Readings

Background

The following texts are intended to encourage out-of-the-box discussion of important current problems with technological components. You may have already read some of these. More technical texts will be used as needed over the course of the semester.

Buy at Amazon Lomborg, Bjorn, ed. Global Crises, Global Solutions. New York, NY: Cambridge University Press, 2004. ISBN: 9780801880094. [Book describing the global prioritization experiment 'Copenhagen Consensus' in which eight expert economists made a prioritized list of 10 global challenges.]

Buy at Amazon Hawken, Paul, Amory Lovins, and L. Hunter Lovins. Natural Capitalism: Creating the Next Industrial Revolution. New York, NY: Little Brown & Company, 2000. ISBN: 9780316353007. [About how we can move towards a sustainable economy taking into account the value of natural resources and processes.]

Conversation Starters

Buy at Amazon Meadows, Donella H., Jorgen Randers, and Dennis L. Meadows. Limits to Growth: The 30-Year Update. White River Junction, VT: Chelsea Green Publishing, 2004. ISBN: 9781931498586.

Buy at Amazon Levitt, Steven D., and Stephen J. Dubner. Freakonomics. New York, NY: Morrow/Avon, 2005. ISBN: 9780060731328.

Buy at Amazon Enriquez, Juan. As the Future Catches You: How Genomics & Other Forces Are Changing Your Life, Work, Health & Wealth. New York, NY: Crown Publishing Group, 2001. ISBN: 9780609609033.

Buy at Amazon Koza, John R. Genetic Programming IV: Routine Human-Competitive Machine Intelligence. New York, NY: Springer, 2003. ISBN: 9781402074462.

Buy at Amazon Wilson, Edward O. Consilience: The Unity of Knowledge. New York, NY: Knopf Publishing Group, 1999. ISBN: 9780679768678.

Buy at Amazon Stock, Gregory. Redesigning Humans. Boston, MA: Houghton Mifflin Company Trade & Reference Division, 2003. ISBN: 978-0618340835.

Buy at Amazon Immortality Institute. The Scientific Conquest Of Death. Buenos Aires, Argentina: LibrosEnRed, 2004. ISBN: 9789875611351.

Buy at Amazon Diamond, Jared M. Collapse: How Societies Choose to Fail or Succeed. New York, NY: Penguin Group (USA) Incorporated, 2005. ISBN: 9780143036555.

Buy at Amazon Gladwell, Malcolm. The Tipping Point: How Little Things Can Make a Big Difference. New York, NY: Little Brown & Company, 2002. ISBN: 9780316346627.

Buy at Amazon Surowiecki, James. The Wisdom of Crowds. New York, NY: Knopf Publishing Group, 2005. ISBN: 9780385721707.

Articles

Series of articles in "Crossroads for Planet Earth." Scientific American 293, no. 3 (September 2005).

Kolbert, Elizabeth. "The Climate of Man." The New Yorker, April 24, 2005.

Briggs, Michael. Widescale Biodiesel Production from Algae. Revised August 2004.

Gibbs, W. W. "Synthetic life." Scientific American 290, no. 5 (May 2004): 74-81.

Collins, Francis S. "Personalized medicine: A new approach to staying well." The Boston Globe, July 17, 2005.

Technical References

Buy at Amazon Tisdall, James. Beginning Perl for Bioinformatics. Cambridge, MA: O'Reilly Media, Inc., 2001. ISBN: 9780596000806.

Buy at Amazon Mount, David W. Bioinformatics: Sequence and Genome Analysis. Woodbury, NY: Cold Spring Harbor Laboratory Press, 2001. ISBN: 9780879696085.

Buy at Amazon Hunter, Lawrence, ed. "Molecular Biology for Computer Scientists." Chapter 1 in Artificial Intelligence and Molecular Biology. Cambridge, MA: MIT Press, 1993. ISBN: 9780262581158.

Buy at Amazon Durbin, Richard, Sean R. Eddy, Anders S. Krogh, and Graeme Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. New York, NY: Cambridge University Press, 1999. ISBN: 9780521629713.

Buy at Amazon Weiss, Neil A. Introductory Statistics. 7th ed. Boston, MA: Addison Wesley, 2004. ISBN: 9780201771312.

Buy at Amazon Gibas, Cynthia and Per Jambeck. Developing Bioinformatics Computer Skills. Cambridge, MA: O'Reilly Media, Incorporated, 2001. ISBN: 9781565926646.

Buy at Amazon Walsh, Linda, ed. The Perl CD Bookshelf, Version 3.0. Cambridge, MA: O'Reilly Media, Incorporated, 2002. ISBN: 9780596003890.

Personalized Medicine

Pollack, Andrew. "A Special Drug Just for You, At the End of a Long Pipeline." New York Times, November 8, 2005.

Burgard, A. P., P. Pharkya, C. D. Maranas. "Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization." Biotechnol Bioeng 84, no. 6 (December 20, 2003): 647-57.

The International HapMap Consortium. "A haplotype map of the human genome." Nature 437 (2005): 1299-1320.

Chung, Young, et al. "Embryonic and extraembryonic stem cell lines derived from single mouse blastomeres." Nature 439, no. 7073 (2006): 216-9.

Wade, Nicholas. "Stem Cell Test Tried on Mice Saves Embryo." New York Times, October 17, 2005.

Rovio, S., I. Kareholt, E. L. Helkala, M. Viitanen, B. Winblad, J. Tuomilehto, H. Soininen, A. Nissinen, and M. Kivipelto. "Leisure-time physical activity at midlife and the risk of dementia and Alzheimer's disease." Lancet Neurol 4, no. 11 (November 2005): 705-11.

Weston, A. D., and L. Hood. "Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine." J Proteome Res 3, no. 2 (March-April 2004): 179-96.

Meyer, J. M., and G. S. Ginsburg. "The path to personalized medicine." Curr Opin Chem Biol 6 (2002): 434-438.

Gibbs, R. "Deeper into the genome commentary on HapMap milestone and where to go next." Nature 437, no. 7063 (October 27, 2005): 1233-4.

Gawande, Atul. "Medicine's money problem." The New Yorker, April 04, 2005.

———. "Bad Medicine." The New Yorker, November 14, 2005. [Atul Gawande writes about who pays the price when patients sue doctors. Here, with Daniel Cappello, he talks about the costs and consequences of medical malpractice.]

Student Readings

Wolfe, C. J., I. S. Kohane, and A. J. Butte. "Systematic survey reveals general applicability of 'guilt-by-association' within gene coexpression networks." BMC Bioinformatics 6 (2005): 227.

Wade, Nicholas. "Genetic Find Stirs Debate on Race-Based Medicine." New York Times, November 11, 2005.

Vernon, John A., and W. Keener Hughen. "The Future of Drug Development: The Economics of Pharmacogenomics." NBER Working Paper No. 11875, December 2005.

Definitions, Background, Requests for Research

NIH DNA Resequencing and Genotyping Service web site

"Sequence specificity." Editorial. Nature Genetics 37, no. 10 (2005): 1013-1013.

"NHGRI's Large-Scale Sequencing Research Network Sets Its Sights on Disease Targets." Press release. NIH News, October 17, 2005.

National Human Genome Research Institute (NHGRI). "Request for Information: Comments on the Identification of Mendelian Disorders by Genomic Sequencing." Notice Number: NOT-HG-05-006, August 2, 2005.

Existing Technologies and Lines of Research

Shendure, Jay, et al. "Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome." Science 309, no. 5741: 1728-1732.

Policy Issues in Implementation - Public Health, Access to Care, Insurance Policy

Sage, William M. "Funding Fairness: Public Investment, Proprietary Rights and Access to Health Care Technology." Virginia Law Review 82, no. 8 (November 1996): 1737-1752. (Symposium on Regulating Medical Innovation.)

Kalb, Paul E. "Controlling Health Care Costs by Controlling Technology: A Private Contractual Approach." The Yale Law Journal 99, no. 5. (March 1990): 1109-1126.

Biehl, João. "The Activist State: Global Pharmaceuticals, AIDS, and Citizenship in Brazil." Social Text 22.3 (2004): 105-132.

Personal Genome Project (PGP)

Church, George M. "Genomes for all." Scientific American 294, no. 1. (January 2006): 46-54. [Article on the Personal Genome project in Scientific American.]

———. "The Personal Genome Project" Mol Syst Biol 2005 doi:10.1038/msb4100040.

The Personal Genome Project page.

HapMap

Montana, Giovanni. "HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients." Bioinformatics 21, no. 23. (2005): 4309-4311.

The International HapMap Consortium. "A haplotype map of the human genome." Nature 437 (2005): 1299-1320.

Gibbs, R. "Deeper into the genome commentary on HapMap milestone and where to go next." Nature 437, no. 7063 (October 27, 2005): 1233-4.

New Energy Sources

Metabolic Engineering Resources

Vunjak-Novakovic, D., Y. Kim, X. Wu, I. Berzin, and J. C. Merchuk. "Air-Lift Bioreactors for Algal Growth on Flue Gas: Mathematical Modeling and Pilot-Plant Studies." Ind Eng Chem Res 44 (2005): 6154-6163.

Fong, S. S., A. P. Burgard, C. D. Herring, E. M. Knight, F. R. Blattner, C. D. Maranas, and B. O. Palsson. "In silico design and adaptive evolution of Escherichia coli for production of lactic acid." Biotechnol Bioeng 91, no. 5 (September 2005): 643-8.

Rozen, D. E., D. Schneider, and R. E. Lenski. "Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism." J Mol Evol 61, no. 2 (August 2005): 171-80.

Burgard, A. P., P. Pharkya, and C. D. Maranas. "Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization." Biotechnol Bioeng 84, no. 6 (December 20, 2003): 647-57.

Martin, V. J., D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. "Engineering a mevalonate pathway in Escherichia coli for production of terpenoids." Nat Biotechnol 21, no. 7 (July 2003): 796-802. [Not exactly personalized medicine, but a very interesting application of systems and synthetic biology for drug production. Ironically, Jay Keasling will be giving a talk at the ICSB 2005 meeting during Week #5 class.]

Price, N., J. Reed, and B. Palsson. "Genome-scale models of microbial cells: evaluating the consequences of constraints." Nature Reviews Microbiology 2 (2004): 886-897. (doi:10.1038/nrmicro1023)

Kurzweil, Ray, and Bill Joy. "Recipe for Destruction." New York Times, October 17, 2005.

Bioremediation Readings

Lovley D. "Cleaning up with genomics: applying molecular biology to bioremediation." Nature Reviews Microbiology 1 (2003): 35-44. (doi:10.1038/nrmicro731) [A survey of the present and future of bioremediation. It seems that the modeling involved in bioremediation would use almost all the same tools as modeling involved in biomass production.]

Benemann, J. R., J. C. Van Olst, M. J. Massingill, J. C. Weissman, and D. E. Brune. "The Controlled Eutrophication Process: Using Microalgae for CO2 Utilization and Agricultural Fertilizer Recycling." Working paper. 2002.

Biodiesel Readings

Tyson, K. S., et al. "Biomass Oil Analysis: Research Needs and Recommendations." National Renewable Energy Laboratory. Report NREL/TP-510-34796, June 2004. [A DOE report on research needs for further development of biomass-oil industry in the United States.]

Sheehan, John, et al. "A Look Back at the U.S. Department of Energy’s Aquatic Species Program: Biodiesel from Algae." National Renewable Energy Laboratory. Report NREL/TP-580-24190, July 1998. [The DOE report on biomass oil from algae, which Briggs draws heavily upon for his article.]

Benemann, J. R., J. C. Van Olst, M. J. Massingill, J. C. Weissman, and D. E. Brune. "The Controlled Eutrophication Process: Using Microalgae for CO2 Utilization and Agricultural Fertilizer Recycling." Working paper. 2002. [The conference paper that discusses algae farms in the desert Southwest, which forms the basis of Briggs's discussion.]

Toda, M., A. Takagaki, M. Okamura, J. N. Kondo, S. Hayashi, K. Domen, and M. Hara. "Green chemistry: biodiesel made with sugar catalyst." Nature 438, no. 7065 (November 10, 2005): 178.

Reuters. "Virgin Airways boss eyes plants for fleet fuel." November 16, 2005. [Discusses the possibility of using vegetable fuel for aircraft as well as for automobiles and ships.]

Schmidt, Lawrence. Biodiesel Vehicle Fuel: GHG Reductions, Air Emissions, Supply and Economic Overview. Climate Change Central. Discussion Paper C3-015. March 11, 2004.

Friedrich, Mag. Stephan. A World Wide Review of the Commercial Production of Biodiesel – A technological, economic and ecological investigation based on case studies. Wien 2004.

Duncan, John. "Costs of Biodiesel Production." Energy Efficiency and Conservation Authority, May 2003.

Krahl, J., et al. "Gaseous Compounds, Ozone Precursors, Particle Number and Particle Size Distributions, and Mutagenic Effects due to Biodiesel." Transactions of the ASAE 44, no. 2 (2001): 179-191. [Particle size and mutagenic effects due to biodiesel. Article suggests potential problems with biodiesel.]

Mansell, G., et al. "Impact of Biodiesel Fuels on Air Quality and Human Health: Task 3 Report, The Impact of Biodiesel Fuels on Ambient Carbon Monoxide Levels in the Las Vegas Nonattainment Area." ENVIRON International Corporation. National Renewable Energy Laboratory. Report NREL/SR-540-33796, May 2003. [This study states that biodiesel emission of CO is not significantly different from ordinary diesel.]

Puppan, Daniel. "Environmental Evaluation of Biofuels." Periodica Polytechnica Ser Soc Man Sci 10, no 1 (2002): 95-116.

Biocomplexity and Randomness Readings

The problem with defining complexity and randomness is that they both already have very precise technical definitions, relating them to algorithmic information theory and Godel's Incompleteness Theorem in surprising and insightful ways.

Gregory Chaitin defines the complexity of something as "the size of the smallest program which computes it or a complete description of it."

Crutchfield, J. P., and Young, K. "Inferring Statistical Complexity." Physical Review Letters 63, no. 2 (1989): 105-108. [In the complexity measure defined by Crutchfield and Young, they attempt to define a measure of the chaos in a system using statistical mechanics.]

Kauffman, Stuart. "Investigations: The Nature of Autonomous Agents and the Worlds They Mutually Create." Santa Fe Institute Preprint, September 13, 1996. [Kauffman defines an molecular autonomous agent as a self-reproducing system that is capable of producing at least one thermodynamic work cycle.]

Buy at Amazon Chaitin, Gregory J. "Toward a Mathematical Definition of 'Life'." In The Maximum Entropy Formalism. Levine, R. D., and M. Tribus, eds. Cambridge, MA: MIT Press, 1978, pp. 477-498. ISBN: 9780262120807.