Biology 182 Lecture I: What is Life?

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Biology 182 Lecture I: What is Life? W. M. Schaffer 1/11/2007 I. Biology. A. The study of living systems: Their form, function, development (ontogeny) and evolution. B. A diverse field composed of numerous sub-disciplines: biochemistry, cell biology, physiology, ecology, etc.

1 Biology 182 Lecture I: What is Life? W. M. Schaffer 1/11/2007 I. Biology. A. The study of living systems: Their form, function, development (ontogeny) and evolution. B. A diverse field composed of numerous sub-disciplines: biochemistry, cell biology, physiology, ecology, etc. II. Levels of Organization. A. Much of this disciplinary diversity reflects the hierarchical nature of biological organization - i.e., the fact biological systems can be studied at different length scales: molecules, cells, tissues, organs, individuals, populations, ecosystems, the entire planet. B. As we move from molecules up, time scales also increase (Figure 1). 1. Doubling time of a bacterium on the order of 15 minutes; 2. Doubling time of even rapidly growing human populations on the order of decades. C. What we observe at any one level of organization can 1. Reflect interactions among elements at that level; 2. Result from activity at a lower level; 3. Be influenced by processes at a higher level. Figure 1. Generation time increases with body size over a wide range of length scales. D. First example: Kinetic Theory of Gases. 1. At the microscopic level, we have molecules often imagined to be hard steel balls moving randomly in some confined volume. In this regard, we can calculate rates of molecular collision from a. Number of molecules; b. Distribution of velocities. 2. At the macroscopic level, we have pressure, volume and temperature, which we can measure on the lab bench. a. Pressure, volume and temperature are macroscopic concepts: they have no meaning at the microscopic level where there is only molecular motion and collision. 1

2 b. Empirically, we can relate these quantities to each other via the Ideal Gas Law, PV = NkT, where N is the number of molecules, and k is the Boltzmann constant ( joule/k ). 3. Remarkably, we can deduce the gas law from a model of molecular motion wherein we assume that a. the distribution of molecular speeds varies with temperature as shown in Figure 2, b. collisions between molecules are perfectly elastic, c. etc. 4. According to this, pressure and the gas law are emergent properties of the microscopic ensemble. Figure 2. Distribution of molecular speeds in an ideal gas. With increasing temperature, T, the distribution is shifted to the right, i.e., more molecules travel at higher speeds. E. Second example: Bee Colony. 1 At the microscopic level, we have individual bees: queen(s), workers and (briefly) drones, and we can study interactions among them. 2 At the macroscopic level, we can study properties of the hive as a whole. These include: a. Activity patterns, e.g., task distributions (who does what and for how long) of the population as a whole as opposed to corresponding patterns of individuals. b. Distribution of brood, pollen and nectar within the colony. c. Temperature and humidity of the colony. 3. Especially interesting is the honey comb itself, which workers build, but cannot see no light in the hive (Figure 3). 4. More generally, no single bee can assess the entire hive there are no apian engineers in control cells monitoring conditions on their computers. 5. Thus, colony-wide properties a. result from local interactions among individuals with limited information b. are emergent properties of the microscopic ensemble. F. The study of emergent properties in complex systems is a hot topic in contemporary biology. Self-organization 1. is ubiquitous think development, consciousness, etc.; 2. offers an alternative to Paley s [p00] watchmaker; 3. alters our perception of natural selection in the sense that changes in fundamental attributes of the ensemble are what induce macroscopic change. 2

Figure 3. A selection of characteristic spatial patterns built by social insects. (a) A termite mound built by Nasutitermes triodiae (northern territory of Australia).

3 Figure 3. A selection of characteristic spatial patterns built by social insects. (a) A termite mound built by Nasutitermes triodiae (northern territory of Australia). (b) A cross-section of Cubitermes spp. nest showing its alveolar structure (Ivory Coast, Africa). (c) A cross-section of a Lasius fuliginosus nest showing its sponge-like structure (France). (d) An external view and a cross-section of an Apicotermes lamani nest (Gabon, Africa). (e) A close-up view of helicoidal ramps connecting successive floors inside an Apicotermes lamani nest (Gabon, Africa). (f ), (g) Two frames showing the characteristic pattern of a centrally located brood surrounded by a band of pollen and a peripheral region of honey in a bee hive (Apis mellifera). (Theraulaz, G., et al The formation of spatial patterns in social insects: from simple behaviours to complex structures. Phil. Trans. R. Soc. Lond. A 361: ). 3

4 III. Complexity. A. The foregoing allows us to better understand what we mean when we say that living systems are complex. B. It s not just that they are complicated they are, of course. C. Rather it is the fact that the interacting entities represent multiple time and length scales that are partially overlapping. 1. The simplification that one observes in many physical systems separation of time and length scales does not apply. 2. More precisely, division of the world into system and environment as shown in Figure 4 is clouded. a. There is almost always a dotted line (from System to Environment) signifying weak / slow effect reciprocal interactions. b. Good example is oxygenation of the earth s atmosphere way back when. 3. There are two important intellectual consequences: a. Increased potential for complex behavior and unpredictability. b. Increased difficulty (for the biologist) in sorting things out. 4. A further consequence (sociology of science) is that biology is an interdisciplinary endeavor (connections among its constituent sub-disciplines) with strong ties to other sciences: chemistry, mathematics, physics, etc. D. All of this begs a more basic question: What is life? Figure 4. Partitioning the world into system and environment requires non-overlapping time and length scales. III. Law of Intermediate Numbers. A. Traditional physics deals with simple systems few or very large numbers of similar, if not identical, objects physicists count one, two, many. B. Living systems are complex with many (but not too many) molecules, organelles, cells, tissues, organs, individuals, populations 1. One, two or many => simple behavior and no statistical uncertainty either the system is deterministic or random variations get averaged out, i.e., the sample mean is the longterm expectation. 2. Intermediate numbers => complex behavior and observable randomness. C. Difference in numbers (between animate and many inanimate systems) complements differences in degree of time / length scale overlap. 4

IV. Breaking the 2 nd Law. A. Equilibria: 1. The term equilibrium refers to the absence of change. 2. Thermodynamic equilibrium, sometimes called heat death, => absence of pattern in time and space.

5 IV. Breaking the 2 nd Law. A. Equilibria: 1. The term equilibrium refers to the absence of change. 2. Thermodynamic equilibrium, sometimes called heat death, => absence of pattern in time and space. Instead, one has infinite sameness. 3. Biological equilibrium involves the maintenance of local order the result of influx of energy and materials in defiance of the 2 nd Law. B. In a series of lectures delivered at the University of Dublin in 1943, Erwin Schrödinger [s47] famously observed that biological order results from two sources: 1. Order from order: a. The existence of a molecular code an aperiodic crystal containing the information necessary for organismal development and function this was before DNA. b. The consumption (by animals) of already organized materials (their food). 2. Order from disorder: The use of energy to create complex structures and orchestrate complex behaviors over time. 3. We now know in addition that the expenditure of energy is further used to preserve integrity of the genetic code. C. Maintaining biological order is an on-going process involving 1. Homeostasis maintenance of internal environment within tolerable limits e.g., variation of metabolic rate with temperature in mamamls (Figure 5) leads to consideration of stability and feedback. 2. Repair 4. These mechanisms generally fall apart as we age which observation leads to consideration of a. Consequences to fitness of increasing reproduction and survival as we age b. Alternative allocation of finite resources. E. Not all biological processes involve expenditure of energy. Some are passive, utilizing potential energy for example, evaporation of water from leaves sets up the flow of water into the roots of plants. But the net is consumption this is true even of primary producers. Figure 5. Maintenance of constant body temperatures in mammals and birds entails the expenditure of energy. At low ambient temperatures, the animal increases its metabolic rate, thereby generating heat. At high temperatures, it pants or perspires. This also results in increased metabolism, but the net effect (up to a point) is evaporative cooling. 5

6 V. Definition of Life. A. Weber [w03] (quoting Harold [01]) gives the following definition: Living organisms are self-constructing, self-maintaining, energy-transducing autocatalytic entities in which information needed to construct the next generation of organisms is stabilized in nucleic acids that replicate within the context of whole cells and work with other developmental resources during the life-cycles of organisms. B. To this he adds, they are also systems capable of evolving by variation and natural selection: selfreproducing entities, whose forms and functions are adapted to their environment and reflect the composition and history of an ecosystem. C. Why the addition? VI. Necessity of Evolution. A. Repair mechanisms notwithstanding, reproduction necessitates duplicating the genetic material and this => heritable variation, i.e., errors. B. In turn, this => differential reproduction / survival and hence, evolution. 1. As soon as one gets individuals that reproduce (i.e., historically), evolution begins. 2. Note that variation comes in many forms ranging from point mutations (affect a single amino acid) to the fusion of formerly free-living individusld (origin of mitochondria and plastids). C. Naively, one might expect progress toward, if not achievement of, the ideal organism. 1. But relative superiority depends on the context. a. If we imagine evolution a game, there are multiple players: b. What s best for A at any time depends on current strategies of B, C, etc. c. Result can be cyclic patterns of change, co-evolutionary arms races. 2. Contiunuing evolution further promoted by environmental change, which includes recurrent catatrophes large and small. VII. Consequences of Evolution. A. Descent with modification and the Tree of Life, which is not always a tree. B. Proximate (physiological, developmental, historical) vs. ultimate (adaptive) explanations of why the world is the way it is. 6

7 References. [h01] Harold, F.M The Way of the Cell: Molecules, Organisms and the Order of Life. Oxford Univ. Press. New York. [p00] Paley, W Natural Theology. [s47] Schrödinger, E What is Life? Cambridge Univ. Press. UK. [w03] Weber, B Life. Stanford Encyclopedia of Philosophy. ( 7

Enduring understanding 1.A: Change in the genetic makeup of a population over time is evolution.

Enduring understanding 1.A: Change in the genetic makeup of a population over time is evolution. The AP Biology course is designed to enable you to develop advanced inquiry and reasoning skills, such as designing a plan for collecting data, analyzing data, applying mathematical routines, and connecting