Difference between revisions of "SynthBioWorkshop2010"

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<strong>Synthetic Biology for Artists and Designers 2</strong>
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=[http://uwujojedeh.co.cc UNDER COSTRUCTION, PLEASE SEE THIS POST IN RESERVE COPY]=
 +
&lt;strong&gt;Synthetic Biology for Artists and Designers 2&lt;/strong&gt;
  
<strong>10th May 2010
+
&lt;strong&gt;10th May 2010
</strong>
+
&lt;/strong&gt;
 
     •  Biology - individual understanding and definition.
 
     •  Biology - individual understanding and definition.
 
     •  Brief History of Biology - Scientists/Microbiologists (Video)
 
     •  Brief History of Biology - Scientists/Microbiologists (Video)
Line 13: Line 14:
 
                     ? Theodore Schwann
 
                     ? Theodore Schwann
 
                     ? Rosalyn Franklin
 
                     ? Rosalyn Franklin
                     ? Watson & Crick
+
                     ? Watson &amp; Crick
 
     •  Evolution – Brief understanding and controversies
 
     •  Evolution – Brief understanding and controversies
 
     •  DNA, Protein – Introduction
 
     •  DNA, Protein – Introduction
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     1. Life: What a concept!
 
     1. Life: What a concept!
  
<strong>11th May 2010</strong>
+
&lt;strong&gt;11th May 2010&lt;/strong&gt;
  
 
     •  Recap of yesterday’s learning
 
     •  Recap of yesterday’s learning
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       2.
 
       2.
  
<strong>12th May 2010</strong>
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&lt;strong&gt;12th May 2010&lt;/strong&gt;
  
 
     •  Video Lecture by David Sadava
 
     •  Video Lecture by David Sadava
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                     ? Somatic and Sex Cells
 
                     ? Somatic and Sex Cells
 
                     ? Virus
 
                     ? Virus
                     ? DNA & its properties
+
                     ? DNA &amp; its properties
 
                     ? Structure of a DNA
 
                     ? Structure of a DNA
 
                     ? Replication of DNA
 
                     ? Replication of DNA
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       2. Online Research
 
       2. Online Research
  
<strong>13th May 2010</strong>
+
&lt;strong&gt;13th May 2010&lt;/strong&gt;
  
 
     1. Video Lecture by David Sadava
 
     1. Video Lecture by David Sadava
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             capability to grow over a period of two months.
 
             capability to grow over a period of two months.
  
<strong>14th May 2010</strong>
+
&lt;strong&gt;14th May 2010&lt;/strong&gt;
  
 
     1. Video Lecture by David Sadava
 
     1. Video Lecture by David Sadava
 
       Genomes – further details
 
       Genomes – further details
 
     ?
 
     ?
       Mutations & Mutagens
+
       Mutations &amp; Mutagens
 
     ?
 
     ?
 
       Cancers caused by mutation of genes by radiation
 
       Cancers caused by mutation of genes by radiation
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       Recombinant DNA
 
       Recombinant DNA
 
     ?
 
     ?
       Stanley Cohen & Herbert Boyer’s Experiment
+
       Stanley Cohen &amp; Herbert Boyer’s Experiment
 
     ?
 
     ?
 
       Goals for making rDNA
 
       Goals for making rDNA
Line 145: Line 146:
 
     ?
 
     ?
  
<strong>17th May 2010-05-17</strong>
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&lt;strong&gt;17th May 2010-05-17&lt;/strong&gt;
  
 
     1. Video Lecture by David Sadava
 
     1. Video Lecture by David Sadava
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Homework – develop and complete creature.
 
Homework – develop and complete creature.
  
<strong>18th May 2010</strong>
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&lt;strong&gt;18th May 2010&lt;/strong&gt;
  
 
     1. Video Documentary – BBC – The Cell – Chemistry of Life
 
     1. Video Documentary – BBC – The Cell – Chemistry of Life
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     3. Discussion of Creatures, peer feedback and progress
 
     3. Discussion of Creatures, peer feedback and progress
  
<strong>19th May 2010</strong>
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&lt;strong&gt;19th May 2010&lt;/strong&gt;
  
<object width="400" height="300"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="http://vimeo.com/moogaloop.swf?clip_id=12045337&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1" /><embed src="http://vimeo.com/moogaloop.swf?clip_id=12045337&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="400" height="300"></embed></object><a href="http://vimeo.com/12045337">Center for Genomic Gastronomy @ Srishti, Bangalore, India</a> from <a href="http://vimeo.com/user3901760">genomic gastronomy</a> on <a href="http://vimeo.com">Vimeo</a>.
+
&lt;object width=&quot;400&quot; height=&quot;300&quot;&gt;&lt;param name=&quot;allowfullscreen&quot; value=&quot;true&quot; /&gt;&lt;param name=&quot;allowscriptaccess&quot; value=&quot;always&quot; /&gt;&lt;param name=&quot;movie&quot; value=&quot;http://vimeo.com/moogaloop.swf?clip_id=12045337&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=&amp;fullscreen=1&quot; /&gt;&lt;embed src=&quot;http://vimeo.com/moogaloop.swf?clip_id=12045337&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=&amp;fullscreen=1&quot; type=&quot;application/x-shockwave-flash&quot; allowfullscreen=&quot;true&quot; allowscriptaccess=&quot;always&quot; width=&quot;400&quot; height=&quot;300&quot;&gt;&lt;/embed&gt;&lt;/object&gt;&lt;a href=&quot;http://vimeo.com/12045337&quot;&gt;Center for Genomic Gastronomy @ Srishti, Bangalore, India&lt;/a&gt; from &lt;a href=&quot;http://vimeo.com/user3901760&quot;&gt;genomic gastronomy&lt;/a&gt; on &lt;a href=&quot;http://vimeo.com&quot;&gt;Vimeo&lt;/a&gt;.
  
 
     1. Presentation by Zac on The center for Genomic Gastronomy
 
     1. Presentation by Zac on The center for Genomic Gastronomy
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     2. Extraction of DNA
 
     2. Extraction of DNA
  
<strong>20th May 2010</strong>
+
&lt;strong&gt;20th May 2010&lt;/strong&gt;
  
 
     1. Presentation of Abstracts of New Creatures
 
     1. Presentation of Abstracts of New Creatures
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         great!
 
         great!
  
<strong>21st May 2010</strong>
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&lt;strong&gt;21st May 2010&lt;/strong&gt;
  
 
Minutes of the Class
 
Minutes of the Class
 
     1. Discussion of ideation on creation of machines.
 
     1. Discussion of ideation on creation of machines.
  
<strong>22nd May 2010</strong>
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&lt;strong&gt;22nd May 2010&lt;/strong&gt;
  
 
Minutes of the Class
 
Minutes of the Class
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             ? Watermarked with 46 authors, web address and mail ID
 
             ? Watermarked with 46 authors, web address and mail ID
 
             ? Significance – vaccine production and Oil Spill reduction
 
             ? Significance – vaccine production and Oil Spill reduction
     2. Artist & other Research
+
     2. Artist &amp; other Research
 
             ? Stellarc
 
             ? Stellarc
 
             ? Symbiotica
 
             ? Symbiotica
 
             ? Orlan
 
             ? Orlan
  
<strong>25th May 2010</strong>
+
&lt;strong&gt;25th May 2010&lt;/strong&gt;
  
 
     1. Visit to NCBS
 
     1. Visit to NCBS
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             ? Tour of other labs with various workflow instruments
 
             ? Tour of other labs with various workflow instruments
  
<strong>26th May 2010</strong>
+
&lt;strong&gt;26th May 2010&lt;/strong&gt;
  
 
Minutes of the Class
 
Minutes of the Class
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             ? PCR and its significance
 
             ? PCR and its significance
 
     2. List of materials required to build the art form made from a living organism
 
     2. List of materials required to build the art form made from a living organism
     3. Artist & other Research
+
     3. Artist &amp; other Research
 
             ? Institution of Applied Autonomy
 
             ? Institution of Applied Autonomy
 
             ? Center for Post Natural History
 
             ? Center for Post Natural History
 
             ? George Gessert
 
             ? George Gessert
  
<strong>27th May 2010</strong>
+
&lt;strong&gt;27th May 2010&lt;/strong&gt;
  
 
Minutes of the Class
 
Minutes of the Class
 
     1. Video Documentary by Kary Mullis on the making of the PCR
 
     1. Video Documentary by Kary Mullis on the making of the PCR
     2. Artist & other Research
+
     2. Artist &amp; other Research
 
             ? Adam Zaretsky
 
             ? Adam Zaretsky
 
             ? Eduardo Kac
 
             ? Eduardo Kac
Line 257: Line 258:
 
     3. Field work on material for art form construction.
 
     3. Field work on material for art form construction.
  
<strong> 1st June </strong>
+
&lt;strong&gt; 1st June &lt;/strong&gt;
  
 
Yeast Growing
 
Yeast Growing
 
http://www.disknet.com/indiana_biolab/b021.htm
 
http://www.disknet.com/indiana_biolab/b021.htm

Revision as of 00:58, 24 November 2010

UNDER COSTRUCTION, PLEASE SEE THIS POST IN RESERVE COPY

<strong>Synthetic Biology for Artists and Designers 2</strong>

<strong>10th May 2010 </strong>

   •  Biology - individual understanding and definition.
   •  Brief History of Biology - Scientists/Microbiologists (Video)
                    ? Anton Von Leeuwenhoek
                    ? Gregor Mendel
                    ? Robert Hooke
                    ? Louis Pasteur
                    ? John Baptiste Van Helmont
                    ? Joseph Jackson Lister
                    ? Theodore Schwann
                    ? Rosalyn Franklin
                    ? Watson & Crick
   •  Evolution – Brief understanding and controversies
   •  DNA, Protein – Introduction
   •  Bacteria E.Coli
   •  Readings – PDF
                    ? Scientific America – Engineering Life
                    ? Synthesizing DNA of microorganisms for various purposes
                    ? Sequencing of DNA
                    ? Cost factors involved
                    ? Comparison to Moore’s Law
                    ? Human Genome
   •  Video – (BBC)-The Cell-The Hidden Kingdom

Homework - Reading (PDF)

   1. Life: What a concept!

<strong>11th May 2010</strong>

   •  Recap of yesterday’s learning
   •  Video lecture by David Sadava
           ? Expression of genes
           ? Phenotypes and Alleles
           ? The Nucleus
           ? Totipotent Cells
           ? Cloning
           ? Genes, chromosomes
           ? Human genetic information
           ? Cell processing
   •  Introduction to Synthetic Biology by Andrew Hessels
   •  Video – Darwin’s theory on evolution

Homework

      1.
      2.

<strong>12th May 2010</strong>

   •  Video Lecture by David Sadava
                   ? Epidemiology
                   ? Lung Cancer gene
                   ? Mutations
                   ? Requirements of a DNA
                   ? Responsibilities of a Protein
                   ? Variety in DNA
                   ? Somatic and Sex Cells
                   ? Virus
                   ? DNA & its properties
                   ? Structure of a DNA
                   ? Replication of DNA
   •  Video of Watson and his story of the discovery of the DNA model at TED.com
   •  Readings – Applying engineering to biology
   •  Reading – Adventures in Synthetic Biology

Homework

      1. Reading
      2. Online Research

<strong>13th May 2010</strong>

   1. Video Lecture by David Sadava
                   ? Spider web theory of protein
                   ? Protein production
                   ? Structure of protein
                   ? Synthesis of Protein
                   ? Human protein synthesis
                   ? Types of proteins
                   ? Expression of Proteins
                   ? Gene – Protein relationship
                   ? Metabolism
                   ? Thermodynamics
                   ? Mechanism, Cell Theory and Evolution
                   ? Ricin and its discovery
                   ? RNA and its role
                   ? Transcription and Translation
                   ? Nirenberg’s Experiment
                   ? Mutations and changes in base pairs
   • Video tutorial on DNA replication
   • Video tutorial on Protein synthesis

Homework

      1. Exercise – Make a piece of art form using any LIVING form that should have the
           capability to grow over a period of two months.

<strong>14th May 2010</strong>

   1. Video Lecture by David Sadava
      Genomes – further details
   ?
      Mutations & Mutagens
   ?
      Cancers caused by mutation of genes by radiation
   ?
      Genetic Damage
   ?
      Leukaemia
   ?
      Scientist Renato del Bucco’s work
   ?
      Hierarchical sequencing
   ?
      Shotgun sequencing – Craig Ventor
   ?
      Bioinformatics
   ?
      Information from a genetic sequence
   ?
      a. Coding sequence
      b. Protein amino acid sequence
      c. Gene control sequences
      Sequential Genomics
   ?
      First genome to be sequenced
   ?
      Hypothetical suggestion of 24000 genes in a human being
   ?
      Synthetic Biology - making artificial genes to bring about a desired result
   ?
      Scientist Werner Arber
   ?
      Restriction Endonuclease
   ?
      How a bacteria prevents Viral infections
   ?
      DNA Mapping
   ?
      Recombinant DNA
   ?
      Stanley Cohen & Herbert Boyer’s Experiment
   ?
      Goals for making rDNA
   ?
      Transgenic animals and plants
   ?
      Naked and Vector DNA
   ?

<strong>17th May 2010-05-17</strong>

   1. Video Lecture by David Sadava
           ? Isolation of genes
           ? PKU and dystrophy
           ? Methods of analyzing DNA
           ? Reverse Genetics
           ? Dystrophine Gene and Utrophine
           ? Gene Therapy
           ? Nucleic Acid Hybridization
           ? Genome Library
           ? DNA Microarray
           ? Metastasis
   2. Exercise - Think of your own creature. Design it. Explain detailed mechanisms using
      diagrams. This organism could be hypothetical. Name it.
   3. Make a scientific paper on your creature
   4. Demonstration of Gabriel’s current prototype of visually representing genetic sequenced
      data of a human mitochondria.

Homework – develop and complete creature.

<strong>18th May 2010</strong>

    1. Video Documentary – BBC – The Cell – Chemistry of Life
    2. Video Documentary – BBC – The Cell – The Spark of Life
    3. Discussion of Creatures, peer feedback and progress

<strong>19th May 2010</strong>

<object width="400" height="300"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="http://vimeo.com/moogaloop.swf?clip_id=12045337&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1%22 /><embed src="http://vimeo.com/moogaloop.swf?clip_id=12045337&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1%22 type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="400" height="300"></embed></object><a href="http://vimeo.com/12045337%22>Center for Genomic Gastronomy @ Srishti, Bangalore, India</a> from <a href="http://vimeo.com/user3901760%22>genomic gastronomy</a> on <a href="http://vimeo.com%22>Vimeo</a>.

    1. Presentation by Zac on The center for Genomic Gastronomy
           ? What is Biotechnolgy
           ? Perspective of food by all living things
           ? Geohackers, Biohackers, Geoengineers, Planetcrafters
           ? Agriculture Biodiversity
           ? Agrinformatics
           ? Metadata and food Genomes
           ? Food System Adaptation
           ? Agriculture Terrorism
           ? First world eating issues
           ? Cuisinformatics
    2. Extraction of DNA

<strong>20th May 2010</strong>

    1. Presentation of Abstracts of New Creatures
           ? The Booster Cell
           ? Supercule
           ? Thermo Cell
    2. Exercise – Create another new creature which does not necessarily have to be a
       microorganism or even possible to exist. Completely hypothetical, imaginary of fantastical is
       great!

<strong>21st May 2010</strong>

Minutes of the Class

    1. Discussion of ideation on creation of machines.

<strong>22nd May 2010</strong>

Minutes of the Class

   1. Video Documentary by Craig Ventor
           ? Scientific Breakthrough – First fully Synthetic Cell to be cultutred.
           ? Genome copied from Mycoplasma Genatalium
           ? Genome synthetically prepared in the lab
           ? Introduced into yeast cells to complete transformation
           ? Introduced into host bacterial cell which transforms to new organism
           ? Watermarked with 46 authors, web address and mail ID
           ? Significance – vaccine production and Oil Spill reduction
   2. Artist & other Research
           ? Stellarc
           ? Symbiotica
           ? Orlan

<strong>25th May 2010</strong>

   1. Visit to NCBS
           ? Tour of the Campus
           ? Meeting with PhD student Mehra and Navneet
           ? Introduction to the lab space
           ? Discussion over Science Institutes and their pros and cons
           ? Tour of other labs with various workflow instruments

<strong>26th May 2010</strong>

Minutes of the Class

   1. Video Tutorial by David Sadava
           ? Bioremediation – using organism to improve the environment
           ? Fluorescence in nature and different organisms
           ? TNT used as example
           ? Degraded by Psuedomonas Putida
           ? Integrated Pest Management
           ? Bacteria in decomposition
           ? Bacteria in Waste Water Treatment
           ? Extremophiles
           ? PCR and its significance
   2. List of materials required to build the art form made from a living organism
   3. Artist & other Research
           ? Institution of Applied Autonomy
           ? Center for Post Natural History
           ? George Gessert

<strong>27th May 2010</strong>

Minutes of the Class

   1. Video Documentary by Kary Mullis on the making of the PCR
   2. Artist & other Research
           ? Adam Zaretsky
           ? Eduardo Kac
           ? Patricia Piccinni
   3. Field work on material for art form construction.

<strong> 1st June </strong>

Yeast Growing http://www.disknet.com/indiana_biolab/b021.htm