CHAPTER 6
Jump in a car: Woods PJE. (1979) The geology of Boulby mine. Economic Geology 74, 409–418.
From the science-fiction cleanliness: The laboratory is run by Sean Paling and his team. Many people need to be thanked, including Emma Meehan, Lou Yeoman, Christopher Toth, Barbara Suckling, Tom Edwards, Jac Genis, David McLuckie, David Pybus, and others who have made our work at Boulby possible.
Here, animal life: Two nice general books on the extremophiles are Gross M. (2001) Life on the Edge: Amazing Creatures Thriving in Extreme Environments. Basic Books, New York; and Postgate JR. (1995) The Outer Reaches of Life. Cambridge University Press, Cambridge.
Life deep down: An excellent book that provides an insight into the history and science of deep subsurface life is Onstott TC. (2017) Deep Life: The Hunt for the Hidden Biology of Earth, Mars, and Beyond. Princeton University Press, Princeton, NJ.
Within the unremarkable sludge: Brock TD, Hudson F. (1969) Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. Journal of Bacteriology 98, 289–297.
Among their ranks: Takai K et al. (2008) Cell proliferation at 122 °C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proceedings of the National Academy of Sciences USA. 105, 10949–10954.
Proteins can be made: For a significant paper that shows how the adaptations of proteins to high temperatures can be explained in terms of physical principles, see Berezovsky IN, Shakhnovich EI. (2005) Physics and evolution of thermophilic adaptation. Proceedings of the National Academy of Sciences 102, 12,742–12,747.
One group of researchers: Cowan DA. (2004) The upper temperature for life—where do we draw the line? Trends in Microbiology 12, 58–60.
At temperatures of around 450°C: For the upper temperature limits of life as set by molecular stability, see Daniel RM, Cowan DA. (2000) Biomolecular stability and life at high temperatures. Cellular and Molecular Life Sciences 57, 250–264.
Life on Earth should: Cockell CS. (2011) Life in the lithosphere, kinetics and the prospects for life elsewhere. Philosophical Transactions of the Royal Society 369, 516–537.
So far, there is no good: A paper quantifying lower temperature limits for life is Price PB, Sowers T. (2004) Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proceedings of the National Academy of Sciences 101, 4631–4636. At very low temperatures, cells reach a point when the rate of energy expenditure by microbes is only just able to keep up with the rate of damage. This trade-off will ultimately determine the lower temperature limit for any given life form to remain intact over long periods.
The challenge that low-temperature life: Another paper that examines this problem considers the challenges caused by liquids that “vitrify,” essentially turn into a glasslike state in cells at low temperatures. Vitrification is likely to seriously limit the movement of gases and nutrients and may set a lower limit for life in many organisms. See Clarke A et al. (2013) A low temperature limit for life on Earth. PLoS One 8, e66207.
This background radiation: The radiation may not be entirely detrimental. The radiolysis of water, or its breaking up by radiation, could release hydrogen, which microbes can use as an energy source. See, for example, Lin L-H et al. (2005) Radiolytic H2 in continental crust: Nuclear power for deep subsurface microbial communities. Geochemistry, Geophysics and Geosystems 6, doi: 10.1029/2004GC000907.
Added to these problems: An example is depurination in the DNA, in which the β-N-glycosidic bond is hydrolytically cleaved, releasing a nucleic base, adenine or guanine, from the DNA structure. See Lindahl T. (1993) Instability and decay of the primary structure of DNA. Nature 362, 709–715; Lindahl T, Nyberg B. (1972) Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610–3618.
After eating your breakfast: Lipids that make up membranes contain fatty acids, long chains of carbon atoms. When we talk about fats in butter, we are talking about the same material—fatty acids.
When exposed to subfreezing: A review that summarizes the variety of challenges and solutions for life at low temperatures is D’Amico S et al. (2006) Psychrophilic microorganisms: Challenges for life. EMBO Reports 7, 385–389.
In this zone, reactions: Including the process of racemization, the tendency for the chirality (L- or D- forms of molecules) to be lost. Remember that amino acids in life are primarily in the L-form. Racemization will tend to produce an equal amount of L- and D-forms. It can happen inexorably over time by thermal effects on molecules. The racemization of amino acids and low-temperature environments is discussed in Brinton KLF, Tsapin AI, Gilichinsky D, McDonald GD. (2002) Aspartic acid racemization and age-depth relationships for organic carbon in Siberian permafrost. Astrobiology 2, 77–82.
No one should be surprised: Grant S et al. (1999) Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 3, 139–145.
Faced with the trauma: The problems of high salt are described in Oren A. (2008) Microbial life at high salt concentrations: Phylogenetic and metabolic diversity. Saline Systems 4, doi: 10.1186/1746-1448-4-2. For the thermodynamic limitations imposed by salt, see Oren A. (2011) Thermodynamic limits to microbial life at high salt concentrations. Environmental Microbiology 13, 1908–1923.
Like scientists enamored: Stevenson A et al. (2015) Is there a common water-activity limit for the three domains of life? ISME J 9, 1333–1351.
By a water activity: Stevenson A et al. (2017) Aspergillus penicillioides differentiation and cell division at 0.585 water activity. Environmental Microbiology 19, 687–697.
These solutions can also cause disorder: Hallsworth JE et al. (2007) Limits of life in MgCl2-containing environments: Chaotropicity defines the window. Environmental Microbiology 9, 801–813.
When investigated by microbiologists: Yakimov MM et al. (2015) Microbial community of the deep-sea brine Lake Kryos seawater–brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA. Environmental Microbiology 17, 364–382.
Indeed, microbiologists have had mixed results: Siegel BZ. (1979) Life in the calcium chloride environment of Don Juan Pond, Antarctica. Nature 280, 828–829.
Yet we find life thriving: Amaral Zettler LA et al. (2002) Microbiology: Eukaryotic diversity in Spain’s River of Fire. Nature 417, 137.
The acid-loving microbes: The adaptations to low pH are summarized well in Baker-Austin C, Dopson M. (2007) Life in acid: pH homeostasis in acidophiles. Trends in Microbiology 15, 165–171. For insights into adaptations from the genome, see Ciaramella M, Napoli A, Rossi M. (2005) Another extreme genome: How to live at pH 0. Trends in Microbiology 13, 49–51.
A trip to Mono Lake: Humayoun SB, Bano N, Hollibaugh JT. (2003) Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Applied and Environmental Microbiology 69, 1030–1042.
In most of Earth’s environments: Some nice work was done by Jesse Harrison, a postdoctoral scientist in my laboratory, to attempt to map the limits of life using growth ranges of known strains of bacteria in the laboratory. You end up with intriguing three-dimensional plots of the boundary space of life: Harrison JP, Gheeraert N, Tsigelnitskiy D, Cockell CS. (2013) The limits for life under multiple extremes. Trends in Microbiology 21, 204–212. This work used only laboratory strains, but natural environments outside the extremes in this paper are known to contain microbes, so there is still much to do to define the physical and chemical boundary space of life.
Microbes have been found: Mesbah NM, Wiegel J. (2008) Life at extreme limits: The anaerobic halophilic alkalithermophiles. Annals of the New York Academy Sciences 1125, 44–57.
Other extremes too: Oger PM, Jebbar M. (2010) The many ways of coping with pressure. Research in Microbiology 161, 799–809.
Pores and transporters: Bartlett DH. (2002) Pressure effects on in vivo microbial processes. Biochimica et Biophysica Acta 1595, 367–381.
The humble Chroococcidiop
sis: Billi D et al. (2000) Ionizing-radiation resistance in the desiccation-tolerant cyanobacterium Chroococcidiopsis. Applied and Environmental Microbiology 66, 1489–1492.
microbe joins: Perhaps the most famous radiation-resistant microbe is Deinococcus radiodurans (a Greek and Latin portmanteau literally meaning “radiation-surviving terrible berry”). See Cox MM, Battista JR. (2005) Deinococcus radiodurans—the consummate survivor. Nature Reviews Microbiology 3, 882–892. However, its capacities are not unique. Other bacteria (including Chroococcidiopsis and Rubrobacter) also have high radiation tolerance.
This zoo: This observation doesn’t contradict the fact that within the confines of the zoo, life is remarkably tenacious and can occupy a startling range of physical and chemical conditions. For a jaunt through these capacities and life’s ability to ride out catastrophes that occur during its tenure on Earth, see Cockell CS. (2003) Impossible Extinction: Natural Catastrophes and the Supremacy of the Microbial World. Cambridge University Press, Cambridge.
CHAPTER 7
In an early paper: Crick FHC. (1965) The origin of the genetic code. Journal of Molecular Biology 38, 367–379.
This apparently odd property: Watson JD, Crick FHC. (1953) A structure for deoxyribose nucleic acid. Nature 171, 737–738.
Surely it is just chance: The number of “letters” in the genetic code is reviewed by Szathmáry E. (2003) Why are there four letters in the genetic code? Nature Reviews in Genetics 4, 995–1001.
In this “RNA world”: Higgs PG, Lehman N. (2015) The RNA World: Molecular cooperation at the origins of life. Nature 16, 7–17
We do not discover: The reader might well retort that the argument is tautological: Of course the models give us results congruent with Earth’s biology because the models we used are based on RNA, the very molecule that Earth life uses! I would reply with the very unscientific “maybe.” However, as is apparent later in this chapter, we can explore many alternative base pairs and molecules, which suggest that the choice of chemicals in the genetic code is not chance. There are some genetic-code-like molecules that have similarities with the other classes of molecules that make life, for example PNA, peptide nucleic acids, which crudely have protein-like qualities with their peptide bonds. However, no one has yet shown that the other major monomers of life that are thought to have been present on the early Earth (e.g., amino acids, lipids, and sugars) can form a genetic code. Among the various organic molecules on offer for the first living things, the ones used in our genetic code seem likely. Nevertheless, we should be open-minded about possible alternative chemistries for genetic codes. I limit myself in this chapter to the observation that once the nucleotides were evolutionarily selected as the basis of the genetic code, the rest of the architecture of the code and its molecular products is highly noncontingent and driven by physical considerations.
Motivated by a desire: Zhang Y et al. (2016) A semisynthetic organism engineered for the stable expansion of the genetic alphabet. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1616443114
The unwieldly named xanthosine: Piccirilli JA et al. (1990) Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343, 33–37.
Some isoguanine and isocytosine: Malyshev DA et al. (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature 509, 385–388.
Scientists at various institutions: Reviewed in Eschenmoser A. (1999) Chemical etiology of nucleic acid structure. Science 284, 2118–2124.
Perhaps the organization of the amino acids: Error minimization as a strong selection pressure for the code is described in a number of papers, for example Freeland SJ, Knight RD, Landweber LF, Hurst LD. (2000) Early fixation of an optimal genetic code. Molecular Biology and Evolution 17, 511–518.
Furthermore, amino acids: Other factors have been proposed. For example, horizontal gene transfer (the movement of genes from one cell or organism to another) can increase the selection for optimal codes. See Sengupta S, Aggarwal N, Bandhu AV. (2014) Two perspectives on the origin of the standard genetic code. Origins of Life and Evolution of Biospheres 44, 287–292.
Of all the codes: In an enticing Las Vegas–style titled paper, this analysis is described in Freeland SJ, Hurst LD. (1998) The genetic code is one in a million. Journal of Molecular Evolution 47, 238–248.
It is easy to get sucked into: A critique of different pressures shaping the early code was made by Knight RD, Freeland SJ, Landweber LF. (1999) Selection, history and chemistry: The three faces of the genetic code. Trends in Biochemical Sciences 24, 241–247, who suggest that different pressures may have dominated at different stages in the origin and early evolution of life. The pathways to the code and the role of coevolution in the process is also discussed by Wong, JT-F et al. (2016) Coevolution theory of the genetic code at age forty: Pathway to translation and synthetic life. Life 6, doi: 10.3390/life6010012. Another excellent review of the problems is Koonin EV, Novozhilov AS. (2009) Origin and evolution of the genetic code: The universal enigma. Life 61, 99–111.
Like much about biology: Schrödinger had a pretty good crack at it. See Schrödinger E. (1944) What Is Life? Cambridge University Press, Cambridge.
Churning out from the RNA: Biological catalysts, or enzymes, perform a vast number of chemical reactions in cells and speed them up to much higher rates than would happen without them.
Curious researchers have long wondered: Amino acids, like many chemicals, come in two types: left-handed (L-amino acids) and right-handed (D-amino acids). In analogy to your two hands, these two forms are mirror images of each other. The left- and right-handed forms rotate polarized light either anticlockwise (to the left, or levorotation) or clockwise (to the right, or dextrorotation), respectively, hence their designation as L- or D-forms. Almost all amino acids in life (barring some in membranes, for instance) are L-amino acids. The preponderance of L-forms was thought to be a matter of chance in life, but some evidence suggests that amino acids in meteorites are partly enriched in L-forms (see, for example, Engel MH, Macko SA. [1997] Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite. Nature 389, 265–268), suggesting an enrichment of the L-form of these amino acids in prebiotic molecules used by life. An alternative explanation is that polarized light in interstellar clouds preferentially destroyed one chiral form over the other, leading to initial enrichment of chiral molecules, later used in prebiotic chemistry (Bonner WA. [1995] Chirality and life. Origins of Life and Evolution of Biospheres 25, 175–190). As life depends on molecular recognition and so is made simpler if all molecules are one form or the other, it is likely that the L-form may have been amplified until it became the predominant form. An interesting question is whether life elsewhere, if it exists, could be made of either L- or D-amino acids. The question strikes at the heart of the basic question of whether contingency or physics drove the early events of evolution. We might equally ask this question about the sugars. Our sugars are predominantly in the D-form.
Initial attempts to discover: An excellent study was Weber AL, Miller SL. (1981) Reasons for the occurrence of the twenty coded protein amino acids. Journal of Molecular Evolution 17, 273–284.
But then in 2011, Gayle Philip: Philip GK, Freeland SJ. (2011) Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology 11, 235–240.
In more recent years, synthetic biologists: See, for example, Tiang Y, Tirrell DA. (2002) Attenuation of the editing activity of the Escherichia coli leucyl-tRNA synthetase allows incorporation of novel amino acids into proteins in vivo. Biochemistry 41, 10,635–10,645.
After all, if some of these new amino acids: I refer here to natural selection. Humans are now making these changes artificially.
The unusual amino acid: Johansson L, Gafvelin G, Amér ESJ. (2005) Selenocysteine in proteins—properties and biotechnological use. Biochimica et Biophysica Acta 1726, 1–13.
Another strange cousin: Srinivasan G, James CM, Krzycki JA. (2002). Pyrrolysine
encoded by UAG in Archaea: Charging of a UAG-decoding specialized tRNA. Science 296, 1459–1462.
Yet as these molecules were uncoiled: The implications of the limited protein folding possibilities for our understanding of evolution is nicely explored in Denton MJ, Marshall CJ, Legge M. (2002) The protein folds as platonic forms: New support for the pre-Darwinian conception of evolution by natural law. Journal of Theoretical Biology 219, 325–342, which also discusses how this knowledge might imply the existence of laws of biology rooted in physical principles.
Helices (termed α-helices): A carboxyl group.
As all these folds collapse: Other factors, such as stability against mutations, may select for certain protein folds. Fascinating papers that explore the reasons for limited protein folds include Li H, Helling R, Tang C, Wingren N. (1996) Emergence of preferred structures in a simple model of protein folding. Science 273, 666–669; and Li H, Tang C, Wingren N. (1998) Are protein folds atypical? Proceedings of the National Academy of Sciences 95, 4987–4990. Weinreich and colleagues, in a study of the mutational trajectories of a bacterial protein, are quite explicit that “this implies that the protein tape of life may be largely reproducible and even predictable” (Weinreich DM, Delaney NF, DePristo MA, Hartl DL. [2006] Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111–113).
Darwinian evolution: Mutations and genetic shuffling and movement such as horizontal gene transfer generate an inexorable increase in diversity. This tendency has even been instantiated into a law (McShea DW, Brandon RN. [2010] Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems. University of Chicago Press, Chicago). However, the degree to which such a tendency can really be a law or merely reflects the inexorable process of mutation that will occur in a code is a matter for debate. If any law drives this proposed biological phenomenon, it is probably the second law of thermodynamics.
The Equations of Life Page 34