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xhttp://www.escience2009.org/ Web Semantics in Action: Web 3.0 in e-Science 11:50 – 12:15 Annamaria Carusi & Anita de Waard: Changing Modes of Scientific Discourse Analysis, Changing Perceptions of ...

xhttp://www.escience2009.org/ Web Semantics in Action: Web 3.0 in e-Science 11:50 – 12:15 Annamaria Carusi & Anita de Waard: Changing Modes of Scientific Discourse Analysis, Changing Perceptions of Science

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    De Waard Carusi De Waard Carusi Presentation Transcript

    • Changing modes of scientific discourse analysis, changing perceptions of science Annamaria Carusi eResearch Centre, Oxford University Anita de Waard Disruptive Technologies, Elsevier Labs Utrecht Institute of Linguistics, U Utrecht
    • Changing modes of scientific discourse analysis
    • Changing modes of scientific discourse analysis
    • Changing modes of scientific discourse analysis • The HypER Project (AdW)
    • Changing modes of scientific discourse analysis • The HypER Project (AdW) • Pragmatic Discourse Analysis (AdW)
    • Changing modes of scientific discourse analysis • The HypER Project (AdW) • Pragmatic Discourse Analysis (AdW) • Rhetoric, discourse, arguments and self-perception (AC)
    • ‘Fact Extraction’ (MEDIE) - is not enough!
    • ‘Fact Extraction’ (MEDIE) - is not enough! Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric
    • ‘Fact Extraction’ (MEDIE) - is not enough! Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.
    • ‘Fact Extraction’ (MEDIE) - is not enough! without some idea of the status of the sentence, it cannot be interpreted! Alteration of nm23, P53, and S100A4 expression may contribute to the development of gastric Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF - Open University: Cohere - Oxford University: CiTO, eLearning/Rhetoric - DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF - Open University: Cohere - Oxford University: CiTO, eLearning/Rhetoric - DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF - Open University: Cohere - Oxford University: CiTO, eLearning/Rhetoric - DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF - Open University: Cohere - Oxford University: CiTO, eLearning/Rhetoric - DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF - Open University: Cohere - Oxford University: CiTO, eLearning/Rhetoric - DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF - Open University: Cohere - Oxford University: CiTO, eLearning/Rhetoric - DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF Hypothesis 22: Intramembrenous Aβ dimer may be toxic. - Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a Open University: Cohere fraction of these Abeta peptides never leave the membrane lipid bilayer after they are - generated, but instead exerteLearning/Rhetoric competing with and compromising Oxford University: CiTO, their toxic effects by the functions of intramembranous segments of membrane-bound proteins that serve - many critical functions. DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • Hypotheses, Evidence and Relationships: - Goal: Align and expand existing efforts on detection and analysis of Hypotheses, Evidence & Relationships - Partners: - Harvard/MGH: SWAN, ARF Hypothesis 22: Intramembrenous Aβ dimer may be toxic. - Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a Open University: Cohere fraction of these Abeta peptides never leave the membrane lipid bilayer after they are - generated, but instead exerteLearning/Rhetoric competing with and compromising Oxford University: CiTO, their toxic effects by the functions of intramembranous segments of membrane-bound proteins that serve - many critical functions. DERI: SALT, aTags - University of Trento: LiquidPub - Xerox Research: XIP hypothesis identifier - U Tilburg: ML for Science - Elsevier, UUtrecht: Discourse analysis of biology
    • HypER Activities: http://hyper.wik.is
    • HypER Activities: http://hyper.wik.is Current activities:
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig ✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig ✓Format for a rhetorical conference paper (SWAN+ SALT + abcde) ‣Parser test of hypothesis identification tools on pharmacology corpus
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig ✓Format for a rhetorical conference paper (SWAN+ SALT + abcde) ‣Parser test of hypothesis identification tools on pharmacology corpus ‣Aligning architectures to exchange hypotheses + evidence
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig ✓Format for a rhetorical conference paper (SWAN+ SALT + abcde) ‣Parser test of hypothesis identification tools on pharmacology corpus ‣Aligning architectures to exchange hypotheses + evidence Further interests:
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig ✓Format for a rhetorical conference paper (SWAN+ SALT + abcde) ‣Parser test of hypothesis identification tools on pharmacology corpus ‣Aligning architectures to exchange hypotheses + evidence Further interests: -Better structure of evidence: MyExperiment, KeFeD, ...
    • HypER Activities: http://hyper.wik.is Current activities: ✓Aligning discourse ontologies: joint task with W3C HCLSSig ✓Format for a rhetorical conference paper (SWAN+ SALT + abcde) ‣Parser test of hypothesis identification tools on pharmacology corpus ‣Aligning architectures to exchange hypotheses + evidence Further interests: -Better structure of evidence: MyExperiment, KeFeD, ... -Granularity of annotation/access: entity, hypothesis, discussion?
    • Pragmatic Discourse Analysis
    • Pragmatic Discourse Analysis - How can we better tell computers what our papers are about?
    • Pragmatic Discourse Analysis - How can we better tell computers what our papers are about? - Science is written in text, as a story
    • Pragmatic Discourse Analysis - How can we better tell computers what our papers are about? - Science is written in text, as a story - Text is created by humans to persuade other humans (peers, that claims are facts)
    • Pragmatic Discourse Analysis - How can we better tell computers what our papers are about? - Science is written in text, as a story - Text is created by humans to persuade other humans (peers, that claims are facts) - To tell the computer how we encode our knowledge, we need to understand:
    • Pragmatic Discourse Analysis - How can we better tell computers what our papers are about? - Science is written in text, as a story - Text is created by humans to persuade other humans (peers, that claims are facts) - To tell the computer how we encode our knowledge, we need to understand: => How do humans tell stories?
    • Pragmatic Discourse Analysis - How can we better tell computers what our papers are about? - Science is written in text, as a story - Text is created by humans to persuade other humans (peers, that claims are facts) - To tell the computer how we encode our knowledge, we need to understand: => How do humans tell stories? => How can we explain what matters, how these stories create knowledge in our heads?
    • 1st Try: Classical Rhetoric APA Style Aristotle Quintilian Cell Guide The introduction of a speech, where one announces the Introducti subject and purpose of the discourse, and where one Introductio prooimion exordium Introduction on usually employs the persuasive appeal of ethos in order to n establish credibility with the audience. The second part of a classical oration, following the introduction or exordium. The speaker here provides a Statement narrative account of what has happened and generally Introductio prothesis narratio Introduction of Facts explains the nature of the case. Quintilian adds that the n narratio is followed by the propositio, a kind of summary of the issues or a statement of the charge. Coming between the narratio and the partitio of a classical propostiti oration, the propositio provides a brief summary of what   Summary Abstract Abstract o one is about to speak on, or concisely puts forth the charges or accusation. Following the statement of facts, or narratio, comes the partitio or divisio. In this section of the oration, the speaker Division/ outlines what will follow, in accordance with what's been Table of   partitio Article Outline outline stated as the status, or point at issue in the case. Quintilian Contents suggests the partitio is blended with the propositio and also assists memory. Following the division / outline or partitio comes the main confirmati Methods, pistis Proof body of the speech where one offers logical arguments as Results o Results proof. The appeal to logos is emphasized here. Following the the confirmatio or section on proof in a Refutatio classical oration, comes the refutation. As the name   refutatio Discussion Discussion
    • 2nd Try: Story Grammar The Story of Goldilocks and Story Grammar Paper The AXH Domain of Ataxin-1 Mediates the Three Bears Neurodegeneration through Its Interaction with Gfi-1/ Senseless Proteins Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully understood, but some general principles have emerged. a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract, She went for a walk in the forest. Location Experimental studied and compared in vivo effects and interactions to those of the Pretty soon, she came upon a setup human protein house. She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1 answered, goal pathogenesis. 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 fully understood. she walked right in. Attempt Hypothesis Atx-1 may play a role in the regulation of gene expression At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in were three bowls of porridge. Files Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain She tasted the porridge from the Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and first bowl. Perrimon, 1993) and compared its effects to those of hAtx-1. This porridge is too hot! she Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives exclaimed. expression in the differentiated R1-R6 photoreceptor cells (Mollereau 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 Atx-1 does not show obvious morphological changes in the photoreceptor cells So, she tasted the porridge from   Data (data not shown), the second bowl. This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28 day
    • 3rd Try: Discourse Segmentation
    • 3rd Try: Discourse Segmentation Goal: ‘one new thought per segment’:
    • 3rd Try: Discourse Segmentation Goal: ‘one new thought per segment’: Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells.
    • 3rd Try: Discourse Segmentation Goal: ‘one new thought per segment’: Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells. a. Figure 4a shows that b. following RASV12 stimulation c. p53 was stabilized and activated d. and the target gene, p21cip1, was induced in all cases, e. indicating an intact p53 pathway in these cells.
    • 3rd Try: Discourse Segmentation Goal: ‘one new thought per segment’: Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells. a. Figure 4a shows that Intratextual b. following RASV12 stimulation Method c. p53 was stabilized and activated Result d. and the target gene, p21cip1, was induced in all cases, Result e. indicating an intact p53 pathway in these cells. Implication
    • 3rd Try: Discourse Segmentation Goal: ‘one new thought per segment’: Figure 4A shows that following RASV12 stimulation, p53 was stabilized and activated, and its target gene, p21cip1, was induced in all cases, indicating an intact p53 pathway in these cells. a. Figure 4a shows that Intratextual b. following RASV12 stimulation Method c. p53 was stabilized and activated Result d. and the target gene, p21cip1, was induced in all cases, Result e. indicating an intact p53 pathway in these cells. Implication
    • Tense and Realm Realm, Segment Type Linguistic Meaning Sample segment timeline Tense Tense Concept Fact Present Eternal Present The TGF-β pathway is a potent inhibitor of epithelial cell proliferation Problem Present Eternal Present Further complicating their discovery are the multifaceted mechanisms by which tumor suppressor genes are inactivated, Hypothesis Present + Modal Hyp Present [Other genes] may be found altered in tumors. Implication Present Present [T]he transcriptional repressor REST/NRSF plays a previously unappreciated role in tumor suppression. Experiment Method (Passive) Past Event Past we inhibited TGF-β signal transduction by alternative mechanisms Result Past Event Past Expression of either cDNA conferred growth in semisolid media Argumentation Reg-Implication Present Event Present we provide evidence that, implying that Reg-Hypothesis Present Event Present Therefore, it is probable that/This supports the hypothesis that Reg-Problem Present Event Present This suggests that Goal To-infinitive Goal To further examine the role of endogenous TGF- β signaling in restraining cell transformation Other research Reg-Others Present perfect Finalised Past disruption of adherens junction components [...] has been linked to cancer progression in a variety of tissues (Cavallaro and Christofori, 2004). Intertextual Present Perfect Finalised Past To date, these models of human cell transformation have incorporated genes already implicated in human tumorigenesis.
    • Biological Discourse Realms: Topic, Discourse Progression, Truth Conceptual Realm Topic Axis Epistemic Axis Discourse Progression Axis Experimental Realm
    • Mythological Realms:Yggdrasil
    • Facts in the Endogenous small RNAs (miRNAs) regulate I sing of golden-throned Hera whom Rhea eternal gene expression by mechanisms conserved bare. Queen of the immortals is she, surpassing present across metazoans. all in beauty: she is the sister and the wife of loud-thundering Zeus, --the glorious one whom all the blessed throughout high Olympus reverence and honor. Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to simple past time investigating a juvenile in the first and gladsome song, and made them merry, and second sessions in experiments waited till evening should come; and as they conducted in the NAC and the striatum: made merry dark evening came upon them. T1 values were 122 ± 6 s and 114 ± 5 s. Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with embedded the RASV12-ERTAM chimera gene, which is sharp bronze, heavy and huge and strong, facts only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of Vita et al, 2005). warriors, with whom she is wroth, she, the daughter of the mighty sire. Attribution miRNAs have emerged as important In this book I have had old stories written in the regulators of development and control down, as I have heard them told by intelligent present processes such as cell fate determination people, concerning chiefs who have held perfect and cell death (Abrahante et al., 2003, dominion in the northern countries, and who Brennecke et al., 2003, Chang et al., 2004, spoke the Danish tongue; and also concerning Chen et al., 2004, Johnston and Hobert, some of their family branches, according to 2003, Lee et al., 1993, ... what has been told me. Implications These results indicate that although Now it is said that ever since then are hedged, miR-372&3 confer complete protection to whenever the camel sees a place where ashes and in the oncogene-induced senescence in a manner have been scattered, he wants to get revenge present similar to p53 inactivation, the cellular with his enemy the rat and stomps and rolls in tense response to DNA damage remains intact the ashes hoping to get the rat
    • Pragmatic Research Article:
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about?
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but...
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but... - Helps increase/jig self-reflection by scientists of their communication
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but... - Helps increase/jig self-reflection by scientists of their communication - New ways of publishing:
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but... - Helps increase/jig self-reflection by scientists of their communication - New ways of publishing: - what should we model/structure/annotate
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but... - Helps increase/jig self-reflection by scientists of their communication - New ways of publishing: - what should we model/structure/annotate - what should we leave alone?
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but... - Helps increase/jig self-reflection by scientists of their communication - New ways of publishing: - what should we model/structure/annotate - what should we leave alone? - author/editor/publisher/user/aggregator - who, what, why?
    • Pragmatic Research Article: - Does this help us tell computers what our papers are about? - Might help identify hypotheses in papers automatically, but... - Helps increase/jig self-reflection by scientists of their communication - New ways of publishing: - what should we model/structure/annotate - what should we leave alone? - author/editor/publisher/user/aggregator - who, what, why? - how can we improve science with these formats?
    • Discourse - Social usage of language (or other symbolic systems); discursive vs linguistic ‘rules’ or regularities - Intentions and epistemic commitments/ meaning - Dialogism (Bakhtin) - Utterances are always directed towards receivers --- meanings of utterances cannot be exhausted by intentions of senders or by linguistic codes - Intertextuality / heteroglossia
    • Rhetoric - Rhetoric has a very long history - It has always been pragmatic -- Aristotle was giving guidelines on how to give a good speech, how to persuade. - Rich: both in terms of making very fine distinctions and in terms of its understanding of discourse in general - And discourse of different genres or types: - poetic - narrative --- eg plot [… and then …] - scientific [… and this shows that ….] - And these can be interestingly intertwined …. 16
    • subject-matter Logos context text speaker/writer listener/reader Ethos Pathos 17
    • Argument - ‘Logos’ in the rhetorical scheme - Intersubjectivity of argument - Combination of elements which are on a continuum from the formalisable (and formalised: eg logical forms) and non- formalisable - Argument extraction and diagramming (formalisation) often require re-writing first; and this requires interpretation
    • The witness said that he had seen Fred in the vicinity of the shop at the time the fire started. But we know this witness has a grudge against Fred, and he has been known to give unreliable evidence in the past. So we cannot rely on this person's statement. Hence Fred must have been somewhere else when the fire was started.
    • Neither shows deductive invalidity of this argument But this does: p: the witness is reliable q: Fred was in the vicinity of the shop at the time of the fire If p, then q [If the witness isfire] shop at the time of the reliable then Fred was in the vicinity of the not p [the witness is unreliable] therefore not q [Fred was not in the vicinity of the shop at the time of the fire] Fallacy of denying the antecedent
    • Scientific self-reflection (1) - Open-ended, ‘gappy’ or relational nature of any utterance or move in a discourse. - Gap between intention and interpretation - Examples: - epistemic force - ‘refute’ : as a relation
    • Figure 3 – Examples of possible relationships between Comment and other SWAN classes. (Ciccarese, Wu & Cla rk 2007
    • Self-reflection (2) - Not liked by the scientists - But neither warranted by argumentation theory - Refutation (to disprove a hypothesis) is not something that one can simply intend or maintain on his/her own - Matter of the wider discourse of science - For Karl Popper, it is also a matter of logic - But what if there is a clash between the two? - Methodological question
    • Self-reflection (3) - In a ‘normal’ discourse situation these implicit understandings of how discourse works are the scaffolding without which interpretation cannot operate, or without which it shifts in status and the acceptance it seems to demand from users. - (Disruptive) technology pushes this background scaffolding to the fore - Impulse may be to hide it or blackbox it: looks like subjectivity creep - But the discourse representation need not be made to look more ‘objective’ and context transcendent than it in fact is -- no need to hide it but rather ensure that it is evident and can be interacted with.
    • Changing modes of scientific discourse analysis
    • Changing modes of scientific discourse analysis - The HypER Project (AdW)
    • Changing modes of scientific discourse analysis - The HypER Project (AdW) - Pragmatic Discourse Analysis (AdW)
    • Changing modes of scientific discourse analysis - The HypER Project (AdW) - Pragmatic Discourse Analysis (AdW) - Rhetoric, Discourse, Arguments and self-perception (AC)
    • Changing modes of scientific discourse analysis - The HypER Project (AdW) - Pragmatic Discourse Analysis (AdW) - Rhetoric, Discourse, Arguments and self-perception (AC)
    • Changing modes of scientific discourse analysis - The HypER Project (AdW) - Pragmatic Discourse Analysis (AdW) - Rhetoric, Discourse, Arguments and self-perception (AC) Questions? Thoughts?