jack_schwartz
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+ | ====== Jack Schwartz (1930 – 2009) ====== | ||
+ | By: Michael Wigler | ||
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+ | | {{: | ||
+ | | Jack Schwartz 1980 | Jack Schwartz 2008 | | ||
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+ | I met Jack Schwartz in 2001, just before he retired from NYU as founder and then chairman of the department of computer science at the Courant Institute of Applied Mathematics. He visited my lab on sabbatical for a period of two years and then subsequently as a visiting scientist, during which time he had a strong influence on me and my group as we turned increasingly to quantitatively and computationally complex methods. Jack was famous for his fundamental mathematical work on linear operators, computer architecture and language, robotics and proof verification. These notes chronicle a slice of his thinking post retirement about other subjects, and document Jack’s far-ranging curiosity and creative analytical abilities, which traits endured far past the time he ceased to care about publishing. | ||
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+ | ===== Genomes as searchable strings ===== | ||
+ | The parallels of an organism’s genetic instructions to a programming language had great appeal to theoretical computer scientists ({{: | ||
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+ | ===== Phylogeny of Mitochondria===== | ||
+ | Beginning with the Human Genome Sequence Initiative there was a National Institutes of Health mandate to place DNA sequence data into the public domain. Jack loved data, especially free data. There was much that could be done with the deposited sequence data, but in particular Jack was interested in phylogeny, as it was natural to organize the genomes by descent. Most phylogenies are based on comparison of protein sequences and nucleic acid sequences, where the distance between strings is measured roughly as the number of mutations, one nucleotide at a time, that convert one string into another. Jack devised different methods. | ||
+ | In the early 2000’s he showed me his results based on study of the circular mitochondrial genome[2]({{: | ||
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+ | =====The Clocks of Evolution===== | ||
+ | Jack discovered other methods of phylogenetic mapping. One was based on the conservation of the intron-exon structure of transcripts[1]. Overall, his various methods can be viewed as clocks that run at different time scales, as do the second, minute and hour hands of a clock. One hand might be useful for measuring fast events, and the other for slow events. What would it say for our confidence in phylogeny if these clocks depicted different trees? Or if the branches were of different duration, depending on the clock used to measure it? The synthesis of these ideas into a coherent theory never occurred under Jack’s watch. He was more interested in the thrill of a logically solid novel insight than in exhausting its implications. But these ideas will eventually be useful in understanding cancer evolution, where the rates of different types of genome instability (point mutation, rearrangements, | ||
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+ | =====Illusions===== | ||
+ | Jack had a keen interest in human cognition, especially vision[4]. This choice was dictated by several considerations: | ||
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+ | =====Memory===== | ||
+ | The organization of memories was a frequent subject of our discussions, | ||
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+ | =====The End Game===== | ||
+ | While Jack loved Cold Spring Harbor, with its invigorating empirical tradition and its natural beauty, his sabbatical ended upon his first serious illness. Once he recognized that his time was limited, he returned home to the city, teeming with the ethnic restaurants he adored, to the project on the application of computational logic to the foundations of mathematics. He maintained his contacts with his colleagues, and continued to visit from time to time, as I did him, often bringing vexing problems or new results. We discussed a myriad of subjects: cellular architecture, | ||
+ | Jack held that a mathematician’s emotional age, often measured in single digits or low teens, was set by the year in which he discovered his intellectual gifts. But Jack escaped this tyranny of arrested development. His intellect was matched by a graceful emotional maturity and an almost serene detachment. A grumpy shrug was the most he would concede to a temporary setback. He drew his ability to grow from his curiosity, his autonomous powers for discovery, and the joy he took in sharing his thoughts and findings with others. By such means, and with the support of a loving wife and family, and highly appreciative friends, he traversed a unique and wonderful life. He died in 2009 of the complications of cancer. At Jack’s memorial service, his granddaughter, | ||
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+ | =====ACKNOWLEDGMENTS===== | ||
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+ | I thank Diana Robinson Schwartz for her help with Jack’s archives, for stimulating my memory, and for her patience. She and Bud Mishra helped with editorial comments and Dennis Sullivan and Jeff Cheeger straightened my mathematics. | ||
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+ | =====FOOTNOTES===== | ||
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+ | 1 Genes are substrings of DNA. DNA is double stranded, so each element of the genome “string” is really a complementary pair of nucleotides. Messenger or coding RNA is made by transcribing one strand of the DNA as template. Parts of the RNA are edited, and the sections of RNA removed are called “introns”, | ||
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+ | 2 Mitochondria are the tiny intracellular “engines” within every eukaryotic cell that produce ATP, the energy currency. They have their own genomes. | ||
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+ | 3 The gene unit itself, being a string, has an orientation. | ||
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+ | 4 Some of Jack’s creations can be found at | ||
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+ | [[http:// | ||
+ | An Analysis of the Cafe Wall Illusion]] | ||
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+ | [[http:// | ||
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+ | [[http:// | ||
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+ | [[http:// | ||
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+ | 5 Roughly speaking, a neuron can be resting and have a low rate of firing, or be recruited into an active state with a high rate of firing. | ||
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+ | 6 See for example | ||
+ | http:// | ||
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+ | =====REFERENCES===== | ||
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+ | Burrows, M. and Wheeler, D.J. (1994). A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation, | ||
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+ | Ferragina, P. and Manzini, G. (2000). Opportunistic data structures with applications. In 41st IEEE Symposium on Foundations of ComputerScience, | ||
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+ | Healy, J., Thomas, E., Schwartz, J.T. and Wigler, M. (2003). Annotating large genomes with exact word matches. Genome Research 13: 2306-2315. | ||
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+ | Hicks, J., Krasnitz, | ||
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+ | Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B. F. and Cedergren, R. (1992). Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. USA. Proc Natl Acad Sci U S A. 89(14): 6575–6579. | ||
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+ | =====RESOURCES===== | ||
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+ | | John Hopkins Presentation | {{: | ||
+ | | Mitochondria Presentation | {{: | ||
+ | | Stanford Presentation | {{: | ||
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+ | [[notes: |