Organization and Levels of Organization Characterization of a mechanism Since the 17th century science often appeals to mechanisms to explain phenomena A mechanism consists of parts entities and operations activities organized to produce a phenomenon Phenomenon what the mechanism does Parts the working parts of the mechanism Operations the work done by the parts that contributes to the activity These parts and operations are organized Multiple mechanisms in the same organ Kidneys perform a number of different phenomena Regulate blood composition keep concentrations of various ions and other metabolites constant Keep water volume constant Remove waste substances urea ammonia drugs toxic substances Keep blood acid base concentration constant Help regulate blood pressure Stimulate the making of red blood cells Maintain body s calcium levels Depending which phenomenon we focus on we will attend to different components and processes different mechanisms 1 Hard to Get Started When You Don t Know the Phenomenon Even Knowing this is a Video Recorder Leaves Lots of Puzzles What are its working parts What does each contribute How do they work together Sometimes You Need to Figure out Operations without Knowing the Parts What are the operations in fermentation 2 Understanding Mechanisms To explain the operation of a mechanism must decompose it into its Working parts Operations Often requires reverse engineering but also empirical inquiry Record operations of possible intermediaries while the mechanism is operating Inhibit possible intermediate processes to see if that stops the reaction lesion experiment Insert possible intermediaries to see if they could produce the end product excitation experiment Mechanisms are organized Mechanisms are not just components each doing their thing The components are organized so that the various operations carried out by the components feed appropriately into the operations of other components It is by virtue of these relations with other entities that they contribute to the performance of some activity Organization is critical to the operation of a lock 3 Organization even more important in a system of active components Using diagrams to portray organization It is very difficult to understand the organization of a complex system from a verbal description Diagrams are able to show in two dimensions the spatial layout of a mechanism Often though diagrams must also show the activity of the mechanism This must usually be done through arrows Organization of energetic reactions lactate pyruvate 2e 2e 2e DPN isocitrate amino acids acetyl Co a CO2 oxalosuccinate cis aconitate citrate fats ADP Kreb s Cycle ketogluterate 2e CYTb ADP succinate oxaloacetate ATP FP 2e fumarate ATP CYTc CYTa Electron Transport Chain glucose ATP ADP CYTa3 malate 2e O2 H2O 4 Diagramming steps in a process in separate diagrams Show organization at successive stages in the process of cell division Use arrows to reflect the progression of stages Mechanisms with multiple states When insulin present fatty acids and glucose are absorbed into fat cells and synthesize triglycerides When insulin absent Hormones enter the cell activating lipases which break down fats into fatty acids and glycerol Diagramming steps in a process in a common diagram Use arrows to trace the movement of components from one location to another here move various RNAs from the DNA of the nucleus to the ribosomes in the cytoplasm 5 Organization creates systems If the organization is appropriate the components comprise a new entity One existing at a higher level of organization Often it is cyclic organization involving later reactions influencing one s earlier in a pathway that turn a set of operations into a system a recognizable entity that does something Nervous system Circulatory system Levels of mechanism The system as a whole engages its environment by performing its activity That system is comprised of components that perform different activities Those components in turn are comprised of components that perform yet different activities Holism versus reductionism Tension Emphasizing organization focuses on the integration of the components into a whole system Emphasizing components focuses on the decomposition of the system into separate components Often conflict between holists vitalists and reductionists Holists charge that reductionists fail to consider the consequences of organization Reductionists charge that holists fails to provide explanations 6 Mechanistic explanations both reductionist and holist To understand a mechanism you must be both a holist and a reductionist Look both Upwards to higher levels of organization in which the mechanism performs its activity and thereby interacts with other entities and Downwards to lower levels of organization in which parts perform their operations in interaction with other parts Delineating the phenomenon of spatial memory To understand spatial memory you must know how it is exhibited including in what larger contexts In the Morris water maze rats quickly learn where the submerged platform is and swim directly to it Going inside to explain the phenomenon Inside the rat s brain one finds a structure the hippocampus that if removed leaves the rat unable to navigate inhibition or lesion experiment Inserting an electrode into the structure one finds cells that respond to specific places recording experiment 7 Molecular changes and long term potentiation Presynaptic neuron releases glutamate Glutamate binds to the NMDA receptor on the post synaptic cell Change in NMDA receptor exposes pore which however remains blocked by Mg ions If the postsynaptic cell fires Mg float out of the channel letting Ca ions enter This initiates a series of biochemical reactions in the postsynaptic cell only some of which are known Multi level account of memory Organisms develop memories Particular parts of their brains are especially important for encoding or storing memories Within these components biochemical changes result in altered systems that behave differently in the future The operations of these components only results in memory insofar as their operations are properly coordinated with each other Organization often produces surprising results from even simple components Beyond Linear Organization Negative Feedback The idea of organizing causal effects to be both forward and backward with backward used for control was rediscovered many times in history Water clocks required constant