Michael Crichton - Jurassic Park

"I see Mr. Nedry has spotted the next phase of our work," Wu said. "How we identify the DNA we have extracted. For that, we use powerful computers."

They went through sliding doors into a chilled room. There was a loud humming sound. Two six-foot-tall round towers stood in the center of the room, and along the walls were rows of waist-high stainless-steel boxes. "This is our high-tech laundromat," Dr. Wu said. "The boxes along the walls are all Hamachi-Hood automated gene sequencers. They are being run, at very high speed, by the Cray XMP supercomputers, which are the towers in the center of the room. In essence, you are standing in the middle of an incredibly powerful genetics factory."

There were several monitors, all running so fast it was hard to see what they were showing. Wu pushed a button and slowed one image.

1 GCGTTGCTGG CGTTTTTCCA TAGGCTCCGC CCCCCTGACG AGCATCACAA AAATCGACGC

61 GGTGGCGAAA CCCGACAGGA CTATAAAGAT ACCAGGCGTT TCCCCCTGGA AGCTCCCTCG

121 TGTTCCGACC CTGCCGCTTA CCGGATACCT GTCCGCCTTT CTCCCTTCGG GAAGCCTGGC

181 TGCTCACGCT GTAGGTATCT CAGTTCGGTG TAGGTCGTTC GCTCCAAGCT GGGCTGTGTG

241 CCGTTCAGCC CGACCGCTGC GCCTTATCCG GTAACTATCG TCTTGAGTCC AACCCGGTAA

301 AGTAGGACAG GTGCCGGCAG CGCTCTGGGT CATTTTCGGC GAGAACCGCT TTCGCTGGAG

361 ATCGGCCTGT CGCTTGCGGT ATTCGGAATC TTGCACGCCC TCGCTCAAGC CTTCGTCACT

421 CCAAACGTTT CGGCGAGAAG CAGGCCATTA TCGCCGGCAT GGCGGCCGAC GCGCTGGGCT

481 GGCGTTCGCG ACGCGAGGCT GGATGGCCTT CCCCATTATG ATTCTTCTCG CTTCCGGCGG

541 CCCGCGTTGC AGGCCATGCT GTCCAGGCAG GTAGATGACG ACCATCAGGG ACAGCTTCAA

601 CGGCTCTTAC CAGCCTAACT TCGATCACTG GACCGCTGAT CGTCACGGCG ATTTATGCCG

661 CACATGGACG CGTTGCTGGC GTTTTTCCAT AGGCTCCGCC CCCCTGACGA GCATCACAAA

721 CAAGTCAGAG GTGGCGAAAC CCGACAGGAC TATAAAGATA CCAGGCGTTT CCCCCTGGAA

781 GCGCTCTCCT GTTCCGACCC TGCCGCTTAC CGGATACCTG TCCGCCTTTC TCCCTTCGGG

841 CTTTCTCAAT GCTCACGCTG TAGGTATCTC AGTTCGGTGT AGGTCGTTCG CTCCAAGCTG

901 ACGAACCCCC CGTTCAGCCC GACCGCTGCG CCTTATCCGG TAACTATCGT CTTGAGTCCA

961 ACACGACTTA ACGGGTTGGC ATGGATTGTA GGCGCCGCCC TATACCTTGT CTGCCTCCCC

1021 GCGGTGCATG GAGCCGGGCC ACCTCGACCT GAATGGAAGC CGGCGGCACC TCGCTAACGG

1081 CCAAGAATTG GAGCCAATCA ATTCTTGCGG AGAACTGTGA ATGCGCAAAC CAACCCTTGG

1141 CCATCGCGTC CGCCATCTCC AGCAGCCGCA CGCGGCGCAT CTCGGGCAGC GTTGGGTCCT

1201 GCGCATGATC GTGCT… CCTGTCGTTG AGGACCCGGC TAGGCTGGCG GGGTTGCCTT

1281 AGAATGAATC ACCGATACGC GAGCGAACGT GAAGCGACTG CTGCTGCAAA ACGTCTGCGA

1341 AACATGAATG GTCTTCGGTT TCCGTGTTTC GTAAAGTCTG GAAACGCGGA AGTCAGCGCC

"Here you see the actual structure of a small fragment of dinosaur DNA," Wu said. "Notice the sequence is made up of four basic compounds-adenine, thymine, guanine, and cytosine. This amount of DNA probably contains instructions to make a single protein-say, a hormone or an enzyme. The full DNA molecule contains three billion of these bases. If we looked at a screen like this once a second, for eight hours a day, it'd still take more than two years to look at the entire DNA strand. It's that big."

He pointed to the image. "This is a typical example, because you see the DNA has an error, down here in line 1201. Much of the DNA we extract is fragmented or incomplete. So the first thing we have to do is repair it-or rather, the computer has to. It'll cut the DNA, using what are called restriction enzymes. The computer will select a variety of enzymes that might do the job."

1 GCGTTGCTGGCGTTTTTCCATAGGGTCCGCCCCCCTGACGAGCATCACAAAAATCGACGC

61 GGTGGCGAAACCCGACAGGACTFITAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCG

NspO4

121 TGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGC

181 TGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCASGCTGGGCTGTGTG

BrontIV

241 CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAA

301 AGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAG

434 DnxTl AoliBn

361 ATCGGCCTGTCGCTTGCGGTATTCGCAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACT

421 CCAAACGTTTCGGCGAGAAGCAGGCCATAATCGCCGGCATGGCGGCCGACGCGCTGGGCT

481 GGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGG

541 CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGHCCATCAGGGACAGCTTCAA

601 CGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCG

Nsp04

661 CACATGGACCCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAA

721 CAAGTCAGAGGTGGCGAAACCCOACAGOACTATAAAGATACCAOOCOTTTCCCCCTGGAA

924 Caoll I DinoLdn

781 GCGCTCTCCTOTTCCOACCCTOCCOCTTACCOGATACCTOTCCOCCTTTCTCCCTTCGGG

841 CTTTCTCAATOCTCACOCTGTABGTATCTCAGTTCGGTOTAGGTCGTTCOCTCCAAOCTO

901 ACGAACCCCCCOTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAOTCCA

961 ACACOACTTAACCOOTTOOCATGGATTGTAGGCGCCGCCCTATACCTTGTCTOCCTCCCC

1021 GCGGTGCATGOAOCCOGOCCACCTCGACCTGAATOGAAGCCGOCGOCACCTCOCTAACOG

1081 CCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGG

1141 CCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCT

1416 DnxTI

SSpd4

1201 GCGCATGATCGTGCT:+=:CCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACT

1281 ATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCT

"Here is the same section of DNA, with the points of the restriction enzymes located. As you can see in line 1201, two enzymes will cut on either side of the damaged point. Ordinarily we let the computers decide which to use. But we also need to know what base pairs we should insert to repair the injury. For that, we have to align various cut fragments, like so."

[picture]

"Now we are finding a fragment of DNA that overlaps the injury area, and will tell us what is missing. And you can see we can find it, and go ahead and make the repair. The dark bars you see arc restriction fragments-small sections of dinosaur DNA, broken by enzymes and then analyzed. The computer is now recombining them, by searching for overlapping sections of code. It's a little bit like putting a puzzle together. The computer can do it very rapidly."

1 GCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGC

61 GGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCG

121 TGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCCTGGC

181 TGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTG

241 CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAA

301 AGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGAACCGCTTTCGCTGGAG

361 ATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACT

421 CCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCT

481 GGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGG

541 CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAA

601 CGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCG

661 CACATGGACGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAA

721 CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATA CCAGGCGTTTCCCCCTGGAA

781 GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGG

841 CTTTCTCAATGCTCACGCTGTAGGTATCTC AGTTCGGTGTAGGTCGTTCGCTCCAAGCTG

901 ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCA

961 ACACGACTTAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCC

1021 GCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGG

1081 CCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGG

1141 CCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCT

1201 GCGCATGATCGTGCTAGCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTT

1281 AGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTG CTGCTGCAAAACGTCTGCGA

1341 AACATGAATGGTCTTCGGTTTCCGTGTTTC GTAAAGTCTGGAAACGCGGAAGTCAGCGCC

"And here is the revised DNA strand, repaired by the computer. The operation you've witnessed would have taken months in a conventional lab, but we can do it in seconds."

"Then are you working with the entire DNA strand?" Grant asked.

"Oh no," Wu said. "That's impossible. We've come a long way from the sixties, when it took a whole laboratory four years to decode a screen like this. Now the computers can do it in a couple of hours. But, even so, the DNA molecule is too big. We look only at the sections of the strand that differ from animal to animal, or from contemporary DNA. Only a few percent of the nucleotides differ from one species to the next. That's what we analyze, and it's still a big job."