Catalyzing Inquiry at the Interface of Computing and Biology

COMPUTATIONAL MODELING AND SIMULATION AS ENABLERS FOR BIOLOGICAL DISCOVERY 199 (^116) E.V. Koonin, N.D. Fedorova, J.D. Jackson, ...

200 CATALYZING INQUIRY modest efficiency and fidelity could evolve a succession of ever-larger genomes and ever-higher repli- ca ...

COMPUTATIONAL MODELING AND SIMULATION AS ENABLERS FOR BIOLOGICAL DISCOVERY 201 fitness ratings. (This phenomenon is known as con ...

202 CATALYZING INQUIRY dispersal declines with distance. Mortality risk is also stochastic and has two elements: random mortal- ...

COMPUTATIONAL MODELING AND SIMULATION AS ENABLERS FOR BIOLOGICAL DISCOVERY 203 Box 5.24 Modeling Challenges for Computer Science ...

204 CATALYZING INQUIRY In the second category, issues related to implementing the model arise. Often such issues involve the act ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 205 205 6A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY Because 21st century bi ...

206 CATALYZING INQUIRY Consider that biological processes, such as catalysis, protein synthesis, and other metabolic sys- tems, ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 207 the science of thermodynamics. Only after energy had been identified and stu ...

208 CATALYZING INQUIRY For example, a simple enzyme protein could be viewed as a computational element that takes an input—the c ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 209 This perspective on cells as computational devices should not be taken as an ...

210 CATALYZING INQUIRY It is also interesting that biological function often relies on what might be called exploration with sel ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 211 behavior, and manifest an evolutionary history.^16 Engineered artifacts serv ...

212 CATALYZING INQUIRY identify the system’s components and their interrelationships and (2) to create representations of the sy ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 213 cells that make up the system. The philosophical notion embedded in the bott ...

214 CATALYZING INQUIRY Important insights into biological organisms can be gained by seeking to identify general principles that ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 215 the building blocks remain more or less stable, while the connectivity among ...

216 CATALYZING INQUIRY FIGURE 6.1 The endomesoderm specification network in the sea urchin species Strongylocentrotus purpuratus ...

A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY 217 approximately 50 genes underlying an early cell-type specification event in ...

218 CATALYZING INQUIRY however, refers to the ability of a structure or process to persist in the face of perturbations of inter ...