cleanup date April 2010 wiktionarypar parsimony Merge to Occam s razor date April 2011 Parsimony is the use ... In science , parsimony is preference for the least complex explanation for an observation. This is generally ... of parsimony however, some argue that parsimony should not be elevated to the status of a general ... , maximum parsimony is a cladistic optimality criterion based on the principle of parsimony. Under maximum parsimony, the preferred phylogenetic tree is the tree that requires the smallest number of evolutionary changes. In biogeography , parsimony is used to infer ancient Historical migration migration ... the minimum amount of total movement. Parsimony is also a factor in statistics in general, mathematical ... be said that applied statisticians such as process control engineers value parsimony quite highly. Lee ... of incomplete data, may even strongly support a false conclusion blockquote When parsimony ... pronouncement, parsimony analysis ceases to be science. blockquote The scientific method In science, parsimony is used as a heuristic rule of thumb to guide scientists in the development of theoretical ... , parsimony was an important heuristic in the formulation of special relativity by Albert Einstein ... name fn 101 In the scientific method, parsimony is an epistemological , Metaphysics metaphysical , or heuristic ... use the idea of parsimony, it only has meaning in a very specific context of inquiry. A number of background assumptions are required for parsimony to connect with plausibility in a particular research problem. The reasonableness of parsimony in one research context may have nothing to do with its ... principle, the demand for simplicity suggested by parsimony cannot be generally sustained. Parsimony cannot help toward a rational decision between competing explanations of the same ... understanding. In the absence of an objective criterion for simplicity and complexity, parsimony ... as an overly complex explanation with senseless additional hypotheses. Parsimony, in this way, becomes ... more details
Lead too short date September 2009 Parsimony is a non parametric statistics non parametric statistical method commonly used in computational phylogenetics for estimating phylogeny phylogenies . Under parsimony ... some observed data. In detail Parsimony is part of a class of character based tree estimation ... as the best estimate of the phylogenetic relationships of the included taxa. Maximum parsimony is used ... mistakenly believed that parsimony assumes that convergence is rare in fact, even convergently derived characters have some value in maximum parsimony based phylogenetic analyses, and the prevalence of convergence does not systematically affect the outcome of parsimony based methods. Ref Cite doi 10.1146 ... which data do not fit the tree is a complex process. Maximum parsimony is one method developed to do this. Character data The input data used in a maximum parsimony analysis is in the form of characters ... two or more states they can have only one, but these characters lend nothing to a maximum parsimony ... a case where the state is simply unknown. Current implementations of maximum parsimony generally ... data are particularly amenable to character based phylogenetic methods such as maximum parsimony because ... The time required for a parsimony analysis or any phylogenetic analysis is proportional to the number ... estimates of the pattern of character changes. The most disturbing weakness of parsimony analysis ... be too suspect to use anyway. Analysis A maximum parsimony analysis runs in a very straightforward ... it to see if the change produces a higher score. The trees resulting from parsimony search are unrooted ... in incorrect relationships on the tree, even if the tree is itself correct in its unrooted form. Parsimony ... by the input trees. Even if multiple MPTs are returned, parsimony analysis still basically produces ..., have been employed with parsimony analysis. The jackknife, which involves resampling without ..., because adding duplicate taxa does not change the result of a parsimony analysis. The bootstrap is much ... more details
Generated by me in XFig This image is placed permanently and irrevocably in the public domain by me. PD self date October 2006 This is an image of a phylogenetic tree used as an example of long branch attraction, a problem with maximum parsimony ... more details
Orphan date February 2009 In maximum parsimony , an informative site is a position in the relevant set of sequences at which there are at least two different character state s at that point in the sequences, and each of those states occurs in at least two of the sequences. References http www.icp.ucl.ac.be opperd private parsimony.html informative Christian de Duve Institute of Cellular Pathology Category Computational phylogenetics Bioinformatics stub ... more details
Stratocladistics is a method of making phylogenetic inferences using both geological and morphobiological data. It follows many of the same rules as cladistics , using Bayesian logic to quantify how good a phylogenetic hypothesis is in terms of debt and parsimony . However, in addition to the morphological debt that is used to determine phylogenetic dissimilarities in cladistics, there is also stratigraphic debt which adds the dimension of time to the equation. Category Phylogenetics ... more details
Three taxon analysis or TTS, or three item analysis is a cladistic based method of phylogenetic reconstruction. Introduced by Nelson and Platnick 1991 ref Nelson and Platnick, 3 Taxon statements a more precise use of parsimony, Cladistics, 1991 ref to reconstruct organisms phylogeny, this method can also be applied to biogeography biogeographic areas . See also Cladistics References references phylo Category Phylogenetics fr Analyse trois l ments ... more details
Haeseler MEGA Molecular Evolutionary Genetics Analysis Distance, Parsimony and Maximum Composite ... population genetics, while others do non phylogenetic multivariate analysis. Maximum parsimony, distance ... inference Maximum parsimony, implied weighting, ratchet http www.cladistics.com aboutNona.htm download ... using parsimony and other methods Maximum parsimony, distance matrix, maximum likelihood http paup.csit.fsu.edu purchase D. Swofford PHYLIP Phylogenetic inference package Maximum parsimony, distance ... Computing nucleotides and aminoacids Maximum likelihood, simple Maximum parsimony http icwww.epfl.ch ... D.H. Huson and D. Bryant TNT Phylogenetic inference Parsimony, weighting, ratchet, tree drift, tree ... matrix and approximate parsimony http bioweb.pasteur.fr seqanal interfaces treealign simple.html server ..., Gene transfer detection Distance, Parsimony and Maximum likelihood http www.trex.uqam.ca T REX ... Nona Maximum parsimony, ratchet http www.cladistics.com aboutWinc.htm download K. Nixon Xrate Phylo ... more details
Context date October 2009 Long branch attraction LBA is a phenomenon in phylogenetic analyses most commonly those employing maximum parsimony when rapidly evolving lineages are inferred to be closely related, regardless of their true evolution ary relationships. For example, in DNA sequence based analyses, the problem arises when sequences from two or more lineages evolve rapidly. There are only four possible nucleotide s and when mutation DNA substitution rates are high, the probability that two lineages will evolve the same nucleotide at the same site increases. When this happens, parsimony erroneously interprets this homoplasy as a synapomorphy i.e., evolving once in the common ancestor of the two lineages . This problem can be minimized by using methods that correct for multiple substitutions at the same site, by breaking up long branches adding taxa related to those with the long branches or by using alternative slower evolving traits. References Bergsten, J. 2005 A review of long branch attraction. Cladistics 21 2 163 193. http www.blackwell synergy.com doi pdf 10.1111 j.1096 0031.2005.00059.x PDF fulltext Felsenstein, J. 2004 Inferring Phylogenies . Sinauer Associates, Sunderland, MA. phylo Category Phylogenetics ca Atracci entre branques llargues es Atracci n de ramas largas fr Attraction des longues branches pl Long branch attraction pt Atra o de ramifica es longas ... more details
program that are available in the package include parsimony , distance matrix , and maximum likelihood ... sequences using the Maximum parsimonyParsimony Method dnapars Estimates phylogenies of DNA sequences using the parsimony method. dnapenny DNA parsimony branch and bound method. Finds all of the most ... construction of phylogenies from nucleic acid sequences, with their evaluation by DNA parsimony ... data pars Unordered multistate discrete characters parsimony method. mix Estimates phylogenies by some parsimony methods for discrete character data with two states 0 and 1 . Allows use of the Wagner parsimony method, the Camin Sokal parsimony method, or arbitrary mixtures of these. penny Branch ... data with two states, for the Wagner, Camin Sokal, and mixed parsimony criteria using the branch and bound ... data with two states 0 and 1 . Evaluates parsimony and compatibility criteria for those phylogenies ... parsimony criteria for discrete character data with two states 0 and 1 . dolpenny Finds ... parsimony criteria using the branch and bound method of exact search. dolmove Interactive ... parsimony criteria. Evaluates parsimony and compatibility criteria for those phylogenies ... more details
taxobox image AristolochiaTomentosa.jpg image width 200px regnum Plant ae unranked divisio Magnoliophyta unranked classis Magnoliid s ordo Piperales familia Aristolochiaceae genus Aristolochia binomial Aristolochia tomentosa species A. tomentosa Aristolochia tomentosa is a species of flowering plant in the Aristolochiaceae family. References C. Neinhuis, S. Wanke1, K. W. Hilu, K. M ller and T. Borsch, 2004 . Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL trnF sequences . Plant Systematics and Evolution, Volume 250, Numbers 1 2. pp. 7 26. Category Aristolochia tomentosa Category Flora of Alabama az Aristolochia tomentosa ... more details
Summary Information Description To quote the authors, a dated molecular supertree for all 34 world pinniped species derived from a weighted matrix representation with parsimony MRP supertree analysis of 50 gene trees, each determined under a maximum likelihood ML framework Source http www.pubmedcentral.nih.gov articlerender.fcgi?tool pubmed&pubmedid 17996107 BMC Evol Biol. 2007 7 216. Published online 2007 November 9. doi 10.1186 1471 2148 7 216. Date 11 9 2007 Author Jeff W Higdon,corresponding author1 Olaf RP Bininda Emonds,2 Robin MD Beck,3 and Steven H Ferguson4 Permission Open Access Creative Commons license PubMed Central other versions Note one purpose of this image is to create a clickable image map. Please update any such map if changing the resolution of this image. Licensing cc by sa 3.0 ... more details
Warren H. Wagner Jr. August 29, 1920 January 8, 2000 , known as Herb Wagner, from his middle name, Herbert, was an eminent American botanist who lived in Michigan . A longtime faculty member at the University of Michigan Ann Arbor , he developed, in the early 1960s, the first algorithm for discerning phylogenetic relationships among species based upon their respective character states observed over a set of characters. This work was honored by James Farris botanist James Farris and Arnold Kluge in their later appellation of related algorithms as Wagner maximum parsimony parsimony . Wagner specialized in the fern s, especially the Botrychiaceae . The standard Binomial nomenclature Authorship in scientific names botanical author abbreviation W.H.Wagner is applied to species he described. Apparently among modern phylogenetic systematists, Wagner is alone in having been mentioned in a Hollywood film A New Leaf , starring Elaine May and Walter Matthau . Note not to be confused with the American botanist http botany.si.edu staff staffPage.cfm?ThisName 47&homepage no Warren L. Wagner 1950 . External links http herbarium.lsa.umich.edu University of Michigan Herbarium Persondata Metadata see Wikipedia Persondata . NAME Wagner, Warren H. ALTERNATIVE NAMES SHORT DESCRIPTION DATE OF BIRTH PLACE OF BIRTH DATE OF DEATH PLACE OF DEATH DEFAULTSORT Wagner, Warren H. Category 1920 births Category 2000 deaths Category American botanists Category Pteridologists Category Botanists with author abbreviations Category University of Michigan faculty US scientist stub es Warren H. Wagner fr Warren Herbert Wagner pt Warren Herbert Wagner ... more details
Other uses Indeterminacy disambiguation The indeterminacy problem is posed as a kind of paradox in the study of the sociology of science sociology and history of science . It is often used as an argument against the rational value of scientific thought. The argument is as follows There are an infinite number of possible theories, There can only be a finite amount of experimental evidence, Therefore it is impossible to disambiguate between all viable theories. While this is true in this abstract form, in practice, parsimony is used to limit the number of theories which are considered useful, and likewise, to limit the number of directions to take experimental research. Occam s Razor , seeking the simplest explanation, forms much of the basis of modern scientific thought a theory which accounts best for all observed phenomena, does not predict disproven phenomena, and does not introduce unobserved phenomena is to be preferred. ref cite book url http books.google.com books?id od68ge7aF6wC&pg PA531&dq parsimonious scientific method v onepage&q &f false title The philosophy of science an encyclopedia, Volume 1 author Sahotra Sarkar, Jessica Pfeifer publisher Routledge isbn 9780415939270 ref Moreover, data obtained by one experiment can be applied to more than one hypothesis, and proven hypotheses can be applied to more than one theory. For example, the theory of gravity has implications for innumerable other theories. There is not an infinite number of possible theories, since the available theories are limited by the ideas which have actually been imagined by scientists. See also Occam s razor Parsimony Negative proof References reflist External links http books.google.com books?q Indeterminacy problem&btnG Search Books Google Books Category Sociology ... more details
Taxobox image Doriopsilla albopunctata mating.jpg image caption Doriopsilla albopunctata regnum Animal ia phylum Mollusca classis Gastropoda unranked familia clade Heterobranchia br clade Euthyneura br clade Nudipleura br clade Nudibranch ia br clade Euctenidiacea br clade Doridacea superfamilia Phyllidioidea familia Dendrodorididae familia authority O Donoghue , 1924 subdivision ranks Genera subdivision See text. synonyms Doridopsidae Alder & Hancock, 1864 Dendrodorididae is a taxonomic family biology family of sea slug s, dorid nudibranch s, marine ocean marine gastropod mollusc s in the order biology Superfamily Phyllidioidea . Genera A Maximum parsimony phylogenetics maximum parsimony analysis of the nucleotide sequence of the 16S mtDNA gene , performed in 2003, has shown that the family Dendrodoridae is paraphyletic . ref cite journal last Vald s first Angel year 2003 title Preliminary molecular phylogeny of the radula less Dorids Gastropoda Opisthobranchia , based on 16S MTDNA sequence data journal Journal of Molluscan Studies publisher Oxford Journals volume 69 issue 1 pages 75 80 issn 1464 3766 url http mollus.oxfordjournals.org cgi content abstract 69 1 75 accessdate 2010 02 01 ref Genera in the family Dendrodorididae presently include Aphelodoris is in Discodorididae Dendrodoris small Christian Gottfried Ehrenberg Ehrenberg , 1831 small Doriopsilla small Rudolph Bergh Bergh , 1880 small References reflist ITIS id 78447 taxon Dendrodorididae Arthur William Baden Powell Powell A. W. B. , New Zealand Mollusca , HarperCollins William Collins Publishers Ltd , Auckland, New Zealand 1979 ISBN 0 00 216906 1 Category Dendrodorididae heterobranchia stub fr Dendrodorididae it Dendrodorididae ... more details
Hickam s dictum is a counterargument to the use of Occam s razor in the medical profession. ref See, e.g., Hickam s Dictum versus Occam s Razor A Case for Occam. W. Bradley Fields, MD, University of Michigan Health System, Ann Arbor, MI 2005 http www.hospitalmedicine.org AM Template.cfm?Section Home&TEMPLATE CM HTMLDisplay.cfm&CONTENTID 5342 Clinical Vignettes ref The principle is commonly stated Patients can have as many diseases as they damn well please . The principle is attributed to John Hickam, MD. Hickam was a faculty member at Duke University in the 1950s, and was later chairman of medicine at Indiana University . ref Journal of Neuro Ophthalmology September 2002 Volume 22 Issue 3 pp 240 246 http www.jneuro ophthalmology.com pt re jneuroophth fulltext.00041327 200209000 00009.htm ref When discussing Occam s razor in contemporary medicine, doctors and philosophers of medicine speak of diagnostic parsimony . Diagnostic parsimony advocates that when diagnosing a given injury, ailment, illness, or disease a doctor should strive to look for the fewest possible causes that will account for all the symptoms. However, this principle has very important limits in medical practice. The actual process that occurs when diagnosing a patient is a continuous flow of hypothesis and testing of that hypothesis, then modifying the hypothesis, and so on. In the context of this method, the principle of Hickam s dictum asserts that at no stage should a particular diagnosis be excluded solely because it doesn t appear to fit the principle of Occam s razor. The principle of Occam s razor, or parsimony, does not demand that the diagnostician necessarily opt for the simplest explanation, but instead guides the medical practitioner to seek explanations, without unnecessary additional assumptions, which are capable of accounting for all relevant evidence. A key reason for using Hickam s dictum as a limiting principle to that of Occam s razor is that it is often statistically more likely ... more details
unref date January 2008 In statistics , an optimality criterion provides a measure of the fit of the data to a given hypothesis. The selection process is determined by the solution that optimizes the criteria used to evaluate the alternative hypotheses. The term has been used to identify the different criteria that are used to evaluate a phylogenetic tree and include maximum likelihood , Bayesian probability Bayesian , maximum parsimony , and minimum evolution . For example, in order to determine the best topology between two phylogenetic trees using the maximum likelihood optimality criterion, one would calculate the maximum likelihood score of each tree and choose the one that had the better score. However, different optimality criteria can select different hypotheses. In such circumstances caution should be exercised when making strong conclusions. Many other disciplines use similar criteria or have specific measures geared toward the objectives of the field. References Empty section date July 2010 See also Optimality in Pareto equilibrium Category Hypothesis testing ru ... more details
Tree rearrangements are used in heuristic algorithm s devoted to searching for an Optimization mathematics optimal tree structure . They can be applied to any set of data that are naturally arranged into a tree, but have most applications in computational phylogenetics , especially in maximum parsimony and maximum likelihood searches of phylogenetic tree s, which seek to identify one among many possible trees that best explains the evolution ary history of a particular gene or species . Basic tree rearrangements gallery Image NNI.svg Nearest Neighbor Interchange NNI Image SPR.svg Sub tree Pruning and Regrafting SPR Image TBR.svg Tree bisection and reconnection TBR gallery The simplest tree rearrangement, known as nearest neighbor interchange , exchanges the connectivity of four subtrees within the main tree. Because there are three possible ways of connecting four subtrees, ref name felsenstein Felsenstein J. 2004 . Inferring Phylogenies Sinauer Associates Sunderland, MA. ref and one is the original connectivity, each interchange creates two new trees. Exhaustively searching the possible nearest neighbors for each possible set of subtrees is the slowest but most optimizing way of performing this search. An alternative, more wide ranging search, subtree pruning and regrafting SPR , selects and removes a subtree from the main tree and reinserts it elsewhere on the main tree to create a new node. Finally, tree bisection and reconnection TBR detaches a subtree from the main tree at an interior node and then attempts all possible connections between branches of the two trees thus created. The increasing complexity of the tree rearrangement technique correlates with increasing computational time required for the search, although not necessarily with their performance. ref name takahashi Takahashi K, Nei M. 2000 . Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number ... more details
unused data authorlink ref Using a parsimony criterion is only one of several methods to infer ... cladogram. ref cite book title Cladistics The Theory and Practice of Parsimony Analysis last Kitching ... data. Algorithms for cladograms include least squares , neighbor joining , parsimony , maximum likelihood , and Bayesian inference . Biologists sometimes use the term parsimony for a specific .... ref cite journal author Stewart, Caro Beth journal Nature title The Powers and Pitfalls of Parsimony ... one. ref cite journal author Nixon K. C. journal Cladistics title The Parsimony Ratchet a new method for rapid parsimony analysis year 1999 volume 15 pages 407 414 doi 10.1111 j.1096 0031.1999.tb00277.x ... more details
. Oxford, Blackwell Publishers. simplicity, parsimony p. 461 462. John Maeda Maeda, J. , 2006 ... . The MIT Encyclopedia of the Cognitive Sciences. Cambridge, Massachusetts, The MIT Press. parsimony ... more details
with extensive anatomical comparisons and by extending their parsimony analysis using PAUP . ref Swofford, D.L. 2002 PAUP phylogenetic analysis using parsimony and other methods Version 4. Sinauer ... more details
Walter M. Fitch May 21, 1929 March 10, 2011 . Until his death he was professor of molecular evolution at the University of California, Irvine . He was also a member of the United States National Academy of Sciences National Academy of Sciences , the American Philosophical Society , and the American Association for the Advancement of Science , and was a Foreign Member of the Linnean Society of London Linnean Society London . He is the co founder of the journal Molecular Biology and Evolution , together with Masatoshi Nei , and was the first president of the Society for Molecular Biology and Evolution . Walter Fitch is noted for his pioneering work on reconstruction of Phylogenetic tree phylogenies evolutionary trees from protein and DNA sequences. Among his achievements are the first major paper on distance matrix methods, which introduced the Fitch Margoliash method which seeks the tree that best predicts a set of pairwise distances among species. He also developed the Fitch parsimony algorithm, which evaluates rapidly and exactly the minimum number of changes of state of a sequence on a given phylogeny. Major papers Fitch, W. M. and E. Margoliash. 1967 . Construction of phylogenetic trees. Science 155 279 284. Fitch, W. M. 1971 . Toward defining the course of evolution minimum change for a specified tree topology. Systematic Zoology 20 406 416 External links http www.faculty.uci.edu profile.cfm?faculty id 2117&name Walter 20M. 20Fitch Faculty page with online publications http ncse.com news 2011 03 walter fitch dies 006544 Obituary at the National Center for Science Education DEFAULTSORT Fitch, Walter M. Category Academics Category Members of the Linnean Society of London Category University of California, Irvine faculty Category 1929 births Category 2011 deaths ... more details
Relevance vector machine RVM is a machine learning technique that uses Bayesian inference to obtain Parsimony parsimonious solutions for Regression analysis regression and Statistical classification classification . The RVM has an identical functional form to the support vector machine , but provides probabilistic classification. It is actually equivalent to a Gaussian process model with covariance function math k mathbf x , mathbf x sum j 1 N frac 1 alpha j phi mathbf x , mathbf x j phi mathbf x , mathbf x j math where is the kernel function usually Gaussian , and x sub 1 sub , , x sub N sub are the input vectors of the training set . Citation needed date February 2010 Compared to that of support vector machine s SVM , the Bayesian formulation of the RVM avoids the set of free parameters of the SVM that usually require cross validation based post optimizations ref group note See the comment of this claim in the Discussion of this page ref . However RVMs use an expectation maximization EM like learning method and are therefore at risk of local minima. This is unlike the standard sequential minimal optimization SMO based algorithms employed by Support vector machine SVM s, which are guaranteed to find a global optimum. Citation needed date February 2010 Notes references group note References cite journal last Tipping first Michael E. last2 Smola first2 Alex title Sparse Bayesian Learning and the Relevance Vector Machine year 2001 journal Journal of Machine Learning Research volume 1 pages 211&ndash 244 url http jmlr.csail.mit.edu papers v1 tipping01a.html doi 10.1162 15324430152748236 Software http dlib.net dlib C Library http www.terborg.net research kml The Kernel Machine Library External links http www.relevancevector.com Tipping s webpage on Sparse Bayesian Models and the RVM http www.tristanfletcher.co.uk RVM 20Explained.pdf A Tutorial on RVM by Tristan Fletcher Category Classification algorithms Category Ensemble learning Category Machine learning Category Non ... more details
Francesco Accolti c. 1416 ref name black cite book first Robert last Black authorlink coauthors year 2002 title Benedetto Accolti and the Florentine Renaissance edition publisher Cambridge University Press isbn 0 521 52227 7 format Paperback page 4 ref 1488 , also called Francesco d Arezzo , was an italy Italian jurist. The brother of Benedetto Accolti the Elder Benedetto Accolti , he professed jurisprudence at Bologna from 1440 to 1445, and afterwards at Ferrara , Siena , and Pisa . He possessed a strong understanding and powerful eloquence. The distinction which he acquired was so great, that he flattered himself with the expectation of obtaining a cardinal s hat, on the accession of Sixtus IV to the pontifical throne and when it was refused him, the pope though it necessary to accompany the refusal with this complimentary apology I would gladly have granted you the honor, had I not feared, that your preferment, by removing you from your school, would have hindered the progress of science. The reputation of Accolti was tarnished by the parsimony with which he amassed vast treasures. He wrote several treatises on law, and translated some of the writings of Chrysostom . ref name genbio genbio Accolti, Francesco ref References reflist See also Accolti , other members of the family DEFAULTSORT Accolti, Francesco Category 1410s births Category 1488 deaths Category People from Arezzo Category Italian jurists Category Italian lawyers Category 15th century Italian people ca Francesco Accolti l aret fr Francesco Accolti it Francesco Accolti sl Francesco Accolti ... more details
Encyclopedia
top
