Chinaman - tome 3 - POUR ROSE (French Edition)

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The straightforward evolutionary search leads to a strongly dichotomous result: i The solution is hyper-abundant so that random sequences can solve the task or ii the solution will almost certainly not be found by an entire planet of bacteria searching for a billion years or more.

How then does evolution discover new functions whose target sequences are not hyper-abundant? Those steps can include point mutations, insertions, deletions, and genomic rearrangements. It could be that some steps need to occur in a particular order, whereas others can occur in any order.

Therefore, the regeneration process can include epistatic interactions between mutations and potentiating mutations We envisage the regeneration process as a sequence of steps that are not individually favored by natural selection. Only the final product is favored by natural selection. If individual steps are already favored, then the evolutionary dynamics would describe the stepwise improvement of an existing function rather than the discovery of a new function.

The incremental adaptation would certainly occur quickly on a geological time scale. Gene duplication A or recombination B generates a starting condition for the search process, at rate w. C From the starting condition, we require k mutational steps, each at rate u , to reach the target sequence, which encodes a new function. At each step, there is the possibility to receive inactivating mutations, at rate v , which destroy the search.

The frequency of the wild type is denoted by x 0. The frequencies of the intermediate steps in the search process are denoted by x i. At steady state and assuming neutrality, we have the following frequencies: and.

Most ensuing searches in the regeneration process will immediately lead away from the target and so fail with high probability. The average time until a single search hits the target would be exponential in L. However, the starting condition is regenerated all the time, with unsuccessful searches being discarded. The result is that we need only polynomially many searches in L to find the target with high probability.

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That is, the search time is exponential in k but not in L. Sexual reproduction and exchange of genetic material can further increase the efficiency of the search processes by a linear factor. With the regeneration process, a planet of bacteria seems well equipped to discover new functional tools on a time scale that is geologically rapid.

Our modeling exercise suggests that as the environment calls for new functions to be advantageous, the relevant sequences might already preexist in the population, either fully or partially formed. The coming together of such sequences in single cells can then lead to genetic machinery able to exploit a new ecological niche. Armed with the preceding results, we can take a closer look at the timing and dynamics of the GOE.

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A growing number of geochemical analyses also suggest that low levels of oxygen built up at least locally and transiently within the water column or in benthic mat communities as early as 3 billion years ago Thus, available geochemical data indicate that either oxygenic photosynthesis evolved 2. In the latter case, the threshold represented by the GOE would reflect a decreasing supply of oxidants from volcanic gases, hydrothermal fluids, and basaltic rocks; increased rates of oxygenic photosynthesis; increased hydrogen escape from the top of the atmosphere; or some combination of these , Total rates of primary production would have been set by nutrient availability, especially P.

Because of adsorption onto iron hydroxides and removal by incorporation into vivianite in anoxic environments, P availability is thought to have been low in Archean oceans, and although somewhat higher in Proterozoic seas, it was still well below Phanerozoic values — Wherever and whenever O 2 first accumulated, life figures prominently in its causation and consequences. Oxygenic photosynthesis is generally accepted as necessary for terrestrial oxygenation , requiring coupled photosystems I and II in all their molecular complexity Similarly, early oxygenation made the origin and expansion of aerobic respiration, as well as the diversification of oxygen-requiring biosynthetic pathways, possible Cyanobacteria are ecosystem engineers: Once O 2 began to accumulate in the surface ocean, alternative electron donors were eliminated.

What, then, governed the timetable of the GOE and its biological consequences? Was it influenced most strongly by the time scale on which mutations could result in adaptations for the production and utilization of oxygen? Or does natural selection discover physiological adaptations quickly, shifting focus onto environmental history?

Given the geochemical evidence that cyanobacteria, and thus oxygenic photosynthesis, preceded the GOE by as much as several hundred million years, it is unlikely that the exact timing and dynamics of the GOE are explained by the evolution of oxygenic photosynthesis per se. Instead, we can imagine that there was a particular steady state between the concentration of oxygen and the biomass of cyanobacteria before GOE. The steady-state level of oxygen is given by the rate of production from cyanobacteria divided by the rate of oxygen removal.

Let x denote the biomass of cyanobacteria and z the concentration of oxygen in the atmosphere. The time derivative of oxygen concentration can then be stated in terms of a simple equation, , where the rate of O 2 production is proportional to the abundance of cyanobacteria, ax , and the O 2 removal rate is proportional to the abundance of oxygen, bz.

The parameters a and b are appropriate rate constants. Given this, the GOE could reflect an increase in the abundance of cyanobacteria as they evolved to be better competitors in the global ecosystem. Another possibility, favored by us, is that the physical environment of the planet changed, leading to a decline in the rate constant, b , for oxygen removal. This could be caused, for example, by the growth of stable continental cratons, a decline in volcanic emissions of reduced gases and ions, a change in the flux of hydrogen out of the top of the atmosphere, or some combination of these processes The accumulation of O 2 in the atmosphere and surface ocean would sweep alternative electron donors from most parts of the photic zone.

The accompanying box and figure present a deliberately oversimplified model for ecosystem change at the GOE. The main inference we draw from this is that whereas rates of oxygen removal might have declined gradually through time, the transition to an oxic atmosphere and surface ocean, with cyanobacteria dominating photosynthesis, would have occurred rapidly once a critical threshold was reached.

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Ward et al. Our simple model of bacterial sequence evolution, introduced above, would suggest that shifting redox conditions would quickly be exploited by bacteria with novel physiologies that make use of oxygen in energy metabolism or biosynthesis. Support for this comes from molecular clock estimates of ca.

In our deliberately simplified model for the GOE, we consider an ecosystem with two major primary producers: anoxygenic photosynthetic bacteria and cyanobacteria. Cyanobacteria obtain the electrons needed for photosynthesis by splitting water. Anoxygenic photosynthetic bacteria and cyanobacteria compete over the limiting resource, phosphate.

The density of anoxygenic photosynthetic bacteria and cyanobacteria is denoted by x 1 and x 2. Their time derivates are and. Their reproductive rates are r 1 and r 2. Considerthe following system of equations. We include small migration rates, u 1 and u 2 , from ecological niches, where cyanobacteria and anoxygenic photosynthetic bacteria could exist independently of each other.

The reproductive rate of anoxygenic photosynthetic bacteria is multiplied by the concentration of ferrous iron, z 1. As discussed in the main text, oxygen is produced by cyanobacteria and removed by both respiration and geophysical events. Thus, the steady-state concentration of oxygen is proportional to the abundance of cyanobacteria. We model the dynamics of the GOE by assuming that the removal rate of oxygen, b , declines over millions of years. The process leads to a slow but continuous increase in the oxygen concentration, slowly reducing the abundance of ferrous iron.

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At this point, cyanobacteria quickly rise to dominance, which causes oxygen levels to increase markedly. The greatly reduced availability in ferrous iron seals the new world order. An illustration of the dynamics of the GOE according to this mechanism is shown in the figure below.

Figure: According to our simple model, the dynamics of the GOE is driven by a slow decline in the removal rate of oxygen from the atmosphere due to geophysical events. The accumulation in oxygen causes a reduction in the abundance of ferrous iron, which leads to a sudden dominance of cyanobacteria over anoxygenic photosynthetic bacteria.

Renewed oxygenation in the Neoproterozoic Era and the temporally associated rise of eukaryotic phytoplankton to ecological prominence could be amenable to modeling broadly similar to that outlined for the GOE.

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However, in general, full oxygenation of ocean basins appears to have been achieved more than transiently only in the Paleozoic Era 48 , Renewed oxygenation could have been driven by supercontinental breakup, increasing organic carbon sequestration in newly formed and rapidly subsiding basins. Increased P supply from the weathering of Neoproterozoic large igneous provinces , could also have pushed Earth system to a new redox state, which, in turn, would have reduced iron-based sinks for P Eukaryotic phytoplankton and macroscopic animals with high demand for oxygen diversified in the context of this change.

Phytoplankton radiations may reflect increased nutrient supply , whereas animal radiation likely reflects the consequent increase in food supply and P O 2 increase above a critical metabolic threshold, as well as a decrease in the incursion of anoxic water masses into the surface ocean and possibly feedbacks of animal evolution onto the environment 51 , That is, on the broadest planetary time scale, the physically driven GOE and NOE together appear to have set the timetable of evolution.

Phanerozoic diversification of animals, plants, and protists documents continuing evolutionary innovation and biological interactions, and these, in turn, reflect, at least in part, the continuing influence of planetary change [for example, see the study of Vrba ], including shifting continents, dynamic climates, and occasional transient geophysical or astrophysical perturbations that drive mass extinctions. Rates of genetic adaptation may be most limiting at the times of rapid and pronounced environmental perturbation that mark mass extinction. As is true for Bacteria and Archaea, a theory explaining the fundamental time scale of evolutionary innovation of eukaryotic organisms remains to be developed.

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Eukaryotic species have smaller population sizes, longer generation times, and a much diminished capacity for horizontal gene transfer. At the same time, they have distinct mechanisms of genetic regulation, which might both facilitate and constrain the evolution of novel morphologies , Evolutionary innovations in plants and animals reflect the accumulation of characters through time and the ecological circumstances under which character change took place Angiosperms, for example, postdate the evolution of seed plants by more than million years, their diversification and remarkable ecological success reflecting the developmentally controlled evolution of fruits and accelerated life cycles, as well as functional innovations in leaves and water transport, bolstered by coevolution with animal pollinators and grazers We suspect that, relative to bacteria, evolutionary timing for plants and animals, fungi, and protists will be governed to a greater extent by the accumulation of complex character combinations and other biological factors, including those that help to define the effective environment of populations this would also be true for younger bacteria, as eukaryotes became important components of their environments.

Nonetheless, the fossil record suggests that eukaryotic evolution has continually been influenced by changes in the physical environment, with rates of genetic discovery sufficiently fast to track most geologically resolvable rates of environmental change. On billion-year time scales, the evolutionary dynamics of a planet is fast and its evolutionary potential is vast; the pace of evolution is primarily determined by the physical history of the planet.

The timetable of evolution, then, is in no small part determined by geophysical events.