Hostname: page-component-8448b6f56d-xtgtn Total loading time: 0 Render date: 2024-04-23T18:18:47.943Z Has data issue: false hasContentIssue false

Big Data Biology: Between Eliminative Inferences and Exploratory Experiments

Published online by Cambridge University Press:  01 January 2022

Abstract

Recently, biologists have argued that data-driven biology fosters a new scientific methodology, namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data-driven studies can be included in the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful generalizations to complement the procedure of prioritization. Overall, this article aims to shed light on the structure of contemporary research in molecular biology.

Type
Research Article
Copyright
Copyright © The Philosophy of Science Association

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

I am extremely grateful to the fellows of the PhD program FOLSATEC (especially Pierre Luc Germain, Federico Boem, Marco Annoni, and Giovanni Boniolo) for their valuable comments on previous drafts, as well as to Michael Weisberg and his group in Philadelphia (especially Emily Parke, Carlos Santana, Jane Reznik, and Alkistis Elliot-Graves). I am in debt also to David Teira for his indispensable comments on advanced drafts.

References

Alberts, Bruce. 2012. “The End of ‘Small Science’?Science 337 (6102): 1583.CrossRefGoogle Scholar
Bechtel, William, and Richardson, Robert C. 2010. Discovering Complexity—Decomposition and Localization as Strategies in Scientific Research. Cambridge, MA: MIT Press.CrossRefGoogle Scholar
Boniolo, Giovanni. 2013. “On Molecular Mechanisms and Contexts of Physical Explanation.” Biological Theory 7 (3): 256–65.10.1007/s13752-012-0073-zCrossRefGoogle Scholar
Boyle, Alan P., et al. 2012. “Annotation of Functional Variation in Personal Genomes Using RegulomeDB.” Genome Research 22 (9): 1790–97.CrossRefGoogle ScholarPubMed
Brenner, Sydney. 1999. “Syllicon Valley Fever.” Current Biology 9 (18): R671.CrossRefGoogle ScholarPubMed
Brookfield, John F. Y. 2010. “Q&A: Promise and Pitfalls of Genome-Wide Association Studies.” BMC Biology 8:41.CrossRefGoogle ScholarPubMed
Ciriello, Giovanni, Miller, Martin L., Aksoy, Bulent Arman, Senbabaoglu, Yasin, Schultz, Nikolaus, and Sander, Chris. 2013. “Emerging Landscape of Oncogenic Signatures across Human Cancers.” Nature Genetics 45 (10): 1127–33.CrossRefGoogle ScholarPubMed
Craver, Carl F., and Darden, Lindley. 2013. In Search of Mechanisms. Chicago: University of Chicago Press.CrossRefGoogle Scholar
Douglas, Heather E. 2009. “Reintroducing Prediction to Explanation.” Philosophy of Science Science 76 (4): 444–63.Google Scholar
Dulbecco, Renato. 1986. “A Turning Point in Cancer Research: Sequencing the Human Genome.” Science 231 (4742): 1055–56.CrossRefGoogle ScholarPubMed
Earman, John. 1992. Bayes or Bust? A Critical Examination of Bayesian Confirmation Theory. Cambridge, MA: MIT Press.Google Scholar
The ENCODE Project Consortium. 2012. “An Integrated Encyclopedia of DNA Elements in the Human Genome.” Nature 489 (7414): 5774.CrossRefGoogle Scholar
Forber, Patrick. 2011. “Reconceiving Eliminative Inference.” Philosophy of Science 78 (2): 185208.10.1086/659232CrossRefGoogle Scholar
Garraway, Levi, and Lander, Eric. 2013. “Lessons from the Cancer Genome.” Cell 153 (1): 1737.CrossRefGoogle ScholarPubMed
Germain, Pierre Luc, Ratti, Emanuele, and Boem, Federico. 2014. “Junk or Functional DNA? ENCODE and the Function Controversy.” Biology and Philosophy 29:807–31.10.1007/s10539-014-9441-3CrossRefGoogle Scholar
Golub, T. 2010. “Counterpoint: Data First.” Nature 464 (7289): 679.10.1038/464679aCrossRefGoogle ScholarPubMed
Gross, Fridolin. 2013. “The Sum of the Parts: Heuristic Strategies in Systems Biology.” PhD diss., University of Milan.Google Scholar
Guessous, Idris, Gwinn, Marta, and Khoury, Muin J. 2009. “Genome-Wide Association Studies in Pharmacogenomics: Untapped Potential for Translation.” Genome Medicine 1 (4): 46.CrossRefGoogle ScholarPubMed
Hanahan, Douglas, and Weinberg, Robert. 2011. “Hallmarks of Cancer: The Next Generation.” Cell 144 (5): 646–74.CrossRefGoogle ScholarPubMed
Hawthorne, James. 1993. “Bayesian Induction Is Eliminative Induction.” Philosophical Topics 21 (1): 99138.CrossRefGoogle Scholar
Hunter, David J., Altshuler, David, and Rader, Daniel. 2008. “From Darwin’s Finches to Canaries in the Coal Mine—Mining the Genome for the New Biology.” New England Journal of Medicine 358:26.10.1056/NEJMp0804318CrossRefGoogle ScholarPubMed
Kandoth, Cyriac, et al. 2013. “Mutational Landscape and Significance across 12 Major Cancer Types.” Nature 502 (7471): 333–39.CrossRefGoogle ScholarPubMed
Keating, Peter, and Cambrosio, Alberto. 2012. “Too Many Numbers: Microarrays in Clinical Cancer Research.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 3751.CrossRefGoogle ScholarPubMed
Kell, D. B., and Oliver, S. G. 2003. “Here Is the Evidence, Now What Is the Hypothesis? The Complementary Roles of Inductive and Hypothesis-Driven Science in the Post-genomic Era.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 26 (1): 99105.CrossRefGoogle Scholar
Kim, Tae-Min, Xi, Ruibin, Luquette, Lovelace, Park, Richard, Johnson, Mark, and Park, Peter J. 2013. “Functional Genomic Analysis of Chromosomal Aberrations in a Compendium of 8000 Cancer Genomes.” Genome Research 23 (2): 217–27.CrossRefGoogle Scholar
Kitcher, Philip S. 1993. The Advancement of Science. New York: Oxford University Press.Google Scholar
Kitsios, Georgios, and Zintzaras, Elias. 2009. “Genome-Wide Association Studies: Hypothesis-Free or ‘Engaged’?Translational Research 154 (4): 161–64.CrossRefGoogle ScholarPubMed
Lawrence, Michael, et al. 2013. “Mutational Heterogeneity in Cancer and the Search for New Cancer-Associated Genes.” Nature 499 (7457): 214–18.CrossRefGoogle ScholarPubMed
Leonelli, Sabina. 2012a. “Classificatory Theories in Data-Intensive Science.” International Studies in the Philosophy of Science 26 (1): 4765.CrossRefGoogle Scholar
Leonelli, Sabina 2012b. “Introduction: Making Sense of Data-Driven Research in the Biological and Biomedical Sciences.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 13.10.1016/j.shpsc.2011.10.001CrossRefGoogle Scholar
Li, Yudong, Zhang, Li, Ball, Robyn, Liang, Xinle, Li, Jianrong, Lin, Zhenguo, and Liang, Han. 2012. “Comparative Analysis of Somatic Copy-Number Alterations across Different Human Cancer Types Reveals Two Distinct Classes of Breakpoint Hotspots.” Human Molecular Genetics 21 (22): 4957–65.CrossRefGoogle ScholarPubMed
Machamer, Peter, Darden, Lindey, and Craver, Carl. 2000. “Thinking about Mechanisms.” Philosophy of Science 67:125.CrossRefGoogle Scholar
McCarthy, Mark I., Abecasis, Goncalo R., Cardon, Lon R., Goldstein, David, Little, Julian, Ioannidis, John P. A., and Hirschhorn, Joel N. 2008. “Genome-Wide Association Studies for Complex Traits: Consensus, Uncertainty and Challenges.” Nature Reviews Genetics 9 (5): 356–69.CrossRefGoogle ScholarPubMed
Mitchell, Sandra D. 1997. “Pragmatic Laws.” Philosophy of Science 64 (Proceedings): S468S479.10.1086/392623CrossRefGoogle Scholar
Norton, John. 1995. “Eliminative Induction as a Method of Discovery: How Einstein Discovered General Relativity.” The Creation of Ideas in Physics, ed. Leplin, Jarrett, 2969. Dordrecht: Kluwer.CrossRefGoogle Scholar
O’Malley, Maureen. 2007. “Exploratory Experimentation and Scientific Practice: Metagenomics and the Proteorhodopsin Case.” History and Philosophy of the Life Sciences 29 (3): 335–58.Google ScholarPubMed
O’Malley, Maureen, and Soyer, Orkun S. 2012. “The Roles of Integration in Molecular Systems Biology.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 5868.CrossRefGoogle ScholarPubMed
Peschard, Isabelle, and van Fraassen, Bas. 2014. “Making the Abstract Complete: The Role of Norms and Values in Experimental Modelling.” Studies in History and Philosophy of Science A 46:310.CrossRefGoogle Scholar
Platt, John R. 1964. “Strong Inference.” Science 146 (3642): 347–53.CrossRefGoogle ScholarPubMed
Pomerantz, M. M., et al. 2009. “The 8q24 Cancer Risk Variant rs6983267 Shows Long-Range Interaction with MYC in Colorectal Cancer.” Nature Genetics 41 (8): 882–84.10.1038/ng.403CrossRefGoogle ScholarPubMed
Pomerantz, M. M. 2010. “Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis.” PLoS Genetics 6 (11): e1001204.CrossRefGoogle ScholarPubMed
Raphael, Benjamin J., Dobson, Jason R., Oesper, Layla, and Vandin, Fabio. 2014. “Identifying Driver Mutations in Sequenced Cancer Genomes: Computational Approaches to Enable Precision Medicine.” Genome Medicine 6 (1): 5.CrossRefGoogle ScholarPubMed
Rheinberger, H.-J. 2011. “Infra-experimentality: From Traces to Data, from Data to Patterning Facts.” History of Science 49 (337).CrossRefGoogle Scholar
Schaub, Marc, Boyle, Alan P., Kundaje, Anshul, Batzoglou, Serafim, and Snyder, Michael. 2012. “Linking Disease Associations with Regulatory Information in the Human Genome.” Genome Research 22 (9): 1748–59.CrossRefGoogle ScholarPubMed
Shmueli, Galit. 2010. “To Explain or to Predict?Statistical Science 25 (3): 289310.CrossRefGoogle Scholar
Smalheiser, Neil R. 2002. “Informatics and Hypothesis-Driven Research.” EMBO Reports 3 (8): 702.10.1093/embo-reports/kvf164CrossRefGoogle ScholarPubMed
Steinle, Friedrich. 1997. “Entering New Fields: Exploratory Uses of Experimentation.” Philosophy of Science 64 (Proceedings): S64S74.CrossRefGoogle Scholar
Strasser, Bruno. 2011. “The Experimenter’s Museum—GenBank, Natural History, and the Moral Economies of Biomedicine.” Isis 102 (1): 6096.CrossRefGoogle ScholarPubMed
Vandin, Fabio, Upfal, Eli, and Raphael, Benjamin J. 2012. “Finding Driver Pathways in Cancer: Models and Algorithms.” Algorithms for Molecular Biology: AMB 7 (1): 23.CrossRefGoogle ScholarPubMed
Vogelstein, Bert, Papadopoulos, Nickolas, Velculescu, Victor E., Zhou, Shibin, Diaz, Luis A. Jr., and Kinzler, Kenneth W. 2013. “Cancer Genome Landscapes.” Science 339 (6127): 1546–58.CrossRefGoogle ScholarPubMed
Waters, C. Kenneth. 2007. “The Nature and Context of Exploratory Experimentation.” History and Philosophy of the Life Sciences 29:19.Google ScholarPubMed
Weinberg, Robert. 2010. “Point: Hypotheses First.” Nature 464 (7289): 678.CrossRefGoogle ScholarPubMed
Zack, Travis I., et al. 2013. “Pan-cancer Patterns of Somatic Copy Number Alteration.” Nature Genetics 45 (10): 1134–40.CrossRefGoogle ScholarPubMed