De Waard Carusi

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

discourse analysis

discourse analysis

• The HypER Project (AdW)

discourse analysis

• Pragmatic Discourse Analysis (AdW)

discourse analysis

• 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.


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


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
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


Current activities:


Current activities:

✓Aligning discourse ontologies: joint task with W3C HCLSSig


Current activities:

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


Current activities:

‣Parser test of hypothesis identiﬁcation tools on pharmacology
corpus


Current activities:

corpus

‣Aligning architectures to exchange hypotheses + evidence


Current activities:

corpus

Further interests:


Current activities:

corpus

Further interests:

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


Current activities:

corpus

Further interests:

-Better structure of evidence: MyExperiment, KeFeD, ...
-Granularity of annotation/access: entity, hypothesis, discussion?

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

papers are about?
- Science is written in text, as a story

papers are about?
- Text is created by humans to persuade other
humans (peers, that claims are facts)

papers are about?
- To tell the computer how we encode our
knowledge, we need to understand:

papers are about?
=> How do humans tell stories?

papers are about?
=> 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

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.

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.

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

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:
- Does this help us tell computers what our
papers are about?

papers are about?
- Might help identify hypotheses in papers
automatically, but...

papers are about?
- Helps increase/jig self-reﬂection by scientists of
their communication

papers are about?
their communication
- New ways of publishing:

papers are about?
their communication
- what should we model/structure/annotate

papers are about?
their communication
- what should we leave alone?

papers are about?
their communication
- author/editor/publisher/user/aggregator - who, what,
why?

papers are about?
their communication
- 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.

discourse analysis
- The HypER Project (AdW)

discourse analysis
- Pragmatic Discourse Analysis (AdW)

discourse analysis
- Rhetoric, Discourse, Arguments and self-perception
(AC)

discourse analysis
- Rhetoric, Discourse, Arguments and self-perception
(AC)

Questions? Thoughts?

De Waard Carusi

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