The Origin of Natural Order

The following sections are included:

• Preface
• Introduction
• Contents

Summary: The basic concept of irreversible thermodynamics is discussed in this chapter. We show that in all movements (processes) of irreversible thermodynamics, there is a giant space in which all changes of thermodynamics obey the principle of equilibrium thermodynamics, but their features cannot be fully explained by it. The new order can be generated in the processes of irreversible thermodynamics. Thus, the origin of natural order can be fully explained by its principle.

Summary: In irreversible thermodynamics, the generation of a sub-system within a thermodynamics system represents the fundamental mechanism for the origin of natural order. According to this theory, the origin of natural order is the most common phenomenon of nature. This new understanding makes us analyze biology theoretically.

Summary: The production of irreversible process is a hierarchical structure. If many types of hierarchical structure can be generated within a system, it is developing system. The nature and living body are developing systems.

Summary: The partition function is a fundamental concept of equilibrium thermodynamics. In the views of traditional thermodynamics, it encodes the particle distribution at different energy levels. However, the behaviors of the complex system of thermodynamics cannot be described by the partition function of a particle. By modifying the partition function of a particle, the partition function of a thermodynamic system has been obtained. It could be utilized to analyze behaviors of a complex thermodynamic system, such as protein conformational state, DNA conformational state. The typical fashions of distributions curves of a thermal system are of great importance and we can judge the properties of a system on the basis of it.

Summary: In view of thermodynamics, all actual changes of nature are irreversible, and our understanding of nature, as well science, is established on the basis of principles of irreversible thermodynamics. Currently there are two different approaches in the field. First is the theory of dissipative structure which represents a dynamic but steady state of a system. Second is thermodynamic structure which represents a static state of a thermal system. The key task of this chapter is to ascertain the validation domains and different usefulness of both theories. The advantages of both theories in diversified area of science are also discussed.

Summary: The system is a basic concept of science. However, until now, there has been scientific definition about it. In this chapter, we discuss its scientific definition on the basis of thermodynamics. According to this definition, a system represents one specific ensemble of matters with its specific structure: logic cycle.

Summary: We show that the fundamental properties of matter cannot logically determine the properties of advanced matter. There is logical discontinuity between different levels of hierarchical structure, which reveals the theoretical limit of scientific model or paradigms. It also shows that we cannot analyze advanced matter by fundamental properties alone.

Summary: All things in nature are systems, but the principles of system have not been formulated mathematically. Here, we formulate a standard paradigm for systems. Basic concept: 1) a system is complex system with its particular structure and it cannot be described by element logic (or axiomatic theory, the traditional logic of mathematics). 2) The relationship of systems can be only described by system logic. The relationship between system logic and element logic are discussed. It provides a new way for our understanding of complexity of things.

Summary: When complex is merged, it is impossible to find absolute model which can account for all matters. In these cases, it is valuable to find conditional models and the logical relationship between different matter could be constructed within these models. These isolated models have great impact on our understanding of nature.

Summary: When polypeptide is synthesized in vivo, the nascent peptide begins to fold itself and finally a folded protein with full biological function is produced. Theoretically speaking, the protein folding is irreversible thermodynamic process and we discuss its principles here. Key thoughts: 1) nature of protein folding can be described by laws of irreversible thermodynamics; 2) a folded protein may be at metastable state in view of thermodynamics; 3) the product of protein folding is protein thermodynamic structure; 4) the Gibbs free energy is not the controlling factor for protein folding.

Summary: A protein has its unique three-dimensional structure and sequence. In protein science, a well-accepted view is that information of protein three dimensional structure and protein folding has been prescribed within sequence of a protein. Thus, some scientists believe that we can find a program, on the basis of which the protein three dimensional structure could be deduced from protein sequence. But the solution for it has not been obtained now. Our conclusion is that we cannot predict all protein three-dimensional structures from protein sequences using one program, nor can we predict protein function from protein three dimensional structure with one program. This represents the logic limit of protein science.

Summary: A protein is not a uniform system of thermodynamics, but is composed of many sub-systems of thermodynamics, called potherse. This sub-system can be structured differently, thus comes the concept of protein thermodynamic structure. In the following chapters of this book, we will show that properties of a protein can be analyzed by applying principle of protein thermodynamic structure theory. Then this chapter will discuss basic principles of protein thermodynamic structure theory.

Summary: The structural features and the biophysical natures of a protein are discussed on the basis of protein thermodynamic structure theory. We have demonstrated that much current knowledge about protein conformation and conformational change can be explained by applying the principles of protein thermodynamic structure theory.

Summary: In the field of biochemistry and molecular biology, much knowledge of protein science has been explained on the basis of the concept of protein conformation. Here, we will study concept of protein conformation on the basis of protein thermodynamic structure theory. The analysis shows that a protein can show numerous types of protein conformations under different conditions.

Summary: Each protein is a complex system of thermodynamics and its behaviours differ from that of common materials in principle. If we use our knowledge of conventional physics when studying protein science, there may be mistakes and controversies. In fact, some thermodynamic natures of protein conformational change have been classified into the dynamic nature of it. Our analysis shows that the dispute about the role of protein dynamics in enzyme activity and protein regulation results from the wrong understanding of dynamic and thermodynamic nature of protein conformational change. There is a direct relation between protein thermodynamics and enzyme activity (a type of protein functioning); the protein dynamics takes its role in enzyme activity by influencing thermodynamic properties of protein conformational states.

Summary: The protein ligand interaction is an important process in biology and is connected to the biological regulation of protein and enzyme. The binding between enzyme and substrate, protein-protein interaction, ligand-receptor are examples of this process. Here we analyze the basic mechanism for it on the basis of the protein conformation concept.

Summary: The receptor activation is an important process in biology. The signaling activity of a receptor is initiated at this step. Many types of biological information or signals are integrated in this process, so it has attracted much attention from scientific community in the past. Many valuable opinions about it have been proposed as well. The receptor activation is a good example of protein thermodynamic reorganization and protein regulation. In this chapter, we will show that the protein thermodynamic structure theory can give satisfactory explanations for much of the knowledge we have obtained in this field. In principle, enzyme regulation is same as the receptor activation and we will discuss some general trend of the receptor and enzyme activation.

Summary: For simple chemical reactions, the catalyst mechanism is rather simple. However, it is more complex for an enzyme catalyzed reaction, where many chemical mechanisms are utilized at same time, which greatly reduce the activation energy of chemical reaction. This chapter will discuss the chemical mechanisms of enzymatic reaction.

Summary: The execution of an enzyme activity requires many steps of protein conformational change by the way of substrate binding conformation, transitional state conformation and product binding conformation. If the pathway of this protein conformational change was modified, thermodynamic and dynamic parameters of enzymatic kinetics, such as k_m, k_cat, activation energy, as well as the affinity between enzyme and substrate will be altered. Thus, we can judge protein conformational change related to an enzyme activity by a change of parameter of enzymatic reaction. Here the basic principles in our understanding of the behaviors of enzyme will be discussed.

Summary: The allosteric regulation model is a tradition model of enzyme regulation. It states that a change of protein conformation at a site can be transmitted into remote areas of the protein because the conformation of a protein can change cooperatively, which is the nature of protein three-dimensional structure. On the basis of the protein thermodynamic structure theory, an allodynamic mechanism for enzyme regulation has been proposed and it is a thermodynamic model for enzyme regulation. It states that a change of protein thermodynamic state at one site can be transmitted into remote sites of the protein via protein thermodynamic structure reorganization. A comprehensive understanding of enzyme regulation can be obtained on the basis of this model.

Summary: A protein can change its properties and transform itself into another species of protein during biological evolution. This chapter discusses the basic and general principle of protein evolution.

Summary: The scientific definition of molecular bio-signals has been made on the basis of protein thermodynamics in this chapter and properties of protein bio-signals will be discussed as well. Within this model, any type of bio-signal corresponds to one potherse or a thermal system within a signaling protein. The signaling activity of a protein represents its physiological activities at a fundamental level. Any physiological activity at different levels of biology is composed of many types signaling activities of proteins.

Summary: Summary: Protein dynamics or flexibility plays an important role in all types of signaling activities of proteins for it alters protein conformational stability and the rate of protein conformational change. In this chapter, we will discuss some signaling activities or biological functions of protein dynamics. The experimental results have indicated that a change of protein flexibility induced by volatile anesthetics is the basis of the working mechanism for anesthesia induction.

Summary: The unified model of signal conduction and the protein model of neural conduction are discussed in this chapter. We will show that neural conduction is not the propagation of electric signals, but the propagation of protein conformational signals. Thus, a systematic and unified knowledge of molecular biology, neuroscience, and physiology, has been successfully developed in this chapter.

Summary: This chapter discusses basic and thermodynamic principle of the biosignal network theory or system biology. In view of the signaling theory, a physiological system that represents a specific signaling network which is thermodynamically stable and shows independence to some degree. The properties of signaling network could be quantitatively described by the law of partition function of a thermal system. Some biological phenomena, such as plant vernalization, canceration, sexualization, and oscillation, are also highlighted in this chapter. (This chapter is a copy of the paper: A Thermodynamic Model of Protein Signaling Network. Reviews in Theoretical Science 4, pp. 1–9, 2016, with minor modification).

Summary: The general principles of biological development are discussed on the basis of the irreversible thermodynamic and signaling network theory. It is shown that the bio-informational flow from a gene to its biological function is a process of informational integration, rather than the translation process. The integration process cannot be described by a unified program (or model), thus the system relation between genes and biological function has been proposed.

Summary: Hybridization is a common process in biological reproduction. The change in the genetic background of an organism has a great impact on all phenotypes and biological functions of the organism. Among all the alterations, which are induced by a change in genetics, hybrid vigor is a well-established phenomenon. The working mechanism of hybridization is discussed on the basis of biological development and the signal network theory. It shows that many mechanisms have made a contribution to the production of heterosis and the main mechanism is the loose control of a physiological activities of organism.

Summary: From the perspective of irreversible thermodynamics, biological evolution is a specific example for the origin of natural order and is an irreversible process. The principle of biological evolution is discussed in this chapter on the basis of irreversible thermodynamics. The essential idea is that any biological species represents a specific signaling network and the behavior of biological evolution can be described and analyzed by applying the principle of system biology.

Summary: Traditional Chinese medical (TCM) theory developed in the ancient times based on our daily experiences and medical practice. It has incorporated these experiences into a unified philosophical theory of biology. In contrast, modern biology developed on the basis of the scientific methods, which, although extremely valuable, are unable to explain our daily experience. A scientific explanation of TCM will be valuable for expanding the scope of medical science and biology. Reconciliation between the scientific approach and TCM is therefore a key task for theoretical biology. Here, we will show that TCM can be explained by applYing principles of biological theory or system biology. The scientific account of TCM provides a comprehensive understanding of biology and medical science.

The following section is included:

• Index