Skip to main content

Pluralism or unity in biology: could microbes hold the secret to life?

Abstract

Pluralism is popular among philosophers of biology. This essay argues that negative judgments about universal biology, while understandable, are very premature. Familiar life on Earth represents a single example of life and, most importantly, there are empirical as well as theoretical reasons for suspecting that it may be unrepresentative. Scientifically compelling generalizations about the unity of life (or lack thereof) must await the discovery of forms of life descended from an alternative origin, the most promising candidate being the discovery of extraterrestrial life. Nonetheless, in the absence of additional examples of life, we are best off exploring the microbial world for promising explanatory concepts, principles, and mechanisms rather than prematurely giving up on universal biology. Unicellular microbes (especially prokaryotes) are by far the oldest, metabolically most diverse, and environmentally tolerant form of life on our planet. Yet somewhat ironically, much of our theorizing about life still implicitly privileges complex multicellular eukaryotes, which are now understood to be highly specialized, fragile latecomers to Earth. The problem with pursuing a pluralist approach to understanding life is that it is likely to blind us to the significance of just those entities and causal processes most likely to shed light on the underlying nature of life.

This is a preview of subscription content, access via your institution.

Notes

  1. 1.

    RNA viruses, which store hereditary information as RNA, are the only known exceptions.

  2. 2.

    The term ‘microbe’ is used loosely even among microbiologists. All microbiologists include prokaryotes (Archaea and Bacteria) and unicellular eukaryotes (e.g., protozoa). Many uses of the label also include acellular viruses, and some include microscopic multicellular eukaryotes (e.g., rotifers) as “microbes.” My focus in this paper is on prokaryotes.

  3. 3.

    Not everyone agrees, however (Kurland et al. 2006).

  4. 4.

    And viruses in turn outnumber them (Edwards and Rohwer 2005; Rohwer and Barott this issue). Viruses are found in large numbers in every microbial community and play a central role in microbial evolution as a source of genetic variation.

  5. 5.

    The concept of species is highly problematic for prokaryotes. I will have more to say about this in the next section.

  6. 6.

    And of course their acellular viral companions, who are critical to the structure and dynamics of the microbial world (Suttle 2007) and are discussed elsewhere in this special issue (Rohwer and Barott this issue).

  7. 7.

    It is important to keep in mind that a scientifically compelling universal theory of life is unlikely to explain all biological phenomena on our particular planet any more than knowledge of basic physics and chemistry can explain all geological phenomena occurring on our planet. Knowledge of the basic chemistry of water, for instance, cannot tell us the source of Earth’s supply of water (volcanism), or what causes monsoons, or droughts. Similarly, knowledge of the chemistry of water cannot tell us whether Mars was ever wet for an extended period of time or whether it merely experienced sudden, high volume flows for brief periods of time; this is a hotly debated question among planetary scientists. The point is it is unrealistic to expect a universal theory of life to explain all the details of life on a particular planet, such as our Earth, since many of them will be contingent upon extraneous conditions. Critics of the prospects for universal biology sometimes ignore this important point.

  8. 8.

    Horizontal gene transfer also goes under the label “lateral gene transfer” (aka LGT).

  9. 9.

    It is important to keep in mind that explaining water in terms of its molecular composition is not the same as identifying water with it (Cleland 2012, pp. 138–139). A single molecule of H2O lacks temperature and pressure. Moreover many of the distinctive phenomenal properties of water (mentioned above) result from secondary structures (dimers, trimers, and hydrogen bonded networks) produced by “weak” hydrogen bonds among H2O molecules, and the purest samples of liquid water are not composed of just H2O molecules because they invariable dissociate into ions (H+, OH, and H3O+) when combined together; for more on the chemistry of water, see (Snoeyink and Jenkins 1980). Nonetheless modern chemistry explains the behavior of water by reference to its molecular composition in the context of molecular theory.

References

  1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2007) Molecular Biology of the Cell (Fourth Addition). Garland Science, New York

    Google Scholar 

  2. Allwood AC, Grotzinger JP, Knoll AH, Burch IW, Anderson MS, Coleman ML, Kanik I (2009) Controls on development and diversity of Early Archean stromatolites. Proc Natl Acad Sci USA 106:9548–9555

    Article  Google Scholar 

  3. Anbar AD, Ariel D, Zahnle KJ, Arnold GL, Mojzsis SJ (2001) Extraterrestrial iridium, sediment accumulation and the habitability of the early Earth’s surface. J Geophys Res 106:3219–3236

    Article  Google Scholar 

  4. Baross JA, Benner SA, Cody GD, Copley SD, Pace NR, Scott JA, Shapiro R, Sogin ML, Stein JL, Summons R, Szostak JW (2007) The limits to organic life in planetary systems. National Academy Press, Washington DC

  5. Benner SA (1994) Expanding the genetic lexicon: incorporating nonstandard amino acids into proteins by ribosome-based synthesis. Trends Biotechnol 12:158–163

    Article  Google Scholar 

  6. Benner SA (2004) Understanding nucleic acids using synthetic chemistry. Acc Chem Res 37:784–797

    Article  Google Scholar 

  7. Benner SA, Hutter D (2002) Phosphates, DNA, and the search for nonterran life: a second generation model for genetic molecules. Bioorg Chem 30:62–80

    Article  Google Scholar 

  8. Benner SA, Ricardo A, Carrigan MA (2004) Is there a common chemical model for life in the universe? Curr Opin Chem Biol 8:672–689

    Article  Google Scholar 

  9. Boto L (2010) Horizontal gene transfer in evolution: facts and challenges. Proc R Soc B 277:819–827

    Article  Google Scholar 

  10. Chicote E, Garcia AM, Moreno DA, Sarró MI, Lorenzo PI, Montero F (2005) Isolation and identification of bacteria from spent nuclear fuel pools. J Ind Microbiol Biotechnol 32:155–162

    Article  Google Scholar 

  11. Cleland CE (2007) Epistemological issues in the study of microbial life: alternative terran biospheres? Stud Hist Philos Biol Biomed Sci 38:847–861

    Google Scholar 

  12. Cleland CE (2012) Life without definitions. Synthese 185:125–144

    Article  Google Scholar 

  13. Cleland CE, Copley SD (2005) The possibility of alternative microbial life on Earth. Int J Astrobiol 4:165–173

    Article  Google Scholar 

  14. Dagan T, Artzy-Randrup Y, Martin W (2008) Molecular networks and cumulative impact of lateral gene transfer in prokaryotic genome evolution. Proc Natl Acad Sci USA 105:10039–10044

    Article  Google Scholar 

  15. Dawkins R (1983) Universal Darwinism. In: Bendall DS (ed) Evolution from molecules to man. Cambridge University Press, Cambridge, pp 403–425

    Google Scholar 

  16. Delong EF, Pace NR (2001) Environmental diversity of Bacteria and Archaea. Syst Biol 50:470–478

    Article  Google Scholar 

  17. Dobzhansky T (1973) Nothing in biology makes sense except in light of evolution. Am Biol Teacher 35:125–129

    Article  Google Scholar 

  18. Doolittle WF, Papke RT (2006) Genomics and the bacterial species problem. Genome Biol 7:116.1–116.7

    Google Scholar 

  19. Dupré J (1993) The Disorder of Things. Harvard University Press, Harvard

    Google Scholar 

  20. Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Microbiol 3:504–510

    Article  Google Scholar 

  21. Ereshefsky M (1998) Species pluralism and anti-realism. Philos Sci 65:103–120

    Article  Google Scholar 

  22. Ereshefsky M (2010) Microbiology and the species problem. Biol Philos 25:553–568

    Article  Google Scholar 

  23. Folse HJ III, Roughgarden J (2010) What is an individual organism? A multilevel selection perspective. Q Rev Biol 85:447–472

    Article  Google Scholar 

  24. Franklin LR (2007) Bacteria, sex, and systematics. Philos Sci 74:69–95

    Article  Google Scholar 

  25. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323:741–746

    Article  Google Scholar 

  26. Hempel CG, Oppenheim P (1948) Studies in the logic of explanation. Philos Sci 15:135–175

    Article  Google Scholar 

  27. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    Google Scholar 

  28. Keller EF (2002) Making Sense of Life: Explaining Biological Development with Models. Harvard University Press, Cambridge, MA, Metaphors and Machines

    Google Scholar 

  29. Knoll AH (2011) The multiple origins of complex multicellularity. Annu Rev Earth Planet 39:217–239

    Article  Google Scholar 

  30. Knoll AH, Javaux EJ, Hewitt D, Cohen P (2006) Eukaryotic organisms in Proterozoic oceans. Philos Trans R Soc B 361:1023–1038

    Article  Google Scholar 

  31. Koonin EV (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res 37:1011–1034

    Article  Google Scholar 

  32. Koonin EV (2010) Origin and early evolution of eukaryotes in the light of metagenomics. Genome Biol 11:1–12

    Article  Google Scholar 

  33. Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709–742

    Article  Google Scholar 

  34. Kurland CG, Collins LJ, Penny D (2006) Genomics and the irreducible nature of eukaryote cells. Science 312:1011–1014

    Article  Google Scholar 

  35. Machamer P, Darden L, Craver CF (2000) Thinking about mechanisms. Philos Sci 67:1–25

    Article  Google Scholar 

  36. Madigan MT, Martinko JM (2006) Brock Biology of Microorganisms. Pearson Prentice Hall, San Francisco

    Google Scholar 

  37. Magner LN (2002) A history of the life sciences. Mercel Dekker, Inc., New York

    Book  Google Scholar 

  38. McDonald D, Vasques-Baeza Y, Walters WA, Caporaso JG, Knight R (this issue) From molecules to dynamic biological communities. Biol Philos. doi: 10.1007/s10539-013-9364-4

  39. Meierhenrich U (2008) Amino Acids and the Asymmetry of Life. Springer-Verlag, Berlin Heidelberg

    Google Scholar 

  40. Mishler BD, Brandon RN (1987) Individuality, pluralism, and the phylogenetic species concept. Biol Philos 2:397–414

    Article  Google Scholar 

  41. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL (1996) Evidence for life on Earth before 3,800 million years ago. Nature 383:55–59

    Article  Google Scholar 

  42. Nagel E (1949) The Meaning of reduction in the natural sciences. In: Stauffer RC (ed) Science and civilization. University of Wisconsin Press, Madison, pp 99–138

    Google Scholar 

  43. Nealson KH, Conrad PG (1999) Life: past, present and future. Philos Trans R Soc B 354:1923–1939

    Article  Google Scholar 

  44. Needham P (2002) The discovery that water is H2O. Int Stud Philos of Sci 16:205–226

    Article  Google Scholar 

  45. Nielsen PE, Egholm M (1999) An introduction to peptide nucleic acid. Current Issue Mol Biol 1:89–1104

    Google Scholar 

  46. O’Malley M, Dupré J (2007) Metagenomics and biological ontology. Stud Hist Philos Biol Biomed Sci 38:834–846

    Google Scholar 

  47. Oren A (2004) Prokaryote diversity and taxonomy: current status and future challenges. Philos Trans R Soc Lond B 359:623–638

    Article  Google Scholar 

  48. Oren A (2009) Systematics of archaea and bacteria. In: Minelli A, Contrfatto G (eds) Biological science fundamentals and systematics (vol. II). EOLSS Pubs, Oxford

  49. Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew S, McLaughlin SH, Herdewijn P, Holliger P (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336:341–344

    Article  Google Scholar 

  50. Pizzarello S, Shock E (2010) The organic composition of carbonaceous meteorities: the evolutionary story ahead of biochemistry. Cold Spring Harb Perspect Biol 2:1–19

    Article  Google Scholar 

  51. Powner MW, Sutherland JD (2011) Prebiotic chemistry: a new modus operandi. Philos Trans R Soc B 366:2870–2877

    Article  Google Scholar 

  52. Rohwer F, Barott K (this issue) Viral information. Biol Philos. doi: 10.1007/s10539-012-9344-0

  53. Rokas A (2008) The origins of multicellularity and the early history of the genetic toolkit for animal development. Annu Rev Genet 42:235–251

    Article  Google Scholar 

  54. Ryder G (2002) Mass flux in the ancient Earth–Moon system and benign implications for the origin of life on Earth. J Geophys Res E 107:1–6

    Article  Google Scholar 

  55. Sapp J (2003) Genesis: the evolution of biology. Oxford University Press, Oxford

    Google Scholar 

  56. Schmitt-Kopplin P, Gabelico Z, Gougeon RD, Fekete A, Kanawati B, Harir M, Gebefuegi I, Eckel G, Hertkorn N (2010) High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall. Proc Natl Acad Sci USA 107:2763–2768

    Article  Google Scholar 

  57. Schultze-Makuch D, Irwin LN (2006) The prospect of alien life in exotic forms in other worlds. Naturwissenschaften 93:155–172

    Article  Google Scholar 

  58. Schultze-Makuch D, Irwin LN (2008) Life in the Universe: Expectations and Constraints. Springer-Verlag, Berlin

    Book  Google Scholar 

  59. Shapiro R (2000) A replicator was not involved in the origin of life. IUBMB Life 49:173–176

    Google Scholar 

  60. Shen B, Dong L, Xiao S, Kowalewksi M (2008) The avalon explosion: evolution of Ediacara morphospace. Science 319:81–84

    Article  Google Scholar 

  61. Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77:1153–1161

    Article  Google Scholar 

  62. Smith E, Morowitz H (2004) Universality in intermediary metabolism. Proc Natl Acad Sci USA 101:13168–13173

    Article  Google Scholar 

  63. Snoeyink VL, Jenkins D (1980) Water chemistry. Wiley, New York

  64. Suttle CA (2007) Marine viruses—major players in the global ecosystem. Nature Rev Microb 5:801–812

    Article  Google Scholar 

  65. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804–810

    Article  Google Scholar 

  66. Wacey D, Kilburn MR, Saunders M, Cliff J, Brasier MD (2011) Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Eestern Australia. Nature Geosci 4:698–702

    Article  Google Scholar 

  67. Ward PD, Brownlee D (2000) Rare Earth: Why complex life is uncommon in the universe. Springer-Verlag, New York

    Google Scholar 

  68. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposals for the domains of Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  Google Scholar 

  69. Yang Z, Chen F, Alvarado JB, Benner SA (2011) Amplification, mutation, and sequencing of a six-letter synthetic genetic system. J Am Chem Soc 133:15105–15112

    Article  Google Scholar 

  70. Zarraonaindia I, Smith DP, Gilbert JA (this issue) Beyond the genome: community-level analysis of the microbial world. Biol Philos. doi: 10.1007/s10539-012-9357-8

Download references

Acknowledgments

I am very grateful to Maureen O’Malley for comments on the manuscript during its development. I would also like to thank two anonymous reviewers for comments on the original version.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Carol E. Cleland.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Cleland, C.E. Pluralism or unity in biology: could microbes hold the secret to life?. Biol Philos 28, 189–204 (2013). https://doi.org/10.1007/s10539-013-9361-7

Download citation

Keywords

  • Archaea
  • Bacteria
  • Eukarya
  • Explanation
  • Prokaryote
  • Eukaryote
  • Pluralism
  • Reduction
  • Universal theory of life