Thank you so much for all of these interesting links! From the first two or three links it became apparent that the date for free oxygen in the environment was settled to be between 2.4 and 2.2 gya – with photosynthesis hacontributions from 3.5-2.7 gya. The NASA link was particularly informative (Biochemical keys to the emergence of complex life). An important excerpt:
If the first 2.5 billion years of Earth history were dominated by an environment in which free oxygen was generally unavailable to the biosphere because of primitive reduced inorganic acceptors or "sinks," then one of the principal strategies of life would have been to adapt to this environment Neither collagen nor extensin would have been possible in the absence of free oxygen, and the fossil record shows that during this period few significant increases in body size were made. After the exhaustion of most primordial inorganic oxygen sinks about 2 billion years ago (Cloud, 1976; Schopf, 1978) and the development of the eucaryotic cell and oxygenic photosynthesis, the major environments of the world began to turn from predominantly reducing to predominantly oxidizing conditions. Multicellularity would have been a priority development and collagen one of its certain prerequisites. The geologic evidence shows that the transition to an oxygenic world did not take place rapidly; if it had, there would be major deposits of reduced carbon in the sediments of the period, and none is found. The buildup of free oxygen is more likely to have been rather slow. With some limited free oxygen present in the environment, limited collagen (and extensin) could have evolved in some organisms where the wide-open ecological niches available and the adaptive advantages being conveyed outweighed the complexities and expense involved in its manufacture. I have already discussed how this may have affected the fossil record (Towe, 1970), but it is worth repeating that in this initially low-oxygen environment, the competition for the low levels of free oxygen by oxidative metabolisms would have restricted most collagen use to small, thin, diffusion-limited organisms unlikely to be found preserved as fossils. As Boaden (1977) has emphasized, the world at this time may have been like the modern thiobios-a sulfide-rich habitat dominated by mostly microscopic, interstitial meiofaunal elements. The biochemistry of collagens from modern near-anaerobic nematodes is instructive in making further comparisons with the Late Precambrian fossil record. Both the cuticle and body wall of Ascaris lumbricoides contain collagen. The body-wall collagen has large amounts of hydroxyproline and hydroxylysine. Adapted to low oxygen tensions, their formation through the [301] hydroxylating enzymes is actually inhibited by too much oxygen (>1%) in the environment (Fujimoto and Prockop, 1969). The cuticle collagen lacks hydroxylysine, contains little hydroxyproline, and appears to be strengthened by disulfide crosslinks (McBride and Harrington, 1967), another adaptation to low-oxygen tensions.
Given this information, one can speculate that the early use of collagen in Late Precambrian low-oxygen environments may have eventually produced "worms" with similarly adapted collagen metabolism, which permitted some of them to attain much larger sizes than the remaining interstitial faunal elements. Perhaps the enigmatic coiled fossils from the billion-year-old Greyson Shale (Walter et al., 1976) or from the Little Dal Group (Hofmann and Aitken, 1979) are rare body fossils of such worms. Or perhaps some of the Late Precambrian burrows were produced by similar worms who had become adapted to the low-oxygen environment and were, like their modern thiobiotic descendants, burrowing to avoid the increasing oxygen tensions that must inevitably have taken place. Burrowing to avoid oxygen at the sediment-water interface in this very early stage of metazoan history seems more likely than burrowing to avoid predators, the types of which are unknown and the fossil evidence for which is otherwise nonexistent.
Ultimately, the further increase in availability of free oxygen as the result of increasing oxygenic photosynthesis would have brought an end to such adaptations, and therefore any experiments toward developing collagens completely free of an oxygen requirement were terminated. At the same time, the high competitive priority of respiratory events for oxygen would have been moderated, allowing many more morphological experiments with collagen to take place in other previously limited metazoan phyla. Even the sclerotization of the arthropod cuticle, which is also inhibited by lack of atmospheric oxygen (Richards, 1951), would have been improved All this would have caused a dramatic worldwide increase in the size and hence ready preservability of numerous organisms. The Late Precambrian-Early Cambrian fossil record can then be interpreted as an explosion of fossils rather than as a sudden eruption of metazoan phylogenesis with highly evolved, diverse, and morphogenetically advanced forms appearing suddenly side by side around the world, few of which have any plausible immediate ancestors as fossils.
All of the above “goes to” the likelihood that the complexity of biological life was due to self-organizing complexity and not happenstance. Also from another link:
Armen Y Mulkidjanian, Dmitry A Cherepanov, and Michael Y Galperin (emphasis mine) In modern concepts of the origin of life, there is an glaring gap between the abiogenic formation of the first building blocks and the origin of the "RNA world" i.e. of the first RNA-like polynucleotides that could undergo a Darwinian-type evolution. Indeed, there is a wealth of experimental evidence for the abiogenic formation of amino acids, nitrogenous bases and carbohydrates from inorganic compounds like cyanide, thiocyanate, and carbon monoxide under reducing and/or neutral conditions (reviewed in ref.). On the other hand, the documented catalytic activity of RNA molecules allows to suggest that primordial ribonucleotides could have initially evolved on their own, without assistance from proteins. What is missing is a physically plausible mechanism for the thermodynamically unfeasible event of formation and accumulation of long oligonucleotide-like polymers.
This problem can be focused even further. Aluminosilicate clays have been shown to catalyze the formation of oligonucleotides of up to 50 units long, when supplied by preformed and pre-activated mononucleotides under optimized laboratory conditions. However, no oligonucleotide formation from pentose phosphates and nitrogenous bases has been reported so far under the supposedly primordial conditions where the formation of amino acids, nitrogenous bases and carbohydrates took place. Furthermore, the current understanding implies that the environmental conditions on the primeval Earth were unfavorable for the survival of oligonucleotide-like polymers. A particularly important factor is that, due to the absence of the ozone layer, the UV flux at the Earth surface must have been approximately 100 times larger than it is now, causing deterioration of most organic molecules. The existing theories consider the high UV level as a major obstacle and offer several different strategies for hiding the first life forms from it (see e.g. ref.). Here we invoke an alternative possibility, i.e. that the UV irradiation played a positive role in the origin of life by serving as a principal selective factor in the formation of pre-biological structures. Moreover, the influx of energy into the system in the form of the UV irradiation could be seen as the driving force required for the gradual complication of the system. These considerations prompted us to analyze the possible effects of the UV irradiation on oligonucleotide formation in primordial conditions.
continuing in the discussion…
Thus, the results of our Monte-Carlo simulation indicate that a mechanism of natural selection, similar to the one that has driven the subsequent biological evolution, could have been responsible for the primordial polymerization. It seems quite unlikely that the extremely effective UV-quenching by all five major nucleobases is just incidental. Accordingly, one can assume that these bases had been selected to perform the UV-protecting function before they became involved in the maintenance and transfer of genetic information. This assumption provides a physically plausible rationale for the primordial enrichment in oligonucleotide-like compounds and also sheds new light on the earliest steps of evolution….
The suggested mechanism turns the high UV levels on primordial Earth from a perceived obstacle to the origin of life (see e.g. ref. [19]) into the selective factor that, in fact, might drive the whole process. Indeed, biochemical condensation reactions proceed with release of water, so that the presence of latter favors hydrolysis of biological polymers. Because of this feature, Bernal [27] and many researchers after him (as reviewed in ref. [10]) advanced the view that life has begun in tidal regions, so that condensation of primordial monomers proceeded under "fluctuating" conditions where the wet periods, enabling the exchange of reagents, alternated with dry ones, favoring the condensation reactions. The awareness of the potential danger of the UV damage, however, prompted other scientists to invoke a UV-protecting water layer (see e.g. ref. [19]), which apparently would impede the condensation reactions. More recently, several authors even moved the point of the life origin to the bottom of the ocean, where the reducing power of minerals and/or of hydrothermal vents was considered to be the energy source for the first condensation events [28,29]. It remained unexplained, though, how inorganic reductants could drive primordial condensation reactions in water in the absence of enzymes (see the discussion in refs. [30,31]).
In a sense, the absence of a consensus on a plausible mechanism for the origin and accumulation of the first RNA-like molecules has significantly hurt the development in the whole field and stimulated proliferation of the Panspermia hypothesis, not to mention various kinds of creationist ideas. It appears that our consideration of the UV irradiation as a positive, selective factor in primordial evolution may suggest a way out of the dead end. This view allows to place the cradle of life onto the sun-illuminated (semi) dry surface of the ancient Earth, as originally considered by Bernal [27]. Indeed, no other known energy source could compete with the UV component of the solar irradiation either in ability to serve simultaneously as both selective and driving force, or in continuity, strength, and access to the whole surface of Earth...
IOW - here, the investigators are turning the UV objection into a positive and suggesting that it is the energy source which (vaguely) drives biological complexity. However, they also indicate that the UV protection “function” must have existed before the UV irradiation actually occurred to protect some. This is what I would call a "just so" story until it is backed up with some empirical investigation. Here are a few more for the discussion: Abiogenesis
[speaking of the Urey-Miller experiments being repeated with success] But the Earth's early atmosphere is nowadays thought to be neutral, consisting mostly of nitrogen and carbon dioxide, instead of hydrogen, ammonia, and methane (reducing), as had been suggested from cosmochemical grounds. Urey-Miller experiments performed with a neutral mixture are much less successful than those with a reducing mixture; however, the early Earth could easily have had reducing microenvironments, like hot springs and hydrothermal vents. There is also the conundrum that bodies of water are poor places for the formation of biomolecules like proteins and nucleic acids, since the "primordial soup" is inevitably very dilute, making it difficult for molecules to "find" each other. This conundrum has led to the "primordial pizza" hypothesis of the origin of life on mineral surfaces like clay surfaces, which organic molecules can easily stick to, and which have catalytic properties that can easily assist in the formation of complex molecules. Günter Wächtershäuser has proposed that the Krebs Cycle (a.k.a. citric acid cycle, tricarboxylic acid cycle) had originated on such mineral surfaces, powered by iron-sulfur chemistry.
And while some biological molecules, like the smaller amino acids and nucleic-acid bases, are readily produced in Urey-Miller experiments, others, like sugars, are not. This means that nucleic acids are difficult to produce, since they contain the sugar ribose and its derivatives; this is a major difficulty with the otherwise-very-attractive "RNA world" hypothesis.
Thus, how to get from there to a complete self-reproducing system is still an unsolved problem, but this question is being actively researched.
Concerning the “primordial pizza” on such mineral surfaces, here’s more on Wächtershäuser. BTW, Intelligent Design theorists ought to get a kick out of this after all the abuse they have taken over lawyers (LOL!)
Günter Wächtershäuser Günter Wächtershäuser, a chemist turned patent lawyer, is mainly known for his groundbreaking and influential work on the origin of life, and in particular his "iron-sulphur world theory", a theory that life on Earth had hydrothermal origins. The theory is consistent with the hypothesis that life originated near submerged hydrothermal vents.
Dr Wächtershäuser, a chemist by training, has been an international patent lawer in Munich since 1970. He has published numerous articles in organic chemistry, genetic engineering and patent law, and has made at least two significant contributions to evolutionary theory: the origins of perception and cognition, and the origin of life.
One of the key ideas advanced by Wächtershäuser is that an early form of metabolism predated genetics. Metabolism here means a cycle of chemical reactions that produce energy in a form that can be harnessed by other processes. The idea is that once a primitive metabolic cycle was established, it began to produce ever more complex compounds.
Wächtershäuser has hypothesized a special role for acetic acid, a simple combination of carbon, hydrogen, and oxygen found in vinegar. Acetic acid is part of the citric acid cycle that is fundamental to metabolism in cells.
And here’s the model for Wächtershäuser’s theory et al (emphasis mine):
Multi-Phase Artificial Chemistry Phase equilibria and the segregation of molecules into different phases probably were of utmost importance in prebiotic evolution. The presence of different phases allows certain species to concentrate to a level necessary for reaction, of which the products can subsequently switch phases to encounter reaction partners which would have before rendered impossible its synthesis. Concentration gradients, in particular pH gradients, between different phases might also have provided the driving force for chemical reactions. Hydrogen cyanide, for example, has been proposed to have polymerized first in an ice phase before its polymerization products continued to react further under warmer conditions [14]. This would avoid the problem possed by its tendency to react with formaldehyde [2]. Allamandola et al. [1] and Trinks et al [15] have also proposed models including different ice mantels in comets or ice phases in the sea.
The most accepted model for the origin of life has been proposed by [13,17] with the primordial ‘soup’. Hot deep sea vents as the birth place of life (the primordial ‘pizza’) were discussed as an interesting alternative [26. However, all these models need a prebiotic chemistry with complicated synthesis. As described in [20] and [21], they cannot occur in single, unpartitioned environment. A sequence of different environments would be important for the orgin of life, just as in the traditional organic synthesis. During such a synthesis a reaction mixture is subjected to certain conditions, then some products are extracted, purified, and/or crystallized, new reagents might be added, and the next step with new conditions begins. We can imagine an analogous situation in prebiotic chemistry, where the different conditions and steps are mimicked by different environments, i.e. phases like hot vents, the atmosphere, and ice, and intermittent evaporation, phase change, crystallization or filtration. This might mitigate the problems of complicated synthesis in prebiotic chemistry.
IMHO, this brings us right back to Luis Rocha
The idea that life may have originated from pure RNA world has been around for a while. In this scenario the first life forms relied on RNA molecules as both symbolic carriers of genetic information, and functional, catalytic molecules. The neutralist hypothesis for the function of RNA editing assumes such a RNA world origin of life. It posits that RNA editing could offer a process by which the dual role of RNA molecules as information carriers and catalysts could more easily co-exist. The key problem for the RNA world origin of life hypothesis is precisely the separation between these two functions of RNA. On the one hand RNA molecules should be stable (non-reactive) to carry information, and on the other hand they should be reactive to perform their catalytic function. RNA editing, could be seen as means to fragment genetic information into several non-reactive molecules, that are later, through RNA editing processes, integrated into reactive molecules. This way, the understanding of this process of mediation between the role of RNA molecules as information carriers and catalytic molecules based on RNA editing, can also offer many clues to the problem of origin of a semiotic code from s dynamic (catalytic) substrate.
IOW, even if one were able to account for the phases necessary to accomplish autonomy and bootstrap a replicating RNA world, in all of this there is not yet proposed a natural origin for the communication (information, Shannon) itself or the semiosis necessary for self-organizing complexity (for those models which eschew happenstance). Where do we go next?
