Darwinism Evolution Intelligent Design Self-Org. Theory

What? Mutations not random? An “enigmatic in-built self-preserving organization”?

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In a conventional science paper…?

Abstract: Mutations underpin the processes in life, be it beneficial or detrimental. While mutations are assumed to be random in the bereft of selection pressures, the genetic code has underlying computable probabilities in amino acid phenotypic changes. With a wide range of implications including drug resistance, understanding amino acid changes is important. In this study, we calculated the probabilities of substitutions mutations in the genetic code leading to the 20 amino acids and stop codons. Our calculations reveal an enigmatic in-built self-preserving organization of the genetic code that averts disruptive changes at the physicochemical properties level. These changes include changes to start, aromatic, negative charged amino acids and stop codons. Our findings thus reveal a statistical mechanism governing the relationship between amino acids and the universal genetic code. –

Kwok-Fong Chan et al., Probability of change in life: Amino acid changes in single nucleotide substitutions, Biosystems, Volumes 193–194, June 2020, 104135 (paywall)

Yeah sure, but it didn’t used to be okay to talk about it without loads of Darwinblather.

Self-organization? See: Natural genetic engineering? Natural popcorn? Or something more important?

Hat tip: Philip Cunningham

14 Replies to “What? Mutations not random? An “enigmatic in-built self-preserving organization”?

  1. 1
    jawa says:

    They ain’t seen nothin’ yet. Poor things.
    In addition to the GCAT-based genetic code for protein synthesis by ribosomes, that translate codons to aminoacids with the help of tRNAs and aminoacyl-tRNA synthetase ( aaRS or ARS ), the DNA also contains promoter regions, enhancer regions, TF-binding sites that are cell type-dependent. Around the DNA there are epigenetic markers. Also the histones are associated with another level of codes.
    Dr Cronin and Dr Szostak must account for all that stuff in their OOL recipes. There yet?

  2. 2
    bornagain77 says:

    As they stated in the second sentence of their paper, a core presupposition of Darwinian evolution is that,

    “mutations are assumed to be random in the bereft of selection pressures”

    And yet, in direct contradiction to that core Darwinian presupposition, they found that,,

    “Our calculations (instead) reveal an enigmatic in-built self-preserving organization of the genetic code that averts disruptive changes at the physicochemical properties level.”

    And as they further stated in the discussion section of their paper, “there are fixed probabilities for the type of change in selection pressure-free conditions that are far from random.”

    Discussion
    We found in-built intrinsic biases and barriers to drastic changes within the genetic code. Within single mutational events, there are fixed probabilities for the type of change in selection pressure-free conditions that are far from random.”
    https://www.sciencedirect.com/science/article/pii/S0303264720300393

    In other words, this is yet another direct falsification of a, if not THE, core Darwinian presupposition.

    As Dr. Cornelius Hinter noted,

    In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual. As Julian Huxley put it, “Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions. … in all cases they are random in relation to evolution. Their effects are not related to the needs of the organisms.” (Huxley, 36) Or as Jacques Monod explained:
    “chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is likely ever to be revised.” (Monod, 112)
    Ronald Fisher wrote that mutations are “random with respect to the organism’s need” (Orr). This fundamental prediction persisted for decades as a recent paper explained: “mutation is assumed to create heritable variation that is random and undirected.” (Chen, Lowenfeld and Cullis)
    But that assumption is now known to be false.
    https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive

    Since this is a direct falsification of a, if not THE, core Darwinian presupposition, I have no idea why the Darwinists on UD are not up in arms trying to discredit this paper, or the authors, in some (dishonest) way, (as they usually do), so as to preserve some semblance scientific respectability for their theory.

    But then again, even though Darwinists, as a core presupposition, have always assumed that mutations were random, that ‘chance postulate’ for mutations, in and of itself, prevented Darwin’s theory from ever truly being considered ‘scientific’ in the first place.

    As Wolfgang (“Not even wrong”) Pauli noted, “While they (Darwinists) pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’”

    Pauli’s ideas on mind and matter in the context of contemporary science – Harald Atmanspacher
    Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’”
    Wolfgang Pauli (pp. 27-28)
    https://pdfs.semanticscholar.org/234f/4989e039089fed5ac47c7d1a19b656c602e2.pdf

    And as Murray Eden of MIT noted, in the paper entitled, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory”, “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”

    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.

    Yet, if Darwinists try to become ‘scientific’ and rigidly define chance against the backdrop of a mathematically defined probability, a backdrop in which a chance event can be said to occur, then they must necessarily presuppose Intelligent Design. As Dr. Egnor, via Aristotle, noted, “Chance presupposes design.”

    Evolution Presupposes Intelligent Design: Case of the Coronavirus – Michael Egnor – April 7, 2020
    Excerpt: Aristotle saw this in his definition of chance in nature — chance is the accidental conjunction of purposeful events. Without purpose there can be no chance. His example is instructive: he considered a farmer who ploughs his field and by chance discovers a treasure buried by someone else. The treasure is discovered by chance, but everything else — the farmer’s ownership of the field, his decision to plough it, the accumulation and burial of the treasure by the other man — is purposeful, and in fact the only reason the accident of discovery happened is because it is embedded in a world of purpose. Chance can’t happen — the word has no meaning — in an entirely accidental world. Chance presupposes design.
    https://evolutionnews.org/2020/04/evolution-presupposes-design-the-case-of-covid-19/

    The fact that chance must necessarily presuppose design is not that hard to understand. After all, randomly choosing a card from a deck, by “chance”, necessarily presupposes a intelligently designed deck of cards to choose from in the first place!

    The same holds for defining a chance event within a cell. As Stephen Talbott noted, “In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.”

    Evolution and the Illusion of Randomness – Talbott – Fall 2011
    Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.”
    In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.”
    This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?”
    http://www.thenewatlantis.com/.....randomness

    In other words, it would be impossible to tell if something happened randomly ‘by chance’ in the cell unless it first happened within the backdrop of the purposely designed “highly regulated, coordinated, integrated, and intensely meaningful biological processes” of the cell.

    In fact, in the current paper in the OP, they tried to find if mutations were random against the backdrop of the intelligently designed genetic code itself and found, even in that limited context, and directly contrary to Darwinian presuppositions, that the mutations “are far from random”

    Thus to repeat what Dr. Egnor, via Aristotle, noted, “Chance presupposes design.”

    So it is very much a damned if you do, damned if you don’t, situation for Darwinists. If they refuse to define chance as a rigidly defined mathematical probability, then they are, as Pauli himself put it, ‘very irrational’ and therefore very unscientific. But if, on the other hand, they try to define chance as a rigidly defined mathematical probability, so as to try to become scientific, then they must first necessarily define that chance against a backdrop of purposeful design.

    In other words, no matter what Darwinian atheists try to do with their primary ‘chance postulate’ that lies at the core of their theory, (in order to try to make their theory ‘scientific’), their efforts will forever be futile. Their theory, because of the ‘chance postulate’ itself, is forever regulated to the realm unscientific pseudo-science.

    Of supplemental note:

    Contrary to how many Darwinists portray chance as being a cause unto itself, chance is not a cause of anything.

    What Is Chance? – Nicholas Nurston
    Excerpt: “The vague word ‘chance’ is used as a substitute for a more precise word such as ’cause’. “To personify ‘chance’ as if we were talking about a causal agent,” notes biophysicist Donald M. MacKay, “is to make an illegitimate switch from a scientific to a quasi-religious mythological concept.”
    Similarly, Robert C. Sproul points out: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’” Others who reasoned in this fashion, Nobel laureate Jacques Monod, for one, used this chance equals cause line of reasoning. “Pure chance, absolutely free but blind, (is) at the root of the stupendous edifice of evolution,”…
    https://books.google.com/books?id=bQ5OAAAAQBAJ&pg=PT25&lpg=PT25

    When Darwinists say that something happened by ‘chance’ they are, in fact, appealing to our ignorance of a known cause instead of appealing to any known cause. Charles Darwin himself admitted that his appeal to ‘chance’ is to “acknowledge plainly our ignorance of the cause “,

    “I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation.”
    Charles Darwin – Origin – Chapter V
    http://darwin-online.org.uk/Va.....-1859.html

    As I stated the other day, a magic show without any magician, (i.e. without chance), to perform the magic is certainly one hell of a magic show for Darwinists to believe in.

    Verses:

    Acts 17:23-25
    For as I walked around and looked carefully at your objects of worship, I even found an altar with this inscription: to an unknown god. So you are ignorant of the very thing you worship—and this is what I am going to proclaim to you.
    “The God who made the world and everything in it is the Lord of heaven and earth and does not live in temples built by human hands. And he is not served by human hands, as if he needed anything. Rather, he himself gives everyone life and breath and everything else.

  3. 3
    PavelU says:

    The authors of the paper cited in the OP lack scientific credentials, hence their conclusions have no authority whatsoever. It’s not surprising that the ID fans so desperately cite such an outdated pseudoscientific paper -published long time ago in an unknown journal- to support their weak proposition.

  4. 4
    JVL says:

    PavelU

    What annoyed me was that we can only access the abstract! I don’t have any reason to cast aspersions on the paper or the authors but I would have liked to read the actual thing and its conclusion.

  5. 5
    PavelU says:

    JVL,
    The alleged authors seem to work in a cheap shop, void of any serious scientific substance that could deserve recognition at the academic level. It seems like a joke. What kind of serious science can one expect from that place? Aren’t those remote exotic places that serve as expensive tourist destination for the financially wealthy people that can afford traveling there?
    And the journal is not a serious scientific publication either.

  6. 6
    PavelU says:

    JVL,

    Here’s the conclusions you asked about:

    CONCLUSION
    We found statistical evidence that showed self-preservation and biases towards various amino acids in the genetic code table. In the event of substitution mutations, the highest probabilities are still conservative to steer away from aromatic, negative amino acids, and both start and stop codons. Such findings demonstrate self- preservation at the amino acid level occurring at the nucleotide level.

    The full text is available online:

    https://www.biorxiv.org/content/biorxiv/early/2019/11/06/729756.full.pdf

    https://www.researchgate.net/publication/335157209_Probability_of_Change_in_Life_amino_acid_changes_in_single_nucleotide_substitutions

    https://www.researchgate.net/profile/Samuel_Ken_En_Gan/publication/335157209_Probability_of_Change_in_Life_amino_acid_changes_in_single_nucleotide_substitutions/links/5d5366a792851c93b62e5e93/Probability-of-Change-in-Life-amino-acid-changes-in-single-nucleotide-substitutions.pdf

  7. 7
    bornagain77 says:

    PavelU, right on cue, being the good dishonest Darwinist that he is, attacks the authors:

    The authors:

    Samuel Ken-En Gan graduated from Temasek Polytechnic[7] with a Diploma in Biotechnology. He attained his BSc (Hons) in Molecular Cell Biology from University College London[8] before embarking on his Masters in Structural Biology from Birkbeck College[9] and Ph.D. in Allergy from King’s College London[10] simultaneously with his BSc (Hons) in Psychology from Open University[11], Graduate Certificate in Academic Practice and the Associate of King’s College, both from King’s College London. Gan is also trained in translation & interpretation, theology, business admin, and commercial law & tech transfer. He is a member of the Higher Education Academy UK, the British Psychological Society, Biochemical Society UK, Allergy & Clinical Immunology Society Singapore, and the New York Academy of Sciences.

    Darius Wen-Shuo Koh
    All-time downloads: 700 (rank: 128,161 (tie) out of 350,615)
    Categories:
    microbiology: 309 (rank: 21,650 (tie) out of 37,869)
    molecular biology: 391 (rank: 8,722 (tie) out of 17,542)
    https://rxivist.org/authors/453682

    Joshua Yi Yeo
    https://www.semanticscholar.org/author/Joshua-Yi-Yeo/9728433

    Kwok-Fong Chan
    https://www.researchgate.net/profile/Kwok_Fong_Chan2

    Stelios Koukouravasa
    https://www.researchgate.net/scientific-contributions/2161238876_Stelios_Koukouravas

    Not too shabby!

    Perhaps PavelU will be good enough to show us his credentials?

  8. 8
    jawa says:

    BA77,

    I don’t think PavelU has to show his credentials, because they are well known already:

    1st degree worldly ignorant troll. 🙂

  9. 9
    bornagain77 says:

    Jawa,

    If PavelU had any education in molecular biology whatsoever, he should have known much better than to ever challenge the fact that DNA is intelligently designed.

    On the efficiency of the genetic code after frameshift mutations. – 2018 (our result demonstrates that the SGC (standard genetic code) appears to be much more than just “one in a million”.)
    Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
    Abstract: (open access) – Geyer R, Madany Mamlouk A. (2018) On the efficiency of the genetic code after frameshift mutations. PeerJ 6:e4825
    https://uncommondescent.com/intelligent-design/the-standard-genetic-code-is-optimized-to-reduce-costly-errors/

    Complex grammar of the genomic language – November 9, 2015
    Excerpt: The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher –,,,
    ,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to.
    Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.
    – per science daily

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi-dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
    http://www.worldscientific.com.....08728_0006

    Collective evolution and the genetic code – 2006:
    Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.
    http://www.pnas.org/content/103/28/10696.full

    Scientists Have Stored a Movie, a Computer OS, and an Amazon Gift Card in a Single Speck of DNA
    “The highest-density data-storage device ever created.”
    – PETER DOCKRILL – 7 MAR 2017
    Excerpt: In turn, Erlich and fellow researcher Dina Zielinski from the New York Genome Centre now say their own coding strategy is 100 times more efficient than the 2012 standard, and capable of recording 215 petabytes of data on a single gram of DNA.
    For context, just 1 petabyte is equivalent to 13.3 years’ worth of high-definition video, so if you feel like glancing disdainfully at the external hard drive on your computer desk right now, we won’t judge.
    http://www.sciencealert.com/sc.....eck-of-dna

    DNA Optimized for Photostability
    Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage.
    – per reasons dot org

    Base-pairing protects DNA from UV damage – Sept. 19, 2014
    Excerpt: researchers have discovered a further function of the base-pairing that holds the two strands of the DNA double helix together: it plays a crucial role in protecting the DNA from the ultraviolet rays of the Sun.,,
    The researchers have now used a combination of femtosecond infrared spectroscopy – a technique which employs ultrashort pulses of infrared light (a femtosecond lasts for a millionth of a billionth of second) to probe the dynamics of excited molecular states – and bioorganic chemistry to elucidate a new function of base-pairing: it protects DNA from photodamage.,,,
    After photoexcitation of this DNA with short laser pulses of UV light, the researchers discovered that the hazardous excited states, which can form in any of the bases, are deactivated by an unexpectedly simple mechanism: Each excited pair – whether it be a G-C or an A-T pair – decays into the ground state in a concerted manner. “Thus, the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy.,,
    Watson-Crick base pairing acts as a natural “sunscreen” and is of fundamental importance in enabling organisms to survive exposure to UV radiation.,,,
    – per physorg

    The Chromosome in Nuclear Space – Stephen L. Talbott
    Excerpt: “If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled?
    Obviously it must be possible, however difficult to conceive — and in fact an endlessly varied packing and unpacking is going on all the time.,,,
    http://natureinstitute.org/txt.....nome_2.htm

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    etc.. etc.. etc..

    After reading that, perhaps PavelU would like to tell us once again how much smarter he is than the authors of the paper since he believes DNA is a kludge of accidents instead of believing that it is intelligently designed?

    I guess you just got to be some kind of super smart Darwinist to not believe what your own eyes are telling you:

    Cross section of DNA compared to the Rose window at York Minster (the largest Gothic cathedral in northern Europe) – picture
    https://reflectionsfrommyporchswing.files.wordpress.com/2012/01/dna-2.jpg

    Verse:

    Romans 1
    18 The wrath of God is being revealed from heaven against all the godlessness and wickedness of people, who suppress the truth by their wickedness, 19 since what may be known about God is plain to them, because God has made it plain to them. 20 For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that people are without excuse.
    21 For although they knew God, they neither glorified him as God nor gave thanks to him, but their thinking became futile and their foolish hearts were darkened. 22 Although they claimed to be wise, they became fools 23 and exchanged the glory of the immortal God for images made to look like a mortal human being and birds and animals and reptiles.

  10. 10
    JVL says:

    PavelU

    I’m sorry but I don’t see the basis for your attacks.

    And besides, we should be evaluating the work not the authors shouldn’t we? I’m not saying this particular paper is going to overthrow the current paradigm but all scientific knowledge is provisional isn’t it?

  11. 11
    Fasteddious says:

    From a quick look, it seems to me that this paper is merely saying that not all substitutional mutations are equally likely, and that in the cases they studied, substitutions that maintained the genetic code were somewhat more likely. This does not mean the mutations are non-random, it just means that the randomness is not uniformly distributed among possible substitutions. That should have been expected given the differences among nucleotides and amino acids.

  12. 12
    PaV says:

    Here’s the paper.

    Here is what they were going after:

    Analysing the genetic code table, we found clear biases to what changes mutations
    can achieve in limited mutation events. It is virtually impossible for ATG (Met) to mutate
    to a codon encoding for Proline (CCA, CCC, CCA, CCG) in a single SNS mutational
    event even though it is possible to become a Lysine (AAG) or Leucine (TTG) within
    one such mutational event. Such limitations show an in-built probabilistic
    predisposition of specified codons to mutate to certain amino acids, demonstrating
    innate mutational constraints. To address this, we analysed the probability of SNS
    induced changes in all 64 codons, with the aim of calculating the probable change
    outcomes of each codon.

    Here’s their rough idea:

    The genetic code has an in-built self-bias to have high probabilities towards change
    within the same physicochemical amino acid group (Figure 3), except for aromatic,
    negatively charged amino acids, and the stop codon. The exceptions showed higher
    probabilities to change to the other group types. Interestingly, aromatic amino acids
    have the highest probability of change to a stop codon while aliphatic amino acids
    have an extremely low probability to change to a stop codon. This suggest that intrinsic
    barriers against certain drastic changes at the amino acid level present even at the
    nucleic acid level.

    I think the authors are more involved in molecular chemistry than even molecular biology. I think they’re on to something, but others with more biological expertise will be needed before the paper’s full signficance can be apprehended.

    DNA is a quantum information system. It acts as such. Given that a.a.’s (amino acids) are also quantum systems suggests that, yes, certain “chemical” (i.e., quantum mechanical) tendencies are in play. But it’s nice to have some of these tendencies come to light.

    Error-correction must be a fundamentally “quantum-mechanical” machine. Maybe we’re inching our way towards understanding this better. But, of course, who can build a “quantum machine”?

    Answer: only a builder!

  13. 13
    jawa says:

    PaV,

    I like your interesting analysis of the paper. Well done!

  14. 14
    jawa says:

    As far as I’m aware of,
    1. the DNA nucleotide sequences that code for pre-mRNAs, which may undergo splicing and other post-transcriptional modifications, before undergoing translation by the ribosomes + tRNAs loaded by the aaRS,
    are just a small part of the DNA information.
    2. Additionally there are DNA nucleotide sequences that code for BC RNAs that are used as either machine parts or regulatory signals.
    3. There are also introns that get removed from the pre-mRNAs during the splicing.
    4. There are promoter regions for recruiting the RNA polymerase.
    5. There are enhancer regions, silencer regions, etc.
    6. There are TF-binding sites that conform a patterning code associated with transduction signaling pathways related to extra cellular signals.
    7. Something else…
    Outside the DNA sequences, there are epigenetic markers along the DNA and also associated to the histones involved in the chromatin remodeling.

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