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Critics of 3ta have failed to fully implement\nit in examples; as a result this criticism is faulty and\ndoes not support the claims made. 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2012 - 3ta Sleeps with the fishes.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Farris - 2012 - 3ta Sleeps with the fishes.pdf", "md5": "7072f4838cb3bc2d2e18fc1873696a83", "mtime": 1328187227881, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/NKDIRXUT" }, "dateAdded": "2012-02-02T12:54:01Z", "dateModified": "2012-02-02T12:54:01Z" } }, { "key": "D6VW722K", "version": 1, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/D6VW722K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/D6VW722K", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Farris", "parsedDate": "2012", "numChildren": 1 }, "data": { "key": "D6VW722K", "version": 1, "itemType": "journalArticle", "title": "3ta Sleeps with the fishes", "creators": [ { "creatorType": "author", "firstName": "J.S.", "lastName": "Farris" } ], "abstractNote": "", "publicationTitle": "Cladistics", "publisher": "", "place": "", "date": "2012", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "8BUQQQTR", "NAA8NPNZ" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/K9F2K5HP" }, "dateAdded": "2012-02-02T12:54:01Z", "dateModified": "2012-02-02T12:54:01Z" } }, { "key": "4RNXJQGC", "version": 1, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/4RNXJQGC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/4RNXJQGC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Jardine", "parsedDate": "1967", "numChildren": 0 }, "data": { "key": "4RNXJQGC", "version": 1, "itemType": "journalArticle", "title": "The concept of homology in biology", "creators": [ { "creatorType": "author", "firstName": "N.", "lastName": "Jardine" } ], "abstractNote": "", "publicationTitle": "British Journal of Philosophical Sciences", "publisher": "", "place": "", "date": "1967", "volume": "18", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "125-139", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "K68PHPPF" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/WB6DXRNC" }, "dateAdded": "2012-02-02T12:42:31Z", "dateModified": "2012-02-02T12:42:31Z" } }, { "key": "TMTEBXBC", "version": 2, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/TMTEBXBC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/TMTEBXBC", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/66889/items/NI3IHE9T", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "TMTEBXBC", "version": 2, "parentItem": "NI3IHE9T", "itemType": "attachment", "linkMode": "imported_file", "title": "Hawkins et al. - 1997 - Primary Homology Assessment, Characters and Charac.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Hawkins et al. - 1997 - Primary Homology Assessment, Characters and Charac.pdf", "md5": "704d06916c84010a151cace73efc9759", "mtime": 1284132604915, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/6FNTRATQ" }, "dateAdded": "2012-02-02T12:42:24Z", "dateModified": "2012-02-02T12:42:24Z" } }, { "key": "NI3IHE9T", "version": 1, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/NI3IHE9T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/NI3IHE9T", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Hawkins et al.", "parsedDate": "1997", "numChildren": 1 }, "data": { "key": "NI3IHE9T", "version": 1, "itemType": "journalArticle", "title": "Primary Homology Assessment, Characters and Character States", "creators": [ { "creatorType": "author", "firstName": "Julie A.", "lastName": "Hawkins" }, { "creatorType": "author", "firstName": "Colin E.", "lastName": "Hughes" }, { "creatorType": "author", "firstName": "Robert W.", "lastName": "Scotland" } ], "abstractNote": "We discuss contrasting approaches to cladistic character\ndefinition and thus to cladistic data matrix compilation.\nThe conventional approach considers character states as\nalternate forms of the “same thing” (the character). A\nreview of the challenges to this convention is presented,\nand their implications evaluated. We argue that the recognition\nof structures which are alternate forms is a vital\nstage of primary homology assessment and is equivalent\nto the conceptualization of a transformational homology.\nSuch a view complies with the demand that characters\nare independent and that character states are hierarchically\nrelated. We identify one justifiable solution to the\ninapplicable data coding problem (coding for organisms\nwhich have red tails, blue tails or no tails), and show that\nalternative approaches to character definition support\nspurious solutions which deny the relation of structures\nwhich are “the same but different”. We propose that the\nterm character can be defined, in a cladistic context, as\nthe descriptive label referring to a transformational\nhomology evidenced by the similarity criterion.", "publicationTitle": "Cladistics", "publisher": "", "place": "", "date": "1997", "volume": "13", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "275-283", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cladistics", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "K68PHPPF" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/XSFTKRUQ" }, "dateAdded": "2012-02-02T12:42:24Z", "dateModified": "2012-02-02T12:42:24Z" } }, { "key": "U93E28JG", "version": 2, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/U93E28JG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/U93E28JG", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/66889/items/AIPF4SHG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "U93E28JG", "version": 2, "parentItem": "AIPF4SHG", "itemType": "attachment", "linkMode": "imported_file", "title": "Roth - 1984 - On homology.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Roth - 1984 - On homology.pdf", "md5": "d8214fa9bb71784949b6a4b8ad60e6f9", "mtime": 1316165092000, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/8U9MNIMP" }, "dateAdded": "2012-02-02T12:42:03Z", "dateModified": "2012-02-02T12:42:03Z" } }, { "key": "AIPF4SHG", "version": 1, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/AIPF4SHG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/AIPF4SHG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Roth", "parsedDate": "1984", "numChildren": 1 }, "data": { "key": "AIPF4SHG", "version": 1, "itemType": "journalArticle", "title": "On homology", "creators": [ { "creatorType": "author", "firstName": "Louise V.", "lastName": "Roth" } ], "abstractNote": "The currently most widely used definitions of homology, which concentrate exclusively on what I\ncall phylogenetic homology, involve comparisons between taxa. Although they share important\nconceptual relationships with phylogenetic homology and their role in evolutionary biology is\nsignificant, serial and other forms of iterative homology have been, by comparison, overlooked.\nThere is need for a more inclusive definition of homology. I propose that the basis of homology in\nthe broad sense is the sharing of pathways of development, which are controlled by genealogicallyrelated\ngenes. Using this definition, one can construct hierarchies of homology, and recognize\ndifferent degrees or strengths of homology. Because different aspects of structures are controlled by\ndistinct developmental programs, it is sometimes necessary to speak of homologies of different\nattributes of specific structures, rather than to homologize the structures per se. For good biological\nreasons, parallelism may be difficult to distinguish from homology, and one must in practice be\nwilling to tolerate some ambiguity between them. The formulation I present leads to some\nunorthodox conclusions about homology in mammalian dentitions and homology between the foreand\nhindlimbs of tetrapods.", "publicationTitle": "Biological Journal of the Linnean Society", "publisher": "", "place": "", "date": "1984", "volume": "22", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "13-29", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "K68PHPPF" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/KB3CS2U8" }, "dateAdded": "2012-02-02T12:42:03Z", "dateModified": "2012-02-02T12:42:03Z" } }, { "key": "GS99B54R", "version": 2, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/GS99B54R", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/GS99B54R", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/66889/items/D97UAJN2", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "GS99B54R", "version": 2, "parentItem": "D97UAJN2", "itemType": "attachment", "linkMode": "imported_file", "title": "Nixon et Carpenter - 2011 - On homology.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Nixon et Carpenter - 2011 - On homology.pdf", "md5": "a43be201f2d0d4f18b2f891ff52c5d96", "mtime": 1316186232000, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/SR2ASPFF" }, "dateAdded": "2012-02-02T12:42:01Z", "dateModified": "2012-02-02T12:42:01Z" } }, { "key": "D97UAJN2", "version": 1, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/D97UAJN2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/D97UAJN2", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Nixon and Carpenter", "parsedDate": "2011", "numChildren": 1 }, "data": { "key": "D97UAJN2", "version": 1, "itemType": "journalArticle", "title": "On homology", "creators": [ { "creatorType": "author", "firstName": "Kevin C.", "lastName": "Nixon" }, { "creatorType": "author", "firstName": "James M.", "lastName": "Carpenter" } ], "abstractNote": "Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not\nsynonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy\nas types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and\nconvergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss\nwhether there is a difference between molecular homology and morphological homology, character state homology, nested\nhomology (additive characters), and serial homology. We conclude by proposing a global definition of homology.", "publicationTitle": "Cladistics", "publisher": "", "place": "", "date": "2011", "volume": "27", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1-10", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cladistics", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "K68PHPPF" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/ZV4UBBZX" }, "dateAdded": "2012-02-02T12:42:01Z", "dateModified": "2012-02-02T12:42:01Z" } }, { "key": "VUGIISXU", "version": 2, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/VUGIISXU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/VUGIISXU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/66889/items/HT6JAVTZ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "VUGIISXU", "version": 2, "parentItem": "HT6JAVTZ", "itemType": "attachment", "linkMode": "imported_file", "title": "Richter - 2005 - Homologies in phylogenetic analyses - concept and .pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Richter - 2005 - Homologies in phylogenetic analyses - concept and .pdf", "md5": "740f0c1f2ce9999472f4c83666fd78b7", "mtime": 1316167936000, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/I28DSGE4" }, "dateAdded": "2012-02-02T12:41:24Z", "dateModified": "2012-02-02T12:41:24Z" } }, { "key": "HT6JAVTZ", "version": 1, "library": { "type": "group", "id": 66889, "name": "cladistics and test of homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/66889/items/HT6JAVTZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cladistics_and_test_of_homology/items/HT6JAVTZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Richter", "parsedDate": "2005", "numChildren": 1 }, "data": { "key": "HT6JAVTZ", "version": 1, "itemType": "journalArticle", "title": "Homologies in phylogenetic analyses - concept and tests", "creators": [ { "creatorType": "author", "firstName": "Stefan", "lastName": "Richter" } ], "abstractNote": "Analyzing morphological characters in a phylogenetic context comprises two steps, character\nanalysis and cladistic analysis, which are equivalent to two independent tests for hypotheses on\nhomology. The concept of homology concerns comparable parts of the same or different organisms\nif their correspondences are the consequence of the same genetic or epigenetic information, and\nconsequently of the same origin. The concept of homology is more inclusive than the character\nconcept. Characters are seen as parts of transformation series. In the first step of morphological\ncharacter analyses correspondences and non-correspondences between two characters are analyzed.\nA range of different examination methods and accurate study contribute to the severity of test. The\nhypothesis that two characters are homologous is corroborated if the correspondences outweigh the\nnon-correspondences because the non-correspondences contradict the homology hypothesis\nwhereas the correspondences contradict the analogy hypothesis. Complex characters possess a\nhigher empirical content than less complex characters because they are more severely testable. The\ncladistic analysis tests characters against other characters which have all passed the first test.\nCharacters which are congruent with the most parsimonious topology are further corroborated;\nincongruent characters are not seen as 'falsified' but as not further corroborated and subject to reanalysis.\nTo test both homologies and topologies repeatedly is consistent with Popperian testability,\nand it is in such cycles of research that hypotheses will be critically re-evaluated.", "publicationTitle": "Theory in Biosciences", "publisher": "", "place": "", "date": "2005", "volume": "124", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "105-120", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "K68PHPPF" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/RUQQUMNE" }, "dateAdded": "2012-02-02T12:41:24Z", "dateModified": "2012-02-02T12:41:24Z" } } ]