Hostname: page-component-586b7cd67f-t7fkt Total loading time: 0 Render date: 2024-12-03T20:32:25.276Z Has data issue: false hasContentIssue false

What Does It Mean to Be 75% Pumpkin? The Units of Comparative Genomics

Published online by Cambridge University Press:  01 January 2022

Abstract

Comparative genomicists seem to be convinced that the unit of measurement employed in their studies is a gene that drives the function of cells and ultimately organisms. As a result, they have come to some substantive conclusions about how similar humans are to other organisms based on the percentage of genetic makeup they share. I argue that the actual unit of measurement employed in the studies corresponds to a structural rather than a functional gene concept, thus rendering many of the implications drawn from comparative genomic studies largely unwarranted, if not completely mistaken.

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

Special thanks to Steve Downes for valuable comments, criticism, and encouragement. I am also grateful to Bryan Benham, Matt Haber, Anya Plutynski, and Jim Tabery for helpful feedback, and most of all to Matt Mosdell, whose healthy skepticism of statistics inspired me to write this article. Earlier versions of this work were presented at ISHPSSB 2007 in Exeter and PSA 2008 in Pittsburgh. Conversations with various audience members helped clarify my ideas on the topic.

References

Auffray, Charles, Imbeaud, Sandrine, Roux-Rouquie, Magali, and Hood, Leroy (2003), “Self-Organized Living Systems: Conjunction of a Stable Organization with Chaotic Fluctuations in Biological Space-Time”, Self-Organized Living Systems: Conjunction of a Stable Organization with Chaotic Fluctuations in Biological Space-Time 361:11251139.Google ScholarPubMed
Beurton, Peter J., Falk, Raphael, and Rheinberger, Hans-Jörg, eds. (2000), The Concept of the Gene in Development and Evolution. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Brett, David, Pospisil, Heike, Valcárcel, Juan, Reich, Jens, and Bork, Peer (2001), “Alternative Splicing and Genome Complexity”, Alternative Splicing and Genome Complexity 30:2930.Google ScholarPubMed
Brown, Terence A. (2002), Genomes. New York: Wiley.Google ScholarPubMed
Burian, Richard M. (1985), “On Conceptual Change in Biology: The Case of the Gene”, in Depew, David J. and Weber, Bruce H. (eds.), Evolution at a Crossroads: The New Biology and the New Philosophy of Science. Cambridge, MA: MIT Press, 2142.Google Scholar
Clark, Melody, ed. (2000), Comparative Genomics. Norwell, MA: Kluwer.CrossRefGoogle Scholar
Downes, Stephen M. (2004), “Alternative Splicing, the Gene Concept, and Evolution”, Alternative Splicing, the Gene Concept, and Evolution 26:91104.Google ScholarPubMed
Durrani, Monise (1999), “Similarity in Diversity”, BBC News, July 5, http://news.bbc.co.uk/2/hi/science/nature/386516.stm.Google Scholar
Dwyer, Rex A. (2002), Genomic Perl: From Bioinformatics Basics to Working Code. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Fogle, Thomas (2001), “The Dissolution of Protein Coding Genes in Molecular Biology”, in Beurton et al. 2000, 325.Google Scholar
Graveley, Brenton R. (2001), “Alternative Splicing: Increasing Diversity in the Proteomic World”, Alternative Splicing: Increasing Diversity in the Proteomic World 17:100107.Google ScholarPubMed
Gregory, Ryan T. (2005), The Evolution of the Genome. Burlington, MA: Elsevier.Google Scholar
Hahn, William M., and Wray, Gregory A. (2002), “The G-value Paradox”, The G-value Paradox 4:7375.Google ScholarPubMed
Hardison, Ross C. (2003), “Comparative Genomics”, Comparative Genomics 1:156160.Google ScholarPubMed
Karplus, Kevin, and Sjolander, Kimmen (1997), “Predicting Protein Structure Using Hidden Markov Models”, Predicting Protein Structure Using Hidden Markov Models 1:134139.Google ScholarPubMed
Keller, Evelyn F. (2000), The Century of the Gene. Cambridge, MA: Harvard University Press.Google Scholar
Kitcher, Philip (1992), “Gene: Current Usages”, in Keller, Evelyn F. and Lloyd, Elizabeth A. (eds.), Keywords in Evolutionary Biology. Cambridge, MA: Harvard University Press, 128131.Google Scholar
Leipzig, Jeremy, Pevzner, Pavel, and Heber, Steffen (2004), “The Alternative Splicing Gallery (ASG): Bridging the Gap between Genome and Transcriptome”, The Alternative Splicing Gallery (ASG): Bridging the Gap between Genome and Transcriptome 32:39773983.Google ScholarPubMed
Lewontin, Richard (2002), The Triple Helix. Cambridge, MA: Harvard University Press.Google Scholar
Marks, Jonathan (2002), What It Means to Be 98% Chimpanzee. Berkeley: University of California Press.Google Scholar
Miller, Webb, Markova, Kateryna D., Nekrutenko, Anton, and Hardison, Ross C. (2004), “Comparative Genomics”, Comparative Genomics 5:1556.Google ScholarPubMed
Moss, Lenny (2003), What Genes Can’t Do. Cambridge, MA: MIT Press.Google Scholar
Neumann-Held, Eva (2001), “Let's Talk about Genes: The Process Molecular Gene Concept and Its Context”, in Oyama, Susan, Griffiths, Paul E., and Gray, Russell D. (eds.), Cycles of Contingency. Cambridge, MA: MIT Press.Google Scholar
Patis, Carrie (2007), “The First Marsupial Genome Sequence”, The First Marsupial Genome Sequence 8:408409.Google Scholar
Pearson, Helen (2006), “Codes and Enigmas”, Codes and Enigmas 444:259261.Google ScholarPubMed
Rheinberger, Hans-Jörg, and Müller-Wille, Staffan (2007), “Gene”, in Edward N. Zalta (ed.), The Stanford Encyclopedia of Philosophy, http://plato.stanford.edu/archives/fall2007/entries/gene/.Google Scholar
Rubin, Gerald M., Yandell, Mark D., Wortman, Jennifer R., Gabor Miklos, George L., Nelson, Catherine R., Hariharan, Iswar K., Fortini, Mark E., et al. (2000), “Comparative Genomics of the Eukaryotes”, Comparative Genomics of the Eukaryotes 287:22042215.Google ScholarPubMed
Sarkar, Sahotra (2005), Molecular Models of Life. Cambridge, MA: MIT Press.Google Scholar
Sivanshankari, Selvarajan, and Shanmughavel, Piramanayagam (2007), “Comparative Genomics—a Perspective”, Comparative Genomics—a Perspective 1:376378.Google Scholar
Stein, Lincoln D., Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R., Chen, Nansheng, Chinwalla, Asif, et al. (2003), “The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics”, The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics 1 (2): E45.Google ScholarPubMed
Stotz, Karola (2006), “With ‘Genes’ like That, Who Needs an Environment? Postgenomics's Argument for the ‘Ontogeny of Information’”, With ‘Genes’ like That, Who Needs an Environment? Postgenomics's Argument for the ‘Ontogeny of Information’ 73:905917.Google Scholar
Stubbs, Lisa (1999), “How Closely Related Are Mice and Humans? How Many Genes Are the Same?”, in Functional and Comparative Genomics Fact Sheet, U.S. Department of Energy Office of Science, http://www.ornl.gov/sci/techresources/Human_Genome/faq/compgen.shtml.Google Scholar
Thomas, C. A. (1971), “The Genetic Organization of Chromosomes”, The Genetic Organization of Chromosomes 5:237256.Google Scholar
Vendrely, Roger, and Vendrely, Collette (1948), “La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales: Techniques et premiers résultats”, La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales: Techniques et premiers résultats 4:434436.Google Scholar
Waters, Kenneth C. (1994), “Genes Made Molecular”, Genes Made Molecular 61:163185.Google Scholar
Waterston, Robert H., Lindblad-Toh, Kerstin, Birney, Ewan, Rogers, Jane, Abril, Josep F., Agarwal, Pankaj, Agarwala, Richa, et al. (2002), “Initial Sequencing and Comparative Analysis of the Mouse Genome”, Initial Sequencing and Comparative Analysis of the Mouse Genome 420:520562.Google ScholarPubMed
Wong, Limsoon (2004), The Practical Bioinformatician. Singapore: World Scientific.CrossRefGoogle Scholar