biosemiotics Cell biology Chemistry Food for thought Functionally Specified Complex Information & Organization ID Foundations Information Origin Of Life Self-Org. Theory

Guest Post — Template-Assisted Ligation: A New OOL Model

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Dr E. Selensky occasionally requests that UD posts an article on his behalf. What follows is his latest:

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Arguably, the RNA world model is excessively complex: it operates too complex structures and involves too complex interactions.

The origin of life, some researchers believe, must have been simpler.

In an attempt to close the gap between chemistry and life by naturalistic means a new model has been proposed recently, yet another one of many, that seeks to explain the rise of RNAs. This model is called template-assisted ligation. It has been proposed by Alexey Tkachenko and Sergei Maslov at American Institute of Physics. They hope it can help shed light on what could have preceded the RNA world.

The crux of the model is as follows. In an environment with cyclic parameter variations (the authors suggest that day-night variations of pH, salinity, luminosity etc. might have occurred in the hypothetical primordial ocean) small-sized polymers could form larger complementary polymer strands that then would undergo cyclic dissociations and associations. The transition from small-sized molecules to larger polymers is hysteretic and, once it happened under suitable conditions, it would no longer be required to maintain the replication of complementary polymer strands.

A schematic drawing of template-assisted ligation, shown in this model to give rise to autocatalytic systems (Credit: Maslov and Tkachenko)

With all due respect, the model falls short of explaining the information processing capability of the living systems.

Autocatalytic replication by itself could not have given rise to a translation from the language of nucleotides to the language of peptides, which takes place in all known organisms today. Template-based replication is observed even in crystals and does not require translation in the above sense. On the contrary, such translation assumes the existence of logical relationships between the code and its referent (see Genetic code). These relationships are categorically different from physico-chemical regularities, which act as the key driver in the appearance of chemical replication in the model under consideration. The realization of the said logical relationships is only possible where the structure of the polymer, recognized by the translator as code, is inert or degenerate towards, arbitrary in relation to and does not chemically depend on the system dynamics.

The genetic information translation system that can be universally observed today includes three major physico-chemically independent components:

  • The code (nucleic acids);

  • The protocol (aminoacyl tRNA synthetases with their tRNAs);

  • The referents (polypeptides).

Additionally, the genetic information translation system is characterized by what is known as semantic closure (semantic self-sufficiency) whereby the code, apart from the other components of the next generation organism, also specifies the translation system itself that will have to recognize and interpret this same code in the subsequent generations. As far as I could see, the template-assisted ligation model does not even address the problem of the origin of biological information translation. It merely illustrates a mechanism of autocatalytic replication.

Many, if not all, known abiogenetic models (chemotons, hyper-cycles, RNA-world, RNA-peptide world, metabolic pathways or template-assisted ligation) fail to recognize that in reality there is no unintelligent non-telic physico-chemical pathway from organic chemistry to life. Information translation — a key property of living systems — is not a consequence of physical or chemical regularities but a result of the organization of the system, in other words, the boundary conditions on system dynamics.

The notoriously evasive complexity leap from organic chemistry to life defies attempts to ‘spread it out’ over a succession of elementary chemical interactions. Simple models do not take into account the necessary starting complexity of life as a whole, while more complex models depart from the original idea of non-telic non-agent-based abiogenetic synthesis: the more complex the model, the further it defeats the naturalistic purpose to represent life as ‘just a bit more complicated’ chemistry.

Finally, let me suggest some further reading.

And, a couple of my previous OPs:

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Serious food for thought on OoL. END

18 Replies to “Guest Post — Template-Assisted Ligation: A New OOL Model

  1. 1
    kairosfocus says:

    F/N: Dr Selensky (in a guest post) on a recent pre-RNA World OoL model: “With all due respect, the model falls short of explaining the information processing capability of the living systems.”

    Expanding:

    Autocatalytic replication by itself could not have given rise to a translation from the language of nucleotides to the language of peptides, which takes place in all known organisms today. Template-based replication is observed even in crystals and does not require translation in the above sense. On the contrary, such translation assumes the existence of logical relationships between the code and its referent (see Genetic code). These relationships are categorically different from physico-chemical regularities, which act as the key driver in the appearance of chemical replication in the model under consideration. The realization of the said logical relationships is only possible where the structure of the polymer, recognized by the translator as code, is inert or degenerate towards, arbitrary in relation to and does not chemically depend on the system dynamics.

    The genetic information translation system that can be universally observed today includes three major physico-chemically independent components:

    The code (nucleic acids);

    The protocol (aminoacyl tRNA synthetases with their tRNAs);

    The referents (polypeptides).

    Additionally, the genetic information translation system is characterized by what is known as semantic closure (semantic self-sufficiency) whereby the code, apart from the other components of the next generation organism, also specifies the translation system itself that will have to recognize and interpret this same code in the subsequent generations. As far as I could see, the template-assisted ligation model does not even address the problem of the origin of biological information translation. It merely illustrates a mechanism of autocatalytic replication.

    Many, if not all, known abiogenetic models (chemotons, hyper-cycles, RNA-world, RNA-peptide world, metabolic pathways or template-assisted ligation) fail to recognize that in reality there is no unintelligent non-telic physico-chemical pathway from organic chemistry to life. Information translation — a key property of living systems — is not a consequence of physical or chemical regularities but a result of the organization of the system, in other words, the boundary conditions on system dynamics.

    The notoriously evasive complexity leap from organic chemistry to life defies attempts to ‘spread it out’ over a succession of elementary chemical interactions.

    That’s the challenge on the table.

    Let the TGIF debate begin.

    KF

  2. 2
    Dionisio says:

    KF,

    Very insightful article by Dr. Selensky.
    Thanks for posting it here.
    Good TGIF reading.

  3. 3
    Dionisio says:

    Eugene S

    Excellent article. Right on target.
    Thanks.

  4. 4
    Dionisio says:

    “the more complex the model, the further it defeats the naturalistic purpose to represent life as ‘just a bit more complicated’ chemistry.”

    Very clear.

  5. 5
    Eugene S says:

    KF, Dionisio,

    Many Thanks for posting and commenting on it!

  6. 6
    Eugene S says:

    The link to D. Abel’s chapter points to the wrong place.

    It should point to here instead.

    Apologies.

  7. 7
  8. 8
    Eugene S says:

    KF

    Excellent. Thanks!

  9. 9
    Dionisio says:

    How do we get the RNA polymerase and the rest of the transcription machinery within this new ool model?
    Thanks

  10. 10
    Dionisio says:

    Is this new OOL model promoted or at least accepted as the new “de facto” OOL scenario by the ‘third way’ folks?
    Thanks

  11. 11
    Dionisio says:

    How is the DNA Polymerase and the rest of the replication machinery accounted for within this new OOL model?
    Thanks.

  12. 12
    Dionisio says:

    “Simple models do not take into account the necessary starting complexity of life as a whole, while more complex models depart from the original idea of non-telic non-agent-based abiogenetic synthesis: the more complex the model, the further it defeats the naturalistic purpose to represent life as ‘just a bit more complicated’ chemistry.”

    The closing statements left little room -if any at all- for counterarguments.

    Perhaps that explains, at least in part, the conspicuous absence of politely dissenting interlocutors, which seem so loud in other threads?

    Well done, Dr. Selensky.

  13. 13
    Dionisio says:

    The whole OOL topic seems above my pay grade. It requires a deep knowledge of chemistry -both organic and inorganic- that I don’t have. It also demands quite a substantial amount of imagination in order to visualize hypothetical scenarios. I lack that too.
    That’s why I usually try to avoid it. Sometimes I may comment against it in harsh terms, arguing that the efforts dedicated to it would be better used to research how the biological systems function.
    However, Dr. Selensky definitely made this otherwise esoteric subject a little more chewable and digestible.
    Well done!

  14. 14
    Dionisio says:

    Sometimes I think that the folks who possess such prolific imaginations to come up with all those OOL models perhaps could have pursued very successful careers working for Disney.
    They could write fairytale scenarios that would render the famous Cinderella story boringly unattractive to most children. After watching one of the OOL-based cartoons, why would a child get excited with a pumpkin turning into an elegant carriage, or mice becoming beautiful horses, or a grasshopper being hired as the ‘cochero’?
    Really, think about it.
    🙂

  15. 15
    Dionisio says:

    In case some readers want to scratch their heads even further, here is the original paper referenced by Dr. Selensky:

    Spontaneous emergence of autocatalytic information-coding polymers
    The Journal of Chemical Physics 143, 045102 (2015); https://doi.org/10.1063/1.4922545
    Alexei V. Tkachenko1 and Sergei Maslov
    http://aip.scitation.org/doi/10.1063/1.4922545

    Here’s the full text PDF:
    http://maslov.bioengineering.i.....P_2015.pdf

    Did somebody say “information-coding”?

  16. 16
    Dionisio says:

    @15 follow up

    The abstract of the referenced paper concludes with this mouthful:

    “The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems.”

    Did somebody say “information encoded”?

  17. 17
    Dionisio says:

    Here’s another paper that cites the authors of the paper referenced in Dr. Selensky’s OP.

    Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

    Elizaveta Guseva, Ronald N. Zuckerman and Ken A. Dill

    PNAS
    vol. 114 no. 36 E7460–E7468,
    doi: 10.1073/pnas.1620179114

    http://www.pnas.org/content/114/36/E7460.full

    PDF full text:
    http://www.pnas.org/content/114/36/E7460.full.pdf

    As one can see, they don’t give up easily. Still keep searching for the black cat in the dark room.

  18. 18
    Dionisio says:

    chemistry-to-biology transition (CTBT)

    CTBT = pop —> Pop —> PoP —> POP —> POP! —> bingo!

    Generously provided by RV+NS+T

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