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The Equations of Life

Page 33

by Charles S. Cockell


  Viruses, small pieces: Viruses contain either DNA or RNA, and these molecules can be in either single- or double-stranded form. For protein coats, note that the assembly of these relatively simple entities can be understood in physical terms. A classic paper describing the geometry of viruses and the mathematical and physical principles that shape their protein coats is Caspar DLD, Klug A. (1962) Physical principles in the construction of regular viruses. Cold Spring Harbor Symposia on Quantitative Biology 27, 1–24.

  The first molecules: In this book, I do not address whether the emergence of life is inevitable. This omission is not a capitulation. I regard the issue as a different question. We do not know whether life is inevitable on a planet with water and clement conditions. It is a profound question at the interface between biology and physics to ask whether suitable physical conditions on a rocky planet will inevitably lead to life. I am interested here in the restrictions on life once it does emerge. However, an intriguing take on the physical and chemical basis of the origin of life is pursued by Pross A. (2012) What Is Life? Oxford University Press, Oxford.

  the 1980s, David Deamer: A detailed account of this work can be found in Deamer D. (2011) First Life: Discovering the Connections Between Stars, Cells, and How Life Began. University of California Press, Berkeley. In this book, Deamer also explores many other conundrums about the origin of life as well as how cellularity allowed for complexity of metabolic processes. A paper summarizing results with self-assembling membranes is Deamer D et al. (2002) The first cell membranes. Astrobiology 2, 371–381.

  Deamer had shown: A paper that takes a theoretical approach to understanding the physics of self-assembling vesicles and even their reproduction is Svetina S. (2009) Vesicle budding and the origin of cellular life. ChemPhysChem 10, 2769–2776.

  Provided that the gases: One of the strangest links between membranes and astronomy is the observation that in the endoplasmic reticulum (the organelle responsible for protein synthesis in eukaryotic cells), layers of membranes are attached to one another in stacks linked with helicoid ramps in a shape resembling a parking garage. Similar structures are thought to exist in the extreme conditions of neutron stars. Whether this similarity of shape is coincidence or reflects some underlying physical principle to do with energy minimization is not known, but the bizarre observation might reflect the common physics underlying patterns in nature: Berry DK et al. (2016) “Parking-garage” structures in nuclear astrophysics and cellular biophysics. Physical Review C 94, 055801.

  Pyruvic acid: Described in Deamer (2011) First Life, above.

  Although these ingenious: Some ideas on the environments and processes leading to the first protocells are nicely described in Black RA, Blosser MC. (2016) A self-assembled aggregate composed of a fatty acid membrane and the building blocks of biological polymers provides a first step in the emergence of protocells. Life 6, 33.

  Some scientists think: Martin W, Russell MJ. (2007) On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical Transactions of the Royal Society 362, 1887–1926.

  Others think: Cockell CS. (2006) The origin and emergence of life under impact bombardment. Philosophical Transactions of the Royal Society 1474, 1845–1855.

  Perhaps Darwin’s “warm little pond”: Darwin described the origin of life in a letter to his friend Joseph Hooker (February 1, 1871): “But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity etc present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter would be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.”

  Deamer’s experiments… schizophrenic molecules: More technically termed amphiphilic.

  The simplicity of these pathways: Smith E, Morowitz HJ. (2004) Universality in intermediary metabolism. Proceedings of the National Academy of Sciences 101, 13,168–13,173.

  By testing thousands: Court SJ, Waclaw B, Allen RJ. (2015) Lower glycolysis carries a higher flux than any biochemically possible alternative. Nature Communications 6, 8427. However, the authors did also show that the route nature uses is not the only possibility. Under different environmental conditions in the cell, other pathways could be used.

  These independent investigations: Similar findings of strong selection based on physical considerations have been reported in studies of the regulatory networks involved in the cell cycle. A high degree of robustness to perturbation was found. See, for example, Li F, Long T, Lu Y, Ouyang Q, Tang C. (2004). The yeast cell-cycle network is robustly designed. Proceedings of the National Academy of Sciences 101, 4781–4786. The information within biological networks may be different from purely random networks and may provide ways of understanding which physical principles are instantiated into biological systems as they emerge. See Walker SI, Kim H, Davies PCW. (2016) The informational architecture of the cell. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, article 0057.

  Nor do these sorts of conclusions: Computational modeling has been used to study how easily one metabolic pathway can change into another and thus whether existing pathways are very much a product of historical quirks. Barve and colleagues conclude their paper with this comment about flexibility of pathways: “Metabolism is thus highly evolvable.… Historical contingency does not strongly restrict the origin of novel metabolic phenotypes.” Barve A, Hosseini S-R, Martin OC, Wagner A. (2014) Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolism. BMC Systems Biology 8, 48.

  Instead, many metabolic process: The pervasive question of predictability in evolutionary possibilities has received some attention at the scale of biochemical pathways. At the metabolic level, with knowledge of an organism’s environment and lifestyle, we can apparently predict with quite surprising accuracy where and how a pathway will develop (Pál C et al. [2006] Chance and necessity in the evolution of minimal metabolic networks. Nature 440, 667–670). An important paper suggests that only a few designs, or topologies, of biochemical pathways are possible. This work suggests that at the very least, the structure of biochemical networks may be quite predictable (Ma W et al. [2009] Defining network topologies that can achieve biochemical adaptation. Cell 138, 760–773).

  When the first cells moved: How the environment might fashion the shape of microbes is beautifully described in Young KD. (2006) The selective value of bacterial shape. Microbiology and Molecular Biology Reviews 70, 660–703.

  One first indefatigable effect: For a discussion on the ethical implications of a hypothetical world in which bacteria are the size of dogs, see Cockell CS. (2008) Environmental ethics and size. Ethics and the Environment 13, 23–39.

  There are many causes: Several essays exploring a range of factors influential in determining cell size are found in: Marshall WF et al. (2012) What determines cell size? BMC Biology 10.101. An excellent and simple discussion of the role of diffusion is Vogel S. (1988) Life’s Devices: The Physical World of Animals and Plants. Princeton University Press, Princeton, NJ.

  A large bag: A fascinating study has suggested that if cells grow larger than about ten micrometers, gravity begins to become significant and may explain why large frog ovary cells, which can be greater than one millimeter in diameter, have a molecular (actin) scaffold around their nucleus to stabilize them against the effects of gravity (Feric M, Brangwynne CP. [2013] A nuclear F-actin scaffold stabilizes ribonucleoprotein droplets against gravity in large cells. Nature Cell Biology 15, 1253–1259). An interesting implication is the speculation that on planets with lower gravity, larger cells may be possible, all other things being equal.

  The larger you are: Beveridge TJ. (1988) The bacterial surface: General considerations towards design and function. Canadian Journal of Microbiology 34, 363–372. Diffusion may be less important a factor than was once supposed. The cell int
erior turns out to be remarkably crowded, and the model of a molecule diffusing passively through a fluid is too simple.

  That smallest theoretical size: This size limit was arrived at by a group of people attempting to define the smallest expected microbe. They were partly motivated to ascertain what the smallest possible biological signature of a cell might be on another planet, for example on Mars. The study is intriguing, as it was provoked by researchers’ desire to set a universal boundary of cell size (National Research Council Space Studies Board [1999] Size Limits of Very Small Microorganisms. National Academies Press, Washington, DC. However, note that a size range of one hundred to three hundred nanometers for the minimum cell was arrived at by Alexander RM. (1985) The ideal and the feasible: Physical constraints on evolution. Biological Journal of the Linnean Society 26, 345–358.

  The estimate actually fits: Do not be fooled. This diminutive creature can reach up to 50 percent of all the biomass in surface water in the oceans. It is immensely important in cycling carbon in the Earth’s oceans.

  When we talk of smallness: Descriptions of these microbes and some discussion of the physics behind their lifestyles are to be found in the very clearly titled paper Schulz HN, Jørgensen BB. (2001) Big bacteria. Annual Reviews of Microbiology 55, 105–137.

  Here, instead of nutrient needs: Described in Persat A, Stone HA, Gitai Z. (2014) The curved shape of Caulobacter crescentus enhances surface colonization in flow. Nature Communications 5, 3824.

  In these places: Kaiser GE, Doetsch RN. (1975) Enhanced translational motion of Leptospira in viscous environments. Nature 255, 656–657.

  These laws: In this context, I refer the reader to fascinating work by Jeremy England and his group, who suggest that adaptation can be realized without selection. Chemical systems can fine-tune their processes in response to their environments as the system establishes resonances with the very environmental factors acting on it. This observation should not be taken as yet another hackneyed attempt to prove that Darwin was wrong. Instead, it shows that organic matter’s ability to evolve may well be aided by its natural tendency to take on forms that reflect its environment, even before the environment has acted to select the forms of that matter that successfully reproduce. England and his colleagues’ work show that biological evolution does not work unexpectedly against disorder, but that emergent complexity in physical systems, including life, favors this process. See, for example, Horowitz JM, England JL. (2017) Spontaneous fine-tuning to environment in many-species chemical reaction networks. Proceedings of the National Academy of Sciences 114, 7565–7570; and Kachman T, Owen JA, England JL. (2017) Self-organized resonance during search of a diverse chemical space. Physical Review Letters 119, 038001.

  In this medley: In some outstanding experiments, Richard Lenski’s group studied populations of the bacterium Escherichia coli to see if they could separate the effects of adaptation, chance, and historical influence in microbial evolution. They found that adaptation was extraordinarily versatile, allowing organisms to mutate to achieve a similar fitness with little effect of contingency or history. However, in traits that were not so important for fitness in these particular experiments, such as cell size (which may, however, be important in more natural environments), contingency could throw up variants presumably because the effects of these mutants were neutral. History could also affect subsequent cell size. Their observations are probably quite generalizable; if a trait has little direct impact on survival to reproductive age in any organisms, then the trait may be more susceptible to chance alterations or it may reflect the idiosyncrasies of past historical attributes. Travisano M, Mongold JA, Bennett AF, Lenski RE. (1995) Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267, 87–89.

  Once the prey: Proposed by Lake JA. (2009) Evidence for an early prokaryotic endosymbiosis. Nature 460, 967–971.

  These chemical products: This alternative idea was suggested by Gupta RS. (2011) Origin of the diderm (Gram-negative) bacteria: Antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Antonie van Leeuwenhoek 100, 171–182.

  In the archaea: The charged heads of the lipids that stick into the water are linked to their long chains by ether linkages in the archaea, rather than the more familiar ester linkages in bacteria. For an in-depth discussion of their chemical differences, see Albers S-V, Meyer BH. (2011) The archaeal cell envelope. Nature Reviews Microbiology 9, 414–426.

  Cooperation, forced: A classic paper presenting a view of the multicellular capacities of bacteria is Shapiro JA. (1998) Thinking about bacterial populations as multicellular organisms. Annual Reviews of Microbiology 52, 81–104. Another view is Aguilar C, Vlamakis H, Losick R, Kolter R. (2007) Thinking about Bacillus subtilis as a multicellular organism. Current Opinion in Microbiology 10, 638–643.

  These patterns and order arise: Like ants, birds, and schooling fish (Chapter 2), bacteria are the focus of physicists studying active matter. Their collective behavior lends itself to modeling and simulation. See Copeland MF, Weibel DB. (2009) Bacterial swarming: A model system for studying dynamic self-assembly. Soft Matter 5, 1174–1187; and Wilking JN et al. (2011) Biofilms as complex fluids. Materials Research Society (MRS) Bulletin 36, 385–391.

  Equations can be used: The responses of large numbers of cells to chemical cues can be modeled. See, for example, Camley BA, Zimmermann J, Levine H, Rappel W-J. (2016) Emergent collective chemotaxis without single-cell gradient sensing. Physical Review Letters 116, 098101.

  domain of the eukaryotes: Prokaryote, literally translated as “before the kernel,” encompasses microbes without a cell nucleus (i.e., most microbes on Earth), in contrast to the eukaryotes (“true nucleus”), organisms whose cells generally contain a nucleus. Eukaryotes do include some single-celled microbes such as algae and some fungi, including yeasts, but these single-celled organisms have a nucleus and other organelles.

  The eukaryotic cell is: It is established that endosymbiosis led to the chloroplast, the photosynthetic apparatus in algae and plants. It began its life as an engulfed cyanobacterium.

  Many hundreds: Lane N, Martin W. (2010) The energetics of genome complexity. Nature 467, 929–934.

  Coupled with this: The potential role of genome complexity as another major difference between prokaryotes and eukaryotes as a critical pathway to animal life is elaborated on in Lynch M, Conery JS. (2003) The origins of genome complexity. Science 302, 1401–1404.

  Microbes that could grab: Photosynthesis using oxygen evolved only once: the early cyanobacteria that mastered this trick eventually became engulfed to make algae and plants. Although photosynthesis has appeared once, it is not necessarily an unlikely evolutionary development, a contingent fluke. Instead, once that feat had been achieved, habitats became filled with photosynthesizers and there may have been few niches left for a second evolution of this pathway to move into.

  Endosymbiosis has happened: Just one such example is Marin BM, Nowack EC, Melkonian M. (2005) A plastid in the making: Evidence for a second primary endosymbiosis. Protist 156, 425–432.

  Then the cells gather: Slime molds can even be used to re-create the most efficient connections between two points. By placing them on maps in the laboratory (where cities and towns are globs of food), they can even be used to predict the best road and rail networks across landscapes such as the Tokyo rail system (Tero A et al. [2010] Rules for biologically inspired adaptive network design. Science 327, 439–442) or Brazilian highways (Adamatsky A, de Oliveira PPB. [2011] Brazilian highways from slime mold’s point of view. Kybernetes 40, 1373–1394). Many other countries’ transport networks have been scrutinized using Physarum plasmodium and P. polycephalum.

  We do not know the exact events: There are many theories for how this might have happened. Insights into cell communication and the genetics of how cells attach and signal are likely to reveal many steps that led from unicellular organisms to true multicellular (differentia
ted) organisms. See, for example, King N. (2004) The unicellular ancestry of animal development. Developmental Cell 7, 313–325; and Richter DJ, King N. (2013) The genomic and cellular foundations of animal origins. Annual Reviews of Genetics 47, 509–537.

  Put simply, the rise of multicellularity: Multicellular structures may emerge from the interaction of physical principles. See Newman SA, Forgacs G, Müller GB. (2006) Before programs: The physical origination of multicellular forms. International Journal of Developmental Biology 50, 289–299.

  A biological arms race: Dawkins R, Krebs JR. (1979) Arms races between and within species. Proceedings of the Royal Society 205, 489–511. Regarding sometimes larger machines, a tendency to become larger may also occur simply because organisms are constrained by the minimum size of cells in becoming smaller so they inevitably move into the larger morphospace of possible forms. See Gould SJ. (1988) Trends as changes in variance: A new slant on progress and directionality in evolution. Journal of Paleontology 62, 319–329. Even this process, though, results from a simple physical principle: organisms become larger to fill available niches that will allow for larger organisms (e.g., on account of energy available for such forms).

  The second claim: We must also be mindful that a planet has a finite lifetime. If the stages along the way between a microbe and a mammoth exceed the time that a planet hosts habitable conditions, then the experiment in evolution will be cut short. This sad end is rooted unambiguously in physics too, the evolution of a star unkindly intercepting the trajectory of life.

  Considering the inevitability: It has been proposed that very few, if any, of the innovations between the origin of life and the numerous key adaptations in multicellular organisms may be unique, that is, singularities in the evolutionary process. See, for example, Vermeij GJ. (2006) Historical contingency and the purported uniqueness of evolutionary innovations. Proceedings of the National Academy of Sciences 103, 1804–1809.

 

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