The Story of Science: A plea for a syntagmatic/paradigmatic analysis of scientific text

Anita de Waard, a.dewaard@elsevier.com Disruptive Technologies Director, Elsevier Labs University of Utrecht, Institute of Linguistics

Thursday, October 21, 2010

Scientific papers are stories, that persuade with data

2

Thursday, October 21, 2010

Scientific papers are stories, that persuade with data

1.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

Thursday, October 21, 2010

Scientific papers are stories, that persuade with data

1.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’

2

Thursday, October 21, 2010

Paradigmatic Approach: story grammar

3

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

Setting

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

Setting

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

Theme

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

Episode 1

Subgoal test the function of the AXH domainShe tasted the porridge from the first bowl.

Attempt

Episode 1

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

Episode 1

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.

Activity

Episode 1

Data (data not shown),

This porridge is too cold, she said

Outcome

Episode 1

Results both genotypes show many large holes and loss of cell integrity at 28 days

So, she tasted the last bowl of porridge.

 Activity

Episode 1

Data (Figures 1B-1D).

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

Outcome

Episode 1

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.  

Episode 1

Data (Figure 1F), Thursday, October 21, 2010

Paradigmatic Approach: story grammar

3

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

Setting

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

Setting

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

Theme

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

Episode 1

Subgoal test the function of the AXH domainShe tasted the porridge from the first bowl.

Attempt

Episode 1

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

Episode 1

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.

Activity

Episode 1

Data (data not shown),

This porridge is too cold, she said

Outcome

Episode 1

Results both genotypes show many large holes and loss of cell integrity at 28 days

So, she tasted the last bowl of porridge.

 Activity

Episode 1

Data (Figures 1B-1D).

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

Outcome

Episode 1

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.  

Episode 1

Data (Figure 1F), Thursday, October 21, 2010

4

Story structure also has a rhetorical goal:

Thursday, October 21, 2010

4

Aristotle QuintilianQuintilian Scientific Paper

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 to ethos in order to establish credibility with the audience.

Introduction: positioning

prothesisStatement of Facts/narratio

The speaker here provides a narrative account of what has happened and generally explains the nature of the case.

Introduction: research question

  Summary/ propostitio

The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents

pistis Proof/ confirmatio

The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here.

Results

  Refutation/ refutatio

As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work

epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.

Discussion: summary, implications.

Story structure also has a rhetorical goal:

Thursday, October 21, 2010

4

Aristotle QuintilianQuintilian Scientific Paper

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 to ethos in order to establish credibility with the audience.

Introduction: positioning

prothesisStatement of Facts/narratio

The speaker here provides a narrative account of what has happened and generally explains the nature of the case.

Introduction: research question

  Summary/ propostitio

The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents

pistis Proof/ confirmatio

The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here.

Results

  Refutation/ refutatio

As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work

epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.

Discussion: summary, implications.

Story structure also has a rhetorical goal:

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Result

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Result

Implication

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Result

Implication

Goal

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Result

Implication

Goal

Reg-Implication

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Result

Implication

Goal

Reg-Implication

Conceptual knowledge

Thursday, October 21, 2010

Paradigmatic approach for science

5

Both 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.

Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),suggesting thatmiR-371-3 expression is a selective event during tumorigenesis.

Fact

Hypothesis

Method

Result

Implication

Goal

Reg-Implication

Conceptual knowledge

ExperimentalEvidence

Thursday, October 21, 2010

Basic Segment Types

6

Thursday, October 21, 2010

Basic Segment TypesSegment Description Example

Fact a known fact, generally without explicit citation

mature miR-373 is a homolog of miR-372

Hypothesis a proposed idea, not supported by evidence

This could for instance be a result of high mdm2 levels

Problem unresolved, contradictory, or unclear issue

However, further investigation is required to demonstrate the exact mechanism of LATS2 action

Goal research goal To identify novel functions of miRNAs,

Method experimental method Using fluorescence microscopy and luciferase assays,

Result a restatement of the outcome of an experiment

all constructs yielded high expression levels of mature miRNAs

Implication an interpretation of the results, in light of earlier hypotheses and facts

our procedure is sensitive enough to detect mild growth differences

6

Thursday, October 21, 2010

Paradigmatic analysis of clausesConceptual discourse Connecting discourse Experimental discourse

Though D3 receptor antagonists can enhance cognitive function,

their sites of action remain unexplored.

This issue was addressed employing a model of social recognition in rats,

and the actions of D3 antagonists were compared to D1 agonists

that likewise possess pro-cognitive properties.

Infusion of the highly selective D3 antagonists, S33084 and SB277,011 (0.04-2.5 µg/side), into the frontal cortex (FCX) dose-dependently reversed the deficit in recognition induced by a delay.By contrast, the preferential D2 antagonist, L741,626 (0.63-5.0) had no effect.The action of S33084 was regionally specific

inasmuch as its injection into the nucleus accumbens or striatum was ineffective.

These data suggest that

D3 receptors modulating social recognition are localized in FCX,

and underpin their pertinence as targets for antipsychotic agents.

Thursday, October 21, 2010

Realms in experimental discourse

Thursday, October 21, 2010

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

Realms in experimental discourse

Thursday, October 21, 2010

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) a. To exclude that

Realms in experimental discourse

Thursday, October 21, 2010

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

(2) a. To exclude that

Realms in experimental discourse

Thursday, October 21, 2010

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

(2) a. To exclude that (3) b. suggesting that

Realms in experimental discourse

Thursday, October 21, 2010

(3) c. miR-371-3 expression is a selective event during tumorigenesis.

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

(2) a. To exclude that (3) b. suggesting that

Realms in experimental discourse

Thursday, October 21, 2010

(3) c. miR-371-3 expression is a selective event during tumorigenesis.

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

Concepts, models, ‘facts’

(2) a. To exclude that (3) b. suggesting that

Realms in experimental discourse

Thursday, October 21, 2010

(3) c. miR-371-3 expression is a selective event during tumorigenesis.

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

Concepts, models, ‘facts’

Experiment

(2) a. To exclude that (3) b. suggesting that

Realms in experimental discourse

Thursday, October 21, 2010

(3) c. miR-371-3 expression is a selective event during tumorigenesis.

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

Concepts, models, ‘facts’

Experiment

Transitions(2) a. To exclude that (3) b. suggesting that

Realms in experimental discourse

Thursday, October 21, 2010

Paradigmatic vs syntagmatic axes: use both?

!

!

Experimental Realm

Syntagmatic Axis

Paradigmatic axis

This issue was addressed….

! Infusion of the highly selective D3 antagonists…!

A similar increase of recognition was obtained upon injection …!

Though D3 receptor antagonists can enhance cognitive function,

D3 receptors modulating social recognition are localized in FCX,

!

These data suggest that !

Conceptual Realm !

their sites of action remain unexplored.

9

Thursday, October 21, 2010

Paradigmatic vs syntagmatic axes: use both?

!

!

Experimental Realm

Syntagmatic Axis

Paradigmatic axis

This issue was addressed….

! Infusion of the highly selective D3 antagonists…!

A similar increase of recognition was obtained upon injection …!

Though D3 receptor antagonists can enhance cognitive function,

D3 receptors modulating social recognition are localized in FCX,

!

These data suggest that !

Conceptual Realm !

their sites of action remain unexplored.

9

Paradigmatic: •repeats itself many times•‘fractal dimension’: •course-grained: Introduction, Results, Discussion•medium-grained: parallel with paradigmatic?•fine-grained: level of clauses.

Thursday, October 21, 2010

Paradigmatic vs syntagmatic axes: use both?

!

!

Experimental Realm

Syntagmatic Axis

Paradigmatic axis

This issue was addressed….

! Infusion of the highly selective D3 antagonists…!

A similar increase of recognition was obtained upon injection …!

Though D3 receptor antagonists can enhance cognitive function,

D3 receptors modulating social recognition are localized in FCX,

!

These data suggest that !

Conceptual Realm !

their sites of action remain unexplored.

9

Paradigmatic: •repeats itself many times•‘fractal dimension’: •course-grained: Introduction, Results, Discussion•medium-grained: parallel with paradigmatic?•fine-grained: level of clauses.

Syntagmatic: • single line?• order is essential•‘medium-grained - ‘story components’

Thursday, October 21, 2010

Three dimensions of (semantic)annotation

measure

Thursday, October 21, 2010

Three dimensions of (semantic)annotation

measure

Thursday, October 21, 2010

document

claim

triple

entity

collection

Granularity

Three dimensions of (semantic)annotation

measure

Thursday, October 21, 2010

document

claim

triple

entity

collection

Granularity

Three dimensions of (semantic)annotation

automated

manual

semi-automated

Meansmeasure

Thursday, October 21, 2010

document

claim

triple

entity

collection

Granularity

Three dimensions of (semantic)annotation

reader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

Thursday, October 21, 2010

document

claim

triple

entity

collection

Granularity

Three dimensions of (semantic)annotation

Web-Based Protein Markup

reader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

Thursday, October 21, 2010

document

claim

triple

entity

collection

Granularity

Three dimensions of (semantic)annotation

Hypothesis markup

Web-Based Protein Markup

reader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

Thursday, October 21, 2010

document

claim

triple

entity

collection

Granularity

Three dimensions of (semantic)annotation

Hypothesis markup

Web-Based Protein Markup

reader/curator/data miningtypesetter/productionauthor/editor

Moment

automated

manual

semi-automated

Meansmeasure

Thursday, October 21, 2010

11

Syntagmatic analysis: W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)

Thursday, October 21, 2010

11

Syntagmatic analysis: W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)

Thursday, October 21, 2010

Syntagmatic enabler: Linked Data (for Elsevier)

Thursday, October 21, 2010

Syntagmatic enabler: Linked Data (for Elsevier)

<ce:section id=#123>

Thursday, October 21, 2010

Syntagmatic enabler: Linked Data (for Elsevier)

<ce:section id=#123> mice like cheesethis says

Thursday, October 21, 2010

Syntagmatic enabler: Linked Data (for Elsevier)

<ce:section id=#123>

said @anita on September 8, 2010

mice like cheesethis says

Thursday, October 21, 2010

but we all know she was wrong then

Syntagmatic enabler: Linked Data (for Elsevier)

<ce:section id=#123>

said @anita on September 8, 2010

mice like cheesethis says

Thursday, October 21, 2010

but we all know she was wrong then

Syntagmatic enabler: Linked Data (for Elsevier)

<ce:section id=#123>

said @anita on September 8, 2010

the xml is fixed, but the structure is open!

mice like cheesethis says

Thursday, October 21, 2010

allows for layers of annotation

but we all know she was wrong then

Syntagmatic enabler: Linked Data (for Elsevier)

<ce:section id=#123>

said @anita on September 8, 2010

the xml is fixed, but the structure is open!

mice like cheesethis says

Thursday, October 21, 2010

Paradigmatic analysis: find segments using Verb form?

13

1. An escape from oncogene-induced senescence is a prerequisite for full transformation into tumor cells.

2. An escape from oncogene-induced senescence was a prerequisite for full transformation into tumor cells.

3. An escape from oncogene-induced senescence may be a prerequisite for full transformation into tumor cells

Thursday, October 21, 2010

Paradigmatic analysis: find segments using Verb form?Manual analysis suggests a correlation:– Present: Fact (82%), Hypothesis (71%), Implication (62%)– Past: Result (82%), Method (76%) - 50% Passive, of

Method 50% Past Perfect– Modal: Hypothesis (44%)

13

1. An escape from oncogene-induced senescence is a prerequisite for full transformation into tumor cells.

2. An escape from oncogene-induced senescence was a prerequisite for full transformation into tumor cells.

3. An escape from oncogene-induced senescence may be a prerequisite for full transformation into tumor cells

Thursday, October 21, 2010

Paradigmatic analysis: find segments using Verb form?Manual analysis suggests a correlation:– Present: Fact (82%), Hypothesis (71%), Implication (62%)– Past: Result (82%), Method (76%) - 50% Passive, of

Method 50% Past Perfect– Modal: Hypothesis (44%)Experiment:

13

1. An escape from oncogene-induced senescence is a prerequisite for full transformation into tumor cells.

2. An escape from oncogene-induced senescence was a prerequisite for full transformation into tumor cells.

3. An escape from oncogene-induced senescence may be a prerequisite for full transformation into tumor cells

Thursday, October 21, 2010

Paradigmatic analysis: find segments using Verb form?Manual analysis suggests a correlation:– Present: Fact (82%), Hypothesis (71%), Implication (62%)– Past: Result (82%), Method (76%) - 50% Passive, of

Method 50% Past Perfect– Modal: Hypothesis (44%)Experiment:–Does verb tense determine perceived segment type?

13

1. An escape from oncogene-induced senescence is a prerequisite for full transformation into tumor cells.

2. An escape from oncogene-induced senescence was a prerequisite for full transformation into tumor cells.

3. An escape from oncogene-induced senescence may be a prerequisite for full transformation into tumor cells

Thursday, October 21, 2010

Paradigmatic analysis: find segments using Verb form?Manual analysis suggests a correlation:– Present: Fact (82%), Hypothesis (71%), Implication (62%)– Past: Result (82%), Method (76%) - 50% Passive, of

Method 50% Past Perfect– Modal: Hypothesis (44%)Experiment:–Does verb tense determine perceived segment type? –Manual classification of 104 tense-manipulated segments:

13

1. An escape from oncogene-induced senescence is a prerequisite for full transformation into tumor cells.

2. An escape from oncogene-induced senescence was a prerequisite for full transformation into tumor cells.

3. An escape from oncogene-induced senescence may be a prerequisite for full transformation into tumor cells

Thursday, October 21, 2010

Paradigmatic analysis: find segments using Verb form?Manual analysis suggests a correlation:– Present: Fact (82%), Hypothesis (71%), Implication (62%)– Past: Result (82%), Method (76%) - 50% Passive, of

Method 50% Past Perfect– Modal: Hypothesis (44%)Experiment:–Does verb tense determine perceived segment type? –Manual classification of 104 tense-manipulated segments:

13

1. An escape from oncogene-induced senescence is a prerequisite for full transformation into tumor cells.

2. An escape from oncogene-induced senescence was a prerequisite for full transformation into tumor cells.

3. An escape from oncogene-induced senescence may be a prerequisite for full transformation into tumor cells

Thursday, October 21, 2010

Summary Fact/Result/Hypothesis classification

14

Thursday, October 21, 2010

Summary Fact/Result/Hypothesis classification

present -> Fact (64-44-76%)

14

Thursday, October 21, 2010

Summary Fact/Result/Hypothesis classification

present -> Fact (64-44-76%)past -> Result (49-44-76%)

14

Thursday, October 21, 2010

Summary Fact/Result/Hypothesis classification

present -> Fact (64-44-76%)past -> Result (49-44-76%)modal -> Hypothesis (33-46-39%)

14

Thursday, October 21, 2010

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

Parallels in tense use between science and mythology

Thursday, October 21, 2010

Biological Discourse Realms relevant to tense use: Topic (syntagmatic), Discourse Progression

(paradigmatic), Truth (trust)

Conceptual Realm

Experimental Realm

Discourse Progression Axis

Epistemic Axis

Topic Axis

16

Thursday, October 21, 2010

Biological Discourse Realms relevant to tense use: Topic (syntagmatic), Discourse Progression

(paradigmatic), Truth (trust)

Conceptual Realm

Experimental Realm

Discourse Progression Axis

Epistemic Axis

Topic Axis

16

Present

Thursday, October 21, 2010

Biological Discourse Realms relevant to tense use: Topic (syntagmatic), Discourse Progression

(paradigmatic), Truth (trust)

Conceptual Realm

Experimental Realm

Discourse Progression Axis

Epistemic Axis

Topic Axis

16

Present

Past

Thursday, October 21, 2010

Biological Discourse Realms relevant to tense use: Topic (syntagmatic), Discourse Progression

(paradigmatic), Truth (trust)

Conceptual Realm

Experimental Realm

Discourse Progression Axis

Epistemic Axis

Topic Axis

16

Present

Past

Past, Present

Thursday, October 21, 2010

Biological Discourse Realms relevant to tense use: Topic (syntagmatic), Discourse Progression

(paradigmatic), Truth (trust)

Conceptual Realm

Experimental Realm

Discourse Progression Axis

Epistemic Axis

Topic Axis

16

Past Perfect

Present

Past

Past, Present

Thursday, October 21, 2010

Mythological Realms: Yggdrasil

17

Thursday, October 21, 2010

Questions?

18

Thursday, October 21, 2010

Questions?

•Can we use these two types of classification - are they even different?

•What structure/ontology/classes?•Valid for which texts? •Apply post-hoc or let authors create? •How do we use: for machine or user access?

18

Thursday, October 21, 2010

Questions?

18

Thursday, October 21, 2010

Questions?

18

a.dewaard@elsevier.comhttp://elsatglabs.com/labs/anita

Thursday, October 21, 2010