Hence the talk of ‘‘genes for any particular character” ought to be omitted, even in cases where no danger of confusion seems to exist. (Johannsen 1911).
Abstract
The word “gene” means different things to different people, and can even be used in multiple ways by the same individual. In this review, I follow a particular thread running through Griffith and Stotz’s “Genetics and Philosophy: an introduction”, which is the way that methods of investigation influence the way we define the concept of “gene”, from nineteen century breeding experiments to twenty-first century big data bioinformatics. These different views lead to a set of gene concepts, which only partially overlap each other, each of which picks up on a different part of gene behaviour, function or scientific utility. This plurality of concepts carries over to the use of the concept of “information” in biology, where the non-overlapping concepts can be connected to whether you view the genome as a blueprint for development, a response to environmental triggers, an engine of heritability, or a document of history.
Similar content being viewed by others
References
Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Boughman J, Brelsford A, Buerkle CA, Buggs R, Butlin RK, Dieckmann U, Eroukhmanoff F, Grill A, Cahan SH, Hermansen JS, Hewitt G, Hudson AG, Jiggins C, Jones J, Keller B, Marczewski T, Mallet J, Martinez-Rodriguez P, Möst M, Mullen S, Nichols R, Nolte AW, Parisod C, Pfennig K, Rice AM, Ritchie MG, Seifert B, Smadja CM, Stelkens R, Szymura JM, Väinölä R, Wolf JBW, Zinner D (2013) Hybridization and speciation. J Evol Biol 26(2):229–246
Ainouche ML, Jenczewski E (2010) Focus on polyploidy. New Phytol 186(1):1–4
Barkman TJ, McNeal JR, Lim SH, Coat G, Croom HB, Young ND, dePamphilis CW (2007) Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evol Biol 7:248
Bass C, Zimmer CT, Riveron JM, Wilding CS, Wondji CS, Kaussmann M, Field LM, Williamson MS, Nauen R (2013) Gene amplification and microsatellite polymorphism underlie a recent insect host shift. Proc Natl Acad Sci USA 110(48):19460–19465
Bates BR, Templeton A, Achter PJ, Harris TM, Condit CM (2003) What does “a gene for heart disease” mean? A focus group study of public understandings of genetic risk factors. Am J Med Genet Part A 119(2):156–161
Baxendale S, Abdulla S, Elgar G, Buck D, Berks M, Micklem G, Durbin R, Bates G, Brenner S, Beck S (1995) Comparative sequence analysis of the human and pufferfish Huntington’s disease genes. Nature Genet 10(1):67–76
Benzer S (1957) The elementary units of heredity. In: McElroy WD, Glass B (eds) The chemical basis of heredity. Johns Hopkins University Press, Baltimore, pp 70–93
Bergstrom CT, Rosvall M (2011) The transmission sense of information. Biol Philos 26(2):159–176
Bodmer W, Bonilla C (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nature Genet 40(6):695–701
Bromham L (2000) Conservation and mutability in molecular evolution. Trends Ecol Evol 15:355
Bromham L (2008) Reading the story in DNA: a beginner’s guide to molecular evolution. Oxford University Press, Oxford
Brunetti CR, Selegue JE, Monteiro A, French V, Brakefield PM, Carroll SB (2001) The generation and diversification of butterfly eyespot color patterns. Curr Biol 11:1578–1585
Cardon LR, Abecasis GR (2003) Using haplotype blocks to map human complex trait loci. Trend Genet 19(3):135–140
Carroll RC (2000) Towards a new evolutionary synthesis. Trends Ecol Evol 15:27–32
Crick FHC (1970) Central dogma of molecular biology. Nature 227:561–563
Cussens J, Bartlett M, Jones EM, Sheehan NA (2013) Maximum likelihood pedigree reconstruction using integer linear programming. Genet Epidemiol 37(1):69–83
Darwin C (1859) The origin of species by means of natural selection: or the preservation of favoured races in the struggle for life. John Murray, London
Demir E, Dickson BJ (2005) Fruitless splicing specifies male courtship behavior in Drosophila. Cell 121(5):785–794
Doolittle WF (2013) Is junk DNA bunk? a critique of ENCODE. Proc Natl Acad Sci USA 110(14):5294–5300
Eddy SR (2013) The ENCODE project: missteps overshadowing a success. Curr Biol 23(7):R259–R261
Friedman JE (2011) Anticipation in hereditary disease: the history of a biomedical concept. Hum Genet 130(6):705–714
Godfrey-Smith P (2000) On the theoretical role of “genetic coding”. Philos Sci 67:26–44
Goldschmidt RB (1946) Position effect and the theory of the corpuscular gene. Cell Mol Life Sci 2(7):250–256
Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E (2013) On the immortality of television sets: “Function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5(3):578–590
Grossniklaus U, Kelly WG, Ferguson-Smith AC, Pembrey M, Lindquist S (2013) Transgenerational epigenetic inheritance: how important is it? Nature Rev Genet 14(3):228–235
Holmes FL (2006) Reconceiving the gene: Seymour Benzer’s adventures in phage genetics. Yale University Press, New Haven
Jasperson KW, Tuohy TM, Neklason DW, Burt RW (2010) Hereditary and familial colon cancer. Gastroenterology 138(6):2044–2058
Johannsen W (1911) The genotype conception of heredity. Am Nat 45(531):129–159
Kunte K, Zhang W, Tenger-Trolander A, Palmer D, Martin A, Reed R, Mullen S, Kronforst M (2014) Doublesex is a mimicry supergene. Nature 507(7491):229–232
Lemos B, Landry CR, Fontanillas P, Renn SCP, Kulathinal R, Brown KM, Hartl DL (2008) Evolution of genomic expression. In: Pagel MD, Pomiankowski A (eds) Evolutionary genomics and proteomics. Sinauer Associates, Sunderland
Lynch M (2007) The origins of genome architecture. Sinauer Associates, Sunderland
Mallet J (2008) Mayr’s view of Darwin: was Darwin wrong about speciation. Biol J Linn Soc 95:3–16
Mallet J (2010) Why was Darwin’s view of species rejected by twentieth century biologists? Biol Philos 25(4):497–527
Maynard Smith J (1958) The theory of evolution. Penguin, London
McClintock B (1983) The significance of responses of the genome to challenge. In: Federoff N, Botstein D (eds) Nobel prize lecture: reprinted in the dynamic genome: Barbara McClintock’s ideas in the century of genetics. 1992. Cold Spring Laboratory Press, New York
Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD (2005) Oscillating evolution of a mammalian locus with overlapping reading frames: an XLas/ALEX relay. PLoS Genet 1(2):e18
Nickrent D, Blarer A, Qiu Y-L, Vidal-Russell R, Anderson F (2004) Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evol Biol 4:1471–2148
Parkinson CN, Osborn RC (1957) Parkinson’s law, and other studies in administration. Houghton Mifflin, Boston
Pickrell JK, Pai AA, Gilad Y, Pritchard JK (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet 6(12):e1001236
Pigliucci M (2007) Do we need an extended evolutionary synthesis? Evolution 62:2743–2749
Ridley R, Frith C, Crow T, Conneally P (1988) Anticipation in Huntington’s disease is inherited through the male line but may originate in the female. J Med Genet 25(9):589–595
Servedio MR, Doorn G, Kopp M, Frame AM, Nosil P (2011) Magic traits in speciation: “magic” but not rare? Trends Ecol Evol 26(8):389–397
Shea N (2011) What’s transmitted? inherited information. Biol Philos 26(2):183–189
Sorek R, Shamir R, Ast G (2004) How prevalent is functional alternative splicing in the human genome? Trends Genet 20(2):68–71
Sterelny K, Kitcher P (1988) The return of the gene. J Philos 85:339–361
Thompson M, Jiggins C (2014) Supergenes and their role in evolution. Heredity 113:1–8
Tricker PJ, López CMR, Gibbings G, Hadley P, Wilkinson MJ (2013) Transgenerational, dynamic methylation of stomata genes in response to low relative humidity. Int J Mol Sci 14(4):6674–6689
Wadhawan S, Dickins B, Nekrutenko A (2008) Wheels within wheels: clues to the evolution of the Gnas and Gnal loci. Mol Biol Evol 25(12):2745–2757
Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M (2011) IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci Int Genet 5(3):170–180
Weinstein LS, Liu J, Sakamoto A, Xie T, Chen M (2004) Minireview: GNAS: normal and abnormal functions. Endocrinology 145(12):5459–5464
Weismann A (1882) Studies in the theory of descent. AMS Press, New York
Wexler NS, Lorimer J, Porter J, Gomez F, Moskowitz C, Shackell E, Marder K, Penchaszadeh G, Roberts SA, Gayan J, Brocklebank D, Cherny SS, Cardon LR, Gray J, Dlouhy SR, Wiktorski S, Hodes ME, Conneally PM, Penney JB, Gusella J, Cha JH, Irizarry M, Rosas D, Hersch S, Hollingsworth Z, MacDonald M, Young AB, Andresen JM, Housman DE, De Young MM, Bonilla E, Stillings T, Negrette A, Snodgrass SR, Martinez-Jaurrieta MD, Ramos-Arroyo MA, Bickham J, Ramos JS, Marshall F, Shoulson I, Rey GJ, Feigin A, Arnheim N, Acevedo-Cruz A, Acosta L, Alvir J, Fischbeck K, Thompson LM, Young A, Dure L, O’Brien CJ, Paulsen J, Brickman A, Krch D, Peery S, Hogarth P, Higgins DS Jr, Landwehrmeyer B (2004) Venezuelan kindreds reveal that genetic and environmental factors modulate Huntington’s disease age of onset. Proc Natl Acad Sci USA 101(10):3498–3503
Wilson Sayres MA, Makova KD (2011) Genome analyses substantiate male mutation bias in many species. Bioessays 33(12):938–945
Xu S, Hu Z (2010) Mapping quantitative trait loci using distorted markers. Int Journal Plant Genomics 2009
Yandell M, Ence D (2012) A beginner’s guide to eukaryotic genome annotation. Nature Rev Genet 13(5):329–342
Acknowledgments
Thanks to Brett Calcott, Kim Sterelny, Paul Griffiths, Karola Stotz and Emma Day for their feedback, and to Silo Kingston for providing an inspirational environment.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bromham, L. What is a gene for?. Biol Philos 31, 103–123 (2016). https://doi.org/10.1007/s10539-014-9472-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10539-014-9472-9