The Equations of Life

by Charles S. Cockell

  The habitable zone: The habitable zone is, like many concepts of its type, too simplified. One of Jupiter’s moons, Europa, contains a giant ocean, and yet Jupiter is far outside the habitable zone. Europa’s internal ocean is not maintained by heating from our Sun, but instead by the buckling and contortions caused by the moon’s gravitational interactions with other Jovian moons. In this moon, there is liquid water far outside the habitable zone. Nonetheless, the habitable zone is useful because it allows us to identify a zone where we might find an Earth-like world around distant stars, a place with giant bodies of liquid water on its surface.

  It is slightly more aged: We need not limit ourselves to the search for merely Earth-like planets. Some may be even more bizarre than our own home world. Just over twenty-two light-years away is a triple star system in which a red dwarf star is orbited by a double or binary star system made up of two K-type stars. Orbiting the red dwarf are at least two super-Earths in its habitable zone, Gliese 667Cb and c. If anything lives on these planets, it may be greeted regularly by the astonishing spectacle of a triple sunset. Even the writers of Star Wars, who so imaginatively conjured up a scene of Luke Skywalker on the moon Tatooine enjoying a double sunset, have been outdone by reality. Anglada-Escudé G et al. (2012) A planetary system around the nearby M Dwarf GJ 667C with at least one super-Earth in its habitable zone. Astrophysical Journal Letters 751, L16.

  The sheer quantity of data: Petigura EA, Howard AW, Marcy GW. (2013) Prevalence of Earth-size planets orbiting Sun-like stars. Proceedings of the National Academy of Sciences 110, 19,273–19,278.

  And astronomers have brilliance: Besides the methods I describe in the main text, there are other ingenious approaches. Gravitational lensing uses the ability of massive objects in the universe to distort light to reveal the small blip in the light of a planet in orbit around a distant star, its light signature magnified briefly by the lensing caused by the focusing power of a massive object lying between it and the observers on Earth. Some exoplanets can be seen directly with telescopes. This is a little more challenging than the transit method, but by blocking out the light from the star, the little light reflected by a planet can be picked up and the pinpricks of individual planets discerned. We can achieve this remarkable feat using coronagraphs, telescopes with colossal sunshades to block out the glare of the central star and allow planets to be more easily detected. Even ground-based telescopes are successfully used to detect brown dwarfs, gassy planets about ten to eighty times the size of Jupiter. By observing them for long enough, we can even see changes in their atmospheres as gases swirl and heat under the influence of their star; in essence, astronomers have been able to observe weather on other planets. As you can imagine, though, direct detection works best with very large planets, thus explaining why the brown dwarfs are some of the more enticing candidates. There is now a legion of popular books describing the search for, and study of, exoplanets. Just one is Perryman M. (2014) The Exoplanet Handbook. Cambridge University Press, Cambridge.

  With all these bizarre new worlds: “One is startled towards fantastic imaginings by such a suggestion: visions of silicon-aluminium organisms—why not silicon-aluminium men at once? wandering through an atmosphere of gaseous sulfur, let us say, by the shores of a sea of liquid iron some thousand degrees or so above the temperature of a blast furnace.” Wells HG. (1894) Another basis for life. Saturday Review, 676.

  Some features may make other Earth-like worlds: Heller R, Armstrong J. (2014) Superhabitable worlds. Astrobiology 14, 50–66.

  Ecologists know well: This is the so-called species-area relationship, a phenomenon itself amenable to modeling and physical interpretation. See, for example, Connor EF, McCoy ED (1979) The statistics and biology of the species-area relationship. American Naturalist 113, 791–833.

  She fell to the ground: Koepcke J. (2011) When I Fell from the Sky. Littletown Publishing, New York.

  There is no better place: A good introductory book on this moon is Lorenz R, Mitton J. (2010) Titan Unveiled: Saturn’s Mysterious Moon Explored. Princeton University Press, Princeton, NJ.

  CHAPTER 12

  That the laws of physics and life: There have been many gallant attempts to find “laws” in biology as distinct new insights. An example is Bejan A, Zane JP. (2013) Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization. Anchor Books, New York, which explores the idea that life evolves toward solutions that enhance “flow” and proposes that this is a unifying factor in all living systems. However, is this just a restatement of the second law of thermodynamics? See also 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. Their “Zero-Force Evolutionary Law” proposes that an increase in diversity and complexity in life observed over evolutionary time periods is a law. Is this merely a statement of the phenomenon that mutations and other changes in the code, DNA, will inexorably produce diversity and variation without natural selection? My own contention is that many attempts to find distinct biological laws are indeed merely elaborated descriptions of phenomena in living things that have their origins in simpler physical principles and might even be better formulated in these terms. Other efforts have been made to use information theory and entropy to describe evolution. See, for example, Brooks DR, Wiley EO. (1988) Evolution as Entropy. University of Chicago Press, Chicago. Examples such as this provide potential mathematical and physical approaches to framing evolutionary questions from the individual organism to the population scale.

  However, ultimately even the material: The presence of life within these inescapable laws of thermodynamics and the tendency toward increased entropy is not a contradiction; nor is it a challenge to those laws. See, for example, Kleidon A. (2010) Life, hierarchy, and the thermodynamic machinery of planet Earth. Physics of Life Reviews 7, 424–460.

  Consider this one from Jan Baptista van Helmont: Quoted in Hall BK. (2011) Evolution: Principles and Processes. Jones and Bartlett, Sudbury, MA, 91. Also mentioned in a wider discussion on the origin of life is Chen IA, de Vries MS. (2016) From underwear to non-equilibrium thermodynamics: Physical chemistry informs the origin of life. Physical Chemistry Chemical Physics 18, 20005.

  In the seventeenth century: Gottdenker P. (1979) Francesco Redi and the fly experiments. Bulletin of the History of Medicine 53, 575–592.

  Just over sixty years after van Leeuwenhoek’s discovery: Needham JT. (1748) A summary of some late observations upon the generation, composition, and decomposition of animal and vegetable substances. Philosophical Transactions of the Royal Society 45, 615–666.

  Transferring some of his gravy: Before the days of health and safety, kitchen food, leftover gravy, and a smorgasbord of festering broths made excellent ways to advance the cause of science.

  After placing wetted seeds: Wetted seeds provide nutrients for a whole range of microbes naturally attached to them to grow, so they were a favored way of getting small creatures growing in vials.

  He then showed: Spallanzani L. (1799) Tracts on the Nature of Animals and Vegetables. William Creech et al., Edinburgh.

  Rather, at this infinitesimal scale: This was a matter that also concerned Niels Bohr, who suggested that biology could not be readily reduced to physics, because, as is the case of quantum uncertainties, any observations of biology at the atomic level would disrupt an organism sufficiently (maybe even kill it), preventing us from taking reliable observations (Bohr N. [1933] Light and life. Nature 131, 457–459). Bohr’s thoughts have been somewhat overshadowed by the enormous number of methods developed since his time. With these methods, scientists can noninvasively study organisms without disrupting their functions sufficiently to make those observations questionable. Bohr made a related point that organisms are so complex compared with many physical systems that a reductionist approach to biology, particularly at the atomic level, is extremely difficult. For example, organisms’ ca
pability to take in gases and release waste products makes it problematic to define which atoms belong to an organism and which do not. However, even on this score, we might note the enormous strides made in biochemistry and biophysics since the 1930s to characterize life’s processes at the atomic and even subatomic level. A recent discussion of Bohr’s ideas in the light of new technology and knowledge can be found in Nussenzveig HM. (2015) Bohr’s “Light and life” revisited. Physica Scripta 90, 118001.

  We can write down simple equations: For the less chemically inclined, this is a different mole from the furry ones I have already written about. In chemistry, a mole is the amount of a substance that contains an Avogadro’s number of atoms, which happens to be 6.022 × 1023 (the number is obtained from the number of atoms in twelve grams of the isotope carbon-12). However, for those with a strange sense of humor, you can find websites that discuss how large a mole of moles would be, and it is very large indeed. In fact, it is so large that such a mass of moles would be of interest to those who spend their time thinking about planet formation. There I will leave this point.

  In the machinery of the cell: Smith TF, Morowitz HJ. (1982) Between history and physics. Journal of Molecular Evolution 18, 265–282, is a well-written and thoroughly interesting paper that explores the interface between biology and physics, citing several authors and works that similarly see both congruence and differences between the two fields. The authors make a strong case for physical determinism at the level of biochemical pathways.

  Some bases (adenine and guanine): These are “depurination” events because they cause the loss of purines (the bases adenine and guanine). They occur through hydrolysis reactions and are one of the main pathways that cause the disintegration of ancient preserved DNA. They also play a role in triggering cancer. Loss of pyrimidine bases (cytosine and thymine) can also occur, but the reaction rates are much slower.

  It was Per-Olov Löwdin: If some mutations in DNA are caused by proton tunneling, namely, the consequences of quantum behavior, then we could perfectly well accept that some variations in organisms at the large scale have their origins in quantum-generated irregularities at the atomic scale. Proton tunneling in DNA base pairs, resulting in mutations, was discussed by Löwdin P-O. (1963) Proton tunnelling in DNA and its biological implications. Reviews of Modern Physics 35, 724–732, and subsequently discussed by many others, for example Kryachko ES. (2002) The origin of spontaneous point mutations in DNA via Löwdin mechanism of proton tunneling in DNA base pairs: Cure with covalent base pairing. Quantum Chemistry 90, 910–923.

  Now sometimes that proton: These are tautomers, chemicals that have the same molecular formula and that readily interconvert.

  Nevertheless, I raise the question: Lambert N et al. (2013) Quantum biology. Nature Physics 9, 10–18; Arndt M, Juffmann T, Vedral V. (2009) Quantum physics meets biology. HFSP Journal 3, 386–400; Davies PCW. (2004) Does quantum mechanics play a non-trivial role in life? BioSystems 78, 69–79. The field of quantum biology may yet yield insights into how other effects at the quantum scale can influence biological processes at the larger scale. Photosynthesis is one process that may be influenced by quantum effects. For example Sarovar M, Ishizaki A, Fleming GR, Whaley KB. (2010). Quantum entanglement in photosynthetic light-harvesting complexes. Nature Physics 6, 462–467.

  As Jacques Monod: Written in the 1970s, when the first insights into protein chemistry and the genetic code were being unraveled, Monod’s book is a beautifully written account of the behavior of life at the molecular level and how this defines a difference with other matter. However, even he succumbs to an astonished bewilderment at how different life is to other matter: “On such a basis, but not on that of a vague ‘general theory of systems,’ it becomes possible for us to grasp how in a very real sense the organism effectively transcends physical laws—even while obeying them—thus achieving at once the pursuit and fulfilment of its own purpose” (Monod J. [1972] Chance and Necessity. Collins, London, 81). If life obeys physical laws, it does not transcend them at any level. Nevertheless, Monod’s book explores many of the general themes advanced by Smith and Morowitz (1982), above, who say that the crucial difference between life and other forms of matter occurs at the molecular level, specifically, the DNA code that fixes errors and generates replicated variety.

  An atomic displacement: However, defects, substitutions of atoms, and other alterations can also sometimes be the source of new properties, including greater strength.

  There is generally no way: Crystals of substances that have a chiral nature can replicate this chiral signature in subsequent crystals. More-complex ideas for self-replicating crystals have been presented. See, for example, Schulman R, Winfree E. (2005) Self-replication and evolution of DNA crystals. In ECAL 2005, edited by M Capcarrere et al. LNAI 3630, 734–743.

  Stephen Jay Gould: For an entertaining and erudite insight into convergence and its possibilities, see Losos J. (2017) Improbable Destinies: How Predictable Is Evolution? Allen Lane, London. Losos believes that evolution is predictable, particularly among closely related lineages, but that there is considerable scope for contingent events to shape the course of evolution. My view is that contingency in the wonderful diversity of life forms is constrained, but that this is not inconsistent with the idea that physical solutions can be sufficiently varied to allow for a mélange of living things.

  He recognized the underlying laws: Gould SJ. (1989) Wonderful Life: The Burgess Shale and the Nature of History. Hutchinson Radius, London, 289–290.

  He elaborated on this: His book on the discovery of the Burgess Shale explores his and his colleagues’ exploits in revealing the hidden treasures: Gould SJ. (1989) Wonderful Life: The Burgess Shale and the Nature of History. Hutchinson Radius, London.

  have a mouth: This predictable structure was pointed out by Gould: “Bilaterally symmetrical creatures with heads and tails are almost always mobile. They concentrate sensory organs up front, and put their anuses behind, because they need to know where they are going and to move away from what they leave behind” (ibid., 156).

  Contingency is there: A point of view expressed by Simon Conway-Morris in a counterpoint to Gould is Conway-Morris S. (1999). The Crucible of Creation: The Burgess Shale and the Rise of Animals. Oxford University Press, Oxford.

  Indeed, since Gould’s paean to contingency: A good summary of the current state of knowledge, which also situates it in modern genetic data, is given by Budd GE. (2013) At the origin of animals: The revolutionary Cambrian fossil record. Current Genomics 14, 344–354.

  In some refinements: For a summary of constraints imposed by the history of an organism, see Maynard Smith J et al. (1985) Developmental constraints and evolution. Quarterly Review of Biology 60, 263–287. The authors also discuss how physical factors limit the spiral structures that can be used in shelled organisms, a particularly visual example of physical (biomechanical) factors driving evolution.

  The historical nuances: But before the reader thinks I am capitulating, this statement is primarily directed at the fine details. For example, one could be overwhelmed by the vast diversity of skeletal structures in vertebrates, but even this diversity can be constrained into a few well-defined forms. A thorough discussion of this limitation can be found in Thomas RDK, Reif W. (1993) The skeleton space. A finite set of organic designs. Evolution 47, 341–356.

  From that increase in surface area: For a fascinating hypothesis on the factors that caused the transition from the Ediacaran to the Cambrian fauna, see Budd GE, Jensen S. (2017) The origin of the animals and a “Savannah” hypothesis for early bilaterian evolution. Biological Reviews 92, 446–473, which provides a mechanism by which the transition out of the “flattened forms” of the Ediacaran could have occurred. A superb book on animal form and body plans is Raff RA. (1996) The Shape of Life: Genes, Development, and the Evolution of Animal Form. University of Chicago Press, Chicago. His book underscores that my statement about producing an invagination and turning a pancake into a more c
omplex organism with internal organs is probably a little flippant. The architecture and history of body plans and their phylogeny is a complex field still in dispute. However, my comment is simply designed to ask whether life really can be railroaded into a dead-end body plan from which it has no escape.

  Whether there are contingencies: Even on present-day Earth, certain organisms, such as jellyfish, have a pancake-like architecture, where the cells of the body are close to the outside surface.

  the whale’s indecision: I highlight again here the difference between mutability in life’s pathways and choices and the narrow limits of life curtailed by physical laws. The two are not contradictory. Life can have the flexibility to break free of past choices, but still be channeled into a limited set of forms.

  A growing compilation of evidence: And these discoveries, particularly in evolutionary developmental biology, raise important questions about whether evolution is just a tinkerer that has no choice but to mess around with existing plans and formats or whether it can act more like an engineer, making something that is completely new and fashioned for its environment (Jacob F. [1977] Evolution and tinkering. Science 196, 1161–1166). Clearly, evolution cannot start from scratch and must use what is there, but the restrictions in attempting new constructions may not be as great as once was thought. Jacob, in considering an alternative evolution, states unequivocally that “despite science fiction, Martians cannot look like us.” However, the devil is in the details. What do we mean by “look like us”? If we mean exactly like us in detail, then we must agree with Jacob. If we mean using the same sorts of sensors, limbs to walk, and structures to support the organism against gravity, then they are likely to seem eerily like us (accepting, of course, that the term “Martians” is used metaphorically to mean aliens in general, not literal Martians, which if they exist at all today are likely to be microbial).