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Biology

From Wikipedia
https://en.wikipedia.org/wiki/Biology

Biology deals with the study of life.

Biology is the scientific study of life. [1] [2] [3] It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. [1] [2] [3] For instance, all living organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. [1] [2] [3] Finally, all living organisms require energy to move, grow, and reproduce, as well as to regulate their own internal environment. [1] [2] [3] [4] [5]

Biologists are able to study life at multiple levels of organization. [1] From the molecular biology of a cell to the anatomy and physiology of plants and animals, and to the evolution of populations. [1] [6] Thus, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they used. [7] [8] [9] Like other scientists, biologists use the scientific method to make observations, pose questions, generate hypotheses, and perform experiments to satisfy their curiosity about the world around them. [1]

Life on Earth, which emerged before 3.7 billion years ago, [10] is immensely diverse. Biologists have sought to study and classify the various forms of life, from prokaryotic organisms such as archaea and bacteria to eukaryotic organisms such as protists, fungi, plants, and animals. These various living organisms contribute to the biodiversity of an ecosystem, where they play specialized roles in the exchange of energy and nutrients.

Etymology

"Biology" derives from the Ancient Greek words of βίος; romanized bíos meaning "life" and -λογία; romanized logía (-logy) meaning "branch of study" or "to speak". [11] [12] Those combined make the Greek word βιολογία; romanized biología meaning biology. Despite this, the term βιολογία as a whole didn't exist in Ancient Greek. The first to borrow it was the English and French (biologie). Historically there was another term for "biology" in English, lifelore; it is rarely used today.

The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus (Carl von Linné) used biologi in his Bibliotheca Botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German use, Biologie, was in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in the preface of a book, Grundzüge der Lehre van der Lebenskraft. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective (Propädeutik zum Studien der gesammten Heilkunst). The term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur (1802–22) by Gottfried Reinhold Treviranus, who announced: [13]

The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, and the causes through which they have been affected. The science that concerns itself with these objects we will indicate by the name biology [Biologie] or the doctrine of life [Lebenslehre].

History

A drawing of a fly from facing up, with wing detail
A Diagram of a fly from Robert Hooke's innovative Micrographia, 1665

Although modern biology is a relatively recent development, sciences related to and included within it have been studied since ancient times. Natural philosophy was studied as early as the ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, and China. However, the origins of modern biology and its approach to the study of nature are most often traced back to ancient Greece. [14] [15] While the formal study of medicine dates back to Pharaonic Egypt, it was Aristotle (384–322 BC) who contributed most extensively to the development of biology. Especially important are his History of Animals and other works where he showed naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences, even into the Middle Ages. [16]

Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany, [17] and Rhazes (865–925) who wrote on anatomy and physiology. Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in upholding a fixed hierarchy of life.

Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining. [18]

Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. Then, in 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory. [19] [20]

Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species. [21] Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Although he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought; his work influenced the evolutionary theories of both Lamarck and Darwin. [22]

In 1842, Charles Darwin penned his first sketch of On the Origin of Species. [23]

Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to present a coherent theory of evolution. [24] He posited that evolution was the result of environmental stress on properties of animals, meaning that the more frequently and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could then be passed on to the animal's offspring, who would further develop and perfect them. [25] However, it was the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell, Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, who forged a more successful evolutionary theory based on natural selection; similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions. [26] [27] Although it was the subject of controversy (which continues to this day), Darwin's theory quickly spread through the scientific community and soon became a central axiom of the rapidly developing science of biology.

The basis for modern genetics began with the work of Gregor Mendel, who presented his paper, "Versuche über Pflanzenhybriden" (" Experiments on Plant Hybridization"), in 1865, [28] which outlined the principles of biological inheritance, serving as the basis for modern genetics. [29] However, the significance of his work was not realized until the early 20th century when evolution became a unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics. [30] In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes. A focus on new kinds of model organisms such as viruses and bacteria, along with the discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics. From the 1950s to the present times, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons. Finally, the Human Genome Project was launched in 1990 with the goal of mapping the general human genome. This project was essentially completed in 2003, [31] with further analysis still being published. The Human Genome Project was the first step in a globalized effort to incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and the bodies of other organisms.

Modern biology

Chemical basis

Atoms and molecules

Model of hydrogen bonds (1) between molecules of water

All living organisms are made up of matter and all matter is made up of elements. [32] Oxygen, carbon, hydrogen, and nitrogen are the four elements that account for 96% of all living organisms, with calcium, phosphorus, sulfur, sodium, chlorine, and magnesium accounting for the remaining 3.7%. [32] Different elements can combine to form compounds such as water, which is fundamental to life. [32] Life on Earth began from water and remained there for about three billions years prior to migrating onto land. [33] Matter can exist in different states as a solid, liquid, or gas.

The smallest unit of an element is an atom, which is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Individual atoms can be held together by chemical bonds to form molecules and ionic compounds. [32] Common types of chemical bonds include ionic bonds, covalent bonds, and hydrogen bonds. Ionic bonding involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities, [34] and is the primary interaction occurring in ionic compounds. Ions are atoms (or groups of atoms) with an electrostatic charge. Atoms that gain electrons make negatively charged ions (called anions) whereas those that lose electrons make positively charged ions (called cations).

Unlike ionic bonds, a covalent bond involves the sharing of electron pairs between atoms. These electron pairs and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. [35]

A hydrogen bond is primarily an electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom or group such as oxygen. A ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule.

Organic compounds

Organic compounds such as glucose are vital to living organisms

With the exception of water, nearly all the molecules that make up each living organism contain carbon. [36] [37] Carbon can form very long chains of interconnecting carbon–carbon bonds, which are strong and stable. The simplest form of an organic molecule is the hydrocarbon, which is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other atoms. When combined with other elements such as oxygen, hydrogen, phosphorus, and sulfur, carbon can form many groups of important biological compounds such as sugars, fats, amino acids, and nucleotides.

Macromolecules

The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.

Molecules such as sugars, amino acids, and nucleotides can act as single repeating units called monomers to form chain-like molecules called polymers via a chemical process called condensation. [38] For example, amino acids can form polypeptides whereas nucleotides can form strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Polymers make up three of the four macromolecules ( polysaccharides, lipids, proteins, and nucleic acids) that are found in all living organisms. Each macromolecule plays a specialized role within any given cell. Some polysaccharides, for instance, can function as storage material that can be hydrolyzed to provide cells with sugar. Lipids are the only class of macromolecules that are not made up of polymers and the most biologically important lipids are fats, phospholipids, and steroids. [38] Proteins are the most diverse of the macromolecules, which include enzymes, transport proteins, large signaling molecules, antibodies, and structural proteins. Finally, nucleic acids store, transmit, and express hereditary information. [38]

Cells

Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division. [39] Most cells are very small, with diameters ranging from 1 to 100  micrometers and are therefore only visible under a light or electron microscope. [40] There are generally two types of cells: eukaryotic cells, which contain a nucleus, and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be single-celled or multicellular. In multicellular organisms, every cell in the organism's body is derived ultimately from a single cell in a fertilized egg.

Cell structure

Structure of an animal cell depicting various organelles

Every cell is enclosed within a cell membrane that separates its cytoplasm from the extracellular space. [41] A cell membrane consists of a lipid bilayer, including cholesterols that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable, allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions. [42] Cell membranes also contains membrane proteins, including integral membrane proteins that go across the membrane serving as membrane transporters, and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell. [43] Cell membranes are involved in various cellular processes such as cell adhesion, storing electrical energy, and cell signalling and serve as the attachment surface for several extracellular structures such as a cell wall, glycocalyx, and cytoskeleton.

Structure of a plant cell

Within the cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids. [44] In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus, which contains a cell's genetic information, or mitochondria, which generates adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play a role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes, another specialized organelle. Plant cells have additional organelles that distinguish them from animal cells such as a cell wall, chloroplasts, and vacuole.

Metabolism

Example of an enzyme-catalysed exothermic reaction

Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic – the building up ( synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts – they allow a reaction to proceed more rapidly – and they also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.

Cellular respiration

Respiration in a eukaryotic cell

Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from oxygen molecules [45] or nutrients into adenosine triphosphate (ATP), and then release waste products. [46] The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy because weak high-energy bonds, in particular in molecular oxygen, [47] are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow, controlled release of energy from the series of reactions.

Nutrients that are commonly used by animal and plant cells in respiration include sugar, amino acids and fatty acids, and the most common oxidizing agent providing most of the chemical energy is molecular oxygen (O2). [45] The chemical energy stored in ATP (the bond of its third phosphate group to the rest of the molecule can be broken allowing more stable products to form, thereby releasing energy for use by the cell) can then be used to drive processes requiring energy, including biosynthesis, locomotion or transport of molecules across cell membranes.

Without oxygen, pyruvate ( pyruvic acid) is not metabolized by cellular respiration but undergoes a process of fermentation. The pyruvate is not transported into the mitochondrion but remains in the cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD+ so it can be re-used in glycolysis. In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD+ for glycolysis. This waste product varies depending on the organism. In skeletal muscles, the waste product is lactic acid. This type of fermentation is called lactic acid fermentation. In strenuous exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic glycolysis, NAD+ regenerates when pairs of hydrogen combine with pyruvate to form lactate. Lactate formation is catalyzed by lactate dehydrogenase in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD+ attaches to hydrogen from lactate to form ATP. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation. The ATP generated in this process is made by substrate-level phosphorylation, which does not require oxygen.

Photosynthesis

Photosynthesis changes sunlight into chemical energy, splits water to liberate O2, and fixes CO2 into sugar.

Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's metabolic activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek phōs ( φῶς), "light", and sunthesis ( σύνθεσις), "putting together". [48] [49] [50] In most cases, oxygen is also released as a waste product. Most plants, algae, and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. [51]

The process of photosynthesis always begins when energy from light is absorbed by proteins called reaction centers that contain green chlorophyll pigments. In plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances, such as water, producing oxygen gas. The hydrogen freed by the splitting of water is used in the creation of two further compounds that serve as short-term stores of energy, enabling its transfer to drive other reactions: these compounds are reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the "energy currency" of cells.

In plants, algae, and cyanobacteria, long-term energy storage in the form of sugars is produced by a subsequent sequence of light-independent reactions called the Calvin cycle. In the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate (RuBP). [52] Using the ATP and NADPH produced by the light-dependent reactions, the resulting compounds are then reduced and removed to form further carbohydrates, such as glucose. In other bacteria, different mechanisms such as the reverse Krebs cycle are used to achieve the same end.

Genetics

Genetics is the science of genes, heredity, and the variation of organisms. [53] [54] It provides research tools used in the investigation of the function of a particular gene, or the analysis of genetic interactions.

Cell cycle

In meiosis, the chromosomes duplicate and the homologous chromosomes exchange genetic information during meiosis I. The daughter cells divide again in meiosis II to form haploid gametes.

The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA ( DNA replication) and some of its organelles, and subsequently the partitioning of its cytoplasm and other components into two daughter cells in a process called cell division.

In cells with nuclei ( eukaryotes), (i.e., animal, plant, fungal, and protist cells), the cell cycle is divided into two main stages: interphase and the mitotic (M) phase (including mitosis and cytokinesis). During interphase, the cell grows, accumulating nutrients needed for mitosis, and replicates its DNA and some of its organelles. During the mitotic phase, the replicated chromosomes, organelles, and cytoplasm separate into two new daughter cells. To ensure the proper replication of cellular components and division, there are control mechanisms known as cell cycle checkpoints after each of the key steps of the cycle that determine if the cell can progress to the next phase. In cells without nuclei ( prokaryotes), (i.e., bacteria and archaea), the cell cycle is divided into the B, C, and D periods. The B period extends from the end of cell division to the beginning of DNA replication. DNA replication occurs during the C period. The D period refers to the stage between the end of DNA replication and the splitting of the bacterial cell into two daughter cells. [55]

The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of a new cycle. Although the various stages of interphase are not usually morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for initiation of the cell division.

In all sexually-reproducing organisms, DNA replication is followed by two rounds of a special type of cell division called meiosis, which produces four daughter cells, each with half the number of chromosomes as the original parent cell. [56] The two meiotic divisions are meiosis I and meiosis II. Meiosis produces haploid gametes (ova or sperm) that contain one set of 23 chromosomes. When two gametes (an egg and a sperm) fuse, the resulting zygote is once again diploid, with the mother and father each contributing 23 chromosomes. This same pattern, but not the same number of chromosomes, occurs in all organisms that utilize meiosis.

Inheritance

Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms.

Classical genetics began with Gregor Mendel's experiments that formulated and defined a fundamental biological concept known as Mendelian inheritance, which is the process in which genes and traits are passed from a set of parents to their offspring. Based on his work with pea plants, Mendel established several principles of inheritance. The first is that genetic characteristics are discrete (e.g., purple vs. white or tall vs. dwarf). Genetic characteristics, which are now called alleles, have alternate forms, each inherited from one of two parents. One allele is dominant over the other. The phenotype reflects the dominant allele. Gametes are created by random segregation. Heterozygotic individuals produce gametes with an equal frequency of two alleles. Different traits have independent assortment. In modern terms, genes are unlinked.

Mendel proposed three laws of inheritance. The first is Law of dominance and uniformity, which states some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele. [57] Then there is Law of segregation, which states that during gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene. Finally, there is the Law of independent assortment, which states that genes of different traits can segregate independently during the formation of gametes.

Gene expression

The extended central dogma of molecular biology includes all the processes involved in the flow of genetic information.

A gene is a unit of heredity that corresponds to a region of DNA that influences the form or function of an organism in specific ways. DNA is found as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as a cell's genome. In eukaryotes, genomic DNA is localized in the cell nucleus, or with small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. [58] The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype. [59] Genes encode the information needed by cells for the synthesis of proteins, which in turn play a central role in influencing the final phenotype of the organism.

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. This process is used by all life— eukaryotes (including multicellular organisms), prokaryotes ( bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. Gene products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, [60] further developed in his 1970 article, [61] and expanded by the subsequent discoveries of reverse transcription [62] [63] [64] and RNA replication. [65] All steps in the gene expression process may be modulated (regulated), including the transcription, RNA splicing, translation, and post-translational modification of a protein. Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on the cellular structure and function.

Biotechnology

Construction of recombinant DNA, in which a foreign DNA fragment is inserted into a plasmid vector.

Biotechnology is the use of cells or living organisms to develop products for humans. [66] It includes tools such as recombinant DNA, which are DNA molecules formed by laboratory methods of genetic recombination such as molecular cloning, which bring together genetic material from multiple sources, creating sequences that would otherwise not be found in a genome. Other tools include the use of genomic libraries, DNA microarrays, expression vectors, synthetic genomics, and CRISPR gene editing. [66] [67] Many of these tools have wide applications such as creating medically useful proteins, or improving plant cultivation and animal husbandry. [66]

Evolution

A central organizing concept in biology is that life changes and develops through evolution, and that all life on Earth, both living and extinct, descended from a last universal common ancestor that lived about 3.5 billion years ago. [68] [69] Biologists regard the ubiquity of the genetic code as evidence of universal common descent for all bacteria, archaea, and eukaryotes. [70] Evolution is now used to explain the great variations of life on Earth.

Evolutionary processes

Natural selection for darker traits.

The term evolution was introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809, [71] and fifty years later Charles Darwin and Alfred Russel Wallace formulated the theory of evolution by natural selection. [72] [73] [74] [75] According to this theory, individuals differ from each other with respect to their heritable traits, resulting in different rates of survival and reproduction. As a results, traits that are better adapted to their environment are more likely to be passed on to subsequent generations. [76] [77] Darwin was not aware of Mendel's work of inheritance and so the exact mechanism of inheritance that underlie natural selection was not well-understood [78] until the early 20th century when the modern synthesis reconciled Darwinian evolution with classical genetics, which established a neo-Darwinian perspective of evolution by natural selection. [79] This perspective holds that evolution occurs when there are changes in the allele frequencies within a population of interbreeding organisms. In the absence of any evolutionary process acting on a large random mating population, the allele frequencies will remain constant across generations as described by the Hardy–Weinberg principle. [80]

Another process that drives evolution is genetic drift, which is the random fluctuations of allele frequencies within a population from one generation to the next. [81] When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward at each successive generation because the alleles are subject to sampling error. [82] This drift halts when an allele eventually becomes fixed, either by disappearing from the population or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone.

Speciation

Speciation is the evolutionary process by which populations evolve to become distinct species. All forms of natural speciation have taken place over the course of evolution. [83] There are several modes of speciation such allopatric speciation, peripatric speciation, parapatric speciation, and sympatric speciation.

The evolutionary history of a species—which describes the characteristics of the various species from which it descended—together with its genealogical relationship to every other species is known as its phylogeny. Widely varied approaches can be used to generate information about phylogeny such as comparisons of DNA sequences and fossils of ancient organisms. [84] Multiple speciation events create a tree structured system of relationships between species.

History of life

The history of life on Earth traces the processes by which organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and life emerged prior to 3.7 billion years ago. [10] [85] [86] The similarities among all known present-day species indicate that they have diverged through the process of evolution from a common ancestor. [87]

Microbal mats of coexisting bacteria and archaea were the dominant form of life in the early Archean Epoch and many of the major steps in early evolution are thought to have taken place in this environment. [88] The earliest evidence of eukaryotes dates from 1.85 billion years ago, [89] [90] and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism. Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions. [91]

Algae-like multicellular land plants are dated back even to about 1 billion years ago, [92] although evidence suggests that microorganisms formed the earliest terrestrial ecosystems, at least 2.7 billion years ago. [93] Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event. [94]

Ediacara biota appear during the Ediacaran period, [95] while vertebrates, along with most other modern phyla originated about 525 million years ago during the Cambrian explosion. [96] During the Permian period, synapsids, including the ancestors of mammals, dominated the land, [97] but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago. [98] During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates; [99] one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods. [100] After the Cretaceous–Paleogene extinction event 66 million years ago killed off the non-avian dinosaurs, [101] mammals increased rapidly in size and diversity. [102] Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. [103]

Diversity

Phylogenies

Bacteria Archaea Eucaryota Aquifex Thermotoga Cytophaga Bacteroides Bacteroides-Cytophaga Planctomyces Cyanobacteria Proteobacteria Spirochetes Gram-positive bacteria Green filantous bacteria Pyrodicticum Thermoproteus Thermococcus celer Methanococcus Methanobacterium Methanosarcina Halophiles Entamoebae Slime mold Animal Fungus Plant Ciliate Flagellate Trichomonad Microsporidia Diplomonad
Phylogenetic tree of all life, based on rRNA data, showing the separation of three domains ( bacteria, archaea, and eukaryotes) as described by Carl Woese.

The dominant classification system is called the Linnaean taxonomy, which includes ranks and binomial nomenclature. Traditionally, living things have been divided into five kingdoms: Monera; Protista; Fungi; Plantae; Animalia. [104] However, many scientists now consider this five-kingdom system outdated. Modern alternative classification systems generally begin with the three-domain system: Archaea (originally Archaebacteria); Bacteria (originally Eubacteria) and Eukaryota (including protists, fungi, plants, and animals). [105] These domains reflect whether the cells have nuclei or not, as well as differences in the chemical composition of key biomolecules such as ribosomes. [105]

Further, each kingdom is broken down recursively until each species is separately classified. The order is: Domain; Kingdom; Phylum; Class; Order; Family; Genus; Species.

Outside of these categories, there are obligate intracellular parasites that are "on the edge of life" [106] in terms of metabolic activity, meaning that many scientists do not actually classify such structures as alive, due to their lack of at least one or more of the fundamental functions or characteristics that define life. They are classified as viruses, viroids, prions, or satellites.

The scientific name of an organism is generated from its genus and species. For example, humans are Homo sapiens, with Homo as the genus and sapiens as the species. By convention, scientific names are italicized, with only the first letter of the genus capitalized. [107] [108]

Bacteria and Archaea

Bacteria Gemmatimonas aurantiaca (-=1 Micrometer)

Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, [109] and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory. [110]

Archaea constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use. [111]

Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi. [112] Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, [113] including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores.

The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.

Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin. [114] Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example. [115]

Protists

Diversity of protists

Protists are eukaryotic organism that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), [116] the exclusion of other eukaryotes means that protists do not form a natural group, or clade. [a] So some protists may be more closely related to animals, plants, or fungi than they are to other protists; however, like algae, invertebrates, or protozoans, the grouping is used for convenience. [117]

The taxonomy of protists is still changing. Newer classifications attempt to present monophyletic groups based on morphological (especially ultrastructural), [118] [119] [120] biochemical ( chemotaxonomy) [121] [122] and DNA sequence ( molecular research) information. [123] [124] Because protists as a whole are paraphyletic, new systems often split up or abandon the kingdom, instead treating the protist groups as separate lines of eukaryotes.

Plant diversity

Diversity of plants

Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae. Botany is the study of plant life, which would exclude fungi and some algae. Botanists have studied approximately 410,000 species of land plants of which some 391,000 species are vascular plants (including approximately 369,000 species of flowering plants), [125] and approximately 20,000 are bryophytes. [126]

Algae is a large and diverse group of photosynthetic eukaryotic organisms. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga. Most are aquatic and autotrophic and lack many of the distinct cell and tissue types, such as stomata, xylem and phloem, which are found in land plants. The largest and most complex marine algae are called seaweeds, while the most complex freshwater forms are the Charophyta.

Nonvascular plants are plants without a vascular system consisting of xylem and phloem. Instead, they may possess simpler tissues that have specialized functions for the internal transport of water. Vascular plants, on the other hand, are a large group of plants ( c. 300,000 accepted known species) [127] that are defined as land plants with lignified tissues (the xylem) for conducting water and minerals throughout the plant. They also have a specialized non-lignified tissue (the phloem) to conduct products of photosynthesis. Vascular plants include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants).

Seed plants (or spermatophyte) comprise five divisions, four of which are grouped as gymnosperms and one is angiosperms. Gymnosperms includes conifers, cycads, Ginkgo, and gnetophytes. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or solitary as in yew, Torreya, Ginkgo. [128] Angiosperms are the most diverse group of land plants, with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species. [127] Like gymnosperms, angiosperms are seed-producing plants. They are distinguished from gymnosperms by having characteristics such as flowers, endosperm within their seeds, and production of fruits that contain the seeds.

Fungi

Diversity of fungi. Clockwise from top left: Amanita muscaria, a basidiomycete; Sarcoscypha coccinea, an ascomycete; bread covered in mold; chytrid; Aspergillus conidiophore.

Fungi are eukaryotic organisms that include microorganisms such as yeasts and molds, as well as the more familiar mushrooms. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (from a monophyletic group). This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds).

Most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment.

The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species. [129] Of these, only about 148,000 have been described, [130] with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. [131]

Animal diversity

Echinoderm Cnidaria Bivalve Tardigrade Crustacean Arachnid Sponge Insect Mammal Bryozoa Acanthocephala Flatworm Cephalopod Annelid Tunicate Fish Bird Phoronida
Diversity of animals. From top to bottom, first column: Echinoderm, cnidaria, bivalve, tardigrade, crustacean, and arachnid. Second column: Sponge, insect, mammal, bryozoa, acanthocephala, and flatworm. Third column: Cephalopod, annelid, tunicate, fish, bird, and phoronida

Animals are multicellular eukaryotic organisms that form the kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs.

Sponges, the members of the phylum Porifera, are a basal Metazoa (animal) clade as a sister of the Diploblasts. [132] [133] [134] [135] [136] They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells.

The majority (~97%) of animal species are invertebrates, [137] which are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include arthropods ( insects, arachnids, crustaceans, and myriapods), mollusks ( chitons, snail, bivalves, squids, and octopuses), annelid ( earthworms and leeches), and cnidarians ( hydras, jellyfishes, sea anemones, and corals). Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata. [138]

In contrast, vertebrates comprise all species of animals within the subphylum Vertebrata ( chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described. [139] Vertebrates include such groups as jawless fishes, jawed vertebrates such as cartilaginous fishes ( sharks, rays, and ratfish), bony fishes, tetrapods such as amphibians, reptiles, birds and mammals.

Viruses

Transmission electron micrograph of bacteriophages attached to a bacterial cell wall.

Viruses are submicroscopic infectious agents that replicate inside the living cells of organisms. [140] Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea. [141] [142] More than 6,000 virus species have been described in detail [143] Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. [144] [145]

When infected, a host cell is forced to rapidly produce thousands of identical copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of the genetic material ( DNA or RNA), a protein coat called capsid, and in some cases an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope, as they are one-hundredth the size of most bacteria.

The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction. [146] Because viruses possess some but not all characteristics of life, they have been described as "organisms at the edge of life", [147] and as self-replicators. [148]

Viruses can spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap, such as aphids; and viruses in animals can be carried by blood-sucking insects. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection.

Plant form and function

A plant's form includes the study of its organs and systems whereas its function involves the study of internal processes such as molecular interactions of photosynthesis and internal diffusion of water, minerals, and nutrients at the smallest scale. At the largest scale are the processes of plant development, seasonality, dormancy, and reproductive control. [149]

Plant body

Diagram of a "typical" eudicot.

Plant morphology treats both the vegetative structures of plants, as well as the reproductive structures. The vegetative (somatic) structures of vascular plants include two major organ systems: a shoot system, composed of stems and leaves, and a root system. These two systems are common to nearly all vascular plants, and provide a unifying theme for the study of plant morphology.

By contrast, the reproductive structures are varied, and are usually specific to a particular group of plants. Structures such as flowers and fruits are only found in the angiosperms; sori are only found in ferns; and seed cones are only found in conifers and other gymnosperms. Reproductive characters are therefore regarded as more useful for the classification of plants than vegetative characters.

Plant nutrition and transport

Different plant cells and tissues are physically and chemically specialized to perform different functions. Roots and rhizoids function to anchor the plant and acquire minerals in the soil. Leaves catch light in order to manufacture nutrients. For both of these organs to remain living, minerals that the roots acquire must be transported to the leaves, and the nutrients manufactured in the leaves must be transported to the roots. Plants have developed a number of ways to achieve this transport, such as vascular tissue, and the functioning of the various modes of transport is studied by plant physiologists. Like animals, plants produce hormones in one part of its body to signal cells in another part to respond. Many flowering plants bloom at the appropriate time because of light-sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene by the plant. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.

Plant development

Plant development is regulated by environmental cues and the plant's own receptors, hormones, and genome. [149] Morever, they have several characteristics that allow them to obtain resources for growth and reproduction such as meristems, post-embryonic organ formation, and differential growth.

Development begins with a seed, which is an embryonic plant enclosed in a protective outer covering. Most plant seeds are usually dormant, a condition in which the seed's normal activity is suspended. [149] Seed dormancy may last may last weeks, months, years, and even centuries. Dormancy is broken once conditions are favorable for growth, and the seed will begin to sprout, a process called germination. Imbibition is the first step in germination, whereby water is absorbed by the seed. Once water is absorbed, the seed undergoes metabolic changes whereby enzymes are activated and RNA and proteins are synthesized. Once the seed germinates, it obtains carbohydrates, amino acids, and small lipids that serve as building blocks for its development. These monomers are obtained from the hydrolysis of starch, proteins, and lipids that are stored in either the cotyledons or endosperm. Germination is completed once embryonic roots called radicle have emerged from the seed coat. At this point, the developing plant is called a seedling and its growth is regulated by its own photoreceptors and hormones. [149]

Plant reproduction

Reproduction and development in sporophytes

Most angiosperms (or flowering plants) engage in sexual reproduction. [150] Their flowers are organs that facilitate reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate two types of pollination: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma of the same flower, or another flower on the same plant. Cross-pollination is the transfer of pollen from the anther of one flower to the stigma of another flower on a different individual of the same species. Self-pollination happened in flowers where the stamen and carpel mature at the same time, and are positioned so that the pollen can land on the flower’s stigma. This pollination does not require an investment from the plant to provide nectar and pollen as food for pollinators. [151]

Plant responses

Many plant organs contain different types of photoreceptors, each of which reacts very specifically to certain wavelengths of light. [152] The photoreceptors relay information such as whether it is day or night, duration of the day, intensity of light available, and the source of light. Shoots generally grow towards light, while roots grow away from it, responses known as phototropism and skototropism, respectively. They are brought about by light-sensitive pigments like phototropins and phytochromes and the plant hormone auxin. [153]

In addition to light, plants can respond to other types of stimuli. For instance, plants can sense the direction of gravity to orient themselves correctly. They can respond to mechanical stimulation. [154]

To function and survive, plants produce a wide array of chemical compounds not found in other organisms. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul-tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.

Animal form and function

Negative feedback is necessary for maintaining homeostasis such as keeping body temperature constant.

The theme of "structure to function" is central to animal biology. In anatomy, the focus is on macroscopic forms of such structures organs and organ systems [155] whereas in animal physiology, the focus is on the mechanical, physical, and biochemical processes that underlie function of the animal and its parts. Individual animals comprise multiple organ systems such as the nervous, immune, endocrine, respiratory, and circulatory systems. These systems often work together to maintain homeostasis, which is the stability of the animal's internal environment. [156] All living organisms, whether unicellular or multicellular, exhibit homeostasis. [157]

Nutrition and digestion

Nutrition is the process by which an organism uses food to support its life. It includes ingestion, absorption, assimilation, biosynthesis, catabolism, and excretion. [158] Digestion is the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the blood plasma. In certain organisms, these smaller substances are absorbed through the small intestine into the blood stream. Digestion is a form of catabolism that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. Mechanical digestion is the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes. Chemical digestion involves enzymes breaking down food into the small molecules that the body can use.

Breathing

Respiratory system in a bird.

The respiratory system consists of specific organs and structures used for gas exchange in animals and plants. The anatomy and physiology that make this happen varies greatly, depending on the size of the organism, the environment in which it lives and its evolutionary history. In land animals the respiratory surface is internalized as linings of the lungs. [159] Gas exchange in the lungs occurs in millions of small air sacs; in mammals and reptiles these are called alveoli, and in birds they are known as atria. These microscopic air sacs have a very rich blood supply, thus bringing the air into close contact with the blood. [160] These air sacs communicate with the external environment via a system of airways, or hollow tubes, of which the largest is the trachea, which branches in the middle of the chest into the two main bronchi. These enter the lungs where they branch into progressively narrower secondary and tertiary bronchi that branch into numerous smaller tubes, the bronchioles. In birds the bronchioles are termed parabronchi. It is the bronchioles, or parabronchi that generally open into the microscopic alveoli in mammals and atria in birds. Air has to be pumped from the environment into the alveoli or atria by the process of breathing which involves the muscles of respiration.

Circulation

Circulatory systems in arthropods, fish, reptiles, and birds/mammals.

The circulatory system permits blood to circulate and transport nutrients (such as amino acids and electrolytes), oxygen, carbon dioxide, hormones, and blood cells to and from the cells in the body to provide nourishment and help in fighting diseases, stabilize temperature and pH, and maintain homeostasis. The circulatory system comprises the blood, heart, and blood vessels. [161] It has two components, a systemic circulation and a pulmonary circulation. [162] While vertebrate animals have a closed cardiovascular system whereby blood never leaves the network of arteries, veins and capillaries, some invertebrate animals have an open cardiovascular system.

Muscle and movement

Asynchronous muscles power flight in most insects. a: Wings b: Wing joint c: Dorsoventral muscles power upstrokes d: Dorsolongitudinal muscles power downstrokes.

In vertebrates, the muscular system consists of skeletal, smooth and cardiac muscles. It permits movement of the body, maintains posture and circulates blood throughout the body. [163] The muscular systems in vertebrates are controlled through the nervous system although some muscles (such as the cardiac muscle) can be completely autonomous. Together with the skeletal system, it forms the musculoskeletal system, which is responsible for movement of the human body. [164]

Skeletal muscle contractions are neurogenic as they require synaptic input from motor neurons. A single motor neuron is able to innervate multiple muscle fibers, thereby causing the fibers to contract at the same time. Once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus, depending on the frequency of action potentials. Unlike skeletal muscles, contractions of smooth and cardiac muscles are myogenic as they are initiated by the smooth or heart muscle cells themselves instead of a motor neuron. Nevertheless, the strength of their contractions can be modulated by input from the autonomic nervous system. The mechanisms of contraction are similar in all three muscle tissues.

In invertebrates such as earthworms and leeches, circular and longitudinal muscles cells form the body wall of these animals and are responsible for their movement. [165] In an earthworm that is moving through a soil, for example, contractions of circular and longitudinal muscles occur reciprocally while the coelomic fluid serves as a hydroskeleton by maintaining turgidity of the earthworm. [166] Other animals such as mollusks, and nematodes, possess obliquely striated muscles, which contain bands of thick and thin filaments that are arranged helically rather than transversely, like in vertebrate skeletal or cardiac muscles. [167] Advanced insects such as wasps, flies, bees, and beetles possess asynchronous muscles that constitute the flight muscles in these animals. [167] These flight muscles are often called fibrillar muscles because they contain myofibrils that are thick and conspicuous. [168]

Nervous system

Mouse pyramidal neurons expressing green fluorescent proteins. Red staining indicates GABAergic interneurons. [169]

The nervous system is a highly complex part of an animal that coordinates its actions and sensory information by transmitting signals to and from different parts of its body. The nervous system detects environmental changes that impact the body, then works in tandem with the endocrine system to respond to such events. [170] At the cellular level, the nervous system is defined by the presence of neurons, which are specialized cells that transmit signals to other cells. They send these signals in the form of electrochemical waves traveling along thin fibers called axons, which cause chemicals called neurotransmitters to be released at junctions called synapses. A cell that receives a synaptic signal from a neuron may be excited, inhibited, or otherwise modulated. The connections between neurons can form neural pathways, neural circuits, and larger networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glial cells (or simply glia), which provide structural and metabolic support.

Nervous systems are found in most multicellular animals, but vary greatly in complexity. [171] In vertebrates, the nervous system consists of the central nervous system, which comprise the brain and spinal cord, and the peripheral nervous system, which consists of nerves that connect the central nervous system to every other part of the body. Nerves that transmit signals from the brain are called motor or efferent nerves, while those nerves that transmit information from the body to the central nervous system are called sensory or afferent. Spinal nerves serve both functions and are called mixed nerves. The peripheral nervous system is divided into three separate subsystems, the somatic, autonomic, and enteric nervous systems. Somatic nerves mediate voluntary movement. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous systems. The sympathetic nervous system is activated in cases of emergencies to mobilize energy, while the parasympathetic nervous system is activated when organisms are in a relaxed state. The enteric nervous system functions to control the gastrointestinal system. Both autonomic and enteric nervous systems function involuntarily. Nerves that exit from the cranium are called cranial nerves while those exiting from the spinal cord are called spinal nerves.

Animal reproduction

Reproduction is the process by which new individual organisms are produced from their parents. There are two forms of reproduction: asexual and sexual. Nearly all animals make use of some form of sexual reproduction. [172] They produce haploid gametes by meiosis. The smaller, motile gametes are spermatozoa and the larger, non-motile gametes are ova. [173] These fuse to form zygotes, [174] which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, and develop into a new sponge. [175] In most other groups, the blastula undergoes more complicated rearrangement. [176] It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm. [177] In most cases, a third germ layer, the mesoderm, also develops between them. [178] These germ layers then differentiate to form tissues and organs. [179] Some animals are capable of asexual reproduction, which often results in a genetic clone of the parent. This may take place through fragmentation; budding, such as in Hydra and other cnidarians; or parthenogenesis, where fertile eggs are produced without mating, such as in aphids. [180] [181]

Animal development

Cleavage in zebrafish embryo.

Animal development begins with the formation of a zygote that results from the fusion of a sperm and egg during fertilization. [182] The zygote undergoes a rapid multiple rounds of mitotic cell period of cell divisions called cleavage, which forms a ball of similar cells called a blastula. Gastrulation occurs, whereby morphogenetic movements convert the cell mass into a three germ layers that comprise the ectoderm, mesoderm and endoderm.

The end of gastrulation signals the beginning of organogenesis, whereby the three germ layers form the internal organs of the organism. [183] The cells of each of the three germ layers undergo differentiation, a process where less-specialized cells become more-specialized through the expression of a specific set of genes. Cellular differentiation is influenced by extracellular signals such as growth factors that are exchanged to adjacent cells, which is called juxtracrine signaling, or to neighboring cells over short distances, which is called paracrine signaling. [184] [185] Intracellular signals consist of a cell signaling itself ( autocrine signaling), also play a role in organ formation. These signaling pathways allows for cell rearrangement and ensures that organs form at specific sites within the organism. [183] [186]

Immune system

Overview of the processes involved in the primary immune response

The immune system is a network of biological processes that detects and responds to a wide variety of pathogens. Many species have two major subsystems of the immune system. The innate immune system provides a preconfigured response to broad groups of situations and stimuli. The adaptive immune system provides a tailored response to each stimulus by learning to recognize molecules it has previously encountered. Both use molecules and cells to perform their functions.

Nearly all organisms have some kind of immune system. Bacteria have a rudimentary immune system in the form of enzymes that protect against virus infections. Other basic immune mechanisms evolved in ancient plants and animals and remain in their modern descendants. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system. Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt to recognize pathogens more efficiently. Adaptive (or acquired) immunity creates an immunological memory leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.

Animal behavior

Brood parasites, such as the cuckoo, provide a supernormal stimulus to the parenting species.

Behaviors play a central a role in animals' interaction with each other and with their environment. [187] They are able to use their muscles to approach one another, vocalize, seek shelter, and migrate. An animal's nervous system activates and coordinates its behaviors. Fixed action patterns, for instance, are genetically determined and stereotyped behaviors that occur without learning. [187] [188] These behaviors are under the control of the nervous system and can be quite elaborate. [187] Examples include the pecking of kelp gull chicks at the red dot on their mother's beak. Other behaviors that have emerged as a result of natural selection include foraging, mating, and altruism. [189] In addition to evolved behavior, animals have evolved the ability to learn by modifying their behaviors as a result of early individual experiences. [187]

Ecology

a colorful cloudfish swimming near a sea anemone
Mutual symbiosis between clownfish of the genus Amphiprion that dwell among the tentacles of tropical sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clown fish from its predators.

Ecology is the study of the distribution and abundance of living organisms, the interaction between them and their environment. [190] An organism shares an environment that includes other organisms and biotic factors as well as abiotic factors such as water, light, radiation, temperature, humidity, atmosphere, acidity, and soil. [191] One reason that biological systems can be difficult to study is that so many different interactions with other organisms and the environment are possible, even on small scales. A microscopic bacterium responding to a sugar gradient is responding to its environment as much as a lion searching for food in the African savanna. For any species, behaviors can be co-operative, competitive, parasitic, or symbiotic. Matters become more complex when two or more species interact in an ecosystem. Ecological systems are studied at several different levels, from the scale of the ecology of individual organisms, to those of populations, to the ecosystems, and finally the biosphere.

Populations

Reaching carrying capacity through a logistic growth curve

A population is a number of organisms of the same group or species living in a particular geographical area and are capable of interbreeding. [192] [193] The area of a sexual population is the area where inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals from other areas. [194] The term population biology is often used interchangeably with population ecology, although population biology is more frequently used in the case of diseases, viruses, and microbes, while the term population ecology is more commonly applied to the study of plants and animals.

The carrying capacity of an environment is the maximum population size of a biological species that can be sustained by that specific environment, given the food, habitat, water, and other resources available. The carrying capacity is defined as the environment's maximal load, which corresponds to the population equilibrium, when the number of deaths in a population equals the number of births (as well as immigration and emigration). The effect of carrying capacity on population dynamics is modelled with a logistic function. Carrying capacity is applied to the maximum population an environment can support in ecology, agriculture and fisheries. [195]

Communities

A community is a group of populations of two or more different species occupying the same geographical area at the same time. A biological interaction is the effect that a pair of organisms living together in a community have on each other. They can be either of the same species (intraspecific interactions), or of different species (interspecific interactions). These effects may be short-term, like pollination and predation, or long-term; both often strongly influence the evolution of the species involved. A long-term interaction is called a symbiosis. Symbioses range from mutualism, beneficial to both partners, to competition, harmful to both partners. [196]

Organisms that are responsible for the introduction of energy into an ecosystem are known as producers or autotrophs. Nearly all such organisms originally draw their energy from the sun. [51] Plants and other phototrophs use solar energy via a process known as photosynthesis to convert raw materials into organic molecules, such as ATP, whose bonds can be broken to release energy. [197] A few ecosystems, however, depend entirely on energy extracted by chemotrophs from methane, sulfides, or other non- luminal energy sources. [198]

Some of the energy thus captured produces biomass and energy that is available for growth and development of other life forms. The majority of the rest of this biomass and energy are lost as waste molecules and heat.

Ecosystems

Fast carbon cycle showing the movement of carbon between land, atmosphere, and oceans of carbon between land, atmosphere, and ocean in billions of tons (gigatons) per year. Yellow numbers are natural fluxes, red are human contributions, white are stored carbon. The effects of the slow carbon cycle, such as volcanic and tectonic activity are not included. [199]

An ecosystem is a community of living organisms in conjunction with the nonliving components of their environment, interacting as a system. [200] These biotic and abiotic components are linked together through nutrient cycles and energy flows. [201] Energy enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present. By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and other microbes. [202] A biogeochemical cycle is a pathway by which a chemical substance is turned over or moves through the biotic ( biosphere) and the abiotic ( lithosphere, atmosphere, and hydrosphere) compartments of Earth. There are biogeochemical cycles for nitrogen, carbon, and water. In some cycles there are reservoirs where a substance remains or is sequestered for a long period of time.

Weather is the day-to-day temperature and precipitation activity, whereas climate is the long-term average of weather, typically averaged over a period of 30 years. [203] [204] Climate change includes both global warming driven by human-induced emissions of greenhouse gases and the resulting large-scale shifts in weather patterns. Though there have been previous periods of climatic change, since the mid-20th century humans have had an unprecedented impact on Earth's climate system and caused change on a global scale. [205] The largest driver of warming is the emission of greenhouse gases, of which more than 90% are carbon dioxide and methane. [206] Fossil fuel burning ( coal, oil, and natural gas) for energy consumption is the main source of these emissions, with additional contributions from agriculture, deforestation, and manufacturing. [207] Temperature rise is accelerated or tempered by climate feedbacks, such as loss of sunlight-reflecting snow and ice cover, increased water vapor (a greenhouse gas itself), and changes to land and ocean carbon sinks.

Conservation biology

Efforts are made to preserve the natural characteristics of Hopetoun Falls, Australia, without affecting visitors' access.

Conservation biology is the study of the conservation of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions. [208] [209] [210] It is concerned with factors that influence the maintenance, loss, and restoration of biodiversity and the science of sustaining evolutionary processes that engender genetic, population, species, and ecosystem diversity. [211] [212] [213] [214] The concern stems from estimates suggesting that up to 50% of all species on the planet will disappear within the next 50 years, [215] which has contributed to poverty, starvation, and will reset the course of evolution on this planet. [216] [217] Biodiversity affects the functioning of ecosystems, which provide a variety of services upon which people depend.

Conservation biologists research and educate on the trends of biodiversity loss, species extinctions, and the negative effect these are having on our capabilities to sustain the well-being of human society. Organizations and citizens are responding to the the current biodiversity crisis through conservation action plans that direct research, monitoring, and education programs that engage concerns at local through global scales. [218] [211] [212] [213]

See also

Notes

  1. ^ The first eukaryotes were "neither plants, animals, nor fungi", hence as defined, protists would include the last eukaryotic common ancestor.

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