1.
Organism
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In biology, an organism is any contiguous living system, such as an animal, plant, fungus, protist, archaeon, or bacterium. All known types of organisms are capable of some degree of response to stimuli, reproduction, growth and development and homeostasis. An organism consists of one or more cells, when it has one cell it is known as an organism. Most unicellular organisms are of microscopic scale and are thus described as microorganisms. Humans are multicellular organisms composed of trillions of cells grouped into specialized tissues. An organism may be either a prokaryote or a eukaryote, prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a cell nucleus. Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes, estimates on the number of Earths current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to five billion species. In 2016, a set of 355 genes from the last universal ancestor of all living organisms living was identified. The term organism first appeared in the English language in 1703 and it is directly related to the term organization. There is a tradition of defining organisms as self-organizing beings. An organism may be defined as an assembly of molecules functioning as a more or less stable whole that exhibits the properties of life. Dictionary definitions can be broad, using such as any living structure, such as a plant, animal, fungus or bacterium, capable of growth. Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the machinery of a host cell for reproduction. A superorganism is an organism consisting of individuals working together as a single functional or social unit. There has been controversy about the best way to define the organism, several contributions are responses to the suggestion that the category of organism may well not be adequate in biology. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction and this controversy is problematic because some cellular organisms are also incapable of independent survival and live as obligatory intracellular parasites
2.
Phylogenetics
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In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks, -lə-/ is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, the result of these analyses is a phylogeny – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a tree can be living organisms or fossils. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, taxonomy is the classification, identification and naming of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline, usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood, and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed, prior to 1990, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses, the term phylogeny derives from the German Phylogenie, introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the phyletic approach. During the late 19th century, Ernst Haeckels recapitulation theory, or biogenetic fundamental law, was widely accepted, but this theory has long been rejected. O. See, Huerta-Cepas, Jaime, Dopazo, Joaquín, Gabaldón, ETE, A python Environment for Tree Exploration. PhylomeDB, A public database hosting thousands of gene phylogenies ranging many different species, See, Huerta-Cepas, J. Capella-Gutierrez, S. Pryszcz, L. P. Denisov, I. Kormes, D. Marcet-Houben, M. Gabaldón, T. PhylomeDB v3.0, An expanding repository of genome-wide collections of trees, alignments, lents, N. H. Cifuentes, O. E. Carpi, A. Teaching the Process of Molecular Phylogeny and Systematics, A Multi-Part Inquiry-Based Exercise
3.
Evolution
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Evolution is change in the heritable characteristics of biological populations over successive generations. Evolutionary processes give rise to biodiversity at every level of organisation, including the levels of species, individual organisms. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all living on Earth. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, existing patterns of biodiversity have been shaped both by speciation and by extinction. More than 99 percent of all species that lived on Earth are estimated to be extinct. Estimates of Earths current species range from 10 to 14 million, more recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. In the mid-19th century, Charles Darwin formulated the theory of evolution by natural selection. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are fitted for the functional roles they perform. The processes by which the changes occur, from one generation to another, are called evolutionary processes or mechanisms, the four most widely recognized evolutionary processes are natural selection, genetic drift, mutation and gene migration. Natural selection and genetic drift sort variation, mutation and gene migration create variation, consequences of selection can include meiotic drive, nonrandom mating and genetic hitchhiking. In the early 20th century the modern evolutionary synthesis integrated classical genetics with Darwins theory of evolution by natural selection through the discipline of population genetics, the importance of natural selection as a cause of evolution was accepted into other branches of biology. Moreover, previously held notions about evolution, such as orthogenesis, evolutionism, evolutionary computation, a sub-field of artificial intelligence, involves the application of Darwinian principles to problems in computer science. The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander, such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura, in contrast to these materialistic views, Aristotelianism considered all natural things as actualisations of fixed natural possibilities, known as forms. This was part of a teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. In the 17th century, the new method of modern science rejected the Aristotelian approach, however, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. The biological classification introduced by Carl Linnaeus in 1735 explicitly recognized the nature of species relationships. Other naturalists of this time speculated on the change of species over time according to natural laws
4.
Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
5.
Taxa
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In biology, a taxon is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is known by a particular name and given a particular ranking, especially if. It is not uncommon, however, for taxonomists to remain at odds over what belongs to a taxon, if a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping. Many modern systematists, such as advocates of phylogenetic nomenclature, use cladistic methods that require taxa to be monophyletic and their basic unit, therefore, is the clade rather than the taxon. Similarly, among those contemporary taxonomists working with the traditional Linnean nomenclature, an example of a well-established taxon that is not also a clade is the class Reptilia, the reptiles, birds are descendants of reptiles but are not included in the Reptilia. The term taxon was first used in 1926 by Adolf Meyer-Abich for animal groups, for plants, it was proposed by Herman Johannes Lam in 1948, and it was adopted at the VII International Botanical Congress, held in 1950. The Glossary of the International Code of Zoological Nomenclature defines a taxon, a taxon encompasses all included taxa of lower rank and individual organisms. A taxon can be assigned a rank, usually when it is given a formal name. Phylum applies formally to any domain, but traditionally it was always used for animals, whereas Division was traditionally often used for plants, fungi. A prefix is used to indicate a ranking of lesser importance, the prefix super- indicates a rank above, the prefix sub- indicates a rank below. In zoology the prefix infra- indicates a rank below sub-, for instance, among the additional ranks of class are superclass, subclass and infraclass. Rank is relative, and restricted to a particular systematic schema, for example, liverworts have been grouped, in various systems of classification, as a family, order, class, or division. Many cladists do not see any need to depart from traditional nomenclature as governed by the ICZN, ICN, etc
6.
Species
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In biology, a species is the basic unit of biological classification and a taxonomic rank. A species is defined as the largest group of organisms in which two individuals can produce fertile offspring, typically by sexual reproduction. While this definition is often adequate, looked at more closely it is problematic, for example, with hybridisation, in a species complex of hundreds of similar microspecies, or in a ring species, the boundaries between closely related species become unclear. Other ways of defining species include similarity of DNA, morphology, all species are given a two-part name, a binomial. The first part of a binomial is the genus to which the species belongs, the second part is called the specific name or the specific epithet. For example, Boa constrictor is one of four species of the Boa genus, Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time, Charles Darwins 1859 book The Origin of Species explained how species could arise by natural selection. Genes can sometimes be exchanged between species by horizontal transfer, and species may become extinct for a variety of reasons. In his biology, Aristotle used the term γένος to mean a kind, such as a bird or fish, a kind was distinguished by its attributes, for instance, a bird has feathers, a beak, wings, a hard-shelled egg, and warm blood. A form was distinguished by being shared by all its members, Aristotle believed all kinds and forms to be distinct and unchanging. His approach remained influential until the Renaissance, when observers in the Early Modern period began to develop systems of organization for living things, they placed each kind of animal or plant into a context. Many of these early delineation schemes would now be considered whimsical, animals likewise that differ specifically preserve their distinct species permanently, one species never springs from the seed of another nor vice versa. In the 18th century, the Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics and he established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships. At the time, however, it was widely believed that there was no organic connection between species, no matter how similar they appeared. However, whether or not it was supposed to be fixed, by the 19th century, naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, described the transmutation of species, proposing that a species could change over time, in 1859, Charles Darwin and Alfred Russel Wallace provided a compelling account of evolution and the formation of new species. Darwin argued that it was populations that evolved, not individuals and this required a new definition of species. Darwin concluded that species are what appear to be, ideas
7.
Linnaean taxonomy
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Linnaean taxonomy can mean either of two related concepts, the particular form of biological classification set up by Carl Linnaeus, as set forth in his Systema Naturae and subsequent works. In the taxonomy of Linnaeus there are three kingdoms, divided into classes, and they, in turn, into orders, families, genera, a term for rank-based classification of organisms, in general. That is, taxonomy in the sense of the word. This term is used as opposed to cladistic systematics, which groups organisms into clades. It is attributed to Linnaeus, although he neither invented the concept of ranked classification nor gave it its present form, in his Imperium Naturae, Linnaeus established three kingdoms, namely Regnum Animale, Regnum Vegetabile and Regnum Lapideum. This approach, the Animal, Vegetable and Mineral Kingdoms, survives today in the mind, notably in the form of the parlour game question, Is it animal. The work of Linnaeus had a impact on science, it was indispensable as a foundation for biological nomenclature. However, the impact he had on science was not because of the value of his taxonomy and his classes and orders of plants, according to his Systema Sexuale, were never intended to represent natural groups but only for use in identification. They were used for that purpose well into the nineteenth century, within each class were several orders. The Linnaean classes for plants, in the Sexual System, were, monandria, flowers with 1 stamen Classis 2. Diandria, flowers with 2 stamens Classis 3, triandria, flowers with 3 stamens Classis 4. Tetrandria, flowers with 4 stamens Classis 5, pentandria, flowers with 5 stamens Classis 6. Hexandria, flowers with 6 stamens Hexandria monogynia pp. 285–352 Hexandria polygynia pp. 342–343 Classis 7, heptandria, flowers with 7 stamens Classis 8. Octandria, flowers with 8 stamens Classis 9, enneandria, flowers with 9 stamens Classis 10. Decandria, flowers with 10 stamens Classis 11, dodecandria, flowers with 12 stamens Classis 12. Icosandria, flowers with 20 stamens, perigynous Classis 13, polyandria, flowers with many stamens, inserted on the receptacle Classis 14. Didynamia, flowers with 4 stamens,2 long and 2 short Classis 15, tetradynamia, flowers with 6 stamens,4 long and 2 short Classis 16. Monadelphia, flowers with the separate, but the filaments united
8.
Phylogenetic nomenclature
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Phylogenetic nomenclature, often called cladistic nomenclature, is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. Phylogenetic nomenclature is not regulated, but the International Code of Phylogenetic Nomenclature is intended to regulate it once it is ratified. Phylogenetic nomenclature ties names to clades, groups consisting of an ancestor and these groups can equivalently be called monophyletic. There are slightly different ways of specifying the ancestor, which are discussed below, once the ancestor is specified, the meaning of the name is fixed, the ancestor and all organisms which are its descendants are included in the named taxon. Listing all these organisms requires the full phylogenetic tree to be known, in practice, there are only one or more hypotheses as to the correct tree. Different hypotheses lead to different organisms being thought to be included in the named taxon, in this sense the name is independent of theory revision. Phylogenetic nomenclature ties names to clades, groups consisting solely of an ancestor, all that is needed to specify a clade, therefore, is to designate the ancestor. There are a number of ways of doing this, commonly, the ancestor is indicated by its relation to two or more specifiers that are mentioned explicitly. The diagram shows three ways of doing this. A node-based definition could read, the last common ancestor of A and B, thus, the entire line below the junction of A and B does not belong to the clade to which the name with this definition refers. Example, The sauropod dinosaurs consist of the last common ancestor of Vulcanodon and Apatosaurus and this ancestor was the first sauropod. C could include other dinosaurs like Stegosaurus, a branch-based definition, often called a stem-based definition, could read, the first ancestor of A which is not also an ancestor of C, and all descendants of that ancestor. Thus, the line below the junction of A and B does belong to the clade to which the name with this definition refers. Example, The rodents consist of the first ancestor of the mouse that is not also an ancestor of the eastern cottontail rabbit together with all descendants of that ancestor. Here, the ancestor is the very first rodent, B is some other descendant, perhaps the red squirrel. An apomorphy-based definition could read, the first ancestor of A to possess trait M that is inherited by A, in the diagram, M evolves at the intersection of the horizontal line with the tree. Thus, the clade to which the name with this definition refers contains that part of the line below the last common ancestor of A and B which corresponds to ancestors possessing the apomorphy M, the lower part of the line is excluded. It is not required that B have trait M, it may have disappeared in the leading to B
9.
Paraphyly
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In taxonomy, a group is paraphyletic if it consists of the groups last common ancestor and all descendants of that ancestor excluding a few—typically only one or two—monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups, the term is commonly used in phylogenetics and in linguistics. The term was coined to apply to well-known taxa like reptiles which, as commonly named and traditionally defined, is paraphyletic with respect to mammals and birds. Reptilia contains the last common ancestor of reptiles and all descendants of that all extant reptiles as well as the extinct synapsids—except for mammals. Other commonly recognized paraphyletic groups include fish, monkeys and lizards, if many subgroups are missing from the named group, it is said to be polyparaphyletic. A paraphyletic group cannot be a clade, which is a monophyletic group, groups that include all the descendants of a common ancestor are said to be monophyletic. A paraphyletic group is a group from which one or more subsidiary clades is excluded to form a separate group. Ereshefsky has argued that paraphyletic taxa are the result of anagenesis in the group or groups. For example, dinosaurs are paraphyletic with respect to birds because birds possess many features that dinosaurs lack, a group whose identifying features evolved convergently in two or more lineages is polyphyletic. More broadly, any taxon that is not paraphyletic or monophyletic can be called polyphyletic and these terms were developed during the debates of the 1960s and 70s accompanying the rise of cladistics. The prokaryotes, because they exclude the eukaryotes, a descendant group, bacteria and Archaea are prokaryotes, but archaea and eukaryotes share a common ancestor that is not ancestral to the bacteria. The prokaryote/eukaryote distinction was proposed by Edouard Chatton in 1937 and was accepted after being adopted by Roger Stanier. The botanical code abandoned consideration of bacterial nomenclature in 1975, currently, dicotyledons are paraphyletic because the group excludes monocotyledons. Dicotyledon has not been used as an ICBN classification for decades, phylogenetic analysis indicates that the monocots are a development from a dicot ancestor. Excluding monocots from the dicots makes the latter a paraphyletic group, the order Artiodactyla, because it excludes Cetaceans. In the ICZN Code, the two taxa are orders of equal rank, molecular studies, however, have shown that the Cetacea descend from the Artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetacean descendants the Artiodactyls must be paraphyletic, the class Reptilia as traditionally defined, because it excludes birds and mammals. In the ICZN Code, the three taxa are classes of equal rank, however, mammals hail from the synapsids and birds are descended from the dinosaurs, both of which are reptiles
10.
Jean-Baptiste Lamarck
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Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, often known simply as Lamarck, was a French naturalist. He was a soldier, biologist, academic, and a proponent of the idea that evolution occurred and proceeded in accordance with natural laws. He gave the term biology a broader meaning by coining the term for special sciences, chemistry, meteorology, geology, Lamarck fought in the Pomeranian War with Prussia, and was awarded a commission for bravery on the battlefield. At his post in Monaco, Lamarck became interested in natural history and he retired from the army after being injured in 1766, and returned to his medical studies. Lamarck developed a particular interest in botany, and later, after he published the three-volume work Flore françoise, Lamarck became involved in the Jardin des Plantes and was appointed to the Chair of Botany in 1788. When the Muséum national dHistoire naturelle was founded in 1793, Lamarck was appointed as a professor of zoology, in 1801, he published Système des animaux sans vertèbres, a major work on the classification of invertebrates, a term he coined. In an 1802 publication, he one of the first to use the term biology in its modern sense. Lamarck continued his work as an authority on invertebrate zoology. He is remembered, at least in malacology, as a taxonomist of considerable stature, however, his idea of soft inheritance was, perhaps, a reflection of the wisdom of the time accepted by many natural historians. Scientists have debated whether advances in the field of transgenerational epigenetics mean that Lamarck was to an extent correct, jean-Baptiste Lamarck was born in Bazentin, Picardy, northern France, as the eleventh child in an impoverished aristocratic family. Male members of the Lamarck family had served in the French army. Lamarcks eldest brother was killed in combat at the Siege of Bergen op Zoom, yielding to the wishes of his father, Lamarck enrolled in a Jesuit college in Amiens in the late 1750s. After his father died in 1760, Lamarck bought himself a horse, and rode across the country to join the French army, Lamarck showed great physical courage on the battlefield in the Pomeranian War with Prussia, and he was even nominated for the lieutenancy. Lamarcks company was exposed to the direct artillery fire of their enemies. When their colonel reached the remains of their company, this display of courage, however, when one of his comrades playfully lifted him by the head, he sustained an inflammation in the lymphatic glands of the neck, and he was sent to Paris to receive treatment. He underwent an operation, and continued his treatment for a year. He was awarded a commission and settled at his post in Monaco and it was there that he encountered Traité des plantes usuelles, a botany book by James Francis Chomel. With a reduced pension of only 400 francs a year, Lamarck resolved to pursue a profession and he attempted to study medicine, and supported himself by working in a bank office
11.
Dendrogram
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A dendrogram is a tree diagram frequently used to illustrate the arrangement of the clusters produced by hierarchical clustering. Dendrograms are often used in biology to illustrate the clustering of genes or samples, sometimes on top of heatmaps. For a clustering example, suppose this data is to be clustered using Euclidean distance as the distance metric, iris dendrogram - Example of using a dendrogram to visualize the 3 clusters from hierarchical clustering using the complete method vs the real species category
12.
Animal
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Animals are multicellular, eukaryotic organisms of the kingdom Animalia. The animal kingdom emerged as a clade within Apoikozoa as the group to the choanoflagellates. Animals are motile, meaning they can move spontaneously and independently at some point in their lives and their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later in their lives. All animals are heterotrophs, they must ingest other organisms or their products for sustenance, most known animal phyla appeared in the fossil record as marine species during the Cambrian explosion, about 542 million years ago. Animals can be divided broadly into vertebrates and invertebrates, vertebrates have a backbone or spine, and amount to less than five percent of all described animal species. They include fish, amphibians, reptiles, birds and mammals, the remaining animals are the invertebrates, which lack a backbone. These include molluscs, arthropods, annelids, nematodes, flatworms, cnidarians, ctenophores, the study of animals is called zoology. The word animal comes from the Latin animalis, meaning having breath, the biological definition of the word refers to all members of the kingdom Animalia, encompassing creatures as diverse as sponges, jellyfish, insects, and humans. Aristotle divided the world between animals and plants, and this was followed by Carl Linnaeus, in the first hierarchical classification. In Linnaeuss original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then the last four have all been subsumed into a single phylum, in 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms, Metazoa and Protozoa. The protozoa were later moved to the kingdom Protista, leaving only the metazoa, thus Metazoa is now considered a synonym of Animalia. Animals have several characteristics that set apart from other living things. Animals are eukaryotic and multicellular, which separates them from bacteria and they are heterotrophic, generally digesting food in an internal chamber, which separates them from plants and algae. They are also distinguished from plants, algae, and fungi by lacking cell walls. All animals are motile, if only at life stages. In most animals, embryos pass through a stage, which is a characteristic exclusive to animals. With a few exceptions, most notably the sponges and Placozoa and these include muscles, which are able to contract and control locomotion, and nerve tissues, which send and process signals
13.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
14.
Kingdom (biology)
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In biology, kingdom is the second highest taxonomic rank below domain. Kingdoms are divided into groups called phyla. Traditionally, textbooks from the United States used a system of six kingdoms while textbooks in Great Britain, India, Australia, Latin America and other countries used five kingdoms. Later two further main ranks were introduced, making the kingdom, phylum or division, class, order, family, genus. In the 1960s a rank was introduced above kingdom, namely domain, prefixes can be added so subkingdom and infrakingdom are the two ranks immediately below kingdom. Superkingdom may be considered as an equivalent of domain or empire or as an independent rank between kingdom and domain or subdomain, in some classification systems the additional rank branch can be inserted between subkingdom and infrakingdom. Taxonomic ranks, including kingdoms, were to be groups of organisms with a common ancestor, based on such RNA studies, Carl Woese thought life could be divided into three large divisions and referred to them as the three primary kingdom model or urkingdom model. In 1990, the domain was proposed for the highest rank. This term represents a synonym for the category of dominion, introduced by Moore in 1974, unlike Moore, Whoese et al. did not suggest a Latin term for this category, which represents a further argument supporting the accurately introduced term dominion. It was also found that the eukaryotes are more related to the Archaea than they are to the Eubacteria. Although the primacy of the Eubacteria-Archaea divide has been questioned, it has been upheld by subsequent research, there is no consensus on how many kingdoms exist in the classification scheme proposed by Woese. In 2004, a article by Simpson and Roger noted that the Protista were a grab-bag for all eukaryotes that are not animals. On this basis, the diagram opposite showed the real kingdoms of the eukaryotes, a classification which followed this approach was produced in 2005 for the International Society of Protistologists, by a committee which worked in collaboration with specialists from many societies. It divided the eukaryotes into the same six supergroups, the published classification deliberately did not use formal taxonomic ranks, including that of kingdom. In this system the multicellular animals are descended from the same ancestor as both the unicellular choanoflagellates and the fungi which form the Opisthokonta, Plants are thought to be more distantly related to animals and fungi. Beyond this, there does not appear to be a consensus, rogozin et al. in 2009 noted that The deep phylogeny of eukaryotes is an extremely difficult and controversial problem. The classification of living things into animals and plants is an ancient one, aristotle classified animal species in his History of Animals, while his pupil Theophrastus wrote a parallel work, the Historia Plantarum, on plants. Carl Linnaeus laid the foundations for biological nomenclature, now regulated by the Nomenclature Codes
15.
Charles Darwin
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Charles Robert Darwin, FRS FRGS FLS FZS was an English naturalist, geologist and biologist, best known for his contributions to the science of evolution. Darwin published his theory of evolution with compelling evidence in his 1859 book On the Origin of Species, by the 1870s, the scientific community and much of the general public had accepted evolution as a fact. In modified form, Darwins scientific discovery is the theory of the life sciences. Darwins early interest in nature led him to neglect his education at the University of Edinburgh, instead. Studies at the University of Cambridge encouraged his passion for natural science, puzzled by the geographical distribution of wildlife and fossils he collected on the voyage, Darwin began detailed investigations and in 1838 conceived his theory of natural selection. Although he discussed his ideas with several naturalists, he needed time for extensive research and he was writing up his theory in 1858 when Alfred Russel Wallace sent him an essay that described the same idea, prompting immediate joint publication of both of their theories. Darwins work established evolutionary descent with modification as the dominant scientific explanation of diversification in nature, in 1871 he examined human evolution and sexual selection in The Descent of Man, and Selection in Relation to Sex, followed by The Expression of the Emotions in Man and Animals. His research on plants was published in a series of books, Darwin has been described as one of the most influential figures in human history, and he was honoured by burial in Westminster Abbey. Charles Robert Darwin was born in Shrewsbury, Shropshire, on 12 February 1809, at his familys home and he was the fifth of six children of wealthy society doctor and financier Robert Darwin and Susannah Darwin. He was the grandson of two prominent abolitionists, Erasmus Darwin on his fathers side, and Josiah Wedgwood on his mothers side, both families were largely Unitarian, though the Wedgwoods were adopting Anglicanism. The eight-year-old Charles already had a taste for history and collecting when he joined the day school run by its preacher in 1817. From September 1818, he joined his older brother Erasmus attending the nearby Anglican Shrewsbury School as a boarder and he found lectures dull and surgery distressing, so neglected his studies. He learned taxidermy in around 40 daily hour-long sessions from John Edmonstone, one day, Grant praised Lamarcks evolutionary ideas. Darwin was astonished by Grants audacity, but had recently read similar ideas in his grandfather Erasmus journals, Darwin was rather bored by Robert Jamesons natural-history course, which covered geology - including the debate between Neptunism and Plutonism. He learned the classification of plants, and assisted with work on the collections of the University Museum, as Darwin was unqualified for the Tripos, he joined the ordinary degree course in January 1828. He preferred riding and shooting to studying, when his own exams drew near, Darwin focused on his studies and was delighted by the language and logic of William Paleys Evidences of Christianity. In his final examination in January 1831 Darwin did well, coming out of 178 candidates for the ordinary degree. Darwin had to stay at Cambridge until June 1831, inspired with a burning zeal to contribute, Darwin planned to visit Tenerife with some classmates after graduation to study natural history in the tropics
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On the Origin of Species
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On the Origin of Species, published on 24 November 1859, is a work of scientific literature by Charles Darwin which is considered to be the foundation of evolutionary biology. Darwins book introduced the theory that populations evolve over the course of generations through a process of natural selection. It presented a body of evidence that the diversity of life arose by common descent through a pattern of evolution. Darwin included evidence that he had gathered on the Beagle expedition in the 1830s and his subsequent findings from research, correspondence, various evolutionary ideas had already been proposed to explain new findings in biology. The political and theological implications were intensely debated, but transmutation was not accepted by the scientific mainstream, the book was written for non-specialist readers and attracted widespread interest upon its publication. As Darwin was an eminent scientist, his findings were taken seriously and the evidence he presented generated scientific, philosophical, and religious discussion. The debate over the book contributed to the campaign by T. H. Huxley, during the eclipse of Darwinism from the 1880s to the 1930s, various other mechanisms of evolution were given more credit. Despite periodic fluctuations, populations remain roughly the same size, resources such as food are limited and are relatively stable over time. Individuals in a population significantly from one another. Much of this variation is heritable and this slowly effected process results in populations changing to adapt to their environments, and ultimately, these variations accumulate over time to form new species. In later editions of the book, Darwin traced evolutionary ideas as far back as Aristotle, Nature was widely believed to be unstable and capricious, with monstrous births from union between species, and spontaneous generation of life. After the turmoil of the English Civil War, the Royal Society wanted to show that science did not threaten religious, in Gods benevolent design, carnivores caused mercifully swift death, but the suffering caused by parasitism was a puzzling problem. The biological classification introduced by Carl Linnaeus in 1735 also viewed species as fixed according to the divine plan. In 1766, Georges Buffon suggested that some species, such as horses and asses, or lions, tigers. The Ussher chronology of the 1650s had calculated creation at 4004 BC, wernerians thought strata were deposits from shrinking seas, but James Hutton proposed a self-maintaining infinite cycle, anticipating uniformitarianism. Charles Darwins grandfather Erasmus Darwin outlined a hypothesis of transmutation of species in the 1790s and this process was later called Lamarckism. Lamarck thought there was an inherent progressive tendency driving organisms continuously towards greater complexity, in parallel, Georges Cuvier strongly disputed such ideas, holding that unrelated, fixed species showed similarities that reflected a design for functional needs. His palæontological work in the 1790s had established the reality of extinction, in Britain, William Paleys Natural Theology saw adaptation as evidence of beneficial design by the Creator acting through natural laws
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Common descent
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Common descent describes how, in evolutionary biology, a group of organisms share a most recent common ancestor. There is evidence of descent that all life on Earth is descended from the last universal common ancestor. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all living on Earth. Common ancestry between organisms of different species arises during speciation, in new species are established from a single ancestral population. Organisms which share a more recent common ancestor are more closely related, the most recent common ancestor of all currently living organisms is the last universal ancestor, which lived about 3.9 billion years ago. Chance, one might say, turned out a vast number of individuals, a much greater number showed neither adaptation nor order, these last have all perished. Thus the species which we see today are but a part of all those that a blind destiny has produced. In 1790, Immanuel Kant wrote in Kritik der Urteilskraft that the analogy of animal forms implies a common original type, furthermore, the genetic code is nearly identical for all known lifeforms, from bacteria and archaea to animals and plants. The universality of this code is generally regarded by biologists as definitive evidence in favor of the theory of common descent. Analysis of the differences in the genetic code has also provided support for universal common descent. An example would be Cytochrome c which most organisms actually share, a statistical comparison of various alternative hypotheses has shown that universal common ancestry is significantly more probable than models involving multiple origins. Similarities which have no adaptive relevance cannot be explained by convergent evolution, such evidence has come from two areas, amino acid sequences and DNA sequences. Proteins with the same three-dimensional structure need not have identical amino acid sequences, in certain cases, there are several codons that code for the same amino acid. Thus, if two species use the same codon at the place to specify an amino acid that can be represented by more than one codon. The universality of many aspects of life is often pointed to as supportive evidence to the more compelling evidence listed above. These similarities include the energy carrier adenosine triphosphate, and the fact that all amino acids found in proteins are left-handed. It is, however, possible that these similarities resulted because of the laws of physics and chemistry, rather than common descent. Another important piece of evidence is that it is possible to construct detailed phylogenetic trees mapping out the proposed divisions and it should be noted, however, that the formal test was criticised for not including consideration of convergent evolution, and Theobald has defended the method against this claim
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Pierre Louis Maupertuis
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Pierre Louis Moreau de Maupertuis was a French mathematician, philosopher and man of letters. He became the Director of the Académie des Sciences, and the first President of the Prussian Academy of Science, Maupertuis made an expedition to Lapland to determine the shape of the Earth. He is often credited with having invented the principle of least action and his work in natural history is interesting in relation to modern science, since he touched on aspects of heredity and the struggle for life. Maupertuis was born at Saint-Malo, France, to a wealthy family of merchant-corsairs. His father, Renė, had involved in a number of enterprises that were central to the monarchy so that he thrived socially and politically. The son was educated in mathematics by a tutor, Nicolas Guisnée. In 1723 he was admitted to the Académie des Sciences and his early mathematical work revolved around the vis viva controversy, for which Maupertuis developed and extended the work of Isaac Newton and argued against the waning Cartesian mechanics. In the 1730s, the shape of the Earth became a flashpoint in the battle among rival systems of mechanics, Maupertuis, based on his exposition of Newton predicted that the Earth should be oblate, while his rival Jacques Cassini measured it astronomically to be prolate. In 1736 Maupertuis acted as chief of the French Geodesic Mission sent by King Louis XV to Lapland to measure the length of a degree of arc of the meridian and his results, which he published in a book detailing his procedures, essentially settled the controversy in his favor. The book included a narrative of the expedition, and an account of the Käymäjärvi Inscriptions. On his return home he became a member of almost all the societies of Europe. He also expanded into the realm, anonymously publishing a book that was part popular science, part philosophy. In 1740 Maupertuis went to Berlin at the invitation of Frederick II of Prussia, and took part in the Battle of Mollwitz, where he was taken prisoner by the Austrians. On his release he returned to Berlin, and thence to Paris, where he was elected director of the Academy of Sciences in 1742, and in the following year was admitted into the Académie française. His position became extremely awkward with the outbreak of the Seven Years War between his country and his patrons, and his reputation suffered in both Paris and Berlin. Finding his health declining, he retired in 1757 to the south of France, but went in 1758 to Basel, Maupertuis difficult disposition involved him in constant quarrels, of which his controversies with Samuel König and Voltaire during the latter part of his life are examples. The brilliance of much of what he did was undermined by his tendency to leave work unfinished and it was the insight of genius that led him to least-action principle, but a lack of intellectual energy or rigour that prevented his giving it the mathematical foundation that Lagrange would provide. He reveals remarkable powers of perception in heredity, in understanding the mechanism by which developed, even in immunology
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Transmutation of species
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The debate over them was an important stage in the history of evolutionary thought and would influence the subsequent reaction to Darwins theory. Transmutation was one of the commonly used for evolutionary ideas in the 19th century before Charles Darwin published On The Origin of Species. Transmutation had previously used as a term in alchemy to describe the transformation of base metals into gold. Transformation is another word used quite as often as transmutation in this context and these early 19th century evolutionary ideas played an important role in the history of evolutionary thought. The terminology did not settle down until some time after the publication of the Origin of Species. The word evolution was quite a late-comer, it can be seen in Herbert Spencers Social Statics of 1851, and there is at least one earlier example, jean-Baptiste Lamarck proposed a hypothesis on the transmutation of species in Philosophie Zoologique. Lamarck did not believe that all living things shared a common ancestor, rather he believed that simple forms of life were created continuously by spontaneous generation. Lamarck also recognized that species were adapted to their environment and he argued that these changes would be inherited by the next generation and produce slow adaptation to the environment. Grant developed Lamarcks and Erasmus Darwins ideas of transmutation and evolutionism, as a young student Charles Darwin joined Grant in investigations of the life cycle of marine animals. Jamesons course closed with lectures on the Origin of the Species of Animals, in 1844 the Scottish publisher Robert Chambers anonymously published an influential and extremely controversial book of popular science entitled Vestiges of the Natural History of Creation. This book proposed a scenario for the origins of the solar system. It claimed that the record showed a progressive ascent of animals with current animals being branches off a main line that leads progressively to humanity. It implied that the lead to the unfolding of a preordained plan that had been woven into the laws that governed the universe. Darwin himself openly deplored the authors poverty of intellect, and dismissed it as a literary curiosity and it also influenced some younger naturalists, including Alfred Russel Wallace, to take an interest in the idea of transmutation. Ideas about the transmutation of species were associated with the radical materialism of the enlightenment and were greeted with hostility by more conservative thinkers. Cuvier attacked the ideas of Lamarck and Geoffroy Saint-Hilaire, agreeing with Aristotle that species were immutable and he also noted that drawings of animals and animal mummies from Egypt, which were thousands of years old, showed no signs of change when compared with modern animals. The strength of Cuviers arguments and his reputation as a leading scientist helped keep transmutational ideas out of the mainstream for decades. Instead, he advocated a form of creation, in which each species had its centre of creation and was designed for this particular habitat
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Erasmus Darwin
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Erasmus Darwin was an English physician. One of the key thinkers of the Midlands Enlightenment, he was also a philosopher, physiologist, slave-trade abolitionist, inventor. His poems included much natural history, including a statement of evolution and he was a member of the Darwin–Wedgwood family, which includes his grandsons Charles Darwin and Francis Galton. Darwin was a member of the Lunar Society of Birmingham. He turned down an invitation of George IIIs to become a physician to the King, Erasmus Darwin House, his home in Lichfield, is now a museum dedicated to Erasmus Darwin and his lifes work. A school in nearby Chasetown recently converted to Academy status and is now known as Erasmus Darwin Academy, Darwin was born at Elston Hall, Nottinghamshire near Newark-on-Trent, England, the youngest of seven children of Robert Darwin of Elston, a lawyer, and his wife Elizabeth Hill. The name Erasmus had been used by a number of his family and derives from his ancestor Erasmus Earle and he obtained his medical education at the University of Edinburgh Medical School. Whether Darwin ever obtained the degree of MD is not known. Darwin settled in 1756 as a physician at Nottingham, but met little success. A few weeks after his arrival, using a course of treatment. This ensured his success in the new locale, Darwin was a highly successful physician for more than fifty years in the Midlands. George III invited him to be Royal Physician, but Darwin declined, in Lichfield, Darwin wrote didactic poetry, developed his system of evolution, and invented amongst other things, a carriage steering mechanism, a manuscript copier and a speaking machine. Darwin married twice and had 14 children, including two daughters by an employee, and, possibly, at least one further illegitimate daughter. In 1757 he married Mary Howard, a governess, Mary Parker, was hired to look after Robert. In 1782, Mary Sr married Joseph Day, a Birmingham merchant, Darwin may have fathered another child, this time with a married woman. A Lucy Swift gave birth in 1771 to a baby, also named Lucy, who was christened a daughter of her mother and William Swift, Lucy Jr. married John Hardcastle in Derby in 1792 and their daughter, Mary, married Francis Boott, the physician. When Edward Pole died, Darwin married Elizabeth and moved to her home, Radbourne Hall, the hall and village are these days known as Radbourne. In 1782, they moved to Full Street, Derby, harriet Darwin, married Admiral Thomas James Maling Darwin died suddenly on 18 April 1802, weeks after having moved to Breadsall Priory, just north of Derby
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Philosophie Zoologique
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Philosophie Zoologique is an 1809 book by the French naturalist Jean-Baptiste Lamarck, in which he outlines his pre-Darwinian theory of evolution now known as Lamarckism. In the book, Lamarck named two supposed laws that would enable animal species to acquire characteristics under the influence of the environment, the first law stated that use or disuse would cause body structures to grow or shrink over the generations. The second law asserted that changes would be inherited. Those conditions together imply that species continuously change by adaptation to their environments, Lamarck was largely ignored by the major French zoologist Cuvier, but he attracted much more interest abroad. The book was read carefully, but its thesis rejected, by nineteenth century including the geologist Charles Lyell. Darwin acknowledged Lamarck as an important zoologist, and his theory a forerunner of Darwins evolution by natural selection and he became known for his work on the taxonomy of the invertebrates, especially of molluscs. He described his theory in his 1802 Recherches sur lorganisation des corps vivants, and in his 1809 Philosophie Zoologique, in the Philosophie Zoologique, Lamarck proposed that species could acquire new characteristics from influences in their environment, in two rules that he named as laws. His first law stated that use or disuse of a bodys structures would cause them to grow or shrink in the course of several generations and his second law held that any changes made in this way would be inherited. Together, Lamarcks laws imply the steady adaptation of animals to their environments and it follows that the species that terminate each branch of the general series are related, at least on one side, to the other neighboring species that shade into them. Lamarck proposed the transmutation of species, but did not believe that all living things shared a common ancestor, rather he believed that simple forms of life were created continuously by spontaneous generation. Page numbers are given in parentheses, VOLUME1 Avertissement Discours Préliminaire Première Partie I. Des Parties de lart dans les productions de la Nature II, De lEspèce parmi les Corps vivans, et de lidée que nous devons attacher à ce mot IV. Généralités sur les Animaux V. Sur lEtat actuel de la Distribution et de la Classification des Animaux VI, dégradation et simplification de lorganisation dune extrémité a lautre de la Chaîne animale VII. De lOrdre naturel des Animaux et de la disposition quil faut donner a leur distribution generale pour la rendre conforme a lordre meme de la nature Seconde Partie Introduction I, comparison des Corps inorganiques avec les Corps vivans, suivie dun Parallele entre les Animaux et les Vegetaux II. De la Vie, de ce qui la constitue, et des Conditions essentielles a son existence dans un corps VOLUME2 III, De la cause excitatrice des mouvemens organiques IV. De lorgasme et de lirritabilité V, du tissu cellulaire, considere comme la gangue dans laquelle toute organisation a ete formee VI. Des generations directes ou spontanees VII, des resultats immediats de la vie dans un corps VIII. Des facultes communes a tous les corps vivans IX, des facultes particulieres a certains corps vivans Troisieme Partie Introduction I
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English-speaking world
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Approximately 330 to 360 million people speak English as their first language. More than half of live in the United States, followed by some 55 million in England. English is the third largest language by number of speakers, after Mandarin. Estimates that include second language speakers vary greatly, from 470 million to more than 1 billion, david Crystal calculates that non-native speakers as of 2003 outnumbered native speakers by a ratio of 3 to 1. When combining native and non-native speakers, English is the most widely spoken language worldwide, there are six large countries with a majority of native English speakers that are sometimes grouped under the term Anglosphere. They are, in descending order of English speakers, the United States, the United Kingdom, Canada, Australia, Ireland, other substantial communities of native speakers are found in South Africa, and Nigeria. Also there are countries where in a part of the territory English became a language, e. g. Colombias San Andrés y Providencia. This was a result of the influence of British colonization in the area, English is one of the eleven official languages that are given equal status in South Africa. It is also the language in current dependent territories of Australia and of the United States. Although the United States federal government has no official languages, English has been official status by 32 of the 50 state governments. It is, by treaty, the official language for aeronautical. English is one of the languages of the United Nations and many other international organizations. In 2012, excluding native speakers,38 percent of Europeans consider that they can speak English, in publishing, English literature predominates considerably with 28 percent of all books published in the world and 30 percent of web content in 2011. This increasing use of the English language globally has had a impact on many other languages, leading to language shift and even language death. English itself has more open to language shift as multiple regional varieties feed back into the language as a whole. Variation in Nonnative Varieties of English, Northern Ireland Statistics and Research Agency. Census 2011, Key Statistics for Northern Ireland December 2012, language in England and Wales,2011. Language Use in the United States,2011, Population by mother tongue and age groups,2011 counts, for Canada, provinces and territories
23.
Vestiges of the Natural History of Creation
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Vestiges of the Natural History of Creation is an 1844 work of speculative natural history and philosophy by Robert Chambers. The ideas in the book were favoured by Radicals, but its presentation remained popular with a wider public. Prince Albert read it aloud to Queen Victoria in 1845, for decades there was speculation about its authorship. Some of the inspiration for the derived from the Edinburgh Phrenological Society whose materialist influence reached a climax between 1825 and 1840. George Combe, the proponent of phrenological thinking, had published his influential The Constitution of Man in 1828. Chambers was closely involved with Combes associates William A. F. Browne, Chambers died in 1871 and is buried in the grounds of St Andrews Cathedral, within the ancient chapel of St Regulus. The book was published by John Spriggs Morss Churchill in London, great pains were undertaken to secure the secret of the authorship from Churchill, and the public. After Chambers completed each section, his wife copied the manuscript, Alexander Ireland of Manchester delivered the manuscript to the publisher. Proofs were delivered by the printer—a Mr. Savill—back to Ireland, Chambers gave the secret to only four people, his wife, his brother William, Ireland, and Robert Cox. All correspondence to and from Chambers went through Ireland as intermediary, the work puts forward a cosmic theory of transmutation as the natural history of creation which we now call evolution. It suggests that everything currently in existence has developed from earlier forms, solar system, Earth, rocks, plants and corals, fish, land plants, reptiles and birds, mammals, and ultimately man. The book begins by tackling the origins of the solar system and it explains the origins of life by spontaneous generation, citing some questionable experiments that claimed to spontaneously generate insects through electricity. It even goes so far as to connect man’s mental reasoning power with the rest of the animals as an evolutionary step that can be traced backwards through the rest of the lower animals. In this sense, the ideas offered in Vestiges aim at being complete. It contains several comments worthy of repetition in light of more recent debates, a candid consideration of all these circumstances can scarcely fail to introduce into our minds a somewhat different idea of organic creation from what has hitherto been generally entertained. In other words, the fact of extinction — which can be observed in the fossil layers —suggests that some designs were flawed. From this, the author concludes, Some other idea must then come to with regard to the mode in which the Divine Author proceeded in the organic creation, but the suggestion is not a mechanism, as Darwin would propose fifteen years later. The author merely notes that a continually active God is unnecessary, surely this idea is too ridiculous to be for a moment entertained
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Robert Chambers (publisher, born 1802)
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Robert and his elder brother William were both born in the rural town of Peebles in the Borders at the turn of the 19th century. The town had changed little in centuries, the town had old and new parts, each consisting of little more than a single street. Peebles was mainly inhabited by weavers and labourers living in thatched cottages and his father, James Chambers, made his living as a cotton manufacturer. Their slate-roofed house was built by James Chambers father as a gift for his son. A small circulating library in the town, run by Alexander Elder, introduced Robert to books and developed his literary interests when he was young. Occasionally his father would buy books for the library. He eagerly read this for many years, William later recalled that for Robert, the acquisition of knowledge was with him the highest of earthly enjoyments. Robert was sent to schools and showed unusual literary taste and ability. His education was typical for the day, the country school, directed by James Gray, taught the boys reading, writing, and, for an additional charge, arithmetic. In grammar school it was the classics – Latin and Ancient Greek, boys bullied one another and the teacher administered corporal punishment in the classroom for unruly behaviour. Although uninspired by the school, Robert made up for this at the bookseller, both Robert and William were born with six fingers on each hand and six toes on each foot. Their parents attempted to correct this abnormality through operations, and while Williams was successful Robert was left partially lame, so while other boys roughed it outside, Robert was content to stay indoors and study his books. Robert surpassed his brother in his education, which he continued for several years beyond Williams. Robert had been destined for the ministry, but at the age of fifteen he dropped this intended career, the arrival of the power loom suddenly threatened James Chambers cotton business, forcing him to close it down and become a draper. During this time, James began to socialise with a number of French prisoners-of-war on parole who were stationed in Peebles, unfortunately, James Chambers lent these exiles a large amount of credit, and when they were abruptly transferred away he was forced to declare bankruptcy. The family moved to Edinburgh in 1813, Robert continued his education at the High School, and William became a booksellers apprentice. In 1818 Robert, at 16 years old, began his own business as a bookstall-keeper on Leith Walk, at first, his entire stock consisted of some old books belonging to his father, amounting to thirteen feet of shelf space and worth no more than a few pounds. By the end of the first year the value of his stock went up to twelve pounds, while Robert built up a business, his brother William expanded his own by purchasing a home-made printing press and publishing pamphlets as well as creating his own type
25.
Tree of life (biology)
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Tree diagrams originated in the medieval era to represent genealogical relationships. Phylogenetic tree diagrams in the evolutionary sense date back to at least the early 19th century, the term phylogeny for the evolutionary relationships of species through time was coined by Ernst Haeckel, who went further than Darwin in proposing phylogenic histories of life. In contemporary usage, tree of life refers to the compilation of comprehensive phylogenetic databases rooted at the last universal ancestor of life on Earth. The Open Tree of Life, first published 2015, is a project to such a database for free public access. The earliest tree of life was published by the French botanist Augustin Augier in 1801 and it shows the relationships between members of the plant kingdom. Jean-Baptiste Lamarck produced the first branching tree of animals in his Philosophie Zoologique and it was an upside-down tree starting with worms and ending with mammals. However, Lamarck did not believe in common descent of all life, instead, he believed that life consists of separate parallel lines advancing from simple to complex. The American geologist Edward Hitchcock published in 1840 the first tree of life based on paleontology in his Elementary Geology, on the vertical axis are paleontological periods. Hitchcock made a separate tree for plants and animals, the plant and the animal tree are not connected at the bottom of the chart. Furthermore, each starts with multiple origins. Hitchcocks tree was more realistic than Darwins 1859 theoretical tree because Hitchcock used real names in his trees and it is also true that Hitchcocks trees were branching trees. However, they were not evolutionary trees, because Hitchcock believed that a deity was the agent of change and that was an important difference with Darwin. It shows a model of development where fish, reptiles. In the text this branching tree idea is tentatively applied to the history of life on earth, there may be branching, however, the image of a branching tree could easily have inspired others to use it explicitly as a representation of the history of life on earth. In 1858, a year before Darwins Origin, the paleontologist Heinrich Georg Bronn published a hypothetical tree labeled with letters, although not a creationist, Bronn did not propose a mechanism of change. Charles Darwin used the concept of a tree of life in the context of his theory of evolution, in On the Origin of Species Chapter IV he presented an abstract diagram of a theoretical tree of life for species of an unnamed large genus. On the vertical axis divisions labelled I – XIV each represent a thousand generations, similarly, the descendants of I have diversified to become the new varieties w10 and z10. The process is extrapolated for a four thousand generations so that the descendants of A and I become fourteen new species labelled a14 to z14
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Thomas Henry Huxley
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Thomas Henry Huxley PC PRS FLS was an English biologist, known as Darwins Bulldog for his advocacy of Charles Darwins theory of evolution. Huxleys famous debate in 1860 with Samuel Wilberforce was a key moment in the acceptance of evolution. Huxley had been planning to leave Oxford on the day, but, after an encounter with Robert Chambers. Wilberforce was coached by Richard Owen, against whom Huxley also debated about whether humans were closely related to apes. Huxley was slow to accept some of Darwins ideas, such as gradualism, and was undecided about natural selection, instrumental in developing scientific education in Britain, he fought against the more extreme versions of religious tradition. Originally coining the term in 1869, Huxley elaborated on agnosticism in 1889 to frame the nature of claims in terms of what is knowable and what is not. Huxley states Agnosticism, in fact, is not a creed, but a method, the fundamental axiom of modern science. In matters of the intellect, follow your reason as far as it will take you, in matters of the intellect, do not pretend that conclusions are certain which are not demonstrated or demonstrable. Use of that term has continued to the present day, Huxley had little formal schooling and was virtually self-taught. He became perhaps the finest comparative anatomist of the latter 19th century and he worked on invertebrates, clarifying relationships between groups previously little understood. Later, he worked on vertebrates, especially on the relationship between apes and humans, after comparing Archaeopteryx with Compsognathus, he concluded that birds evolved from small carnivorous dinosaurs, a theory widely accepted today. Thomas Henry Huxley was born in Ealing, which was then a village in Middlesex and he was the second youngest of eight children of George Huxley and Rachel Withers. Like some other British scientists of the century such as Alfred Russel Wallace. His father was a teacher at Ealing School until it closed. As a result, Thomas left school at age 10, after two years of formal schooling. Despite this unenviable start, Huxley was determined to educate himself and he became one of the great autodidacts of the nineteenth century. At first he read Thomas Carlyle, James Huttons Geology, in his teens he taught himself German, eventually becoming fluent and used by Charles Darwin as a translator of scientific material in German. He learned Latin, and enough Greek to read Aristotle in the original, later on, as a young adult, he made himself an expert, first on invertebrates, and later on vertebrates, all self-taught
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Archaeopteryx
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Archaeopteryx, sometimes referred to by its German name Urvogel, is a genus of bird-like dinosaurs that is transitional between non-avian feathered dinosaurs and modern birds. The name derives from the ancient Greek ἀρχαῖος meaning ancient, and πτέρυξ, between the late nineteenth century and the early twenty-first century, Archaeopteryx had been generally accepted by palaeontologists and popular reference books as the oldest known bird. Older potential avialans have since been identified, including Anchiornis, Xiaotingia, similar in size to a Eurasian magpie, with the largest individuals possibly attaining the size of a raven, the largest species of Archaeopteryx could grow to about 0.5 m in length. Despite their small size, broad wings, and inferred ability to fly or glide and these features make Archaeopteryx a clear candidate for a transitional fossil between non-avian dinosaurs and birds. Thus, Archaeopteryx plays an important role, not only in the study of the origin of birds and it was named from a single feather in 1861. That same year, the first complete specimen of Archaeopteryx was announced, over the years, ten more fossils of Archaeopteryx have surfaced. Despite variation among these fossils, most experts regard all the remains that have been discovered as belonging to a single species, most of these eleven fossils include impressions of feathers. Because these feathers are of a form, these fossils are evidence that the evolution of feathers began before the Late Jurassic. The type specimen of Archaeopteryx was discovered just two years after Charles Darwin published On the Origin of Species, Archaeopteryx was roughly the size of a raven, with broad wings that were rounded at the ends and a long tail compared to its body length. It could reach up to 500 millimetres in length, with an estimated mass of 0.8 to 1 kilogram. Archaeopteryx feathers, although less documented than its other features, were similar in structure to modern-day bird feathers. Despite the presence of numerous features, Archaeopteryx had many non-avian theropod dinosaur characteristics. Unlike modern birds, Archaeopteryx had small teeth, as well as a bony tail. Because it displays features common to both birds and non-avian dinosaurs, Archaeopteryx has often considered a link between them. For instance, it has an ascending process of the ankle bone, interdental plates, an obturator process of the ischium. In particular, Ostrom found that Archaeopteryx was remarkably similar to the theropod family Dromaeosauridae, specimens of Archaeopteryx were most notable for their well-developed flight feathers. They were markedly asymmetrical and showed the structure of feathers in modern birds. The tail feathers were asymmetrical, again in line with the situation in modern birds
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Hesperornis
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Hesperornis is a genus of flightless aquatic birds that spanned the first half of the Campanian age of the Late Cretaceous period. One of the discoveries of the paleontologist O. C. Marsh in the late 19th century Bone Wars, it was a find in the history of avian paleontology. Locations for Hesperornis fossils include the Late Cretaceous marine limestones from Kansas, nine species are recognised, eight of which have been recovered from rocks in North America and one from Russia. Hesperornis was a bird, reaching up to 1.8 metres in length. It had virtually no wings, and swam with its hind legs. Fossil evidence shows that the toes were probably lobed, as in todays grebes, like many other Mesozoic birds such as Ichthyornis, Hesperornis had teeth as well as a beak, which were used to hold prey. The teeth of Hesperornis were present along nearly the entire lower jaw, the front portion of the upper jaw and tip of the lower jaw lacked teeth and were probably covered in a beak. Studies of the surface show that at least the tips of the jaws supported a hard. The palate contained small pits that allowed the teeth to lock into place when the jaws were closed. They also retained a dinosaur-like joint between the jaw bones. It is believed that this allowed them to rotate the back portion of the mandible independently of the front, the first Hesperornis specimen was discovered in 1871 by Othniel Charles Marsh. Marsh was undertaking his second expedition, accompanied by ten students. The team headed to Kansas where Marsh had dug before, aside from finding more bones belonging to the flying reptile Pteranodon, Marsh discovered the skeleton of a large fossil bird, at least five feet in height. The specimen was large, wingless, and had strong legs—Marsh considered it a diving species, unfortunately, the specimen lacked a head. Marsh named the find Hesperornis regalis, or regal western bird, Marsh headed back west with a smaller party the following year. In western Kansas, one of Marshs four students, Thomas H. Russell and this specimen had enough of its head intact that Marsh could see that the creatures jaws had been lined with teeth. Marsh saw important evolutionary implications of this find, along with Benjamin Mudges find of the toothed bird Ichthyornis, in an 1873 paper Marsh declared that the fortunate discovery of these interesting fossils does much to break down the old distinction between Birds and Reptiles
29.
Bird
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Birds, a subgroup of Reptiles, are the last living examples of Dinosaurs. Birds live worldwide and range in size from the 5 cm bee hummingbird to the 2.75 m ostrich. They rank as the class of tetrapods with the most living species, at ten thousand. Birds are the closest living relatives of crocodilians, the fossil record indicates that birds evolved from feathered ancestors within the theropod group of saurischian dinosaurs. True birds first appeared during the Cretaceous period, around 100 million years ago, Birds, especially those in the southern continents, survived this event and then migrated to other parts of the world while diversifying during periods of global cooling. Primitive bird-like dinosaurs that lie outside class Aves proper, in the broader group Avialae, have been found dating back to the mid-Jurassic period, around 170 million years ago. Birds have wings which are more or less developed depending on the species, the digestive and respiratory systems of birds are also uniquely adapted for flight. Some bird species of aquatic environments, particularly seabirds and some waterbirds, have evolved for swimming. Many species annually migrate great distances, Birds are social, communicating with visual signals, calls, and bird songs, and participating in such social behaviours as cooperative breeding and hunting, flocking, and mobbing of predators. The vast majority of species are socially monogamous, usually for one breeding season at a time, sometimes for years. Other species have breeding systems that are polygynous or, rarely, Birds produce offspring by laying eggs which are fertilised through sexual reproduction. They are usually laid in a nest and incubated by the parents, most birds have an extended period of parental care after hatching. Some birds, such as hens, lay eggs even when not fertilised, songbirds, parrots, and other species are popular as pets. Guano is harvested for use as a fertiliser, Birds prominently figure throughout human culture. About 120–130 species have become extinct due to human activity since the 17th century, human activity threatens about 1,200 bird species with extinction, though efforts are underway to protect them. Recreational birdwatching is an important part of the ecotourism industry, the first classification of birds was developed by Francis Willughby and John Ray in their 1676 volume Ornithologiae. Carl Linnaeus modified that work in 1758 to devise the taxonomic classification system currently in use, Birds are categorised as the biological class Aves in Linnaean taxonomy. Phylogenetic taxonomy places Aves in the dinosaur clade Theropoda, Aves and a sister group, the clade Crocodilia, contain the only living representatives of the reptile clade Archosauria
30.
Genomics
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Genomics is an interdisciplinary field of science focusing on genomes. A genome is a set of DNA within a single cell of an organism, and as such genomics is a branch of molecular biology concerned with the structure, function, evolution. Genomics aims at the collective characterization and quantification of genes, which direct the production of proteins with the assistance of enzymes, proteins in turn make up body structures like organs and tissues as well as control chemical reactions and carry signals between cells. If a cells DNA is mutated, a protein may be produced. Advances in genomics have triggered a revolution in discovery-based research to understand even the most complex systems such as the brain. The field includes efforts to determine the entire DNA sequence of organisms, the field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. From the Greek ΓΕΝ gen, gene meaning become, create, creation, birth, following Rosalind Franklins confirmation of the helical structure of DNA, James D. In 1964, Robert W. Holley and colleagues published the first nucleic acid sequence ever determined, extending this work, Marshall Nirenberg and Philip Leder revealed the triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in their experiments. In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. Fiers group expanded on their MS2 coat protein work, determining the complete nucleotide-sequence of bacteriophage MS2-RNA and Simian virus 40 in 1976 and 1978, in 1975, he and Alan Coulson published a sequencing procedure using DNA polymerase with radiolabelled nucleotides that he called the Plus and Minus technique. This involved two closely related methods that generated short oligonucleotides with defined 3 termini and these could be fractionated by electrophoresis on a polyacrylamide gel and visualised using autoradiography. The procedure could sequence up to 80 nucleotides in one go and was a big improvement, nevertheless, in 1977 his group was able to sequence most of the 5,386 nucleotides of the single-stranded bacteriophage φX174, completing the first fully sequenced DNA-based genome. For their groundbreaking work in the sequencing of nucleic acids, Gilbert, the advent of these technologies resulted in a rapid intensification in the scope and speed of completion of genome sequencing projects. The first complete genome sequence of an organelle, the human mitochondrion, was reported in 1981. In 1992, the first eukaryotic chromosome, chromosome III of brewers yeast Saccharomyces cerevisiae was sequenced, the first free-living organism to be sequenced was that of Haemophilus influenzae in 1995. As of October 2011, the sequences are available for,2,719 viruses,1,115 archaea and bacteria. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models, yeast has long been an important model organism for the eukaryotic cell, while the fruit fly Drosophila melanogaster has been a very important tool. The worm Caenorhabditis elegans is an often used model for multicellular organisms
31.
Multiple sequence alignment
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A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences shared evolutionary origins, Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. Multiple sequence alignment also refers to the process of aligning such a sequence set, MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. A direct method for producing an MSA uses the dynamic programming technique to identify the optimal alignment solution. For nucleotide sequences a similar gap penalty is used, but a much simpler substitution matrix, for n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, to find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a method that uses pairwise alignments to constrain the n-dimensional search space. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment and has implemented in a software program for constructing multiple sequence alignments. The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique developed by Paulien Hogeweg, progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or UPGMA, progressive alignments are not guaranteed to be globally optimal. The primary problem is that errors are made at any stage in growing the MSA. Performance is also particularly bad when all of the sequences in the set are rather distantly related and this corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a scale for many sequences. Progressive alignment services are available on publicly accessible web servers so users need not locally install the applications of interest. Different portals or implementations can vary in user interface and make different parameters accessible to the user, current version of Clustal family is ClustalW2. EMBL-EBI announced that CLustalW2 will be expired in August 2015 and they recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments
32.
Thomas Cavalier-Smith
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Thomas Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow, is a Professor of Evolutionary Biology in the Department of Zoology, at the University of Oxford. He is well known for his system of classification of all organisms, Cavalier-Smith was born on 21 October 1941 in London. His parents were Alan Hailes Spencer and Mary Maude Cavalier-Smith and he was educated at Norwich School, Gonville and Caius College, Cambridge and Kings College London. He was under the supervision of Sir John Randall for his PhD thesis between 1964-1967, his thesis was entitled Organelle Development in Chlamydomonas reinhardii, from 1967 to 1969, he was a guest investigator at Rockefeller University. He became Lecturer of biophysics at King’s College London in 1969 and he was promoted to Reader in 1982. In 1989 he was appointed Professor of botany at the University of British Columbia, in 1999, he joined the University of Oxford, becoming Professor of evolutionary biology in 2000. He received the International Prize for Biology from the Emperor of Japan in 2004, and he was appointed Fellow of the Canadian Institute for Advanced Research between 1998-2007, and Advisor of the Integrated Microbial Biodiversity of CIFAR. He won the 2007 Frink Medal of the Zoological Society of London, Cavalier-Smith has written extensively on the taxonomy and classification of protists. One of his contributions to biology was his proposal of a new kingdom of life. He also introduced a new group for primitive eukarytes called the Chromalveolata, as well as Opisthokonta, Rhizaria, though fairly well known, many of his claims have been controversial and have not gained widespread acceptance in the scientific community to date. His taxonomic revisions often lead to changes in the classification of all life forms. Cavalier-Smiths first major classification system was the division of all organisms into eight kingdoms, in 1993, he revised his system particularly in the light of the general acceptance of Archaebacteria as separate group from Bacteria. In addition, some protists lacking mitochondria were discovered, as a result, these amitochondriate protists were separated from the protist kingdom, giving rise to the, at the same time, superkingdom and kingdom Archezoa. This was known as the Archezoa hypothesis, the eight kingdoms became, Eubacteria, Archaebacteria, Archezoa, Protozoa, Chromista, Plantae, Fungi, and Animalia. However, kingdom Archezoa is now defunct and he now assigns former members of the kingdom Archezoa to the phylum Amoebozoa. By 1998, Cavalier-Smith had reduced the number of kingdoms from eight to six, Animalia, Protozoa, Fungi, Plantae, Chromista. He created three new animal phyla, Acanthognatha, Brachiozoa, and Lobopoda and recognized a total of 23 animal phyla, in this scheme they reintroduced the division of prokaryotes into two kingdoms, Bacteria and Archaea. This is based on the consensus in the Taxonomic Outline of Bacteria and Archaea, in 2006, Cavalier-Smith proposed that the last universal common ancestor to all life was a non-flagellate negibacterium with two membranes
33.
G. G. Simpson
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George Gaylord Simpson was an American paleontologist. He was an expert on extinct mammals and their intercontinental migrations and he anticipated such concepts as punctuated equilibrium and dispelled the myth that the evolution of the horse was a linear process culminating in the modern Equus caballus. He coined the word hypodigm in 1940, and published extensively on the taxonomy of fossil, Simpson was influentially, and incorrectly, opposed to Alfred Wegeners theory of continental drift. He was Professor of Zoology at Columbia University, and Curator of the Department of Geology and Paleontology at the American Museum of Natural History from 1945 to 1959. He was Curator of the Museum of Comparative Zoology at Harvard University from 1959 to 1970, in 1943 Simpson was awarded the Mary Clark Thompson Medal from the National Academy of Sciences. For his work, Tempo and mode in evolution, he was awarded the Academys Daniel Giraud Elliot Medal in 1944 and he was awarded the Linnean Society of Londons prestigious Darwin-Wallace Medal in 1958. At the University of Arizona, Tucson, the Gould-Simpson Building was named for Arizona geologist Lawrence M. Gould, Simpson was noted for his work in the field of paleogeography and continental evolution relationships. In the 1960s, Simpson rubbished the then-nascent science of exobiology and he was raised as a Christian but later became an agnostic. Molecules and monkeys, George Gaylord Simpson and the challenge of molecular evolution, History & Philosophy of the Life Sciences. Laporte, L. O. F. Simpson on species, journal of the History of Biology. Olson, E. C. George Gaylord Simpson, June 16, laporte, Léo F. George Gaylord Simpson as mentor and apologist for paleoanthropology. Laporte, L. F. Simpsons Tempo and Mode in Evolution revisited, proceedings of the American Philosophical Society. Gershenowitz, H. George Gaylord Simpson and Lamarck, indian journal of history of science. George Gaylord Simpson — full and comprehensive biography by L. F. George Gaylord Simpson — Open Library
34.
Ernst Mayr
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Not to be confused with Ernst Mayr, Ernst Mayer, Ernst Meyer, Ernest Mayer or Ernest May. Ernst Walter Mayr was one of the 20th centurys leading evolutionary biologists and he was also a renowned taxonomist, tropical explorer, ornithologist, philosopher of biology, and historian of science. Although Charles Darwin and others posited that multiple species could evolve from a common ancestor. Ernst Mayr approached the problem with a new definition for species, the most significant and rapid genetic reorganization occurs in extremely small populations that have been isolated. Mayr was the son of Helene Pusinelli and Dr. Otto Mayr. His father was a jurist but took an interest in natural history and he learnt all the local birds in Würzburg from his elder brother Otto. He also had access to a history magazine for amateurs. His father died just before he was thirteen, the family then moved to Dresden and he studied at the Staatsgymnasium in Dresden-Neustadt and completed his high school education there. In April 1922, while still in school, he joined the newly founded Saxony Ornithologists’ Association. Here he met Rudolf Zimmermann, who became his ornithological mentor, in February 1923, Mayr passed his high school examination and his mother rewarded him with a pair of binoculars. On 23 March 1923 on the lakes of Moritzburg, the Frauenteich, the species had not been seen in Saxony since 1845 and the local club argued about the identity. Raimund Schelcher of the club suggested that Mayr visit his classmate Erwin Stresemann on his way to Greifswald. After a tough interrogation, Stresemann accepted and published the sighting as authentic, Stresemann was very impressed and suggested that, between semesters, Mayr could work as a volunteer in the ornithological section of the museum. Mayr wrote about this event, It was as if someone had given me the key to heaven, Mayr was endlessly interested in ornithology and chose Greifswald at the Baltic for my studies for no other reason than that. It was situated in the ornithologically most interesting area, although he ostensibly planned to become a physician, he was first and foremost an ornithologist. During the first semester break Stresemann gave him a test to identify treecreepers, Stresemann declared that Mayr was a born systematist. Mayr completed his doctorate in ornithology at the University of Berlin under Dr. Carl Zimmer, on 1 July he accepted the position offered to him at the museum for a monthly salary of 330.54 Reichsmark. In New Guinea, Mayr collected several thousand bird skins and, during his stay in New Guinea, he was invited to accompany the Whitney South Seas Expedition to the Solomon Islands
35.
Vertebrate
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Vertebrates /ˈvɜːrtᵻbrᵻts/ comprise all species of animals within the subphylum Vertebrata /-ɑː/. Vertebrates represent the majority of the phylum Chordata, with currently about 66,000 species described. Vertebrates include the fish and the jawed vertebrates, which include the cartilaginous fish. A bony fish known as the lobe-finned fishes is included with tetrapods, which are further divided into amphibians, reptiles, mammals. Extant vertebrates range in size from the frog species Paedophryne amauensis, at as little as 7.7 mm, to the blue whale, vertebrates make up less than five percent of all described animal species, the rest are invertebrates, which lack vertebral columns. The vertebrates traditionally include the hagfish, which do not have proper vertebrae due to their loss in evolution, though their closest living relatives, hagfish do, however, possess a cranium. For this reason, the vertebrate subphylum is sometimes referred to as Craniata when discussing morphology, molecular analysis since 1992 has suggested that hagfish are most closely related to lampreys, and so also are vertebrates in a monophyletic sense. Others consider them a group of vertebrates in the common taxon of craniata. The word origin of vertebrate derives from the Latin word vertebratus, the Proto-Indo-European language origins are still unclear. Vertebrate is derived from the vertebra, which refers to any of the bones or segments of the spinal column. All vertebrates are built along the basic body plan, a stiff rod running through the length of the animal, with a hollow tube of nervous tissue above it. In all vertebrates, the mouth is found at, or right below, the remaining part of the body continuing after the anus forms a tail with vertebrae and spinal cord, but no gut. However, a few vertebrates have secondarily lost this anatomy, retaining the notochord into adulthood, such as the sturgeon, jawed vertebrates are typified by paired appendages, but this trait is not required in order for an animal to be a vertebrate. All basal vertebrates breathe with gills, the gills are carried right behind the head, bordering the posterior margins of a series of openings from the pharynx to the exterior. Each gill is supported by a cartilagenous or bony gill arch, the bony fish have three pairs of arches, cartilaginous fish have five to seven pairs, while the primitive jawless fish have seven. The vertebrate ancestor no doubt had more arches than this, as some of their relatives have more than 50 pairs of gills. In amphibians and some primitive fishes, the larvae bear external gills. These are reduced in adulthood, their function taken over by the gills proper in fishes, some amphibians retain the external larval gills in adulthood, the complex internal gill system as seen in fish apparently being irrevocably lost very early in the evolution of tetrapods
36.
Paleontology
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Paleontology or palaeontology is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene Epoch. It includes the study of fossils to determine organisms evolution and interactions with each other, paleontological observations have been documented as far back as the 5th century BC. The science became established in the 18th century as a result of Georges Cuviers work on comparative anatomy, and developed rapidly in the 19th century. The term itself originates from Greek παλαιός, palaios, i. e. old, ancient, ὄν, on, i. e. being, creature and λόγος, logos, i. e. speech, thought, study. Paleontology lies on the border between biology and geology, but differs from archaeology in that it excludes the study of modern humans. It now uses techniques drawn from a range of sciences, including biochemistry, mathematics. The final quarter of the 20th century saw the development of molecular phylogenetics, molecular phylogenetics has also been used to estimate the dates when species diverged, but there is controversy about the reliability of the molecular clock on which such estimates depend. The simplest definition is the study of ancient life, paleontology is one of the historical sciences, along with archaeology, geology, astronomy, cosmology, philology and history itself. This means that it aims to describe phenomena of the past, hence it has three main elements, description of the phenomena, developing a general theory about the causes of various types of change, and applying those theories to specific facts. Sometimes the smoking gun is discovered by an accident during other research. Paleontology lies on the boundary between biology and geology since paleontology focuses on the record of past life but its source of evidence is fossils. In addition paleontology often uses techniques derived from other sciences, including biology, osteology, ecology, chemistry, techniques developed in engineering have been used to analyse how ancient organisms might have worked, for example how fast Tyrannosaurus could move and how powerful its bite was. As knowledge has increased, paleontology has developed specialised subdivisions, vertebrate paleontology concentrates on fossils of vertebrates, from the earliest fish to the immediate ancestors of modern mammals. Invertebrate paleontology deals with fossils of such as molluscs, arthropods. Paleobotany focuses on the study of plants, but traditionally includes the study of fossil algae. Palynology, the study of pollen and spores produced by plants and protists. Micropaleontology deals with all microscopic fossil organisms, regardless of the group to which they belong, one example is the development of oxygenic photosynthesis by bacteria, which hugely increased the productivity and diversity of ecosystems. This also caused the oxygenation of the atmosphere, together, these were a prerequisite for the evolution of the most complex eukaryotic cells, from which all multicellular organisms are built
37.
Taxonomic rank
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In biological classification, rank is the relative level of a group of organisms in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, order, class, phylum, kingdom, domain, a given rank subsumes under it less general categories, that is, more specific descriptions of life forms. Above it, each rank is classified within more general categories of organisms, the rank of any species and the description of its genus is basic, which means that to identify a particular organism, it is usually not necessary to specify ranks other than these first two. Consider a particular species, the red fox Vulpes vulpes, its next rank, as one group of the class Mammalia, all of the above are classified among those with backbones in the Chordata phylum rank, and with them among all the animals in the Animalia kingdom rank. Finally, all of the above will find their earliest relatives somewhere in their domain rank Eukarya, today, nomenclature is regulated by the nomenclature codes. There are seven main ranks, kingdom, phylum or division, class, order, family, genus. In addition, the domain is now used as one of the fundamental ranks. Also, this represents a synonym for the category of dominion. Unlike Moore, Whoese et al. did not suggest a Latin term for this category, a taxon is usually assigned a rank when it is given its formal name. The basic ranks are species and genus, when an organism is given a species name it is assigned to a genus, and the genus name is part of the species name. The species name is called a binomial, that is. For example, the name for the human species is Homo sapiens. This is usually italicized in print and underlined when italics are not available, in this case, Homo is the generic name and it is capitalized, sapiens indicates the species and it is not capitalized. There are definitions of the taxonomic ranks in the International Code of Zoological Nomenclature, superfamily, family, subfamily, tribe, subtribe, genus, subgenus. The International Code of Zoological Nomenclature divides names into family-group names, genus-group names, in the genus group and species group no further ranks are allowed. At higher ranks a lower level may be denoted by adding the prefix infra, meaning lower, a taxon above the rank of species has a scientific name in one part. A species has a composed of two parts, generic name + specific name, for example Canis lupus. A subspecies has a composed of three parts, generic name + specific name + subspecific name, for example Canis lupus familiaris
38.
Alfred Romer
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Alfred Sherwood Romer was an American paleontologist and biologist and a specialist in vertebrate evolution. Romer joined the department of geology and paleontology at the University of Chicago as a professor in 1923. He was a researcher and teacher. His collecting program added important Paleozoic specimens to the Walker Museum of Paleontology, in 1934 he was appointed professor of biology at Harvard University. In 1946, he became director of the Harvard Museum of Comparative Zoology. In 1954 Romer was awarded the Mary Clark Thompson Medal from the National Academy of Sciences and he was awarded the Academys Daniel Giraud Elliot Medal in 1956. Romer was very keen in investigating vertebrate evolution and he always emphasized the evolutionary significance of the relationship between the form and function of animals and the environment. Through his textbook Vertebrate Paleontology Romer laid the foundation for the classification of vertebrates. He drew together the widely scattered taxonomy of the different vertebrate groups and combined them in a scheme, emphasizing orderliness. Based on his research of early amphibians, he reorganised the labyrinthodontians, Romers classification was followed by many subsequent authors, notably Robert L. Carroll, and is still in use. A genus of early captorhinids is named Romeria after Romer, as is Romeriida, the finding of these fossils was hailed as a breakthrough proving dinosaurs and other dinosauromorphs lived together for as long as 15 million to 20 million years. The early Pennsylvanian Romeriscus was also named after Romer and it was initially described as the oldest known amniote, but this is because limnoscelids were, at that time, considered amniotes by some authors. A subsequent study showed that the fossil lacks diagnostic characters and can only be assigned to Tetrapoda. Romer was the first to recognise the gap in the record between the tetrapods of the Devonian and the later Carboniferous period, a gap that has borne the name Romers gap since 1995. Notes and Comments on Vertebrate Paleontology, http, //people. wku. edu/charles. smith/chronob/ROME1894. htm Alfred Romer — Biographical Memoirs of the National Academy of Sciences
39.
Microbiology
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Microbiology is the study of microscopic organisms, those being unicellular, multicellular, or acellular. Microbiology encompasses numerous sub-disciplines including virology, mycology, parasitology, microbiologists traditionally relied on culture, staining, and microscopy. However, less than 1% of the present in common environments can be cultured in isolation using current means. Microbiologists often rely on extraction or detection of nucleic acid, either DNA or RNA sequences, viruses have been variably classified as organisms, as they have been considered either as very simple microorganisms or very complex molecules. As an application of microbiology, medical microbiology is often introduced with medical principles of immunology as microbiology and immunology, otherwise, microbiology, virology, and immunology as basic sciences have greatly exceeded the medical variants, applied sciences. The existence of microorganisms was hypothesized for many centuries before their actual discovery, the existence of unseen microbiological life was postulated by Jainism which is based on Mahavira’s teachings as early as 6th century BCE. Paul Dundas notes that Mahavira asserted existence of unseen microbiological creatures living in earth, water, air, in 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission. However, early claims about the existence of microorganisms were speculative, actual observation and discovery of microbes had to await the invention of the microscope in the 17th century. In 1676, Anton van Leeuwenhoek, who lived most of his life in Delft, Holland, observed bacteria and other microorganisms using a single-lens microscope of his own design. While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the bodies of moulds. It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe micro-organisms and he was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses. One of his books contains a chapter in Latin, which reads in translation – Concerning the wonderful structure of things in nature, here, he wrote who would believe that vinegar and milk abound with an innumerable multitude of worms. He also noted that material is full of innumerable creeping animalcule. These observations antedate Robert Hookes Micrographia by nearly 20 years and were published some 29 years before van Leeuwenhoek saw protozoa and 37 years before he described having seen bacteria. Joseph Lister was the first person who said infectious diseases are caused by micro-organism and was first person who used phenol as disinfectant on the wounds of patients. Cohn was also the first to formulate a scheme for the classification of bacteria. Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are considered to be the father of microbiology and medical microbiology. Pasteur is most famous for his series of experiments designed to disprove the widely held theory of spontaneous generation
40.
Biochemistry
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Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through biochemical signaling and the flow of energy through metabolism. Biochemistry is closely related to biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Depending on the definition of the terms used, molecular biology can be thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate. The chemistry of the cell depends on the reactions of smaller molecules. These can be inorganic, for water and metal ions, or organic, for example the amino acids. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism, the findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases, in nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control. However, biochemistry as a scientific discipline has its beginning sometime in the 19th century, or a little earlier. Gowland Hopkins on enzymes and the nature of biochemistry. The term biochemistry itself is derived from a combination of biology, the German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister. Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea and these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle. Another significant historic event in biochemistry is the discovery of the gene and this part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, in 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92 naturally occurring elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life, while a few common ones are not used, most organisms share element needs, but there are a few differences between plants and animals
41.
Willi Hennig
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Emil Hans Willi Hennig was a German biologist who is considered the founder of phylogenetic systematics, also known as cladistics. In 1945 as a prisoner of war, Hennig began work on his theory of cladistics, with his works on evolution and systematics he revolutionised the view of the natural order of beings. As a taxonomist, he specialised in dipterans, Hennig was born in Dürrhennersdorf, Upper Lusatia. His mother Marie Emma, née Groß, worked as a maid and, later and his father Karl Ernst Emil Hennig was a rail worker. Willi had two brothers, Fritz Rudolf Hennig, who became a minister, and Karl Herbert, who went missing at Stalingrad in 1943, in the spring of 1919, Willi Hennig started school in Dürrhennersdorf, and subsequently was at school in Taubenheim an der Spree and Oppach. Rudolf Hennig described the family as calm, his father possessed an even temperament, as of 1927, Willi Hennig continued his education at the Realgymnasium and boarding school in Klotzsche near Dresden. Here he met his first mentor M. Rost, a science teacher, Rost had an interest in insects and introduced Hennig to Wilhelm Meise, who worked as a scientist at the Dresdener Museum für Tierkunde. In 1930, Hennig skipped a year, and graduated on February 26,1932, as early as 1931, Willi Hennig composed an essay entitled Die Stellung der Systematik in der Zoologie as part of his school work, published posthumously in 1978. It showed his interest as well as his treatment of systematic problems. From the summer semester of 1932 onwards, Hennig read zoology, botany and he would continue to visit the Museum in Dresden. There, he met the curator of the collection, the Dipteran expert Fritz Isidor van Emden. Hennig saw him regularly until van Emden was expelled from National Socialist Germany for having a Jewish mother, Hennig developed a deep friendship with Emdens successor, Klaus Günther. Hennig concluded his studies with a dissertation entitled, Beiträge zur Kenntnis des Kopulationsapparates der cyclorrhaphen Dipteren, by this time, Hennig had published eight scientific papers. Besides his 300-page revision of the Tylidae, there were papers on Diptera. After his studies, Hennig was Volontär at the State Museum for Zoology in Dresden, on January 1,1937, he obtained a scholarship from the Deutsche Forschungsgemeinschaft to work at the German Entomological Institute of the Kaiser-Wilhelm-Gesellschaft in Berlin-Dahlem. On May 13,1939, Hennig married his fellow student Irma Wehnert. By 1945, they had three sons, Wolfgang, Bernd and Gerd, Willi Hennig was drafted in 1938 to train for the infantry and concluded this course in 1939. As of the start of World War II, he was deployed in the infantry in Poland, France, Denmark and Russia
42.
Monophyly
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In common cladistic usage, a monophyletic group is a taxon which forms a clade, meaning that it consists of an ancestral species and all its descendants. The term is synonymous with the uncommon term holophyly, monophyletic groups are typically characterized by shared derived characteristics. Monophyly is contrasted with paraphyly and polyphyly, as shown in the second diagram, a paraphyletic group consists of all of the descendants of a common ancestor minus one or more monophyletic groups. These definitions have taken time to be accepted. When the cladistic school of thought became mainstream in the 1960s, indeed, taxonomists sometimes used terms without defining them, leading to confusion in the early literature, a confusion which persists. On the broadest scale, definitions fall into two groups, willi Hennig defined monophyly as groups based on synapomorphy. Some authors have sought to define monophyly to include paraphyly as any two or more groups sharing a common ancestor, however, this broader definition encompasses both monophyletic and paraphyletic groups as defined above. Therefore, most scientists today restrict the term monophyletic to refer to groups consisting of all the descendants of one common ancestor, however, when considering taxonomic groups such as genera and species, the most appropriate nature of their common ancestor is unclear. Assuming that it would be one individual or mating pair is unrealistic for sexually reproducing species, some argue that using a broader definition, such as a species and all its descendants, does not really work to define a genus. According to D. M. Glossary of scientific naming Clade Paraphyly Polyphyly Crown group Abbey, graphical explanation of basic phylogenetic terms. Carr, Steven M. Concepts of monophyly, polyphyly & paraphyly
43.
Amphibian
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Amphibians are ectothermic, tetrapod vertebrates of the class Amphibia. They inhabit a variety of habitats, with most species living within terrestrial, fossorial, arboreal or freshwater aquatic ecosystems. Thus amphibians typically start out as larvae living in water, the young generally undergo metamorphosis from larva with gills to an adult air-breathing form with lungs. Amphibians use their skin as a respiratory surface and some small terrestrial salamanders and frogs lack lungs. They are superficially similar to lizards but, along with mammals and birds, reptiles are amniotes, the earliest amphibians evolved in the Devonian period from sarcopterygian fish with lungs and bony-limbed fins, features that were helpful in adapting to dry land. They diversified and became dominant during the Carboniferous and Permian periods, over time, amphibians shrank in size and decreased in diversity, leaving only the modern subclass Lissamphibia. The three modern orders of amphibians are Anura, Urodela, and Apoda, the number of known amphibian species is approximately 7,000, of which nearly 90% are frogs. The smallest amphibian in the world is a frog from New Guinea with a length of just 7.7 mm. The largest living amphibian is the 1.8 m Chinese giant salamander, the study of amphibians is called batrachology, while the study of both reptiles and amphibians is called herpetology. The word amphibian is derived from the Ancient Greek term ἀμφίβιος, the term was initially used as a general adjective for animals that could live on land or in water, including seals and otters. Traditionally, the class Amphibia includes all tetrapod vertebrates that are not amniotes, the numbers of species cited above follows Frost and the total number of known amphibian species is over 7,000, of which nearly 90% are frogs. With the phylogenetic classification, the taxon Labyrinthodontia has been discarded as it is a group without unique defining features apart from shared primitive characteristics. Classification varies according to the phylogeny of the author and whether they use a stem-based or a node-based classification. The phylogeny of Paleozoic amphibians is uncertain, and Lissamphibia may possibly fall within groups, like the Temnospondyli or the Lepospondyli. If the common ancestor of amphibians and amniotes is included in Amphibia, all modern amphibians are included in the subclass Lissamphibia, which is usually considered a clade, a group of species that have evolved from a common ancestor. The three modern orders are Anura, Caudata, and Gymnophiona, although the fossils of several older proto-frogs with primitive characteristics are known, the oldest true frog is Prosalirus bitis, from the Early Jurassic Kayenta Formation of Arizona. It is anatomically similar to modern frogs. The oldest known caecilian is another Early Jurassic species, Eocaecilia micropodia, the earliest salamander is Beiyanerpeton jianpingensis from the Late Jurassic of northeastern China
44.
Amniote
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Amniotes are a clade of tetrapod vertebrates comprising the reptiles, birds, and mammals that lay their eggs on land or retain the fertilized egg within the mother. They are distinguished from the anamniotes, which lay their eggs in water. Older sources, particularly prior to the 20th century, may refer to amniotes as higher vertebrates and anamniotes as lower vertebrates, based on the discredited idea of the Great Chain of Being. Amniotes are tetrapods that are characterised by having an egg equipped with an amnion, amniotes include synapsids and sauropsids, as well as their ancestors, back to amphibians. Amniote embryos, whether laid as eggs or carried by the female, are protected and aided by several extensive membranes, in eutherian mammals, these membranes include the amniotic sac that surrounds the fetus. These embryonic membranes and the lack of a larval stage distinguish amniotes from tetrapod amphibians, the first amniotes, referred to as basal amniotes, resembled small lizards and evolved from the amphibian reptiliomorphs about 312 million years ago, in the Carboniferous geologic period. Their eggs could survive out of the water, allowing amniotes to branch out into drier environments, the eggs could also breathe and cope with wastes, allowing the eggs and the amniotes themselves to evolve into larger forms. From this point the amniotes spread around the globe, eventually to become the dominant land vertebrates, very early in the evolutionary history of amniotes, basal amniotes diverged into two main lines, the synapsids and the sauropsids, both of which persist into the modern era. Amniotes can be characterized in part by embryonic development that includes the formation of several extensive membranes, the amnion, chorion, and allantois. Amniotes develop directly into a form with limbs and a thick stratified epithelium. In amniotes, the transition from a two-layered periderm to cornified epithelium is triggered by thyroid hormone during embryonic development and their kidneys and large intestines are also well-suited to water retention. Most mammals do not lay eggs, but corresponding structures may be found inside the placenta, the ancestors of true amniotes, such as Casineria kiddi, which lived about 340 million years ago, evolved from amphibian reptiliomorphs and resembled small lizards. At the late Devonian mass extinction 360 million years ago, all known tetrapods were essentially aquatic, indeed, many modern day amniotes are dependent on moisture to keep their eggs from desiccating. Although some modern amphibians lay eggs on land, they all lack advanced traits like an amnion, the amniotic egg was formed through a series of evolutionary steps. This allowed the egg to both its size and the rate of gas exchange, permitting a larger, metabolically more active embryo to reach full development before hatching. Further development of the design, like extraembryonic membranes and a shell, were not essential. The only way for the eggs to increase in size would be to develop new internal structures specialized for respiration, as this happened, it would also affect how much the juveniles could grow before they reached adulthood. In fish and amphibians there is one inner membrane, the embryonic membrane
. PMID 20008390.
