Friday, July 13, 2007

Evolution and energy transformation in the Biosphere

As we previously showed Vernadsky postulated the biosphere regulates the transformation of energy on the planet.

The Biosphere is devoted to calculations on the fraction of total solar energy used by photosynthesizing organisms to produce biomass. In the context of these calculations Vernadsky argues that it is an inherent characteristic of the biosphere that living matter is distributed on the Earth’s surface in a way that solar radiation is completely captured. In order to optimize the utilization of solar energy and to create a sufficient surface, green biomass appears in different forms in different biotopes. On land, plants have to develop three-dimensional structures in order to create a sufficiently thick film for optimal use of solar radiation. In oceans, primary production is dominated by phytoplankton because it can easily distribute over the depth of the photic zone.

Arguments against solar variance is on the basis of minimal changes to the overall energy transfer in the sun-earth coupling, however the changes are dominant in the spectra that are transformers of cellular growth i.e. the biosphere attenuation and amplification.

The extensive scientific discussion of global warming causes a natural wish to relate this process to possible changes in the amount and dynamics of terrestrial and oceanic vegetation. Does this process influence variations in the amount and diversity of plants? Plausible yes, from a metrological perspective. However this is a subset of the total ecosystem and has less importance then either biogeochemical, or biologic parameters.

In 1961, (the paradox of the plankton) Hutchinson posed his classic question: "How is it possible for a number of species to coexist in a relatively isotrophic or unstructured environment, all competing for the same sorts of materials?"

Hutchinson gave the particular example of the phytoplankton, from which the paradox is named. Most species of phytoplankton are autotrophic, requiring light, CO2 and about 17 mineral elements, not all of which will be limiting in any particular waters. Yet considerably more species than implied by this can coexist, although in a continued state of increasing and decreasing populations in self organization away from equilibrium in response to environmental and competitive changes ranging from seconds to centuries.

Changes to absorption and emission of nutrients are also responsive to changes in both the type and spectra of radiation, these inhibit some populations and enhance others.Indeed what we can see is the ecological communities of microflora, changing rapidly to meet their changing levels of nutrients and energy is a Belousov-Zhabotinsky reaction diffusion mechanism.

Recent work by two theoretical ecologists (Huisman & Weissing, 1999; 2001),has shown that competition for resources by as few as three species can result in long-term oscillations, even in the traditionally convergent models of plankton species growth. For as few as five species, apparently chaotic behavior can emerge. Huisman and Weissing propose these phenomena as one possible new explanation of the paradox of the plankton, in which the number of co-existing plankton species far exceeds the number of limiting resources, in direct contradiction of theoretical predictions. Continuously fluctuating species levels can support more species than a steady, stable equilibrium distribution.

Their results show that external factors are not necessary to maintain non-equilibrium conditions; the inherent complexity of the "simple" model itself can be sufficient.
The publication of dubious 'catastrophic 'predictions for the oceans ability to maintain its biological role of atmospheric moderation are simply "creationist wastepaper" the ability of biogenic adaptability is already genetically available "banked for a rainy day so to speak". Been there done that, got the T-shirt and the DNA!

The high proportion of duplicate genes within plant and algae genomes is indicative of a high rate of retention of duplicate genes (Lynch and Connery, 2000). Gene duplications contribute to the establishment of new gene functions, and may underlie the origin of evolutionary novelty. Duplicate genes can exist stably in a partially redundant state over a protracted evolutionary period (Moore and Purugganan, 2005). A half-life to silencing and loss of a plant gene duplicate is estimated at 23.4 million years such that remnant duplicate genes, which can be reactivated by environmental conditions to encode calcification within coccolithophores under “ancestral” conditions representative 60 Ma, appears reasonable.

The theory of self-organization and adaptivity has grown out of a variety of disciplines, including thermodynamics, cybernetics and computer modelling.. Self-organization can be defined as the spontaneous creation of a globally coherent pattern out of local interactions. Because of its distributed character, this organization tends to be robust, resisting perturbations. The dynamics of a self-organizing system is typically non-linear, because of circular or feedback relations between the components. Positive feedback leads to an explosive growth, which ends when all components have been absorbed into the new configuration, leaving the system in a stable, negative feedback state. Non-linear systems have in general several stable states, and this number tends to increase (bifurcate) as an increasing input of energy pushes the system farther from its thermodynamic equilibrium.

To adapt to a changing environment, the system needs a variety of stable states that is large enough to react to all perturbations but not so large as to make its evolution uncontrollably chaotic. The most adequate states are selected according to their fitness, either directly by the environment, or by subsystems that have adapted to the environment at an earlier stage. Formally, the basic mechanism underlying self-organization is the (often noise-driven) variation which explores different regions in the system’s state space until it enters an attractor. This precludes further variation outside the attractor, and thus restricts the freedom of the system’s components to behave independently. This is equivalent to the increase of coherence, or decrease of statistical entropy, that defines self organization.

In the case where the self-organizing system does not reach an equilibrium, the solution is less obvious. The Belgian thermodynamicist Ilya Prigogine received a Nobel Prize for his investigation, starting in the 1950s, of that problem. Together with his colleagues of the “Brussels School” of thermodynamics, he has been studying what he called dissipative structures. These are patterns such as the Brusselator, which exhibit dynamic self-organization. Such structures are necessarily open systems: energy and/or matter are flowing through them. The system is continuously generating entropy, but this entropy is actively dissipated, or exported, out of the system. Thus, it manages to increase its own organization at the expense of the order in the environment. The system circumvents the second law of thermodynamics simply by getting rid of excess entropy. The most obvious examples of such dissipative systems are living organisms. Plants and animals take in energy and matter in a low entropy form as light or food. They export it back in a high entropy form, as waste products. This allows them to reduce their internal entropy, thus counteracting the degradation implied by the second law.

Indeed as we see here the evolutionary memory is a further complication in the "Paradox of the Plankton"

The analysis of DNA sequences from tiny green algae have provided new insights into the mystery of how new species of plankton evolve—and further highlights their critical role in managing the global cycling of carbon. These findings, by a group led by the DOE Joint Genome Institute (DOE JGI); the Scripps Institution of Oceanography, University of California, San Diego; and the Pierre & Marie Curie University, were published this week in the Proceedings of the National Academy of Sciences (PNAS).

Ocean-dwelling phytoplankton from the genus Ostreococcus emerge at the primitive root of the green plant lineage, dating back nearly 1.5 billion years. Today, these microscopic, free-living creatures, among the smallest eukaryotes ever characterized, barely a micron in diameter, contribute to a significant share of the world’s total photosynthetic activity. These “picophytoplankton” also exhibit great diversity that contrasts sharply with the dearth of ecological niches available to them in aquatic ecosystems. This observation, known as the “paradox of the plankton,” has long puzzled biologists.

Plumbing the depths of molecular-level information of related species, genomics offers a novel glimpse into this paradox. The researchers compared the genomes of two Ostreococcus species, O. lucimarinus and O. tauri, and saw dramatic changes in genome structure and metabolic capabilities.

“We found several striking features of genome organization,” said DOE JGI’s Igor Grigoriev, the PNAS paper’s senior author.


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