rationalist
Member
Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life
https://******************************/t1279p75-abiogenesis-is-mathematically-impossible#7759
Life: What A Concept! https://jsomers.net/life.pdf
Craig Venter: To me the key thing about Darwinian evolution is selection. Biology is a hundred percent dependent on selection. No matter what we do in synthetic biology, synthetic genomes, we're doing selection. It's just not
natural selection anymore. It's an intelligently designed selection, so it's a unique subset. But selection is always part of it.
My comment:
In regards to the prebiotic synthesis of the basic building blocks of life, I list 23 problems directly related to the lack of a selection mechanism on the prebiotic earth. This is one of the unsolvable problems of abiogenesis.
Selecting the right materials is absolutely essential. But a prebiotic soup of mixtures of impure chemicals would never purify and select those that are required for life. Chemicals and physical reactions have no "urge" to join, group, and start interacting in a purpose and goal-oriented way to produce molecules, that later on would perform specific functions, and generate self-replicating factories, full of machines, directed by specified, complex assembly information. This is not an argument from ignorance, incredulity, or gaps of knowledge.
William Dembski: The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability. Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other.
http://www.discovery.org/a/1256
Out of the 27 listed problems of prebiotic RNA synthesis, 8 are directly related to the lack of a mechanism to select the right ingredients.
1.How would prebiotic processes have purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
2.How did fortuitous accidents select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
3.How did unguided random events select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
4.How did stochastic coincidence select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
5.How would these functional bases have been separated from the confusing jumble of similar molecules that would also have been made?
6.How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
7.How were the correct nitrogen atom of the base and the correct carbon atom of the sugar selected to be joined together?
8.How could right-handed configurations of RNA and DNA have been selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )
Out of the 27 listed problems of prebiotic amino acid synthesis, 13 are directly related to the lack of a mechanism to select the right ingredients.
1. How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
2. How were bifunctional monomers, that is, molecules with two functional groups, so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
3. How could achiral precursors of amino acids have produced/selected and concentrated only left-handed amino acids? ( The homochirality problem )
4. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
5. How would natural causes have selected twenty, and not more or less amino acids to make proteins?
6. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
7. How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
8. How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
9. How could achiral precursors of amino acids have produced and concentrated/selected only left-handed amino acids? (The homochirality problem)
10. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
11. How would natural causes have selected twenty, and not more or less amino acids to make proteins?
12. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
13. How did nature "know" that the set of amino acids selected appears to be near ideal and optimal?
Out of the 12 listed problems of prebiotic cell membrane synthesis, 2 are directly related to the lack of a mechanism to select the right ingredients.
1. How did prebiotic processes select hydrocarbon chains which must be in the range of 14 to 18 carbons in length? There was no physical necessity to form carbon chains of the right length nor hindrance to join chains of varying lengths. So they could have been existing of any size on the early earth.
2. How would random events start to produce biological membranes which are not composed of pure phospholipids, but instead are mixtures of several phospholipid species, often with a sterol admixture such as cholesterol? There is no feasible prebiotic mechanism to select/join the right mixtures.
https://******************************/t1279p75-abiogenesis-is-mathematically-impossible#7759
Life: What A Concept! https://jsomers.net/life.pdf
Craig Venter: To me the key thing about Darwinian evolution is selection. Biology is a hundred percent dependent on selection. No matter what we do in synthetic biology, synthetic genomes, we're doing selection. It's just not
natural selection anymore. It's an intelligently designed selection, so it's a unique subset. But selection is always part of it.
My comment:
In regards to the prebiotic synthesis of the basic building blocks of life, I list 23 problems directly related to the lack of a selection mechanism on the prebiotic earth. This is one of the unsolvable problems of abiogenesis.
Selecting the right materials is absolutely essential. But a prebiotic soup of mixtures of impure chemicals would never purify and select those that are required for life. Chemicals and physical reactions have no "urge" to join, group, and start interacting in a purpose and goal-oriented way to produce molecules, that later on would perform specific functions, and generate self-replicating factories, full of machines, directed by specified, complex assembly information. This is not an argument from ignorance, incredulity, or gaps of knowledge.
William Dembski: The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability. Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other.
http://www.discovery.org/a/1256
Out of the 27 listed problems of prebiotic RNA synthesis, 8 are directly related to the lack of a mechanism to select the right ingredients.
1.How would prebiotic processes have purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
2.How did fortuitous accidents select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
3.How did unguided random events select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
4.How did stochastic coincidence select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
5.How would these functional bases have been separated from the confusing jumble of similar molecules that would also have been made?
6.How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
7.How were the correct nitrogen atom of the base and the correct carbon atom of the sugar selected to be joined together?
8.How could right-handed configurations of RNA and DNA have been selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )
Out of the 27 listed problems of prebiotic amino acid synthesis, 13 are directly related to the lack of a mechanism to select the right ingredients.
1. How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
2. How were bifunctional monomers, that is, molecules with two functional groups, so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
3. How could achiral precursors of amino acids have produced/selected and concentrated only left-handed amino acids? ( The homochirality problem )
4. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
5. How would natural causes have selected twenty, and not more or less amino acids to make proteins?
6. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
7. How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
8. How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
9. How could achiral precursors of amino acids have produced and concentrated/selected only left-handed amino acids? (The homochirality problem)
10. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
11. How would natural causes have selected twenty, and not more or less amino acids to make proteins?
12. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
13. How did nature "know" that the set of amino acids selected appears to be near ideal and optimal?
Out of the 12 listed problems of prebiotic cell membrane synthesis, 2 are directly related to the lack of a mechanism to select the right ingredients.
1. How did prebiotic processes select hydrocarbon chains which must be in the range of 14 to 18 carbons in length? There was no physical necessity to form carbon chains of the right length nor hindrance to join chains of varying lengths. So they could have been existing of any size on the early earth.
2. How would random events start to produce biological membranes which are not composed of pure phospholipids, but instead are mixtures of several phospholipid species, often with a sterol admixture such as cholesterol? There is no feasible prebiotic mechanism to select/join the right mixtures.