With natural selection as the sole criterion and

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with natural selection as the sole criterion and consider their work done when they concoct a plausible story.“ -> Optimality models define a quantitative test for agreement with observations -> Population genetics can define criteria -> Falsifiable predictions are required Criticism on adaptionist arguments in biology Gould and Lewontin, Proc. Roy, Soc. (1979)
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60 Rejection of one story leads to another: “The rejection of one adaptive story usually leads to its replacement by another, rather than to a suspicion that a different kind of explanation might be required. Since the range of adaptive stories is as wide as our minds are fertile, new stones can always be postulated. And if a story is not immediately available, one can always plead temporary ignorance and trust that it will be forthcoming.“ -> Science proceeds by rejection of theories and replacement with new ones. -> Over-fitting and fine tuning should be avoided -> Adequacy and predictive power assessed by community Criticism on adaptionist arguments in biology Gould and Lewontin, Proc. Roy, Soc. (1979)
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61 Drift-selection balance (Michael Brenner)
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62 Fungal spores shape
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63 Understanding network structure: optimality in metabolism
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Solution to Pentose Phosphate game in 7 steps Corresponds to natural pathway Doesn't explain why the rules exist Supports the idea of simplicity
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65 Are there simplifying principles to structure of central carbohydrate metabolism network? But what do you mean simplifying principles? - handturn.html? ex=1354856400&en=c9a577b0fac3b645&ei=5090&part ner=rssuserland&emc=rss
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66 Searching for design principles in networks Analogy: Many stations connected in “shortest paths” But not all Finding sets of shortest relates to function (modules=lines, hub=down town)
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67 We develop a method to find shortest path from A to B
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68 All possible reaction types are explored aldehyde dehydrogenase (CoA): pyruvate ↔ acetyl-CoA + CO 2 isomerase (keto to enol): pyruvate ↔ enolpyruvate kinase (carboxyl): pyruvate ↔ pyruvate-P
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69 EC classes define 27 possible enzymatic reaction families
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70 Optimization function finds minimal number of steps between any two metabolites The shortest path can be found efficiently using a customized BFS (breadth first search) Fitness (3)
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71 Are all pairs of metabolites connected by shortest possible paths? (as allowed by biochemistry classes)
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72 Are all pairs of metabolites connected by shortest possible paths? (as allowed by biochemistry classes) Some pairs are connected by possible shortest paths Other pairs can be connected in less steps via shortcuts Cluster together pairs that contain shortest paths Define these as optimality modules
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73 Optimality modules are defined to contain shortest paths Only metabolites connected by shortest possible paths are contained in an optimality module Existing reactions (in organism) Possible EC reactions (biochemistry) Optimality modules A B C D E F A B C D E F A B C D E F
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74 GAP 3PG (EC 1.2) is biochemically feasible (exists in plants), but is not part of E. coli
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