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Lifeness signatures and the roots of the tree of life

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Abstract

Do trees of life have roots? What do these roots look like? In this contribution, I argue that research on the origins of life might offer glimpses on the topology of these very roots. More specifically, I argue (1) that the roots of the tree of life go well below the level of the commonly mentioned ‘ancestral organisms’ down into the level of much simpler, minimally living entities that might be referred to as ‘protoliving systems’, and (2) that further below, a system of roots gradually dissolves into non-living matter along several functional dimensions. In between non-living and living matter, one finds physico-chemical systems that I propose to characterize by a ‘lifeness signature’. In turn, this ‘lifeness signature’ might also account for a diverse range of biochemical entities that are found to be ‘less-than-living’ yet ‘more-than-non-living’.

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Notes

  1. The term “protoliving system” has been used in origins of life studies with the meaning of rudimentary, primordial -and potentially minimal- living systems (Fox 1991) It is with this meaning that I use the term here. This meaning might be found to be synonymous to that of “protocell” even though protoliving systems do not require, strictly speaking, to be cell-like. Also, the term “protocell” is now often used in synthetic biology with a broader meaning, for instance including systems made out of non-prebiotically compatible compounds or resulting from artificial life research (e.g. Rasmussen et al. 2009) than the initial meaning it had in origins of life studies (e.g. Krampitz and Fox 1969; Stillwell 1980; de Duve 1991).

  2. Such dimensions might correspond to properties of “list-based” definitions or relate to the functioning characteristics of the models involved in “model-based” definitions of life.

References

  • Ashkenasy G, Jagasia R, Yadav M, Ghadiri MR (2004) Design of a directed molecular network. Proc Natl Acad Sci USA 101(30):10872–10877

    Article  Google Scholar 

  • Augier A (1801) Essai d’une nouvelle classification des végétaux. Bruyset, Lyon

    Google Scholar 

  • Bachmann PA, Luisi PL, Lang J (1992) Autocatalyic self-replicating micelles as models for prebiotic structures. Nature 357:57–59

    Article  Google Scholar 

  • Bernal JD (1967) The origin of life. Weidenfeld and Nicolson, London

    Google Scholar 

  • Brasier M, McLoughlin N, Green O, Wacey D (2006) A fresh look at the fossil evidence for early Archaean cellular life. Phil Trans R Soc B 361(1470):887–902

    Article  Google Scholar 

  • Bruylants G, Bartik K, Reisse J (2010) Is it useful to have a clear-cut definition of life? On the use of fuzzy logic in prebiotic chemistry. Orig Life Evol Biosph 40(2):137–143

    Article  Google Scholar 

  • Commeyras A, Taillades J, Collet H, Boiteau L, Vandenabeele-Trambouze O, Pascal R, Rousset A, Garrel L, Rossi JC, Biron JP, Lagrille O, Plasson R, Souaid E, Danger G, Selsis F, Dobrijévic M, Martin H (2004) Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. Orig Life Evol Biosph 34:35–55

    Article  Google Scholar 

  • Crick F (1981) Life itself: its origin and nature. Simon and Schuster, New York

    Google Scholar 

  • Darwin CR (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, 1st edn. John Murray, London. http://darwin-online.org.uk/

  • de Duve C (1991) Blueprint for a Cell: The Nature and Origin of Life. Patterson, Burlington NC

    Google Scholar 

  • Deamer D (1985) Boundary structures are formed by organic components of the Murchison carbonaceous chondrite. Nature 317:792–794

    Article  Google Scholar 

  • Despois D, Gargaud M (2006) A synthetic interdisciplinary ‘‘chronological frieze’’: an attempt. Earth Moon Planets 98:291–297

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Dworkin JP, Lazcano A, Miller SL (2003) The roads to and from the RNA world. J Theor Biol 222:127–134

    Article  Google Scholar 

  • Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Microbiol 3(6):504–510

    Article  Google Scholar 

  • Eschenmoser A (2007) The search for the chemistry of life’s origin. Tetrahedron 63:12821–12844

    Article  Google Scholar 

  • Farmer JD, Belin A (1992) Artificial life: the coming evolution. In: Langton CG, Taylor C, Farmer JD, Rasmussen S (eds) Artificial life II, Santa Fe Institute studies in the sciences of complexity proceedings, vol X. Addison-Wesley, Redwood City, pp 815–838

    Google Scholar 

  • Fitch WM, Upper K (1987) The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harb Symp Quant Biol 52:759–767

    Google Scholar 

  • Forterre P (2002) The origin of DNA genomes and DNA replication proteins. Curr Opin Microbiol 5:525–532

    Article  Google Scholar 

  • Forterre P, Philippe H (1999) The last universal common ancestor (LUCA), simple or complex? Biol Bull 196:373–377

    Article  Google Scholar 

  • Fox SW (1991) Synthesis of life in the lab? Defining a protoliving system. Q Rev Biol 66(2):181–185

    Article  Google Scholar 

  • Gánti T ([1971] 2003) The principles of life. Oxford University Press, Oxford

  • Gilbert W (1986) The RNA world. Nature 319:618

    Article  Google Scholar 

  • Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226–2238

    Google Scholar 

  • Haeckel E (1866) Generelle Morphologie der Organismen: allgemeine Grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte Descendenz-Theorie. Georg Reimer, Berlin

    Google Scholar 

  • Hanczyc M, Szostak JW (2004) Replicating vesicles as models of primitive cell growth and division. Curr Opin Chem Biol 8(6):660–664

    Article  Google Scholar 

  • Hargreaves WR, Mulvihill SJ, Deamer DW (1977) Synthesis of phospholipids and membranes in prebiotic conditions. Nature 266:78–80

    Article  Google Scholar 

  • Itaya M (1995) An estimation of minimal genome size required for life. FEBS Lett 362:257–260

    Article  Google Scholar 

  • Jordan IK, Rogozin IB, Wolf YI, Koonin EV (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12:962–968

    Google Scholar 

  • Kandler O (1994) Cell wall biochemistry in Archaea and its phylogenetic implications. J Biol Phys 20:165–169

    Article  Google Scholar 

  • Kasting J (2005) Methane and climate during the Precambrian era. Precambrian Res 137(3–4):119–129

    Article  Google Scholar 

  • Kauffman SA (1993) The origins of order: self-organization and selection in evolution. Oxford University Press, New York

    Google Scholar 

  • Kim DE, Joyce GF (2004) Cross-catalytic replication of an RNA ligase ribozyme. Chem Biol 11(11):1505–1512

    Article  Google Scholar 

  • Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev 1:127–136

    Article  Google Scholar 

  • Koshland DE Jr (2002) The seven pillars of life. Science 295:2215–2216

    Article  Google Scholar 

  • Krampitz G, Fox SW (1969) The condensation of the adenylates of the amino acids common to protein. Proc Natl Acad Sci USA 62:299–406

    Article  Google Scholar 

  • La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D (2008) The virophage as a unique parasite of the giant mimivirus. Nature 455(7209):100–104

    Article  Google Scholar 

  • Lee D, Granja JR, Martinez JA, Severin K, Ghadiri MR (1996) A self-replicating peptide. Nature 382:525–528

    Article  Google Scholar 

  • Leipe DD, Aravind L, Koonin EV (1999) Did DNA replication evolve twice independently? Nucleic Acids Res 27:3389–3401

    Article  Google Scholar 

  • Luisi PL (1998) About various definitions of life. Orig Life Evol Biosph 28:613–622

    Article  Google Scholar 

  • Luisi PL (2002) Emergence in chemistry: chemistry as the embodiment of emergence. Found Chem 4:183–200

    Article  Google Scholar 

  • Martin W, Russell MJ (2003) On the origin of cells: an hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond A 358B:27–85

    Google Scholar 

  • Maturana H, Varela F (1973) Autopoiesis: the organization of the living. Reidel, Dordrecht

    Google Scholar 

  • Mayr E (1982) The growth of biological thought: diversity, evolution, and inheritance. The Belknap Press, Cambridge

    Google Scholar 

  • Monnard PA, Deamer DW (2002) Membrane self-assembly processes: steps toward the first cellular life. Anat Rec 268:196–207

    Article  Google Scholar 

  • Monod J (1970) Le hasard et la nécessité. Le Seuil, Paris

    Google Scholar 

  • Morange M (2003) La vie expliquée : 50 ans après la double hélice. Odile Jacob, Paris

    Google Scholar 

  • Moreira D, Lopez-Garcia P (2006) The last common ancestor. In: Pascal R, Boiteau L, Forterre P, Gargaud M, Lazcano A, Lopez-Garcia P, Moreira D, Maurel MC, Pereto J, Prieur D, Reisse J (eds) Prebiotic chemistry—biochemistry—emergence of life (4.4-2 ga). Earth Moon Planets 98:153–203

  • Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93:10268–10273

    Article  Google Scholar 

  • Noireaux V, Bar-Ziv R, Godefroy J, Salman H, Libchaber A (2005) Toward an artificial cell based on gene expression in vesicles. Phys Biol 2:P1–P8

    Article  Google Scholar 

  • Nooner DW, Oro J (1979) Synthesis of fatty acids by a closed system Fischer-Tropsch process. In: Kugler EL, Steffgen FW (eds) Hydrocarbon synthesis from carbon monoxide and hydrogen. Am Chem Soc, Washington DC, pp 159–171

    Chapter  Google Scholar 

  • Norman A, Hansen LH, Sørensen SJ (2009) Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond A 364:2275–2289

    Article  Google Scholar 

  • Oparin AI (1961) Life: its nature, origin and development. Academic Press, New York

    Google Scholar 

  • Ourisson G, Nakatani Y (1994) The terpenoid theory of the origin of cellular life: the evolution of terpenoids to cholesterol. Chem Biol 1(1):11–23

    Article  Google Scholar 

  • Pace NR (2001) The universal nature of biochemistry. Proc Natl Acad Sci USA 98:805–808

    Article  Google Scholar 

  • Palyi G, Zucchi C, Caglioti L (eds) (2002) Fundamentals of life. Elsevier, Paris

    Google Scholar 

  • Popa R (2004) Between chance and necessity: searching for the definition and origin of life. Springer, Heidelberg

    Google Scholar 

  • Rajamani S, Vlassov A, Benner S, Coombs A, Olasagasti F, Deamer DW (2008) Lipid-assisted synthesis of RNA-like polymers from mononucleotides. Orig Life Evol Biosph 38(1):57–74

    Article  Google Scholar 

  • Raoult D, Forterre P (2008) Redefining viruses: lessons from Mimivirus. Nat Rev Microbiol 6:315–319

    Article  Google Scholar 

  • Rasmussen S, Chen L, Nilsson M, Abe S (2003) Bridging nonliving and living matter: new browser window will open. Artif Life 9:269–316

    Article  Google Scholar 

  • Rasmussen S, Bedau MA, Chen L, Deamer D, Krakauer DC, Packard NH, Stadler PF (2009) Protocells: bridging nonliving and living matter. MIT, Cambridge

    Google Scholar 

  • Rode BM (1999) Peptides and the origin of life. Peptides 20:773–786

    Article  Google Scholar 

  • Rohmer M, Bouvier P, Ourisson G (1979) Molecular evolution of biomembranes: structural equivalents and phylogenetic precursors of sterols. Proc Natl Acad Sci USA 76(2):847–851

    Article  Google Scholar 

  • Ruiz-Mirazo K, Pereto J, Moreno A (2004) A universal definition of life: autonomy and open-ended evolution. Orig Life Evol Biosph 34(3):323–346

    Article  Google Scholar 

  • Sacerdote MG, Szostak JW (2005) Semipermeable lipid bilayers exhibit diastereo-selectivity favoring ribose. Proc Natl Acad Sci USA 102:6004–6008

    Article  Google Scholar 

  • Sagan C ([1970] 1986) Life. In: Encyclopedia Britannica, 15th edn., vol 22. Encyclopedia Britannica Inc., Chicago, pp 985–1002

  • Schopf J (2006) Fossil evidence of Archaean life. Phil Trans R Soc B 361(1470):869–885

    Article  Google Scholar 

  • Segré D, Ben-Eli D, Deamer DW, Lancet D (2001) The lipid world. Orig Life Evol Biosph 31:119–145

    Article  Google Scholar 

  • Shapiro R (1986) Origins: a skeptic’s guide to the creation of life on earth. Summit Books, New York

    Google Scholar 

  • Sievers D, Von Kiedrowski G (1994) Self-replication of complementary nucleotide oligomers. Nature 369:221–224

    Article  Google Scholar 

  • Stevens PF (1983) Augustin Augier’s ‘Arbre Botanique’ (1801), a remarkable early botanical representation of the natural system. Taxon 32:203–211

    Article  Google Scholar 

  • Stillwell W (1980) Facilitated diffusion as a method for selective accumulation of materials from the primordial oceans by a lipid-vesicle protocell. Orig Life Evol Biosph 10:277–292

    Article  Google Scholar 

  • Szostak J, Bartel D, Luisi PL (2001) Synthesizing Life. Nature 409:387–390

    Article  Google Scholar 

  • Woese CR (1998) The universal ancestor. Proc Natl Acad Sci USA 95:6854–6859

    Article  Google Scholar 

  • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74(11):5088–5090

    Article  Google Scholar 

  • Yao S, Ghosh I, Zutshi R, Chmielewski J (1998) Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature 396:447–450

    Article  Google Scholar 

  • Yjivikua T, Ballester P, Rebek J Jr (1990) A self-replicating system. J Am Chem Soc 112:1249–1250

    Article  Google Scholar 

Download references

Acknowledgments

An earlier version of this paper was presented at the Perspectives on the Tree of Life workshop, sponsored by the Leverhulme Trust and held in Halifax, July 2009. I am indebted to several participants for valuable comments, and to Maureen O’Malley and John Dupré for providing such a valuable brainstorming platform. I also thank Jacques Reisse of the Université Libre de Bruxelles and Jean Gayon at the Université Paris 1—Panthéon Sorbonne for stimulating discussions, as well as two anonymous referees for their insightful comments. Support from the CNRS interdisciplinary program “Origines des planètes et de la vie” and from the Fondation Louis D. of the Institut de France is gratefully acknowledged.

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    Christophe Malaterre

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Malaterre, C. Lifeness signatures and the roots of the tree of life. Biol Philos 25, 643–658 (2010). https://doi.org/10.1007/s10539-010-9220-8

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