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mso-layout-grid-align:none;text-autospace:none'><b style='mso-bidi-font-weight: normal'><span style='font-size:24.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman";color:#74120F'>Evolution and Computation</span></b><span style='font-size:16.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal align=center style='text-align:center;mso-pagination:none; mso-layout-grid-align:none;text-autospace:none'><b style='mso-bidi-font-weight: normal'><span style='font-size:24.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman";color:#74120F'>&nbsp;</span></b><span style='font-size:16.0pt; font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p><b><span style='font-size:18.0pt'>Instructor:&nbsp;</span></b> <span style='font-size:13.5pt'><a href="http://www.cs.berkeley.edu/%7Echristos">Christos H. Papadimitriou</a></span><span class=GramE><span class=grame>&nbsp; </span></span><br> <span style='font-size:13.5pt'>Soda 689,&nbsp;</span> <span style='font-size: 13.5pt'><a href="mailto:%20christos@cs.berkeley.edu"><span class=SpellE><span class=spelle><span style='color:blue'>christos@cs</span></span></span></a>, (510) 642-1559</span><o:p></o:p></p> <p><b><span style='font-size:18.0pt'>Office Hours:&nbsp; </span></b><span style='font-size:13.5pt'>Mondays and Thursdays 5-6pm, and by appointment</span> <o:p></o:p></p> <p><b><span style='font-size:18.0pt'>Meets:</span></b><span style='font-size: 13.5pt'>&nbsp; Thursdays 5:00-7:00pm, in Soda 320. </span><o:p></o:p></p> <p><b><span style='font-size:18.0pt'>Units:&nbsp; </span></b><span style='font-size:13.5pt'>two.</span><o:p></o:p></p> <p><span class=GramE><span class=grame><b><span style='font-size:18.0pt'>Course&nbsp; Format</span></b></span></span><b><span style='font-size:18.0pt'>:&nbsp; </span></b><span style='font-size:14.0pt'>A reading course.<span style="mso-spacerun:yes"> </span>Each meeting will be a two-hour discussion of the week s readings.&nbsp; <span style="mso-spacerun:yes"></span></span><o:p></o:p></p> <p><b><span style='font-size:18.0pt'>Purpose</span></b><b><span style='font-size:14.0pt'>:<span style="mso-spacerun:yes"> </span></span></b><span style='font-size:14.0pt;font-family:"Times New Roman"'>Evolution is one of the greatest problems in science, as well as a flourishing research endeavor, and sophisticated mathematics have been employed in its development.&nbsp; Computational formalisms have also been used, albeit mostly for processing, as in genomics and phylogeny.<span style="mso-spacerun:yes"> </span>A leading thinker of the field has recently noticed that evolution has relied for too long on the mathematics of physics, that is, the kind used to study rolling balls.<span style="mso-spacerun:yes"> </span>During this semester, the Simons Institute at UC Berkeley has a semester-long program on <a href="http://simons.berkeley.edu/programs/evolution2014">Evolutionary Biology and the Theory of Computing</a> bringing together some of the world s leading scientists in this discipline.<span style="mso-spacerun:yes"> </span>One of the purposes of this course is to make this opportunity more accessible to the department s students.</span><span style='font-size:14.0pt'><o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><b style='mso-bidi-font-weight:normal'><span style='font-size:18.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>Course Requirements:</span></b><span style='font-size:18.0pt; font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'>&nbsp; <o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:16.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoListParagraph style='text-indent:-18.0pt;mso-pagination:none; mso-list:l0 level1 lfo1;mso-layout-grid-align:none;text-autospace:none'><![if !supportLists]><span style='font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span style='font-size:14.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>Each week read the assigned readings, and <span class=GramE>write</span> a one-page essay whose purpose is to convince the reader that you have comprehensively absorbed the assigned reading and you have thought creatively about it (due:<span style="mso-spacerun:yes"> </span>Thursday 5pm).<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoListParagraph style='text-indent:-18.0pt;mso-pagination:none; mso-list:l0 level1 lfo1;mso-layout-grid-align:none;text-autospace:none'><![if !supportLists]><span style='font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span style='font-size:14.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>Attend all meetings, participate in the discussion, and contribute to it.<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoListParagraph style='text-indent:-18.0pt;mso-pagination:none; mso-list:l0 level1 lfo1;mso-layout-grid-align:none;text-autospace:none'><![if !supportLists]><span style='font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span style='font-size:14.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>By the end of the semester, write a longer essay on an advanced topic of your choice.<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:16.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><b style='mso-bidi-font-weight:normal'><span style='font-size:18.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>Contents </span></b><span style='font-size:12.0pt; font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'>(as it looks right now)</span><b style='mso-bidi-font-weight:normal'><span style='font-size:18.0pt;font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>:<o:p></o:p></span></b></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:16.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>First three weeks, the classics:&nbsp; Darwin (Get <i style='mso-bidi-font-style:normal'>The Origin of Species</i>.<span style="mso-spacerun:yes"> </span>Make sure your copy has the 1959 foreword by Huxley), Weismann, Mendel, more.&nbsp; <span style="mso-spacerun:yes"></span>Also note the Simons Institute program s <a href="http://simons.berkeley.edu/workshops/evolution2014-boot-camp">boot camp</a> starting the same day as the course.<span style="mso-spacerun:yes"> </span>Make sure to attend as much as you can, it will be invaluable help in this class.<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>Next five weeks, molecular and quantitative foundations:<span style="mso-spacerun:yes"> </span><span class=SpellE>Graur</span> and Li  Fundamentals of Molecular Evolution second edition, Chapters 1 and 2.<span style="mso-spacerun:yes"> </span>We ll also read classics <span class=SpellE>likeWatson</span> and Crick, Fisher, Wright, etc. <o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>Next two weeks, Haldane s  The cost of Natural Selection and  Why sex and recombination? by Barton and <span class=SpellE>Charlesworth</span>, among others.<span style="mso-spacerun:yes"> </span>In parallel, we ll read about organisms (to remember that all this science is about wondrous, amazing, beautiful life& ).<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>Next three weeks:&nbsp; Computational theories of evolution.&nbsp; Selection from:&nbsp; Valiant's theory of <span class=SpellE>evolvability</span>, Evolutionary algorithms, <span class=SpellE>Livnat's</span> theory of <span class=SpellE>mixability</span>, evolutionary game theory, Artificial Life, etc.<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>&nbsp;<o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>Final four weeks:<span style="mso-spacerun:yes"> </span>Selection from other advanced topics.</span><span style='font-size:14.0pt;font-family:"Times New Roman Bold Italic";mso-bidi-font-family: "Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span class=SpellE><span class=GramE><b style='mso-bidi-font-weight: normal'><span style='font-size:14.0pt;font-family:"Times New Roman Bold Italic"; mso-bidi-font-family:"Times New Roman";color:red'>Wanna</span></b></span></span><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt;font-family: "Times New Roman Bold Italic";mso-bidi-font-family:"Times New Roman"; color:red'> smile?</span></b><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><span style="mso-spacerun:yes"> </span>Evolutionists gather around wall stain in the image of Charles Darwin <a href="http://www.theonion.com/content/news/evolutionists_flock_to_darwin">(from <i style='mso-bidi-font-style:normal'>The Onion</i>)</a><o:p></o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='mso-pagination:none;mso-layout-grid-align:none; text-autospace:none'><span style='font-size:14.0pt;font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span style='color:black'><o:p></o:p></span></p> <p class=MsoNormal><span style='color:black'><o:p>&nbsp;</o:p></span></p> </div> </body> </html>