User:Anthony.Sebastian/Life/draft/Sebastian Notes

The Information Processing Perspective

• Define information
• Relate to entropy
• Define entopy

===Self-Organization==Living systems organize themselves spontaneously. Molecular self-organization in cells emerges in part from the chemical properties of the proteins encoded in genes. Those proteins make their appearance by a genetic transcription-translation machinery, which itself represents a self-organized function emerging in part from the chemical properties of proteins and other molecules. Molecules can interact through the formation and breaking of strong covalent bonds and also through weaker, nonstable noncovalent electromagnetic forces, like hydrogen bonding and van der Waals forces and many othersThose weaker ‘supramolecular’ interactions give physical properties to molecular aggregates and make possible many intracellular and intercellular biological processes.

The qualifier, ‘in part’, in the preceding paragraph reflects the need to invoke not only molecular self-assembly but also evolutionary mechanisms selecting genes that yield proteins whose chemical properties entail interactions that tend to optimize functional self-organization—in other words, adaption to circumstances. One must also invoke local real-time selective processes that confer stability and appropriate functionality to molecular self-assembly. Self-organization and adaptation functionally conjoin.

One way to the self-organization of cell structure and function is to view the genome metaphorically as a computer, the genome functioning as a ‘program’ that constructs critical components of the cell that can arrange themselves in a way that accords with their chemical properties. With the tinkering comprising local trial-and-error and evolution’s handiwork, that arrangement can then carry out integrative functions not explicitly encoded in the genome itself.

As Oxford professor Denis Noble reminds us, the Nobel Prize-winning geneticist, Sidney Brenner, expressed the computer metaphor this way:

• ”…biological systems can be viewed as special computing devices. This view emerges from considerations of how information is stored in and retrieved from the genes. Genes can only specify the properties of the proteins they code for, and any integrative properties of the system must be 'computed' by their interactions. This provides a framework for analysis by simulation and sets practical bounds on what can be achieved by reductionist models.”

The patterns of structure and behavior that develop in self-organized systems require no master and no prepared recipes that explicitly specify the organized structure and dynamics of the system, which emerge from the interactions among the components dictated by their physical properties as dynamically modified by consequences of the emerging organization embedded in its environment.

Self-organization tends to breed greater degrees of self-organization—breeding more complexity. Genes not only express proteins that organize themselves into a functional unit but also express proteins that organize themselves to regulate that functional unit, as in transcription regulatory circuits. Protein networks interact in a self-organizing way to produce networks of networks with complex levels of coordination. Cells communicate with other cells, either in free-living cellular communities or in multicellular organisms—communicative activities that self-organize in virtue of the properties, functions and behaviors of the cells, selected for fitness by evolutionary mechanisms, and responsive to downward regulation by environmental influences on the whole system.

The single-celled zygote self-organizes into a multicellular living system as the properties of the genetically encoded proteins interact in accord with their physical properties, responding to changing influences stemming from the changing environment generated by growing multicellularity—self-organizing into a network of multiple cell-types doing cooperative work.

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Thermodynamic

Biologists sometimes view living things from the perspective of thermodynamics---the science of interactions among energy (capacity to do work, a driving force), heat (thermal energy), work (movement through force), entropy (degree of disorder) and information (degree of order). The interactions define what the system can and cannot do in the process of interconverting energy and work. For example, by the First Law of thermodynamics we know that when a process converts one form of energy to another, it results in no net loss of energy, and no net gain.

Appreciation of the penetrating insight the thermodynamic perspective gives to explaining what constitutes a living entity requires a basic understanding of the laws of thermodynamics that scientists discovered through experiment, debate, mathematical formulation and refinement, and that Albert Einstein believed stood as an edifice of physical theory that could never topple.

Most pertinent, the Second Law of Thermodynamics, has several expressions:

• Heat flows spontaneously—i.e., without external help—from a region or body of higher temperature to one of lower temperature, and never so flows spontaneously in the reverse direction. That holds for other forms of energy as well (e.g., electromagnetic, chemical, etc.)—concentrations of energy disperse themselves to lower energy levels, flowing “into the cool”, so to speak.
• When heat as input to a system causes the system to perform work (e.g., a steam engine), part of the heat disperses as ‘exhaust’, unused and unusable by the system for further work. That holds as well for other forms of energy doing work. Some of the energy always turns into ‘exhaust’, typically heat. Energy conversion to work in a system can never proceed at 100% efficiency—an empirical fact.
• The degree of order or organization of a system and its surroundings cannot spontaneously increase; it either remains the same or decreases. Scientists have learned to put a number on the degree of ΄΄disorder΄΄ of a system, and refer to it as ΄΄entropy΄΄. Water vapor, with its water molecules in more or less random distribution, has a higher entropy value than liquid water, with its molecules distributed less randomly, and has a higher entropy value than ice, with its molecules distributed in a more organized crystal array. Left to itself, ice tends to spontaneously melt, and liquid water to evaporate. Order tends to disorder, with the Universe as a whole tending to exhaust itself into an ‘equilibrium’ state of randomness.

Those three expressions of the Second Law in effect restate each other as tenets of classical thermodynamics reflecting the empirical fact that high energy and order spontaneously flow downhill—down a ‘gradient’—toward eliminating the gradient, as if nature abhors gradients of energy and order. Upon gradient elimination, all energy and order has degraded, all tendencies to change disappear, no further change occurs, an equilibrium state ensues.

Given the universality of the Second Law, how then do living entities manage to come into existence, develop from an ‘embryonic’ state to one of greater degrees of order and lesser degrees of entropy, and to perpetuate their order and increase in order, if only by manufacturing replacements of themselves? How do they thwart the Second Law?

They don’t. They appear to do it by exploiting the Universe’s gradients of energy and order, by their location along those gradients, between the energy input and exhaust. Like a steam engine, they ‘import’ the available energy and order, converting it to the work of internal organization, reducing their entropy. But all along emitting enough exhaust to more than compensatorily increasing the disorder and entropy of their surroundings, so that the total entropy of the living system and its surroundings increase—in keeping with the Second Law.

Science has formalized that concept in the special field of 'non-equilibrium' thermodynamics. It describes many of the characteristics of living systems that remain, for a more or less long time (a lifespan), in a steady-state of organized functional activity. A living system performs its organized functional activities far from the 'equilibrium' state of activity of the system that would obtain if it did not have access to and ability to store and utilize available energy (including mass-energy) from outside the system. Such systems can store energy and perform work on themselves and outside; the available outside energy ultimately supplies the driving force that keeps the system functioning far-from-equilibrium and in disequilibrium with its environment.

Biological cells qualify as non-equilibrium thermodynamic systems because they must consume energy to live, and because they reach an equilibrium state only in death---whereupon all parts relate to each other according to spontaneous physicochemical processes. Viewing living systems from this perspective gives biologists mathematical tools to work with to learn how the system organizes itself. Those tools may help find ways to eliminate accumulated dysfunctions in the organizational activity of a living system that eventually causes it fail to maintain its optimal organization sufficiently to keep the system organized and therefore far-from-equilibrium. Slowing or eliminating dysfunctions of organizational activities might increase lifespan.

We can, then, view a living system as a state of organizational activity (non-randomness) that is maintained by importing, storing and transforming energy and matter from its external environment into the work and structures required to sustain its organizational activity. In doing so, living systems produce waste and export it to the external environment, lowering the organizational state of the environment. The living system thus maintains its internal organization at the expense of that of the external environment, leaving the environment more disorganized than the gain in organization of the living system--in keeping with the second law of thermodynamics that the total disorder (system plus environment) always increases.

Thus, the following could serves as a fundamental characterization of life, or of living systems:

• The ability to remain for a time (a "lifespan") as an organized, coordinated functioning system, in which spontaneous tendencies and external forces that tend to disturb its organization are opposed by built-in self-correcting mechanisms fueled by external resources (energy, matter) and facilitated by production and exportation of waste (disorder)---thus all the while operating far-from an ever-approaching equilibrium (the state that we call "death").