The phenotype of an organism is the composite of the organism's observable characteristics or traits, including its morphology or physical form and structure. An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, the influence of environmental factors, which may interact, further affecting phenotype; when two or more different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented polymorphism is Labrador Retriever coloring. Richard Dawkins in 1978 and again in his 1982 book The Extended Phenotype suggested that bird nests and other built structures such as caddis fly larvae cases and beaver dams can be considered as "extended phenotypes"; the genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm and somatic cells.
The genotype-phenotype distinction should not be confused with Francis Crick's central dogma of molecular biology, a statement about the directionality of molecular sequential information flowing from DNA to protein, not the reverse. The term "phenotype" has sometimes been incorrectly used as a shorthand for phenotypic difference from wild type, bringing the absurd statement that a mutation has no phenotype. Despite its straightforward definition, the concept of the phenotype has hidden subtleties, it may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable and are thus part of the phenotype, it may seem that this goes beyond the original intentions of the concept with its focus on the organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits that can be made visible by some technical procedure.
A notable extension to this idea is the presence of "organic molecules" or metabolites that are generated by organisms from chemical reactions of enzymes. Another extension adds behavior to the phenotype. Behavioral phenotypes include cognitive and behavioral patterns; some behavioral phenotypes may characterize psychiatric syndromes. Phenotypic variation is a fundamental prerequisite for evolution by natural selection, it is the living organism as a whole that contributes to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection; the interaction between genotype and phenotype has been conceptualized by the following relationship: genotype + environment → phenotype A more nuanced version of the relationship is: genotype + environment + genotype & environment interactions → phenotype Genotypes have much flexibility in the modification and expression of phenotypes.
The plant Hieracium umbellatum is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy with broad leaves and expanded inflorescences; these habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine the phenotype that grows. An example of random variation in Drosophila flies is the number of ommatidia, which may vary between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments; the concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, silent mutations that do not change the corresponding amino acid sequence of a gene may change the frequency of guanine-cytosine base pairs; these base pairs have a higher thermal stability than adenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.
Richard Dawkins described a phenotype that included all effects that a gene has on its surroundings, including other organisms, as an extended phenotype, arguing that "An animal's behavior tends to maximize the survival of the genes'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it." For instance, an organism such as a beaver modifies its environment by building a beaver dam. When a bird feeds a brood parasite such as a cuckoo, it is unwittingly extending its phenotype.
In biology, an organism is any individual entity that exhibits the properties of life. It is a synonym for "life form". Organisms are classified by taxonomy into specified groups such as the multicellular animals and fungi. All types of organisms are capable of reproduction and development, some degree of response to stimuli. Humans are multicellular animals composed of many trillions of cells which differentiate during development into specialized tissues and organs. An organism may be either a eukaryote. Prokaryotes are represented by two separate domains -- archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles. Fungi and plants are examples of kingdoms of organisms within the eukaryotes. Estimates on the number of Earth's 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 over five billion species, that lived are estimated to be extinct.
In 2016, a set of 355 genes from the last universal common ancestor of all organisms was identified. The term "organism" first appeared in the English language in 1703 and took on its current definition by 1834, it is directly related to the term "organization". There is a long tradition of defining organisms as self-organizing beings, going back at least to Immanuel Kant's 1790 Critique of Judgment. 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 phrases such as "any living structure, such as a plant, fungus or bacterium, capable of growth and reproduction". Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the biochemical machinery of a host cell for reproduction. A superorganism is an organism consisting of many individuals working together as a single functional or social unit. There has been controversy about the best way to define the organism and indeed about whether or not such a definition is necessary.
Several contributions are responses to the suggestion that the category of "organism" may well not be adequate in biology. Viruses are not considered to be organisms because they are incapable of autonomous reproduction, growth or metabolism; this controversy is problematic because some cellular organisms are incapable of independent survival and live as obligatory intracellular parasites. Although viruses have a few enzymes and molecules characteristic of living organisms, they have no metabolism of their own; this rules out autonomous reproduction: they can only be passively replicated by the machinery of the host cell. In this sense, they are similar to inanimate matter. While viruses sustain no independent metabolism and thus are not classified as organisms, they do have their own genes, they do evolve by mechanisms similar to the evolutionary mechanisms of organisms; the most common argument in support of viruses as living organisms is their ability to undergo evolution and replicate through self-assembly.
Some scientists argue. In fact, viruses are evolved by their host cells, meaning that there was co-evolution of viruses and host cells. If host cells did not exist, viral evolution would be impossible; this is not true for cells. If viruses did not exist, the direction of cellular evolution could be different, but cells would be able to evolve; as for the reproduction, viruses rely on hosts' machinery to replicate. The discovery of viral metagenomes with genes coding for energy metabolism and protein synthesis fueled the debate about whether viruses belong in the tree of life; the presence of these genes suggested. However, it was found that the genes coding for energy and protein metabolism have a cellular origin. Most these genes were acquired through horizontal gene transfer from viral hosts. Organisms are complex chemical systems, organized in ways that promote reproduction and some measure of sustainability or survival; the same laws that govern non-living chemistry govern the chemical processes of life.
It is the phenomena of entire organisms that determine their fitness to an environment and therefore the survivability of their DNA-based genes. Organisms owe their origin and many other internal functions to chemical phenomena the chemistry of large organic molecules. Organisms are complex systems of chemical compounds that, through interaction and environment, play a wide variety of roles. Organisms are semi-closed chemical systems. Although they are individual units of life, they are not closed to the environment around them. To operate they take in and release energy. Autotrophs produce usable energy using light from the sun or inorganic compounds while heterotrophs take in organic compounds from the environment; the primary chemical element in these compounds is carbon. The chemical properties of this element such as its grea
A skill is the ability to carry out a task with determined results within a given amount of time, energy, or both. Skills can be divided into domain-general and domain-specific skills. For example, in the domain of work, some general skills would include time management and leadership, self-motivation and others, whereas domain-specific skills would be used only for a certain job. Skill requires certain environmental stimuli and situations to assess the level of skill being shown and used. People need a broad range of skills to contribute to a modern economy. A joint ASTD and U. S. Department of Labor study showed that through technology, the workplace is changing, identified 16 basic skills that employees must have to be able to change with it. Three broad categories of skills are suggested and these are technical and conceptual; the first two can be substituted with soft skills, respectively. Hard skills called technical skills, are any skills relating to a specific task or situation, it involves both understanding and proficiency in such specific activity that involves methods, procedures, or techniques.
These skills are quantifiable unlike soft skills, which are related to one's personality. These are skills that can be or have been tested and may entail some professional, technical, or academic qualification. Skilled workers have long had historical import as electricians, carpenters, bakers, coopers and other occupations that are economically productive. Skilled workers were politically active through their craft guilds. An ability and capacity acquired through deliberate and sustained effort to smoothly and adaptively carryout complex activities or job functions involving ideas, and/or people. See competence. According to the Portland Business Journal, people skills are described as: understanding ourselves and moderating our responses talking and empathizing building relationships of trust and productive interactions. A British definition is "the ability to communicate with people in a friendly way in business." The term is not listed yet in major US dictionaries. The term people skills is used to include both psychological skills and social skills but is less inclusive than life skills.
Social skill is any skill facilitating communication with others. Social rules and relations are created and changed in verbal and nonverbal ways; the process of learning such skills is called socialization. Soft skills are a combination of interpersonal people skills, social skills, communication skills, character traits, career attributes and emotional intelligence quotient among others. Skills can be categorized based on the level of motivation; the highest level of engagement corresponds to the craftsman. About 2% of people reach the highest level. Communication skills Deskilling DISCO - European Dictionary of Skills and Competences Dreyfus model of skill acquisition Game of skill Online skill-based game Procedural knowledge Transferable skills analysis American Society for Training & Development Australian National Training Authority NCVER's Review of generic skills for the new economy SKILLS EU Research Integrated Project
Allometric engineering is the process of experimentally shifting the scaling relationships, for body size or shape, in a population of organisms. More the process of experimentally breaking the tight covariance evident among component traits of a complex phenotype by altering the variance of one trait relative to another. Body size is one of the two traits; the measurements of the two traits are plotted against each other and the scaling relationship can be represented as: l o g = m l o g + l o g. Manipulations of this sort alter the scaling relationships either by shifting the intercept, slope or both to create novel variants; these novel variants can be tested for differences in performance or fitness. Through careful testing, one could sequentially test each component of a trait suite to determine how each part contributes to the function of the entire complex phenotype, the fitness of the organism; this technique allows for comparison within or among biological groups differing in size by adjusting morphology to match one another and comparing their performances.
Allometric engineering has been used to test David Lack's hypothesis in the lizard Sceloporus occidentalis. In this study, two populations were "engineered" to fit the morphology of the other by manipulating egg yolk quantity, removing effect of size difference between groups. After manipulation, they found. Maternal investment was "allometrically engineered" by surgically removing an ovary in cockroaches; this reduced number of progeny and increased resource allocation to each offspring. They coupled this manipulation with group effects, found that maternal investment can overcome group effect; the male long-tailed widowbird has exceptionally long tail feathers half a meter in length. Male tail feathers were cropped and glued and those with artificially enhanced tail lengths secured the most matings, demonstrating female preference; the fly Zonosemata vittigera has a banding pattern on its wings, found to mimic movements of a jumping spider. Greene et al. engineered novel phenotypes, breaking correlation between a behavior and morphology, by cutting and transplanting the wings of this fly with the common housefly.
This manipulation demonstrated that it was behavior coupled with the banding pattern that deterred jumping spiders from attacking, though not other predators. Current uses have involved truncation or cropping, yolk manipulation, hormonal treatments, maternal allocation, temperature manipulation, or altering the nutritional states; each method undoubtedly has its merits and pitfalls to consider before designing an experiment, but these techniques are opening new avenues of research in comparative and evolutionary biology. Allometry Cline Phenotypic plasticity
Philosophy of science
Philosophy of science is a sub-field of philosophy concerned with the foundations and implications of science. The central questions of this study concern what qualifies as science, the reliability of scientific theories, the ultimate purpose of science; this discipline overlaps with metaphysics and epistemology, for example, when it explores the relationship between science and truth. There is no consensus among philosophers about many of the central problems concerned with the philosophy of science, including whether science can reveal the truth about unobservable things and whether scientific reasoning can be justified at all. In addition to these general questions about science as a whole, philosophers of science consider problems that apply to particular sciences; some philosophers of science use contemporary results in science to reach conclusions about philosophy itself. While philosophical thought pertaining to science dates back at least to the time of Aristotle, philosophy of science emerged as a distinct discipline only in the 20th century in the wake of the logical positivism movement, which aimed to formulate criteria for ensuring all philosophical statements' meaningfulness and objectively assessing them.
Thomas Kuhn's 1962 book The Structure of Scientific Revolutions was formative, challenging the view of scientific progress as steady, cumulative acquisition of knowledge based on a fixed method of systematic experimentation and instead arguing that any progress is relative to a "paradigm," the set of questions and practices that define a scientific discipline in a particular historical period. Karl Popper and Charles Sanders Peirce moved on from positivism to establish a modern set of standards for scientific methodology. Subsequently, the coherentist approach to science, in which a theory is validated if it makes sense of observations as part of a coherent whole, became prominent due to W. V. Quine and others; some thinkers such as Stephen Jay Gould seek to ground science in axiomatic assumptions, such as the uniformity of nature. A vocal minority of philosophers, Paul Feyerabend in particular, argue that there is no such thing as the "scientific method", so all approaches to science should be allowed, including explicitly supernatural ones.
Another approach to thinking about science involves studying how knowledge is created from a sociological perspective, an approach represented by scholars like David Bloor and Barry Barnes. A tradition in continental philosophy approaches science from the perspective of a rigorous analysis of human experience. Philosophies of the particular sciences range from questions about the nature of time raised by Einstein's general relativity, to the implications of economics for public policy. A central theme is; that is, can chemistry be reduced to physics, or can sociology be reduced to individual psychology? The general questions of philosophy of science arise with greater specificity in some particular sciences. For instance, the question of the validity of scientific reasoning is seen in a different guise in the foundations of statistics; the question of what counts as science and what should be excluded arises as a life-or-death matter in the philosophy of medicine. Additionally, the philosophies of biology, of psychology, of the social sciences explore whether the scientific studies of human nature can achieve objectivity or are shaped by values and by social relations.
Distinguishing between science and non-science is referred to as the demarcation problem. For example, should psychoanalysis be considered science? How about so-called creation science, the inflationary multiverse hypothesis, or macroeconomics? Karl Popper called this the central question in the philosophy of science. However, no unified account of the problem has won acceptance among philosophers, some regard the problem as unsolvable or uninteresting. Martin Gardner has argued for the use of a Potter Stewart standard for recognizing pseudoscience. Early attempts by the logical positivists grounded science in observation while non-science was non-observational and hence meaningless. Popper argued; that is, every genuinely scientific claim is capable of being proven false, at least in principle. An area of study or speculation that masquerades as science in an attempt to claim a legitimacy that it would not otherwise be able to achieve is referred to as pseudoscience, fringe science, or junk science.
Physicist Richard Feynman coined the term "cargo cult science" for cases in which researchers believe they are doing science because their activities have the outward appearance of it but lack the "kind of utter honesty" that allows their results to be rigorously evaluated. A related question is what counts as a good scientific explanation. In addition to providing predictions about future events, society takes scientific theories to provide explanations for events that occur or have occurred. Philosophers have investigated the criteria by which a scientific theory can be said to have explained a phenomenon, as well as what it means to say a scientific theory has explanatory power. One early and influential theory of scientific explanation is the deductive-nomological model, it says that a successful scientific explanation must deduce the occurrence of the phenomena in question from a scientific law. This view has been subjected to substantial criticism, resulting in several acknowledged counterexamples to the theory.
It is challenging to characterize what is meant by an explanation when the thing to be explained cannot be deduc
Deoxyribonucleic acid is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development and reproduction of all known organisms and many viruses. DNA and ribonucleic acid are nucleic acids; the two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases, a sugar called deoxyribose, a phosphate group; the nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA; the complementary nitrogenous bases are divided into two groups and purines. In DNA, the pyrimidines are cytosine. Both strands of double-stranded DNA store the same biological information.
This information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences; the two strands of DNA are thus antiparallel. Attached to each sugar is one of four types of nucleobases, it is the sequence of these four nucleobases along the backbone. RNA strands are created using DNA strands as a template in a process called transcription. Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms store most of their DNA inside the cell nucleus as nuclear DNA, some in the mitochondria as mitochondrial DNA, or in chloroplasts as chloroplast DNA. In contrast, prokaryotes store their DNA only in circular chromosomes.
Within eukaryotic chromosomes, chromatin proteins, such as histones and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed. DNA was first isolated by Friedrich Miescher in 1869, its molecular structure was first identified by Francis Crick and James Watson at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, a post-graduate student of Rosalind Franklin. DNA is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic theorem and the theory of elasticity; the unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro- and nano-fabrication. Among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a long polymer made from repeating units called nucleotides.
The structure of DNA is dynamic along its length, being capable of coiling into tight loops and other shapes. In all species it is composed of two helical chains, bound to each other by hydrogen bonds. Both chains are coiled around the same axis, have the same pitch of 34 angstroms; the pair of chains has a radius of 10 angstroms. According to another study, when measured in a different solution, the DNA chain measured 22 to 26 angstroms wide, one nucleotide unit measured 3.3 Å long. Although each individual nucleotide is small, a DNA polymer can be large and contain hundreds of millions, such as in chromosome 1. Chromosome 1 is the largest human chromosome with 220 million base pairs, would be 85 mm long if straightened. DNA does not exist as a single strand, but instead as a pair of strands that are held together; these two long strands coil in the shape of a double helix. The nucleotide contains both a segment of the backbone of a nucleobase. A nucleobase linked to a sugar is called a nucleoside, a base linked to a sugar and to one or more phosphate groups is called a nucleotide.
A biopolymer comprising multiple linked nucleotides is called a polynucleotide. The backbone of the DNA strand is made from alternating sugar residues; the sugar in DNA is 2-deoxyribose, a pentose sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings; these are known as the 3′-end, 5′-end carbons, the prime symbol being used to distinguish these carbon atoms from those of the base to which the deoxyribose forms a glycosidic bond. When imagining DNA, each phosphoryl is considered to "belong" to the nucleotide whose 5′ carbon forms a bond therewith. Any DNA strand therefore has one end at which there is a phosphoryl attached to the 5′ carbon of a ribose and another end a
In biology, histones are alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be long. For example, each human diploid cell has about 1.8 meters of DNA. When the diploid cells are duplicated and condensed during mitosis, the result is about 120 micrometers of chromosomes. Five major families of histones exist: H1/H5, H2A, H2B, H3, H4. Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1/H5 are known as the linker histones; the core histones all exist as dimers, which are similar in that they all possess the histone fold domain: three alpha helices linked by two loops. It is this helical structure that allows for interaction between distinct dimers in a head-tail fashion; the resulting four distinct dimers come together to form one octameric nucleosome core 63 Angstroms in diameter.
Around 146 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn to give a particle of around 100 Angstroms across. The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure; the most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with 50 base pairs of DNA separating each pair of nucleosomes. Higher-order structures include the 30 nm fiber and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins. Histones are subdivided into canonical replication-dependent histones that are expressed during the S-phase of cell cycle and replication-independent histone variants, expressed during the whole cell cycle. In animals, genes encoding canonical histones are clustered along the chromosome, lack introns and use a stem loop structure at the 3’ end instead of a polyA tail.
Genes encoding histone variants are not clustered, have introns and their mRNAs are regulated with polyA tails. Complex multicellular organisms have a higher number of histone variants providing a variety of different functions. Recent data are accumulating about the roles of diverse histone variants highlighting the functional links between variants and the delicate regulation of organism development. Histone variants from different organisms, their classification and variant specific features can be found in "HistoneDB 2.0 - Variants" database. The following is a list of human histone proteins: The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer, forming two nearly symmetrical halves by tertiary structure; the H2A-H2B dimers and H3-H4 tetramer show pseudodyad symmetry. The 4'core' histones are similar in structure and are conserved through evolution, all featuring a'helix turn helix turn helix' motif, they share the feature of long'tails' on one end of the amino acid structure - this being the location of post-translational modification.
Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack into a tall superhelix onto which DNA coils in a manner similar to nucleosome spools. Only some archaeal histones have tails, it has been proposed that histone proteins are evolutionarily related to the helical part of the extended AAA+ ATPase domain, the C-domain, to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. Despite the differences in their topology, these three folds share a homologous helix-strand-helix motif. Using an electron paramagnetic resonance spin-labeling technique, British researchers measured the distances between the spools around which eukaryotic cells wind their DNA, they determined the spacings range from 59 to 70 Å. In all, histones make five types of interactions with DNA: Helix-dipoles form alpha-helixes in H2B, H3, H4 cause a net positive charge to accumulate at the point of interaction with negatively charged phosphate groups on DNA Hydrogen bonds between the DNA backbone and the amide group on the main chain of histone proteins Nonpolar interactions between the histone and deoxyribose sugars on DNA Salt bridges and hydrogen bonds between side chains of basic amino acids and phosphate oxygens on DNA Non-specific minor groove insertions of the H3 and H2B N-terminal tails into two minor grooves each on the DNA moleculeThe basic nature of histones, aside from facilitating DNA-histone interactions, contributes to their water solubility.
Histones are subject to post translational modification by enzymes on their N-terminal tails, but in their globular domains. Such modifications include methylation, acetylation, phosphorylation, SUMOylation, ADP-ribosylation; this affects their function of gene regulation. In general, genes that are active have less bound histone, while inactive genes are associated with histones during interphase, it a