Published Modelling Biology – working through (in-)stabilities and frictions

Just had our paper on Com­pu­ta­tion­al Bio­logy pub­lished in the online journ­al Com­pu­ta­tion­al Cul­ture.

Alex S. Taylor, Jas­min Fish­er, Byron Cook, Sam­in Ish­tiaq and Nir Piter­man (2014) Mod­el­ling Bio­logy – work­ing through (in-)stabilities and fric­tions. Com­pu­ta­tion­al Cul­ture, 1 (4).


Abstract: Com­pu­ta­tion­al bio­logy is a nas­cent field reli­ant on soft­ware cod­ing and mod­el­ling to pro­duce insights into bio­lo­gic­al phe­nom­ena. Extreme claims cast it as a field set to replace con­ven­tion­al forms of exper­i­ment­al bio­logy, see­ing soft­ware mod­el­ling as a (more con­veni­ent) proxy for bench-work in the wet-lab. In this art­icle, we deep­en and com­plic­ate the rela­tions between com­pu­ta­tion and sci­en­ti­fic ways of know­ing by dis­cuss­ing a com­pu­ta­tion­al bio­logy tool, BMA, that mod­els gene reg­u­lat­ory net­works. We detail the instabil­it­ies and fric­tions that sur­face when com­pu­ta­tion is incor­por­ated into sci­en­ti­fic prac­tice, fram­ing the ten­sions as part of knowing-in-progress—the prac­tic­al back and forth in work­ing things out. The work exem­pli­fies how soft­ware studies—and care­ful atten­tion to the mater­i­al­it­ies of computation—can shed light on the emer­ging sci­ences that rely on cod­ing and com­pu­ta­tion. Fur­ther, it puts to work a stand­point that sees com­pu­ta­tion as tightly entangled with forms of sci­en­ti­fic know­ing and doing, rather than a whole­sale replace­ment of them.

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