Main topics on abiogenesis
https://reasonandscience.catsboard.com/t2678-maintopics-on-abiogenesis
Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution, page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.
A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life
All things considered, my assessment of the current state of the art in the study of the origins of replication and translation is rather somber. Notwithstanding relevant theoretical models and suggestive experimental results, we currently do not have a credible solution to these problems and do not even see with any clarity a path to such a solution.
Eugene V. Koonin, The Logic of Chance: page 219
The emergence of cells is the epitome of the problems encountered by all explanations of the evolution of complex biological structures. Among modern biological entities, we do not see any intermediates between macromolecules and cells, and to imagine how such intermediates might operate is a huge challenge.
Bayesian analysis of the astrobiological implications of life’s early emergence on Earth
2012 Jan 10
the evidence is inconclusive and indeed is consistent with an arbitrarily low intrinsic probability of abiogenesis for plausible uninformative priors. Finding a single case of life arising independently of our lineage (on Earth, elsewhere in the solar system, or on an extrasolar planet) would provide much stronger evidence that abiogenesis is not extremely rare in the universe. 4
The data are consistent (under plausible priors) with life being extremely rare. Thus, a Bayesian enthusiast of extraterrestrial life should be significantly encouraged by the rapid appearance of life on the early Earth but cannot be highly confident on that basis.
Origin and evolution of the genetic code: the universal enigma
Koonin, 2009 Feb; 6
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology. 1
The genetic code is one in a million
1998 Sep
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. 2
On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
2007 May 31
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. 3
A calculation of the probability of spontaneous biogenesis by information theory
Hubert P. Yockey 7 August 1977
The Darwin-Oparin-Haldane “warm little pond” scenario for biogenesis is examined by using information theory to calculate the probability that an informational biomolecule of reasonable biochemical specificity, long enough to provide a genome for the “protobiont”, could have appeared in 109 years in the primitive soup. Certain old untenable ideas have served only to confuse the solution of the problem. Negentropy is not a concept because entropy cannot be negative. The role that negentropy has played in previous discussions is replaced by “complexity” as defined in information theory. A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. Previous calculations based on simple combinatorial analysis over estimate the number of sequences by a factor of 105. The number of cytochrome c sequences is about 3·8 × 10^61. The probability of selecting one such sequence at random is about 2·1 ×10^65. The primitive milieu will contain a racemic mixture of the biological amino acids and also many analogues and non-biological amino acids. Taking into account only the effect of the racemic mixture the longest genome which could be expected with 95 % confidence in 109 years corresponds to only 49 amino acid residues. This is much too short to code a living system so evolution to higher forms could not get started. Geological evidence for the “warm little pond” is missing. It is concluded that belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.
There are only two possible explanations as to how life arose: Spontaneous generation was scientifically disproved 120 years ago by Louis Pasteur and others, but that just leaves us with only one other possibility…that life came as a supernatural act of creation by God, BUT I CAN’T ACCEPT THAT PHILOSOPHY BECAUSE I DO NOT WANT TO BELIEVE IN GOD. Therefore I choose to believe in that which I know is scientifically impossible, spontaneous generation leading to evolution. –George Wald (AD 1906 – 1997/ professed atheist/ 1967 Nobel Physiology or Medicine Prize).
Ironically, George Wald was first to observe the three-color sensing pigments in the three different types of human retina cones (yes, this is another imprimatur). Each of the three types of cone receptors contains the protein photopsin, with variations in its conformation causing differences in the optimum wavelengths absorbed.
The secret of life won't be cooked up in a chemistry lab
Paul Davies Sun 13 Jan 2013
The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry. Therefore chemistry alone will not explain life's origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program.
https://www.theguardian.com/commentisfree/2013/jan/13/secret-life-unveiled-chemistry-lab
Thomas Nagel, New York University professor:
It “highly implausible that life is a result of a sequence of physical accidents combined with natural selection”
The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true.
Chemist Wilhelm Huck, professor at Radboud University Nijmegen
"A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity,"
Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.
Chemical evolution: The mechanism of the formation of adenine under prebiotic conditions
September 6, 2007
How did life on earth begin? The presence of biomolecules was a prerequisite, but the origin of even the simplest of these remains a fascinating but unsolved puzzle 6
Abiogenesis is virtually impossible
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-impossible
The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument
The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-the-possible-mechanisms-to-explain-the-origin-of-life
Calculations of life beginning through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-calculations-of-life-beginning-through-unguided-natural-random-events
The cell is irreducibly complex
https://reasonandscience.catsboard.com/t1299-the-cell-is-irreducibly-complex
The irreducible, code-instructed process to make cell factories and machines points to intelligent design
https://reasonandscience.catsboard.com/t2364-the-irreducible-code-instructed-process-to-make-cell-factories-and-machines-points-to-intelligent-design
Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind
All cellular functions are irreducibly complex
https://reasonandscience.catsboard.com/t2179-the-cell-is-a-interdependent-irreducible-complex-system
The Cell membrane, irreducible complexity
https://reasonandscience.catsboard.com/t2128-membrane-structure#3798
The Interdependency of Lipid Membranes and Membrane Proteins
https://reasonandscience.catsboard.com/t2397-the-interdependency-of-lipid-membranes-and-membrane-proteins
Factory and machine planning and design, and what it tells us about cell factories and molecular machines
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-liness
Genome information, protein synthesis, the biosynthesis pathways in biology, and the analogy of human programming, engineering, and factory robotic assembly lines
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines
What might be a Cell’s minimal requirement of parts?
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts
How Cellular Enzymatic and Metabolic networks point to design
https://reasonandscience.catsboard.com/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design
Amazing molecular assembly lines and nonribosomal amino-acid chain formation pathways come to light
https://reasonandscience.catsboard.com/t2445-new-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-light
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
2. http://www.ncbi.nlm.nih.gov/pubmed/9732450
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258618/
5. http://www.sciencedirect.com/science/article/pii/0022519377900443
6. http://www.pnas.org/content/104/44/17272.full
https://reasonandscience.catsboard.com/t2678-maintopics-on-abiogenesis
Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution, page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.
A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life
All things considered, my assessment of the current state of the art in the study of the origins of replication and translation is rather somber. Notwithstanding relevant theoretical models and suggestive experimental results, we currently do not have a credible solution to these problems and do not even see with any clarity a path to such a solution.
Eugene V. Koonin, The Logic of Chance: page 219
The emergence of cells is the epitome of the problems encountered by all explanations of the evolution of complex biological structures. Among modern biological entities, we do not see any intermediates between macromolecules and cells, and to imagine how such intermediates might operate is a huge challenge.
Bayesian analysis of the astrobiological implications of life’s early emergence on Earth
2012 Jan 10
the evidence is inconclusive and indeed is consistent with an arbitrarily low intrinsic probability of abiogenesis for plausible uninformative priors. Finding a single case of life arising independently of our lineage (on Earth, elsewhere in the solar system, or on an extrasolar planet) would provide much stronger evidence that abiogenesis is not extremely rare in the universe. 4
The data are consistent (under plausible priors) with life being extremely rare. Thus, a Bayesian enthusiast of extraterrestrial life should be significantly encouraged by the rapid appearance of life on the early Earth but cannot be highly confident on that basis.
Origin and evolution of the genetic code: the universal enigma
Koonin, 2009 Feb; 6
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology. 1
The genetic code is one in a million
1998 Sep
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. 2
On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
2007 May 31
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. 3
A calculation of the probability of spontaneous biogenesis by information theory
Hubert P. Yockey 7 August 1977
The Darwin-Oparin-Haldane “warm little pond” scenario for biogenesis is examined by using information theory to calculate the probability that an informational biomolecule of reasonable biochemical specificity, long enough to provide a genome for the “protobiont”, could have appeared in 109 years in the primitive soup. Certain old untenable ideas have served only to confuse the solution of the problem. Negentropy is not a concept because entropy cannot be negative. The role that negentropy has played in previous discussions is replaced by “complexity” as defined in information theory. A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. Previous calculations based on simple combinatorial analysis over estimate the number of sequences by a factor of 105. The number of cytochrome c sequences is about 3·8 × 10^61. The probability of selecting one such sequence at random is about 2·1 ×10^65. The primitive milieu will contain a racemic mixture of the biological amino acids and also many analogues and non-biological amino acids. Taking into account only the effect of the racemic mixture the longest genome which could be expected with 95 % confidence in 109 years corresponds to only 49 amino acid residues. This is much too short to code a living system so evolution to higher forms could not get started. Geological evidence for the “warm little pond” is missing. It is concluded that belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.
There are only two possible explanations as to how life arose: Spontaneous generation was scientifically disproved 120 years ago by Louis Pasteur and others, but that just leaves us with only one other possibility…that life came as a supernatural act of creation by God, BUT I CAN’T ACCEPT THAT PHILOSOPHY BECAUSE I DO NOT WANT TO BELIEVE IN GOD. Therefore I choose to believe in that which I know is scientifically impossible, spontaneous generation leading to evolution. –George Wald (AD 1906 – 1997/ professed atheist/ 1967 Nobel Physiology or Medicine Prize).
Ironically, George Wald was first to observe the three-color sensing pigments in the three different types of human retina cones (yes, this is another imprimatur). Each of the three types of cone receptors contains the protein photopsin, with variations in its conformation causing differences in the optimum wavelengths absorbed.
The secret of life won't be cooked up in a chemistry lab
Paul Davies Sun 13 Jan 2013
The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry. Therefore chemistry alone will not explain life's origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program.
https://www.theguardian.com/commentisfree/2013/jan/13/secret-life-unveiled-chemistry-lab
Thomas Nagel, New York University professor:
It “highly implausible that life is a result of a sequence of physical accidents combined with natural selection”
The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true.
Chemist Wilhelm Huck, professor at Radboud University Nijmegen
"A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity,"
Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.
Chemical evolution: The mechanism of the formation of adenine under prebiotic conditions
September 6, 2007
How did life on earth begin? The presence of biomolecules was a prerequisite, but the origin of even the simplest of these remains a fascinating but unsolved puzzle 6
Abiogenesis is virtually impossible
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-impossible
The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument
The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-the-possible-mechanisms-to-explain-the-origin-of-life
Calculations of life beginning through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-calculations-of-life-beginning-through-unguided-natural-random-events
The cell is irreducibly complex
https://reasonandscience.catsboard.com/t1299-the-cell-is-irreducibly-complex
The irreducible, code-instructed process to make cell factories and machines points to intelligent design
https://reasonandscience.catsboard.com/t2364-the-irreducible-code-instructed-process-to-make-cell-factories-and-machines-points-to-intelligent-design
Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind
All cellular functions are irreducibly complex
https://reasonandscience.catsboard.com/t2179-the-cell-is-a-interdependent-irreducible-complex-system
The Cell membrane, irreducible complexity
https://reasonandscience.catsboard.com/t2128-membrane-structure#3798
The Interdependency of Lipid Membranes and Membrane Proteins
https://reasonandscience.catsboard.com/t2397-the-interdependency-of-lipid-membranes-and-membrane-proteins
Factory and machine planning and design, and what it tells us about cell factories and molecular machines
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-liness
Genome information, protein synthesis, the biosynthesis pathways in biology, and the analogy of human programming, engineering, and factory robotic assembly lines
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines
What might be a Cell’s minimal requirement of parts?
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts
How Cellular Enzymatic and Metabolic networks point to design
https://reasonandscience.catsboard.com/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design
Amazing molecular assembly lines and nonribosomal amino-acid chain formation pathways come to light
https://reasonandscience.catsboard.com/t2445-new-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-light
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
2. http://www.ncbi.nlm.nih.gov/pubmed/9732450
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258618/
5. http://www.sciencedirect.com/science/article/pii/0022519377900443
6. http://www.pnas.org/content/104/44/17272.full
