Living Systems

Systems Biology

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Abstract

Thermodynamics of living systems probably can be better understood through Gibbs ensembles approach and systems biology.

DMR Sekhar
 
 

Introduction

George Wald described1 living organism as an intricate machine during 1954. During 1980 Hanawalt wrote2,”The phenomenon of life may be traced to the coordinated behavior of molecules within cells. The cell is the self- contained and self–reproducing  fundamental unit of life…… The molecules in the cells are guided by the same basic laws of chemistry and physics that apply through out the universe…… The mystery lies rather in the programmed coordination of the myriad of chemical reactions necessary for the metabolic activities of the cells.” In 1983 Volkenshtein wrote3 that if it is alone for thermodynamics G-C content in the DNA should have increased during evolution. Human genome is apparently4 losing G-C rich regions.
 
 

Systems Biology

Living things are in fact living systems. A system is a group of parts5 that come together interacting and interdependent to form a more complex whole unit. A system is more than the sum of its parts. A system exhibits emergent properties which can not be reduced to its individual parts. A system is said to be complex if its emergent properties are unpredictable.
 
 

Statistical Thermodynamics

From the stand point of molecular statistics it may be stated6, “the self compression of a gas is not absolutely impossible”. For the study of statistical behavior of thermodynamic systems Gibbs proposed the method of ensembles. According to Gibbs6, an ensemble is a sufficiently large set of microstates which are compatible with a particular thermodynamic or macroscopic state. More clearly the thermodynamic state of a macro system [say ensemble] if in equilibrium does not change in time but the constituent myriad elements [say individual reactions] of the system may be in continuously changing microstates but in such a way that the macro state remains unaltered. Ensembles are classified as [1] micro canonical, [2] canonical and [3] grand canonical ensemble. The grand canonical ensemble is in both thermal and material equilibrium with the surroundings and can exchange both energy and matter.
 
 

Living cell as grand canonical ensemble

A living cell may be analogically visualized as grand canonical ensemble and a macro system. The myriad chemical reactions that go on in the cell may be viewed as a family of reactions in micro states which allows us to presume that the entropy change of these reactions follow normal distribution, hence follow hierarchy without disturbing the thermodynamic equilibrium of the cell  with its surroundings but a living cell dies if isolated from its enviornment indicating that the living cell is in steady state. Obviously some reactions at the extreme tail end of the distribution curve will have to move towards decreased entropy. It must be noted here that cells age over time that is they do change though very slowly.
 
 
The genome [a discrete sub system] of higher organism with higher percent of A-T pairs than thermodynamically favored G-C pairs indicates that genomic processes are non spontaneous that take entropy [change] to less than zero and to maintain this state cell processes are directed by the genome to expend work. Recent experimental work of Craig Venter and his team clearly proves7 that genomic processes have primacy over cell processes so much so that cell structure and functions are reorganized as per the genetic programmes.
 
 

Summary

The genome [a discrete sub system] in a cell of higher organism with higher percent of A-T pairs than thermodynamically favored G-C pairs is similar to an air plane in flight or pumping water to over head tank which are non spontaneous. The difference is that genome and cell are self operating. Life is not about the individual chemical reactions that go on in the cell but is about the non spontaneous functioning of the genome. Genome and the cell as living systems are more than the individual chemical reactions that go on inside them. Self programmability and self drive are the emergent system’s properties of the genome. Failure to recognize non spontaneous functioning of genome leads to vain science.
 
A living cell is akin to Gibbs grand canonical ensemble which is also a living system due to the emergent properties self programmability, consciousness and will. A cell maintains thermal and material equilibrium with its surroundings under the control of genome which acts non spontaneously. An ensemble may or may not evolve into a system. More clearly self programmability, consciousness and will are emergent properties of the system of organised matter [including energy] when it is in the state of life.
 
 

References

  1. George Wald, The origin of life, Molecules to living cells, W.H. Freeman and Company, 1980, San Francisco.
  2. Philip C Hanawalt, Protein Structure and Function: Assembly of Viruses and Ribosomes, 1980, ibid.
  3. Volkenshtein, M.V., Bio physics, MIR Publishers, 1983, Moscow.
  4. Arndt, P.F., Hwa, T., Petrov, D.A., Substantial Regional Variation in Substitution Rates in the Human Genome : Importance of GC content, Gene Density, and Telomere-Specific Effects, J. Mol. Evol. 2005, 60: 748-763.
  5. Yeremin, E.N., Fundamentals of Chemical Thermodynamics, MIR Publishers, 1983, Moscow.
  6. Daniel G. Gibson, et al, Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome, / http://www.sciencexpress.org / 20 May 2010 / Page 1 / 10.1126/science. 1190719.
 

Other Important References

  1. May see this link for quick reference to Venter’s experiment: Venter builds Wald’s Machine, http://knol.google.com/k/dmr-sekhar/venter-builds-wald-s-machine/3ecxygf1lxcn2/39?collectionId=3ecxygf1lxcn2.36# in this collection.
  2. May see this link for quick reference on ensembles: http://en.wikipedia.org/wiki/Statistical_ensemble_(mathematical_physics) & http://en.wikipedia.org/wiki/Statistical_mechanics#Statistical_ensembles
  3. Gladyshev, Georgi. WHAT IS LIFE? BIO-PHYSICAL PERSPECTIVES [Internet]. Version 21. Knol. 2009 Oct 16. Available from: http://knol.google.com/k/georgi-gladyshev/what-is-life-bio-physical-perspectives/3hr52gyju6t3d/3
  4. Gladyshev, Georgi. Science, evolution and reality, http://knol.google.com/k/georgi-p/science-evolution-and-reality/169m15f5ytneq/12#
  5. Gladyshev, Geogi. Synergetics is the knowledge in pictures, http://knol.google.com/k/georgi-gladyshev/synergetics-is-the-knowledge-in-pictures/3hr52gyju6t3d/19#
  6. Bose,J.C. 1927, The Unity of Life,[ as reproduced in], Every man’s Science , Vol.XXXIX,NO.4,Oct.-Nov.2004, https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0Bwimo6n_JQscZWVmZjE3OWUtYTgzZi00MTA4LThmNDItNjQ4ZWI3MWEwZDI2&hl=en
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