Biology – biocab.org

The classical definition of Biology is:

Biology is the science of life.

A more realistic and accurate definition of Biology is the reductionist definition:

Biology is the natural science that studies the no-spontaneous transfer of energy and the quasi-stable systems that experience it.

Now that we have inferred a realistic definition of life, things will go easier. My definition of life is based on careful observations about the behavior of the state of equilibrium in biosystems.

In general, we knew that life was related to the thermodynamic descriptions assigned to the evolution of the universe.

Thus, many things that the theory of life had not elucidated now are solved. For example, the origin of life, when the inert coacervates, or primitive protobionts, were converted into bionts (living beings), why currently living beings do not emerge by non-biological synthesis; if a virus is or it is not a living being; the meaning of biological death, etc.

IMPORTANCE OF BIOLOGY

Biological disciplines imply a significant responsibility for the protection and welfare of all living species. The knowledge about the diversity of life forms and their conservation-exploitation is of great importance for our day by day life.

Have you gotten sick some time? Well, all we have got ill some times and in order that our doctor was able to accomplish a good diagnosis from our illness, he or she had to be familiar with the normal organic functions that we consider within the homeostatic parameters. This normal state, or homeostasis, is investigated by Biology.

The study on the origin of diseases and plagues is also answerable by means of Biology, for example the etiology of cancer, infections, functional problems, the damage to fruits, the pathologies of farm animals, plants, trees, etc.

Food resources and quality, factors that cause illnesses, plagues, sustainable exploitation of natural resources, the enhancement and development of useful species, the discovery and production of medicines, the study of the functions of living beings, their inheritance, etc., all are fields of research through Biology.

The food that we consume are materials produced by living beings, the Biology studies the living beings and the processes implied in the production of those nutritional substances. Besides, by means of the Biotechnology, the Biologists search for methods that make to the producers to be more efficient in the elaboration of food and other supplies for humans.

The Biology covers the study of all the living beings and their interactions into the biosphere. This it is a very important task because we are able to know the behavior or functioning of each population when it faces to other individuals from other populations or communities and how the populations or the specific sectors of the biosphere are affected and/or benefited by that behavior or functioning of the populations into a community..

The Biology also investigate the environmental factors that surround the living beings; and, by means of conservationism, it seeks for more effective ways to understand the variations or new conditions of the environment that can threaten the existence of living beings on our planet.

WHAT IS LIFE?

The interaction of charged particles, electrons and protons, through uncharged particles, expressly through photons, determines the positions and momentums of the energy during the performance of the Proton Motive Force.

Life is a delay of the spontaneous diffusion or dispersion of the internal energy of the biomolecules towards more potential microstates.

An operational definition is a description of a variable, a term, or an object in terms of the specific process or the set of corroboration assessments used to determine its existence and quantity. The properties described by an operational definition should be publicly accessible so that one or more persons other than the person that defined the concept- can measure it or test it independently at will, for themselves.

An operational definition is generally designed to model a conceptual definition, to be precise, by using words and concepts to describe a variable.

Phase Space is the space at which all the possible states of a system are represented. The phase space is produced by the general positions and their corresponding conjugated moments.

A conjugated moment derives from the difference between the kinetic energy and the potential energy in relation to an integral coordinate.

Delaying is not the same as revert; although revert could cause a delay, it is not the behavior of processes or states in nature. Many authors say that life involves a violation of the second law of thermodynamics, or that it follows trajectories against entropy, which is not factual. The referred law indicates that the energy always flows from a space or system with a high density of energy toward another space or system with a lower density of energy, which is precisely how life occurs. The Universe has a higher density of energy than that of the biosystems. If it were not thus, then life would not be possible.

The confusion was originated when some properties associated with the entropy were subordinated like alternatives to explain biotic features; for example, order, complexity, etc. However, to acquire order or to be more complex, the biosystem should transfer disorder toward the Universe and it has to take complexity from the Universe. Seen in this way, there is not any violation at the second principle of thermodynamics, every time that the biosystems are more disordered than the Universe and its disorder flows from the most disorderly system (the biosystems) toward the less disorderly system (the Universe). The major order of the Universe -as a whole- in contrast with any of its components, is specified by the theory of the energy density of the Higgs fields.

Given that life implies a state of the energy, it is precise that we know what energy is. Energy is the capability to do work, that is to say, a function of the quantifiable properties of a provided system.

Another term used in the conceptualization of life, essentially important for its formulation, is Quantum Energy. The term refers to the sum of the kinetic energy and the potential energy in a particle, which can be fermions or bosons.

The quantum energy (to be precise, the energy contained by a particle or a quantum) is proportional to the frequency of the electromagnetic radiation at which that particle of energy corresponds.

The formula to obtain the value of the quantum Energy is E = h f, where E is the quantum energy of a photon, h is the constant of Planck (6.626 X 10e-34 J.s) and f is the frequency of vibration of the radiant energy.

In the operational definition of life I used the concept of internal energy: internal energy of a system is the energy associated to the movement of the molecules in a thermodynamic system, that is to say, the energy subordinated to the temperature of such system. In an energy transfer, the internal energy of a biosystem is the energy that has already been transferred through the real or imaginary limits of that system (toward the inside of that system). For example, a multicellular biont has an external protector cover that isolates it partially from the environment. Each cell of a multicellular biont has a membrane or a wall that constitutes its real limits. There are organelles, as mitochondria, chloroplasts, etc. into each cell that have their own membranes as real limits, etc.

In the definition of internal energy I avoided to mention the words disorderly, random and chaos in relation to the molecular movement because the movements at a mesoscopic level are determined by microscopic fundamental laws that can be formally described by the mathematical notions of natural phenomena; therefore, the molecular movements are not chaotic, disordered or accidental. A small variation in the initial conditions can produce a change in the displacement of the particles, whether that we perceive or not that microscopic oscillation or the law that governs it.

What we call quantum state is the position, movement and energy density that follow a wave trajectory in discrete magnitudes or quanta. In this case, we refer to particles -like the fermions and the bosons- that establish the function of distribution of the energy in the intervals of delay in the spontaneous transfer of that energy.

The fermions are particles that have an intrinsic angular momentum that, calculated in units of Spin, is equal to an odd number from a fraction (1/2 or 0.5, 3/2 or 1.5, etc.) and that obey at the Exclusion Principle of Pauli. The fermions cannot coexist in the same position. Fermions are particles that comprise matter; for example, electrons, quarks, leptons, protons, neutrons, etc.

On the other hand, the bosons are particles whose angular momentum is always a whole number (0, 1, 2, 3, etc...), then, they do not obey the Exclusion Principle of Pauli and can coexist in the same position. For example, photons, gluons, particles w- and w+, gravitons, etc.

Angular Moment of Spin refers to the presence of angular momentum in an elementary quantized particle and not to a rotational movement. The magnitude of the spin of a quantized particle is obtained by the relation,

L = s (s + 1)

Where is the Reduced Plancks constant [ = h/2 = 1.054572 x 10-27 g-cm^2/s] and s is an integral or a non negative half-integral.

h = 6.6260693 x 10-34 J.s

p = 3.1415926535897932384626433832795

Energy Density is the quantity of energy stored in a given system, or in a spatial region expressed per mass or volume units. For example, the liquid Hydrogen has an energy density of 120 MJoules per kilogram. The glucose has 17 MJoules per kilogram, etc.

A spontaneous process is that in which the energy always is dispersed toward more potential microstates. By this, when I talk about life, I am referring to no-spontaneous processes. For a spontaneous process to occur, it is not required the aggregation of energy of the environment, but of the transfer of energy toward the environment (exergonic process). In contrast, the life processes are endergonic, that is to say, processes that requires of the input of energy from the environment, or no-spontaneous processes.

In the definition of life I also introduced the concept of interval. An interval is a subset of states situated amid an initial state and a final state.

Finally, the quantum state of the energy in a biotic system is established by the flow of fermions and bosons that possess a quasi-stable density of energy during the transfer and storage of the energy through limited periods of time. For example, in the process of Transquantum Thermal Biotransfer of photosynthesis we study the positions, density and movements of the internal energy of a boson (photon) and of the fermions (electrons and protons) implied in the successive biotransfer of the energy freed by that boson. In the Transquantum Thermal Biotransfer of fermentation we study the density and the movements of the internal energy of the fermions, etc.

When we examine particles of matter, or with mass, we can only study a kind of particle, a given position or a given movement at once. Similarly, on studying the functions at some stage in the transfer and storage of the energy we can only study a function at one time. Once we have completed the study of each particle and each function, we integrate immediately the whole set to formulate the complete process.

CHARACTERISTICS OF LIVING BEINGS:

ORGANIZATION: The living beings present a functional and structural organization. Both, structure and function, are narrowly interrelated.

The organization of the structures and the linkage of their function distinguish to living beings from inert beings more than an upper order or exceptional complexities. The molecules self organize to construct cells, the cells to form tissues, the tissues to form out organs, the organs apparatuses and systems, and the assembly of all the interconnected systems makes an individual. There are individuals that are constituted by only one cell, for example bacteria, protists and some fungi (for example yeasts and molds); however, although in quantity and/or volume a multicellular organism possesses more matter, they will not be more complex or more ordered than a unicellular individual.

It is feasible to find well organized inert beings, by which we need to include other contextual-to-life characteristics. The observation of the whole set of characteristics permits us to distinguish between living beings and inert beings. The other characteristics that will help us are Reproduction and Evolution, although we even can find well organized inert beings that self reproduce and evolve, there is another characteristic that an inert being cannot cover, the no-spontaneous manipulation of the energy to continue getting it from the environment.

REPRODUCTION: Reproduction is the characteristic of living beings that permits the individuals to make replicas of their kind. Although some organic molecules are able to make replicas from themselves, they lack of the other characteristics of living beings.

Life only proceeds from life, the living beings cannot be originated from inert matter. This is a biological axiom called Biogenesis.

The continuity of life depends on the transmission of the hereditary characteristics, which is based on the DNA molecules.

EVOLUTION: Living beings interact with their environment. As the environmental conditions change, the organisms have to adapt to those changes. The evolution refers to the changes that should occur in the organisms so that they adapt to the changes of the environment.

So that those changes in the organism be considered in the context of the evolutionary adaptation, they should occur in the DNA. In this way, the change will be inherited to the progeny.

Then what are the differences between inert thermodynamic systems and living thermodynamic systems?

The last should be explained by an example: Consider an inert system to confront a selective pressure from the environment, for example, a protein exposed to a temperature of 50 C. As an inert system, it will experience a phase transition to a phase known as denaturalization, or it will go through a phase of disintegration. These will be limited spontaneous trajectories available for the inert thermodynamic systems to evolve as a reaction before a pressure from the environment. It will be determined by the universal spontaneous tendency towards equilibrium.

Now consider a living thermodynamic system, for example a bacterium. As the bacterium is exposed to 50 C, she will respond through many spontaneous mechanisms for defending herself from the hostile variation in her environment to continue being alive. One of them is by adopting a macrostate denominated spore; another way consists of a biochemical adaptation to that condition by producing proteins that will help her to tolerate higher temperatures. Another trajectory will be by trying to elude the area where the pressure takes place, etc. As we can see, the living thermodynamic systems also bear the spontaneous tendency towards equilibrium, but they can block the tendency by longer periods than inert thermodynamic systems can, because the inert beings permits without restraint the spontaneous increase of its available microstates.

Nevertheless, all of this is ambiguous and exhausting. Indeed, there is only one sure difference between living beings and inert beings:

Living beings are able to set no-spontaneously (autonomously) a transitory quasi-steady sequence of intervals that delays the spontaneous transference of thermal equilibrium by means of inner operators.

LEVELS OF ORGANIZATION IN BIOLOGY

The biologists do not come to an agreement on this issue. Many of them say that the levels of organization in Biology begin with the cell; however, the best part of the authors thinks that the biological levels begin with the molecules. Well, anyway, the knowledge does not hurt; then, we will begin with the study of the molecules.

We can see a Biological order in every organism in the world, and we can find levels of organization from the atoms to the largest living thing. The atoms are organized to form molecules, the molecules to form cells, the cells to form tissues, the tissues to form organs, the organs to form apparatuses and systems, and these form the whole called an organism, a group of individuals that share the same genetic characteristics (of one species) forms a population, a group of different populations forms a community, the communities interact with their environment to constitute an Ecosystem, the sum of all ecosystems and communities on Earth is the Biosphere. The biosphere is the largest level of organization in biology.

MOLECULAR LEVEL: Atoms from the same kind (element) or from different kinds (compound) link to form a molecule.

There are some elemental molecules in nature formed by only one atom (monatomic molecules), like krypton, argon, helium, neon, xenon, etc. Nevertheless, most molecules are formed by two or more atoms (like hydrogen, oxygen, sugar, oil, amino acids, etc.).

When different atoms combine to form molecules, we call them compounds. A typical example for a compound is the water. Water is formed by one atom of oxygen and two atoms of hydrogen.

There are two kinds of compounds: Organic compounds and inorganic compounds.

Organic molecules have carbon atoms in their structure, while inorganic molecules do not have carbon atoms. Living things' structures are built with organic compounds; this is to say with carbon based molecules:

CHEMISTRY OF LIFE

Living beings are constituted by matter.

Matter is a form of energy which has substance and mass, and occupies a portion of space.

Matter is constituted by minuscule aggregates of stored energy known as particles which stack together to form larger particles called nuclei. Nuclei attract and capture other particles identified as electrons, which are placed into orbital layers surrounding nuclei, and form atoms.

Atoms are the structural units forming all matter configurations existing in the known Universe.

An element is a substance constituted by atoms of the same species; for example, carbon, iron, zinc, calcium, hydrogen, etc. A compound is a substance that is constituted by two or more species of atoms; for example, water (H2O), carbon dioxide (CO2), sulfuric acid (H2SO4), etc.

From 92 known natural elements, only 25 elements are found in living matter. From those 25 elements, four elements, Carbon, Oxygen, Hydrogen and Nitrogen, are present in 97% of life molecules. The remaining elements represent only 3% of living matter, being Phosphorus, Potassium, Calcium, and Sulfur the most important.

The main organic compounds are:

a) Carbohydrates

b) Lipids

c) Proteins

d) Nucleic Acids

CARBOHYDRATES

The carbohydrates, or Hydrates of Carbon, are organic molecules constituted by atoms of Carbon, Oxygen and Hydrogen. Carbohydrates also are called Saccharides, Glycids, or Sugars.

The basic formula for carbohydrates is CH2O. We can distinguish three kinds of carbohydrates: Monosaccharides (one saccharide), Disaccharides (two molecules of saccharide) and polysaccharides (three or more molecules of saccharides).

PROTEINS

Proteins constitute more than the 50% of cells' solid matter. Proteins are the more complex and functionally more versatile among biomolecules, as for cell composition, because proteins form structures like membranes, micro fibers, skeletons, cilia, flagellums, etc., as for functions like storage of energy, transportation of other substances, signaling, protection, hormonal functions, etc. Proteins also are a critical part of all metabolic processes because they work as enzymes, which are proteins that selectively accelerate or slow down chemical reactions.

Proteins are formed by sub units called amino acids. Amino acids are organic molecules composed by two groups, one carboxyl group and one amino group. The general formula for an amino acid is as follows:

C2H4O2N-R

R means a chain of one or more atoms of Carbon, which can combine with other elements, as H, O, P and S, but that are not part of the carboxyl group.

Example of aminoacids:

Amino Group-----> H - N - C - C = O <-----Carboxyl Group

GLYCINE (Gly)

There are 20 amino acids in nature from which all proteins are built. Polymers constructed by two or more amino acids, joined by peptide bonds, are called polypeptides.

Important proteins for living beings are enzymes, hormones, Collagen, Chlorophyll and Hemoglobin.

CELLULAR LEVEL

Molecules are highly organized to build structural membranes (organelles), which possess specific functions, according to the materials with which they are formed.

BIOMEMBRANES AND CELL WALLS:

Cells have a watery medium called cytosol that contains the necessary factors for their survival. This internal cellular environment should be maintained segregated from the external environment to avoid the chemical changes that, if that barrier did not exist, would occur spontaneously, ending in the disorganization of the whole system.

The internal environment of the cells should be maintained in a quasi-stable state because the capture energy and its biotransfer are highly specific. If the internal environment of the cell remained unprotected, e.g., when the cell membrane or the cell wall rips open, the cell dies immediately because the compounds disaggregate into the external medium being separated from other biomolecules with which they interact. Besides, many biomolecules change or lose their biotic properties and their organization when remaining exposed to the action of the environmental factors or under unstable conditions.

All cells have biomembranes that segregate their internal environment from the surroundings. Bacteria have a single membrane and a peripheral wall made of peptidoglycan (proteins + oligosaccharides). Both structures, the membrane and the wall, enclose the cytosol. Some bacteria have an outer single membrane, a transitional wall and an external single membrane. All eukaryotic cells own an external bilayered phospholipidic membrane. The eukaryotic plant cells own the bilayered phospholipidic membrane and an outer cell wall made of cellulose.

The prokaryotic cells do not have membranous organelles, although their membranes have invaginations that extend into the cytosol. Those invaginations determine certain functions, like the secretion of substances and the synthesis of DNA and RNA.

The plasma membrane is constituted by a phospholipidic bi-layer with proteins incrusted through it from outside to inside. Imagine the cell's plasma membrane as an avocado sandwich, in which the two slices of bread are the "heads" (hydrophilic) of the phospholipidic bi-layer, and the avocado represents the "tails" (hydrophobic) of the phospholipidic bi-layer, one layer is fixed to the other by the tails. To complete our sandwich, we insert olives from one side to another, and some fragments of toothpick incrusted in the upper slice and other fragments in the lower slice. Olives represent important protein membrane structures identified as permeases.

Permeases are enzymes that transport substances across the cell membrane, whether forward or outward the cell and they are highly specialized in their function. Besides, cell membranes operate as containers and as a protection for the cytoplasm.

Toothpick fragments represent carbohydrates, glycoproteins, and glycolipids.

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Biology - biocab.org