Biological Networks: An Introductory Review

1. Introduction

2. Types of network systems

A. Natural networks

B. Artificial networks

C. Biological networks

3. Biological networks

4. Characteristic features of biological networks

5. Design of biological networks

6. Structural and functional distortion of biological networks

7. Mechanisms of regulation of biological networks

7.1. Regulatory roles of ribozymes and riboswitches

7.2. Regulation of higher genomic regulatory networks

8. Types and classification of biological networks

9. Temporal classification of biological networks

10. Functional classification of biological networks

10.1. Genome preserving networks

10.2. Transcription regulatory networks or transcriptome networks

10.3. Translation regulatory networks or proteome networks

10.4. Developmental networks

10.4.1. Characteristics and regulation of developmental networks

10.4.2. Developmental signaling pathways

10.5. Signal transduction networks

10.5.1. Characteristics of signal transduction mechanisms

10.5.2. Important signal transduction networks

10.6. Apoptosis networks

10.6.1. Cascade of signaling mechanisms of apoptosis

10.6.2. Characteristic features of apoptosis

10.7. Oscillatory rhythm networks

10.7.1. Circadian rhythm networks

10.7.2. Intrinsic rhythm networks

10.8. Executive networks

10.9. Metabolic networks

10.9.1. Functional regulation of metabolic networks

10.9.1 A. Quantitative regulation of functions of metabolic networks

10.9.1 B. Qualitative regulation of functions of metabolic networks

10.9.2. Metabolic disorders

10.9.2 A. Congenital metabolic disorders

10.9.2. B. Acquired metabolic disorders

10.9.3. Pathogenesis of metabolic disorders

10.9.4. Classification of metabolic disorders

10.10. Preserving and repair networks of the genome, the transcriptome and the proteome

10.10.1. Anti-mutation networks of the genome

10.10.2. Transcriptome preserving and repair networks

10.10.3. Proteome preserving and repair networks

10.11. Neuronal brain networks

11. Proposed hypothesis of mechanisms of function of neuronal networks

12. Challenges to defining key regulatory molecules of biological networks

13. Importance of studying and analysis of biological networks

14. References

A network is an organized deterministic system composed of many structural components, units and sub-units, working in a predefined programmed and recurring manner to perform specific function(s) according to regulatory rules controlling functions/responses/interactions and cooperation of its components. There are many different kinds of network systems, for example engineered networks, electrical networks, mechanical networks, industrial networks, communication networks, natural ecological networks and biological networks. Each kind of network systems is constructed and controlled according to system-specific standards to perform the required function(s). Biological networks are organized deterministic systems that constitute the framework of life activities of the whole structural spectrum of living matter that includes biomolecules, e.g., nucleic acids and proteins, cell organelles, e.g., mitochondria and cytoskeleton, whole cells, tissues, organs and, at last, the whole organism (Figure 1 & Figure 2).

Figure 1.The design of biological networks

Figure 2.The concept of biological/biochemical pathways

The concept of the network is a universal basic frame-work within which the actions/ reactions/interactions of related objects or components of existing systems exert their activities. Moreover, it also regulates interactions between different groups of apparently un-related systems. For example, apart from being a component of the cosmic networks that regulate the behavior of similar systems in the milky way galaxy, the specific networks of the solar system responsible for regulating too many parameters concerning heat production and light emission by the sun are intimately related to a large number of vital networks responsible for regulating biological activities of nearly all living creatures on the earth. Although the rules that govern these interactions between apparently unrelated networks are not known, the effects of the networks responsible for initiating/maintaining/regulating heat production in the sun have a crucial impact on all network systems on the earth including biological networks regulating the life of human beings, animals, plants, and other simpler organisms as well as physical networks that regulate light and temperature input and distribution allover all solid parts and water stores of the earth.

In spite of the marked differences between different types of networks, they share common features including a basic model design reflecting composition and assemblage of variable numbers of structural units, each consisting of a number of nodes organized into modules. The modular design of the network characterizes specialized functional units coordinated to regulate and control the behavior of the network. Other shared features between different network systems include presence of key regulatory components, continuity of network action(s) as long as balance between input data/substrates and output data/products is maintained, preservation of network performance provided that internal/external optimal functioning conditions are conserved, and presence of stringent surveillance and control modules to optimize network function(s) and, in some instances, to minimize possible hazards that may result from malfunctioning of any unit or component of the network.

A comprehensive architectural design of key structural units and key regulatory components of any/all artificially structured/engineered networks is a prerequisite and a predefined characteristic of the network system. However, the same does not apply to either natural networks or biological networks. In natural networks that constitute the framework of actions and interactions of natural ecological systems, many key structural units and key regulatory components of these networks are, largely, speculative. This is attributed to the fact that a considerable proportion of the spectrum of natural forces that constitute and control natural phenomena is, still, ill defined. Biological networks, probably, are the least as regards availability of sufficient and satisfactory interpretation of data concerning their structural designs, their functional capabilities, their regulatory units, and the mechanisms of synchronization and coordination of their components. In spite of the continuing gush of tremendous sources of information in the field of biology, too little is known about the exact nature, the functional potential, the hierarchical organization and the flexibility of responses to external effectors of the extremely wide spectrum of network systems encompassing and controlling the innumerable groups of biological networks responsible for mediating the countless numbers of cellular life activities in both physiological as well as pathological conditions of human and other living organisms.

However, it must be emphasized that a considerable difficulty in study of biological networks from a medical point of view resides in the fact that analysis of network systems in general is carried out by theorists in physics and mathematics who use advanced and complex mathematical analysis and algorithmic approaches for constructing computational design models of network systems that fit, primarily, to artificially engineered networks. Additionally, technical terminology used within this context does not coincide with the more simple descriptive terminology used for characterization of biological processes. For example, the definition of the network as a (set of nodes and a set of directed or undirected edges between the nodes) seems quite ambiguous, or even meaningless, from a medical/genetic/physiological point of view that describes biological networks in a more simpler, descriptive and applicable terms, e.g., a biological network is an organized system composed of a number of proteins/enzymes/other molecules that act in a coordinated pattern within a specific cellular compartment to perform specific physiological functions.

Difficulties in discovery and characterization of biological networks, whether individually or as clusters of functionally related networks, are related to the colossal wide spectrum of the variable structural components of these networks that comprises thousands of genes, probably similar numbers of different categories of RNAs, and much more larger numbers of different types of proteins. Advances in molecular diagnostic techniques represented a major breakthrough in trials to disclose and define a large portion of these components, and diagnostic approaches based on more advanced analytical methods, e.g., quantum dynamics and nano-dynamics based techniques and computational genomics, are expected to offer greater diagnostic capabilities in this regard.

Classification of network systems is not an easy task because of the multiple and different criteria that define and characterize each type of network systems. Examples of such criteria include, for instance: structural components, motif patterns, hierarchical design, modularity, robustness, perception and sensitivity to external stresses, redundancy of components, functional performance, automation, scale-free nature of the network, in addition to many other criteria. Accordingly, many different categories of networks could be identified and delineated depending on the particular criteria used for classification. However, it must be emphasized that no satisfactory or a globally accepted classification scheme of networks is agreed upon, and that the classification framework of networks presented here is a tentative suggested approach taking into consideration the basic features that characterize each type. Within this context, three distinct categories of networks, with many subcategories of each, could be identified and delineated:

A. Natural Networks or naturally existing ecological systems that constitute, define and regulate the framework of all and varying aspects of earth ecology like climate networks, animal-plant and microbial biome networks and aquatic networks.

B. Artificial Networks that are designed, constructed, engineered and structured for specific purposes like electrical networks, industrial networks and computer-informatics networks.

C. Biological Networks that mediate and regulate all life activities of living organisms. Examples of biological networks include genomic networks, proteome networks, metabolic networks, regulatory networks, neuronal networks, inter-cellular networks and many others.

The basic essence of the concept of biological networks resides in the fact that all aspects of life activities in living cells are mediated/executed and regulated by a vast number of networks, comprising a wide spectrum of components, starting with simple biomolecules and ending with the whole organism, and functioning within a precisely organized tight framework. On the cellular level, all life activities are precisely and tightly connected and interconnected in many different specific programmed predetermined mechanisms, e.g., cascade-loop reactions/stimulus-response reactions/threshold-effect reactions and feedback-loop reactions. Proper mediation of cellular activities necessitates their inclusion within the context of structured and organized network systems capable of regulating/coordinating and synchronizing the countless numbers of biological processes occurring within living cells (Figure 3).

Figure 3.Genetic regulation of life activities and the concept of biological networks

The number of biological networks and pathways within the living cell is considerably huge, being dependent on the structural complexity and functional capabilities of the cell. Each network/pathway performs a specific physiological function within the global frame of cellular activities. The biological frame of life activities encompasses three major aspects in living organisms:

1.Keeping the vital structural design and integrity of different cellular components and cell organelles, e.g., cell nucleus and sub-nuclear structures, cell cytoskeleton, mitochondria, cell membranes, Golgi body, endoplasmic reticulum, cell pores and transport channels and intercellular connections etc.

2.Maintaining optimal functional performance of the whole spectrum of cellular activities including cell growth, division, proliferation, differentiation, migration, apoptosis and single and multicellular responses to, and interactions with, environmental effectors.

3.Integrating andcomplementing functions of all components of multicellular and higher organisms, cells-tissues-organs, to ensure optimal biological fitness of the organism.

Pathogenesis and progression of human diseases result from functional disturbances of biological networks within the cell. Disturbed network function leads to deleterious effects on physiological processes dependent on, and mediated by, affected network(s). Ensuing pathological processes, defined by the nature of disturbed networks and the specific organs or tissues affected, pave the way for the development of pathognomonic and characteristic disease entities. As most network functions are dependent on relatively small number of key regulatory biomolecules, i.e. enzymes/proteins and signal transducing factors, it follows that functional disturbances of biological networks and pathogenesis of disease states can be attributed, in most instances, to quantitative and/or qualitative abnormalities of these key regulatory molecules.

In spite of the remarkable differences between individual network categories, and even between secondary networks and sub-pathways within each category as regards its structural design and its functional spectrum, biological networks, in general, have and share common characteristic dynamic features determined by natural laws of thermodynamics. These features include, for example, basic similar dynamic mechanisms responsible for initiation of reaction cascades of different components of the network and synchronization of these cascades for multistage networks, maintaining rate limiting reactions at optimal performance levels, synchronization of network function(s) with other functionally related networks or pathways, ensuring efficient and optimal balance between substrate input and product output of the network, maintaining optimal and efficient loop of supply-flow-consumption of energy by the network, adapting network performance to physiological needs and to emergent changes in reaction environment and, finally, termination of reactions and interactions of different pathways of the network after attaining its predefined targets and performing its functions.

Study, analysis, and characterization of biological networks must take into consideration a major difference that characterizes this category of networks from other types of network systems; viz. biological networks are living systems and not merely constructed materialistic systems designed for performing specific functions. Many significant consequences of the living nature of biological networks follow this delineation, and can be summarized in the following observations:

4.1. Though biological networks are constructed from living units and subunits composed of biomolecules that show limited qualitative variations being composed of structural proteins, catalytic enzymes, ribozymes, and nucleic acids, they show wide quantitative variations from small local intracellular networks composed of few biomolecules, e.g., metabolic networks mediating enzymatic conversion of one compound to another, to exceedingly large networks composed of large numbers of biomolecules exerting their functions across many tissues and organs, or even on the level of the whole organism, like hormonal and neuronal networks.

4.2. The unique nature of the living design of biological network systems imparts to them peculiar characteristics that differentiate and characterize their performance from that of artificially structured network systems, irrespective of the apparently wider quantitative structural complexity of artificial networks. The differences stem from differences in flexibility to external stresses due to differences in modularity design of the two network systems, existence of alternative pathways for possible functional defect in any of the units/subunits composing the system, and presence of unique dynamic regulatory mechanisms exerted and controlled by two major, among many other, life preserving systems; viz. the neural and the endocrinal systems.

4.3. A crucial feature of biological networks resides in their ability to anticipate, and interact to, possible causes of performance inefficiency of the network due to many reasons like changes in input, e.g., nutritional deficiency, or changes in surrounding environment, e.g., infection. These predictive and corrective responses are initiated and conducted by many different mechanisms. Sensing networks that act in precise synchrony and cooperation with functionally related executive networks, constitute major life preserving measures of utmost importance for living organisms. For instance, sensory neuronal and metabolic networks responsible for sensing hypoglycemia, hypocalcemia or hypothermia, and the functionally related executive networks responsible for, and responding by, enhancing glycogenolysis, increasing blood calcium level and ATP production, respectively, reveal this crucial feature which reflects the wide range of flexibility of biological networks to changing external and/or internal effectors and working conditions.

4.4. The round the clock continuous dynamic changes of the input/output parameters and conditions of life activities of living organisms necessitates presence of precise master systems responsible for surveillance, detection and correction of any ensuing defects in structural design or functional performance of the network. Examples of these master regulatory networks include DNA/RNA/Protein proofreading and repair network systems, e.g., DNA repair enzymes, guide RNA and chaperones. These real time dynamic responses of biological networks to existing and to evolving changes are indispensable for maintaining vital homeostasis needed for proper regulation of life processes in living cells, as well as for prevention of occurrence or progression of detrimental errors that can lead to pathogenesis of disease.

4.5. The pivotal role played by enzymes in mediation and regulation of all biological networks in living organisms, without exception, has no counterpart in artificially constructed networks. Though many types of natural networks that shape and control main ecological bio-systems of the earth involve actions of enzymes, many natural networks do not involve enzymes as part of their design, and those that do involve it as an implicit component of some of its constituent units.

The crucial roles attributed to enzymes in constructing, mediating and regulating functional performance of biological networks resides in their peculiar ability to compose/decompose/change/reshape/locate/relocate other simple and complex biomolecules in a unidirectional as well as in a bidirectional manner within reaction environment as well as within cellular components hosting these reactions. This feature of enzyme action is responsible for the exquisite precision and efficiency of functional performance of biological networks. In addition, an important feature of enzyme dynamics that have crucial roles in network functions is the ability of enzymes to undergo transient association into multifaceted, more stable functional complexes that lead to marked increase in functional efficiency of the network. The presence of multiple functionally related isoforms of most enzymes involved in metabolic regulation represents a protective mechanism to preserve the integrity of the metabolic network in the face of mutations that can cause defective or deficient synthesis of one of the isoforms. Another major feature of enzyme dynamics allowing them to act as central regulatory/executive units of biological networks is their rapid, sometimes, instantaneous responses to changes in performance requirements. Enzymes act as catalysts that allow biochemical reactions to proceed, and allow rapid regulation of metabolic pathways in response to changes in the cell's environment or extrinsic signaling input from other cells, because enzymes exist as preexisting components, the activation of which is a much faster process compared to activation/regulation of gene expression for synthesis of required enzyme proteins.

4.6. An important feature of biological networks that might have important implications in diagnosis and treatment of many diseases is their conformation, as a complex organized system, to some rules different from, sometimes even contradictory to, some basic rules of artificial network dynamics. This argument debates the alleged assumption that ordered systems are generally less controllable/regulated than disordered ones. For instance, the hypothesis that this assumption could be applied to cancer therapy trials ¹ is obviously unreasonable, because progression of carcinogenesis reflects ongoing decomposition of the cellular systems of malignant cells, i.e. progression from order to more disorder and basic clinical facts of cancer therapy clearly shows that treatment of early cancer, i.e. relatively more ordered system, is much more effective than later intervention when cancer cell systems become more disordered, due to involvement of more cellular components and networks in development of the malignant phenotype, thus adding more disorder to the system.

4.7. Most cellular networks are confined to the intracellular environment, even to specific cell organelles either individually or in concert to accomplish specific physiological processes, e.g., metabolic networks responsible for fatty acid oxidation within the mitochondria and regulatory/proofreading networks responsible for post-translation modifications of proteins during their sequential passage along the endoplasmic reticulum and Golgi apparatus. However, biological networks might comprise distant units and subunits dispersed within many tissues and organs, that are tightly interconnected, synchronized and functionally coordinated via neural/endocrinal regulatory motifs. For example, preservation of blood and body fluid osmolality has a critical impact on life activities of cells and its precise regulation is attained through a crucial water homeostasis network comprising the brain, the kidney, the skin, the heart and the eyes as well. In pathophysiological conditions causing hyper-osmolality states, physiological alterations due to sensation of thirst/diminished water content of skin/decreased intraocular pressure due to diminished secretion of intraocular fluid/diminished volume sensation of auricles and ventricles of the heart/diminished pressure in blood vessels due to fall in blood pressure, all trigger local signaling pathways in affected dehydrated cells and tissues. Network modules responsible for maintaining network function, i.e. preservation of proper blood/fluid osmolality, begin to exert their corrective roles via different processes, e.g., stimulation of osmo-receptor nodes of neural networks of the hypothalamus responsible for synthesizing the prepro-form of vasopressin, or antidiuretic hormone, and for controlling its conversion to the mature form and its release by the posterior pituitary. Other hormones taking part in maintaining water homeostasis and participating in regulating water excretion by the kidney and prophylaxis against pathological consequences of plasma hyper-osmolality, e.g., renin/aldosterone/secretin/aquaporins, might also constitute additional/alternative/subsidiary subunits or modules of the water homeostasis network, and are affected in a similar way. Following these responses, vasopressin and other hormones begin to exert their corrective functions to restore network performance and function(s) according to their predefined roles, e.g., affecting permeability of renal tubules to water, augmenting sensitivity of collecting ducts to vasopressin and the like.

4.8. A crucial feature that characterizes biological networks is the marked degree of flexibility of performance of the network in response to changes of functioning conditions, and to a lesser extent, to changes involving structural units, e.g., biomolecules and organelles of the network. For instance, flexibility of performance of artificially engineered networks is limited by the predefined design features of the network, and unexpected external stress or change of functioning conditions could be tolerated up to a limit followed by failure of network function. Though the traditional definition of chaos or deterministic chaos states that in absence of random events, the future behavior of deterministic systems is determined by their initial conditions, predictability of this behavior is not possible or, at least, hard to measure. The question of whether biological systems, including the genome, the proteome, the transcriptome and other biome networks, can be dealt with as deterministic systems or not has no definite or universally accepted answer. On one hand, in contrast to the modularity of engineered networks that have no or limited performance flexibility in response to stress, biological networks are fully flexible networks. Even with unexpected random events, e.g., external environmental mutagenic effects, these systems have a precise degree of predictability of their behavior, e.g., DNA repair mechanisms. Many factors underlie functional flexibility of biological networks. First, presence of multiple regulatory modules, nearly of all parts and along all reaction steps of the network to detect early malfunctioning signs of the network. Second, existence of varying and different corrective processes triggered by signaling pathways and conducted by efficient functional responses of major components of the network system, e.g., the genome, the proteome and the transcriptome.

4.9. An important feature of many biological networks is the multifunctionalcapabilities ofsome of its key components. For instance, many proteins and enzymes that constitute parts of important regulatory/signaling networks have many functions and can regulate or affect many other components/pathways of the network. A prominent example is Glyceraldehyde 3-phosphate dehydrogenase, (GAPDH or G3PDH), an enzyme involved in glycolysis and energy production through break down of glucose. In addition to this metabolic function, GAPDH has been found implicated in performing other non-related physiological functions including neuronal transmission, intracellular trafficking of translated proteins, transcription activation, iron homeostasis and initiation of apoptosis.

Though the traditional interpretation of this multifunctional property of enzymes/proteins rests mostly on the presence of multiple functional domains each capable of mediating a specific function, other plausible interpretations could, also, be assumed, e.g., binding to another protein/enzyme thus forming a novel functional catalytic component, structural conformational change thus offering more functional options like binding to membranes/cell pores/cytoskeleton regions, or even degradation or disassembly to smaller different but, still, functionally specialized units.

A relatively recent postulation attributes this multifunctional property to a vague hypothesis termed gene sharing, i.e. a single gene is sharing in performing multiple/different/unrelated functions via its encoded protein product ². The prominent examples of proteins within this context are the moonlighting proteins. Though the main function of moonlighting proteins is enzymatic catalysis, they also serve other non-enzymatic functions in view of their many functional categories which include membrane receptors, ion channel regulators, chaperones and initiators of apoptosis ³.

Meticulous analysis of the gene sharing hypothesis, however, reveals that the essence of the hypothesis seems unreasonable because it is based on unnecessary theoretical postulations trying to deduce new concepts to explain findings already interpretable by the traditional dogmas of biochemistry and physiology. The postulation argues that most, if not all, proteins perform a variety of functions in the same and in different species, and that this is a fundamental necessity for evolution. However, the cardinal examples of the hypothesis, crystallins and actin, that have diverse unrelated functions are not unique in this respect, as multitudes of proteins already have this multifunctional property and perform diverse unrelated functions including regulation of gene expression, e.g., p53 ⁴, fragile X mental retardation protein (FXMR1) ⁵, and many others.

The Gene sharing hypothesis represents another desperate attempt to support the irrational concept of evolution by postulating unreasonable assumptions that have no logical support. More advanced analytical measures will, probably, reveal that the underlying molecular mechanisms of this multifunctional property of proteins/enzymes are mediated, and can be interpreted within the context of the aforementioned classic dogmas of biochemistry and physiology.

4.10. A hierarchical master regulatory system responsible for controlling network function(s) probably exists for most, if not all, biological networks within living cells. Though the exact mechanisms through which this presumed control system exerts its effects are vaguely defined, a tentative hypothetical frame based on accumulating observations might be postulated in this regard. Within the context of this postulated hypothesis, all biological networks in the cell are considered as subordinate entities constructed and organized according to the information embodied within the genome. The genome, as the prime entity in this hierarchical system, defines all types of networks needed for mediating all life processes in the cell. Genome function(s), in turn, are probably regulated by genomic regulatory networks composed of, and controlled by, different constituents, e.g., microRNA/histones/proteins, that regulate and maintain structural and functional integrity of the genome. These genomic regulatory networks mediate critical tasks encompassing a wide variety of genome functions and behavior like regulation of DNA replication/regulation of DNA repair/regulation of cell division, and many others.

4.11. In contrast to the modularity of artificially engineered networks, that have no or limited performance flexibility in response to external stresses or to ensuing changes in internal performance, biological networks are fully flexible networks. Even with unexpected random events, e.g. external mutagenic effects, these systems have a precise degree of predictability of their behavior, e.g. DNA repair mechanisms. Sometimes, recognition or detection of this flexibility in behavior is blurred upon looking to the effects of mutation in general. Mutation-induced genetic disorders should not, and could not, be considered as chaotic behavior, in the scientific sense, of the genome. Rather, they reflect and represent precisely predefined behavior in response to random events determined by the initial conditions of the system.

4.12. Although the genome defines the proteome that constitutes the structural components of the majority of developmental/metabolic/ signaling networks all through the life cycle of the cell, auto-regulatory subsidiary circuits and modulator pathways, composed of protein by-products of a network, can mediate some integral functions within the mother network. Self-exerted auto-regulation, mediated by a wide variety of biomolecules including proteins/enzymes/microRNAs, is a critical mechanism that seems to plays an important role in regulating and fine tuning the function of most biological networks. These functions include, for instance, rate-limiting effects/feedback potentiation or inhibition/signaling and synchronization, among other functions. The source as well as the behavior of this postulated inherent auto-regulation exerted by proteome components on biological networks, including even genomic regulatory networks, has no clear interpretation. Postulations that attribute this behavior to mere conformation with biochemical/biophysical laws ruling the network/reaction environment can, partly, offer an explanation but they can not interpret the persistence of this behavior in different pathophysiological conditions. Regulatory protein by-products of parent networks are, obviously, out of control of the genome as they are not synthesized by genes, and their apparent roles might be controlled by information embodied within the proteome, rather than the genome, of the cell.

4.13. The genome of the cell defines and controls synthesis of its proteome through a strict precise hierarchical pathway system including many networks that act in accurate temporal sequence to regulate gene function via gene activation and start of transcription, post-transcription modifications of mRNA, translation, post-translation modifications of synthesized proteins and, finally, intracellular/extracellular trafficking and localization of synthesized proteins. Following the final structural organization of the proteome of the cell, intracellular networks regulating vital processes in the cell are formed. These networks comprise the vast majority of executive cellular networks responsible for energy production/maintenance of optimal physical characteristics of the cytosol/preservation of the proper balanced biochemical composition of all cellular components/regulation of metabolism/regulation of transport across cell membrane and membranes of cell organelles/synthesis, construction and maintenance of cytoskeleton components of the cell/regulation of excretory processes/regulation of secretory processes/regulation of apoptosis and regulation of all other vital processes required to maintain proper and optimal performance of life activities and cellular functions.

The last level of the hierarchical organization of cellular networks within this context of gene function includes networks responsible for regulating intercellular and extracellular processes. Intercellular networks regulate contact and communication between cells, synchronization of cellular responses to changes in extracellular microenvironment and global mass cellular behavior like cell growth, cell differentiation, cell migration and apoptosis. Similarly, extracellular regulatory networks control vital processes necessary for homeostasis of life environment of multicellular organisms including global mass cellular behavior like cell growth, cell differentiation, cell migration and apoptosis during embryonic and fetal development, regulation of cardiac output, blood pressure and local perfusion of tissues, regulation of blood osmolality and electrolyte balance, regulation of neuronal transmission, regulation of immune defense mechanisms like quorum sensing and mass cellular aggregation in inflammatory conditions, regeneration and differentiation of stem cells in certain pathological states, and regulation of an endless list of other vital functions in multicellular organisms.

4.14. Study and analysis of biological networks in accordance to the classic definition of network systems has to recall and put into consideration additional peculiar features that characterize some subcategories of these networks. Some types of biological networks, mostly metabolic pathways, are temporarily formulated and constructed to perform specific functions, e.g., metabolism of drugs or other administered foreign substances. Following performing the required task(s), the network is disassembled to its component units/subunits. This fate is important to save energy, recycle network components for other purposes and to avoid possible conflict with other pathways. Accordingly, large numbers of biological networks have no enduring or permanent structural framework, they ate formulated and constructed to face temporary or contingent specific cellular requirements. The significance of this feature raises many questions regarding the functional potential of the genome/proteome profile of the cell. For instance: are there hidden networks and pathways that appear only upon need, e.g., upon exposure to extrinsic stressful effects, and if so, are there predefined/preprogrammed genomic/genetic registry data ready for transcription/translation upon need. This feature denotes the unlimited reactive potential and the countless synthetic capabilities of the genetic material in response to environmental stresses and offers an explanation to the existence and persistence of huge numbers of living organisms in spite of unfavorable environmental conditions. The temporary nature of this phenomenon contradicts its consideration within any evolutionary context as it does not become a consistent fixed part of the life frame of the organism.

4.15. Although most aspects of the postulated hierarchical system responsible for regulating functions and interactions of biological networks are well defined on cellular level, little is known as regards its mechanisms of action on the whole organism level. In humans and other multicellular organisms, two major regulatory systems, viz. the nervous and the endocrinal systems, exert coordinated and synchronized regulatory functions though via different mechanisms. A master regulatory hierarchical system dominating both these systems does not exist, and hypotheses postulating domination of higher brain/cortical regions over these systems might offer partial interpretation in this regard. Existence of a predefined programmed master regulatory scheme dictated by the life code embodied within the genome, and probably also within the proteome, of the cell might be a more comprehensive hypotheses. Unfortunately, currently available knowledge of the structure/function/behavior of the genetic material in unicellular, as well as in multicellular, organisms are far from being sufficient to offer plausible postulations as regards the nature, the location, the structure or the mechanisms of action of this hypothesized master life regulatory system.

The structural homogeneity of all components of the human genome rules out presence of any peculiar regions that can be alleged responsible for coding or defining such a master regulatory scheme. However, the marked functional heterogeneity of different components of the genome might suggest a provisional frame of such a master regulatory scheme. Within this context, three distinctive functional genome components that have crucial impact on genome size/genome structure/genome functions might participate in this presumed regulatory scheme. These include: 1. different classes of non-coding RNAs, short or microRNAs and long non-coding RNAs (lncRNAs). 2. different classes of the transposons. 3.Pyknons.

Non-coding RNAs exert crucial regulatory functions over genomic networks, and spontaneous or induced activities of transposons can affect genome size and homogeneity considerably particularly during development. Though very little is known about the functional significance of pyknons, their considerable sizable proportion in the genome and their peculiar structural features might suggest an important role played by pyknons as global regulators of gene function. They probably represent non-classic genes or non-classic transcriptional units capable of coding for, and regulating synthesis of, some microRNAs species for specific biological activities including regulation of genomic networks.

A plausible hypothesis regarding the nature of the postulated master scheme of life in living organisms is difficult to formulate in view of the marked paucity of current information concerning the detailed structural and functional organization of the genome, the different classes of RNA, and the proteome of living cells. Obviously, if a master dominating system responsible for defining the functional framework of the neural and endocrinal networks involved in regulating and mediating all life activities within the cell do exist, it must be located within, still functionally unidentified, regions of the brain. A marked different pattern of structural organization of the genome and RNA classes of cells constituting these master regions and a much wider spectrum of functional capabilities of their proteome might exist. Though current knowledge of the structures and functions of different regions of the human brain do not offer any helpful clues in this regard, future advances in molecular scanning techniques based on nano-scanners and nano-sensors capable of detecting the smallest, even the tiniest, structural deviations of the genome and the proteome, from currently known ordinary patterns, might reveal and disclose some of the mysterious aspects in this regard, and might even offer some answers to questions about the possible source and the exact nature of this postulated master scheme of life in living creatures.

The predefined designs of biological networks in living cells are dictated by information databases constituting a critical portion of the bioinformatics databases of life processes, probably contained within the genetic material of the cell. Unfortunately, the nature of these specific information databases defining all aspects of biological networks within specific cells or distinct organisms are ambiguous and largely unidentified. However, few rules can be delineated from accumulating observations in this regard. In general, biological networks conform, both structurally and functionally, to the general scheme of network systems though they have peculiar characteristics that differentiate them from other kinds of networks. Although all network systems are designed according to the functional requirements, biological networks are unique as they are formulated, constructed and regulated by preexisting programed designs contained within the cell/organism. The genome of the cell/organism comprises within its functional spectrum the databases needed for defining all network systems necessary for initiation/progression/preservation of life activities, as well as databases of networks responsible for inducing apoptosis, or programed termination, of these activities at certain stages of cellular life. The hierarchical design of life of all living organisms, with the exception of some viruses, has a more or less solid frame represented by the classic dogma of life at the molecular level which states that the genetic commands of the databases embodied within the structural/functional components of the genome are transcribed first to the transcriptome, then translated to the proteome that mediates all life activities of the cell/organism. All steps, and every step, of this design are under strict control of regulatory, proofreading, executive and corrective/repair networks composed of, and comprising all, structural/functional components of the cell. As processes and mechanisms of construction and maintenance of each structural component of the cell are mediated by network systems, nearly every cellular/subcellular component of the cell has its peculiar spectrum of networks mediating these mechanisms. The same applies to functional activities of the cell which are mediated and regulated by varying numbers of networks depending on the spectrum of cellular activities. The exceedingly large number of structural and functional biological networks in living cells function in concert, they are coordinated, interconnected and synchronized within a precise, punctilious context aiming at preserving the cardinal features of life at the molecular level as well as the whole organism level.

Biological networks have common routine functional features irrespective of the life activities mediated and regulated by these networks. Each network is composed of a varying number of structural proteins, catalytic enzymes, signaling molecules, and other organic/inorganic regulatory molecules necessary for network functions. The constituents of the network communicate with each other either directly for adjacent complexes, e.g., through structural conformational changes of proteins, or via signaling molecules that transport commands from regulatory units of the network, e.g., key proteins, to executive units, e.g., enzymes. Main products or secondary products of network function, e.g., ATP or metabolites, are either handled by other networks for specific physiological purposes or function as input substrates for renewal of network functions.

Although the major portion of the spectrum of biochemical and physiological regulatory networks and pathways through which the genome/transcriptome/proteome dominates all life activities at the molecular level inside the cell has been disclosed, and in spite of defining the major part of the spectrum of neural and endocrinal regulatory mechanisms of network functions on the whole organism level, the exact nature of the molecular mechanisms responsible for sensing and anticipating network demands by specific components, and the exact nature of the molecular mechanisms responsible for perception of these demands by executive components of the network remain extremely mysterious. Though occurrence of structural conformational changes in a protein, an enzymes or an organelle membranes upon contact, or interaction, with another biomolecule can be interpreted in terms of thermodynamics, and sometimes according to classic dynamics, occurrence of comprehensive organized and coordinated responses of all network components upon triggering/activating/initiating the first step in the pathway is hard to interpret by any currently available materialistic explanations.

The predefined structural and functional design of biological networks aims primarily at ensuring optimal performance outcomes under variable working conditions. However, attaining and maintaining optimal functioning conditions of biological networks are dependent on presence of many factors and fulfillment of many conditions including: first: presence of properly constructed executive networks comprising all needed constituents, second: presence of intact regulatory networks or pathways necessary for controlling function(s) of executive networks, third: availability of properly adjusted continuous/interrupted flow of input substrates needed for initiation and keeping of network function(s), fourth: proper coordination with other functionally related networks or pathways responsible for handling output products of the network, fifth: properly synchronized renewal and replacement of network components, or biomolecules, that become structurally distorted and functionally inefficient over time.

Deviations from the proper predefined design of biological networks happen all the time throughout the whole life span of the living cell. These distortions are expected, or even inevitable, in view of the persistently dynamic nature of the network and the continuously changing circumstances of the cellular compartments enclosing the network(s). Underlying causes of these deviations can be deduced from analysis of factors participating in formation, regulation and disassembly of the network. Defects in the general framework design of the network affecting its mechanism of action might be inherited, e.g., congenital genetic disorders, or might be acquired following fertilization and zygote formation. Mutation-induced defects and abnormalities can present at any time and in any tissue/organ depending on the function(s) of affected networks. Similarly, mutations affecting genes or sets of genes responsible for synthesis of protein-enzyme components of the network or microRNA-protein regulatory factors have peculiar temporal and spatial profiles depending on the functions/localization of the network. Variations in environmental conditions of cellular compartments enclosing biological networks might be triggered and initiated by external factors like physical stresses, e.g., temperature changes, chemical stresses, e.g., changes in pH status, or biological stresses, e.g., viral or bacterial infections. These variations are dealt with, more or less efficiently, by networks specifically designed for these purposes as long as they occur within the predefined functional spectrum and the tolerable threshold limits of the network design. Over the threshold quantitative changes of these environmental variations, or exposure to external variations that can not be dealt with by the network, can result in a graded spectrum of functional deterioration of network performance starting with reduced outcome and ending with complete ravage, degradation or damage of the network. Exposure to ionizing radiations, for instance, leads to breakage of the sugar-phosphate backbone of DNA. Within limits, DNA repair systems or DNA repair networks can repair the resulting damage via the efficient DNA repair mechanisms comprising endonucleases/polymerases/ligases, among many other components of the repair system. Overexposure to lethal or intolerable doses of ionizing radiations, however, can cause widespread damage to DNA that can not be repaired, leading to irreversible devastating and drastic changes of the genome. The same scenario applies also to protein components of the networks, where exposure of living cells to lethal or damaging external stresses, like high temperature or irradiation, can lead to a wide range of detrimental consequences including damage of structural conformation of the proteins, disassembly and disorientation of the proper design of the different domains of the protein molecules, and loss of the external water envelope that constitutes an integral functional component of the molecule. Ensuing damage of the structural components of the network results in progressive failure in network performance, failure of physiological functions mediated by the network with consequent pathophysiological alterations and pathogenesis of pathognomonic disease depending on the functional spectrum of affected networks.

The cooperative and synchronized performance of functionally related sets or groups of networks, either locally in single cells or more globally in tissues/organs/organisms, is precisely controlled by, still unidentified, regulatory system(s) that ensures proper flow of input requirements or substrates to specific networks and parallel flow of metabolites or end products to other networks for final usage. Attaining and maintaining optimal life processes in living cells depend on the closed circle-like dynamic nature of this functional design of biological networks. Deviations from the predefined framework of this design or distortion of one or more of its constituent networks underlies the development of pathophysiological alterations and pathogenesis of disease. For instance, mutation-induced defective or deficient synthesis of components of an executive or input network will result in deficiency of products, biomolecules or ATP, necessary for functioning of other related networks or for provision of energy needed for performing, any and all, life processes in the cell. Similarly, mutation-induced defective or deficient synthesis of components of intermediary or output handling networks will lead to accumulation of products of executive networks and marked disturbances in the thermodynamic equilibria of involved reactions. Mutation-induced defective or deficient synthesis of structural components of regulatory networks, also, has a more widespread deleterious effects on all networks dependent on structural and functional integrity of these regulatory networks. The abovementioned examples reveal, in brief, some of the causes and effects of distortion of, or damage to, different types of biological networks and their role in pathogenesis of genetic as well as of non-genetic disorders consequent to these structural and functional alterations.

Regulation of biological networks comprises nearly all functional aspects of the networks including initiation, activation, augmentation, inhibition, persistence, coordination and synchronization of function with related network groups, and termination of network function when required tasks are accomplished. Key networks might regulate function(s) of subsidiary networks through regulatory activator/terminator proteins, enzymes and microRNA. Inorganic components like heavy metals can also act as key regulatory molecules of some network functions ⁶. These regulatory proteins might exert their roles via acting as substrates or competitors of key enzymes of the network. Network activation depends on the type of the network, the nature of the regulatory network, the functional spectrum of the network, and the nature of the regulatory factors participating in defining network outcome. Metabolic networks are usually activated when the primary substrate is availed to the first initiating enzyme of the reaction cascade. Though all components of metabolic networks are synthesized under strict control of genomic regulatory networks, metabolic networks have a considerable degree of self-automation as long as the substrate resources and structural network components, enzymes/proteins/biomolecules, are available within the reaction environment. However, although core components of signaling networks, including signal receptors, are similarly synthesized under strict control of genomic regulatory networks, signaling networks do not have similar self-automation behavior like metabolic networks because they are primarily designed so as to elicit temporary and instantaneous regulatory responses. The second messenger outcomes of signaling pathways, also, do not have such degrees of self-automation because their effects are conditioned by many other factors like availability of transcription microRNA molecules, structural integrity of targeted genes, concomitant complementary and synchronized signaling pathways participating in the same task(s), and augmentation/inhibition by specific key regulatory molecules.

Classification of biological networks is difficult and perplexing in view of the exceedingly large numbers of primary/central/pivotal key networks and corresponding, even larger, numbers of secondary/subsidiary/ temporary networks present in each living cell. Additionally, the wide spectrum of structural and functional characteristics that distinguish each of these network categories and subcategories makes their comprehensive classification an arduous task. Many cellular networks function in concert within a common and shared context imposing functional complementation to mediate specific tasks within a larger network system, e.g., cell cycle regulating network. Moreover, functional complementation of networks may comprise different network categories, e.g., transcription regulatory networks and signal transducing networks, or similar category networks working in succession in a cascade manner, e.g., metabolic networks.

No single reasonable and acceptable classification of biological networks could be formulated because of the many different parameters relied upon for classification. For example, classification may depend on network function, e.g., regulatory/developmental/executive networks, or on structural components of the network, e.g., protein-enzyme networks, protein-microRNA networks and mixed network comprising other components like inorganic signaling molecules. Other parameters of classification schemes include complexity of the network, e.g. major/subsidiary/intermediary networks, and cellular location of the network, e.g., nuclear/mitochondrial/ cytoplasmic networks. Each of these network categories could be classified, further, into many subtypes according to peculiar characteristic features of the network. Overlapping and interlacement of network subtypes is common because many networks share common features with other apparently distinctive network types. For example, metabolic networks could be classified according to their structural components as protein-enzyme networks and as executive networks based on their functional specialization. Some metabolic networks function as major pivotal or central networks while other less important metabolic pathways serve as subsidiary networks. In addition, metabolic networks could be, also, classified as cytoplasmic, mitochondrial or nuclear metabolic networks according to their location within the cell compartments.

Another classification scheme of biological networks worthy of consideration is based on the temporal nature and persistence of network function. According to this classification scheme, four main categories of biological networks could be identified with clear discrimination between the peculiar characteristics of each of them: 1. Continual unceasing networks functioning all through the life span of the cell, e.g., energy producing networks and cell division regulatory networks. 2. Temporary networks that function during particular stages of the life span of the cell, e.g., developmental networks. 3. Circadian rhythm networks implicated in regulating physiological activities characterized by having nighttime/daytime cyclic endogenous physiological rhythms, e.g., sleep/wakefulness, blood pressure fluctuations, rhythmic secretion of hormones/endorphins, and entrainment or synchronization of these activities with environmental cycles of light and dark. 4. Oscillatory rhythm networks that work in an interrupted recurring pattern in response to external environmental changes, e.g., temperature cycles, or in retroaction to internal changes in cellular homeostasis, e.g., electrolyte balance. However, functional classification of biological networks seems to be the most reasonable as functional specificity of the network is the main determinant of its importance within the life frame of the cell [Table 1].

The aforementioned resume of different network categories in the living cell outlines, in brief, what could be referred to as the dynamics of life processes in living cells cell. Analysis of the classic dogma of life cycle, traditionally and illogically referred to as the classic dogma of molecular biology, reveals the three major structural components responsible for mediating life activities in living creatures, i.e. the genome, the transcriptome and the proteome. It also defines the major network categories which guarantee precise and optimal performance of these activities. Additionally, it delineates the temporal relations between the biological implications and the dynamic cascades of these vital life activities. Within this context, a time-dependent or time-related temporal classification of biological networks might be assumed to comprise the following postulated network categories hierarchically arranged according to the temporal cascades of their functions:

A. Crucial Stage or Genome Preserving Network Category composed of many different types of networks responsible for maintaining the identity, the integrity and the stability of the genome. This life sustaining and maintaining obligation starts at fertilization and continues till cell death occurs.

B.  Transcription Stage Network Category also composed of many different types of networks that regulate all aspects of transcription including initiation/enhancing/silencing and termination of transcription, post-transcription modifications and availing mRNA to protein synthesis machinery in the cytoplasm.

C. Translation Stage Network Category composed of regulatory and executive networks responsible for controlling translation. Translation of mRNA coding for proteins results in synthesis of the exceedingly large number of structural and catalytic proteins which compose the proteome. The proteome provides the structural protein components of all the biological networks responsible for direct execution and mediation of all life activities of the cell.

D. Executive Stage Network Category which comprises all types of networks and pathways directly involved in regulation and performance of all life activities in the cell. This category includes the vast majority and the largest portion of biological networks in the cell.

E. Final Stage Network Category including networks responsible for initiation and completion of apoptosis of senescent and heavily mutated cells. Apoptosis networks and pathways are a subcategory of executive biological networks that finalize the life cycle of the cell and put an end to the biological existence at the cellular level.

Functional classification of biological networks, probably, represents the most plausible approach in this regard. As referred to earlier, the classic dogma of life cycle denotes the presence of three major structural and functional components in the living cell responsible for controlling all life activities of the cell, viz. the genome, the transcriptome and the proteome. Consequently, three main network categories in the cell could be identified and delineated comprising genomic, transcriptomic and proteomic networks. Analysis of the nature, the composition, the dynamics and the functions of each of these three main network categories reveals that each category has distinctive characteristic features defined, primarily, by their basic functions. Functional characterization of each of these three basic network categories and the subsidiary networks and pathways dependent on, and regulated by, each of them discloses, with very few exceptions, the global framework of life processes in living cells. Presence of secondary/subsidiary/tributary and intermediary networks tightly connected and properly synchronized to ensure optimal performance of their functions is mandatory in view of the complexity and multistage nature of life processes in the cell. However, it must be emphasized that this classification is speculative and is meant for educational purposes in the first place. In fact, sharp demarcations between the individual spectra of each of these categories is practically, and even theoretically, impossible because of the intimate and cooperative relationships between their functional spectra which are widely intermingled and complementary (Figure 6, Figure 7, Figure 8).

Figure 6.Functional Classification of Genomic Regulatory Networks

In view of the characteristic features and distinctive nature of the wide spectrum of structural and functional properties of the nervous system of higher organisms, in general, and of the human brain in particular, few apparently plausible hypotheses regarding mechanisms of development and mediation of higher intellectual functions in human brain might be proposed as follows:

1.  Perception, propagation and flow of information, gained from endogenous sources and external stimuli, to neurons occur first as specific defined patterns of electric impulses. Metabolic changes in the extra-neuronal environment might, also, be conveyed to the inside of the neuron first as electrical input to be translated to specific proteomic responses via signaling networks within the neuron.

2. Dendritic input to the neuron might elicit, through certain signaling pathways, specific proteomic responses that functionally relate particular proteins to specific patterns of information input. Contrary to the majority of physiological processes mediated by the activity of single enzymes, or few enzymes and protein molecules, the complex and intricate nature of mental processes make them difficult to be executed by single or few proteins and considerable number of proteins might be involved in these processes.

3.  Recognition of specific patterns of information input may cause relevant specific neuronal network(s), composed of afferent nerves, dendrites, signaling pathways, and particular arrays of certain proteins, to get into work and a specific imprint formulated by the combined electric and proteomic responses to information input of particular situations is constructed and preserved.

4. The huge, unimaginable quantitative and qualitative spectra of information flow and input to the brain necessitates involvement and participation of multiple specific information imprints, each devoted for specific input state, in formulation of other particular imprints for other different situations. Thus, few or variable numbers of imprints, where each is peculiar for a specific input state, might be collectively and/or selectively combined to formulate and characterize a different mental, cognitive or intellectual condition.

5. This presumed team work design of neuronal functions postulates presence of functional specialization of the large numbers of neurons constituting particular components of the brain. A structural-functional design of the human brain according to this assumption is built on the postulation that within each cellular neuronal component of the brain, e.g., the cerebral cortex/nuclei of cranial nerves/the amygdala/the thalamus/the hypothalamus etc., functionally predefined groups of neurons do exist. Each functionally specialized neuronal group probably works on network basis, i.e. they form a well- defined structured functional network composed of the neurons and their functionally related nerve fibers/dendritic processes and ramifications/support and regulatory glial cells and, probably, other poorly defined regulatory or signaling pathways necessary for combining/synchronizing and harmonizing their functions with other groups.

6. Perception, storage and archiving of different types of information with formulation of specific functional imprints and specialized networks, each being selectively responsible for handling one or more distinctive type of information input to the neuronal group(s), might represent the afferent limb of information storing mechanism(s) of the brain. The exceedingly large number of neurons composing the human brain, estimated to count around one billion neurons, and the much more extensive inter-neuronal connections amounting to more than one trillion connections, allow for efficient handling, processing and storing of the unimaginable flow of daily, sometimes hourly, information input and flow to the human brain. Theoretically, millions and even billions of information-handling specialized neuronal networks with comparable numbers of specific imprints for all possible kinds of information-processing mental operations confronted with in daily life, could be constructed and formulated in the human brain in view of the huge numbers of neurons and inter-neuronal connections composing the nervous system.

7. According to these preliminary hypotheses, storing/processing/archiving of information in the neuron seem to be a dynamic conditioned process controlled by specialized neuronal networks comprising proteins as one of their components, rather than a static process depending on lasting presence of certain proteins specialized in storing information. The network concept, instead of the protein concept, as regards information handling by the neuron seems more palatable for many reasonable considerations:

a. The number of proteins needed to execute different stages of information handling, e.g., perception/recognition/archiving/formulation of specific imprints/storage etc, by the neuron would be huge enough to cause considerable spatial and functional encroachment on other neuronal functions needed to sustain its essential life activities.

b. A sizable portion of the genome would be needed and devoted for synthesis of required proteins with consequent deleterious effects on synthesis of proteins mediating other life activities of the cell.

c. The multistage dynamic nature of information handling cascade inside the neuron necessitates and imposes many dynamic communications and mutual interactions between many different related components, e.g., proteins/signaling molecules/regulatory molecules/modulating pathways etc. Obviously, efficient and proper execution of these stages and processes could only be mediated and performed according to basic rules and mechanisms of network functioning. Attributing the ability to execute these mechanisms to structured designs of static proteins, whether in groups or in scattered patterns in the cytosol, seems unreasonable as it contradicts the basic principles of physics, chemistry and efficient energy consumption rules of thermodynamics.

8. Hypotheses regarding the nature of mechanisms implicated in, and responsible for, recall and retrieval of information imprints stored within the neurons are much more difficult to formulate. Normal physiological and pathological interpretations of mechanisms of neuronal control of other body organs in health and disease, respectively, provide relatively acceptable explanations of the nature of neuronal responses and brain function within the context of known functional mechanisms of the nervous system. Neurological regulation of somatic and autonomic body functions is exerted by many different mechanisms including, for example, autonomic and somatic reflex arcs initiated and conducted by monosynaptic and polysynaptic pathways, feedback potentiation or inhibition of afferent or efferent pathways, neuro-endocrinal regulation of secretory functions of endocrine glands, and the like. Unfortunately, no comparable assumptions as regards possible mechanisms involved in storage, processing, recall and retrieval of stored information generated by higher cognitive and intellectual functions, e.g., recognition, intuition, thinking, reasoning talking, learning, writing, memory, emotions and imagination, could be speculated or formulated. In spite of the currently available flood of information regarding the fine structure of the nervous system, and to a lesser extent, its functional capabilities, sufficient knowledge of the structural and functional designs of the brain at the molecular level is grossly lacking. Unavailability of more specific non-invasive diagnostic techniques and analytical approaches to disclose these mysterious aspects of the human brain at more deeper insights represents a major obstacle in this respect. It is hoped that disclosure of intra-neuronal structural and functional specialization of the neuro-proteome, and possible network systems responsible for higher functions of the brain, would add great wealth of data indispensable for formulating better hypotheses regarding the nature and sources of these functions. It would, also, be of great help in postulating better assumptions regarding the construction, development, and the mechanisms of action(s) of neuronal brain networks responsible for intellectual functions of the brain.

9. The abovementioned hypothetical postulations regarding possible mechanisms of information processing in the brain might offer a partial interpretation of some memory recall and retrieval defects like temporary and/or recurrent amnesia and Alzheimer disease. Degradation of key proteins that participate in neuronal networks responsible for performing specific memory-storage and recall functions, might explain temporary amnesia due to interruption with function of these networks. Re-synthesis and replacement of degraded/denatured/deficient proteins might, in a similar way, explain regaining lost functions related to memory recall and retrieval. However, if considerable loss of functions of genes responsible for synthesis of these proteins, e.g., due to un-repairable mutation-induced damage, happens, permanent loss of memory for many events, depending on the magnitude and the spectrum of these events, may occur.

Defining key regulatory molecules of networks implicated in pathogenesis and progression of the majority of genetic, as well as most non-genetic, diseases lacking obvious clues as regards possible underlying etiology, represents a hard task and a real challenge because of many difficulties including (Table 5):

1. The exceedingly large number of biological networks within the cell.

2. The ever changing dynamic frame of interactions/interconnections and communications between large numbers of functionally related networks within the cell and subcellular compartments.

3. The complex nature of networks that control and synchronize the functional performance of the tremendous pathways mediating intercellular/inter-tissues/inter-organs connections and behavior.

4. The, still, undisclosed nature and designs of the mysterious genetically-determined master network systems responsible for regulating and harmonizing functions of all other biological networks of all body components.

5. The enigmatic nature and the, largely, unknown codes and rules of the predefined and pre-programmed frame of life that guarantees fulfillment of the essential requirements of optimal biological fitness of living creatures.

Meticulous study of biological networks represents an important and integral aspect in study of biology. Interpretation and analysis of basic information deduced from observing and analyzing structural designs and functional characteristics and dynamics of biological networks discloses and defines the basic framework within which life activities in living cells are initiated, adapted to physiological requirements, maintained, and terminated upon completion of their aims. More important, however, is the contribution of this information to proper understanding of the different mechanisms responsible for regulating and synchronizing the functions and performances of the vast spectrum of different network categories within the cell.

Study and analysis of the structural designs and the functional mechanisms of biological networks would have crucial and important impacts on many theoretical and applied aspects of biology, in general, and of medical sciences in particular. As regards medical genetics, these aspects include many diagnostic, therapeutic, prophylactic, biotechnological and theoretical applications. For example, discovering and defining the key pivotal structural and regulatory molecules within life-mediating networks, and along different pathways responsible for controlling functional dynamics of the network, represent an indispensable approach insistent for designing proper therapeutic approaches to diseases caused by network defects. This approach has been successfully adopted and resorted to since decades for treatment of many genetic diseases, e.g., enzyme replacement therapy for metabolic errors due to enzyme deficiencies and protein replacement therapy for protein deficiency disorders like immunodeficiency and hemophilia.

In a parallel way, defining key regulatory molecules of biological networks in normal conditions would have a pivotal impact on diagnostic approaches to diseases caused by qualitative and/or quantitative defects of these molecules. For instance, comparative analysis of normal profiles of these molecules with their profiles in specific disease conditions can point out defects leading to qualitative and/or quantitative abnormalities in their synthesis. Furthermore, in a way similar to the concept of reverse genetic engineering, categories of RNAs involved in translation and synthesis of these molecules and even abnormal/mutated genes involved in coding and defining their structural designs and functional roles can be detected and defined in ambiguous disease states caused by defective proteins coded by, still, undefined genes.

Within a global context, success in defining the whole proteome spectrum of specific cells would have a great and crucial impact on both diagnostic and therapeutic approaches to some dreadful human diseases that represent real challenges to researches aiming at their early diagnosis and effective treatment. If this goal can be achieved, early and accurate diagnosis of specific cancers, for instance, might be possible upon comparing the whole proteome of suspected malignant cells with their counterpart of normal cells. Comparative analysis of observed deviations of malignant proteomes might even disclose unapparent aspects of tumor progression and ongoing changes of the malignant phenotype more accurately and at much earlier stages than can be achieved by currently available traditional diagnostic techniques. This same approach might prove useful for other mystical disease conditions including, for instance, many neurological and autoimmune disorders.

Defining and characterizing biological networks and biochemical pathways responsible for mediating specific stages of embryonic and fetal development can have a great impact on prophylactic approaches aiming at obviating pathogenesis of congenital abnormalities caused by defective or deficient synthesis of structural proteins/catalytic enzymes of these networks and pathways. Achieving this goal necessitates, firstly, construction of normal developmental proteome maps composed by complete and accurate characterization of the structural components of the vast majority of these regulatory networks and pathways at different temporal stages of growth and development for different tissues and organs. Comparing databases of these normal developmental proteome maps with their counterparts of embryonic or fetal developmental maps for the same temporal stage of development of specific tissues or organs can offer an early and accurate diagnostic, and possibly prophylactic, approach to structural and/or functional congenital defects of tissues or organs with abnormal and deviant developmental maps. A major obstacle in this regard is the restriction imposed by the time limits that govern the transfer of embryonic/fetal cells to maternal circulation where they can be separated and analyzed.

Construction of genomic developmental maps composed of databases of expression states of genes/genome parts during specific temporal stages of development might prove to be the ultimate proper and effective approach for proper and accurate preparation/selection/engineering of specific stem cells suitable for replacement therapy of diseased tissues or organs in post-natal life. The genomes of stem cells are strictly organized under extreme and strict programming rules that regulate and define their final expression states at time of their formation during embryonic/fetal life and during their latency in post-natal life, as well. The specific genome of a specific stem cell comprises thousands of active genes and similar number of temporally, and spatially, imprinted inactive genes. This state of pre-programmed and pre-defined selective activation and selective repression of the genomes of stem cells occurs only within an exquisite environment comprising the actions of thousands of genes of the genome and their interactions with similar number of genes of other effector or regulatory genomes at specific times of growth and development, a situation nearly impossible to imitate in vitro or even in vivo in post-natal life. Proposed approaches to construct genomic developmental maps might prove useful in re-engineering the genomes of stem cells to render them capable of re-performing their roles during development in post-natal life.

Hypothetical aspects regarding possible impacts of studying biological networks on eugenics might become a field of research and experimentation in the near future. For instance, theoretical proposals aiming at improving human capabilities, fitness, and adaptation to drastic environmental conditions by genetic engineering techniques that can improve the performance and efficiency of native genomic and proteomic networks of human beings, can be formulated and rendered applicable for in vitro then for in vivo experimentation. Researches in this regard might be directed basically towards improving somatic characteristics of human beings via engineering human genome and proteome to acquire characteristics of genomes and proteomes of animals that have better somatic features and capabilities than human beings. For example, reengineering human proteome networks responsible for hearing or vision or smelling to mimic those of animals characterized by supreme capabilities of these senses might be tried, in spite of the short term eugenic consequences of such trials as they are limited by the short life span and relatively rapid turnover rates of engineered protein components of the proteome networks. Trials aiming at reengineering proteome networks, or genome networks, of human beings for eugenic purposes might seem attractive for many obvious reasons, but they implicate considerable risks that can neither be ignored nor tolerated for ethical, health, and medical reasons in view of the unique identity of the human race compared with identities of all other species. In view of the current state of vague and scanty knowledge available as regards the structural/functional/regulatory aspects of the human genome and human proteome, researches directed to disclose details of these aspects would represent the proper attitude towards defining the best diagnostic, therapeutic, and prophylactic approaches for human diseases.

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