Autogenesis
Questions concerning the nature and origin of living systems and the hierarchy of their evolutionary processes are considered, and several problems which arise in connection with formerly developed theories--the autopoiesis of Maturana & Varela, the POL theory of Haukioja and the earlier developed evolutionary theory of Csányi--are discussed. The organization of living systems, the use of informational terms and the question how reproduction can enter into their characterization, problems of autonomy and identity are included in the list. It is suggested that replication--a copying process achieved by a special network of interrelatedness of components and component-producing processes that produces the same network as that which produced them--characterizes the living organization. The information "used" in this copying process, whether it is stored by special means or distributed in the whole system, is called replicative information. A theoretical model is introduced for the spontaneous emergence of replicative organization, called autogenesis. Autogenesis commences in a system by an organized "small" subsystem, referred to as AutoGenetic System Precursor (AGSP), which conveys replicative information to the system. During autogenesis, replicative information increases in system and compartment(s) form. A compartment is the co-replicating totality of components. The end state of autogenesis is an invariantly self-replicating organization which is unable to undergo further intrinsic organizational changes. It is suggested that replicative unities--such as living organisms--evolve via autogenesis. Levels of evolution emerge as a consequence of the relative autonomy of the autogenetic unities. On the next level they can be considered as components endowed with functions and a new autogenetic process can commence. Thus evolution proceeds towards its end state through the parallel autogenesis of the various levels. In terms of applications, ontogenesis is dealt with in detail as an autogenetic process as is the autogenesis of the biosphere and the global system.
autogenesis
Depictions of two hypothetical forms of simple autogenetic (i.e. self-reproducing) viruses with polyhedral (left panel) and tubular (middle panel) capsid structure. The chemical logic of simple autogenesis is depicted in the diagram in the right panel. Molecule a is
So autogenesis provides what amounts to a constraint production and preservation ratchet. During the dynamical phase new components are produced but because of their co-dependent relationships to one another the constraints that provide the reciprocal boundary conditions are also produced as the probability of occurrence of the component self-organizing processes increases. Together these reciprocal and recursive relationships would make autogenic viruses minimally evolvable.
This analogy is instructive in another sense. It demonstrates that the competence to interpret immediate conditions to be about correlated conditions is dependent on the more basic interpretive competence to re-present self. It is the self-correcting, self re-presenting capacity of simple autogenesis that enables the correlation between changes in capsid fragility to be about the value of the environment for that self and its interpretive capacity. To put this in semiotic terms, it suggests that indexical interpretive competence (grounded on correlational affordance) depends on more basic iconic interpretive competence (grounded on isomorphic affordance). As we will see below, this pattern of nested dependency in which different levels of semiosis are hierarchically constructed can be recursively iterated level upon level.
Consider the following enhancement of simple autogenesis. If another of the side products produced by autogenic reciprocal catalysis is a molecule like the nucleotides ATP and GDP that can acquire and give up energy carried in pyrophosphate bonds, the availability of this generic free energy could potentially facilitate more effective catalysis and drive otherwise energetically unfavorable reactions. This could provide a sort of energy-assisted autogenesis which would tend to out-perform spontaneous autogenesis and be favored by natural selection. This could also enable a wider variety of potential substrate molecules to be useful, because the energy to drive reciprocal catalysis would not need to be derived from substrate lysis. The logic of this hypothetical energy-assisted autogenesis is diagramed in Fig. 6.
But the availability of high-energy molecules is only useful during dynamic endergonic processes and can be disruptive of exergonic reactions and stable molecular structures. So energetic phosphates could cause potential damage during the inert phase of autogenesis. To be preserved safely and intact so they can be available when again catalysis is required they need to be somehow stored in an nonreactive form.
The capacity to transfer constraints from one physical medium to another quite different one makes possible the transfer of the holistically embodied dynamical constraints of autogenesis onto a different sort of material substrate such as a nucleotide polymer.
In summary: these variations on the autogenic model system exemplify a three tiered interpretive logic by which referential and instructional information can be derived and evolved. First there is simple autogenesis which is entirely determined by holistically embodied isomorphic (similarity) constraints distributed in its many components that preserve their own codependence despite damage and substrate replacement. Second there is context sensitive autogenesis which is determined by an augmentation of simple autogenesis in which the capsid surface presents structures with forms that are similar to the forms of useful substrates facilitating their binding to the surface where binding weakens capsid integrity. And third there is template-mediated autogenesis in which catalyst interaction constraints become offloaded onto a molecular structure. Offloading is afforded because complementary structural similarities between catalysts and regions of the template molecule facilitate catalyst binding in a particular order that by virtue of their positional correlations biases their interaction probabilities. In this way modifications of the structure of the template molecules can indirectly suppress potentially non beneficial interactions in favor of those that are conducive to autogenic repair and reproduction. The offloading of interaction constraints onto a physically separate and distinct structure preserves referential continuity while linking it to unrelated sign vehicle properties that can be harnessed for distinct semiotic functions, including semiotic recursion.
2015 Elsevier B.V. The Mississippi River fluvial-marine sediment-dispersal system (MRS) has become the focus of renewed research during the past decade, driven by the recognition that the channel, alluvial valley, delta, and offshore regions are critical components of North American economic and ecological networks. This renaissance follows and builds on over a century of intense engineering and geological study, and was sparked by the catastrophic Gulf of Mexico 2005 hurricane season, the 2010 Deep Water Horizon oil spill, and the newly recognized utility of source-to-sink concepts in hydrocarbon exploration and production. With this paper, we consider influences on the MRS over Neogene timescales, integrate fluvial and marine processes with the valley to shelf to deepwater regions, discuss MRS evolution through the late Pleistocene and Holocene, and conclude with an evaluation of Anthropocene MRS morphodynamics and source-to-sink connectivity in a time of profound human alteration of the system. In doing so, we evaluate the effects of tectonic, climatic, and anthropogenic influences on the MRS over multiple timescales.The Holocene MRS exhibits autogenic process-response at multiple spatial and temporal scales, from terrestrial catchment to marine basin. There is also ample evidence for allogenic influence, if not outright control, on these same morphodynamic phenomena that are often considered hallmarks of autogenesis in sedimentary systems. Prime examples include episodes of enhanced Holocene flooding that likely triggered avulsion, crevassing, and lobe-switching events at subdelta to delta scales.The modern locus of the Mississippi fluvial axis and shelf-slope-fan complex was established by Neogene crustal dynamics that steered sediment supply. Dominant Miocene sediment supply shifted west to east, due to regional subsidence in the Rockies. Then, drier conditions inhibited sediment delivery from the Rocky Mountains, and Appalachian epeirogenic uplift combined with wetter conditions to enhance sediment delivery from the Appalachians.Climatic influences came to the forefront during Pleistocene glacial-interglacial cycles. The fluvial system rapidly responded to sea-level rises and falls with rapid and extensive floodplain aggradation and fluvial knickpoint migration, respectively. More dramatically, meltwater flood episodes spanning decades to centuries were powerful agents of geomorphic sculpting and source-to-sink connectivity from the ice edge to the deepest marine basin. Differential sediment loading from alluvial valley to slope extending from Cretaceous to present time drove salt-tectonic motions, which provided additional morphodynamic complexity, steered deep-sea sediment delivery, diverted and closed canyons, and contributed to modern slope geometry.Despite the best efforts from generations of engineers, the leveed, gated, and dammed Mississippi still demonstrates the same tendency for self-regulation that confronted 19th century engineers. This is most apparent in the bed-level aggradation and scour associated with changes in sediment cover and stream power in river channels, and in the upstream migration of channel depocenters and fluvial and sediment outlets at the expense of downstream flow, that will ultimately lead to delta backstepping. Like other source-to-sink systems, upstream control of sediment supply is impacting downstream morphology. Even within the strait-jacketed confines of the modern flood control system, the Mississippi River still retains some independence. 041b061a72