Computational Phylogenetics, Phylogenetic Inference
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Computational Phylogenetics, Phylogenetic Inference
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm). Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. An especially well-known discipline of the study of computation is computer science. Physical process of Computation Computation can be seen as a purely physical process occurring inside a closed physical system called a computer. Examples of such physical systems are digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, microfluidics-based computers, analog computers, and wetware computers. This point of view has been adopted by the physics of computation, a branch of theoretical physics, as well as the field of natural computing. An even more radical point of view, pancomputationalism (inaudible word), is the postulate of digital physics that argues that the evolution of the universe is itself a ...
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Arithmetic
Arithmetic () is an elementary part of mathematics that consists of the study of the properties of the traditional operations on numbers— addition, subtraction, multiplication, division, exponentiation, and extraction of roots. In the 19th century, Italian mathematician Giuseppe Peano formalized arithmetic with his Peano axioms, which are highly important to the field of mathematical logic today. History The prehistory of arithmetic is limited to a small number of artifacts, which may indicate the conception of addition and subtraction, the best-known being the Ishango bone from central Africa, dating from somewhere between 20,000 and 18,000 BC, although its interpretation is disputed. The earliest written records indicate the Egyptians and Babylonians used all the elementary arithmetic operations: addition, subtraction, multiplication, and division, as early as 2000 BC. These artifacts do not always reveal the specific process used for solving problems, but t ...
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Digital Physics
Digital physics is a speculative idea that the universe can be conceived of as a vast, digital computation device, or as the output of a deterministic or probabilistic computer program. The hypothesis that the universe is a digital computer was proposed by Konrad Zuse in his 1969 book ''Rechnender Raum'' ("''Calculating Space''"). The term ''digital physics'' was coined by Edward Fredkin in 1978, who later came to prefer the term digital philosophy. Fredkin encouraged the creation of a digital physics group at what was then MIT's Laboratory for Computer Science, with Tommaso Toffoli and Norman Margolus as primary figures. ''Digital physics'' suggests that there exists, at least in principle, a program for a universal computer that computes the evolution of the universe. The computer could be, for example, a huge cellular automaton. Extant models of digital physics are incompatible with the existence of several continuous characters of physical symmetries, e.g., rotational symm ...
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Finite State Automaton
A finite-state machine (FSM) or finite-state automaton (FSA, plural: ''automata''), finite automaton, or simply a state machine, is a mathematical model of computation. It is an abstract machine that can be in exactly one of a finite number of '' states'' at any given time. The FSM can change from one state to another in response to some inputs; the change from one state to another is called a ''transition''. An FSM is defined by a list of its states, its initial state, and the inputs that trigger each transition. Finite-state machines are of two types— deterministic finite-state machines and non-deterministic finite-state machines. A deterministic finite-state machine can be constructed equivalent to any non-deterministic one. The behavior of state machines can be observed in many devices in modern society that perform a predetermined sequence of actions depending on a sequence of events with which they are presented. Simple examples are vending machines, which dispense p ...
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Pushdown Automaton
In the theory of computation, a branch of theoretical computer science, a pushdown automaton (PDA) is a type of automaton that employs a stack. Pushdown automata are used in theories about what can be computed by machines. They are more capable than finite-state machines but less capable than Turing machines (see below). Deterministic pushdown automata can recognize all deterministic context-free languages while nondeterministic ones can recognize all context-free languages, with the former often used in parser design. The term "pushdown" refers to the fact that the stack can be regarded as being "pushed down" like a tray dispenser at a cafeteria, since the operations never work on elements other than the top element. A stack automaton, by contrast, does allow access to and operations on deeper elements. Stack automata can recognize a strictly larger set of languages than pushdown automata. A nested stack automaton allows full access, and also allows stacked values to be ...
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Turing Machine
A Turing machine is a mathematical model of computation describing an abstract machine that manipulates symbols on a strip of tape according to a table of rules. Despite the model's simplicity, it is capable of implementing any computer algorithm. The machine operates on an infinite memory tape divided into discrete cells, each of which can hold a single symbol drawn from a finite set of symbols called the alphabet of the machine. It has a "head" that, at any point in the machine's operation, is positioned over one of these cells, and a "state" selected from a finite set of states. At each step of its operation, the head reads the symbol in its cell. Then, based on the symbol and the machine's own present state, the machine writes a symbol into the same cell, and moves the head one step to the left or the right, or halts the computation. The choice of which replacement symbol to write and which direction to move is based on a finite table that specifies what to do for each comb ...
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Model Of Computation
In computer science, and more specifically in computability theory and computational complexity theory, a model of computation is a model which describes how an output of a mathematical function is computed given an input. A model describes how units of computations, memories, and communications are organized. The computational complexity of an algorithm can be measured given a model of computation. Using a model allows studying the performance of algorithms independently of the variations that are specific to particular implementations and specific technology. Models Models of computation can be classified into three categories: sequential models, functional models, and concurrent models. Sequential models Sequential models include: * Finite state machines * Post machines (Post–Turing machines and tag machines). * Pushdown automata * Register machines ** Random-access machines * Turing machines * Decision tree model Functional models Functional models include: * Abstract re ...
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Theory Of Computation
In theoretical computer science and mathematics, the theory of computation is the branch that deals with what problems can be solved on a model of computation, using an algorithm, how efficiently they can be solved or to what degree (e.g., approximate solutions versus precise ones). The field is divided into three major branches: automata theory and formal languages, computability theory, and computational complexity theory, which are linked by the question: ''"What are the fundamental capabilities and limitations of computers?".'' In order to perform a rigorous study of computation, computer scientists work with a mathematical abstraction of computers called a model of computation. There are several models in use, but the most commonly examined is the Turing machine. Computer scientists study the Turing machine because it is simple to formulate, can be analyzed and used to prove results, and because it represents what many consider the most powerful possible "reasonable" mo ...
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Brain
A brain is an organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as vision. It is the most complex organ in a vertebrate's body. In a human, the cerebral cortex contains approximately 14–16 billion neurons, and the estimated number of neurons in the cerebellum is 55–70 billion. Each neuron is connected by synapses to several thousand other neurons. These neurons typically communicate with one another by means of long fibers called axons, which carry trains of signal pulses called action potentials to distant parts of the brain or body targeting specific recipient cells. Physiologically, brains exert centralized control over a body's other organs. They act on the rest of the body both by generating patterns of muscle activity and by driving the secretion of chemicals called hormones. This centralized control allows rapid and coordinated respon ...
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Multiple Realizability
Multiple realizability, in the philosophy of mind, is the thesis that the same mental property, state, or event can be implemented by different physical properties, states, or events. Philosophers of mind have used multiple realizability to argue that mental states are not the same as — and cannot be reduced to — physical states. They have also used it to defend many versions of functionalism, especially '' machine-state functionalism''. In recent years, however, multiple realizability has been used to attack functionalism, the theory that it was originally used to defend. As a result, functionalism has fallen out of favor in the philosophy of mind. The notion of multiple realizability The multiple realizability thesis in the philosophy of mind is the thesis that the same mental state can be realized by different physical states; another way of putting it is that there is a many-to-one mapping from physical states to mental states. Multiple realizability in general is not ...
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Mechanical Philosophy
The mechanical philosophy is a form of natural philosophy which compares the universe to a large-scale mechanism (i.e. a machine). The mechanical philosophy is associated with the scientific revolution of early modern Europe. One of the first expositions of universal mechanism is found in the opening passages of ''Leviathan'' by Thomas Hobbes, published in 1651. Some intellectual historians and critical theorists argue that early mechanical philosophy was tied to disenchantment and the rejection of the idea of nature as living or animated by spirits or angels. Other scholars, however, have noted that early mechanical philosophers nevertheless believed in magic, Christianity and spiritualism. Mechanism and determinism Some ancient philosophies held that the universe is reducible to completely mechanical principles—that is, the motion and collision of matter. This view was closely linked with materialism and reductionism, especially that of the atomists and to a large extent, st ...
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Semantics
Semantics (from grc, σημαντικός ''sēmantikós'', "significant") is the study of reference, meaning, or truth. The term can be used to refer to subfields of several distinct disciplines, including philosophy Philosophy (from , ) is the systematized study of general and fundamental questions, such as those about existence, reason, knowledge, values, mind, and language. Such questions are often posed as problems to be studied or resolved. Some ..., linguistics and computer science. History In English, the study of meaning in language has been known by many names that involve the Ancient Greek word (''sema'', "sign, mark, token"). In 1690, a Greek rendering of the term ''semiotics'', the interpretation of signs and symbols, finds an early allusion in John Locke's ''An Essay Concerning Human Understanding'': The third Branch may be called [''simeiotikí'', "semiotics"], or the Doctrine of Signs, the most usual whereof being words, it is aptly enough ter ...
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Jerry Fodor
Jerry Alan Fodor (; April 22, 1935 – November 29, 2017) was an American philosopher and the author of many crucial works in the fields of philosophy of mind and cognitive science. His writings in these fields laid the groundwork for the modularity of mind and the language of thought hypotheses, and he is recognized as having had "an enormous influence on virtually every portion of the philosophy of mind literature since 1960." Until his death in 2017 he held the position of State of New Jersey Professor of Philosophy, Emeritus, at Rutgers University. Fodor was known for his provocative and sometimes polemical style of argumentation. He argued that mental states, such as beliefs and desires, are relations between individuals and mental representations. He maintained that these representations can only be correctly explained in terms of a language of thought (LOT) in the mind. Furthermore, this language of thought itself is an actually existing thing that is codified in the b ...
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