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COB4

COB4

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Published by Ilya Korsunsky
Notes on lecture in computational biology
Notes on lecture in computational biology

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Published by: Ilya Korsunsky on May 29, 2013
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05/29/2013

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Ilya  Korsunsky   COB  reflection  paper  4   Justin  Jee  3/12/13     Justin  presented  his  work  on  2  disparate  yet  intimately

 related  topics,  the  evolution   of  the  genetic  code  and  the  evolution  of  ideas  as  evidenced  through  text  corpora.   One  of  the  most  interesting  themes  in  both  is  the  dominance  of  suboptimal   equilibria.  In  the  genetic  code,  some  messages  are  not  robust  to  error  and  therefore   small  mistakes  in  the  code  could  lead  to  large  mistakes  in  the  encoded  protein.  In   the  cultureomics  example,  the  idea  that  odors  spread  disease  dominated  over  the   less  popular  idea  that  physical  contact  spread  disease,  until  more  evidence  for  the   latter  appeared.  He  explained  this  in  a  game  theoretic  way.  The  utility  of  the   suboptimal  solution  is  high  enough  to  be  stable  and  changing  the  convention   radically  might  cause  more  harm  than  good  in  the  short  term.  For  instance,  changing   the  genetic  code  to  a  more  optimal  one  now  would  render  many  proteins  inactive   and  useless  and  thus  render  most  physiological  processes  unviable.  Thus,  the   suboptimal  solution  gets  stuck  and  may  never  be  replaced  by  the  optimal  one.       I  am  curious  as  to  what  kind  of  conditions  would  allow  the  genetic  code  to  optimize   even  further.  Historically,  this  seemed  to  happen  twice.  However,  the  evolution  of   ideas  seems  to  happen  much  more  frequently.  This  suggests  that  either  there  is  less   of  a  barrier  to  change  in  cultureomics  or  that  we  are  in  a  sort  of  Cambrian  explosion   of  ideas.  The  latter  suggests  that  this  flux  in  ideas  will  cool  down  and  we  will   eventually  settle  on  a  coherent  understanding  of  the  universe.    

 Longer  polypeptides  lead  to  a  greater  variety  of  proteins  that  can  do  different   things.  in  the   genetic  code.  with  a  bound  on  the  distortion.  it  makes  sense  to   favor  longer.  On  the  other  hand.  it  is  more  desirable.  In  information   theory.  which  is  the  length  of  the   gene.  after  all.  longer   messages  allow  for  description  of  more  complex  concepts.  which  is  clearly  evolutionarily  favorable.  the  complexity  of  the  action.  more  complex  messages.  as  they  lead  to  a  greater  behavior  repertoire.  In  particular.  which  is  the  length  of  the  resulting   polypeptide.  In  light  of  this.     .  is  linear  in  the  complexity  of  the  message.An  interesting  discussion  came  up  during  the  talk.  to  pack  as  much  information  into  a  short  a   message  as  possible.  A  participant  asked  why   messages  of  longer  length  should  be  considered  more  favorable.

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