Hostname: page-component-5d59c44645-klj7v Total loading time: 0 Render date: 2024-02-29T10:49:38.284Z Has data issue: false hasContentIssue false

Causation and Single Nucleotide Polymorphism Heritability

Published online by Cambridge University Press:  01 January 2022

Abstract

Genome-wide association studies (GWAS) of human complex traits have provided us with new estimates of heritability. These estimates foreground the question of genetic causation. After having presented in simple terms the rationale underlying this way of estimating heritability, I assess the extent to which relationships between genes and phenotypes established with GWAS satisfy several dimensions of causal relationships—namely, range of influence, specificity, and stability—distinguished within the interventionist account of causation. The upshot is that if these relationships are causal in some sense, my analysis shows the extent to which they do not represent paradigmatic causal relationships.

Type
Biological Sciences and Medicine
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 thankful to the Theory and Method in Biosciences group at the University of Sydney who provided useful feedback on previous versions of the manuscript and in particular Stefan Gawronski who proofread the final manuscript. I am also thankful to Lucas Matthews for organizing the symposium and the audiences at the PSA 2019 conference and at the Genetics and Human Agency 2019 annual meeting for feedback. This research was supported by a Macquarie University Research Fellowship and a Large Grant from the John Templeton Foundation (grant 60811).

References

Bourrat, Pierrick. 2019a. “Heritability, Causal Influence and Locality.” Synthese. https://doi.org/10.1007/s11229-019-02484-3.CrossRefGoogle Scholar
Bourrat, Pierrick. 2019b. “On Calcott’s Permissive and Instructive Cause Distinction.” Biology and Philosophy 34 (1): 1. https://doi.org/10.1007/s10539-018-9654-y.CrossRefGoogle Scholar
Bourrat, Pierrick. 2019c. “Variation of Information as a Measure of One-to-One Causal Specificity.” European Journal for Philosophy of Science 9 (1): 11. https://doi.org/10.1007/s13194-018-0224-6.CrossRefGoogle Scholar
Bourrat, Pierrick, and Lu, Qiaoying. 2017. “Dissolving the Missing Heritability Problem.” Philosophy of Science 84 (5): 1055–67.10.1086/694007CrossRefGoogle Scholar
Bourrat, Pierrick, Lu, Qiaoying, and Jablonka, Eva. 2017. “Why the Missing Heritability Might Not Be in the DNA.” BioEssays 39 (7). https://doi.org/10.1002/bies.201700067.CrossRefGoogle Scholar
Bush, William S., and Moore, Jason H.. 2012. “Chapter 11: Genome-Wide Association Studies.” PLOS Computational Biology 8 (12): e1002822. https://doi.org/10.1371/journal.pcbi.1002822.CrossRefGoogle Scholar
Downes, S. M. 2009. “Heritability.” In Stanford Encyclopedia of Philosophy, ed. Zalta, Edward N.. Stanford, CA: Stanford University. https://plato.stanford.edu/entries/heredity/.Google Scholar
Elgin, Sarah C. R., and Reuter, Gunter. 2013. “Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila.” Cold Spring Harbor Perspectives in Biology 5 (8). https://doi.org/10.1101/cshperspect.a017780.CrossRefGoogle ScholarPubMed
Falconer, Douglas S., and Mackay, Trudy F. C.. 1996. Introduction to Quantitative Genetics. 4th ed. Essex: Longman.Google Scholar
Griffiths, P. E., and Neumann-Held, E. M.. 1999. “The Many Faces of the Gene.” Bioscience 49:656–62.10.2307/1313441CrossRefGoogle Scholar
Griffiths, P. E., and Stotz, K.. 2013. Genetics and Philosophy: An Introduction. New York: Cambridge University Press.CrossRefGoogle Scholar
Hesslow, Germund. 1988. “The Problem of Causal Selection.” In Contemporary Science and Natural Explanation: Commonsense Conceptions of Causality, ed. Hilton, Denis J., 1132. New York: New York University Press.Google Scholar
Iannuzzi, Michael C., et al. 1991. “Two Frameshift Mutations in the Cystic Fibrosis Gene.” American Journal of Human Genetics 48 (2): 227–31.Google ScholarPubMed
Lee, James J., and Chow, Carson C.. 2013. “The Causal Meaning of Fisher’s Average Effect.” Genetics Research 95 (2–3): 89109.10.1017/S0016672313000074CrossRefGoogle ScholarPubMed
Lewontin, Richard C. 1974. “The Analysis of Variance and the Analysis of Causes.” American Journal of Human Genetics 26 (3): 400411.Google ScholarPubMed
Lu, Qiaoying, and Bourrat, Pierrick. 2018. “The Evolutionary Gene and the Extended Evolutionary Synthesis.” British Journal for the Philosophy of Science 69 (3): 775800.10.1093/bjps/axw035CrossRefGoogle Scholar
Lynch, Kate E., and Bourrat, Pierrick. 2017. “Interpreting Heritability Causally.” Philosophy of Science 84 (1): 1434.CrossRefGoogle Scholar
Maher, Brendan. 2008. “Personal Genomes: The Case of the Missing Heritability.” Nature News 456 (7218): 1821.10.1038/456018aCrossRefGoogle ScholarPubMed
Mathieson, Iain, and McVean, Gil. 2012. “Differential Confounding of Rare and Common Variants in Spatially Structured Populations.” Nature Genetics 44 (3): 243–46.CrossRefGoogle ScholarPubMed
Matthews, Lucas J., and Turkheimer, Eric. 2019. “Across the Great Divide: Pluralism and the Hunt for Missing Heritability.” Synthese. https://doi.org/10.1007/s11229-019-02205-w.CrossRefGoogle Scholar
Morgan, Angela, Fisher, Simon E., Scheffer, Ingrid, and Hildebrand, Michael. 1993. “FOXP2-Related Speech and Language Disorders.” In GeneReviews, ed. Adam, Margaret P. et al. Seattle: University of Washington.Google ScholarPubMed
Nudel, Ron, and Newbury, Dianne F.. 2013. “FOXP2.” Wiley Interdisciplinary Reviews 4 (5): 547–60.Google ScholarPubMed
Pocheville, Arnaud, Griffiths, Paul E., and Stotz, Karola. 2017. “Comparing Causes—an Information-Theoretic Approach to Specificity, Proportionality and Stability.” In Proceedings of the 15th Congress of Logic, Methodology and Philosophy of Science, ed. Leitgeb, Hannes, Niiniluoto, Ilkka, Sober, Elliott, and Seppälä, Päivi, 260–75. London: College.Google Scholar
Rosenberg, Henry, Davis, Mark, James, Danielle, Pollock, Neil, and Stowell, Kathryn. 2007. “Malignant Hyperthermia.” Orphanet Journal of Rare Diseases 2 (April): 21. https://doi.org/10.1186/1750-1172-2-21.CrossRefGoogle Scholar
Sesardic, Neven. 2005. Making Sense of Heritability. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Turkheimer, Eric. 2011. “Still Missing.” Research in Human Development 8 (3–4): 227–41.10.1080/15427609.2011.625321CrossRefGoogle Scholar
Vargha-Khadem, Faraneh, Gadian, David G., Copp, Andrew, and Mishkin, Mortimer. 2005. “FOXP2 and the Neuroanatomy of Speech and Language.” Nature Reviews Neuroscience 6 (2): 131–38.CrossRefGoogle ScholarPubMed
Visscher, Peter M., Wray, Naomi R., Zhang, Qian, Sklar, Pamela, McCarthy, Mark I., Brown, Matthew A., and Yang, Jian. 2017. “10 Years of GWAS Discovery: Biology, Function, and Translation.” American Journal of Human Genetics 101 (1): 522.10.1016/j.ajhg.2017.06.005CrossRefGoogle Scholar
Walker, Francis O. 2007. “Huntington’s Disease.” Lancet 369 (9557): 218–28.CrossRefGoogle ScholarPubMed
Woodward, James. 2002. “What Is a Mechanism? A Counterfactual Account.” Philosophy of Science 69 (Proceedings): S366S377.10.1086/341859CrossRefGoogle Scholar
Woodward, James. 2003. Making Things Happen: A Theory of Causal Explanation. New York: Oxford University Press.Google Scholar
Woodward, James. 2010. “Causation in Biology: Stability, Specificity, and the Choice of Levels of Explanation.” Biology and Philosophy 25 (3): 287318.10.1007/s10539-010-9200-zCrossRefGoogle Scholar
Yang, Jian, Zeng, Jian, Goddard, Michael E., Wray, Naomi R., and Visscher, Peter M.. 2017. “Concepts, Estimation and Interpretation of SNP-Based Heritability.” Nature Genetics 49 (9): 1304–10.10.1038/ng.3941CrossRefGoogle ScholarPubMed
Yang, Jian, et al. 2010. “Common SNPs Explain a Large Proportion of the Heritability for Human Height.” Nature Genetics 42 (7): 565–69.10.1038/ng.608CrossRefGoogle ScholarPubMed