Tree of life (biology) in the context of "Evolutionary progress"

Orthogenesis, also known as orthogenetic evolution, progressive evolution, evolutionary progress, or progressionism, is an obsolete biological hypothesis that organisms have an innate tendency to evolve in a definite direction towards some goal (teleology) due to some internal mechanism or "driving force". According to the theory, the largest-scale trends in evolution have an absolute goal such as increasing biological complexity. Prominent historical figures who have championed some form of evolutionary progress include Jean-Baptiste Lamarck, Pierre Teilhard de Chardin, and Henri Bergson.

The term orthogenesis was introduced by Wilhelm Haacke in 1893 and popularized by Theodor Eimer five years later. Proponents of orthogenesis had rejected the theory of natural selection as the organizing mechanism in evolution for a rectilinear (straight-line) model of directed evolution. With the emergence of the modern synthesis, in which genetics was integrated with evolution, orthogenesis and other alternatives to Darwinism were largely abandoned by biologists, but the notion that evolution represents progress is still widely shared; modern supporters include E. O. Wilson and Simon Conway Morris. The evolutionary biologist Ernst Mayr made the term effectively taboo in the journal Nature in 1948, by stating that it implied "some supernatural force". The American paleontologist George Gaylord Simpson (1953) attacked orthogenesis, linking it with vitalism by describing it as "the mysterious inner force". Despite this, many museum displays and textbook illustrations continue to give the impression that evolution is directed.

On the Origin of Species (or, more completely, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life) is a work of scientific literature by Charles Darwin that is considered to be the foundation of evolutionary biology. It was published on 24 November 1859. Darwin's book introduced the scientific theory that populations evolve over the course of generations through a process of natural selection, although Lamarckism was also included as a mechanism of lesser importance. The book presented a body of evidence that the diversity of life arose by common descent through a branching pattern of evolution. Darwin included evidence that he had collected on the Beagle expedition in the 1830s and his subsequent findings from research, correspondence, and experimentation.

Various evolutionary ideas had already been proposed to explain new findings in biology. There was growing support for such ideas among dissident anatomists and the general public, but during the first half of the 19th century the English scientific establishment was closely tied to the Church of England, while science was part of natural theology. Ideas about the transmutation of species were controversial as they conflicted with the beliefs that species were unchanging parts of a designed hierarchy and that humans were unique, unrelated to other animals. The political and theological implications were intensely debated, but transmutation was not accepted by the scientific mainstream.

Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.

In biological taxonomy, a domain (/dəˈmeɪn/ or /doʊˈmeɪn/) (Latin: regio or dominium), also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.

According to the domain system, the tree of life consists of either three domains, Archaea, Bacteria, and Eukarya, or two domains, Archaea and Bacteria, with Eukarya included in Archaea. In the three-domain model, the first two are prokaryotes, single-celled microorganisms without a membrane-bound nucleus. All organisms that have a cell nucleus and other membrane-bound organelles are included in Eukarya and called eukaryotes.

The two-domain system is a biological classification of all organisms in the tree of life into two domains: Archaea, which includes eukaryotes in this classification, and Bacteria. It emerged from development of knowledge of archaea diversity and challenges the widely accepted three-domain system that classifies life into Bacteria, Archaea, and Eukarya. It was preceded by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system, due to evidence at the time. Better understanding of archaea, especially of their roles in the origin of eukaryotes through symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became more widely accepted after the discovery of a large kingdom of archaea called Promethearchaeati in 2017, which evidence suggests to be the evolutionary root of eukaryotes, thereby making eukaryotes members of the domain Archaea.

While the features of promethearchaea do not completely rule out the three-domain system, the notion that eukaryotes originated within Archaea has been strengthened by genetic and proteomic studies. Under the three-domain system, Eukarya is mainly distinguished by the presence of "eukaryotic signature proteins" that are not found in Archaea and Bacteria. However, promethearchaea contain genes that code for multiple such proteins.

Evolutionary thought, the recognition that species change over time and the perceived understanding of how such processes work, has roots in antiquity. With the beginnings of modern biological taxonomy in the late 17th century, two opposed ideas influenced Western biological thinking: essentialism, the belief that every species has essential characteristics that are unalterable, a concept which had developed from medieval Aristotelian metaphysics, and that fit well with natural theology; and the development of the new anti-Aristotelian approach to science. Naturalists began to focus on the variability of species; the emergence of palaeontology with the concept of extinction further undermined static views of nature. In the early 19th century prior to Darwinism, Jean-Baptiste Lamarck proposed his theory of the transmutation of species, the first fully formed theory of evolution.

In 1858 Charles Darwin and Alfred Russel Wallace published a new evolutionary theory, explained in detail in Darwin's On the Origin of Species (1859). Darwin's theory, originally called descent with modification, is known contemporarily as Darwinism or Darwinian theory. Unlike Lamarck, Darwin proposed common descent and a branching tree of life, meaning that two very different species could share a common ancestor. Darwin based his theory on the idea of natural selection: it synthesized a broad range of evidence from animal husbandry, biogeography, geology, morphology, and embryology. Debate over Darwin's work led to the rapid acceptance of the general concept of evolution, but the specific mechanism he proposed, natural selection, was not widely accepted until it was revived by developments in biology that occurred during the 1920s through the 1940s. Before that time most biologists regarded other factors as responsible for evolution. Alternatives to natural selection suggested during "the eclipse of Darwinism" (c. 1880 to 1920) included inheritance of acquired characteristics (neo-Lamarckism), an innate drive for change (orthogenesis), and sudden large mutations (saltationism). Mendelian genetics, a series of 19th-century experiments with pea plant variations rediscovered in 1900, was integrated with natural selection by Ronald Fisher, J. B. S. Haldane, and Sewall Wright during the 1910s to 1930s, and resulted in the founding of the new discipline of population genetics. During the 1930s and 1940s population genetics became integrated with other biological fields, resulting in a widely applicable theory of evolution that encompassed much of biology—the modern synthesis.

The inception of Darwin's theory occurred during an intensively busy period which began when Charles Darwin returned from the survey voyage of the Beagle, with his reputation as a fossil collector and geologist already established. He was given an allowance from his father to become a gentleman naturalist rather than a clergyman, and his first tasks were to find suitable experts to describe his collections, write out his Journal and Remarks, and present papers on his findings to the Geological Society of London.

At Darwin's geological début, the anatomist Richard Owen's reports on the fossils showed that extinct species were related to current species in the same locality, and the ornithologist John Gould showed that bird specimens from the Galápagos Islands were of distinct species related to places, not just varieties. These points convinced Darwin that transmutation of species must be occurring, and in his Red Notebook he jotted down his first evolutionary ideas. He began specific transmutation notebooks with speculations on variation in offspring "to adapt & alter the race to changing world", and sketched an "irregularly branched" genealogical branching of a single evolutionary tree.

The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes (later classified as Thermoproteota, a group of archaea). After his team at the University of California, Los Angeles discovered eocytes in 1984, James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: prokaryotes, which include Bacteria and Archaea, and karyotes, that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria.

Lake's hypothesis was based on an analysis of the structural components of ribosomes. It was largely ignored, being overshadowed by the three-domain system which relied on more precise genetic analysis. In 1990, Carl Woese and his colleagues proposed that cellular life consists of three domains—Eucarya, Bacteria, and Archaea – based on the ribosomal RNA sequences. The three-domain concept was widely accepted in genetics, and became the presumptive classification system for high-level taxonomy, and was promulgated in many textbooks.