Citation practices and the

construction of scientific factJodi Schneider

European Conference on Argumentation preconference: status, relevance, and authority of facts

Fribourg, Switzerland2017-06-19

jschneider@pobox.comhttp://jodischneider.com/jodi.html

@jschneider

“[Y]ou can transform a fact into

fiction or a fiction into fact just by

adding or subtracting references”- Bruno Latour

Slide credit: Anita DeWaard: Epistemics, https://www.slideshare.net/anitawaard/epistemics/6

Latour is Science in Action: How to Follow Scientists and, p 33

... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).

Raver-Shapira et.al, JMolCell 2007

miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)

Yabuta, JBioChem 2007:

As claims get cited, they become facts:

To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...

Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Voorhoeve et al, Cell, 2006:

Hypothesis

Implication

Cited Implication

Fact

Slide credit: Anita DeWaard: 'Stories that persuade with data' - talk at CENDI meeting January 9 2014https://www.slideshare.net/anitawaard/stories-that-persuade-with-data-talk-at-cendi-meeting-january-

9-2014/6

Miscitation & bad assumptions

“False claims regarding a causal link between game playing and obesity have propagated in the literature on exertion games.”

“While the causal link between game play and obesity is not supported by evidence from health research, a version of this argument is presented many times in published exertion game literature, complete with supporting citations from public health research.”

Marshall, J., & Linehan, C. (2017). Misrepresentation of health research in exertion games literature. In Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems (pp. 4899-4910). ACM.

Miscitation & bad assumptions

“False claims regarding a causal link between game playing and obesity have propagated in the literature on exertion games.”

“While the causal link between game play and obesity is not supported by evidence from health research, a version of this argument is presented many times in published exertion game literature, complete with supporting citations from public health research.”

Marshall, J., & Linehan, C. (2017). Misrepresentation of health research in exertion games literature. In Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems (pp. 4899-4910). ACM.

How well do we cite?

Haussmann, N. S., McIntyre, T., Bumby, A. J., & Loubser, M. J. (2013). Referencing practices in physical geography: how well do we cite what we write?. Progress in Physical Geography, 37(4), 543-549.

How might miscitation happen?

• Reading errors

• Hasty literature reviews

• Reviewer errors

• Cherry picking to justify pre-existing agenda

Marshall, J., & Linehan, C. (2017). Misrepresentation of health research in exertion games literature. In Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems (pp. 4899-4910). ACM.

Citing fake science harms people

A paper about a clinical trial for renal disease was retracted because:“‘the trial had not been approved by the ethics committee, the involvement of a statistician could not be verified, [and] the trial was not a double-blind study, because Dr Nakao knew the treatment allocation’.”

“Nevertheless, the COOPERATE study was cited by 173 review articles and 58 secondary clinical studies that enrolled a total of 35,929 patients.”

“The harm done by COOPERATE is thus 4-fold:

• patients were enrolled in an experimental therapy for a condition which already had an accepted therapy;

• time, energy and money were wasted by patients and investigators;

• false information pervaded the literature;

• and combination therapy was accepted more quickly and used more widely than it might have been otherwise.”

Steen, R. G. (2011). Retractions in the medical literature: how many patients are put at risk by flawed research?. Journal of Medical Ethics, 37(11), 688-692.

Citing fake science harms people

A paper about a clinical trial for renal disease was retracted because:“‘the trial had not been approved by the ethics committee, the involvement of a statistician could not be verified, [and] the trial was not a double-blind study, because Dr Nakao knew the treatment allocation’.”

“Nevertheless, the COOPERATE study was cited by 173 review articles and 58 secondary clinical studies that enrolled a total of 35,929 patients.”

“The harm done by COOPERATE is thus 4-fold:

• patients were enrolled in an experimental therapy for a condition which already had an accepted therapy;

• time, energy and money were wasted by patients and investigators;

• false information pervaded the literature;

• and combination therapy was accepted more quickly and used more widely than it might have been otherwise.”

Steen, R. G. (2011). Retractions in the medical literature: how many patients are put at risk by flawed research?. Journal of Medical Ethics, 37(11), 688-692.

“The conversion of hypothesis to

fact through citation alone.”

- Stephen Greenberg

Greenberg, Steven A. "Understanding belief using citation networks." Journal of evaluation in clinical practice 17.2 (2011): 389-393.http://dx.doi.org/10.1111/j.1365-2753.2011.01646.x

“The conversion of hypothesis to fact through citation alone.”

- Stephen Greenberg

Greenberg, Steven A. "How citation distortions create unfounded authority: analysis of a citation network." BMJ 339 (2009): b2680.

https://doi.org/10.1136/bmj.b2680

Funded grants with citation bias & citation distortion.

Greenberg, Steven A. "How citation distortions create unfounded authority: analysis of a citation network." BMJ 339 (2009): b2680.

https://doi.org/10.1136/bmj.b2680

Can we do better?

Boyce, R.D.: A Draft Evidence Taxonomy and Inclusion Criteria for the

Drug Interaction Knowledge Base (DIKB),

http://purl.net/net/drug-interaction-knowledge-base/evidence-types-and-

inclusion-criteria

Ask: What evidence is relevant

for a given purpose?

Ask: What evidence is strong

enough?

Figure credit: SUNY Downstate Medical Center. Medical Research

Library of Brooklyn. Evidence Based Medicine Course. A Guide to

Research Methods: The Evidence Pyramid:

http://library.downstate.edu/EBM2/2100.htm

Ask: Can we

model scientific

arguments and

evidence?

Clark, Tim, Paolo N. Ciccarese, and Carole A. Goble.

"Micropublications: a semantic model for claims, evidence, arguments

and annotations in biomedical communications." Journal of Biomedical

Semantics 5.28 (2014). http://dx.doi.org/10.1186/2041-1480-5-28

Jodi Schneider, Paolo Ciccarese, Tim Clark, Richard D. Boyce. “Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base.” Linked Science at ISWC 2014 http://ceur-ws.org/Vol-1282/lisc2014_submission_8.pdf

Modeling arguments and

evidence

SEPIO – evidence lines

Brush, Matthew, Kent Shefchek, and Melissa Haendel. "SEPIO: a

semantic model for the integration and analysis of scientific

evidence." International Conference on Biomedical Ontology and BioCreative. 2016. http://ceur-ws.org/Vol-1747/IT605_ICBO2016.pdf

“A proposition has_evidence

one or more evidence lines, which have_supporting_data

one or more data items used in evaluation of the

proposition’s truth.”

SEPIO – evidence lines example

Brush, Matthew, Kent Shefchek, and Melissa Haendel. "SEPIO: a

semantic model for the integration and analysis of scientific

evidence." International Conference on Biomedical Ontology and BioCreative. 2016. http://ceur-ws.org/Vol-1747/IT605_ICBO2016.pdf

“A simplified account of existing evidence related to this proposition is presented below,

presenting summaries of five evidence lines (E1-E5) from five studies relevant to the

classification of the variant for Fabry Disease:

E1. Six affected individuals with the variant were found to have reduced GLA enzyme

activity.

E2. The variant was absent from 528 unaffected controls.

E3. The variant is predicted to cause abnormal splicing that inserts additional sequence.

E4. Pedigree analyses showed Fabry Disease phenotypes segregating with the variant.

E5. Population databases show high frequency of individuals homozygous for the variant.”

SEPIO – evidence lines example

Brush, Matthew, Kent Shefchek, and Melissa Haendel. "SEPIO: a

semantic model for the integration and analysis of scientific

evidence." International Conference on Biomedical Ontology and BioCreative. 2016. http://ceur-ws.org/Vol-1747/IT605_ICBO2016.pdf

“A simplified account of existing evidence related to this proposition is presented below,

presenting summaries of five evidence lines (E1-E5) from five studies relevant to the

classification of the variant for Fabry Disease:

E1. Six affected individuals with the variant were found to have reduced GLA enzyme

activity.

E2. The variant was absent from 528 unaffected controls.

E3. The variant is predicted to cause abnormal splicing that inserts additional sequence.

E4. Pedigree analyses showed Fabry Disease phenotypes segregating with the variant.

E5. Population databases show high frequency of individuals homozygous for the variant.”

Modeling arguments and

evidence

SEE

Bölling, Christian, Michael Weidlich, and Hermann-Georg Holzhutter.

"SEE: structured representation of scientific evidence in the biomedical

domain using Semantic Web techniques." Journal of Biomedical Semantics 5.1 (2014): 1.

SEE

Bölling, Christian, Michael Weidlich, and Hermann-Georg Holzhutter.

"SEE: structured representation of scientific evidence in the biomedical

domain using Semantic Web techniques." Journal of Biomedical Semantics 5.1 (2014): 1.

Ask: Can we structure the

arguments

• “An ontology is a formal, explicit

specification of a shared conceptualisation.”

- (Gruber, 1993)

• Make clear the lines of argument

• Enable formal reasoning (OWL reasoners)

Gruber, Thomas R. "Toward principles for the design of ontologies used

for knowledge sharing?." International journal of human-computer

studies 43.5-6 (1995): 907-928. DOI:10.1006/ijhc.1995.1081

Ask: Should the evidence be

aggregated?

Figure credit: Forest plot from Underhill, Kristen, Paul

Montgomery, and Don Operario. "Sexual abstinence only

programmes to prevent HIV infection in high income countries: systematic review." BMJ 335.7613 (2007): 248.

Figure credit: Duke University Medical Center Library. Introduction to

Evidence-based Practice. What is Evidence-Based Practice (EBP)? http://guides.mclibrary.duke.edu/c.php?g=158201&p=1036021

Contextualize evidence with

values and expertise