Hostname: page-component-cd9895bd7-fscjk Total loading time: 0 Render date: 2024-12-26T17:58:53.884Z Has data issue: false hasContentIssue false

With ‘Genes’ Like That, Who Needs an Environment? Postgenomics's Argument for the ‘Ontogeny of Information’

Published online by Cambridge University Press:  01 January 2022

Abstract

The linear sequence specification of a gene product is not provided by the target DNA sequence alone but by the mechanisms of gene expressions. The main actors of these mechanisms, proteins and functional RNAs, relay environmental information to the genome with important consequences to sequence selection and processing. This ‘postgenomic’ reality has implications for our understandings of development not as predetermined by genes but as an epigenetic process. Critics of genetic determinism have long argued that the activity of ‘genes’ and hence their contribution to the phenotype depends on intra- and extraorganismal ‘environmental’ elements. As will be shown here, even the mere physical existence of a `gene' is dependent on its phenotypic context.

Type
Advances in Genomics and Its Conceptual Implications for Development and Evolution
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 grateful to the Biology Studies Reading Group at Indiana University, especially Lisa Lloyd and Colin Allen, for comments on an earlier draft. This research was supported by National Science Foundation grants 0217567 and 0323496 and supplemental funding by the University of Pittsburgh. Any opinions, findings, and conclusions or recommendations expressed in this material are mine and do not necessarily reflect the views of the National Science Foundation.

References

Ambros, Victor (2004), “The Function of Animal Micro RNAs,” Nature 431:350355.CrossRefGoogle Scholar
Baranov, Pavel V., Gurvich, Olga L., Hammer, Andrew W., Gesteland, Raymond F., and Atkins, John F. (2003), “Recode 2003,” Nucleic Acids Research 31 (1): 8789..CrossRefGoogle ScholarPubMed
Blumenthal, Thomas, and Thomas, Jeffrey (1988), “Cis and Trans mRNA Splicing in C. elegans,” Trends in Genetics 4 (11): 305308..CrossRefGoogle ScholarPubMed
Coelho, Paulo S. R., Bryan, Anthony C., Kumar, Anuj, Shadel, Gerald S., and Snyder, Michael (2002), “A Novel Mitochondrial Protein, TAR1p, Is Encoded on the Antisense Strand of the Nuclear 25S rDNA,” Genes and Development 16:27552760.CrossRefGoogle ScholarPubMed
Communi, Didier, Suarez-Huerta, Nathalie, Dussossoy, Danielle, Savi, Pierre, and Boeynaems, Jean-Marie (2001), “Cotranscription and Intergenic Splicing of Human P2Y(11) SSF1 Genes,” Journal of Biological Chemistry 276 (19): 1656116566..CrossRefGoogle ScholarPubMed
Davidson, Eric R. (2001), Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.Google Scholar
Dillon, Niall (2003), “Positions, Please,” Nature 425: 457.CrossRefGoogle ScholarPubMed
Falk, Raphael (2000), “The Gene: A Concept in Tension,” in Beurton, Peter, Falk, Raphael, and Rheinberger, Hans-Jörg (eds.), The Concept of the Gene in Development and Evolution. Cambridge: Cambridge University Press, 317348.CrossRefGoogle Scholar
Finta, Csaba, Warner, S. C., and Zaphiropoulos, Peter G. (2002), “Intergenic mRNAs: Minor Gene Products or Tools of Diversity?Histology and Histopathology 17 (2): 677682..Google ScholarPubMed
Finta, Csaba, and Zaphiropoulos, Peter G. (2000), “The Human Cytochrome P450 3A Locus: Gene Evolution by Capture of Downstream Exons,” Gene 260 (1–2): 1323.CrossRefGoogle ScholarPubMed
Flomen, R., Knight, J., Sham, P., Kerwin, R., and Makoff, A. (2004), “Evidence That RNA Editing Modulates Splice Site Selection in the 5-HT2C Receptor Gene,” Nucleic Acids Research 32 (7): 21132122..CrossRefGoogle ScholarPubMed
Flouriot, G., Brand, H., Seraphin, B., and Gannon, F. (2002), “Natural Trans-spliced mRNAs Are Generated from the Human Estrogen Receptor-Alpha (hER Alpha) Gene,” Journal of Biological Chemistry 277 (29): 2624426251..CrossRefGoogle ScholarPubMed
Francastel, Claire, Schübeler, Dirk, Martin, David I. K., and Groudine, Mark (2000), “Nuclear Compartmentalization and Gene Activity,” Cell Biology 1: 137.Google ScholarPubMed
Gagen, Michael J., and Mattick, John S. (2004), “Imperatives and Inherent Limitations of Accelerating Networks in Biology, Engineering and Society,” unpublished paper.Google Scholar
Gibbs, W. W. (2003), “The Unseen Genome: Gems among the Junk,” Scientific American 289 (5): 4653..CrossRefGoogle ScholarPubMed
Gilbert, Scott F., and Sarkar, Sahotra (2000), “Embracing Complexity: Organicism for the 21st Century,” Developmental Dynamics 219:19.3.0.CO;2-A>CrossRefGoogle ScholarPubMed
Gray, M. W. (2003), “Diversity and Evolution of Mitochondrial RNA Editing Systems,” IUBMB Life 55 (4–5): 227233.CrossRefGoogle ScholarPubMed
Handa, H., Bonnard, G., and Grienenberger, J. M. (1996), “The Rapeseed Mitochondrial Gene Encoding a Homologue of the Bacterial Protein Cell Is Divided into Two Independently Transcribed Reading Frames,” Molecular and General Genetics 252 (3): 292302..CrossRefGoogle ScholarPubMed
Hazzalin, Catherine A., and Mahadevan, Louis C. (2002), “MAPK-Regulated Transcription: A Continuously Variable Gene Switch?Nature 3:3041.Google ScholarPubMed
Jablonka, Eva, and Lamb, Marion J. (2005), Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge, MA: MIT Press.Google Scholar
Kim, D. D. Y., Kim, T. T. Y., Walsh, T., Kobayashi, Y., Matise, T. C., Buyske, S., and Gabriel, A. (2004), “Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome,” Genome Research 14 (9): 17191725..CrossRefGoogle ScholarPubMed
Leipzig, Jeremy, Pevzner, Pavel, and Heber, Steffen (2004), “The Alternative Splicing Gallery (ASG): Bridging the Gap between Genome and Transcriptome,” Nucleic Acids Research 32 (13): 39773983..CrossRefGoogle ScholarPubMed
Lemon, B., Inouye, C., King, D. S., and Tjian, R. (2001), “Selectivity of Chromatin-Remodeling Cofactors for Ligand-Activated Transcription,” Nature 414:924928.CrossRefGoogle ScholarPubMed
Levy, David E., and Darnell, J. E. Jr. (2002), “STATS: Transcriptional Control and Biological Impact,” Nature Reviews: Molecular Cell Biology 3:651662.CrossRefGoogle ScholarPubMed
Luscombe, Nicholas M., Badu, M. Madan, Yu, Haiyuan, Snyder, Michael, Teichmann, Sarah A., and Gerstein, Mark (2004), “Genomic Analysis of Regulatory Network Dynamics Reveals Large Topological Changes,” Nature 431:308312.CrossRefGoogle ScholarPubMed
Magrangeas, Florence, Pitiot, Gilles, Dubois, Sigrid, Bragado-Nilsson, Elisabeth, Cherel, Michel, Jobert, Severin, Lebeau, Benoit et al. (1998), “Cotranscription and Intergenic Splicing of Human Galactose-1 Phosphate Uridylyltransferase and Interleukin-11 Receptor Alpha-Chain Genes Generate a Fusion mRNA in Normal Cells,” Journal of Biological Chemistry 273 (26): 1600516010..CrossRefGoogle ScholarPubMed
Mandal, Maumita, and Breaker, Ronald R. (2004), “Gene Regulation by Riboswitches,” Nature Reviews: Molecular Cell Biology 5:451463.CrossRefGoogle ScholarPubMed
Mansfield, S. G., Clark, R. H., Puttaraju, M., and Mitchell, L. G. (2002), “Spliceosome-Mediated RNA Trans-splicing (SMaRT): A Technique to Alter and Regulate Gene Expression,” Blood Cells, Molecules and Diseases 28 (3): 338348..Google Scholar
Martens, Joseph A., Laprade, Lisa, and Winston, Fred (2004), “Intergenic Transcription Is Required to Repress the Saccharomyces cerevisiae SER3 Gene,” Nature 429:571574.CrossRefGoogle ScholarPubMed
Mattick, John S. (2003), “Challenging the Dogma: The Hidden Layer of Non-protein-coding RNAs in Complex Organisms,” BioEssays 25 (10): 930939..CrossRefGoogle ScholarPubMed
Mattick, John S. (2004), “RNA Regulation: A New Genetics?Nature Reviews Genetics 5 (4): 316323..CrossRefGoogle ScholarPubMed
Meaney, Michael J. (2001), “Maternal Care, Gene Expression, and the Transmission of Individual Differences in Stress Reactivity across Generations,” Annual Review of Neuroscience 24:11611192.CrossRefGoogle Scholar
Moss, Lenny (2003), What Genes Can’t Do. Cambridge, MA: MIT Press.Google Scholar
Mottus, Randy C., Whitehead, Ian P., O'Grady, Michael, Sobel, Richard E., Burr, Rod H. L., Spiegelman, George B., and Grigliatti, Thomas A. (1997), “Unique Gene Organization: Alternative Splicing in Drosophila Produces Two Structurally Unrelated Proteins,” Gene 198 (1–2): 229236.CrossRefGoogle ScholarPubMed
Müller, Gerd B., and Olsson, Lennart (2003), “Epigenesis and Epigenetics,” in Hall, Brian K. and Olson, Wendy M. (eds.), Keywords and Concepts in Evolutionary Developmental Biology. Cambridge, MA: Harvard University Press, 114123.Google Scholar
Nelson, Craig E., Hersh, Bradley M., and Carroll, Sean B. (2004), “The Regulatory Content of Intergenic DNA Shapes Genome Architecture,” Genome Biology 5 (4): R25.CrossRefGoogle ScholarPubMed
Novina, Carl D., and Sharp, Phillip A. (2004), “The RNAi Revolution,” Nature 430:161164.CrossRefGoogle ScholarPubMed
Oyama, Susan ([1985] 2000), The Ontogeny of Information: Developmental Systems and Evolution. 2nd ed. Durham, NC: Duke University Press.Google Scholar
Pirrotta, V. (2002), “Trans-splicing in Drosophila,” BioEssays 24 (11): 988991..CrossRefGoogle ScholarPubMed
Robert, Jason S. (2004), Embryology, Epigenesis and Evolution: Taking Development Seriously. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Samuel, C. E. (2003), “RNA Editing Minireview Series,” Journal of Biological Chemistry 278 (3): 13891390..CrossRefGoogle ScholarPubMed
Sharpless, Norman E., and DePinho, Ronald A. (1999), “The INK4A/ARF Locus and Its Two Gene Products,” Current Opinion in Genetics and Development 9:2230.CrossRefGoogle ScholarPubMed
Stern, David (2003), “Gene Regulation,” in Hall, B. K. and Olson, W. M. (eds.), Keywords and Concepts in Evolutionary Developmental Biology. Cambridge, MA: Harvard University Press, 145151.Google Scholar
Stotz, Karola (forthcoming), “Molecular Epigenesis: A Break in the Central Dogma,” History and Philosophy of the Life Sciences 26 (4).Google Scholar
Stotz, Karola, Bostanci, Adam, and Griffiths, Paul E. (2006), “Tracking the Shift to `Post-genomics’,” Community Genetics 9 (3): 190196..Google Scholar
Sturm, N. R., and Campbell, D. K. (1999), “The Role of Intron Structures in Trans-splicing and Cap 4 Formation for the Leishmania Spliced Leader RNA,” Journal of Biological Chemistry 274 (27): 1936119367..CrossRefGoogle ScholarPubMed
Takahara, T., Kasahara, D., Mori, D., Yanagisawa, S., and Akanuma, H. (2002), “The Trans-spliced Variants of Sp1 mRNA in Rats,” Biochemical and Biophysical Research Communications 298 (1): 156162..CrossRefGoogle Scholar
Thieffry, Denis, and Sarkar, Sahotra (1998), “Forty Years under the Central Dogma,” Trends in Biochemical Sciences 23 (August): 312316.CrossRefGoogle ScholarPubMed
Wray, Gregory A., Hahn, Matthew W., Abouheif, Ehab, Balhoff, James P., Pizer, Margaret, Rockman, Matthew V., and Romano, Laura A. (2003), “The Evolution of Transcriptional Regulation in Eukaryotes,” Molecular Biology and Evolution 20 (9): 13771419..CrossRefGoogle ScholarPubMed
Zhang, Cheng, Xie, Youmei M., Martignetti, John A., Yeo, Tracy T., Massa, Stephen M., and Longo, Frank M. (2003), “A Candidate Chimeric Mammalian mRNA Transcript Is Derived from Distinct Chromosomes and Is Associated with Nonconsensus Splice Junction Motifs.” DNA and Cell Biology 22 (5): 303315..CrossRefGoogle ScholarPubMed