Skip to main content
Log in

Size doesn’t matter: towards a more inclusive philosophy of biology

  • Review
  • Published:
Biology & Philosophy Aims and scope Submit manuscript

Abstract

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Adl S.M., Simpson G.B., Farmer M.A. et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52: 399–451

    Google Scholar 

  • Adler J. (1969) Chemoreceptors in bacteria. Science 166: 1588–1597

    Google Scholar 

  • Allers T., Mevarech M. (2005) Archaeal genetics – the third way. Nat. Rev. Genet.6: 58–73

    Google Scholar 

  • Amann R.I., Ludwig W., Scleifer K.-H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microb. Rev. 59: 143–169

    Google Scholar 

  • Ameison J.C. (2002) On the origin, evolution, and nature of programmed cell death: a timeline of four billion years. Cell Death Differ. 9: 367–393

    Google Scholar 

  • Amend J.P., Shock E.L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthemophilic Archaea and Bacteria. FEMS Microbiol. Rev. 25: 175–243

    Google Scholar 

  • Andersson J.O. (2000) Is Buchnera a bacterium or an organelle? Curr. Biol. 10: R866–R868

    Google Scholar 

  • Andrews J.H. (1998) Bacteria as modular organisms. Annu. Rev. Microbiol. 52: 105–126

    Google Scholar 

  • Aravind L., Anantharaman V., Iyer L.M. (2003) Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective. Curr. Opin. Microbiol. 6: 490–497

    Google Scholar 

  • Atlas R.M., Bartha R. (1998) Microbial Ecology: Fundamentals and Applications (4th edn.). Benjamin/Cummings, Menlo Park, CA

    Google Scholar 

  • Avery O.T., MacLeod C.M., McCarty M. (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type III. J. Exp. Med. 79: 137–158

    Google Scholar 

  • Bäckhed F., Ley R.E., Sonnenburg J.L. et al. (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915–1920

    Google Scholar 

  • Baker M.D., Wolanin P.M., Stock J.B. (2005) Signal transduction in bacterial chemotaxis. BioEssays 28: 9–22

    Google Scholar 

  • Bassler B.L. (2002) Small talk: cell-to-cell communication in bacteria. Cell 109: 421–424

    Google Scholar 

  • Beadle G., Tatum E. (1941) Genetic control of biochemical reactions in Neurospora. PNAS 27: 499–506

    Google Scholar 

  • Beiko R.G., Harlow T.J., Ragan M.A. (2005) Highways of gene sharing in prokaryotes. PNAS 102: 14332–14337

    Google Scholar 

  • Béjà O., Aravind L., Koonin E.V. et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902–1906

    Google Scholar 

  • Bell S.D., Jackson S.P. (1998) Transcription and translation in archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6: 222–228

    Google Scholar 

  • Ben-Jacob E., Cohen I., Golding I. et al. (2000) Bacterial cooperative organization under antibiotic stress. Physica A 282: 247–282

    Google Scholar 

  • Berg R.D. (1996) The indigenous gastrointestinal microflora. Trends Microbiol. 4: 430–435

    Google Scholar 

  • Biagini G.A., Bernard C. (2000) Primitive anaerobic protozoa: a false concept? Microbiology 146: 1019–1020

    Google Scholar 

  • Bonner J.T. (1998) The origins of multicellularity. Integr. Biol. 1: 27–36

    Google Scholar 

  • Boucher Y., Nesbø C.L., Doolittle W.F. (2001) Microbial genomes: dealing with diversity. Curr. Opin. Microbiol. 4: 285–289

    Google Scholar 

  • Brandon R.N. (1999) The units of selection revisited: the modules of selection. Biol. Philos. 14: 167–180

    Google Scholar 

  • Brandon R.N., Burian R.M. (eds.) (1984) Genes, Organisms, Populations: Controversies over the Unit of Selection. MIT Press, Cambridge, MA

    Google Scholar 

  • Brehm-Stecher B.F., Johnson E.A. (2004) Single-cell microbiology: tools, technologies and applications. Microbiol. Mol. Biol. Rev. 68: 538–559

    Google Scholar 

  • Breitbart M., Felts B., Kelley S. et al. (2004) Diversity and population structure of a near-shore marine-sediment viral community. Proc. Roy. Soc. London B 271: 565–574

    Google Scholar 

  • Breitbart M., Hewson I., Felts B. et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185: 6220–6223

    Google Scholar 

  • Brock T.D. (1966) Principles of microbial ecology. Prentice-Hall, Englewood Cliffs, NJ

    Google Scholar 

  • Brock T.D. (1987) The study of microorganisms in situ: progress and problems. Sym. Soc. General Microbiol. 41: 1–17

    Google Scholar 

  • Brock T.D. (1990) The Emergence of Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Bromham L. (2002) The human zoo: endogenous retroviruses in the human genome. Trends Ecol. Evol. 17: 91–97

    Google Scholar 

  • Brown J.H. (1932) The biological approach to bacteriology. J. Bacteriol. XXIII: 1–10

    Google Scholar 

  • Brown J.R. (2001) Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst. Biol. 50: 497–512

    Google Scholar 

  • Brown S.P., Johnstone R.A. (2001) Cooperation in the dark: signalling and collective action in quorum-sensing bacteria. Proc. Roy. Soc. London B 268: 961–965

    Google Scholar 

  • Brune A., Friedrich M. (2000) Microecology of the termite gut: structure and function on a microscale. Curr. Opin. Microbiol. 3: 263–269

    Google Scholar 

  • Bryant C. (eds) (1991) Metazoan Life without Oxygen. Chapman & Hall, London

    Google Scholar 

  • Bryant D., Moulton V. (2004) Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol 21: 255–265

    Google Scholar 

  • Buckley M.R. (2004) The Global Genome Question: Microbes as the Key to Evolution and Ecology. American Academy of Microbiology, Washington, DC

    Google Scholar 

  • Bull A.T., Slater J.H. (1982a) Historical perspectives on mixed cultures and microbial communities. In: Bull A.T., Slater J.H. (eds) Microbial Interactions and Communities. Academic Press, London, UK, pp. 1–12

    Google Scholar 

  • Bull A.T., Slater J.H. (1982b) Microbial interactions and community structure. In: Bull A.T., Slater J.H. (eds) Microbial Interactions and Communities. Academic Press, London, UK, pp. 13–44

    Google Scholar 

  • Bult C.J., White O., Olsen G.J. et al. (1996) Complete genome sequence of the methanogenic archaeon. Methanococcus jannaschii, Science 273: 1058–1072

    Google Scholar 

  • Bushman F. (2001) Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Buss L.W. (1987) The Evolution of Individuality. Princeton University Press, Princeton

    Google Scholar 

  • Caldwell D.E., Atuku E., Wilkie D.C. et al. (1997) Germ theory vs. community theory in understanding and controlling the proliferation of biofilms. Adv. Dent. Res. 11: 4–13

    Article  Google Scholar 

  • Caldwell D.E., Costerton J.W. (1996) Are bacterial biofilms constrained to Darwin’s concept of evolution through natural selection? Microbiología SEM 12: 347–358

    Google Scholar 

  • Carlile M.J. (1980) From prokaryote to eukaryote: gains and losses. In: Gooday G.W., Lloyd D., Trinci A.P.J. (eds) The Eukaryotic Microbial Cell. Cambridge University Press, Cambridge, pp. 1–40

    Google Scholar 

  • Carroll S.B. (2001) Chance and necessity: the evolution of morphological complexity and diversity. Nature 409: 1102–1109

    Google Scholar 

  • Casadesús J., D’Ari R. (2002) Memory in bacteria and phage. BioEssays 24: 512–518

    Google Scholar 

  • Charlebois R.L., Beiko R.G., Ragan M.A. (2003) Microbial phylogenomics: branching out. Nature 421: 217

    Google Scholar 

  • Cho J.-C., Tiedje J.M. (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66: 5448–5456

    Google Scholar 

  • Cleland, C.E. and Copley, S.D.:2005, The possibility of alternative microbial life on earth, Int. J. Astrobiol 4: 165--173

    Google Scholar 

  • Coenye T., Gevers D., de Peer Y.V. et al. (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29: 147–167

    Google Scholar 

  • Cohan F.M. (2002) What are bacterial species? Annu. Rev. Microbiol. 56: 457–487

    Google Scholar 

  • Collins J.P. (2003) What can we learn from community genetics? Ecology 84: 574–577

    Google Scholar 

  • Colwell R.R. (1997) Microbial diversity: the importance of exploration and conservation. J. Indust. Microb. Technol. 18: 302–307

    Google Scholar 

  • Conway Morris S. (1998) The evolution of diversity in ancient ecosystems: a review. Philos. Trans. Roy. Soc. London B 353: 327–345

    Google Scholar 

  • Conway-Morris S. (2003) The Cambrian ‘explosion’ of metazoans and molecular biology: would Darwin be satisfied? Int. J. Dev. Biol. 47: 505–515

    Google Scholar 

  • Corliss J.O. (1999) Biodiversity, classification, and numbers of species of protists. In: Raven P.H. (eds) Nature and Human Society: The Quest for a Sustainable World. National Academy Press, Washington, DC, pp. 130–155

    Google Scholar 

  • Costerton B. (2004) Microbial ecology comes of age and joins the general ecology community. PNAS 101: 16983–16984

    Google Scholar 

  • Costerton J.W., Lewandowski Z., Caldwell D.E., Korber D.R., Lappin-Scott H.M. (1995) Microbial biofilms. Annu. Rev. Microbiol. 49: 711–745

    Google Scholar 

  • Croal L.R., Gralnick J.A., Malasarn D., Newman D.K. (2004) The genetics of geochemistry. Annu. Rev. Genet. 38: 175–202

    Google Scholar 

  • Crespi B.J. (2001) The evolution of social behaviour in microorganisms. TREE 16: 178–183

    Google Scholar 

  • Cutler D.W., Crump L.M. (1935) Problems in Soil Microbiology. Longmans, Green & Co., London

    Google Scholar 

  • Daims H., Lücker S., Wagner M. (2006) daime, a novel image analysis program for microbial ecology and biofilm research.Environ. Microbiol. 8: 200–213

    Google Scholar 

  • Daniel R. (2004) The soil metagenome – a rich resource for the discovery of novel natural products. Curr. Opin. Biotechnol. 15: 199–204

    Google Scholar 

  • Davey M.E., O’Toole G.A. (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol. Mol. Biol. Rev. 64: 847–867

    Google Scholar 

  • Davies D.G. (2000) Physiological events in biofilm formation. In: Allison D.G., Gilbert P., Lappin-Scott H.M., Wilson M. (eds) Community Structure and Cooperation in Biofilms. CUP, Cambridge, pp. 37–52

    Google Scholar 

  • DeLong E.F. (2002) Towards microbial systems science: integrating microbial perspective from genomes to biomes. Environ. Microbiol. 4: 9–10

    Google Scholar 

  • DeLong E.F. (2004) Reconstructing the wild types. Nature 428: 25–26

    Google Scholar 

  • DeLong E.F. (2005) Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3: 459–469

    Google Scholar 

  • DeLong E.F., Pace N.R. (2001) Environmental diversity of Bacteria and Archaea. Syst. Biol. 50: 470–478

    Google Scholar 

  • Diaz-Torres M.L., McNab R., Spratt D.A. et al. (2003) Novel tetracycline resistance determinant from the oral metagenome. Antimicrob. Agents chemother. 47: 1430–1432

    Google Scholar 

  • Dijkshoorn L., Ursing B.M., Ursing J.B. (2000) Strain, clone and species: comments on three basic concepts of bacteriology. J. Med. Microbiol. 49: 397–401

    Google Scholar 

  • Doney S.C., Abbott M.R., Cullen J.J. et al. (2004) From genes to ecosystems: the ocean’s new frontier. Front. Ecol. Environ. 2: 457–466

    Google Scholar 

  • Dixon B. (1994) Power Unseen: How Microbes Rule the World. Freeman, Oxford

    Google Scholar 

  • Doolittle W.F. (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2128

    Google Scholar 

  • Doolittle W.F. (2002) Diversity squared. Environ. Microbiol. 4: 10–12

    Google Scholar 

  • Doolittle W.F. (2005) If the tree of life fell, would we recognize the sound. In: Sapp J. (eds) Microbial Phylogeny and Evolution: Concepts and Controversies. OUP, Oxford, pp. 119–133

    Google Scholar 

  • Doolittle W.F., Boucher Y., Nesbø C.L. et al. (2003) How big is the iceberg of which organellar genes are but the tip? Philos. Trans. Roy. Soc. London B358: 39–58

    Google Scholar 

  • Douglas A.E., Raven J.A. (2002) Genomes at the interface between bacteria and organelles. Philos. Trans. Roy. Soc. London B 358: 5–18

    Google Scholar 

  • Drews G. (2000) The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. FEMS Microbiol. Rev. 24: 225–249

    Google Scholar 

  • Dunny G.M., Leonard B.A.B. (1997) Cell-cell communication in gram-positive bacteria. Annu. Rev. Microbiol. 51: 527–564

    Google Scholar 

  • Dunny, G.M. and Winans, S.C. 1999. Bacterial life: Neither lonely nor boring. In: G.M. Dunny and S.C. Winans (eds), Cell-Cell Signalling in Bacteria, ASM, Washington, DC, pp. 1–5

  • Dupré J. (2002) Humans and Other Animals. OUP, Oxford

    Google Scholar 

  • Dworkin M. (1985) Developmental Biology of the Bacteria. Benjamin/Cummings, Reading, MA

    Google Scholar 

  • Dworkin M. (1996) Recent advances in the social and developmental biology of the Myxobacteria. Microbiol. Rev. 60: 70–102

    Google Scholar 

  • Dworkin M. (1997) Multiculturism versus the single microbe. In: Shapiro J.A., Dworkin M. (eds) Bacteria as Multicellular Organisms. OUP, NY, pp. 3–13

    Google Scholar 

  • Dykhuizen D.E. (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73: 25–33

    Google Scholar 

  • Ehlers L.J. (2000) Gene transfers in biofilms. In: Allison D.G., Gilbert P., Lappin-Scott H.M., Wilson M. (eds) Community Structure and Co-operation in Biofilms. CUP, Cambridge, pp. 215–256

    Google Scholar 

  • Ehrlich P.R., Wilson E.O. (1991) Biodiversity studies: science and policy. Science 253: 758–762

    Google Scholar 

  • Eisenbach, M.:2005, Bacterial chemotaxis, Encylopedia of Life Sciences, doi: 10.1038/npg.els. 0003952

  • Engelberg H., Hazan R. (2003) Cannibals defy starvation and avoid sporulation. Science 301:467–468

    Google Scholar 

  • Faguy D.M., Jarrell K.F. (1999) A twisted tale: the origin and evolution of motility and chemotaxis in prokaryotes. Microbiology 145: 279–281

    Article  Google Scholar 

  • Falke J.J., Bass R.B., Butler S.L. et al. (1997) The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases and adaptation enzymes. Annu. Rev. Cell Develop. Biol. 13: 457–512

    Google Scholar 

  • Falkowski P.G., de Vargas C. (2004) Shotgun sequencing in the sea: a blast from the past? Science 304: 58–60

    Google Scholar 

  • Federle M.J., Bassler B.L. (2003) Interspecies communication in bacteria. J. Clin. Invest. 112: 1291–1299

    Google Scholar 

  • Feil E.J., Spratt B.G. (2001) Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 55:561–590

    Google Scholar 

  • Fenchel T. (1996) Eukaryotic life: anaerobic physiology. In: Roberts D.M., Sharp P., Alderson G., Collins M.A. (eds) Evolution of Microbial Life. CUP, Cambridge, pp. 185–203

    Google Scholar 

  • Figge R.M., Gober J.W. (2003) Cell shape, division and development: the 2002 American Society for Microbiology (ASM) conference on prokaryotic development. Mol. Microbiol. 47: 1475–1483

    Google Scholar 

  • Finlay B.J., Clarke K.J. (1999) Ubiquitous dispersal of microbial species. Nature 400: 828

    Google Scholar 

  • Finlay B.J., Maberly S.C., Cooper J.I. (1997) Microbial diversity and ecosystem function. Oikos 80: 209–213

    Google Scholar 

  • Fleischmann R.D., Adams M.D., White O. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496–512

    Google Scholar 

  • Fox G.E., Stackebrandt E., Hespell R.B. et al. (1980) The phylogeny of prokaryotes. Science 209: 457–463

    Google Scholar 

  • Fraser C.M., Gocayne J.D., White O. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397–403

    Google Scholar 

  • Gans J., Wolinsky M., Dunbar J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387–1390

    Google Scholar 

  • Genereux D.P., Logsdon Jr. J.M. (2003) Much ado about bacteria-to-vertebrate lateral gene transfer. Trends Genet. 19: 191–195

    Google Scholar 

  • Gevers D., Cohan F.M., Lawrence J.G. et al. (2005) Re-evaluating prokaryote species. Nat. Rev. Microbiol. 3: 733–739

    Google Scholar 

  • Gogarten J.P., Doolittle W.F., Lawrence J.G. (2002) Prokaryotic evolution in the light of gene transfer. Mol. Biol. Evol. 19: 2226–2238

    Google Scholar 

  • Gogarten J.P., Townsend J.P. (2005) Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3: 679–687

    Google Scholar 

  • Goodnight C.J., Stevens L. (1997) Experimental studies of group selection: what do they tell us about group selection in nature? Am. Nat. 150(Supplement): S59–S79

    Google Scholar 

  • Gould S.J. (1994) The evolution of life on earth. Sci. Am. 271: 84–91

    Google Scholar 

  • Gray K.M. (1997) Intercellular communication and group behaviour in bacteria. Trends Microbiol. 5: 184–188

    Google Scholar 

  • Grebe T.W., Stock J. (1998) Bacterial chemotaxis: the five sensors of a bacterium. Curr. Biol. 8: R154–R157

    Google Scholar 

  • Gregory T.R. (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. 76: 65–101

    Google Scholar 

  • Griffiths D.J. (2001) Endogenous retroviruses in the human genome sequence. Genome Biol. 2: 1017.1–1017.5

    Google Scholar 

  • Griffin A.S., West S.A., Buckling A. (2004) Cooperation and competition in pathogenic bacteria. Nature 430: 1024–1027

    Google Scholar 

  • Handelsman J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669–685

    Google Scholar 

  • Handelsman J., Rondon M.R., Brady S.F. et al. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5: R245–249

    Google Scholar 

  • Hausner M., Wuertz S. (1999) High rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis. Appl. Environ. Microbiol. 65: 3710–3713

    Google Scholar 

  • Henke J.M., Bassler B.L. (2004) Bacterial social engagements. Trends Cell Biol. 14: 648–656

    Google Scholar 

  • Hooper L.V., Bry L., Falk P.G., Gordon J.I. (1998) Host-microbial symbiosis in the mammalian intestine: exploring an internal ecosystem. BioEssays 20: 336–343

    Google Scholar 

  • Hooper L.V., Gordon J.I. (2001) Commensal host-bacterial relationships in the gut. Science 292: 1115–1118

    Google Scholar 

  • Hooper L.V., Wong M.H., Thelin A. et al. (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881–884

    Google Scholar 

  • Horikoshi K., Grant W.D. (eds) (1998) Extremophiles: Microbial Life in Extreme Environments. Wiley-Liss, NY

    Google Scholar 

  • Hugenholtz, Goebels B.M., Pace N.R. (1998) The impact of culture-independent studies on the emerging phylogenetic view of biodiversity. J. Bacteriol. 180: 4765–4774

    Google Scholar 

  • Hull D.L. (1987a) The ideal species concept – and why we can’t get it. In: Claridge M.F., Dawah H.A., Wilson M.R. (eds) Species: The Units of Biodiversity. Chapman and Hall, London, pp. 357–380

    Google Scholar 

  • Hull D.L. (1987b) Genealogical actors in ecological roles. Biol. Philos. 2: 168–183

    Google Scholar 

  • Huson D.H. (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68–73

    Google Scholar 

  • Iyer L.M., Aravind L., Coon S.L. et al. (2004) Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role? Trends Genet. 20: 292–299

    Google Scholar 

  • Jannasch H.W., Jones G.E. (1959) Bacterial populations in sea water as determined by different methods of enumeration. Limnol. Oceanogr. 4: 128–139

    Google Scholar 

  • Koshland Jr. D.E. (1979) A model regulatory system: bacterial chemotaxis. Physiol. Rev. 59: 811–862

    Google Scholar 

  • Jefferson K.K. (2004) What drives bacteria to produce a biofilm? FEMS Microbiol. Lett. 236: 163–173

    Google Scholar 

  • Joseph S.J., Hugenholtz P., Sangwan P. et al. (2003) Laboratory cultivation of widespread and previously uncultured bacteria. Appl. Environ. Microbiol. 69: 7210–7215

    Google Scholar 

  • Kaeberlein T., Lewis K., Epstein S.S. (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296: 1127–1129

    Google Scholar 

  • Kaiser D. (2001) Building a multicellular organism. Annu. Rev. Genet. 35: 103–123

    Google Scholar 

  • Kämpfer P., Rosselló-Mora R. (2004) The species concept for prokaryotic microorganisms – an obstacle for describing diversity? Poiesis Prax 3: 62–72

    Google Scholar 

  • Kasting J.F., Siefert J.L. (2002) Life and the evolution of earth’s atmosphere. Science 296: 1066–1068

    Google Scholar 

  • Keim C.N., Abreu F., Lins U. et al. (2004) Cell organization and ultrastructure of a magnetotactic multicellular organism. J. Struct. Biol 145: 254–262

    Google Scholar 

  • Kerr R.A. (2005) The story of O2. Science 308: 1730–1732

    Google Scholar 

  • Kitano, H. and Oda, K.: 2006, Robustness trade-offs and host-microbial symbiosis in the immune system, Molecular Systems Biology 2: 2006.0022

  • Kohler Jr. R.E. (1973) The enzyme theory and the origin of biochemistry. Isis 64: 181–196

    Google Scholar 

  • Kolenbrander P.E. (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu. Rev. Microbiol. 54: 413–437

    Google Scholar 

  • Konstantinidis K.T., Tiedje J.M. (2005) Genomic insights that advance the species definition for prokaryotes. PNAS 102: 2567–2572

    Google Scholar 

  • Koonin E.V., Makarova K.S., Aravind L. (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55: 709–742

    Google Scholar 

  • Kreft J.-U. (2004) Conflict of interest in biofilms. Biofilms 1: 265–276

    Google Scholar 

  • Kroos L., Maddock J.R. (2003) Prokaryotic development: emerging insights. J. Bacteriol. 185: 1128–1146

    Google Scholar 

  • Lan R., Reeves P.R. (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8: 396–401

    Google Scholar 

  • Lan R., Reeves P.R. (2001) When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9: 419–424

    Google Scholar 

  • Lawrence J.G. (2002) Gene transfer in bacteria: speciation without species? Theoret. Popul. Biol. 61: 449–460

    Google Scholar 

  • Lawrence J.G., Hendrickson H. (2003) Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50: 739–749

    Google Scholar 

  • Lawrence J.G., Hendrickson H. (2005) Genome evolution in bacteria: order beneath chaos. Curr. Opin. Microbiol. 8: 1–7

    Google Scholar 

  • Leadbetter J.R. (2003) Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr. Opin. Microbiol. 6: 274–281

    Google Scholar 

  • Lederberg J., Tatum E.L. (1946) Novel genotypes in mixed cultures of biochemical mutants of bacteria. Cold Spring Harbor Symp. Quant. Biol. 11: 113–114

    Google Scholar 

  • Lee K. (2004) There is biodiversity and biodiversity: implications for environmental philosophers. In: Oksanen M., Pietarinen J. (eds) Philosophy and Biodiversity. CUP, NY, pp. 152–171

    Google Scholar 

  • Lee M.S., Morrison D.A. (1999) Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J. Bacteriol. 181: 5004–5016

    Google Scholar 

  • Levin B.R., Bergstrom C.T. (2000) Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. PNAS 97: 6951–6985

    Google Scholar 

  • Lewis C.S. (1945) That Hideous Strength. Scribner, NY

    Google Scholar 

  • Lewis K. (2000) Programmed death in bacteria. Microbiol. Mol. Biol. Rev. 64: 503–514

    Google Scholar 

  • Lloyd D. (2004) ‘Anaerobic protists’: some misconceptions and confusions. Microbiology 150: 1115–1116

    Google Scholar 

  • Lloyd E.A. (1989) A structural approach to defining units of selection. Philos. Sci. 56: 395–418

    Google Scholar 

  • Lloyd E.A. (2000) Groups on groups: some dynamics and possible resolution of the units of selection debates in evolutionary biology. Biol. Philos. 15: 389–401

    Google Scholar 

  • Looijen R.C. (2000) Holism and Reductionism in Biology and Ecology: The Mutual Dependence of Higher and Lower Level Research Programmes. Kluwer, Dordrecht

    Google Scholar 

  • Loreau M., Naeem S., Inchausti P. et al. (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294: 804–808

    Google Scholar 

  • Luria S.E. (1947) Recent advances in bacterial genetics. J. Bacteriol. 11: 1–40

    Google Scholar 

  • Luria S.E., Darnell J.E., Baltimore D., Campbell A. (eds) (1978) General Virology (3rd edn.). John Wiley & Sons, NY

    Google Scholar 

  • Luria S.E., Delbrück M. (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28: 491–511

    Google Scholar 

  • Magasanik B. (1999) A midcentury watershed: the transition from microbial biochemistry to molecular biology. J. Bacteriol. 181: 357–358

    Google Scholar 

  • Maier R.M., Pepper I.L., Gerba C.P. (2000) Environmental Microbiology. Academic Press, San Diego

    Google Scholar 

  • Manchester K.L. (2000) Biochemistry comes of age: a century of endeavour. Endeavour 24: 22–27

    Google Scholar 

  • Margulis L. (1970) Origin of Eukaryotic Cells. Yale University Press, New Haven

    Google Scholar 

  • Martin W., Russell M.J. (2003) On the origin of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos. Trans. Roy. Soc. London B. 358: 59–85

    Google Scholar 

  • Martiny J.B.H., Bohannan B.J.M., Brown J.H. et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4: 102–112

    Google Scholar 

  • Maynard Smith J. (1995) Do bacteria have population genetics? In: Baumberg S., Young J.P.W., Saunders J.R., Wellington E.M.H. (eds) Population Genetics of Bacteria, Society for General Microbiology Symposium 52. CUP, Cambridge, pp. 1–12

    Google Scholar 

  • Maynard Smith J., Feil E.J., Smith N.H. (2000) Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22: 1115–1122

    Google Scholar 

  • Maynard Smith J., Smith N.H., O’Rourke M., Spratt B.G. (1993) How clonal are bacteria? Proc. Nat. Acad. Sci. 90: 4384–4388

    Google Scholar 

  • Maynard Smith J. and Szathmáry, E. 1995. The Major Transitions in Evolution. W. H. Freeman, NY

  • Mayr E. (1998) Two empires or three? PNAS 95: 9720–9723

    Google Scholar 

  • McFall-Ngai M.J. (2001) Identifying ‘prime suspects’: symbioses and the evolution of multicellularity. Compar. Biochem.Physiol. Part B 129: 711–723

    Google Scholar 

  • McFall-Ngai M.J. (2002) Unseen forces: the influence of bacteria on animal development. Develop. Biol. 242: 1–14

    Google Scholar 

  • McShea D.W. (2004) A revised Darwinism. Biol. Philos. 19: 45–53

    Google Scholar 

  • Medini D., Donati C., Tettelin H. et al. (2005) The microbial pan-genome. Curr. Opin. Genet. Develop. 15: 589–594

    Google Scholar 

  • Michod R.E. (1997a) Cooperation and conflict in the evolution of individuality. I. Multilevel selection of the organism. Am. Nat. 149: 607–645

    Google Scholar 

  • Michod R.E. (1997b) Evolution of the individual. Am. Nat. 150: S5–S21

    Google Scholar 

  • Miller M.B., Bassler B.L. (2001) Quorum sensing in bacteria. Annu. Rev. Microbiol. 55: 165–199

    Google Scholar 

  • Molin S., Tolker-Nielsen T. (2003) Gene transfer occurs with enhanced efficiency in biofilms and induces stabilisation of the biofilm structure. Curr.Opin. Biotechnol. 14: 255–261

    Google Scholar 

  • Myers G., Paulsen I., Fraser C. (2006) The role of mobile DNA in the evolution of prokaryotic genomes. In: Caporale L.H. (eds) The Implicit Genome. OUP, Oxford, pp. 121–137

    Google Scholar 

  • Nanney D. (1999) When is a rose?: the kinds of Tetrahymena. In: Wilson R.A. (eds) Species: New Unterdisciplinary Essays. MIT Press, Cambridge, MA, pp. 97–118

    Google Scholar 

  • Nee S. (2004) More than meets the eye. Nature 429: 804–805

    Google Scholar 

  • Nee S. (2005) The great chain of being. Nature 435: 429

    Google Scholar 

  • Newman D.K., Banfield J.F. (2002) Geomicrobiology: how molecular scale interactions underpin biogeochemical systems. Science 296: 1071–1077

    Google Scholar 

  • Nisbet E.G., Sleep N.H. (2001) The habitat and nature of early life. Nature 409: 1083–1091

    Google Scholar 

  • Ochman H., Lawrence J.G., Groisman E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304

    Google Scholar 

  • O’Donnell A.G., Goodfellow M., Hawksworth D.L. (1994) Theoretical and practical aspects of the quantification of biodiversity among microorganisms. Philos.Trans. Roy. Soc. London B 345: 65–73

    Google Scholar 

  • Okasha S. (2003) Recent work on the levels of selection problem. Human Nat. Rev. 3: 349–356

    Google Scholar 

  • Okasha, S. 2004. Multi-level selection and the major transitions in evolution. Proceedings PSA 19th Biennial Meeting – PSA 2004: PSA Contributed Papers, Austin, Texas, PSA

  • Oksanen M., Pietarinen J. (2004) Philosophy and Biodiversity. CUP, NY

    Google Scholar 

  • Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R. (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337–365

    Google Scholar 

  • Olsen G.J., Woese C.R., Overbeek R. (1994) The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176: 1–6

    Google Scholar 

  • O’Malley M.A., Boucher Y. (2005) Paradigm change in evolutionary microbiology. Stud. Hist. Philos. Biol. Biomed. Sci. 36: 183–208

    Google Scholar 

  • O’Toole G., Kaplan H.B., Kolter R. (2000) Biofilm formation as microbial development. Annu. Rev. Microbiol. 54: 49–79

    Google Scholar 

  • Pääbo S. (2001) The human genome and our view of ourselves. Science 291: 1219–1220

    Google Scholar 

  • Pace N.R. (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740

    Google Scholar 

  • Palys T., Nakamura L.K., Cohan F.M. (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47: 1145–1156

    Article  Google Scholar 

  • Papke R.T., Ward D.M. (2004) The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48: 293–303

    Google Scholar 

  • Park S., Wolanin P.M., Yuzbashyan E.A., Silberzan P., Stock J.B., Austin R.H. (2003) Motion to form a quorum. Science 301: 188

    Google Scholar 

  • Parker V.T. (2004) The community of an individual: implications for the community concept. Oikos 104: 27–34

    Google Scholar 

  • Parsek M.R., Fuqua C. (2004) Biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life. J. Bacteriol. 186: 4427–4440

    Google Scholar 

  • Pauling L., Zuckerkandl E. (1963) Chemical paleogenetics: molecular “restoration studies” of extinct forms of life. Acta Chem. Scand. 17: S9–S16

    Article  Google Scholar 

  • Penn M., Dworkin M. (1976) Robert Koch and two visions of microbiology. Bacteriol. Rev. 40: 276–283

    Google Scholar 

  • Peterson S.N., Sung C.K., Kline R. et al. (2004) Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays. Mol. Microbiol. 51: 1051–1070

    Google Scholar 

  • Postgate J.R. (1976) Death in macrobes and microbes. In: Gray T.R.G., Postgate J.R. (eds) The Survival of Vegetative Microbes. Cambridge University Press, Cambridge, pp. 1–18

    Google Scholar 

  • Price P.B. (2000) A habitat for psychrophiles in deep Antarctic ice. PNAS 97: 1247–1251

    Google Scholar 

  • Queller D.C. (2004) Kinship is relative. Nature 430: 975–976

    Google Scholar 

  • Raoult D., Audic S., Robert C. et al. (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306: 1344–1350

    Google Scholar 

  • Reanney D.C., Roberts W.P., Kelly W.J. (1982) Genetic interactions among microbial communities. In: Bull A.T., Slater J.H. (eds) Microbial Interactions and Communities. Academic Press, London, UK, pp. 287–322

    Google Scholar 

  • Redfield R.J. (2002) Is quorum sensing a side effect of diffusion sensing? Trends Microbiol. 10: 365–370

    Google Scholar 

  • Relman D.A., Falkow S. (2001) The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 9: 206–208

    Google Scholar 

  • Rice K.C., Bayles K.W. (2003) Death’s toolbox, examining the molecular components of bacterial programmed cell death. Mol. Microbiol. 50: 729–738

    Google Scholar 

  • Riesenfeld C.S., Schloss P.D., Handelsman J. (2004) Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525–552

    Google Scholar 

  • Robert J.S. (2004) Embryology, Epigenesis, and Evolution: Taking Development Seriously. CUP, Cambridge

    Google Scholar 

  • Rodríguez-Valera F. (2002) Approaches to prokaryotic diversity: a population genetics approach. Environ. Microbiol. 4: 628–633

    Google Scholar 

  • Rodríguez-Valera F. (2004) Environmental genomics: the big picture. FEMS Microbiol. Lett. 231: 153–158

    Google Scholar 

  • Rohwer F. (2003) Global phage diversity. Cell 113: 141

    Google Scholar 

  • Roselló-Mora R., Amann R. (2001) The species concept for prokaryotes. FEMS Microbiol. Rev. 25: 39–67

    Google Scholar 

  • Sapp J. (1987) Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. OUP, NY

    Google Scholar 

  • Sapp J. (2003) Genesis: The Evolution of Biology. OUP, Oxford

    Google Scholar 

  • Sapp J. (2005) The prokaryote-eukaryote dichotomy: meanings and mythology. Microbiol. Mol. Biol. Rev. 69: 292–305

    Google Scholar 

  • Sarkar S. (2002) Defining “biodiversity”: assessing biodiversity. Monist 85: 131–155

    Google Scholar 

  • Saunders N.J., Boonmee P., Peden J.F., Jarvis S.A. (2005) Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori. BMC Genomics 6(1): 9

    Google Scholar 

  • Savage D.C. (1977) Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31: 107–133

    Google Scholar 

  • Schloss P.D., Handelsman J. (2004) Status of the microbial census. Microbiol. Mol. Biol. Rev. 68: 686–691

    Google Scholar 

  • Schmeisser C., Stöckigt C., Raasch C. et al. (2003) Metagenome survery of biofilms in drinking-water networks. Appl. Environ. Microbiol. 69: 7298–7309

    Google Scholar 

  • Schoolnik G.K. (2001) The accelerating convergence of genomics and microbiology. Genome Biol. 2: 4009.1–4009.2

    Google Scholar 

  • Schulz H.N., Jørgensen B.B. (2001) Big bacteria. Annu. Rev. Microbiol. 55: 105–137

    Google Scholar 

  • Shapiro J.A. (1997) Multicellularity: the rule, not the exception. In: Shapiro J.A., Dworkin M. (eds) Bacteria as Multicellular Organisms. OUP, NY, pp. 14–49

    Google Scholar 

  • Shapiro J.A. (1998) Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52: 81–104

    Google Scholar 

  • Shapiro J.A., Dworkin M. (eds) (1997) Bacteria as Multicellular Organisms. OUP, NY

    Google Scholar 

  • Shimkets L.J. (1999) Intercellular signalling during fruiting-body development of Myxococcus xanthus. Annu. Rev. Microbiol. 53: 525–549

    Google Scholar 

  • Shimkets L.J., Brun Y.V. (2000) Prokaryotic development: strategies to enhance survival. In: Brun Y.V., Shimkets L.J. (eds) Prokaryotic Development. ASM Press, Washington, DC

    Google Scholar 

  • Shiner E.K., Rumbaugh K.P., Williams S.C. (2005) Interkingdom signaling: deciphering the language of acyl homoserine lactones. FEMS Microbiol. Rev. 29: 935–947

    Google Scholar 

  • Simpson A.G.B., Roger A.J. (2004) The real ‘kingdoms’ of eukaryotes. Curr. Biol. 14: R693–R696

    Google Scholar 

  • Slater J.H., Bull A.T. (1978) Interactions between microbial populations. In: Bull A.T., Meadow P.M. (eds) Companion to Microbiology: Selected Topics for Further Study. Longman, London, pp. 181–206

    Google Scholar 

  • Sober E., Wilson D.S. (1994) A critical review of philosophical work on the units of selection problem. Philos. Sci. 61: 534–555

    Google Scholar 

  • Solomon J.M., Grossman A.D. (1996) Who’s competent and when: regulation of natural competence in bacteria. Trends Genet. 12: 150–155

    Google Scholar 

  • Sonea S., Mathieu L.G. (2001) Evolution of the genomic systems of prokaryotes and its momentous consequences. Int. Microbiol. 4: 67–71

    Google Scholar 

  • Stackebrandt E., Frederisksen W., Garrity G.M. et al. (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043–1047

    Google Scholar 

  • Staley J.T. (1997) Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol. 8: 340–345

    Google Scholar 

  • Stahl D.A., Lane D.J., Olsen G.J., Pace N.R. (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl. Environ. Microbiol. 49: 1379–1384

    Google Scholar 

  • Stahl D.A., Tiedje J.M. (2002) Microbial Ecology and Genomics: A Crossroads of Opportunity. American Academy of Microbiology, Washington, DC

    Google Scholar 

  • Staley J.T., Gosink J.J. (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53: 189–215

    Google Scholar 

  • Staley J.T., Konopka A. (1985) Measurements of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39: 321–346

    Google Scholar 

  • Stanier R.Y., Doudoroff M., Adelberg E.A. (1957) The Microbial World. Prentice-Hall, Englewood Cliffs, NJ

    Google Scholar 

  • Stanier R.Y., Van Niel C.B. (1941) The main outlines of bacterial classification. J. Bacteriol. 42: 437–466

    Google Scholar 

  • Stanier R.Y., van Niel C.B. (1962) The concept of a bacterium. Archiv für Mikrobiol. 42: 17–35

    Google Scholar 

  • Sterelny K. (1999) Species as ecological mosaics. In: Wilson R.A. (eds) Species: New Interdisciplinary Essays. MIT Press, Cambridge, MA, pp. 119–138

    Google Scholar 

  • Sterelny K. (2004) Symbiosis, evolvability and modularity. In: Schlosser G., Wagner G.P. (eds) Modularity in Evolution and Development. University of Chicago Press, Chicago, pp. 490–518

    Google Scholar 

  • Sterelny K., Griffiths P.E. (1999) Sex and Death: An Introduction to the Philosophy of Biology. University of Chicago Press, Chicago

    Google Scholar 

  • Stewart P.S., Costerton J.W. (2001) Antibiotic resistance of bacteria in biofilms. The Lancet 358: 135–138

    Google Scholar 

  • Stoodley P., Sauer K., Davies D.G., Costerton J.W. (2002) Biofilms as complex differentiated communities. Annu. Rev. Microbiol. 56: 187–209

    Google Scholar 

  • Summers W.C. (1991) From culture as organism to organism as cell: historical origins of bacterial genetics. J. Hist. Biol. 24: 171–190

    Google Scholar 

  • Suttle C.A. (2005) Viruses in the sea. Nature 437: 356–644

    Google Scholar 

  • Thomas C.M., Nielsen K.M. (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3: 711–721

    Google Scholar 

  • Travisano M., Velicer G.J. (2004) Strategies of microbial cheater control. Trends Microbiol. 12: 72–78

    Google Scholar 

  • Tyson G.W., Chapman J., Hugenholz P. et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43

    Google Scholar 

  • Underwood A.J. (1996) What is a community? In: Raup D.M., Jablonski D. (eds) Patterns and Processes in the History of Life. Springer-Verlag, Berlin, pp. 351–367

    Google Scholar 

  • van Haastert P.J.M., Devreotes P.N. (2004) Chemotaxis: signalling the way forward. Nat. Rev. Mol. Cell Biol. 5: 626–634

    Google Scholar 

  • Vandamme P., Pot B., Gillis M. et al. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407–438

    Google Scholar 

  • Velicer G.J. (2003) Social strife in the microbial world. Trends Microbiol. 11: 330–337

    Google Scholar 

  • Venter J.C., Remington K., Heidelberg J.F. et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74

    Google Scholar 

  • Villarreal L.P. (2004a) Are viruses alive? Sci. Am. 291: 100–105

    Article  Google Scholar 

  • Villarreal L.P. (2004b) Can viruses make us human? Proc. Am. Philos. Soc. 148: 296–323

    Google Scholar 

  • Visick K.L., Fuqua C. (2005) Decoding microbial chatter: cell-cell communication in bacteria. J. Bacteriol. 187: 5507–5519

    Google Scholar 

  • Wadhams G.H., Armitage J.P. (2004) Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 5: 1024–1037

    Google Scholar 

  • Waggoner B. (2001) Eukaryotes and multicells: origins, Encyclopedia of Life Sciences, http://www.els.net

  • Wainwright M. (2003) An alternative view of the early history of microbiology. Adv. Appl. Microbiol. 52: 333–355

    Google Scholar 

  • Walsh D.A., Doolittle W.F. (2005) The real ‘domains’ of life. Curr. Biol. 15: R237–R240

    Google Scholar 

  • Ward B.B. (2002) How many species of prokaryotes are there? PNAS 99: 10234–10236

    Google Scholar 

  • Ward D.M. (1998) A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1: 271–277

    Google Scholar 

  • Ward N., Fraser C.M. (2005) How genomics has affected the concept of microbiology. Curr. Opin. Microbiol. 8: 564–571

    Google Scholar 

  • Watnick P., Kolter R. (2000) Biofilm, city of microbes. J. Bacteriol. 182: 2675–2679

    Google Scholar 

  • Webb J.S., Givskov M., Kjelleberg S. (2003) Bacterial biofilms: prokaryotic adventures in multicellularity. Curr. Opin. Microbiol. 6: 578–585

    Google Scholar 

  • Webre D.J., Wolanin P.M., Stock J.B. (2003) Bacterial chemotaxis. Curr. Biol. 13: R47–R49

    Google Scholar 

  • Weinbauer M.G., Rassoulzadegan F. (2004) Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6: 1–11

    Google Scholar 

  • Wertz J.E., Goldstone C., Gordon D.M., Riley M.A. (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J. Evol. Biol. 16: 1236–1248

    Google Scholar 

  • Whitaker R.J., Grogan D.W., Taylor J.W. (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976–978

    Google Scholar 

  • Whitham T.G., Young W.P., Martinsen G.D. et al. (2003) Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 84: 559–573

    Google Scholar 

  • Whitman W.B., Coleman D.C., Wiebe W.J. (1998) Prokaryotes: the unseen majority. PNAS 95: 6578–6583

    Google Scholar 

  • Wilkins J.S. (2003) How to be a chaste species pluralist-realist: the origin of species modes and the synapomorphic species concept. Biol. Philos.18: 621–638

    Google Scholar 

  • Wilson D.S. (1997) Altruism and organism: disentangling the themes of multilevel selection theory. Am. Nat. 150(Supplement): S122–S134

    Google Scholar 

  • Wimpenny J. (2000) An overview of biofilms as functional communities. In: Allison D.G., Gilbert P., Lappin-Scott H.M., Wilson M. (eds) Community Structure and Cooperation in Biofilms. CUP, Cambridge, pp. 1–24

    Google Scholar 

  • Woese C.R. (1987) Bacterial evolution. Microb. Rev. 51: 221–271

    Google Scholar 

  • Woese C.R. (2005) Evolving biological organization. In: Sapp J. (eds) Microbial Phylogeny and Evolution: Concepts and Controversies. OUP, Oxford, pp. 99–117

    Google Scholar 

  • Woese C.R., Fox G.G. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS 11: 5088–5090

    Google Scholar 

  • Woese C.R., Kandler O., Wheelis M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 87: 4576–4579

    Google Scholar 

  • Xu J., Gordon J.I. (2003) Honor thy symbionts. PNAS 100: 10452–10459

    Google Scholar 

  • Young J.M. (2001) Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int. J. Syst. Evol. Microbiol. 51: 945–953

    Google Scholar 

  • Zuckerkandl E., Pauling L. (1965) Molecules as documents of evolutionary history. J. Theoret. Biol. 8: 357–366

    Google Scholar 

Download references

Acknowledgements

Many thanks to our anonymous referee for very helpful advice and detailed comments; to Staffan Müller-Wille, Jane Calvert and Jim Byrne for feedback; and also to the audiences at the first International Biohumanties Conference (Queensland, 2005) and the International Society for the History, Philosophy and Social Studies of Biology conference (Guelph, 2005). We gratefully acknowledge research support from the UK Economic and Social Research Council (ESRC), the Arts and Humanities Research Council (AHRC), and Overseas Conference Funding from the British Academy. The research in this paper was part of the programme of the ESRC Research Centre for Genomics in Society (Egenis).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Maureen A. O’Malley.

Rights and permissions

Reprints and permissions

About this article

Cite this article

O’Malley, M.A., Dupré, J. Size doesn’t matter: towards a more inclusive philosophy of biology. Biol Philos 22, 155–191 (2007). https://doi.org/10.1007/s10539-006-9031-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10539-006-9031-0

Keywords

Navigation