Home » Intelligent Design » Here is That New Paper on Synonymous Nucleotides

Here is That New Paper on Synonymous Nucleotides

One of the most common tests evolutionists use, when studying how genes are supposed to have evolved, is to compare the non-synonymous and synonymous genetic differences. That is, if a gene that codes for a particular protein is found in several species, then evolutionists interpret differences in the gene, across those species, as the result of mutations in the evolutionary process. And while most mutations cause a change in the resulting protein amino acid sequence, some mutations do not affect the amino acid that is coded for. These two kinds of mutations are referred to as non-synonymous and synonymous, respectively, and their relative proportions are important to evolutionists. They believe that the while the non-synonymous mutations are important, because they change the resulting protein, the synonymous mutations on the other hand are not important. Therefore, if the ratio of the non-synonymous to synonymous mutations is high, then evolutionists think most of the mutations are important and so the gene is undergoing strong selection which is driving significant evolutionary change. But if the ratio of the non-synonymous to synonymous mutations is low, then evolutionists think most of the mutations are not important and so the gene is undergoing purifying selection which rejects most changes because the lower fitness. In that case the synonymous mutations occur merely because they don’t change the protein. As you can see this entire approach is deeply wedded to evolutionary assumptions and its main result is an inference about how genes evolved. If evolution is true then that is useful information, but if not then the entire exercise is a waste. Well for several years evidence has been growing that this approach and its results do, in fact, have much less meaning than evolutionists believe and, as we discussed here, there is a much better way.  Read more

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4 Responses to Here is That New Paper on Synonymous Nucleotides

  1. Besides falsifying evolutionary presuppositions about synonymous mutations, there is another finding in this paper that places further constraint on neo-Darwinian evolution:

    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

    Besides multifunctionality being found for synonymous positions, it is now found, by ENCODE, that the majority of protein coding regions are ‘overlapping’ with one another:

    Time to Redefine the Concept of a Gene? – Sept. 10, 2012
    Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!
    While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.
    http://networkedblogs.com/BYdo8

    It is readily apparent that this ‘overlapping multifunctionality’ places severe constraint on Darwinian evolution:

    If we were to actually get a proper ‘beneficial mutation’ in a ‘overlapping multifunctional’ gene we would be encountering something akin to this illustration found on page 141 of the book “Genetic Entropy” by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Which is translated ;
    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.
    This ancient puzzle, which dates back to 79 AD, reads the same four different ways. Thus, if we change (randomly mutate) any single letter we may get a new meaning for a single reading read any one way but we will consistently destroy the other 3 readings (functions) of the message with the new mutation (save for the center letter).
    For Darwinist to continue to believe in ‘random’ mutations to generate the staggering level of ‘overlapping multifunctionality’ we find in life is absurd in the highest order!

    As to Theistic Evolutionists(TEs), who believe God guides evolution in a ‘bottom up’ fashion, (apparently in a way that is undetectable to humans), all I ask TEs to consider is do you think that it would be easier for God to incrementally change a ‘overlapping multifunctional’ gene of any organism in a bottom up manner or do you think it would be easier for Him to design each kind of organism in a top down manner? Especially considering the fact that many genes are usually associated for any given phenotypic trait?

    Notes:

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
    R. Milner, Encyclopedia of Evolution (1990)

    Epistasis between Beneficial Mutations – July 2011
    Excerpt: We explored epistasis for beneficial mutations by constructing genotypes with pairs of mutations that had been previously identified as beneficial to the ssDNA bacteriophage ID11 and by measuring the effects of these mutations alone and in combination. We constructed 18 of the 36 possible double mutants for the nine available beneficial mutations. We found that epistatic interactions between beneficial mutations were all antagonistic—the effects of the double mutations were less than the sums of the effects of their component single mutations. We found a number of cases of decompensatory interactions, an extreme form of antagonistic epistasis in which the second mutation is actually deleterious in the presence of the first. In the vast majority of cases, recombination uniting two beneficial mutations into the same genome would not be favored by selection, as the recombinant could not outcompete its constituent single mutations.
    http://www.plosgenetics.org/ar.....en.1002075

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    Testing Evolution in the Lab With Biologic Institute’s Ann Gauger – podcast with link to peer-reviewed paper
    Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger’s paper, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,”.
    http://intelligentdesign.podom.....4_13-07_00

    Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009
    Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own.
    http://www.discovery.org/a/9951

    ——-

    Moreover, it should be noted that,,,

    Time to Redefine the Concept of a Gene? – Sept. 10, 2012
    Excerpt: Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance.
    http://networkedblogs.com/BYdo8

    Yet, as radical as that ‘redefinition to the RNA transcript,’ of the fundamental unit of inheritance would be to undermining the entire edifice of the modern synthesis upon which neo-Darwinism is built (genetic reductionism), the fact of the matter is, as much as I would love to see that undermining happen, that these current findings present us with yet another irreducibly complex situation in that ANY changes to DNA nucleotides, as Dr. Hunter has pointed out, effect RNA in a multifunctional way, yet, on the other hand, the RNA is regulating the gene in a multifunctional way.,,, Needless to say, this puts neo-Darwinists, once again, between the proverbial ‘rock and a hard place’!,,,
    Perhaps, after getting beat to a pulp with the rock of empirical evidence time after time, it is time for Darwinists to choose to ‘work with with the rock’ instead of choosing to get repeatedly beat to a pulp with it?

    Music, verse and video:

    5th service band Featuring TRU-SERVA – Solid Rock
    http://www.youtube.com/watch?v=G4jD70Y-mQ0

    Matthew 7:24
    “Therefore everyone who hears these words of Mine and acts on them, may be compared to a wise man who built his house on the rock.

    But to the unwise???,,, well perhaps this cartoon will help get the point across,,,

    Wile E. Coyote – cartoon video
    http://www.youtube.com/watch?v=hz65AOjabtM

  2. OT: Free will: Philosopher Alvin Plantinga responds to New Atheist’s book denying free will –
    Denyse O’Leary
    http://www.thebestschools.org/.....ying-free/

  3. Supplemental notes:

    A genome-wide study of dual coding regions in human alternatively spliced genes. – 2006
    Excerpt: Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcripts and show that approximately 7% of alternatively spliced genes contain dual (multiple) coding regions.
    http://www.ncbi.nlm.nih.gov/pubmed/16365380

    Dual-Coding Genes in Mammalian Genomes – 2007
    Excerpt: A textbook human gene encodes a protein using a single reading frame. Alternative splicing brings some variation to that picture, but the notion of a single reading frame remains. Although this is true for most of our genes, there are exceptions. Like viral counterparts, some eukaryotic genes produce structurally unrelated proteins from overlapping reading frames. The examples are spectacular (G-protein alpha subunit [Gnas1] or INK4a tumor suppressor), but scarce. The scarcity is anthropogenic in origin: we simply do not believe that dual-coding genes can occur in eukaryotes. To challenge this assumption, we performed the first genome-wide scan for mammalian genes containing alternative reading frames located out of frame relative to the annotated protein-coding region. Using a newly developed statistical framework, we identified 40 such genes. Because our approach is very conservative, this number is likely a significant underestimate, and future studies will identify more alternative reading frame–containing genes with fascinating biology.
    http://www.plosone.org/article.....bi.0030091

  4. In the biological sciences lew generalizations are absolute and we have already noted strange bases in RNA in addition to the usual — A, C, G and U (Fig. 5–1). For many purposes DNA can be considered solely in terms of its four major bases — A, C, G and T. However, in written languages single letters arc sometimes qualified with accents. We should not be surprised to find that there are similar qualifications in the DNA language. The most evident of these is methy Icytosine, where the base C acquires a chemical grouping (mcthyl) [2]. Thus, in many organisms DNA has five letters — A, C, Me-C, G and T. Apart from the pattern of the four regular bases, there is a pattern of methylation at intervals along a DNA sequence. A brief consideration of the fifth letter is needed to conclude our discussion of evolutionary bioinformatics.

    The Fifth Letter

    A Simplified Description of DNA Methylation

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