A The cell: structural organization

Complex biology are highly organized assemblies of specialized cells. In spite of these differences, every cells re-publishing common an essential properties and also represent a “unit” in living organisms. They are surrounded by a plasma membrane, usage DNA together their genetic material, and employ the same basic mechanisms for power metabolism. There are two species of cells: the eukaryotic cell (which participates in the development of complicated organisms and also contains a nucleus, cytoplasmic organelles, and also a cytoskeleton) and the anuclear prokaryotic cell (bacteria), i beg your pardon lacks these components.

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To maintain integrity, cells are surrounded by lipid membranes that type a shell and also separate the cell interior from the environment (Figure 8.1). The principal structure blocks that membranes room phospholipids, which room amphipathic molecules consisting of two hydrophobic long fatty acid chains linked to a phosphate-containing hydrophilic head group. These molecules spontaneously form a bi-layer by orienting the fee head groups to interact with the bordering water, and also fatty mountain tails to kind a hydrophobic interior. In addition, the membrane the mammalian cells includes glycolipids and cholesterol, which boost the rigidity. Vital property of membrane is that they behave as 2D fluids and also their fluidity is affected by temperature and lipid composition.



Figure 8.1. Structural organization of the mammalian cell. The major elements room schematically indicated.


In mammalian cells, membrane not only segregate the cell interior from the environment however surround intracellular organelles. This facilitates substantial subcellular compartmentalization and allows mammalian cells to role efficiently. The biggest organelle is the nucleus, which harbors the cell genome (DNA) and is the site of warrior (RNA synthesis). Only the final stages the gene expression, the synthetic of proteins (translation), take location in the cytoplasm. Hence, the nucleus not just serves come store hereditary information however controls cellular responses. By separating the genome from the cytoplasm, post-transcriptional adjustments such together RNA splicing can take place before the messenger (m)RNA is transported to the cytoplasm, where protein synthetic occurs and also the accessibility of proteins to the genetic material is limited.

In contrast to bacteria, which lack a nucleus, this opens up novel methods for the regulation the gene expression in mammalian cells, including the selected transfer of transcription determinants from the cytoplasm come the nucleus. Another big organelle existing in multiple duplicates in the cytosol that mammalian cells room mitochondria, in which most of the cellular ATP is created by oxidation of small molecules. Therefore, mitochondria are pertained to as the “power plant” of the cell. A large network of interconnected membrane fastened tubules develops the endoplasmic reticulum (ER), which extends indigenous the atom membrane transparent the cytosol. The significant task that the ER is sorting of protein destined for secretion indigenous the plasma membrane. Polypeptide chains space translocated into the ER, where protein folding and also processing takes place. Native the ER, proteins room transported within membranous vesicles come the Golgi apparatus and further ceded to the cell surface ar membrane or room secreted.

In addition to the membrane-enclosed organelles, a network that protein filaments extends through the cytoplasm, creating the cytoskeleton and also providing an additional level of organization. The cytoskeleton offers a structural structure determining the cabinet shape and also cellular movements, including transport the organelles. In comparison to the strict implications, the cytosekeleton undergoes constant remodeling and also thus mirrors a very dynamic entity. There room three principal varieties of protein filaments: actin filaments, intermediate filaments, and also microtubules. Actin filaments are produced by head-to-tail polymerization the actin monomers creating a helical structure. Assembly and disassembly of these filaments is tightly regulated by actin binding proteins.

Upon communication with the engine protein myosin, actin filaments support a range of movements of cells. Intermediate filaments room polymers of different proteins expressed in various cell types and own a rope-like structure. They space not involved in moving movement, but provide mechanical support. Microtubules are created by reversible polymerization the tubulin in dependency of GTP hydrolysis. They are extended outward indigenous a centrosome and the mitotic spindle forms throughout mitosis the is responsible because that chromosomal separation. Two households of engine proteins, kinesins and dyneins, associate v microtubules and also promote movement and also positioning of oribel in the cytoplasm.


*

The overall scheme is a feedback cycle v two inputs: the goal, which stands for the preferred values of the system's necessary variables, and also the disturbances, which was standing for every the procedures in the environment that the mechanism does not have actually under control but that can affect these variables. The device starts through observing or sensing the variables that it desire to control since they impact its preferred state. This step of perception creates an interior representation the the external situation. The information in this depiction then have to be processed in order come determine: (1) in what method it may influence the goal and also (2) what is the ideal reaction to safeguard the goal.

Based ~ above this interpretation, the system then decides on an appropriate action. This activity affects some part of the environment, which in turn affects other parts of the environment through the normal causal procedures or dynamics of that environment. This dynamics are affected by the collection of unknown variables which we have called the disturbances. This dynamical interaction affects amongst others the variables the the mechanism keeps under observation. The change in these variables is again viewed by the system, and this again root cause interpretation, decision and also action, thus closing the regulate loop.

This basic scheme of manage may incorporate buffering, feedforward and feedback regulation. Buffering is implicit in the dynamics, which identify to what level the disturbances affect the observed variables. The it was observed variables must encompass the essential variables the the system wants to keep under manage (feedback or error-controlled regulation) in stimulate to avoid error accumulation. However, they will certainly in general also include assorted nonessential variables, to duty as early warning signals for anticipated disturbances. This implements feedforward regulation.

The components of this scheme deserve to be as basic or as complex as needed. In the thermostat, perception is just a sensing that the one-dimensional change room temperature; the goal is the set-point temperature the the thermostat tries to achieve; info processing is the trivial procedure of deciding whether the regarded temperature is lower than the preferred temperature or not; and action consists of one of two people heating, if the temperature is lower, or act nothing. The impacted variable is the lot of heat in the room. The disturbance is the lot of heat exchanged with the outside. The dynamics is the procedure by which within heating and heath exchange with the external determine inside temperature.

For a more complex example, us may take into consideration a board of director whose score is come maximize the long-term revenue of your company. Their actions consist of of miscellaneous initiatives, such together publicity campaigns, rental managers, beginning up manufacturing lines, saving on governmental costs, etc. This influence the basic functioning the the company. However this work is also impacted by factors that the plank does not regulate such as the financial climate, the tasks of competitors, the needs of the clients, etc. With each other these disturbances and also the efforts of the board determine the success that the company, i m sorry is indicated by variables such as amount that orders, working costs, manufacturing backlog, agency reputation, etc. The board, together a manage system, will interpret each of these variables with reference to your goal the maximizing profits, and also decide around actions come correct any type of deviation from the desired course.

Note that the manage loop is completely symmetric: if the system in Fig. 2 is rotated over 180°, atmosphere becomes mechanism while disturbance becomes goal, and also vice versa. Therefore, the scheme could likewise be taken as two interacting systems, every of i beg your pardon tries come impose its goal on the other one. If the two purposes are incompatible, this is a version of dispute or competition; otherwise, the interaction may settle into a mutually satisfactory equilibrium, providing a model of weaken or cooperation.

But in control we normally mean to suggest that one mechanism is an ext powerful than the various other one, qualified of suppressing any type of attempt through the other mechanism to i have loaded its preferences. To accomplish this, one asymmetry need to be developed into the regulate loop: the actions of the mechanism (controller) should have much more effect on the state of the environment (controlled) than the other means around. This can likewise be perceived as an amplification the the signal travelling with the regulate system: weak perceptual signals, carrying details but almost no energy, lead to powerful actions, delivering plenty the energy. This asymmetry can be achieved by weakening the affect of the environment, e.g., through buffering the actions, and also by increase the plot of the system, e.g., by giving it v a powerful energy source. Both instances are illustrated by the thermostat: the walls carry out the essential insulation from external perturbations, and also the fuel supply provides the volume to generate enough heat. No thermostatic regulate would be feasible in a room without wall surfaces or without power supply. The exact same requirements used to the an initial living cells, which essential a protective membrane come buffer disturbances, and also a food supply for energy.


This section deals with the finite-element modeling of several dynamic procedures that occur during embryonic development, such as cell division and migration. The sequence of occasions that begins with a single fertilized ovum and also culminates in a complex organism is quiet shrouded in mystery. The breaches in our knowledge span the fields of genetics, molecular biology, and biochemistry, as well as biomechanics. During the initial stage of development, the fertilized ovum, or zygote, undergoes cleavage by mitotic division to form a multicell aggregate, the blastula. Cleavage and cell department are putatively initiated by the formation of a contractile ring the actin microfilaments beneath the plasmalemma. In teamwork with molecule motors, the convulsion of ring induces the formation of a groove between the 2 nascent daughter cells and also eventually pinches castle off. This model was conceived throughout the critical century and has because been extended and refined <48>. Albeit so, the specific manner in i m sorry the cytoplasm divides during cell department is still a matter of debate, due to the fact that different mechanisms of ingression have the right to yield the very same end result (Fig. 11.7).



Several investigators have used finite-element modeling come test miscellaneous hypotheses. The reliability of this analyses depends, the course, on knowledge of the product properties of the cell in question and also on the border conditions. The physics properties that the target cells and embryos have thus been subjected to scrutiny, because that which objective the adhering to techniques have actually been employed: micropipette aspiration, atomic force microscopy, laser-tracking micro-rheology, needle poking, and magnetic twisting cytometry. In the embryos the sea urchins, a highly sophisticated finite-element simulation that the first cleavage has been created by He and also Dembo <48>. Their design simulated the flow of the hyaloplasm, the polymerization and also the depolymerization the the cytoskeleton, the friction existing between the cytoskeletal network and also the aqueous phase of the cytoplasm, and the viscosity and also the contractility that the cytoskeletal network. It has been used to probe several aspects of the cleavage process, such together the duty of cytoskeletal flow during the formation of the contractile ring and also the biomechanical nature of the latter.


As the process of cleavage continues and the total variety of cells increases, an nearly spherical blastula is formed, which at some point invaginates to productivity a gastrula (Fig. 11.8).



Several mechanisms have been proposed come account for the shape transforms that occur throughout gastrulation <49>. The study that was carried out by Davidson et al. Illustrates an especially well the great potential of finite-element modeling in this field. Utilizing optical sections through the blastula of Lytechinus pictus, the investigators modeled that is three-dimensional configuration. Since the product properties of the different materials of the epithelial template were not fully known, castle were set using worths that had been identified by various other investigators using assorted systems and methodologies, such as compression of the life cells between parallel plates, the suctioning that neutrophils and endothelial cells, and also the surveillance of low-frequency dynamic modulii in purified cytoskeletal components. The last epithelial template was then offered as a model to test 5 of the proposed instrument of invagination. By adjusting the mechanical properties the the various embryonic components, invagination can be achieved according to every of the experiment mechanisms. These simulations revealed each hypothesis to be characterized by a specific combination of mechanically properties. By identify the requisite material properties for various other prospective mechanisms, these could be reduced in number come the couple of that were crucial in the process of invagination. A comprehensive, biomechanically orientated evaluation of gastrulation in different types has been created by Keller et al. <50>.

In species with one axial concerned system, gastrulation is followed by neurulation, which entails the formation of the tubular rudiment the the nerve cord. Both gastrulation and neurulation indicate a folding and reshaping the the epithelial sheets that the embryo (Fig. 11.8). Back the outcomes that the tissue movements and the rearrangements that are associated in gastrulation and also neurulation differ, the basic mechanisms are probably comparable and subject to similar constraints. Because that this reason, identical modeling techniques have actually been offered to simulate every process. In 1993, Clausi and also Brodland <51> simulated neurulation using technique resembling that embraced for the modeling the gastrulation. The neuronal plate, namely, the part of the embryonic epithelium that gives rise come the neural pipe by neurulation, is composed of hundreds of cells. Due to the fact that the limitations of hardware would render impracticable the separation, personal, instance modeling of all cells, the investigators simulated small patches of these with like volumes. Each simulated patch had apical and also proximal contractile frameworks to mimic the actin and tubulin filaments. The neural plate to be simulated in both the dorsal and the transverse planes. Number of models to be established, each of which to be designed to check a details hypothesis appertaining come the pressures that drive neurulation and to gauge the susceptibility the the mechanical system to alters in the nature of the tissue. Finite-elements have likewise been supplied to research such embryological phenomena together cell sorting and also checkerboard patterning. If two different species of embryonic cell space artificially dissociated, randomly mixed, and also reaggregated, castle spontaneously combine to reestablish a meaningful homogeneous tissue. One explanation the this phenomenon is furnished through the theory of differential adhesion, i m sorry assumes cell movement to be pushed by differences in cell–cell adhesion (reviewed by Ref. <52>). The phenomenon could likewise be explained by the hypothesis differential tension, i m sorry was occurred by the finite-element modeling of mechanically interactions in between cells within multicell aggregates <53>. Follow to this model, microfilaments lie close come the cabinet surface have the right to generate a contractile force that would affect cell–cell adhesion <54>.


Göran Akusjärvi, in Encyclopedia the Physical science and modern technology (Third Edition), 2003

I Introduction

Expression of the hereditary information has actually been summary in the so-called main dogma, which postulates the the hereditary information in a cabinet is sent native the DNA to an RNA intermediary to protein. A major difference between basic and complicated organisms is the presence of a cell nucleus. Thus, prokaryotes, which encompass the bacteria and also the blue-green algae, do not have a nucleus, vice versa, eukaryotes, which encompass animals, plants, and fungi, have cells through a nucleus that encapsulates the DNA. The simple mechanisms to regulate gene expression in eukaryotes and prokaryotes are very similar, although eukaryotes usually use more sophisticated techniques to to express out an ext information native the DNA sequence. In prokaryotes on–off switches that transcription appear to be the vital mechanism to regulate gene activity, although other mechanisms likewise contribute come the control of gene expression: transcriptional attenuation, transcriptional terminations, and posttranscriptional effects. In eukaryotes similar mechanisms room in operation. However, a crucial difference in between prokaryotes and also eukaryotes is the substantial use that RNA handling to generate a mature mRNA. Thus, eukaryotic genes space encoded through discontinuous DNA segment that require a posttranscriptional tires to create a functional mRNA. As will be questioned later in this review, the requirement for RNA splicing may be a crucial to the development of a highly distinguished organism choose humans. The general postulate that one gene renders one protein was acquired from hereditary studies the bacteriophages and also does not use to higher eukaryotes. Due to the fact that of alternative RNA processing events a large portion of eukaryotic gene encode because that multiple proteins (see ar V).


Frank Dellaert, Randall D. Beer, in on Growth, form and Computers, 2003

20.1 Introduction

Development is crucial and integral component of biological evolution. Genetic transforms are not straight manifested in phenotypic changes, as is often assumed in population genetics, and in most autonomous agent occupational involving man-made evolution. Rather, facility developmental machine mediates in between genetic information and phenotype and also this has countless consequences. It provides robustness by filtering the end genetic changes (i.e. Part genetic changes make small or no difference to the last phenotype; over there is an equifinality come development). It also provides a natural method to shot out a spectrum of mutations, i.e. The same form of genetic mutation can create anything from no effect to a very huge effect in the phenotype, depending on when the affected gene acts during development. Furthermore, breakthrough provides a compact genetic encoding of complex phenotypes, permits incremental structure of facility organisms and supports symmetry and also modular designs.

For these reasons, over there is a farming interest in modelling development (Lyndenmayer and Prusinkiewicz, 1989; Wilson, 1989; Mjolsness et al., 1991; deBoer et al., 1992; Fleischer and Barr, 1994; Kitano, 1994). Countless ongoing initiatives aimed at including basic developmental models in evolutionary simulations deserve to be found in the literature (Belew, 1993; Cangelosi et al., 1993; Gruau and also Whitley, 1993; DeGaris, 1994; Kodjabachian and also Meyer, 1994; Nolfi et al., 1994; Sims, 1994; Jakobi, 1995).

Much that the latter work has concentrated on modelling neural development, however in biology, bodies and nervous equipment co-evolve. Body morphology and also nervous systems can constrain and shape one another. Somatic and also genetic determinants can interact and this occurs not only during development, however on an evolutionary range as well. Troubles posed by advancement can be addressed by a mix of body and neural changes. Permitting both body and also nervous system to co-evolve can carry out a smoother and more incremental route for an extensive changes.

Also, much of the existing work-related is extremely abstracted indigenous biological development (e.g. Utilizing grammars). While over there are an excellent reasons for this (familiarity, simplicity, computational speed, emphasis on performance no biology, etc.), too tiny is at this time understood about development to understand what space the ideal abstractions come make. Development fully transforms the framework of the room that is being searched. If we room lucky, this transformation will enable us come evolve amazing agents much more easily. However if we are unlucky, we could actually make the search trouble harder. Due to the fact that so tiny is right now understood around the all at once ‘logic’ of development, it is crucial that we explore numerous different level of abstraction to gain a feeling of the tradeoffs involved. Critical aspect the this expedition should it is in to discover developmental models that are an ext biologically reality in their straightforward structure 보다 the highly abstract models the have at this time been explored.

Thus, in this thing we current a design of advance that has actually been provided to evolve useful autonomous agents, complete with a morphological structure and also a neural regulate system. Earlier work that associated a much more biologically defensible yet more facility model is contrasted v a new and simplified technique that performs how amazing better. In the following section we provide a short overview that the general strategy that we have adjusted to model a developmental procedure for autonomous agents. That is usual to both models we comment on in the chapter. Section 20.3 gift a biologically defensible model of development, finish with a system for the development of a nervous system influenced by axonal development cones. The expressiveness that the model is demonstrated by means of a hand-designed genome, may be to straight the advancement of a functional and complete agent that can execute a simple task in a simulated world. In Section 20.4, we discuss a simplified version that addresses some of the problems of the previously model and also show that it have the right to be used to evolve functional agents native scratch. We display the example of an agent developed to execute a line adhering to task. Section 20.5 discusses some of the lessons we learned native this work and suggests some avenues for additional research.


Olaf Wolkenhauer, Allan Muir, in ideology of facility Systems, 2011

Preface

The structure of the essay is as follows:

Introduction: The intricacy of cell-biological systems has an “inherent” basis, concerned the nature of cell (large number and range of components, nonlinear, spatio-temporal interactions, constant modification that the components) and arises additionally from the method we have actually for examining cells (technological and methodological limitations).

Section 1: Ontological and also epistemological inquiries are intertwined: to examine the nature of living systems, we call for modeling and also abstraction, i beg your pardon in turns calls for assumptions and choices that will certainly influence/constrain what we deserve to know around cells. We research cells, organs and organisms in ~ a particular, liked level, are compelled to select subsystems/parts that a bigger whole, and also pick a minimal range of technologies to create observations. The examine of cell biological systems calls for a pragmatic form of reductionism and the translate of data and models is subsequently connected to a context. The framework to build (mathematical) models is solution theory.

Systems concept is the study of organization per se. When investigations right into the structural (material) organization of molecules and cells have dominated molecular and also cell biology to this day, v the appearance of solution biology there is a change of emphasis towards an expertise of the functional organization that cells and cell populations, i.e., the procedures (“laws” and “mechanisms”) that identify the cell's or organ's behavior. The need to pick a level and also subsystem, leads inevitably come a theoretical close in the concept of dynamical systems: by classifying observables into dependent, independent and also invariant persons (parameters) we attract a boundary in between an interior and also exterior.

The main challenge is then to rally a coherent whole from an (partial) understanding of that parts. We argue the this is only feasible through an iterative procedure of modeling, style of experiments, additional modeling and also so on, in which hypotheses about the entirety guide interim models.

Section 2: using systems theory to molecular and also cell biology, we seek an understanding of structural and also functional company of the subcellular and macroscale level. The cell's functional company at subcellular level can be grouped into three great of processes: gene expression, metabolism, and also cell signaling. This classification involves a selection of modern technologies for each class, causing an operational division.

Section 3: The conservation of genomic properties v evolution motivates the id of “model organisms”. Unfortunately, even the simplest version organism is very facility and us give examples of the handy considerations connected in knowledge so referred to as “pathways”. Not just are pathways, cells, guts or biology complex, the structures of knowing are an in similar way complex. The concept of a “gene” and the concept of a “pathway” are examples of devices for knowledge that develop. Our conversation highlights the prestige of discussing how we shot to make sense of monitorings in molecular and cell biology.

Section 4: with hundreds or thousands of materials that need to be thought about as gibbs in a pathway/network/subsystem, regardless of how innovative the modern technologies are, our cognitive an abilities and mathematical devices seem very restricted to two-dimensional visualizations and only a grasp of device variables. We slam the ide that methods of “artificial intelligence” can avoid thinking of the experimentalist — data execute not speak because that themselves. Mathematics modeling stays an art that (fortunately) cannot be automated.

Section 5: In systems theory objects and also relations between objects have actually identical ontological status. We emphasized above the focus on the cell's behavior (functionality) as a an effect of spatio-temporal interactions of molecules. At any type of level the a organism, that subsystems are interacting objects whose relationships and properties space largely determined by their duty in the whole. When we have the right to study a liver cabinet in isolation to investigate its stimulus-response behavior, we will certainly only recognize the cell's function completely by considering the cell and its setting as an undivided whole. The whole-part partnership emerges together a major stumbling block in handling the intricacy of cell organic systems.

Section 6: The cells an essential functions incorporate growth, proliferation, differentiation and also apoptosis. Mathematics modeling of any type of of these processes seeks simplifications to alleviate their actions to that essence, come extract a principle that serves together an explanation. Us argue that mathematical modeling is the arts of making appropriate assumptions, balancing important reductions/approximations due to experimental/methodological limitations with abstractions serving explanatory purposes. This is true for any level (atoms, molecules, cells, orgas, and organisms) and since at any level over there is another level above or below, every design is calculation macroscopic or phenomenological. While physics-style mechanial models of connecting mass points are not coherent in solution biology, the attribute “phenomenological” does not indicate arbitrariness in the building and construction of these models and also their explanatory strength — come paraphrase G. E. Box: every models space wrong, some room useful.

Section 7: In previous sections us highlighted the reality that living systems deserve to be investigated at different levels, but also processes in ~ subcellular and also macroscale deserve to be interpreted in terms of business levels (e.g. Gene expression, metabolic networks and also signal transduction pathways). The concept of a domain the autonomy for different levels, says a systems-theoretic frame to recognize levels the bounded autonomy together subsystems that can be studied in family member isolation, while keeping a opportunity to recognize the larger entirety from knowledge around domains of autonomy. A rudimentary body of theory exists and also we think further research right into such theoretical concepts and their applications in equipment biology can lead to helpful tools, taking us a little step additional in an effort to resolve the tight whole-part relationship debated in vault sections.

Section 8: while previous sections focused on dealing with complexity, the necessary reduction come subsystems will present uncertainty. The isolated check out of subsystems, the need of skipping observables, the inability to keep outside variables consistent in an speculative set-up, motivate stochastic design formalisms to capture uncertainty in kind of stochasticity. While this type of stochasticity emerges from epistemological considerations, development is an example of purposeful randomness (required to generate alternatives/variations). Us briefly discuss the semantics that deterministic vs. Stochastic models.

Section 9 concludes our conversation with a review of an essential points and also an outlook top top the field of solution biology. The tight whole-part relationship and also the fact that ontological aspects of molecular and also cell-biological equipment are linked with epistemological questions lets us finish that theorists of scientific research could actively contribute come the breakthroughs of the life sciences. There is a long background of dynamical and mathematical systems theory throughout which ideas of self-organization, emergence, feedback or system identification have been developed. Examining the difference between physical and also biological systems, in between living and non-living systems and also studying the way by i m sorry we have investigated together systems, could improve our chances of regulating the intricacy of cell-biological systems. In the indigenous of Ludwig Wittgenstein: “The fact that us can describe the activities of the people using Newtonian mechanics tells united state nothing around the world. The truth that us do, go tell united state something around the world.”


Exergy is characterized as the amount of work-related ( = entropy–free energy) a system deserve to perform as soon as it is carried into thermodynamic equilibrium through its environment. As a reservoir, recommendation state, the is valuable in ecology to select the exact same system however at thermodynamic equilibrium, i.e. That all materials are inorganic and also at the highest oxidation state, if sufficient oxygen is current (nitrogen together nitrate, sulfur together sulfate and so on); watch Fig. 1. The applications of this reference state means that one more exergy, various other than that usually used in engineering, is found. That is named ecoexergy to distinguish it from the technical exergy. The referral state will certainly in this situation correspond come the ecosystem there is no life forms and also with every chemical power utilized or as an ‘inorganic soup’. Usually, it means that we take into consideration T = To, and also p = po, which method that the ecoexergy becomes same to the distinction of Gibbs complimentary energy the the system and also the same system at thermodynamic equilibrium, or the chemical energy content included the thermodynamic info (see below) that the system. The ecoexergy becomes, v this definition, a measure up of how far the ecosystem is indigenous thermodynamic equilibrium, i.e. Just how much (complex) company the ecosystem has construct up in the form of organisms, complex biochemical compounds and also the complex ecological network. All procedures are irreversible, which means that exergy or ecoexergy is shed (and entropy is produced). Ns of ecoexergy and production that entropy space two various descriptions that the same reality, namely the all processes are irreversible, and also we unfortunately constantly have part loss of power forms that can do work-related to power forms the cannot do work (heat at the temperature that the environment) (see likewise Ref. <9>). So, the formulation the the 2nd law that thermodynamic by use of ecoexergy is: “All real processes are irreversible, which implies that ecoexergy inevitably is lost. Exergy and also ecoexergy are not conserved,” while energy of course is conserved by all procedures according come the an initial law the thermodynamics. Every transfers of ecoenergy suggest that ecoexergy is lost due to the fact that energy is transformed to warmth at the temperature the the environment. The ecoexergy the the system steps the contrast—it is the difference in complimentary energy if there is no distinction in pressure and temperature, as might be assumed because that an ecosystem or an ecological system and also its environment—against the neighboring environment. If the system is in equilibrium with the surrounding environment the exergy is, that course, zero.



This summary of ecoexergy advance in ecosystems provides it pertinent to evaluate the ecoexergy that ecosystems. That is not possible to measure up ecoexergy directly—but it is possible to compute it. Together the chemical energy embodied in the organic components and the organic structure contributes far an ext to the ecoexergy content of the system, there appears to be no factor to i think a (minor) temperature and pressure difference between the system and the recommendation environment. Under these circumstances we can calculate the ecoexergy content of the device as coming completely from the chemistry energy:


This to represent the nonflow chemical ecoexergy. It is identified by the difference in chemistry potential (μc – μco) between the ecosystem and the same mechanism at thermodynamic equilibrium. This difference is determined by the concentrations of the thought about components in the system and in the recommendation state (thermodynamic equilibrium), together is the situation for every chemical processes. We can measure the concentrations in the ecosystem, but the concentration in the recommendation state (thermodynamic equilibrium) can be based on the usual use of chemical equilibrium constants. If we have the process:


The concentration of ingredient A in ~ thermodynamic equilibrium is complicated to find, but we can, based ~ above the ingredient of A, find the concentration of ingredient A in ~ thermodynamic equilibrium native the probability of forming A native the inorganic components.


We find by these calculations the ecoexergy that the system compared with the same system at the very same temperature and also pressure however in the kind of an inorganic soup without any type of life, biological structure, information or organic molecules. Together (μc – μco) have the right to be found from the an interpretation of the chemical potential replacing tasks by concentrations, we gain the complying with expressions for the ecoexergy:


where R is the gas continuous (8.317 J/K mole = 0.08207 l atm/K mole), T is the temperature that the atmosphere (and the system; view Fig. 1), if Ci is the concentration that the i-th ingredient expressed in a suitable unit, e.g. Because that phytoplankton in a lake Ci might be expressed as mg/l or as mg/l the a focal length nutrient. Ci,o is the concentration of the i-th ingredient at thermodynamic equilibrium and also n is the variety of components. Ci,o is, the course, a very small concentration (except because that i = 0, which is thought about to cover the inorganic compounds), equivalent to a very low probability that forming facility organic compound spontaneously in an inorganic soup at thermodynamic equilibrium. Ci,o is even lower because that the various organisms, since the probability of developing the organisms is an extremely low through their embodied information, which means that the hereditary code have to be correct.


By making use of this particular ecoexergy based on the same device at thermodynamic equilibrium together reference, the ecoexergy becomes dependent just on the chemical potential the the numerous biochemical materials that are characteristic that life. This is continuous with Boltzmann’s statement, that life is the struggle for complimentary energy.

The total ecoexergy of an ecosystem cannot be calculated exactly, together we cannot measure the concentrations of every the contents or determine all feasible contributions come ecoexergy in an ecosystem. If we calculate the ecoexergy that a fox, for instance, the over shown calculations will certainly only give the contributions comes from the biomass and also the information embodied in the genes, however what is the donation from the blood pressure, the sex-related hormones and also so on? these properties space at the very least partially covered by the genes yet is that the whole story? We have the right to calculate the contributions from the dominant components, for instance by the use of a model or measurements that consists the many essential contents for a focal length problem. The difference in ecoexergy by comparison of 2 different feasible structures (species composition) is below decisive. Moreover, ecoexergy computations always give only relative values, together the ecoexergy is calculated loved one to the recommendation system.

As we understand that ecosystems as result of the throughflow of power have the tendency to move away indigenous thermodynamic equilibrium shedding entropy or getting ecoexergy and information, we have the right to at this phase formulate the adhering to proposition of relevance for ecosystems: “Ecosystems effort to construct toward a greater level of ecoexergy”.


In 1957, Turing <68> propose a mathematical design for morphogenesis, which explains the advance of complicated organisms indigenous a solitary shell. He speculated that localized peaks in concentration the a chemical substance, recognized as an inducer or morphogen, could be responsible for a team of cells developing differently native the surrounding cells. He climate demonstrated, with straight analysis, how a nonlinear reaction diffusion device like (1.3) might possibly create such diverted peaks. Later on in 1972, Gierer and also Meinhardt <21> prove the existence of such equipment numerically for the following (so-called Gierer–Meinhardt system)


Gierer–Meinhardt mechanism was provided in <21> to version head formation in the hydra. Hydra, an pet of a few millimeters in length, is consisted of of approximately 100,000 cells of about fifteen different types. It consists of a “head” an ar located at one end along the length. Common experiments top top hydra show off removing component of the “head” an ar and transplanting the to various other parts of the human body column. Then, a new “head” will type if and also only if the transplanted area is sufficiently much from the (old) head. This observations have actually led come the presumption of the presence of two chemical substances—a slowly diffusing (i.e., ε ≪ 1) activator a and a fast diffusing (i.e., D ≫ ε) inhibitor h.


To recognize the dynamics of (GM), the is valuable to consider an initial its equivalent “kinetic system”


This system has a unique consistent steady state a ≡ 1, h ≡ 1. For0τqr(p−1)(s+1) that is straightforward to check out that the constant solution a ≡ 1, h ≡ 1 is secure as a stable state that (ODE).

However, if∈D is small, that is not difficult to see that the continuous steady state a ≡ 1, h ≡ 1 that (GM) i do not care unstable and also bifurcation may occur. This phenomenon is typically referred to together Turing's diffusion-driven instability. (A basic criteria for this have the right to be found in Murray's publication <47>.)

There are countless other reaction–diffusion systems which exhibition Turing's diffusion-driven instability: they encompass Gray–Scott design from chemistry reactor theory, Schnakenberg model, Sel′kov model, Lengyl–Epstein model, thomas model, Keener–Tyson model, Brusselator, Oregonator, etc. For introduction and discussion on these basic Turing models, we refer to the publication <47>. A survey of math modeling of biological and chemical phenomena using reaction–diffusion systems is provided in <38>. Mathematical modeling of trends in biological morphogenesis using extensions of GM version are discussed in <36> and <48>.

Several common qualities of Turing type reaction–diffusion systems include: first, they space nonvariational, i.e., they do not have actually Lyapunov or power functional so standard variational (or energy) an approach cannot it is in applied; second, they room noncooperative, i.e., they execute not have actually Maximum ethics so sub-super-solution technique cannot it is in applied; third, they support finite-amplitude spatial-temporal fads of exceptional diversity and also complexity, such as steady spikes, layers, stripes, spot-splitting, travel waves, etc. (See <63>.) The research of these RD systems not only rises our knowledge on Turing patterns, but likewise induces brand-new tools and also techniques to address other problems which might share comparable characteristics.

The most amazing phenomena connected with (GM) is the presence of secure spikes and stripes. The numerical studies of <21> and an ext recent those of <31> have revealed the in the border ε → 0, the (GM) device seems to have stable stationary solutions with the building that the activator concentration is localized roughly a finite number of points in Ω¯. Moreover, as ε → 0, the pattern exhibits a “spike great phenomenon” through which we mean that the activator concentration is localized in narrower and narrower regions approximately some points and also eventually shrinks come a certain variety of points as ∈ → 0, vice versa, the maximum worth of the activator concentration quarter to +∞.

Such type of point-condensation phenomena has generated a many interests both mathematically and biologically in current years. The objective of this chapter is come report top top the present trend and also status of such researches (up to June, 2006). We shall not give most that proofs. For more details, please view the references and also therein.

In the study of spiky patterns (or concentration phenomena), two an essential methods emerge. The an initial one is the so-called “Localized energy Method”, or LEM in short. LEM is a combination of timeless Lyapunov–Schmidt reduction technique with variational techniques. This is a really useful device to construct remedies with miscellaneous concentration behavior, such as spikes, layers, or vortices. The second technique is the so-called “Nonlocal Eigenvalue problem Method”, or NLEP in short. This deals with eigenvalue difficulties which room nonselfadjoint. The plays an essential role in the examine of security of spike patterns. In this survey, i shall show these two methods in details in the hope the they may discover applications in other problems.


Andres Kriete, in Biosystems, 2013

6 Body size as a source for robustness

Complex organisms space not just optimized v respect to a power of forced traits and also control mechanisms, but also in regards to physical and physiological structure and also function. This optimizations contribute to lifespan together a measure of robustness. Lifespan for individuals in a course of types is variable, contributing to the stochastic nature that aging (Herndon et al., 2002) and is figured out by many failures bring about a catastrophic breakdown, and the procedure of aging rises the opportunity for an unified failures come occur. However, median lifespan is quantifiable in populations, which deserve to be used to define one border of the viable state an are in which every organisms reside. Typical lifespan have the right to by to express by allometric scaling laws, which define a biological property in relationship to body mass (Mb) and also a scaling exponent α. The exponent takes multiples of 1/4 power, such as basal metabolic price (α ~ 3/4), DNA and also nucleotide substitution rates (α ~ 3/4), densities of mitochondria and also ribosomes (α ~ −1/4), and also heart rate (α ~ −1/4), to surname a few, and also has been amended by finite size corrections (Savage et al., 2008). West, Brown and also Enquist (West et al., 1999) had actually reasoned that the geometry and function of it is provided networks (vascular tree, branching in bronchial tree that lung, hepatic, renal, neural but additionally intracellular systems) space at the root of such relationships. It is renowned in physiology that in the style of branching supply systems boost of cross-sections in branches rises the all at once volume of the tool to be transported, while palliation in cross-sections boosts resistance, hence there is a physics optimum i m sorry minimizes transport connected costs. In organisms such relationships provide networks for optimized distribution, room filling, and also minimization of power dissipation to invariant finish units (cells) constraining your metabolism, leading to performance gains with enhancing body size (West et al., 2003). Because that mammals, allometric scalings extend over 7 assignment of magnitude in mass, from shrew (2 g) come whale (200 t), the end of 27 orders applicable to biology (West and Brown, 2005). Sports in lifespan because that mammals, within a total variety of 3 orders of magnitude, shows an evolution optimization the structural and also functional properties specifying one border for robustness in mammalian state space.


For mammalian expectation the exponent α is about 1/4, indicating boost of lifespan through body size and also an absolute predictor for organism robustness in terms of lifespan potential (RabsLS) is proportional to:


This measure up is inversely related to metabolism every unit weight per day (specific metabolic rate), which is greater in the computer mouse (133 kcal kg−1 day−1) than it is in elephants (7.4 kcal kg−1 day−1), identify the price of aging decline. Interestingly, the thickness of mitochondria scales through a an unfavorable exponent (Mb−1/4), which deserve to be directly linked with development in lifespan identified by a hopeful exponent (Mb1/4) (Kriete et al., 2006).


One characteristics of allometric scaling legislations is the emergence of invariant quantities, which consists of heartbeats per life time for mammals or total variety of turnovers in the respiratory complexes. Similarly, we deserve to express a loved one measure the robustness (RrelLS) by basal power consumed every uni-mass the an animal over its expectancy potential:


This expression for loved one robustness of expectancy is invariant and approximately 2 × 105 kcal kg−1 lifespan−1 for every mammals. Types with comparable relative robustness belong come the same optimality class. Rise of robustness in biological and technical solution is no only restricted to the optimization the traits and also control mechanisms, however can also be achieved by modularity, decoupling and also redundancy (Kitano, 2004). The over defined invariance demonstrates the body size acquired by enhancing the overall variety of cellular systems in conjunction v optimized supply systems is a redundancy resource for mammals, which boosts lifespan by reduce the (per cell) metabolism, improving energetic efficiency and also lessening several of the damaging effects occurring from cellular specialization.

However, adding redundancies becomes raising burden for the mechanism as a whole and also benefits are not farming linearly as an ext and more resources room being added. Because that instance, environmental niches because that very big animals space sparse and also such animals would be constrained by accessibility of nutrients and risk extinction despite increased metabolic efficiency, which constitutes population-level tradeoffs and reduces the thickness of larger varieties (Clauset and Erwin, 2008). While body mass and also base metabolism end up being factors identify longevity, the environmental conditions and also their changes, and the carefully tuned balance of properties inherited genetically constitute added factors influencing the rate of aging and lifespan. This introduces a variance around the allometric regression line, reducing its right (R2 value), but not that is statistical definition (p value). Varieties diverting from the best-fit line space of major interest to inspection genetic and environmental factors contributing come aging, such together the bat or naked mole rat in mammals. The lengthy lifespan in humans, exceeding loved one robustness by around three times end the predicted mean value, arised only recently by improved living conditions, hygiene, clinical support and nutritional balance. In enhancement to environmental problems the procedure of aging is affected by identifiable proteins and pathways promoting longevity (Li and de Magalhaes, 2011) and also further modulated by hereditary variants deciphered in long-lived centenarians. These variants appear to introduce a buffer – or robustness – against the detrimental impact of age-related disease genes (Bergman et al., 2007; Christensen et al., 2006; Sebastiani et al., 2012) and may indicate strategies for healthy and balanced aging.

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D. Guidolin, ... L.F. Agnati, in Biosystems, 2019

Abstract

The rather recent (at the very least on the evolution time scale) development of nervous systems in facility organisms allowed the living beings to build a wide-ranging design of the external human being in order to predict and also evaluate the outcomes of their actions. Together a procedure likely represents a real coding activity, since, by suitable handling the information, the generates a mapping in between the exterior environment and also internal cerebral task patterns. The trends of neural activity that correspond to the final maps, however, arise from the holistic assembly of a multilevel useful organization. Nerve tissue components, indeed, show up organized in compartments, additionally called useful modules (FM), the contain device components and circuits of different miniaturizations not only arranged to job-related together one of two people in parallel or in series but also nested within every other. At least three levels have the right to be known in a functional module and also it is feasible to point out that such a hierarchical organization that the brain circuits might be mirrored by a equivalent hierarchical company of biocodes. This function can additionally suggest the theory that the exact same logic might operate also at mechanism level to incorporate FM into functional mind areas and to associate locations to generate the last map provided by humans to image the outside world and to imagine untestable worlds.