https://gcat.davidson.edu/GcatWiki/api.php?action=feedcontributions&feedformat=atom&user=Mlewis14 2026-05-05T19:32:36Z User contributions MediaWiki 1.28.2 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7891 2009-05-19T02:49:26Z

<p>Mlewis14: </p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1 (on or off).<br /> <br /> maximize 2 + a - 2*b*c + b<br /> <br /> This is an example from a small max 2-sat problem where all the logical constraints have been translated into a fitness function. What values of ''a, b'' and ''c'' maximize this function? Did you consider this a challenging problem? (ans: a = b = 1, c = 0 for an objective value of 4)<br /> <br /> Is there a way to program e. coli to evolve where their fitness is measured by this or some other function? <br /> <br /> Is there a way to try, in parallel, the many possible solutions (different values for the 2^n combinations) and choose the one that has maximized the given function?</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7890 2009-05-19T02:49:06Z

<p>Mlewis14: </p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1 (on or off).<br /> <br /> maximize 2 + a - 2*b*c + b<br /> <br /> This is an example from a small max 2-sat problem where all the logical constraints have been translated into a fitness function. What values of ''a, b'' and ''c'' maximize this function? Did you consider this a challenging problem? (ans: a = b = 1, c = 0 for an objective value of 4)<br /> <br /> Is there a way to program e. coli to evolve where their fitness is measured by this or some other equation? <br /> <br /> Is there a way to try, in parallel, the many possible solutions (different values for the 2^n combinations) and choose the one that has maximized the given function?</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7737 2009-04-09T17:04:01Z

<p>Mlewis14: </p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1.<br /> <br /> minimize 2 - a + 2*b*c - b<br /> <br /> This is an example from a small max 2-sat problem where all the logical constraints have been translated into a fitness function. What values of ''a, b'' and ''c'' minimize this function? Did you consider this a challenging problem? <br /> <br /> Is there a way to program e. coli to evolve according to their fitness as measured by this equation? Note that a minimization is easily transposed to a maximization via the negation of the function, if that helps the biologists.</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7736 2009-04-09T17:00:59Z

<p>Mlewis14: </p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1.<br /> <br /> minimize 2 - a + 2*b*c - b<br /> <br /> This is an example from a small max 2-sat problem where all the logical constraints have been translated into a fitness function. What values of ''a, b'' and ''c'' minimize this function? Did you consider this a challenging problem? Here is a link to the [[Media:max 2-sat version of this problem in Excel]], wherein you can try different values of ''a, b'' and ''c''.<br /> <br /> Is there a way to program e. coli to evolve according to their fitness as measured by this equation? Note that a minimization is easily transposed to a maximization via the negation of the function, if that helps the biologists.</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7735 2009-04-09T16:59:21Z

<p>Mlewis14: </p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1.<br /> <br /> minimize 2 - a + 2*b*c - b<br /> <br /> This is an example from a small max 2-sat problem [[where all the logical constraints have been translated into a fitness function]]. What values of ''a, b'' and ''c'' minimize this function? Did you consider this a challenging problem?<br /> <br /> Is there a way to program e. coli to evolve according to their fitness as measured by this equation? Note that a minimization is easily transposed to a maximization via the negation of the function, if that helps the biologists.</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7734 2009-04-09T16:55:51Z

<p>Mlewis14: </p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1.<br /> <br /> minimize 2 - a + 2*b*c - b<br /> <br /> This is an example from a small max 2-sat problem. What values of ''a, b'' and ''c'' minimize this function? Did you consider this a challenging problem?<br /> <br /> Is there a way to program e. coli to evolve according to their fitness as measured by this equation? Note that a minimization is easily transposed to a maximization via the negation of the function.</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Can_we_get_bacteria_to_solve_a_problem_large_enough_to_challenge_a_person%3F&diff=7733 2009-04-09T16:54:14Z

<p>Mlewis14: Introduction of a fitness function with a small max 2-sat example</p> <hr /> <div>If bacteria can be used to optimize, that is minimize or maximize a function, then we are looking at a significant contribution. Even if the bacteria can get reasonably good solutions to a function, i.e. a heuristic approach, that is significant. For example, consider the following very small &quot;fitness&quot; function where the variables ''a, b'' and ''c'' are either 0 or 1.<br /> <br /> minimize 2-a+2*b*c -b<br /> <br /> This is an example from a small max 2-sat problem. What values of ''a, b'' and ''c'' minimize this function? Did you consider this a challenging problem?<br /> <br /> Is there a way to program e. coli to evolve according to their fitness as described by this equation? Note that a minimization is easily transposed to a maximization via the negation of the function.</div>

Mlewis14 https://gcat.davidson.edu/GcatWiki/index.php?title=Missouri_Western/Davidson_iGEM2009&diff=7732 2009-04-09T16:41:37Z

<p>Mlewis14: Adding a link</p> <hr /> <div>This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.<br /> <br /> [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] &lt;br&gt;<br /> [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] &lt;br&gt;<br /> [http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] &lt;br&gt;<br /> [http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-along Freezer Stocks]&lt;br&gt;<br /> <br /> <br /> We need to learn more about these topics:<br /> &lt;center&gt;'''Biology-based'''&lt;/center&gt;<br /> #[[What is msDNA?]]<br /> #[[How is msDNA normally produced?]]<br /> #[[How is msDNA stored in E. coli?]] <br /> #[[How many copies are carried per cell?]] <br /> #[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]]<br /> #[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]]<br /> #[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]<br /> #[[Can we solve a 3-SAT problem with supressor logic?]]<br /> #[[What role can physical modeling of protein structure play in our project?]]<br /> <br /> <br /> <br /> &lt;center&gt;'''Math-based'''&lt;/center&gt;<br /> #What interesting challenges or problems does origami offer?<br /> #Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?<br /> #What has been done before and how can we improve upon that?<br /> #We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).<br /> #Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?<br /> #How has 3SAT been addressed with a DNA computer? Can we use those methods?<br /> #[[Can we get bacteria to solve a problem large enough to challenge a person?]]<br /> #Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?<br /> <br /> <br /> &lt;center&gt;'''Behavior-based'''&lt;/center&gt;<br /> #[[What constructs are we testing?]]<br /> #[[What school districts do we have access to?]]<br /> #[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]<br /> #[[Do you need any more input from the veterans before the survey is ready?]]</div>

Mlewis14