A syntagmatic and paradigmatic analysis of scientific text

The Story of Science: A plea for a syntagmatic/paradigmatic analysis of scientific textAnita de Waard, a.dewaard@elsevier.com Disruptive Technologies Director, Elsevier Labs University of Utrecht, Institute of LinguisticsThursday, October 21, 2010Scientific papers are stories, that persuade with data2Thursday, October 21, 2010Scientific papers are stories, that persuade with data1.Paradigmatic approach (Tropp)/story grammar (Rumelhart, Thorndyke): ‘ systematic assignment of constituent structure”• Sequential components• Order in text is key factor• Granularity: one or more paragraphs (?)2Thursday, October 21, 2010Scientific papers are stories, that persuade with data1.Paradigmatic approach (Tropp)/story grammar (Rumelhart, Thorndyke): ‘ systematic assignment of constituent structure”• Sequential components• Order in text is key factor• Granularity: one or more paragraphs (?)2.Syntagmatic approach: “groups of relations between actors and events are sought throughout the text” (Lévi-Strauss, 1955)• Groups are found throughout the text• Relationship types between actors/events are key• Granularity: ‘shortest possible sentences’2Thursday, October 21, 2010Paradigmatic Approach: story grammarThe Story of Goldilocks StoryGrammarPaperThe AXH Domain of Ataxin-1 Mediates and the Three BearsNeurodegeneration through Its Interaction with Gfi-1/Senseless ProteinsOnce upon a timeTimeSettSet int gBackgroundThe mechanisms mediating SCA1 pathogenesis are stil not ful y understood, but some general principles have emerged. a little girl named GoldilocksCharactersObjects of studythe Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract, She went for a walk in the LocationExperimental studied and compared in vivo effects and interactions to those of forest. Pretty soon, she came setupthe human proteinupon a house.She knocked and, when no one GoalThT emeResearchGain insight into how Atx-1's function contributes to SCA1 answered, goalpathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not ful y understood.she walked right in. AttemptHypothesisAtx-1 may play a role in the regulation of gene expressionAt the table in the kitchen, there NameEpE isode 1e NamedAtX-1 and hAtx-1 Induce Similar Phenotypes When were three bowls of porridge. Overexpressed in Files Goldilocks was hungry. SubgoalSubgoaltest the function of the AXH domainShe tasted the porridge from AttemptMethodoverexpressed dAtx-1 in flies using the GAL4/UAS system (Brand the first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1. This porridge is too hot! she OutcomeResultsOverexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives exclaimed.expression in the differentiated R1-R6 photoreceptor cel s (Mol ereau et al., 2000 and O'Tousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after eclosion, overexpression of either So, she tasted the porridge ActivityDataAt(dx-1ata dnoet s nsh oo t w shn),o w obvious morphological changes in the from the second bowl.photoreceptor cel sThis porridge is too cold, she OutcomeResultsboth genotypes show many large holes and loss of cel integrity at said28 days So, she tasted the last bowl of  ActivityData(Figures 1B-1D). porridge.Ahhh, this porridge is just right, OutcomeResultsOverexpression of dAtx-1 using the GMR-GAL4 driver also induces she said happily and eye abnormalities. The external structures of the eyes that 3overexpress dAtx-1 show disorganized ommatidia and loss of she ate it al up.interommatidial bristles  Data(Figure 1F), Thursday, October 21, 2010Paradigmatic Approach: story grammarThe Story of Goldilocks StoryGrammarPaperThe AXH Domain of Ataxin-1 Mediates and the Three BearsNeurodegeneration through Its Interaction with Gfi-1/Senseless ProteinsOnce upon a timeTimeSettSet int gBackgroundThe mechanisms mediating SCA1 pathogenesis are stil not ful y understood, but some general principles have emerged. a little girl named GoldilocksCharactersObjects of studythe Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract, She went for a walk in the LocationExperimental studied and compared in vivo effects and interactions to those of forest. Pretty soon, she came setupthe human proteinupon a house.She knocked and, when no one GoalThT emeResearchGain insight into how Atx-1's function contributes to SCA1 answered, goalpathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not ful y understood.she walked right in. AttemptHypothesisAtx-1 may play a role in the regulation of gene expressionAt the table in the kitchen, there NameEpE isode 1e NamedAtX-1 and hAtx-1 Induce Similar Phenotypes When were three bowls of porridge. Overexpressed in Files Goldilocks was hungry. SubgoalSubgoaltest the function of the AXH domainShe tasted the porridge from AttemptMethodoverexpressed dAtx-1 in flies using the GAL4/UAS system (Brand the first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1. This porridge is too hot! she OutcomeResultsOverexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives exclaimed.expression in the differentiated R1-R6 photoreceptor cel s (Mol ereau et al., 2000 and O'Tousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after eclosion, overexpression of either So, she tasted the porridge ActivityDataAt(dx-1ata dnoet s nsh oo t w shn),o w obvious morphological changes in the from the second bowl.photoreceptor cel sThis porridge is too cold, she OutcomeResultsboth genotypes show many large holes and loss of cel integrity at said28 days So, she tasted the last bowl of  ActivityData(Figures 1B-1D). porridge.Ahhh, this porridge is just right, OutcomeResultsOverexpression of dAtx-1 using the GMR-GAL4 driver also induces she said happily and eye abnormalities. The external structures of the eyes that 3overexpress dAtx-1 show disorganized ommatidia and loss of she ate it al up.interommatidial bristles  Data(Figure 1F), Thursday, October 21, 2010Story structure also has a rhetorical goal:4Thursday, October 21, 2010Story structure also has a rhetorical goal:Aristotle QuintilianScientific PaperThe introduction of a speech, where one announces the Introduction: prooimion Introduction subject and purpose of the discourse, and where one usual y / exordiumemploys the persuasive appeal to ethos in order to positioningestablish credibility with the audience. Introduction: research prothesisStatement of The speaker here provides a narrative account of what has Facts/narratio happened and general y explains the nature of the case. question Summary/ The propositio provides a brief summary of what one is about propostitioto speak on, or concisely puts forth the charges or accusation. Summary of contentsThe main body of the speech where one offers logical pistisProof/ Resultsconfirmatioarguments as proof. The appeal to logos is emphasized here. Refutation/ As the name connotes, this section of a speech was devoted to refutatioanswering the counterarguments of one's opponent.Related WorkFol owing the refutatio and concluding the classical oration, the Discussion: summary, epilogosperoratio peroratio conventional y employed appeals through pathos, and often included a summing up.implications.4Thursday, October 21, 2010Story structure also has a rhetorical goal:Aristotle QuintilianScientific PaperThe introduction of a speech, where one announces the Introduction: prooimion Introduction subject and purpose of the discourse, and where one usual y / exordiumemploys the persuasive appeal to ethos in order to positioningestablish credibility with the audience. Introduction: research prothesisStatement of The speaker here provides a narrative account of what has Facts/narratio happened and general y explains the nature of the case. question Summary/ The propositio provides a brief summary of what one is about propostitioto speak on, or concisely puts forth the charges or accusation. Summary of contentsThe main body of the speech where one offers logical pistisProof/ Resultsconfirmatioarguments as proof. The appeal to logos is emphasized here. Refutation/ As the name connotes, this section of a speech was devoted to refutatioanswering the counterarguments of one's opponent.Related WorkFol owing the refutatio and concluding the classical oration, the Discussion: summary, epilogosperoratio peroratio conventional y employed appeals through pathos, and often included a summing up.implications.4Thursday, October 21, 2010Paradigmatic approach for scienceBoth seminomas and the EC component of nonseminomas share features with ES cells. To exclude that the detection of miR-371-3 merely reflects its expression pattern in ES cells, we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004). In many of the m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.5Thursday, October 21, 2010