Please see the note and apology at the end of this post.
I have not yet had time to parse through all this, other than to note that most of what Alicia discusses below was already granted for discussion purposes in my Abiogenesis Challenge. Thus, even if we were to grant the very questionable and optimistic claims, it still does not address the central issues needed for the origin of life, including the issue of information content.
That said, I appreciate Alicia taking time to put together the below and would invite commenters to weigh in, both with respect to the evidentiary claims made, as well as the relevance to a materialistic origins scenario.
The language below is directly from Alicia, although I have added paragraph numbers to allow comments to focus on particular claims and to facilitate discussion.
Here’s a very brief overview of the basic supporting work done on abiogenesis and I have taken it a step further for EA at the end and talk briefly about a simplified example of the evolution of the first living organism. Enjoy.
1. Miller-Urey demonstrated that methane, ammonia, and hydrogen gases in a highly favorable early earth model could produce cyanide, formaldehyde, and amino acids. Subsequent studies demonstrated similar results in more realistic models. Amino acids are repeatedly produced by early earth models and have also been found in meteorites. Mimicking volcanic gases flowing through rock crevices produces amino acids and in fact, it tends to produce some of the natural amino acids over the other, unnatural residues. UV light in early earth models produce aldehydes, which are still important intermediates in amino acid synthesis. Polymerization of amino acids, although unfavorable, can be driven by certain conditions. Simply through energy input in the presence of minerals, researchers have demonstrated the formation of protein polymers. We have also observed amino acid polymerization at hydrothermal vents. Amino acids in cooler water have been shown to polymerize when carbon and sulfur-containing gases (commonly ejected by hydrothermal vents) are also present.
2. Important reactants have been hypothesized to accumulate on layers of mineral deposits in the early earth environment; dissolved gases are attracted to these minerals which helps to concentrate them to drive chemical reactions. The minerals function as catalysts as they are reactive in solution and their importance can still be seen at the active site of many enzymes today.
3. The production of acetic acid from dissolved carbon dioxide and hydrogen is spontaneous and still used today by bacteria. Acetic acid is also an important intermediate in the pathway that produces acetyl-CoA, a molecule still used by all living organisms. Recent research has shown that a variety of larger organic molecules can be produced by early earth models, including those important to the eventual synthesis of nucleotides.
4. Free radical production is much more likely in the early earth atmosphere, where there is no ozone layer. Free radicals are highly reactive and computer models have demonstrated the formation of formaldehyde through these types of reactions. In the presence of heat or UV radiation, formaldehyde molecules are able to link together, forming more complicated organic molecules such as sugars. Both 5- and 6-carbon sugars are produced in these models and other studies have shown that enrichment of the 5-carbon sugars occurs on minerals outside of hydrothermal vents. 3-carbon ketoses and other molecules related to sugars have also been found in meteorites.
5. Hydrogen cyanide was also likely produced in the early earth atmosphere as shown in Miller-Urey, and it is an important precursor for nucleic base production. Early earth atmospheric models eventually led to the production of all five nucleic bases. Prebiotic simulations have demonstrated activation of nucleotides through addition of phosphate groups, and further studies have shown that these nucleotides can polymerize in the presence of minerals. Even without nucleotide activation, polymerization of nucleic acids over 90 bases long has been demonstrated to occur when both heat and small lipids are included.
6. Recent studies have shown that, starting with a ribozyme capable of joining two ribonucleotides together, random mutations and copying produces ribozymes capable of replication activity. This enzyme is now capable of using itself as a template, to copy fragments of itself. Other studies have demonstrated molecular evolution by starting with random pools of nucleic acids and selection of nucleic acids that connect uracil base to ribose sugar. After 11 rounds of selection, the ribozyme population was 1,000,000x better at catalyzing the reaction in comparison to the uncatalyzed reaction. Numerous other studies have produced ribozymes with a host of different catalytic activities.
7. Simple lipids have been produced through early earth model systems using hydrogen, carbon dioxide and mineral catalysts. Lipids with amphipathic properties have also been discovered in meteorites. These molecules form simple membrane structures spontaneously due to the hydrophobic effect and provide an environment more suitable for life inside the first protocells. These early cell membranes provide the ability to concentrate reactants and protect products of chemical reactions. Membrane permeability of small molecules can be altered by simple proteins that span the hydrophobic layer and also by temperature changes. Simple vesicles can join together, in essence “growing” and vibrations of the surrounding media can cause them to replicate. Ions and ribonucleotides are known to diffuse through fatty acid membranes and the formation of these membranes is facilitated by minerals as well.
8. It is hypothesized that the first replicating molecule did not consist of RNA, but instead was made up of simpler nucleic acids, which consisted of simpler nucleotide molecules. Nucleic acid-polypeptide hybrid molecules have been proposed, in which nucleic bases are connected by peptide bonds instead of phosphodiester bonds. These simpler molecules are capable of both catalytic activity and acting as a template; and their ability to direct synthesis of RNA as we know it today has been demonstrated, as they have similar 3D geometries. This would allow for evolution from a pre-RNA world to an RNA world. The catalytic repertoire of ribozymes seen in nature today is quite small, however synthetic ribozymes have demonstrated a wide variety of reactions, even rivaling proteins. The distinction between proteinaceous enzymes and ribozymes seems to be the efficiency with which they catalyze reactions, not the range of possible reactions. The ability of ribozymes to catalyze their own replication has been demonstrated, but only in fragments. Ribozymes able to ligate short nucleotide strands, which has already been demonstrated, would piece these fragments together, producing more replicating ribozymes. The efficiency of this ligation reaction would be increased by containing the replicating ribozyme and nucleic acid fragments within a membrane consisting of fatty acids or some derivative of these amphipathic molecules. This would be the first living cell.
9. Sealing these ribozymes into protocells allows for evolution of these first organisms based on not just structure of subcellular components, but also how these components interact with each other. Replication of these protocells would be driven by physical agitation, unevenly splitting the intracellular components into new protocells and providing more variation for selection to act on.
10. Experiments have demonstrated that selection from pools of random RNA molecules can produce RNA polymers that bind tightly to amino acids. These RNA molecules tend to have sequences identical to the codons still used by today’s translational system. This shows the potential for a limited genetic code, of which the remnants cans still be seen today. Synthetic ribozymes have been shown to catalyze tRNA charging, moving the early translational system closer to the more efficient system seen today. Evolution of this early translational system would make protein synthesis more efficient and eventually lead to a protein-dominated world.
EA Note for Readers:
I was away from UD for several weeks and just this week realized that the above post was still in my “Drafts” section in my UD Dashboard, with a date stamp of November 24, 2015. I did not get time to review Alicia’s discussion as I had hoped, and then forgot I hadn’t published this, in between the Thanksgiving trip with the in-laws, various obligations in early December and then Christmas and New Year’s.
My sincere apologies to Alicia for the long delay. Alicia, if there is anything you would like to add to your description, having had a few additional weeks to think about it, please let me know and I will add it to your above description.