BOTANY VOLUME 1 - CELL BIOLOGY. ANATOMY. MORPHOLOGY - 2007

INTRODUCTION

Botany as a Biological Science

Botany is the science of plants. This name was coined by Dioscorides (1st century AD), who used it to denote The Study of (medicinal) herbs. In fact, the Greek word "botanē" originally meant a grass, specifically any forage or useful plant. The general Greek term for a plant, however, is "phyton"; hence, it has repeatedly been proposed to name plant biology "phytology," contrasting it with zoology as the science of animals.

METABOLISM/2.html">THE CONCEPT OF "plants" originally encompassed all organisms whose Cells contain, alongside a true Cell Nucleus with a membrane and multiple Chromosomes, Plastids. These are either present as Chloroplasts or can develop into them under appropriate conditions. Chloroplasts are Organelles (cellular Organs) that perform Photosynthesis, i.e., The conversion of light energy into chemical energy and the associated synthesis of Organic compounds (carbon assimilation). Green plants are photolithotrophic (photoautotrophic). In contrast to animals and all other heterotrophic (chemoorganoheterotrophic) organisms, green plants do not require organic Nutrition.

Traditionally, Fungi are also included in the plant kingdom, even though they lack plastids. Fungi are heterotrophic and obtain their nutrition either from dead organic material (saprotrophically) or from living organisms (parasitically). (The authors use the older term "saprophytic" here. In scientific literature, including Russian, the term "saprotrophic" is now increasingly preferred. Indeed, the word "saprophyte" implies a plant that feeds on dead matter. Since many of these organisms are no longer considered plants—specifically fungi—the more inclusive term "saprotroph" was introduced, meaning simply "one that feeds on dead matter." — Trans. note) Evolutionarily, fungi are closer to animals, but they share certain features with plants, such as vacuoles within cells enclosed by a rigid Cell wall, and the uptake of nutrients in dissolved form.

Among unicellular organisms (protists), the distinction between plants and animals is problematic. Within flagellates, sometimes even within the same genus—that is, among closely related species—there are forms without plastids and forms with chloroplasts, designated respectively as zooflagellates and phytoflagellates (e.g., Euglena, Fig. 1). In Bacteria and archaebacteria (archaea), any meaningful assignment to either the plant or animal kingdom is altogether impossible. These organisms possess cells that are generally smaller and structurally much simpler than the cells of all animals, fungi, and plants, even unicellular ones (Fig. 2). Bacteria and archaebacteria lack a true cell nucleus; neither nuclear nor Cell Division occurs here in the manner found in other organisms, and phototrophic forms lack plastids, etc. Therefore, the cells of these groups are sometimes called protocytes in contrast to the eucytes of all other organisms. Bacteria and archaebacteria, as prokaryotes, are contrasted with eukaryotes (plants, fungi, animals, and all protists with a true cell nucleus). In the modern (recent) living world, there are no transitional forms between pro- and eukaryotes.

Class="center">Fig. 1. Euglena gracilis (after G. F. Leedale)

Fig. 2. Comparison of prokaryotic and Introduction/5.html">Eukaryotic Cell sizes: A—bacterial cells from a hay infusion (enrichment culture of hay bacillus); B—cells of a moss leaf (Mnium undulatum); three Characteristic Features of The plant cell can be noted: cell walls, chloroplasts, and central vacuoles. Both photographs are shown at the same magnification (380x). Under dark-field illumination, only those cellular structures that scatter and refract side-incident light are visible

This is a eukaryotic unicellular Organism possessing chloroplasts, which produce paramylon—a substance structurally similar to starch—as a reserve product. The locomotor flagellum emerges from the "gullet" (anterior reservoir). Its movements are controlled by a light-sensitive organelle (the red stigma, often incorrectly called an eyespot, coupled with a photoreceptor on the short, non-moving flagellum). A cell wall is absent. Contractile vacuoles ensure Water excretion. Euglenas are capable of both swimming and crawling, undergoing profound changes in shape during locomotion (2100x).

Nevertheless, the earliest eukaryotes evolved from prokaryotes. The study of microscopically small organisms—both eukaryotic and prokaryotic—is the domain of a specialized biological science: microbiology. This field also encompasses Viruses, which are subcellular systems positioned on the boundary between the living and the non-living.

Despite all the differences between prokaryotic and Eukaryotic cells, they share numerous fundamental features, and even more are shared between the cells of higher animals and plants, which often exhibit completely different shapes and Functions. Everywhere we encounter similar classes of molecules, and

many core functions of living systems are conserved across all organisms. The same holds true for numerous genes (heredity factors). This reflects the fundamental unity of All living organisms, evidencing their common descent; all extant organisms apparently evolved from a single common ancestor (monophyletic origin).

What is Life?

As living organisms ourselves, we have a direct connection to the fundamental question of biology: what is life? Yet, answering this question turns out to be quite difficult. While every living system possesses a specific set of properties, it is only the totality of these attributes that allows us to distinguish the living from non-living systems or structures. Let us outline the classic characteristics of life.

• Chemical composition. The dry mass of all living organisms is dominated by Proteins, Nucleic Acids, Polysaccharides, and Lipids. In addition, There is a large, heterogeneous pool of other organic molecules and ions. Complex organic molecules, particularly macromolecules, are synthesized in nature exclusively by living organisms (Biosynthesis via specialized catalysts called Enzymes).

• Complex structured systems. Life is invariably associated with living organisms. Even simple entities are distinguished by complex structures of a systemic nature. This means that Molecular and supramolecular components are functionally interconnected and coordinated with one another. Only through their proper interaction—that is, cooperatively—can they perform the functions that sustain the living state. None of the individual components, let alone isolated substances, would be capable of this on its own. A system is fundamentally more than just the sum of its parts, and life is always a systemic activity. Below the level of cellular Organization, independent life does not exist: cells are elementary organisms. They invariably contain information-bearing structures, a complete Complement of necessary enzymes, and are delimited from the environment by selectively permeable membranes. (This does not contradict the fact that in most multicellular plants, tissue cells are interconnected by plasmodesmata—cytoplasmic channels through cell walls—forming supracellular symplasts.)

• Nutrition. Viewed from the perspective of energy and Entropy changes, the existence of living organisms might seem highly improbable. They consist of energy-rich, unstable molecules; the high Structural and functional orderliness of living organisms corresponds to a low entropy level. Maintaining this labile state is possible only through a continuous influx of energy. Consequently, living systems are fundamentally open systems, meaning they take in energy-rich photons or chemical substances and release energy-depleted substances (e.g., CO₂, H₂O; an analogy being a candle flame). Energy Metabolism is inextricably linked with material metabolism (metabolism). Metabolism does not lead to stationary equilibrium. Rather, it continuously maintains a non-equilibrium state (dynamic equilibrium with irreversible partial processes). Metabolism and Energy Exchange make it possible to couple the energy-demanding biosynthetic processes of organism-specific (macro)molecules (anabolism, assimilation) with energy-yielding processes—the capture of solar energy and/or The breakdown of energy-rich compounds (Catabolism, dissimilation). The low entropy content of living organisms is maintained by releasing (dissipating) excess entropy into the environment. Only as dissipative structures can living organisms avoid the destructive chaos that threatens them. Thus, "life" is ultimately not a state, but always a process. While the external form of organisms often changes quite slowly, a continuous reorganization takes place at THE MOLECULAR LEVEL through the replacement of degraded substances with newly synthesized ones (turnover).

• Movement. Every actively living organism and every individual cell is capable of movement. To be sure, many cells/organisms can enter a resting state, forming structures such as seeds, spores, or cysts. During such stages of latent (dormant) life, not only are any movements undetectable, but all other manifestations of life are temporarily suspended.

• Irritability and responsiveness. To maintain their viability, all organisms and cells are equipped with specialized receptors to perceive environmental signals and respond to them with appropriate reactions. The Diversity of the corresponding mechanisms is extraordinarily vast.

• Development. Living organisms are incapable of permanently maintaining a once-achieved Structure. No organism looks identical across different phases of its life cycle. A new cell resulting from division grows up to the size of the mother cell (growth). Multicellular Organisms initiate their individual development in most cases from a single cell (a fertilized egg—zygote; or a spore). Through cell proliferation, they attain their definitive size, accompanied by changes in their external appearance. Development into a sexually mature multicellular organism involves morphogenetic processes. At THE CELLULAR LEVEL, this is manifested by the fact that initially identical embryonic cells acquire increasingly distinct characteristics (differentiation).

• Reproduction. Successive generations consist of interconnected life cycles. Through reproduction, life persists despite the impossibility of permanently maintaining a specific developmental stage in individual specimens and despite the inevitable death of every individual in many multicellular organisms. This constitutes The final stage of ontogeny. "Physiological death," in contrast to "catastrophic death," is frequently driven by internal causes resulting from the execution of a genetically predetermined self-destruction program. Conversely, organisms can arise exclusively as descendants of similar ancestors. Spontaneous generation (The Emergence of living systems from non-living matter) is currently extremely unlikely on Earth and has furthermore never been documented: omne vivum e vivo (all life comes from life). This now self-evident principle has not always been accepted

as such. For instance, prior to the groundbreaking research of L. Pasteur and G. Hoffmann in the mid-19th century, it was widely believed that microorganisms (as well as fungi and worms) could spontaneously arise in decaying and fermenting liquids (a notion disproved by experiments involving the Sterilization of Nutrient media).

• Reproduction. Reproduction is typically associated with an increase in the number of individuals. Only in this way is the continuation of a species possible, despite various losses caused to a greater or lesser extent by environmental impacts. Everywhere we observe very high rates of reproduction (especially in small organisms). Under optimal conditions, bacterial cells often divide every 20 min. This means that if reproduction goes completely unimpeded, a single cell can produce within just two days a progeny whose volume would reach that of the entire Earth. In larger organisms, The rate of reproduction is generally significantly lower, which is why the life of each individual is better protected by various kinds of adaptations.

• Heredity. Individual development proceeds more or less identically across a succession of generations. The Genetic information of all cellular organisms (PROKARYOTES AND EUKARYOTES) is contained in The sequence of bases (NUCLEOTIDES) of deoxyribonucleic acid molecules (DNA). We are referring here to linear or cyclic macromolecules consisting of two strands (double-stranded DNA, dsDNA). In viruses, genetic information may also be transmitted via a single-stranded DNA molecule, as well as through Ribonucleic Acids (RNA, consisting of one or two strands).

• Evolution. The copying (Replication) and subsequent transmission of genetic information are carried out with high precision; however, over a sequential series of several generations, changes may arise that are inherited (Mutations). Over a long period of time, populations exhibit significant differences among individuals, which subsequently have varying chances of leaving offspring. According to the theory of natural Selection, established in 1859 by C. Darwin and independently by A.R. Wallace, forms that are increasingly adapted to preserving the species constantly accumulate in nature. This leads to Changes in the characteristics of species representatives and, ultimately, to the emergence of new species: evolution, phylogenetic development (phylogeny).

The capacity for reproduction inherent in all organisms can apparently be regarded as the most crucial criterion of life. All other characteristics represent either preconditions or consequences of this central property. In all organisms, genetic information contains the developmental blueprint for a highly complex molecular machinery whose primary function is self-reproduction. Life (at least on present-day Earth) can only be proven and conceived as a continuum. This is emphasized by the irreversibility of individual death and the extinction of species.

Mathematician J. von Neumann developed a general theory of self-replicating systems. The "Neumann machine" comprises four components: (1) devices for producing all system elements; (2) the information necessary for this; (3) a multiplying device for the precise reproduction of (2); (4) a regulator for the corresponding sequence program of all individual processes. The joint functioning of these four components leads to cyclical processes in which the system reproduces itself. A living cell is a Neumann machine¹.

¹ In our country, under the supervision of Academician V. B. Kudryavtsev, a theory of cellular automata based on the same principles has been developed. — Editor's note.

Origin and Evolution of Life

The modern (recent) living world is the result of an unimaginably long evolution. Based on natural radioactivity and the COMPOSITION OF THE most ancient rock formations, the age of the Earth is estimated at 4.6 billion years. The Study of the remains of various organisms (fossils: paleontology) in deposits of different ages shows that in earlier epochs of Earth's history, plants and animals lived here that were distinct from modern ones. Phyletic continuity is manifested in the fact that the floras and faunas of past epochs are less similar to the modern world of organisms the further removed they are from us in time. Larger multicellular organisms appear only toward the end of the Precambrian (approx. 570 million years ago). Prior to that, unicellular organisms dominated, and among them, prokaryotes above all. Indications of extensive cyanobacterial mats already exist from the Archean (>3 billion years ago): deposits of such age in Australia and South Africa contain layered stromatolites up to 30 cm and more in size. These are characteristic biogenous deposits that are still formed today in warm water bodies by dense formations of phototrophic cyanobacteria and other organisms (cyanobacterial mats).

How could life have arisen? Biology attempts to approach this fundamental question through experiments that reproduce (model) the conditions that presumably prevailed on primordial Earth¹. A prerequisite for The formation of the simplest self-replicating systems was the presence of organic (macro-)molecules. In contrast to the present day, organic compounds could have arisen abiogenically on the still-hot primeval Earth. Alongside water vapor, the early atmosphere contained primarily carbon dioxide and nitrogen, presumably also minor proportions of reducing gases, but practically no free oxygen. Consequently, there was no ozone layer to absorb the energy-rich ultraviolet radiation of the Sun. Under such conditions, various organic compounds could form spontaneously. Even in aqueous mixtures of carbon monoxide, hydrogen sulfide, and metal sulfides—such as those expelled by deep-sea hydrothermal vents—acetic acid and energy-rich thioester bonds between molecules can arise abiogenically. Such compounds apparently accumulated in certain locations on the primeval Earth, especially since living organisms that would consume them for nutrition did not yet exist, preventing their destruction through oxidation.

¹ Experiments simulating the conditions under which the first organic molecules arose were first conducted in our country by Academician A. I. Oparin. The theory described here belongs to him. — Editor's note.

Purely speculatively, the simplest cells—roughly like those of living saprotrophic Mycoplasmas (see below)—are already so complexly structured that their emergence from a chaotic mixture of molecular components As a result of a single chance event seems utterly improbable. However, the Origin of the simplest self-replicating systems can be explained, at least speculatively, as a sequence of hypothetical intermediate stages: the multistage hypothesis. If the necessary individual steps of this prebiotic evolution were sufficiently small, the probability of them occurring over very long periods of time becomes quite high. Some molecules that could have arisen abiogenically possess enzymatic activity, i.e., they act as biocatalysts. Certain RNA molecules (ribozymes) can thereby catalyze certain Chemical Reactions on their own and, together with heavy Metal Ions, even direct their own reproduction, albeit in a very imperfect manner ("RNA world"). The decisive step toward life proper was taken when efficient and precise Nucleic Acid Replication became possible with the participation of protein catalysts, while the synthesis of these protein enzymes began to be carried out based on the information encoded in nucleic acids. Thanks to this dual progress, which presumably resulted from many individual minor steps, a mutual relationship between proteins and nucleic acids emerged, forming The basis of all life in its modern form. Now there was a Genetic Code for translating nucleic acid sequences into polypeptide sequences of proteins, and a Separation of the Gene (hereditary factor) and the phen (trait arising on the basis of hereditary information) took place.

While the abiotic formation of organic molecules was taking place, the first reproduction-capable systems—hypothetical progenotes—and the prokaryotes that eventually evolved from them could live organotrophically. However, with the progressive consumption and exhaustion of organic nutrient sources, phototrophic forms began to come to the fore, including those that split water during photosynthesis and released oxygen. As a result, the atmosphere became increasingly oxidizing, creating the prerequisites for a significantly more efficient acquisition of energy from organic substances via cellular Respiration. At the same time, an ozone layer formed in the stratosphere¹, which began to absorb the intense mutagenic ultraviolet radiation of the Sun and thereby made the colonization of land possible.

¹ The emergence of the ozone layer is a later event than the emergence of respiration. Calculations show that 0.2% O₂ in the atmosphere is sufficient for respiration (Pasteur point), whereas 1–2% O₂ is required for the Formation of the ozone layer. — Editor's note.

Fossil finds from the long Precambrian evolution are, of course, rare and correspondingly fragmentary. However, by comparing PROTEIN AND NUCLEIC acid sequences, one can establish the degree of kinship among modern organisms and reconstruct the course of evolution. The more the sequences of corresponding proteins, DNA, and RNA differ, the earlier the last common ancestors of the organisms being compared must have lived. Changes during the course of evolution could occur at varying rates across different (particular) sequences; therefore, to reconstruct early phylogeny, researchers select sequences (or sequence regions) that change very slowly and remain largely similar even in completely dissimilar modern organisms. From a comparison of such highly conserved sequences, it can be concluded that the divergence of archaea and bacteria occurred more than 3 billion years ago¹. In modern eukaryotic cells, plastids and Mitochondria (the organelles of photosynthesis and cellular respiration, respectively) possess their own genetic information and synthesize a portion of their own proteins. They can arise only from like entities and thus occupy a (semi-)autonomous position within eukaryotic cells. Furthermore, they exhibit numerous prokaryotic properties, such as their mode of division and details of chemical composition. At least plastids are evidently the descendants of once-free-living bacteria that invaded primitive eukaryotic cells more than a billion years ago as intracellular symbionts and gradually evolved into cell organelles (endosymbiotic theory).

¹ These quantitative estimates are derived based on the assumption that mutations in genes occur uniformly over time. The THEORETICAL FOUNDATIONS OF DNA sequence comparison were laid by Kimura (Japan): the neutral theory. — Editor's note.

Remains of multicellular macroorganisms are found only in deposits no older than a billion years. Such organisms are exclusively eukaryotes. Their evolution, which is becoming increasingly reconstructible thanks to paleontological data, likewise proceeded primarily through the interplay of random mutations and direction-Setting selection (selection theory, Darwinism). It is believed that evolution is the result of the summation of countless minor changes (gradualism). Macroevolutionary aromorphoses (major evolutionary transitions) also occur constantly, differing not in their mode of Implementation, but rather in their effect compared to gradual evolutionary changes. Although aromorphoses occurred significantly less often than other gradual evolutionary steps, they had far-reaching consequences. Evidently, reproductive units that had previously developed independently gradually became enclosed within increasingly larger and significantly more complex structures. As a result, entirely new systems emerged that could become starting points for evolutionary lines of a different type.

A clear example of such a major transition is the emergence of multicellular organisms from unicellular ones during evolution. An individual cell, which prior to this transition constituted a complete organism, becomes merely one of many elements of the whole body in multicellular organisms. Selection acts no longer on individual cells as before, but on the overall supra-cellular system. If it dies, all its cells die with it. By integrating into a larger system that ensures stable living conditions, cells largely lose their independence. The system as a whole determines, for example, the division of individual cells, their specific functions, and their lifespan in performing diverse tasks. In doing so, an important function of such systems is realized: the "division of labor" takes place. In multicellular organisms, individual cells can specialize to perform specific tasks, while the remaining cells do not participate in them. As a result, not only can particular processes of important metabolic pathways be carried out with greater efficiency, but synergistic potentials can also be utilized more fully. During further phylogeny, differentiated cells or entire Tissues increased or decreased in quantitative terms, and they could move within the overall system like modules (Building Blocks of a "constructor") or be recombined anew. Such combinatorics, given a relatively small number of differing elements, fosters The Development of an almost infinitely large number of diverse systems. This is associated with the extraordinarily large diversity of species and forms of macroorganisms that surround us.

Other major evolutionary changes are associated with Symbiosis. Through the close cohabitation of unrelated organisms, fundamentally new systems with a higher level of organization can arise. The aforementioned endosymbiotic theory is a good example of this. In light of the symbiogenesis theory, Eukaryotic cells are not actually single cells; they should be viewed as mosaic entities resulting from the intracellular symbiosis of Cells of the most ancient eukaryotes ("urkaryotes") with bacterial cells. The hypothesis is even discussed that the first eukaryotic cells, in turn, were the result of a symbiosis between archaebacteria and eubacteria.

The Boundaries of Life

The question of the boundaries of life has a twofold meaning: on the one hand, as a question concerning the Limits of the distribution of living organisms, and on the other hand, as a question concerning the smallest or largest living organisms. The first aspect forms the Subject Matter of ecology; one can say that, despite the exceptionally great

age of adaptation mechanisms, the general requirements of living organisms remain within very narrow limits. They are determined primarily by water content maxima and minima, Temperature, and light. The optimum for most organisms lies in the range of moderate temperatures (10–40°C) and high water availability. Accordingly, foodstuffs can be preserved from decomposition by various organisms in a usable state in a refrigerator (particularly a freezer), or by drying (legumes, grains, flour, bread, pasta; hay), or by heat sterilization (milk...). In the wild, particularly cold and dry regions are sparsely populated or completely lifeless. At the same time, resting stages of many organisms can survive at temperatures close to absolute zero, whereas vital functions become impossible at temperatures ranging from 0 to -10°C. Temperatures up to 100°C and higher, which occur in only a few places on Earth (hot springs, volcanoes), can, conversely, be habitable for thermophilic organisms. Some archaebacteria have a temperature optimum around 100°C; this capability may have been preserved as a relict from the earliest times of Earth's history. Since phototrophic organisms serve to a large extent as the sole producers of organic material (biomass)¹, life is predominantly restricted to well-lit areas of the land surface and oceans. The Earth is covered by a relatively thin layer of the biosphere. The latter constitutes less than a hundredth of a percent of the Earth's volume.

¹ There is evidence that chemoautotrophic organisms play a significant—and perhaps even greater than photoautotrophs—role as producers of organic material, being particularly widespread in the deep waters of the world's oceans. — Translator's Note.

Particularly large organisms are found among fossil and extant vertebrate forms (dinosaurs, baleen whales), coniferous and deciduous trees (even in a significantly greater number of species and individuals)—though this is less noticeable at first glance—among interconnected clones of certain plants (e.g., Lombardy poplars, reeds, bracken fern) and fungi. Tree giants (sequoias, cryptomerias, certain eucalyptus trees¹) simultaneously possess the greatest mass. (Despite their enormous mass, giant whales do not have such a high density; their weight is compensated by buoyancy.)

¹ There is evidence that certain specimens of Douglas fir (Pseudotsuga menziesii) reach the greatest heights—up to 145–150 m. — Translator's note.

For theoretical biology, the question of how small living organisms can exist is more important: where does the lower limit of complex self-reproducing biosystems lie? The smallest cells possess a prokaryotic organization. They are found in mycoplasmas. The diameter of these cell wall-deficient Prokaryotic Cells is on the order of 0.3 µm; their DNA can encode only about 500 different proteins. This is close to the minimum required for DNA replication, the realization of the genetic information contained within it, the maintenance of heterotrophic metabolism and energy, and a simple cellular structure (approximately 350 genes). For comparison: typical bacterial cells have a diameter on the order of 2 µm and contain over 3,000 different proteins; the diameter of most eukaryotic cells, meanwhile, falls within 10 and 100 µm, and they can produce up to 30,000 and more different proteins. The fully sequenced genome of thale cress (Arabidopsis thaliana) contains about 25,000 genes, which is 11,000 more than in Drosophila.

Viruses have a significantly simpler organization than mycoplasma cells, and most of them are also much smaller. However, a virion (virus particle) is not a cell. While even the simplest cell contains both DNA (as the carrier of genetic information) and RNA (for its realization), a virion possesses only a single type of nucleic acid: either DNA or RNA. The nucleic acid is often associated with just a single type of protein, as in the tobacco mosaic virus (TMV, Fig. 3), or it is surrounded by a protein coat (capsid) consisting of a single protein or a few different proteins. The viral capsid formed in this way often exhibits crystalline Symmetry. Viruses, including (bacterio)phages (viruses that infect prokaryotic cells), only partially meet the criteria of life. They do not carry out metabolism and energy conversion, lack the intrinsic ability for replication and Protein Synthesis, and therefore cannot reproduce independently. They perform this function solely by utilizing the metabolism and energy of living cells, making them Obligate Intracellular Parasites (“borrowed life”). Outside of living cells, virions, which serve as the dispersal form, are lifeless organic systems.

Fig. 3. Tobacco mosaic virus (TMV) (electron micrographs A – F by F. Amelunxen; B – by C. Weichan)

Under Electron Microscopy (EM), virus particles appear as rod-like structures. The virion contains a helical RNA molecule along which, in undamaged virions, 2,130 identical protein molecules are arranged in a row, each consisting of 158 amino acid residues. The central axial channel formed by the RNA helix is clearly visible in these negatively stained preparations

The simplest Levels of organization are achieved by Viroids — infectious nucleic acids (RNA) devoid of accompanying proteins. These very short circular RNA molecules do not encode any proteins. Among viroids, there are dangerous plant parasites.

Despite their particularly simple organization, VIRUSES AND VIROIDS cannot be considered as ancestral forms of life, since their reproduction presupposes the presence of living cells. Rather, they are genetic elements that may have partially separated from their host cells (selfish genetic elements). In fact, many (and likely all) eukaryotes and prokaryotes possess segments of genetic information that either inherit independently of the main gene-bearing structures (chromosomes, genophores) or can, at least temporarily, detach from them. This heterogeneous group includes, on the one hand, Plasmids of many bacteria and certain eukaryotes, and on the other hand, so-called insertion sequences and Transposons (“jumping genes”).

Biology as a Natural Science

Living nature impresses us first and foremost with the immense diversity of organisms. The study, description, and systematic arrangement of all currently living and extinct species of organisms constitute a vast, never-to-be-fully-completed task of biology, primarily of systematics. However, the goal of biology is not limited to merely registering what exists; rather, researchers strive to uncover the regularities underlying this diversity. Alongside ordinary observation and comparison, experimentation plays a role here — the observation of processes under artificially created or varying conditions. Admittedly, the results of experiments or observations provide only the raw material for constructing hypotheses and theories, i.e., for elucidating causal relationships. (H. Poincaré: “Science is built up of facts, as a house is of stones — but a collection of facts is no more a science than a heap of stones is a house.”) By discovering regular interrelationships and ultimately formulating them as natural laws, countless data from special observations can be generalized and comprehended in a concise, intuitive form. Without this abstraction, intellectual penetration into the real world, with its fundamentally immeasurable Abundance of structures and events, would be impossible. Only the discovery of natural laws enables the understanding of natural states and processes (explanation), the prediction of events, and, finally, the rational application of scientifically achieved results. Upon this rests the colossal importance of the natural sciences in our time. Modern biology occupies a special place in this regard (keywords: biotechnology, Genetic Engineering).

The sum of established natural laws (not isolated data!) and their interpretations creates the scientific worldview — a simplified reflection of nature in concepts, symbols, and mental models. This worldview is the highest expression of our knowledge of nature. It allows us to perform mental operations (thought experiments) that would be costly, dangerous, or altogether impossible in the real world. The scientific worldview is inherently open (dynamic), meaning that with the progress of research and new interpretations, it is constantly expanding and changing; therefore, it inevitably remains provisional and fragmentary in character and can never be regarded as final. Nevertheless, it is simultaneously the best that humanity has at its disposal in this field. The fragmentary Nature of the scientific worldview is connected not only with arbitrary — though not always conscious and acknowledged — boundaries of scientific objectives (e.g., the absence of aesthetic, ethical, and transcendental parameters), but also with methodological limitations, above all the mode of seeking new knowledge. Such a search in foundational research, aimed at understanding the world rather than changing it and mastering it, may be indirect, since the goal (the ultimate result) is not known in advance. In indirect searches, testable attempts at explanation are made in the form of hypotheses (from Greek hypothesis — a supposition). However, a hypothesis, or generally a scientific concept, may prove incompatible with so many consistent data that the number of supporting facts remains negligible compared to the infinitely large number of conceivable contradictions. Conversely, a universal statement (generalization) can be refuted by a single contradictory result (the Asymmetry of verification and falsification: K. R. Popper). The assertion “All roses are red” cannot be proven even by the existence of a thousand red roses, but is disproven by the existence of a single yellow or white rose.

Correlations express regular relationships at the level of observable phenomena (e.g., cigarette smoking/Lung Cancer; stork frequency/birth rates in certain localities). Correlations may, but do not necessarily, imply a causal relationship. If variables B and C correlate, then B may be the cause of C, or vice versa. However, B and C may also share a third, hitherto unconsidered variable A as a common cause; in that case, although they correlate, neither is causally linked to the other. Thus, while an absence of correlation indicates a lack of causal relationship, even a statistically significant correlation does not yet serve as proof of it, i.e., it cannot constitute verification of the corresponding assumption.

Due to the asymmetry of verification and falsification, cognitive progress is achieved not through a direct path, but indirectly by refuting inadequate hypotheses (the trial-and-error method). The goal — veridical knowledge and explanatory understanding — can be attained only through disappointment and roundabout paths (the Greek word “methodos” signifies not only “thorough investigation” but also “a roundabout way”).

Of course, with each failed attempt at falsification, the probability increases that the hypothesis is correct, especially if it can be successfully applied to experiments from other scientific fields conducted independently of it. Generalizing hypotheses that, despite many attempts, have not been falsified are treated as theories. Theories are elements of the scientific worldview. Starting from a given theory (e.g., The Theory of evolution, which is central to biology), a multitude of data can be explained. Based on a scientific theory, numerous experimentally testable propositions can be formulated. In scientific-theoretical terms, a theory represents a disciplinary matrix — a paradigm — which establishes the intellectual framework for further experimental work in the respective field. Since purposeful observations and deliberate experiments can be conducted only on the basis of hypotheses or theories, a large part of research is surprisingly non-inductive (i.e., it does not originate from experience nor lead directly to veridical understanding), but rather deductive. Above all, these experiments are not aimed at discovering the unexpected and new, but serve to Supplement or re-examine a previously established paradigm. Of course, even theories considered “reliable” and universally accepted occasionally turn out to be falsified. In such cases, a new, more comprehensive theory must be found. However, such scientific revolutions (L. Fleck, T. S. Kuhn) succeed only when the new theory is able to explain why its predecessor accounted for so many facts. It often turns out that the old theory remains valid within certain boundaries that were not initially recognized. The history of scientific biology contains many Examples of such revolutions, notably the development of Cell Theory and genetics.

The arguments presented here form a part of epistemology (the theory of the possibilities and limits of human cognition), which occupies a central position not only in the theoretical natural sciences but also in philosophy (e.g., in I. Kant). For a long time, it remained a puzzle why there exist experience-independent logic, mathematics, and other disciplines that nevertheless apply universally to living nature. (A. Einstein: “The most incomprehensible thing about the world is that it is comprehensible.”) This puzzle was fundamentally resolved by the evolutionary theory of knowledge originating from biology (K. Lorenz, G. Vollmer, and others): even statements of logic and mathematics that are independent of individual experience (a priori) are ultimately based on experience that was, in fact, accumulated during hominid evolution over many generations and, through constant confirmation, was eventually genetically fixed¹ because it conferred a powerful selective advantage.

“¹ One might argue with the German author here, since logic is embedded in The structure of language. Language is a system for the non-genetic transmission of information from generation to generation. The capacity for logic and mathematics is developed through training. — Ed. note.”

The Special Status of Biology

The special position of living organisms in nature corresponds to the special status of biology among the natural sciences. The question is frequently raised whether living systems are governed by laws different from those operating in inanimate nature, and special vital forces are often postulated (vitalism). At the same time, to this day, no case has been found where Physical and Chemical laws fail to operate among living organisms. On the other hand, however, an incredible complexity and systemic character are introduced into the world of living organisms, so that biology manifests regularities observed nowhere else. We are speaking of emergent properties. An important consequence of The complexity of living systems is that The Essence of biology cannot be grasped logically or through mathematical Methods in the same way as the objects of physics and chemistry². Admittedly, biology is essentially an exact nomothetic (law-seeking) natural science, yet observation, description, and comparison play a significantly larger role in it than, say, in physics. The complete reduction of all biological phenomena to the laws known from chemistry and physics, as demanded by consistent reductionism, remains an illusion in any case.

“² Such a contrast between biology and physics/chemistry seems debatable to us. On the one hand, a large degree of “unsaid” remains in the complete mathematical and logical description of objects in chemistry and physics (otherwise theoretical research in these sciences would cease). On the other hand, biologists still strive insufficiently to understand the living through logic and mathematics, which is why the corresponding sections of the “Mathematics of Living Systems” are still underdeveloped. — Ed. note.”

In characterizing living organisms as self-reproducing systems, we approach another point that elucidates their special status: biological teleonomy. Living organisms behave purposefully, react adaptively, and appear intelligently designed. Alongside the question “why?” (causality), the question “what for?” (finality) is also meaningful and legitimate in biology (and among the natural sciences, only in biology). This is ultimately grounded in the cyclical development of living organisms (cf. The concepts of “developmental, reproductive, or generational cycles”). Starting from a given initial state, these cycles lead, along genetically determined developmental pathways, back to similar initial states (e.g., unicellular forms, spores). As a result, quasi-cyclical chains of events and causal chains emerge. For example, a certain developmental state B arises not only as a consequence of the preceding state A, but also via subsequent states C, D... and simultaneously acts anew as a cause for repeated (even if not temporally ordered) manifestations of A. The finalistic mode of consideration thus appears in biology almost on an equal footing with the causal one. In inanimate nature, cyclical processes (e.g., oscillations) lack mechanisms that would compensate for losses due to damping processes and ultimately reach a state of rest¹. By contrast, living organisms are even able to increase their population numbers during reproduction.

“¹ On the macro-level, the inanimate nature of the Earth has not yet reached a state of rest: the water cycle (river flow and glaciers), plate tectonics, atmospheric currents apparently served as the prerequisite for THE ORIGIN OF life on our planet. — Ed. note.”

Biology also occupies an unusual position among the natural sciences when studying evolution and the origin of life. While physics and chemistry primarily reveal regularities characterized by regular repetitions of structures or processes, here singular, chance events often play a decisive role. This is connected with the reproduction and selection of organisms. Natural Mutations are random events — singular and unpredictable. If a mutation leads to favorable consequences for its carrier, then, according to the theory of selection, it confers advantages repeatedly in successive generations. Living organisms “function” in this respect as extraordinarily potent amplifiers: many (all?) of the heritable traits observed in them originate from extremely improbable and correspondingly rare random events (singular occurrences) which, however, subsequently spread and became amplified extraordinarily through reproductive processes. It is quite possible, for instance, that the origin of life or the “discovery” of The Genetic Code — which exhibits virtually no deviations across all organisms — were based on singular events fixed during the course of terrestrial life and massively replicated through organismal reproduction. The ORIGIN AND EVOLUTION of life are prime examples of deterministic chaos which, although governed by laws and not devoid of causality, is neither predictable nor fully understandable due to determining random events.

Animals and Plants

After overcoming (more historically than objectively) the specialized division of science into zoology and botany, modern biology is dominated by an interdisciplinary general approach: genetic, biophysical, biochemical, and physiological data form the broad foundation of general biology; similarly, evolutionary biology, developmental biology, molecular biology, and cell biology transcend the BOUNDARIES OF THE “classical” disciplines of botany and zoology. Nevertheless, despite this Classification, one should not forget that the typical animal and the typical plant (both terms understood in the colloquial sense) exhibit numerous fundamental differences.

A typical animal is capable of locomotion; therefore, its body is compactly constructed, and all organs, except for Sense Organs designed to perceive signals from the external environment, are located inside the organism. To examine the structure of an animal’s body, it must be dissected (anatomy — from the Greek word meaning “dissection”). Extensive surfaces required for respiration, nutrition, and excretion develop as invaginations into the interior of the body. The external surface is reduced to a minimum: an animal is a “closed” organism. This compact body structure ensures the central Location of organs for Circulation and excretion. Likewise, The Nervous system, which enables rapid coordination, shows a tendency toward centralization during phylogeny. Most organs are formed in limited numbers. Body symmetry is predominantly bilateral and dorsoventral, corresponding to two mutually perpendicular vectors of gravity and movement. In the strict sense, radially symmetrical forms are found almost exclusively among attached or suspended aquatic forms. The specialization of tissues and organs is highly advanced. Even generative tissues are often specialized for the subsequent formation of strictly defined cell types (stem cells of the Blood and immune system, Skin, intestinal epithelium, etc.). The lifespan even of large animals is limited. Regenerative functions in highly developed animals are minimal. In them, certain highly differentiated cells remain active throughout life and typically do not regenerate once mature (large Neurons; striated Muscle fibers; cells of the eye lens).

A typical plant, by contrast, leads a sessile lifestyle. It develops many of its organs (roots, leaves, flowers) in large numbers and freely outwards. The body surface is maximized through outgrowths and branching. A plant is an “open” organism. Perennial plants continue to grow during each vegetation period, possessing numerous growth points (in trees: annual growth of all shoots, annual wood rings, etc.). The open ORGANIZATION OF THE plant body limits the development of central organs; plants possess neither a Heart nor Kidneys, nor any organs analogous to a nervous system. Metabolic waste products must be eliminated by each individual cell independently; instead of centralized excretion, there is localized, cellular excretion. The body is most frequently radially symmetrical; bilateral organs generally form only when the vectors of gravity and growth are oriented perpendicularly to each other (laterally positioned leaves, many flowers). The capacity for regeneration is immense: every growth point can, in principle, develop into a complete new plant, which forms the basis of vegetative propagation via cuttings, layers, bulbils, etc., commonly applied in horticulture and agriculture generally. Furthermore, in randomly proliferating cells (callus tissue) that typically form initially following injury, new growth points can arise de novo. As a result, whole plants can regenerate from plant cell cultures, which is impossible in animal cell and tissue cultures. Plants aged several centuries or even millennia are frequently found not only among trees and shrubs, but also among herbaceous perennials.

Animals and plants also differ significantly in the Structure and function of their cells. A general comparison based on typical features makes it clear that plant cells (phytocytes) differ not only by the presence of plastids. They are not only phototrophic but also osmotrophic, meaning they absorb substances exclusively in dissolved form, whereas animal cells (zoocytes) are phagotrophic, meaning they can take up nutrients in particulate form. Characteristically, flagellates exhibit so-called mixotrophic nutrition, possessing both forms of cellular nutrition (Fig. 4). A mature plant cell features a central vacuole, which often accounts for over 90% of The Cell volume, and a rigid cell wall. The cell wall mechanically resists the hydrostatic pressure of the vacuole (turgor), which would otherwise tear the cell apart. Turgor is the result of osmotic phenomena; the total molar concentration of the cell sap in the vacuole is significantly higher than that of aqueous solutions within the cell walls. Animal tissue cells possess neither large vacuoles (and are therefore usually much smaller than plant tissue cells) nor rigid cell walls that serve to stabilize individual cells. Their turgor is negligible because they are filled with isotonic body and tissue fluids. Massive extracellular matrices of connective and supporting tissue in animals serve to reinforce supracellular structures rather than individual cells. During cell division, the initial cell plate in plant and fungal cells forms between daughter cells via “internal” secretion of cell wall substances. By contrast, the typical mode of cell division in animals is constriction (Cleavage) of the mother cell. Moreover, while plant body cells remain fixed almost without exception at the site of their formation, Animal Embryonic Development involves cell displacement and migration.

Fig. 4. Poterioochromonas malhamensis (Interference contrast micrograph by W. Herth)

This is a mixotrophic flagellate belonging to the order Chrysomonadales (cf. Fig. 11.74) with two flagella of unequal length and feeding pseudopodia (lobopodia L) at the anterior end, as well as a posterior attachment stalk (magnification 1160×). In the cell on the left, one can distinguish The Nucleus (N) with a nucleolus, a plastid (P), and a storage vacuole (V). The cell on the right shows a large food vacuole containing a partially digested algal cell.

Except for the absence of plastids and the inability to carry out phototrophy, fungal cells are remarkably similar to typical plant cells: they are vacuolated, osmotrophic cells with rigid cell walls, which typically divide not by cell plate formation (cytokinesis via cell plate), but through the internal secretion of cell wall components.

Subdisciplines and Significance of Botany

The study of plants, fungi, and protists can be approached from many different Perspectives, much like biology as a whole. For instance, the entire spectrum of biological research can be viewed through the hierarchy of the structures under investigation (Table 1). Basic (fundamental) research aims to understand form and function in their mutual interdependence, realization, and diversity, with the object of study taking center stage. Applied research, on the other hand, deals with the PRACTICAL USE OF plants, fungi, and microorganisms for Human nutrition and useful animals; medicinal, poisonous, and narcotic plants as the foundation of pharmacology; cultivation, genetic manipulation, and biotechnology; agriculture in the broadest sense and forestry; phytopathology, pest control, pathogens, and weed management; landscape maintenance, nature conservation, species protection, and modern ecology. Fundamental research provides the foundational knowledge for applied research of any kind.

Table 1. Directions of biological research and levels of organization of objects (after J. Lengeler)

This textbook begins by describing the General Principles of structural organization, covering a vast spectrum from the atomic to the macroscopic level: following An Overview of the molecular foundations, the architecture and ULTRASTRUCTURE OF THE cell (Cytology) are examined, followed by plant tissues (histology) and, finally, their macroscopic, externally visible structure (morphology). Our approach focuses primarily on general foundational principles rather than an overwhelming variety of forms, with descriptive analysis taking precedence.

Structural concepts are presented throughout the textbook in conjunction with their general roles in metabolism and energy exchange, morphological changes, and movement. In the realm of physiology, the dynamics of life processes take center stage. A detailed examination of metabolic physiology is followed by developmental physiology and, finally, movement physiology. The concluding, in many respects particularly timely section is dedicated to allelophysiology—that is, the diverse physiological interactions between various organisms in nature.

In Structuring this textbook of botany into parts and chapters, the authors have kept in mind the inherently interdisciplinary nature of modern biology. Once-distinct fields of knowledge converge to create new and particularly fruitful areas of research. For instance, the fusion of descriptive cell biology (cytology), biochemistry, and molecular biology has given rise to modern cell biology.

Botanical systematics occupies a prominent place in the material covering evolutionary theory, the mechanisms and causes of speciation, and their genetic basis. As the science of the evolutionary relationships among organisms, it draws upon data from all other disciplines and deals with the description, nomenclature, and classification of over 500,000 currently known plant species. This systematic classification is guided by the reconstructed evolutionary history (phylogeny) of the plant kingdom. Here, comparisons of nucleic acid and protein sequences (molecular phylogeny) and the study of fossil plant remains (paleobotany) play a dominant role. The systematic section provides insights into actively researched areas focusing on specific groups of organisms (microbiology and bacteriology, mycology, etc.), as well as applied disciplines that investigate the practical importance of plants to humanity.

Finally, plant ecology explores the Interactions Between Plants, entire plant communities, and their biotic and abiotic environment. Ecological botany seeks to understand the factors, patterns, and causes governing the distribution and coexistence of plants on Earth across space and time. Given the critical importance of natural ecosystems in today's overpopulated world, the final section of the textbook is dedicated to this vital field of research and its intersecting disciplines (such as biotic interactions, vegetation science, and global change biology).

Closely tied to plant ecology is an aspect that clearly demonstrates the unique significance of botany in the contemporary world. Energetically, all life on Earth depends on phototrophic organisms, and almost entirely on plants: they serve as the sole primary producers at the base of nearly all FOOD CHAINS AND form the foundation of all ecological pyramids. This has been the case for at least a billion years. Not least through their immense diversity (biodiversity), plants ensure the Maintenance of the structure and function of major ecosystems. Today, however, this diversity, along with the functioning of individual organisms, is increasingly threatened on multiple fronts by the profound impact of over 6 billion people on the biosphere. Ironically, humans are among the organisms that depend most critically on a stable environment for their survival as individuals and as a species. Under these conditions, environmental protection grounded in the deepest possible scientific understanding is paramount—dictated not only by an ethics of responsibility for all life on Earth, but also by sheer self-preservation, lest we undermine the very foundations of our own existence. Naturally, this complex subject is easily hijacked by unrealistic utopians and emotional demagogues if serious science fails to contribute adequately to solving ecological problems.

Botany continues to play a vital role in the advancement of the biological sciences. Many fundamental biological principles were established primarily through the study of plants. For instance, discoveries concerning the cell and cell nucleus, chromosomes, Mitosis and Meiosis, osmosis, and the laws of heredity were all first made in plants. Even though today the most suitable model systems for solving numerous problems in modern biology are often found among microorganisms and certain animals, and while many critical questions regarding cancer, The Immune System, memory, and consciousness must naturally be investigated using (higher) animals, botany nevertheless remains a fertile ground for exploring the fundamentals of biology. Applied research in this field remains exceptionally important. In biotechnology, plants and fungi consistently play a central role. It is hardly surprising that genetic engineering in agriculture is also gaining rapidly growing importance (“green genetic engineering”). Furthermore, as everywhere in modern biology, genome sequencing (Genomics) is increasingly complemented by the study of diverse protein profiles across different cells within the same organism (Proteomics).

Finally, we must not overlook the fact that plants—those quiet and often exceptionally beautiful subjects of botanical study—continue to exert a powerful emotional impact on human beings. If botany was once famously dubbed “scientia amabilis” (the amiable science), it owes this title to the aesthetic appeal of trees and flowers, which transcends pure natural science yet remains deeply meaningful to humanity.

Morphology, the biological study of form, encompasses all structures characteristic of living organisms, ranging from Biomolecules to massive organisms. A classic example is the cellular structure of a leafy liverwort leaf (Plagiochila asplenioides, bottom); all cells contain numerous chloroplasts and translucent, grape-like clusters of oil bodies containing various Terpenes. At the top is the external appearance of a cauliflower “one” (Brassica oleracea var. botrytis). This structure represents an extensive inflorescence in which the elongation of axis elements is initially suppressed (though not entirely in the “Minaret” cultivar shown here). This bud cluster forms a “fractal” structure in which the morphogenesis of the main SHOOT is repeated in all lateral shoots, in their lateral shoots again, and so on. In this single illustration snippet alone, a suitable magnification would reveal nearly 500,000 growing tips. Both images illustrate structural patterns that recur in endless variations across a vast array of living organisms.