• This project has TWO options: 1) Using a predefined sequence or 2) using the genetic code.

Proposal: Thursday, April 24, 2003

Completed Project: Thursday, May 8, 2003

Inspiration:

Joe Davis, artist/researcher at MIT created an artwork called Riddle of Life.
Here is the text he wrote to describe it for Ars Electronica, 2000:

"Riddle of Life, is the culmination of an interesting but little known episode in the history of science. In the fall of 1958, biophysicist Max Delbrück sent a mysterious telegram to George W. Beadle at the Nobel prize ceremonies in Stockholm, Sweden. Delbrück had composed his telegram in a form that reflected some new and exciting ideas about the nature of DNA and the operation of the genetic code. It was also an important precedent for the idea that extrabiological information - in this case, English language - could be contained in genetic form. The telegram was sent as one continuous 'word' with 229 letters:

The key to unraveling the message was that it mimicked the triplet operation of DNA. In Stockholm, Beadle managed to crack Delbrück's code and read the English sentence:

"BREAK-THIS-CODE-OR-GIVE-BACK-NOBEL-PRIZE-LEDERBERG-GO-HOME-MAX-MARKO-STERLING."

Beadle replied with a slightly different triplet code of his own. When Beadle's telegram arrived at Delbrück's laboratory at Caltech, the return message was deciphered:

"GWBTOMDIMSUREITSAFINEMESSAGEIFICOULDDOTHEFINALSTEP"

Evidently, Delbrück and the group at Caltech weren't ready to let the recent Nobel laureate have the last word. So, they rallied with yet another mysterious message. At a formal lecture after the Nobel prize ceremonies in Stockholm, Beadle was presented with a molecular model constructed from toothpicks (Delbrück had airmailed it to the presiding officer). Each toothpick was stained with one of four colors. Like the coded telegrams, the toothpick model also contained an English language message, but with a code made up of colors rather than letters. This time, Delbrück chose to encode a poetic message that embodied a theme important to the history of both the sciences and the arts. The model contained the message,

"I am the riddle of life. Know me and you will know yourself."

Delbrück and Beadle had ingenious ideas for expressing human language in the form of DNA, but in 1958 no synthetic, or artificially constructed nucleic acids were available. I organized a project to create DNA corresponding to Max Delbrück's toothpick molecule with the Laboratory of Molecular Structure at MIT Biology (Alexander Rich Laboratory), and the Burghardt Wittig Laboratory at the Institute for Molecular Biology and Biochemistry at the Free University of Berlin, Germany. Max Delbrück's RIDDLE OF LIFE molecule that was first conceived of over 40 years ago actually first came into existence in Berlin in December/January, 1993-4 . [1]

Source: http://www.aec.at/festival2000/texte/artistic_molecules_2_e.htm

 

Instructions

Option 1 - Use a DNA sequence as the basis for an original design/creative exploration.

• You will each be using the unique sequence of the Ammonifex Degensii genomic fragment that you isolated in the Fall quarter (2002) and that were sequenced and annotated in the Winter quarter (2003).

Option 2 - Use the genetic code as a system to create a sequence from an original work( e.g. a short poem or phrase, equation, idea, image etc.) or something that inspires you which you will then use to build your design/creative exploration.

(Note: We will decide how much of the DNA sequence below to use in class.)

1. Select a medium you are comfortable working in and create 4 distinct elements with that medium to represent each of the DNA bases, A, C, T, and G.
   • Examples: images (hand drawn, Xerox copies, digital images, etc.), words/phrases, alphanumeric characters, sound, video, computer code, equations, pipe cleaners, buttons, stones, cards etc. Or if you are going to do this algorithmically, you could devise a schema of functions to represent the four bases, so that the sequence guides the result of your programming, or program four elements to represent the bases and use them to build your design. How you create all this is up to you. Use a medium that you are familiar with and enjoy. See how far you can take this and do what is most interesting to you.
2. Make a "legend" to identify which DNA base corresponds to each of your elements and how they will pair. Assign one of your elements to each of the 4 DNA bases, A, C, T, and G. Work out how these elements pair with each other, similar to the DNA pairing rules in which A pairs with T, G pairs with C. Prepare this to bring to class. Initially this can be in a descriptive format as long as it is very clear what you are working with. When you present the completed project you should include a completed legend. Note: your elements may change as you work on the project further. If this happens, you will need to update this legend for the completion of the project.
   • If you are working on Option 1 - continue with step 4, if working on Option 2 - continue with step 3.
3. If you choose option 2 - look at the structure of the genetic code (see below) and create a schema to encode your non-DNA material into DNA information. Document this as part of your project. E.g. You could make another "legend" or chart. Record the resulting DNA sequence and
4. Assemble your design via the process of DNA replication. Using the DNA sequence below or the one you generated using the schema you created with the genetic code:
• Single strand: Build a single strand of the sequence using each of your four elements.
• Replication: Build your design by creating the opposing strand using the element pairing rules from your legend.
5. Mutation and derivatives: Mutation results in a change in DNA, usually in its sequence, the number of copies of a sequence that are present, how the DNA is arranged, or its location (which chromosome). Use one or more of the following methods for mutating your design then build both the resulting single strand and "duplex":
• Point mutation: substitute an individual base with another. Some common substitutions: A for C; A for G; C for T; G for T, A for T; G for C.
• Deletion: delete a segment of the sequence
• Inversion: invert a segment of the sequence, keeping its place in the overall order
• Transposition: move a segment of the sequence from one place to the other in the overall order.
• Duplication: repeat a section of the sequence one or more times
• Insertion: insert another sequence into this on
6. Write an Artist Statement:
   • The statement must include y our name, the project title, the project description (dimensions, materials) and a written statement that details the conceptual foundation and motivations for your artwork, the strategies/processes used to construct it, and your interpretation of the work. It would also include your thoughts about the use of genetic information as a structure to guide what you are designing and any other reflections you have about your creative process in the making of this work.Some things to think about: Is the "mutated" design different in what it evokes than the "original?" Does it convey the same meaning you originally intended? What was it like to have this kind of preexisting structure determine you creative direction.
7. Bring the following to class on the due date:
   • Legend of your 4 elements and their pairing rules; and if you did option 2) the schema you worked out to correspond to the genetic code, including your source material and the DNA sequence that resulted from it- Write this up so we can include it in the web page documenting your project.
   • "Duplex" original version
   • "Duplex" mutated version
   • Your initial concept sketches etc. so we can document the process.
   • Your artist statement
   • Also - e-mail your artist statement in MS-word format to the instructor by the due date.

Some additional information on DNA and the Genetic Code:

DNA Bases: A, C, T, G,

DNA molecules are large polymers. They have a backbone of alternating sugar and phosphate residues. The sugar is deoxyribose, which has 5 carbons. Sugars are linked to each other. Attached to each sugar is a nitrogenous base at carbon atom 1' (one prime). There are four kinds of bases: Adenine (A); Cytosine (C), Guanine (G), and Thymine (T). A sugar with its attached base is a nucleoside. A nucleoside with a phosphate group attached to its 5' or 3' carbon is a nucleotide, or the basic building block of the DNA strand. DNA is an antiparallel double helix. The opposing strands have opposite directions for the linking of the 3' to 5' carbon on the sugars.

DNA Pairing: A pairs with T, G pairs with C.

Note: sources for images is: http://www.accessexcellence.org

The Genetic Code: [11]

Legend:

Amino acids specified by each codon sequence on mRNA. Key for the above table:

Ala: Alanine	Cys: Cysteine	Asp: Aspartic acid	Glu: Glutamic acid
Phe: Phenylalanine	Gly: Glycine	His: Histidine	Ile: Isoleucine
Lys: Lysine	Leu: Leucine	Met: Methionine	Asn: Asparagine
Pro: Proline	Gln: Glutamine	Arg: Arginine	Ser: Serine
Thr: Threonine	Val: Valine	Trp: Tryptophane	Tyr: Tyrosisne

A = adenine G = guanine C = cytosine T = thymine U = uracil

DNA transfers information to mRNA in the form of a code defined by a sequence of nucleotides bases. During protein synthesis, ribosomes move along the mRNA molecule and "read" its sequence three nucleotides at a time (codon) from the 5' end to the 3' end. Each amino acid is specified by the mRNA's codon, and then pairs with a sequence of three complementary nucleotides carried by a particular tRNA (anticodon).

Since RNA is constructed from four types of nucleotides, there are 64 possible triplet sequences or codons (4x4x4). Three of these possible codons specify the termination of the polypeptide chain. They are called "stop codons". That leaves 61 codons to specify only 20 different amino acids. Therefore, most of the amino acids are represented by more than one codon. The genetic code is said to be degenerate.