de waard carusi

Changing modes of scientific discourse analysis,

changing perceptions of science

Annamaria CarusieResearch Centre, Oxford University

Anita de WaardDisruptive Technologies, Elsevier Labs

Utrecht Institute of Linguistics, U Utrecht

Changing modes of scientific discourse analysis



• The HypER Project (AdW)


• The HypER Project (AdW)• Pragmatic Discourse Analysis (AdW)


• The HypER Project (AdW)• Pragmatic Discourse Analysis (AdW)• Rhetoric, discourse, arguments and self-perception

(AC)

‘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.



Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53.


without some idea of the status of the sentence, it cannot be interpreted!

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



- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags







- Partners:




- DERI: SALT, aTags





Hypothesis 22: Intramembrenous Aβ dimer may be toxic.

Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a fraction of these Abeta peptides never leave the membrane lipid bilayer after they are generated, but instead exert their toxic effects by competing with and compromising the functions of intramembranous segments of membrane-bound proteins that serve many critical functions.



- Partners:




- DERI: SALT, aTags





Hypothesis 22: Intramembrenous Aβ dimer may be toxic.

Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a fraction of these Abeta peptides never leave the membrane lipid bilayer after they are generated, but instead exert their toxic effects by competing with and compromising the functions of intramembranous segments of membrane-bound proteins that serve many critical functions.

HypER Activities: http://hyper.wik.is

http://hyper.wik.is

http://hyper.wik.is


Current activities:

http://hyper.wik.is

http://hyper.wik.is


Current activities:

✓Aligning discourse ontologies: joint task with W3C HCLSSig

http://hyper.wik.is

http://hyper.wik.is


Current activities:


✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)

http://hyper.wik.is

http://hyper.wik.is


Current activities:



‣Parser test of hypothesis identification tools on pharmacology corpus

http://hyper.wik.is

http://hyper.wik.is


Current activities:




‣Aligning architectures to exchange hypotheses + evidence

http://hyper.wik.is

http://hyper.wik.is


Current activities:





Further interests:

http://hyper.wik.is

http://hyper.wik.is


Current activities:





Further interests:

-Better structure of evidence: MyExperiment, KeFeD, ...

http://hyper.wik.is

http://hyper.wik.is


Current activities:





Further interests:

-Better structure of evidence: MyExperiment, KeFeD, ...

-Granularity of annotation/access: entity, hypothesis, discussion?

http://hyper.wik.is

http://hyper.wik.is

Pragmatic Discourse Analysis


- How can we better tell computers what our papers are about?



- Science is written in text, as a story



- Science is written in text, as a story- Text is created by humans to persuade other

humans (peers, that claims are facts)




humans (peers, that claims are facts)- To tell the computer how we encode our

knowledge, we need to understand:





knowledge, we need to understand:=> How do humans tell stories?





knowledge, we need to understand:=> How do humans tell stories? => How can we explain what matters, how these

stories create knowledge in our heads?

Aristotle Quintilian Cell APA Style Guide

prooimion Introduction

exordium

The introduction of a speech, where one announces the subject and purpose of the discourse, and where one

usually employs the persuasive appeal of ethos in order to establish credibility with the audience.

Introduction

Introduction

prothesisStatement of Facts

narratio

The second part of a classical oration, following the introduction or exordium. The speaker here provides a narrative account of what has happened and generally

explains the nature of the case. Quintilian adds that the narratio is followed by the propositio, a kind of summary of

the issues or a statement of the charge.

Introduction

Introduction

Summary propostitio

Coming between the narratio and the partitio of a classical oration, the propositio provides a brief summary of what

one is about to speak on, or concisely puts forth the charges or accusation.

Abstract Abstract

Division/outline

partitio

Following the statement of facts, or narratio, comes the partitio or divisio. In this section of the oration, the speaker

outlines what will follow, in accordance with what's been stated as the status, or point at issue in the case. Quintilian

suggests the partitio is blended with the propositio and also assists memory.

Table of Contents

Article Outline

pistis Proof confirmatio

Following the division / outline or partitio comes the main body of the speech where one offers logical arguments as

proof. The appeal to logos is emphasized here.Results Methods,

Results

Refutatio

nrefutatio

Following the the confirmatio or section on proof in a classical oration, comes the refutation. As the name connotes, this section of a speech was devoted to

answering the counterarguments of one's opponent.

Discussion Discussion

epilogos peroratio

Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals

through pathos, and often included a summing up (see the figures of summary, below).

Discussion Discussion

1st Try: Classical Rhetoric

http://rhetoric.byu.edu/Canons/Arrangement/Exordium.htm

http://rhetoric.byu.edu/Canons/Arrangement/Exordium.htm

http://rhetoric.byu.edu/Canons/Arrangement/Narratio.htm

http://rhetoric.byu.edu/Canons/Arrangement/Narratio.htm

http://rhetoric.byu.edu/Canons/Arrangement/Partitio.htm

http://rhetoric.byu.edu/Canons/Arrangement/Partitio.htm

http://rhetoric.byu.edu/Canons/Arrangement/Confirmatio.htm




http://rhetoric.byu.edu/Canons/Arrangement/Refutatio.htm

http://rhetoric.byu.edu/Canons/Arrangement/Refutatio.htm

The Story of Goldilocks and the Three Bears

Story Grammar Paper The AXH Domain of Ataxin-1 Mediates 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. Pretty soon, she came upon a house.

Location Experimental setup

studied and compared in vivo effects and interactions to those of the human protein

She knocked and, when no one answered,

Goal Theme Researchgoal

Gain insight into how Atx-1's function contributes to SCA1 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 were three bowls of porridge.

Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in Files

Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain

She tasted the porridge from the first bowl.

Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1.

This porridge is too hot! she exclaimed.

Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives 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 the second bowl.

Data (data not shown),

This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28 days

So, she tasted the last bowl of porridge.

Data (Figures 1B-1D).

Ahhh, this porridge is just right, she said happily and

Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eye abnormalities. The external structures of the eyes that overexpress dAtx-1 show disorganized ommatidia and loss of interommatidial bristles

she ate it all up. Data (Figure 1F),

2nd Try: Story Grammar

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 thatb. following RASV12 stimulationc. p53 was stabilized and activatedd. and the target gene, p21cip1, was induced in all cases,e. indicating an intact p53 pathway in these cells.






IntratextualMethod

Result Result

Implication





IntratextualMethod

Result Result

Implication



Realm, timeline

Segment Type Linguistic Tense

Meaning Tense

Sample segment

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.

Discourse Intratextual Present, Imperative

Performative (see below);(see Table S1 in the Supplemental Data available with this article online)

Tense and Realm

Biological Discourse Realms: Topic, Discourse Progression, Truth

Conceptual Realm

Experimental Realm

Discourse Progression Axis

Epistemic Axis

Topic Axis

Mythological Realms: Yggdrasil

Facts in the eternal present

Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans.

I sing of golden-throned Hera whom Rhea bare. Queen of the immortals is she, surpassing 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 simple past

Vehicle-treated animals spent equivalent time investigating a juvenile in the first and second sessions in experiments conducted in the NAC and the striatum: T1 values were 122 ± 6 s and 114 ± 5 s.

Now the wooers turned to the dance and to gladsome song, and made them merry, and waited till evening should come; and as they made merry dark evening came upon them.

Events with embedded facts

We also generated BJ/ET cells expressing the RASV12-ERTAM chimera gene, which is only active when tamoxifen is added (De Vita et al, 2005).

And she took her mighty spear, tipped with sharp bronze, heavy and huge and strong, wherewith she vanquishes the ranks of men-of warriors, with whom she is wroth, she, the daughter of the mighty sire.

Attribution in the present perfect

miRNAs have emerged as important regulators of development and control processes such as cell fate determination and cell death (Abrahante et al., 2003, Brennecke et al., 2003, Chang et al., 2004, Chen et al., 2004, Johnston and Hobert, 2003, Lee et al., 1993, ...

In this book I have had old stories written down, as I have heard them told by intelligent people, concerning chiefs who have held dominion in the northern countries, and who spoke the Danish tongue; and also concerning some of their family branches, according to what has been told me.

Implications are hedged, and in the present tense

These results indicate that although miR-372&3 confer complete protection to oncogene-induced senescence in a manner similar to p53 inactivation, the cellular response to DNA damage remains intact

Now it is said that ever since then whenever the camel sees a place where ashes have been scattered, he wants to get revenge with his enemy the rat and stomps and rolls in the ashes hoping to get the rat

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:





- New ways of publishing: - what should we model/structure/annotate





- New ways of publishing: - what should we model/structure/annotate - what should we leave alone?





- New ways of publishing: - what should we model/structure/annotate - what should we leave alone? - author/editor/publisher/user/aggregator - who, what, why?





- 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

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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 ….

17

subject-matterLogos

listener/readerPathos

speaker/writer Ethos

textcontext

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 argumentBut this does: p: the witness is reliableq: Fred was in the vicinity of the shop at the time of the fireIf p, then q [If the witness is reliable then Fred was in the vicinity of the shop at the time of the fire]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.



- The HypER Project (AdW)


- The HypER Project (AdW)- Pragmatic Discourse Analysis (AdW)


- The HypER Project (AdW)- Pragmatic Discourse Analysis (AdW)- Rhetoric, Discourse, Arguments and self-perception

(AC)



(AC)



(AC)

Questions? Thoughts?