, but we seem to be heading toward some kind of world view climax instead.

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