Clones Clones The protein sequencer ran the letters off on the monitor screen. Alone the amino acids meant nothing, but combined they became words in a genetic statement. How they were put together was a mystery until now. Some would be dominant andbe expressed, others would lie quiet never to be heard from. Dennis watched the monitor as the letters came off, and occasionally jotted a few notes down in his journal. In the background a timer ticked constantly every time one of the sequences were added to the list growing on the screen. He returned to his notes and thought, If A were to be expressed here then the E would have to be silent. It doesnt make any sense. Perhaps if I started the whole sequence over,and changed the timing, perhaps varying from just iambic pentameter. He thought about the young woman for a while before he returned to his unfinished poem.

I hate the formatting when you submitt something. It always screws your type up.

Being technical here, but... "The protein sequencer ran the letters off on the monitor screen. Alone the amino acids meant nothing..." The letters would be nitrogenous bases, not the amino acids. "Some would be dominant andbe expressed..." Unclear. Neither proteins nor amino acids are expressed. It is genes that are expressed. "every time one of the sequences were added to the list..." Should be "one...was." Also, are sequences being added to the list, or individual letters as in the first sentence? "If A were to be expressed here then the E would have to be silent." I'm not sure what A and E are supposed to refer to. If nucleic acid bases, there is an A, but no E. I see the tie to musical notes, but the original E confuses me. Interesting plot thread going on here, but I'm not sure I can wrap my brain around it enough to understand it yet.

Adenine, guanine, thiamine, cystosine and sometimes uracil are amino acids... the protein sequencer reads the base pairs as the DNA unravels just as a cell would read those pairs constructing a protein. This wasn't meant to be a Biology paper but a twist on where poetry comes from. It's all in combining the letters.

The poetry of life, eh? Nice concept. I can't speak to the science of it all, but understood where you were going. However, that may be partly due to following the poetry challenges and ensuing discussions. ;-) The last line did confuse me, however. Maybe I'm dense, but the young woman lost me. jon

"Adenine, guanine, thiamine, cystosine and sometimes uracil are amino acids... the protein sequencer reads the base pairs as the DNA unravels just as a cell would read those pairs constructing a protein." TJ, still gotta disagree with you. Adenine, Guanine, Thymine, and Cytosince, and yes, Uracil in RNA instead of T in DNA, are NOT amino acids. They are, as you next say, the bases in the base pairs. In transcription, mRNA codons formed of 3 bases are constructed from the matching triplet in DNA. The codons in the mRNA are read in the ribosomes during translation, along with the help of tRNA which brings the amino acid that corresponds to the codon/anticodon pair in question. The sequence of amino acids assembles into a protein.

I like the interwoven ideas of letters/information/words/rhythm/poetry. I picture in my mind a guy who is neither left nor right brain dominant here, the artistic-scientific type, in the middle of a couple of simultaneous projects. Are the clone of the title, the owner of the protein sequence being elaborated, and the young woman of the penultimate line one and the same? I lean toward prose, so I'm wondering if you could shed a little light here on what you were thinking. Aha! Light goes on. The silent E. And paragraph/stanza one refers to the protein sequence, while number three refers to the poem, with parallel ideas. The structure is making a little more sense, now.

The turn was meant to be quick on a huh? I was thinking the machine reading off a-a-a-g-g-c-c-c some combinations mean something, some nonsense, some their actions masked by other combinations. On the thousands of possible combinations like if you have an allele that says produce this protein and its activity is countered by another that says bond a sequence that makes that protien useless. Not every combination is expressed. Anyways back in the seventies when I went through that part of my rotation every part of the genetic lab was so "primative" most of the methods are probably historical. I know what a sequencer does and can imagine the young man's boredom because I used to sit watching bubbles flow though the tubes of an autoanalyzer, watching the printout of sugar, bun, creatinine, sgot, sgpt,ldh and the mind did wander. All you had to do was keep up the fluids and replace the sample tray when it ran out....occassionally checking a standard or a control to make sure the quality control was in. Do you see where I'm going. If I can draw an allegory between each bubble being a specimen, a person, people, running through the tubes and a city...cars traffic. Anyways I took genetics back in 1977. Every once in a while my mind fades back to the day...but back then I had my trusty bowmar brain and a wang to do all the calculations in the lab. There were no PC's and I used punch cards to put results in the computer which took up an entire room and handled millions of calculations per minute. (Apollo 13).

And T-rna only handles 3 pairs...tell me how many T-rna's does one utilize to come up with iambic pentameter, which is five feet of one unstressed followed by one stressed syllable? Wouldn't a three foot syllable work better? something like an amphibranch being u/u or a anapest being /uu. And is there a genetic sequence for love? This could be fun...Oh, by the way,"u" means an unstressed foot not uracil. Where are you Chuck and D' I'm on a roll.

OK, I think readers would pick up the multitasking in the midst of boredom, but I'm not sure they would get to the metaphor of the bubbles in the tubes. Too much is automated today. I understand that the technical fallout from the human genome project has resulted in sequencers that would spit out bases probably faster than our poet could read. I think they will pick up on the expressed/unexpressed metaphor, whether we're dealing with junk sequences (introns vs. exons), feedback loops for gene regulation, or dominance and recessiveness as nu-be suggested. I thought from the start that iambic was all wrong. Definitely anapestic, or else dactylic, since the beginning and end of each codon are crucial. Is he in the mood for a dactylic waltz, or an anapestic cha-cha-CHA!?

Something about getting a readout of tyr-cys-leu-cys-isoleu-cys-guan...just didn't seem to go with that silent E. Every small column of liquid between the bubbles is a sample, each sample comes from an individual,all those samples running the tubes could be seen as the people they represent Where are they going in such a hurry? That coil leads into the flame photometer? Are they all doomed to a hellish incandescence? The protime counter ticking in the background was too fast. I thing the sample probe coming down into in SMAC was too slow...couldn't maintain the rhythm. And if I would've thought about it for a few minutes I probably would have had to explain how Mr. T took the message from Hannibal on how to make their super secret compound.

For those really interested the whole process is explained at http://www.starsandseas.com/SAS%20Genetics/SAS%20protein_synth/proteinsynth.htm I've read it over and over and without any graphics, even using the Mr T taking the message idea to illustrate what's going on, it still reads like stereo instructions. There's alot of work for us out there.