Skip to main content
SpringerLink
Log in

A Trip Through Chemical Space: Why Life Has Evolved the Chemistry That It Has

  • Chapter
  • First Online:
Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life

Abstract

Earth life is built from a quite restricted set of chemicals. Is this an accident of evolution, or are there reasons for the patterns of similarity and diversity in metabolism? I summarize several studies looking at how life has explored “chemical space”, and seeking explanations for the nature of biochemistry. The properties of synthetic alternatives to DNA have lead to a hypothesis about what the features that any genetic material must have, providing a rationale for the incorporation of phosphate into DNA. Synthesis and computational studies of possible amino acids have been synergistic in understanding the limits to which the 20 main proteinaceous amino acids are chemically inevitable and the extent to which they are a frozen accident from the origin of life. A broader exploration of chemical space including all of metabolism shows that metabolism is actually crowded into a limited region of the space of possible chemicals. Using a wide dataset of measurement of the toxicity of chemicals, I have shown that this crowding has important implications for how new chemistry can be added to life, which could in principle be developed into a set of constraints on how any metabolism could evolve. Biochemistry is often constrained to specific chemical function, but not always limited to one molecule to carry out that function. These initial results provide hope that there are computationally tractable approaches to understanding why biochemistry is as it is.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    This was originally termed “substrate independence”, but that earlier phrase implied that an organism could grow on anything, which clearly is not true.

  2. 2.

    In a prokaryotic cell internal compartment, anyway. In compartmentalized eukaryotic cells, each compartment only ‘sees’ a subset of metabolism.

References

  • Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, le Gall L, Lynn DH, McManus H, Mitchell EAD, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW (2012) The revised classification of eukaryotes. J Eukaryot Microbiol 59:429–514

    Article  PubMed Central  PubMed  Google Scholar 

  • Akers KS, Sinks GD, Schultz TW (1999) Structure–toxicity relationships for selected halogenated aliphatic chemicals. Environ Toxicol Pharmacol 7:33–39

    Article  CAS  PubMed  Google Scholar 

  • Allred AL, Rochow EG (1958) A scale of electronegativity based on electrostatic force. J Inorg Nucl Chem 5:264–268

    Article  CAS  Google Scholar 

  • Amend JP, Shock EL (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiol Ecol 25:175–243

    Google Scholar 

  • Bains W (2004) Many chemistries could be used to build living systems. Astrobiology 4:137–167

    Article  CAS  PubMed  Google Scholar 

  • Bains W (2013) What do we think life is? A simple illustration and its consequences. Int J Astrobiol (in press)

    Google Scholar 

  • Bains W, Seager S (2012) A combinatorial approach to biochemical space: description and application to the redox distribution of metabolism. Astrobiology 12:271–281

    Article  CAS  PubMed  Google Scholar 

  • Bains W, Seager S (2013) Correction: a combinatorial approach to biochemical space: description and application to the redox distribution of metabolism. Astrobiology 13:792

    Article  Google Scholar 

  • Bains W, Tacke R (2003) Silicon chemistry as a novel source of chemical diversity in drug design. Curr Opin Drug Discov Devel 6:526–543

    CAS  PubMed  Google Scholar 

  • Bedau MA (2010) An Aristotelian account of minimal chemical life. Astrobiology 10:1011–1020

    Article  PubMed  Google Scholar 

  • Benner S, Bains W, Seager S (2013) Models and standards of proof in cross-disciplinary science: the case of arsenic DNA. Astrobiology 13:510–513

    Article  CAS  PubMed  Google Scholar 

  • Benner S, Battersby TR, Eschgfäller B, Hutter D, Kodra JT, Lutz S, Arslan T, Bäschlin DK, Blättler M, Egli M, Hammer C, Held HA, von Krosigk U, Lutz MJ, Macpherson LJ, Moroney SE, Müller E, Nambiar KP, Piccirilli JA, Switzer C, Vögel JJ, Richert C, Roughton AL, Schmidt J, Schneider KC, Stackhouse J (1998) Redesigning nucleic acids. Pure Appl Chem 70:263–266

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Benner SA (2010) Defining life. Astrobiology 10:1021–1030

    Article  PubMed Central  PubMed  Google Scholar 

  • Berends AG, Boutonnet JC, Rooij CGD, Thompson RS (1999) Toxicity of trifluoroacetate to aquatic organisms. Environ Toxicol Chem 18:1053–1059

    Article  CAS  Google Scholar 

  • Blackman GE, Parke MH, Garton G (1955) The physiological activity of substituted phenols. I. relationships between chemical structure and physiological activity. Arch Biochem Biophys 54:45–54

    Article  CAS  PubMed  Google Scholar 

  • Böck A, Forchhammer K, Heider J, Leinfelder W, Sawers G, Veprek B, Zinoni F (1991) Selenocysteine: the 21st amino acid. Mol Microbiol 5:515–520

    Article  PubMed  Google Scholar 

  • Boudreau TM, Sibley PK, Mabury SA, Muir DGC, Solomon KR (2003) Laboratory evaluation of the toxicity of perfluorooctane sulfonate (PFOS) on Selenastrum capricornutum, Chlorella vulgaris, Lemna gibba, Daphnia magna, and Daphnia pulicaria. Arch Environ Contam Toxicol 44:0307–0313

    Article  CAS  Google Scholar 

  • Brain RA, Johnson DJ, Richards SM, Hanson ML, Sanderson H, Lam MW, Young C, Mabury SA, Sibley PK, Solomon KR (2004a) Microcosm evaluation of the effects of an eight pharmaceutical mixture to the aquatic macrophytes Lemna gibba and Myriophyllum sibiricum. Aquat Toxicol 70:23–40

    Article  CAS  PubMed  Google Scholar 

  • Brain RA, Johnson DJ, Richards SM, Sanderson H, Sibley PK, Solomon KR (2004b) Effects of 25 pharmaceutical compounds to Lemna gibba using a seven-day static-renewal test. Environ Toxicol Chem 23:371–382

    Article  CAS  PubMed  Google Scholar 

  • Caux PY, Weinberger P, Carlisle DB (1988) A physiological study of the effects of triton surfactants on Lemna minor L. Environ Toxicol Chem 7:671–676

    Article  CAS  Google Scholar 

  • Chase MWJ (1998) NIST-JANAF thermochemical tables, fourth edition. J Chem Phys Ref Data Monograph Number 9:1–1951

    Google Scholar 

  • Church GM, Regis E (2012) Regenesis: how syntehtic biology will reinvent nature and ourselves. Basic Books, New York

    Google Scholar 

  • Chyba CF, McDonald GD (1995) The origin of life in the solar system: current issues. Ann Rev Earth Planet Sci 23:215–249

    Article  CAS  Google Scholar 

  • Committee on the origins and evolution of life (2007) The limits of organic life in planetary systems. National Research Council, Washington

    Google Scholar 

  • Cowgill UM, Milazzo DP, Landenberger BD (1991) The sensitivity of Lemna gibba G-3 and four clones of Lemna minor to eight common chemicals using a 7-day test. Res J Water Pollut Fed 63:991–998

    CAS  Google Scholar 

  • Cronin MTD, Netzeva TI, Dearden JC, Edwards R, Worgan ADP (2004) Assessment and modeling of the toxicity of organicchemicals to Chlorella vulgaris: development of a novel database. Chem Res Tox 17:545–554

    Article  CAS  Google Scholar 

  • Das RN, Roy K (2014) Predictive modeling studies for the ecotoxicity of ionic liquids towards the green algae Scenedesmus vacuolatus. Chemosphere 104:170–176

    Google Scholar 

  • Geoffroy L, Teisseire H, Couderchet M, Vernet G (2002) Effect of oxyfluorfen and diuron alone and in mixture on antioxidative enzymes of Scenedesmus obliquus. Pestic Biochem Physiol 72:178–185

    Article  CAS  Google Scholar 

  • Gould SJ (1989) Wonderful life: the burgess shale and the nature of history. Norton & Co, New York

    Google Scholar 

  • Hanson ML, Solomon KR (2004) Haloacetic acids in the aquatic environment part I: macrophyte toxicity. Environ Pollut 130:371–383

    Article  CAS  PubMed  Google Scholar 

  • Higgs PG, Pudritz RE (2009) A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9:483–490

    Article  CAS  PubMed  Google Scholar 

  • Hitchcock DR, Lovelock JE (1967) Life detection by atmospheric analysis. Icarus 7:149–150

    Article  Google Scholar 

  • Hopkins AL, Mason JS, Overington JP (2006) Can we rationally design promiscuous drugs? Curr Opin Struct Biol 16:127–136

    Article  CAS  PubMed  Google Scholar 

  • Hu R, Seager S, Bains W (2012) Photochemistry in terrestrial exoplanet atmospheres. i. photochemistry model and benchmark cases. Astrophys J 761:166

    Article  Google Scholar 

  • Ilardo MA, Freeland S (2014) Testing for adaptive signatures of amino acid alphabet evolution using chemistry space. J Syst Chem 5: doi:10.1186/1759-2208-5-1

  • Kirby MF, Sheahan DA (1994) Effects of atrazine, isoproturon, and mecoprop on the macrophyte Lemna minor and the alga Scenedesmus subspicatus. Bull Environ Contam Toxicol 53:120–126

    CAS  PubMed  Google Scholar 

  • Kulacki KJ, Lamberti GA (2008) Toxicity of imidazolium ionic liquids to freshwater algae. Green Chem 10:104–110

    Article  CAS  Google Scholar 

  • Larson JH, Frost PC, Lamberti GA (2008) Variable toxicity of ionic liquid-forming chemicals to Lemna minor and the influence of dissolved organic matter. Environ Toxicol Chem 27:676–681

    Article  CAS  PubMed  Google Scholar 

  • Lazcano A, Miller SL (1996) The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85:793–798

    Article  CAS  PubMed  Google Scholar 

  • Leeson PD, Springthorpe B (2007) The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discovery 6:881–890

    Article  CAS  Google Scholar 

  • Li X, Ping X, Xiumei S, Zhenbin W, Liqiang X (2005) Toxicity of cypermethrin on growth, pigments, and superoxide dismutase of Scenedesmus obliquus. Ecotoxicol Environ Saf 60:188–192

    Article  CAS  PubMed  Google Scholar 

  • Liu CC, Schultz PG (2010) Adding new chemistries to the genetic code. Ann Rev Biochem 79:413–444

    Article  CAS  PubMed  Google Scholar 

  • Longo LM, Lee J, Blaber M (2013) Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proc Natl Acad Sci 110:2135–2139

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lu G-H, Yuan X, Zhao Y-H (2001) QSAR study on the toxicity of substituted benzenes to the algae (Scenedesmus obliquus). Chemosphere 44:437–440

    Article  CAS  PubMed  Google Scholar 

  • Lu Y, Freeland S (2006) On the evolution of the standard amino-acid alphabet. Genome Biol 7:102

    Article  PubMed Central  PubMed  Google Scholar 

  • Ma J (2005) Differential sensitivity of three cyanobacterial and five green algal species to organotins and pyrethroids pesticides. Sci Total Environ 341:109–117

    Article  CAS  PubMed  Google Scholar 

  • Ma J, Lu N, Qin W, Xu R, Wang Y, Chen X (2006) Differential responses of eight cyanobacterial and green algal species, to carbamate insecticides. Ecotoxicol Environ Saf 63:268–274

    Article  CAS  PubMed  Google Scholar 

  • Ma J, Wang P, Chen J, Sun Y, Che J (2007) Differential response of green algal species Pseudokirchneriella subcapitata, Scenedesmus quadricauda, Scenedesmus obliquus, Chlorella vulgaris and Chlorella pyrenoidosa to six pesticides. Polish J Environ Stud 16:847–851

    CAS  Google Scholar 

  • Ma J, Zheng R, Xu L, Wang S (2002) Differential sensitivity of two green algae, Scenedesmus obliqnus and Chlorella pyrenoidosa, to 12 pesticides. Ecotoxicol Environ Saf 52:57–61

    Article  CAS  PubMed  Google Scholar 

  • Machery E (2012) Why i stopped worrying about the definition of life… and why you should as well. Synthese 185:145–164

    Article  Google Scholar 

  • Martin W, Russell MJ (2007) On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc B Biol Sci 362:1887–1926

    Article  CAS  Google Scholar 

  • McConkey BJ, Duxbury CL, Dixon DG, Greenberg BM (1997) Toxicity of a pah photooxidation product to the bacteria photobacterium phosphoreum and the duckweed Lemna gibba: effects of phenanthrene and its primary photoproduct, phenanthrenequinone. Environ Toxicol Chem 16:892–899

    Article  CAS  Google Scholar 

  • Meringer M, Cleaves HJI, Freeland SJ (2013) Beyond terrestrial biology: charting the chemical universe of α-amino acid structures. J Chem Inf Model 53:2851–2862

    Article  CAS  PubMed  Google Scholar 

  • Metzler DE, Metzler CM (2001) Biochemistry—the chemical reactions of living cells, vol 1, 2nd edn. Harcourt Academic Press, San Diego

    Google Scholar 

  • Orgel LE (1998) The origin of life—a review of facts and speculations. Trends Biochem Sci 23:491–495

    Article  CAS  PubMed  Google Scholar 

  • Philip GK, Freeland S (2011) Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology 11:235–240

    Article  CAS  PubMed  Google Scholar 

  • Pillard DA, Dufresne DL (1999) Toxicity of formulated glycol deicers and ethylene and propylene glycol to Lactuca sativa, Lolium perenne, Selenastrum capricornutum, and Lemna minor. Arch Environ Contam Toxicol 37:29–35

    Article  CAS  PubMed  Google Scholar 

  • Qi P, Wang Y, Mu J, Wang J (2011) Aquatic predicted no-effect-concentration derivation for perfluorooctane sulfonic acid. Environ Toxicol Chem 30:836–842

    Article  CAS  PubMed  Google Scholar 

  • Ramirez TORO GI, Leather GR, Einhellig FA (1988) Effects of three phenolic compounds on Lemna gibba G3. J Chem Ecol 14:845–853

    Article  CAS  PubMed  Google Scholar 

  • Rawlins P (2010) Current trends in label-free technologies. Drug Discov World 2010:17–26

    Google Scholar 

  • Robinson NE (2002) Protein deamidation. Proc Nat Acad Sci USA 99:5283–5288

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Saçan MT, Özkul M, Erdem SS (2007) QSPR analysis of the toxicity of aromatic compounds to the algae (Scenedesmus obliquus). Chemosphere 68:695–702

    Article  PubMed  Google Scholar 

  • Schultz-Mukuch D, Irwin LN (2008) Life in the universe: expectations and constraints, 2nd edn. Springer, Berlin

    Google Scholar 

  • Schultz TW (1999) Structure—toxicity relationships for benzenes evaluated with Tetrahymena pyriformis. Chem Res Toxicol 12:1262–1267

    Article  CAS  PubMed  Google Scholar 

  • Schultz TW, Cronin MTD, Netzeva TI, Aptula AO (2002) Structure—toxicity relationships for aliphatic chemicals evaluated with Tetrahymena pyriformis. Chem Res Toxicol 15:1602–1609

    Article  CAS  PubMed  Google Scholar 

  • Schultz TW, Netzeva TI, Roberts DW, Cronin MTD (2005) Structure—toxicity relationships for the effects to Tetrahymena pyriformis of aliphatic, carbonyl-containing, α, β-unsaturated chemicals. Chem Res Toxicol 18:330–341

    Article  CAS  PubMed  Google Scholar 

  • Sharma HA, Barber JT, Ensley HE, Polito MA (1997) A comparison of the toxicity and metabolism of phenol and chlorinated phenols by Lemna gibba, with special reference to 2,4,5-trichlorophenol. Environ Toxicol Chem 16:346–350

    Article  CAS  Google Scholar 

  • Sherman F, Stewart JW, Tsunasawa S (1985) Methionine or not methionine at the beginning of a protein. BioEssays 3:27–31

    Article  CAS  PubMed  Google Scholar 

  • Stephenson J, Freeland S (2013) Unearthing the root of amino acid similarity. J Mol Evol 77:159–169

    Article  CAS  PubMed  Google Scholar 

  • Tadros MG, Philips J, Patel H, Pandiripally V (1994) Differential response of green algal species to solvents. Bull Environ Contam Toxicol 52:333–337

    CAS  PubMed  Google Scholar 

  • Tong Z, Hongjun J (1997) Use of duckweed (Lemna minor L.) growth inhibition test to evaluate the toxicity of acrylonitrile, sulphocyanic sodium and acetonitrile in China. Environ Pollut 98:143–147

    Article  CAS  Google Scholar 

  • van de Plassche EJ, de Bruijn JHM, Stephenson RR, Marshall SJ, Feijtel TCJ, Belanger SE (1999) Predicted no-effect concentrations and risk characterization of four surfactants: Linear alkyl benzene sulfonate, alcohol ethoxylates, alcohol ethoxylated sulfates, and soap. Environ Toxicol Chem 18:2653–2663

    Article  Google Scholar 

  • Wang C, Lu G, Tang Z, Guo X (2008) Quantitative structure-activity relationships for joint toxicity of substituted phenols and anilines to Scenedesmus obliquus. J Environ Sci 20:115–119

    Article  Google Scholar 

  • Wang W (1990) Literature review on duckweed toxicity testing. Environ Res 52:7–22

    Article  CAS  PubMed  Google Scholar 

  • Weber A, Miller S (1981) Reasons for the occurrence of the twenty coded protein amino acids. J Mol Evol 17:273–284

    Article  CAS  PubMed  Google Scholar 

  • Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178

    Article  CAS  PubMed  Google Scholar 

  • Wojciechowski F, Leumann CJ (2011) Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications. Chem Soc Rev 40:5669–5679

    Article  CAS  PubMed  Google Scholar 

  • Wolfenden R (2006) Degrees of difficulty of water-consuming reactions in the absence of enzymes. Chem Rev 106:3379–3396

    Article  CAS  PubMed  Google Scholar 

  • Xu Y, Lay JP, Korte F (1988) Fate and effects of xanthates in laboratory freshwater systems. Bull Environ Contam Toxicol 41:683–689

    Article  CAS  PubMed  Google Scholar 

  • Yan X-F, Xiao H-M, Gong X-D, Ju X-H (2005) Quantitative structure–activity relationships of nitroaromatics toxicity to the algae (Scenedesmus obliguus). Chemosphere 59:467–471

    Article  CAS  PubMed  Google Scholar 

  • Yuan J, O’donoghue P, Ambrogelly A, Gundllapalli S, Sherrer RL, Palioura S, Simonović M, Söll D (2010) Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems. FEBS Lett 584:342–349

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang W, Zhang M, Lin K, Sun W, Xiong B, Guo M, Cui X, Fu R (2012) Eco-toxicological effect of carbamazepine on Scenedesmus obliquus and Chlorella pyrenoidosa. Environ Toxicol Pharmacol 33:344–352

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

My thanks to Janusz Petkowski (ETH, Zurich) for many useful discussions, to the attendees of the Gordon Research Conference on Synthetic Biology (Summer 2013) for helpful comments, to Sara Seager (MIT) for the continued and unstinting support, to Pierre Pontarotti and the organizers of the 17th Evolutionary Biology Meeting (2013, Marseilles) for inviting me, and to Alan Wilson (Llhasa Ltd) for not believing a word of it.

Author information

Authors and Affiliations

  1. Massachusetts Institute of Technology, 54-1726, 77 Mass Avenue, Cambridge, MA, 02139, USA

    William Bains

Authors
  1. William Bains
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to William Bains .

Editor information

Editors and Affiliations

  1. CNRS, Laboratoire Évolution Biologique et Modélisation, Université d'Aix-Marseille, Marseille, France

    Pierre Pontarotti

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Bains, W. (2014). A Trip Through Chemical Space: Why Life Has Evolved the Chemistry That It Has. In: Pontarotti, P. (eds) Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. Springer, Cham. https://doi.org/10.1007/978-3-319-07623-2_18

Download citation

Publish with us

Policies and ethics

Search

Navigation