Saturday, March 31, 2007

Belousov-Zhabotinsky Reaction in Ecological communities self organization or chaos

The ecological communities of microflora, change rapidly to meet their changing levels of nutrients and energy. This is observable as shown by Ilya Prigorine and the Brusselator model of the BZ reaction.

A Belousov-Zhabotinsky reaction, or BZ reaction, is one of a class of reactions that serve as a classical example of non-equilibrium thermodynamics, resulting in the establishment of a nonlinear chemical oscillator. The only common element in these oscillating systems are the inclusion of bromine and an acid. The reactions are theoretically important in that they show that chemical reactions do not have to be dominated by equilibrium thermodynamic behavior. These reactions are far from equilibrium and remain so for a significant length of time. In this sense, they provide an interesting chemical model of nonequilibrium biological phenomena, and the mathematical model of the BZ reactions themselves are of theoretical interest.

An essential aspect of the BZ reaction is its so called "excitability"- under the influence of stimuli, patterns develop in what would otherwise be a perfectly quiescent medium. Some clock reactions such as Briggs-Rauscher and BZ using the chemical ruthenium bipyridyl as catalyst can be excited into self-organising activity through the influence of light.

Levich in his lectures on theoretical biology analyses Baeurs ideas on the non equilibrium of biological systems .

In "Theoretical Biology" E. Bauer confidently stated that biology was not applied physics or chemistry. He also stated that "all special laws, which would be revealed in certain fields of biology would display the general laws of motion, appropriate to living matter" [4, p.8]. The urgent problem of theoretical biology was, according to E. Bauer, the development of general laws of motion for living matter.

"Only living systems never reach equilibrium, for they constantly work against stability" [4, p.43]. According to Bauer, the source of free energy(or” the work of structuring forces" and "structural energy" are the synonyms) is the nonequilibrium of molecular structure of living matter

What is the source of the nonequilibrium of "living matter"? Firstly it is the activation of molecules of food caused by levelling processes. Energy of these molecules maintains nonequilibrium (here the molecules of living matter in "active, deformed state" are considered [4, p.127]. However, the unavoidable result of metabolism is, according to E. Bauer, the lowering of the potential of free energy of nonequilibrium. "The more intensive metabolism is, the higher rates of the free energy depletion are. This free energy of living matter exists because of the deformed nonequilibrium structure of its molecules" [4, p.129]. "During assimilation the structural energy of a system can be used. This energy is necessary for the reconstruction of nonliving substance" [4, p.144].The total amount of energy that can be assimilated is limited. This amount of energy is species-specific parameter of organism (Rubner constant) (see [4, p.131; 37] and is "proportional to the free energy of an ovicell" [4, p.130].

This means that the problem of the source of living matter's nonequilibrium cannot be reduced to the possibility of nonequilibrium's replenishment with free energy of food. Another source of nonequilibrium is required. The utilization of this source should regulate the organism's ability to make up for free energy losses with food. Concerning deeper nonequilibrium one can propose several possibilities of its origination in organism. They might be the following:

- the law of nonincrease (or conservation) of structural energy and transfer of it from generation to generation;

- the possibility of external replenishment of structural energy during the origination or fertilization of the ovicell in addition to an explanation of Bauer's theory, according to which fetal cells, possessing maximum initial potential, originate due to dying or, in other words, dissimilation of the body tissues" [4, p. 144].

- to reject the idea of the impossibility of structural energy replenishment during the life period, and then to find the ways of such replenishment, for instance, the mechanism of structural energy assimilation by autotrophs and its farther spreading in the biosphere through the food chains.

In the second and third proposals, and in other cases, allowing the structural energy replenishment, the question about the sources of such replenishment remains.
When considering the problem of understanding the stable nonequilibrium principle, another problem arises, that is the search for the sources of nonequilibrium. This problem is connected with time, its flow and becoming. One of the possible hypotheses dealing with this problem's consideration consists of the substantial time construction [28; 29].


In modeling of biological systems that oscillate from state to state seemingly random in appearance, are actually showing self organization of the ecologic community to variation of resource and both evolution and devolution.

As scientists at MIT have created an ocean model so realistic that the virtual forests of diverse microscopic plants they "sowed" have grown in population patterns that precisely mimic their real-world counterparts.

This model of the ocean is the first to reflect the vast diversity of the invisible forests living in our oceans-tiny, single-celled green plants that dominate the ocean and produce half the oxygen we breathe on Earth. And it does so in a way that is consistent with the way real-world ecosystems evolve according to the principles of natural selection.

Scientists use models such as this one to better understand the oceans' biological and chemical cycles and their role in regulating atmospheric carbon dioxide, an important greenhouse gas.

The output of the new model, the brainchild of oceanographer Mick Follows, has been tested against real-world patterns of a particular species of phytoplankton, called prochlorococcus, which dominates the plant life of some ocean regions.

Follows and co-authors report this work, part of the MIT Earth System Initiative's new Darwin Project, in the March 30 issue of Science. The Darwin Project is a new cross-disciplinary research project at MIT connecting systems biology, microbial ecology, global biogeochemical cycles and climate.

"The guiding principle of our model is that its ecosystems are allowed to self-organize as in the natural world," said Follows, a principal research scientist in MIT's Department of Earth, Atmospheric and Planetary Sciences (EAPS), lead author on the paper and creator of the model. "The fact that the phytoplankton that emerge in our model are analogous to the real phytoplankton gives us confidence in the value of our approach."

One of Follows' collaborators, Penny Chisholm, the Lee and Geraldine Martin Professor of Civil and Environmental Engineering and Biology and director of the Earth Systems Initiative, has made prochlorococcus her focus of study for 20 years. Stephanie Dutkiewicz, a research scientist in EAPS, and Scott Grant, a graduate student at the University of Hawaii, who was an MIT physics undergraduate during this project, collaborated with Chisholm and Follows on the new model.

Chisholm believes that because previous ocean models did not convey the diversity of phytoplankton, they did not well represent the systems they modeled. The new model remedies that.

"Now we are finally modeling the ocean systems in a way that is consistent with how biologists think of them-water filled with millions of diverse microbes that wax and wane in relative abundance through interactions with each other, and the environment, as dictated by natural selection," said Chisholm.

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