Saturday, January 29, 2005

Biotechnology Project I / Cryptography Project I / Religion Project I

Background:

Your vocabulary words are highlighted in maroon.

DNA is a linear polymer which encodes the information by which cells make specific proteins. These proteins are also linear polymers of amino acids. The particular sequence of amino acids in a protein determines its properties.

DNA codes the information for amino acids by means of bases, which are four in number: adenine, cytosine, guanine, and thymine. These bases are often abbreviated as A, C, G, and T. These bases are read in groups of three, which are called codons. Sixty-one of the sixty-four possible codons specify an amino acid, with the remaining three being the signal to terminate production of a protein.

Amino acids are often abbreviated using single letters of the alphabet. The abbreviations, along with the DNA codons for them, are below:

alanine (A) encoded by GCA, GCC, GCG, GCT
cysteine (C) encoded by TGC, TGT
aspartic acid (D) encoded by GAC, GAT
glutamic acid (E) encoded by GAA, GAG
phenylalanine (F) encoded by TTC, TTT
glycine (G) encoded by GGA, GGC, GGG, GGT
histidine (H) encoded by CAC, CAT
isoleucine (I) encoded by ATA, ATC, ATT
lysine (K) encoded by AAA, AAG
leucine (L) encoded by CTA, CTC, CTG, CTT, TTA, TTG
methionine (M) encoded by ATG1
asparagine (N) encoded by AAC, AAT
proline (P) encoded by CCA, CCC, CCG, CCT
glutamine (Q) encoded by CAA, CAG
arginine (R) encoded by AGA, AGG, CGA, CGC, CGG, CGT
serine (S) encoded by AGC, AGT, TCA, TCC, TCG, TCT
threonine (T) encoded by ACA, ACC, ACG, ACT
valine (V) encoded by GTA, GTC, GTG, GTT
tryptophan (W) encoded by TGG
tyrosine (Y) encoded by TAC, TAT

The stop codons are TAA, TAG, and TGA.

You will need:

computer
paper
floppy disk (optional)

1) The first step in the process is to expand the genetic "alphabet" to include the letters B, J, O, U, X, and Z, which are not currently assigned to amino acids. You may do this in one of two ways:

1A) (preferred) Assign the unassigned alphabetic characters to whichever amino acid abbreviation most closely resembles it. For example, the letter U might be encoded by valine (V). I recommend the following: encode B with P, J with I, O with Q, U with V, X with Y, and Z with N.
1B) (alternate) You may also, if you wish, assign specific codons to the letters which remain. For example, you could specify that AGA and AGG, which are normally codons for the amino acid arginine (R), will instead be specific for the letter B in your text. If you do this, please bear in mind that you must supply me with a list of the codons so assigned, and you must not reassign codons for amino acids which have only one (e.g. tryptophan). More advanced students may wish to assign redundant codons to punctuation (space, question mark, comma, digits) as well, though this will reduce the length of the text you can encode.
1C) (alternate) You may also bypass reassignment of codons or characters by choosing a text which does not include the letters B, J, O, U, X, or Z; however, finding such texts will be extraordinarily difficult, owing to the frequency of the letters O and U in English.

2) Select your religious text for encoding. Remember that it must meet the following specifications: a) it must be no longer than 4000 bases (1333 codons). b) It must come from a scripture which is regarded as authoritative, or which has been regarded as authoritative in the past, by some substantial number of people. c) It must exist in a form which utilizes standard English letters, whether by translation or originally. This means that it will not be possible, within the scope of this project, to translate texts which utilize other alphabets (Russian, Hebrew, Greek), unless the texts have been subsequently translated into English. d) It must begin with the letter "M," or else you must write a short identifying tag at the beginning of the text which begins with the letter "M."

3) Proceeding one letter at a time, select a codon for each and write it down in sequential order.

4) When completed, you may double-check your sequence using an on-line DNA translator tool, as for example this one. Cut and paste from your document into the translation window, select "compact" from the pull-down menu for "output format," and verify that at least one of the sequences displayed matches the intended text.

5) Submit your sequence (by e-mail or floppy disk!) to me for verification and grading. You must include the following information: source of the text, intended translation of the text, and a paragraph or two identifying which method you used to encode the "missing" letters (B, J, O, U, X, and Z), as well as any special characters you may have included. Your sequence will then be evaluated and a grade assigned.

1 Methionine also serves as the initiator codon and is required to begin a protein.


Elaboration (choose any three):

1) Write an essay no longer than five pages in which you discuss the potential religious impact, if any, of splicing your text into the genome of a living organism, for example, the bacterium E. coli. Would it change your understanding of the text you have selected if you knew that every twenty minutes, a bacterium kept in an acceptable climactic and nutritional environment could reproduce your text in its progeny, or exchange your text with other bacteria through the bacterial equivalent of sexual intercourse?

2) Order your text from an on-line company which specializes in production of short sequences of DNA (one possibility is Integrated DNA Technologies). For long sequences, you may need to break your text into multiple small pieces and join them together later; alternately, you might enquire as to whether the company would link your sequence together for an additional charge. You may use my name and the address of the school for your shipping information; however, I will not supply a credit card for your order.
Any DNA sequences so obtained will be presented to the class in short (approximately five minutes) presentations, in which you will display the DNA, read its translated text, and explain why you selected that particular text for encoding.

3) As with 2), except use the DNA you obtain to splice your text into a living organism. Students selecting this option will receive a grade of incomplete for the course, until transfection of the text can be verified. Students will then receive all known organisms containing the text, and will be given a grade of A+ for the course.

4) Write a creative short story (less than 10 pages) set after the extinction of the human race, in which aliens land on Earth and discover your encoded message in bacteria. Describe the implications for the alien race.

5) Mutations in DNA sequence can be induced by a wide variety of causes, including chemicals, radiation (including cosmic rays, x-rays, radioactive decay), internal rearrangement of bases, and mistakes made by proofreading enzymes. There are four main types of mutation:

insertion of a base, or set of bases, into the sequence (for example, ACATAG --> ACAGTAG)
deletion of a base of set of bases (ACATAG --> ACAG)
substitution of a base (ACATAG --> AGATAG)
duplication of a base or set of bases (ACATAG --> ACATCATTAG)


"Mutate" your text at least five times with each of the above methods so that a new message with a different meaning is formed. Supply the sequences for the mutations, and identify which type of mutation has led to the new message.

6) Not all mutations result in changes to the protein sequence, or impair the function of the protein produced. Explain how this is possible in a short (300 words) essay. You may find pp. 1156-1175 of your textbook useful.

A sample text and translation, with mutations, is included in the comments. I have included punctuation and spaces which are not, strictly speaking, encoded in the DNA sequence in order to enhance readability.

Tuesday, January 18, 2005

Music Project I

You will need:

scissors
plastic ballpoint pen
scotch tape
a piece of music, recorded on cassette, or a blank cassette tape and a musical selection on CD
a stereo or boom box capable of cassette playback
a stereo or boom box capable of recording to cassette (optional; may be the same as the playback device)

1. If you have a pre-recorded cassette, and you are willing to lose the music on the cassette, this cassette will now be referred to as the Primary Cassette: proceed to step 3. If you have music on a cassette which you are not willing to potentially destroy, or music on a CD, proceed to step 2.

2. Use the recording device to record a copy of the music from CD or cassette to the blank cassette. The blank cassette will now be called the Primary Cassette.

3. Rewind the Primary Cassette to the beginning of the tape.

4. Turn the tape upside down, so that the side of the tape which contacts the magnetic head is facing you. The tape which is visible should lack the brown or grayish magnetic coating which records the music: it is often light pink or blue in color, though it may be other colors. If you are in doubt, ask your instructor.

5. Pull a loop of tape about an inch long from the center of the tape, just above where the magnetic head contacts the magnetic tape.

6. Take two small lengths of scotch tape from your scotch tape dispenser, and attach them on a clean nearby surface so that a substantial portion of the tape is hanging free in the air.

7. Place your index finger in the center of the loop of tape. Hold the tape steady on either side with your thumb and middle finger. Slide the scissors under the loop of tape, and cut through the tape.

8. Pick up one of the pieces of scotch tape from step 6. Put it on one of the loose ends of the magnetic tape. The alignment does not have to be precise, but it should be adequate to cover the full width of the end.

9. Rotate the end with the scotch tape on it one half-turn, in either direction, and then attach the unrotated other end to the same piece of scotch tape, making the alignment of the second end as close to parallel as possible.

10. Fold the scotch tape over the cut. Use scissors to trim away any excess scotch tape from the sides of the magnetic tape. Try to make the reconstituted magnetic tape as straight as possible.

11. You should now have a cassette tape into which a single half-turn has been inserted. If you do not, consult your instructor.

12. This is the boring part: carefully advance the tape, manually, to the opposite side. I.e., you are to rewind to the beginning of the other side of the tape. While doing this:

DO NOT allow the turn to become wound around the spindles of the cassette.
DO NOT attempt to advance the tape too rapidly, as this may cause it to kink or fold.


13. When you reach the other end of the cassette, repeat steps 4 to 10 on the other end of the magnetic tape, but instead of adding another half-turn, remove it. If you rotated the cut end of the tape counterclockwise in step 9, you will need to rotate the opposite side clockwise in this step.

14. At this point, you should have a cassette where the central portion of the magnetic tape has been rotated 180 degrees relative to its ends. Wait for your instructor to confirm that you have performed the procedure correctly before proceeding to step 15.

15. Place the cassette into a playback device and press play. You may need to fast-forward, if you did not have music on the entire Primary Cassette when you began.

Answer the following questions:
1. Why is the music now being played backwards?
2. Do you hear any messages, Satanic or otherwise, in the music? (If so: ask one of your classmates to listen to the same section of your tape, without telling them the message you believe you hear. Do your classmates hear the same thing you hear? If not, how is their interpretation different? Do your results reinforce 1970s/80s-era hysteria about so-called "backward masking" in music, or discredit it?)
3. ADVANCED STUDENTS: Is your recording missing most of its high-frequency sounds? If so, research music recording on magnetic tape in the library or on the internet, and explain why this might happen.