How Life is Different

Vitaly Shubin

• Publisher: CRC Press
• Year: 2021
• ISBN:
  9781000401424
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Cell Biology
• Index: Biological Sciences

The book examines basic principles of the structure and organization of living organisms and their differences from objects of inanimate nature. It covers how a single program-information structure permeates all evolutionary stages of life, including the cell, multicellular organisms and humans. The author explains how this structure is arranged and how it functions, as well as the role of the information system.

KEY FEATURES

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• Reviews persistent questions and addresses fundamental themes in biology

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• Provides systematic coverage

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• Includes original insights into basic principles of living organization and structure

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• Demonstrates the applicability of a proposed approach to particular evolutionary grades

RELATED TITLES

J.W. Schopf, Life in Deep Time: Darwin's "Missing" Fossil Record (ISBN 978-1-138-38549-8)

C.H. Waddington, ed., The Origin of Life: Toward a Theoretical Biology (ISBN 978-0-202-36302-8)

J. Wiegel, A.W.W. Michael, eds., Thermophiles: The Keys to the Molecular Evolution and the Origin of Life (ISBN 978-0-7484-0747-7)

1Cell and Unicellular Organisms

WHAT IS THE DIFFERENCE BETWEEN CHEMICAL LABORATORIES IN A CELL AND VOLCANO?

Judging by the title of the book, the author is going to express his thoughts on the structure of life, specifically, on the living part of the observed world.

Because life is a collection of organisms and their vital functions, and the body is just set of cells, the cell is the basis of all life systems.

Therefore, in order to answer the question of the chapter, we need to examine what happens in the cell.

In the cell, there are plants and laboratories that produce products and carry out operations for the growth and functioning of the cell throughout the entire cell cycle. Moreover, the words factories and laboratories should be used without quotation marks, because they are much better in organization, efficiency and product quality than the most modern human plants and laboratories, furthermore we can take into account the minimization of working space and energy costs as well as strict quality control indicators in cell plants and factories.

Indeed, we humans have a lot to learn, for example, in assembly production, taking a protein assembly as a model, or in the process of organizing transport by observing various cellular solutions to the problem of delivering large and small molecules and ions to the right places in the cell compartments, The processes of management of both individual operations and the functioning of cellular systems and the whole cell also deserve close attention.

It should be noted that this particular work of cellular plants is being thoroughly studied and quite successful, but the examination of the system's structure is somewhat lagging behind.

Still, the main processes happening in the cell are considered biochemical reactions of decomposition, catabolism and synthesis, anabolism, carried out with the help of enzymes which are mainly proteins and complexes based on them. This is so, but they do not explain rather striking differences between a living cell laboratory and non-living one, for example, in a volcano.

Why not to compare them? In both cases, we observe chemical reactions and mechanical movements of interacting particles and bodies as well as changes in their forms and characteristic features. Also, the presence of analogues of enzymes – catalysts in a volcanic laboratory is not excluded.

However, the difference among the laboratories is enormous.

Systematic, regulated, that is precise in time and space activity in the cell leads to exact reproducible results and stochastic processes occurring in random time and space, lead to result of the emergence of unexpected gifts, such as porous tuffs with different colors, or glassy black obsidian in a volcanic laboratory.

Well, we have touched, as we see it, the fundamental differences between the stochastic process in the inanimate world and the regulated live process, hereinafter referred to as the program.

Let us try to give definitions of both, as well as related definitions.

STOCHASTIC PROCESS AND A PREDICTABLE PROGRAM

The process – at least one equivalent, interchangeable interaction of two arbitrary bodies or objects, occurring at an indefinite time in an indefinite place, accompanied by the conservation of energy while taking into account its dissipation and leading to the result.

The result of the process and its consequence is determined by the characteristics of two interacting bodies and their interaction and may consist in changing the spatial parameters of the bodies: acceleration, speed, position (coordinates) and/or changes in their characteristics: size, shape, chemical state, etc., including combining two interacting objects into one or dividing them into several objects.

The result of the process as well as the process itself is not predetermined in advance, i.e., it is random, stochastic both in essence and in place and time of its realization.

The program is at least one predetermined, regulated action made by a specific performer (maker) with respect to a predetermined object at a predetermined time in a predetermined place in space – the program execution site, mainly accompanied by the absorption of energy stored by special energy programs (EPs).

The result of the program may consist in changing the spatial parameters of the object: acceleration, speed, position (coordinates) and/or changes in its characteristics: size, shape, chemical state, etc., including dividing the object into several objects or combining the object and the performer, and, in accordance with the definition of the program, it is predetermined in its essence, time and place of implementation.

An important clarification! Here we are considering the initial natural process, which has not been subjected to human study, and all the more so to the impact, which is based precisely on the program approach. In other words, the result of observation and study of the initial stochastic non-living process bears the subjective traces of the program approach. The essence of the program approach in science will be discussed in more detail in the third chapter of this book.

INFORMATIONAL ORGANIZATION OF LIVING

First, we must note that a large part, and perhaps all actions of performers over an object by nature or as we will speak further on modality, correspond to the interactions observed in inanimate nature. These are primarily mechanical and chemical interactions, leading to movement, change in shape and separation into parts, association, change in chemical activity, etc., in bodies and objects involved in interactions. At the same time, the material molecular, atomic and field basis of the program living world, completely match with that for its inanimate part.

So what kind of life-giving water turns the stochastic inanimate process into a living and ordered program?

Such life-giving water is information – a system of instructions and signals, in accordance with which programs are reproduced and are consistent with each other. The information in turn is the result of the implementation of specific information programs that are part of the program system of the cell and any organism.

The basic part of the information system (IS) is the instructions according to which the performer (maker) recognizes his object and/or performs the necessary program steps and actions.

The most important example of instruction is information of the DNA gene, according to which special programs reproduce blanks for the manufacture of all the makers – ribonucleic acid (RNA) and proteins.

A common example of informational signals are ions or molecules that activate or inactivate a given maker, thereby controlling the frequency or intensity of its execution of a program in accordance with the needs of it for the entire cellular program system (CPS) or its part.

At the same time, in addition to effective maker domain responsible for the implementation of regulated actions on an object, there are information domain (ID) for reading instructions and responding to signals.

We can say that the makers created by the information instruction, performing their actions with regard to the information signals, reproduce all the cell programs and ensure the functioning of the CPS.

Thus, the information organization permeates the entire program structure, its functioning and forms programs.

PROGRAM PARTS AND COMPONENTS

The main components and elements of the program are maker, object, action, and site.

We remind you that we are considering only the cell.

The main active elements of the programs are makers. They are proteins, RNAs and assemblies created on their basis, which are also created as a result of executing programs, the key of which are transcription and translation programs performed by complex makers – polymerase and ribosome, respectively.

Why, instead of introducing the new term “maker,” didn’t the author use the traditional term “enzyme,” which would be, in its own way, logical, since we are talking about the same biochemical formations?

The reason lies in the fact that the author sees in these well-known biochemical objects new, non-traditional functions and capabilities that are fundamental for the developed program concept.

First, this is a significant expansion of the actions performed by the maker in comparison with the enzyme in its classical definition and presentation, in transport, assembly, signal and other programs.

Second, this is the most important property that allows the maker, the performer of its basic program to participate additionally in information programs as an active performer, for example, when reading instructive DNA information, or a passive object when reacting to the signal of the control program.

The maker, generally, performs program actions in relation to a single object, i.e., the structure and functioning of each maker are very specific, which is reflected in the diversity of protein molecules and the complexes formed from them, even in the simplest prokaryotic cells.

The objects of programs can be a variety of cellular components: large and small molecules, atoms, ions and including the makers themselves, for example, as already noted with control programs.

The changes that have occurred with the object are the result of the program, while the maker does not change and after the execution of the next program, he is able to perform similar program once more.

We should mention some more properties and features of the makers and their variants.

At the lower level of the program hierarchy there is a principle: one program – one maker – one object. It corresponds to the situation when a simple maker performing single action on an object, for example, one stage of catabolism, execute a simple program that have an intermediate result.

Other simple programs that are also performed by simple makers use this result. A chain of such simple programs is formed, at the output of which the main, final result is achieved such as, for example, the Krebs catabolic cycle. In this case, we can speak of a complex result program consisting of components of simple programs that are executed sequentially by several simple makers.

In turn, composite programs can be combined into task programs to solve specific cellular problems, for example, breathing.

In the future, we will adhere to such hierarchical organization of programs. Task programs, often executed in different sites and receiving the final result, consist of composite programs that implement intermediate results, usually in the same site, but using a number of makers. Composite programs include program components executed by a single maker.

Both composite and task programs can be formed from the programs of the lower hierarchy by a sequential, parallel or mixed principle.

In the considered variants of programs, simple programs with simple makers performing one action were meant at the lowest hierarchical level.

However, there are well-known makers who perform several actions. For example, the already mentioned ribosome in the translation program performs a series of actions, being essentially a multifunctional complex maker of a composite broadcast program.

Some of the simple one-process programs are performed by different sections of the ribosome, and some, for example, the delivery of amino acids for the formation of a peptide chain, are performed by independent makers – transport RNA.

Thus, we can say that there is a variety of multifunctional, complex makers that perform composite, task and implementing the final result types of the program. In addition to the ribosome, these include RNA polymerase or adenosine triphosphate (ATP) synthase. In some cases, the maker works with two or more objects.

Auto-assembly programs, for example, microtubules or complexes of proteins and RNA, the author considers as programs with a maker and an object. In this case, the role of the maker is performed by the next component that is included in the assembly, and the object is the growing seed of the assembly. Maker identifies the place for assembly and sits on it, fulfilling the task of further formation of the object.

The main actions of the performers can be mechanical, chemical and mixed. Mechanical actions help the movement of the object, chemical actions create common reactions such as oxidation, reduction, phosphorylation and others. Mixed actions lead to the mechanical unification or separation of objects, the mechanism of which is most often concern with the weakening or strengthening of the chemical interaction among individual objects or parts of one object.

Most programs require certain amounts of energy. Typically, energy amounts transmit to makers or objects “energy particles” of ATP.

Localization of the execution of programs is achieved by the presence of various membrane structures of the cell which create its organelles.

Programs can be carried out both inside organelles and directly on the membranes which form them.

Cell membranes, which are based on lipid layers, are assembled by appropriate programs.

Special transport programs collect into according sites all the necessary missing components of the programs running on these sites.

In a number of the following sections of this chapter, instead of the terms “maker”, “performer”, and sometimes “the working element of the program”, we will use traditional definitions such as enzyme, protein, transport protein, synthetase, kinase, etc., implying that any program is always performed by the maker.

POOL OF BASIC “PRODUCTION” CELL PROGRAMS

In order for every program in each cell's life moment to have all the necessary components: makers, objects, energy and sites their reproducing programs included in the pool of “basic” programs should work intensively. To this base pool, we also add transport programs that ensure the delivery of components and their elements to sites and call the programs of this pool – production programs. Let us consider the examples of programs in this pool in more detail.

We will begin our consideration with the programs that make perfor...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Dedication Page
• Contents
• Preface
• Chapter 1 Cell and Unicellular Organisms
• Chapter 2 Multicellular Organisms
• Chapter 3 Man
• Chapter 4 Program-Information Unity of Living
• Provisions of the Program Approach
• Reading List
• Index