Lone Piper
I disagree with a number of your statements and your unchecked and unreasoned bias is amazing (did you even look at the research paper?) but for the sake of time I'll just try to answer your question and I'll use non-creationist since you seem to throw them out without even considering their work. I'm becoming more and more convinced that your problem (not just you, but the other atheist here as well) with theism and devotion to evolution has very little to do with scientific evidence. but anyway....
I assume that the question you wanted answered deals with the Abiogenesis since that's the one you think I am avoiding.
there are number of major problems:
1) The assumption that there was no free oxygen. This is the assumption of all the experiments that I have seen that simulating creating basic building blocks of life. O2 totally stops and destroys the production of organic compounds. There is strong geological evidence that significant amounts of oxygen was present in the earth's early atmosphere. For instance, many minerals react with oxygen (such as the rusting of iron), and the resulting oxides are found in rocks dated earlier than the origin of life. (J.H. Carver, "Prebiotic Atmosphere Oxygen Levels," Nature 292 (1981):136-38; & James F. Kasting, "Earth's Early Atmosphere," Science 259 (1993): 920-26.)
--The oceans have an equilibrium with the atmosphere, so the oceans would have had the same amount of O2 as the atmosphere. (this would destroy any organic compounds that moved out of anoxic conditions)
-- if there was not oxygen in the Atmosphere, then there would have been no Ozone. Ozone forms a protective shield from the ultraviolet radiation from the sun. Without it life/organic compounds would be destroyed from the high levels, yet life clearly flourished on early earth. (which would also destroy organic compunds in anoxic environments)
--the Miller-Urey experiment is now dismissed by many origin-of-life researchers because "the early atmosphere looked nothing like the Miller-Urey simulation." (Jon Cohen, "Novel Center Seeks to Add Spark to Origin of Life," Science 270 (1995):1925-26.)
--to claim anaerobic conditions for the formation of life greatly limits the places and opportunity for these random processes to form and stay protected from being destroyed. This would mean that the first life also had to form in these conditions or else suffer the effects of O2. But that's fine if that claim gets around oxygen. I'll let you take it for the sake of argument, even though there is no empirical evidence for that claim.
---organic chemicals from metiorites gets you around this O2 problem for their basic formation, but it doesn't stop their destruction once here on earth. It also doesn't solve the problem of the chemicals being stopped or destroyed form forming into life. So what if you have some chemicals slam into earth, you still have to deal with the O2 to get any more complex for life.
2)Reactions are reversible. the creation of organic chemicals would take some form of energy. The sun, lightning, or heat from volcanic activity are the three big ones normally used. While some chemical reactions form easily under these conditions, they also break easily. Energy is a two-edged sword that can create and destroy just as readily. The simulated experiments normally take or collect the created compounds and get them away from the destructive forces used to create them. Taking this into account the "prebiotic soup" would favor simple molecules and work against complex ones. (this would affect anoxic environments)
3)Interfering Cross-Reactions: While many reaction needed for biologically important compounds have been observed under artificial laboratory conditions. In nature many reactions that occur in nature work against the formation of biologically important compounds. Amino acids, for instance, do not readily react with each other. They do readily reach with other substances like sugars. But for life to form the amino acids would need to only reach with each other. They would not just float around in some type or soup and only react with other amino acids. They would react with anything they come in contact with making all sorts of cross-reactions. This would tie them up and make them useless for any type of biologically useful function, it would just make a useless tar. Even in the carefully planed primitive atmosphere experiments confirm this. Most of what they form is a tar with only some very small peptides. If the scientist in a controlled environment can't do it, it cast real doubt on it happening naturally. (this also covers your far-fetched self-replicating non-amino acid molecules theory even if in anoxic conditions) (Alan W. Schwarts, "Interactable Mixtures and the Origin of Life," Chemistry and Biodiversity 4(4) (2007):656. He is the editor of Origins of Life and Evolution of Biospheres;also Robert Shapiro, "A Simpler Origin of Life," Scientific American (Feb 12, 2007)
4)Racemic Mixtures: Amino acids, sugars, proteins, and DNA are not simply bundles of chemicals. they exhibit very specific 3-D structures. Even if they have all the right pieces, they don't always have the right structure. The problem is that that amino acids (and sugars) appear in two forms (chiralities). they can exists as mirror images of each other, sort of like a right and left handed glove, they are actually referred to as right handed or left handed amino acids. In simulated experiments(such as Miller and Urey) the "left" and "right" appear about 50/50 for both amino acids and sugars. Scientist have not been able to get concentrations of one or the other in "natural" simulations. The reason this is a problem is that only the Left handed amino acids are used in life. If even one of the right handed forms get involved in the structure of the protein, it diminished and often completely destroys the function of it. To add to this problem living things include only right-handed sugars in life(such as the sugar phosphate backbone in DNA). How did living things exclusively prefer one form to the other when there should have been an even mixture. Life shows characteristics that are alien to anything known to be produced under ordinary material conditions. (this would affect anoxic environments)
5)The synthesis of polymers problem: even if you had all the correct amino acids(Left handed) and sugars(right handed) you run into the staggering complexity of organizing them in the right sequence with only the correct bonds. Amino acids can chemically join together in a number of ways, but only the "peptide bond" is in functional proteins. You have to solve the problem of only the correct bond before you can even touch the problem of the correct order of amino acids. Living cells solve this problem using enzymes (which are proteins). In nature or a prebiotic soup you don't have this luxury. Things get even more complicated when we talk about the nucleotides found in DNA.
In a small protein consisting of 100 subunits, and using only the 20 amino acid found in life. the number of different sequences (with only peptide bonds) is 20 raised to the 100. (or about 10 raised to the 130). MIT biochemist Robert Sauer applied a technique that took into account the variations that would be tolerated at a given protein site. His number that the probability of forming a 100-subunit functional protein is only 1 in 10 raised to the 65. While that is much better it is still an infinitesimally small probability. Just for reference it has been estimated that there are 10 raise to the 65 atoms in the universe. (if you want to claim amino acids from meteors helped form life, then you have even more problems because the Murchison meteorite had over 70 amino acids, which make the possible combinations significantly larger and even more improbable)[J. Bowie and R. Sauer, "Identifying Determinants of Folding and Actiity for a Protein of Unknown Sequences:Tolerance to Amino Acid Substitution," Proceedings of the National Academy of Science 86 (1989): 2152-56.; J. Bowie, J. reidhaar-Olson, W. Lim, and R. Sauer, "Deciphering the Message in Protein sequences: Tolerance to Amino Acid Substitution," Science 247 (1990):1306-10.; J. Reidhaar-Olson and R. Sauer, "Functionally Acceptable Solutiions in Two Alpha-Helical regions of Lambda Repressor," Proteins, Structure, Function, and Genetics 7 (1990): 306-10. see also Hubert Yockey, Information Theory and Molecular Biology (cambridge: Cambridge University Press, 1992) 246-58.]
These are major problems that you cannot just wave off as if they don't matter or say well we just don't have enough information yet. These problems have arisen because of all the information we do have, This is not an ignorance problem. You can deny the evidence and still hold to the spontaneous generation (abiogeneis) that Darwin claimed out of ignorance to the true complexity of life, but you must realize and admit that you do so on grounds other than the scientific evidence. As I said before I think the true issue with theism is not a scientific one, but either emotionally based or philosophically based.
I disagree with a number of your statements and your unchecked and unreasoned bias is amazing (did you even look at the research paper?) but for the sake of time I'll just try to answer your question and I'll use non-creationist since you seem to throw them out without even considering their work. I'm becoming more and more convinced that your problem (not just you, but the other atheist here as well) with theism and devotion to evolution has very little to do with scientific evidence. but anyway....
I assume that the question you wanted answered deals with the Abiogenesis since that's the one you think I am avoiding.
there are number of major problems:
1) The assumption that there was no free oxygen. This is the assumption of all the experiments that I have seen that simulating creating basic building blocks of life. O2 totally stops and destroys the production of organic compounds. There is strong geological evidence that significant amounts of oxygen was present in the earth's early atmosphere. For instance, many minerals react with oxygen (such as the rusting of iron), and the resulting oxides are found in rocks dated earlier than the origin of life. (J.H. Carver, "Prebiotic Atmosphere Oxygen Levels," Nature 292 (1981):136-38; & James F. Kasting, "Earth's Early Atmosphere," Science 259 (1993): 920-26.)
--The oceans have an equilibrium with the atmosphere, so the oceans would have had the same amount of O2 as the atmosphere. (this would destroy any organic compounds that moved out of anoxic conditions)
-- if there was not oxygen in the Atmosphere, then there would have been no Ozone. Ozone forms a protective shield from the ultraviolet radiation from the sun. Without it life/organic compounds would be destroyed from the high levels, yet life clearly flourished on early earth. (which would also destroy organic compunds in anoxic environments)
--the Miller-Urey experiment is now dismissed by many origin-of-life researchers because "the early atmosphere looked nothing like the Miller-Urey simulation." (Jon Cohen, "Novel Center Seeks to Add Spark to Origin of Life," Science 270 (1995):1925-26.)
--to claim anaerobic conditions for the formation of life greatly limits the places and opportunity for these random processes to form and stay protected from being destroyed. This would mean that the first life also had to form in these conditions or else suffer the effects of O2. But that's fine if that claim gets around oxygen. I'll let you take it for the sake of argument, even though there is no empirical evidence for that claim.
---organic chemicals from metiorites gets you around this O2 problem for their basic formation, but it doesn't stop their destruction once here on earth. It also doesn't solve the problem of the chemicals being stopped or destroyed form forming into life. So what if you have some chemicals slam into earth, you still have to deal with the O2 to get any more complex for life.
2)Reactions are reversible. the creation of organic chemicals would take some form of energy. The sun, lightning, or heat from volcanic activity are the three big ones normally used. While some chemical reactions form easily under these conditions, they also break easily. Energy is a two-edged sword that can create and destroy just as readily. The simulated experiments normally take or collect the created compounds and get them away from the destructive forces used to create them. Taking this into account the "prebiotic soup" would favor simple molecules and work against complex ones. (this would affect anoxic environments)
3)Interfering Cross-Reactions: While many reaction needed for biologically important compounds have been observed under artificial laboratory conditions. In nature many reactions that occur in nature work against the formation of biologically important compounds. Amino acids, for instance, do not readily react with each other. They do readily reach with other substances like sugars. But for life to form the amino acids would need to only reach with each other. They would not just float around in some type or soup and only react with other amino acids. They would react with anything they come in contact with making all sorts of cross-reactions. This would tie them up and make them useless for any type of biologically useful function, it would just make a useless tar. Even in the carefully planed primitive atmosphere experiments confirm this. Most of what they form is a tar with only some very small peptides. If the scientist in a controlled environment can't do it, it cast real doubt on it happening naturally. (this also covers your far-fetched self-replicating non-amino acid molecules theory even if in anoxic conditions) (Alan W. Schwarts, "Interactable Mixtures and the Origin of Life," Chemistry and Biodiversity 4(4) (2007):656. He is the editor of Origins of Life and Evolution of Biospheres;also Robert Shapiro, "A Simpler Origin of Life," Scientific American (Feb 12, 2007)
4)Racemic Mixtures: Amino acids, sugars, proteins, and DNA are not simply bundles of chemicals. they exhibit very specific 3-D structures. Even if they have all the right pieces, they don't always have the right structure. The problem is that that amino acids (and sugars) appear in two forms (chiralities). they can exists as mirror images of each other, sort of like a right and left handed glove, they are actually referred to as right handed or left handed amino acids. In simulated experiments(such as Miller and Urey) the "left" and "right" appear about 50/50 for both amino acids and sugars. Scientist have not been able to get concentrations of one or the other in "natural" simulations. The reason this is a problem is that only the Left handed amino acids are used in life. If even one of the right handed forms get involved in the structure of the protein, it diminished and often completely destroys the function of it. To add to this problem living things include only right-handed sugars in life(such as the sugar phosphate backbone in DNA). How did living things exclusively prefer one form to the other when there should have been an even mixture. Life shows characteristics that are alien to anything known to be produced under ordinary material conditions. (this would affect anoxic environments)
5)The synthesis of polymers problem: even if you had all the correct amino acids(Left handed) and sugars(right handed) you run into the staggering complexity of organizing them in the right sequence with only the correct bonds. Amino acids can chemically join together in a number of ways, but only the "peptide bond" is in functional proteins. You have to solve the problem of only the correct bond before you can even touch the problem of the correct order of amino acids. Living cells solve this problem using enzymes (which are proteins). In nature or a prebiotic soup you don't have this luxury. Things get even more complicated when we talk about the nucleotides found in DNA.
In a small protein consisting of 100 subunits, and using only the 20 amino acid found in life. the number of different sequences (with only peptide bonds) is 20 raised to the 100. (or about 10 raised to the 130). MIT biochemist Robert Sauer applied a technique that took into account the variations that would be tolerated at a given protein site. His number that the probability of forming a 100-subunit functional protein is only 1 in 10 raised to the 65. While that is much better it is still an infinitesimally small probability. Just for reference it has been estimated that there are 10 raise to the 65 atoms in the universe. (if you want to claim amino acids from meteors helped form life, then you have even more problems because the Murchison meteorite had over 70 amino acids, which make the possible combinations significantly larger and even more improbable)[J. Bowie and R. Sauer, "Identifying Determinants of Folding and Actiity for a Protein of Unknown Sequences:Tolerance to Amino Acid Substitution," Proceedings of the National Academy of Science 86 (1989): 2152-56.; J. Bowie, J. reidhaar-Olson, W. Lim, and R. Sauer, "Deciphering the Message in Protein sequences: Tolerance to Amino Acid Substitution," Science 247 (1990):1306-10.; J. Reidhaar-Olson and R. Sauer, "Functionally Acceptable Solutiions in Two Alpha-Helical regions of Lambda Repressor," Proteins, Structure, Function, and Genetics 7 (1990): 306-10. see also Hubert Yockey, Information Theory and Molecular Biology (cambridge: Cambridge University Press, 1992) 246-58.]
These are major problems that you cannot just wave off as if they don't matter or say well we just don't have enough information yet. These problems have arisen because of all the information we do have, This is not an ignorance problem. You can deny the evidence and still hold to the spontaneous generation (abiogeneis) that Darwin claimed out of ignorance to the true complexity of life, but you must realize and admit that you do so on grounds other than the scientific evidence. As I said before I think the true issue with theism is not a scientific one, but either emotionally based or philosophically based.
"An unexamined life is not worth living." - Socrates
