Abstract
Jack Schwartz was drawn to the biological science late in life. He took a two year sabbatical at Cold Spring Harbor Laboratory, where he demonstrated how computer generated graphics could provide a window into visual processing, and found signatures in the permutation of mitochondrial gene order useful for phylogenetic analysis. He made a lasting impact on computational genomics at the lab by emphasizing the utility of the sort and exact matching. This led to the application of the Burrough-Wheeler algorithm, now a central component to many widely used genome mapping algorithms.
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Notes
- 1.
Jack defined an expert as someone who has made every possible mistake.
- 2.
See for example Jack’s 8th and 9th slides from his presentation at Johns Hopkins at http://roma.cshl.edu/jack.
- 3.
Genes are substrings of DNA. DNA is double stranded, so each element of the genome “string” is really a complementary pair of single stranded 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”, leaving intact but joining together the “exons”. Only then is the RNA is used to make protein.
- 4.
Mitochondria are the tiny intracellular “engines” within every eukaryotic cell that produce ATP, the energy currency. They have their own genomes.
- 5.
The gene unit itself, being a string, has an orientation.
- 6.
See for example Jack’s slide talk at IBM. http://roma.cshl.edu/jack. Recently, I looked again at the difficulty of computing precise distances between species, measured as the number of applications of Jack’s rule. I now concur with his opinion about its difficulty.
- 7.
- 8.
Roughly speaking, a neuron can be resting and have a low rate of firing, or be in an active state with a high rate of firing.
- 9.
Jack summarized his experience as Director this way: “The fastest way to make enemies is to give away money.”
- 10.
See for example http://www.settheory.com/drum_machine/drums.html.
References
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Hicks, J., Krasnitz, A., Lakshmi, B., Navin, N., Riggs, M., Leibu, E., Esposito, D., Alexander, J., Troge, J., Grubor, V., Yoon, S., Wigler, M., Ye, K., Børresen-Dale, A.-L., Naume, B., Schlicting, E., Norton, L., Hagerstrom, T., Skoog, L., Auer, G., Maner, S., Lundin, P., Zetterberg, A.: Novel patterns of genomic rearrangement and their association with survival in breast cancer. Genome Res. 16, 1465–1479 (2006)
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Acknowledgements
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. Dennis Sullivan and Jeff Cheeger helped me to understand the depth of the mathematics implicit in mitochondrial phylogeny.
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Wigler, M. (2013). The Last Ten Yards. In: Davis, M., Schonberg, E. (eds) From Linear Operators to Computational Biology. Springer, London. https://doi.org/10.1007/978-1-4471-4282-9_10
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