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Science as metaphor
Sean Gibbons
5 posts
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- October 9, 2011
- 07:30 PM
- 272 views
Laser Worms!
by Sean Gibbons in Ars Scientifica
The blossoming field of optogenetics was Nature Methods "Method of the Year" in 2010.... Read more »
Stirman, J., Crane, M., Husson, S., Wabnig, S., Schultheis, C., Gottschalk, A., & Lu, H. (2011) Real-time multimodal optical control of neurons and muscles in freely behaving Caenorhabditis elegans. Nature Methods, 8(2), 153-158. DOI: 10.1038/nmeth.1555
- August 12, 2011
- 12:30 AM
- 924 views
A Case for BioHydrogen
by Sean Gibbons in Ars Scientifica
The hydrocarbon economy is faltering as oil reserves dwindle worldwide (Hirsch, 2008). Commodity prices have begun to fluctuate drastically due to the uncertain cost of petroleum, which resulted in food riots around the world in 2008. With a steadily decreasing energy supply and the demands on energy systems continually growing, the planet is in dire economic, geopolitical, and environmental straits. In order to halt the advance of climate change, prevent ecological collapse, rescue the globa........ Read more »
Agapakis, C., Ducat, D., Boyle, P., Wintermute, E., Way, J., & Silver, P. (2010) Insulation of a synthetic hydrogen metabolism circuit in bacteria. Journal of Biological Engineering, 4(1), 3. DOI: 10.1186/1754-1611-4-3
Asada, Y. (2000) Heterologous expression of clostridial hydrogenase in the cyanobacterium Synechococcus PCC7942. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1490(3), 269-278. DOI: 10.1016/S0167-4781(00)00010-5
Atsumi, S., Higashide, W., & Liao, J. (2009) Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nature Biotechnology, 27(12), 1177-1180. DOI: 10.1038/nbt.1586
Bendall, D., Howe, C., Nisbet, E., & Nisbet, R. (2008) Introduction. Photosynthetic and atmospheric evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1504), 2625-2628. DOI: 10.1098/rstb.2008.0058
Blankenship, R., & Hartman, H. (1998) The origin and evolution of oxygenic photosynthesis. Trends in Biochemical Sciences, 23(3), 94-97. DOI: 10.1016/S0968-0004(98)01186-4
Brioukhanov, A., & Netrusov, A. (2007) Aerotolerance of strictly anaerobic microorganisms and factors of defense against oxidative stress: A review. Applied Biochemistry and Microbiology, 43(6), 567-582. DOI: 10.1134/S0003683807060014
Cho, M. (1999) GENETICS:Ethical Considerations in Synthesizing a Minimal Genome. Science, 286(5447), 2087-2090. DOI: 10.1126/science.286.5447.2087
Cleaves, H., Chalmers, J., Lazcano, A., Miller, S., & Bada, J. (2008) A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres. Origins of Life and Evolution of Biospheres, 38(2), 105-115. DOI: 10.1007/s11084-007-9120-3
Cohen, M., Wallis, J., Campbell, E., & Meeks, J. (1994) Transposon mutagenesis of Nostoc sp. strain ATCC 29133, a filamentous cyanobacterium with multiple cellular differentiation alternatives. Microbiology, 140(12), 3233-3240. DOI: 10.1099/13500872-140-12-3233
Enderlin, C., & Meeks, J. (1983) Pure culture and reconstitution of the Anthoceros-Nostoc symbiotic association. Planta, 158(2), 157-165. DOI: 10.1007/BF00397709
Fontecilla-Camps, J., Amara, P., Cavazza, C., Nicolet, Y., & Volbeda, A. (2009) Structure–function relationships of anaerobic gas-processing metalloenzymes. Nature, 460(7257), 814-822. DOI: 10.1038/nature08299
Ghirardi, M., Posewitz, M., Maness, P., Dubini, A., Yu, J., & Seibert, M. (2007) Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms . Annual Review of Plant Biology, 58(1), 71-91. DOI: 10.1146/annurev.arplant.58.032806.103848
Hirsch, R. (2008) Mitigation of maximum world oil production: Shortage scenarios. Energy Policy, 36(2), 881-889. DOI: 10.1016/j.enpol.2007.11.009
Huang, H., Camsund, D., Lindblad, P., & Heidorn, T. (2010) Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Research, 38(8), 2577-2593. DOI: 10.1093/nar/gkq164
Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga-Canut, M., & Serrano, L. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature, 452(7189), 840-845. DOI: 10.1038/nature06847
King, P., Posewitz, M., Ghirardi, M., & Seibert, M. (2006) Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System. Journal of Bacteriology, 188(6), 2163-2172. DOI: 10.1128/JB.188.6.2163-2172.2006
MAKARIEVA, A., GORSHKOV, V., & LI, B. (2008) Energy budget of the biosphere and civilization: Rethinking environmental security of global renewable and non-renewable resources. Ecological Complexity, 5(4), 281-288. DOI: 10.1016/j.ecocom.2008.05.005
Mimuro, M., Tomo, T., & Tsuchiya, T. (2008) Two unique cyanobacteria lead to a traceable approach of the first appearance of oxygenic photosynthesis. Photosynthesis Research, 97(2), 167-176. DOI: 10.1007/s11120-008-9311-4
Mukherji, S., & van Oudenaarden, A. (2009) Synthetic biology: understanding biological design from synthetic circuits. Nature Reviews Genetics. DOI: 10.1038/nrg2697
NISBET, E., GRASSINEAU, N., HOWE, C., ABELL, P., REGELOUS, M., & NISBET, R. (2007) The age of Rubisco: the evolution of oxygenic photosynthesis. Geobiology, 5(4), 311-335. DOI: 10.1111/j.1472-4669.2007.00127.x
Oliveira, P., & Lindblad, P. (2007) An AbrB-Like Protein Regulates the Expression of the Bidirectional Hydrogenase in Synechocystis sp. Strain PCC 6803. Journal of Bacteriology, 190(3), 1011-1019. DOI: 10.1128/JB.01605-07
Picataggio, S. (2009) Potential impact of synthetic biology on the development of microbial systems for the production of renewable fuels and chemicals. Current Opinion in Biotechnology, 20(3), 325-329. DOI: 10.1016/j.copbio.2009.04.003
Schutz, K., Happe, T., Troshina, O., Lindblad, P., Leitao, E., Oliveira, P., & Tamagnini, P. (2004) Cyanobacterial H2 production ? a comparative analysis. Planta, 218(3), 350-359. DOI: 10.1007/s00425-003-1113-5
Tamagnini, P., Leitao, E., Oliveira, P., Ferreira, D., Pinto, F., Harris, D., Heidorn, T., & Lindblad, P. (2007) Cyanobacterial hydrogenases: diversity, regulation and applications. FEMS Microbiology Reviews, 31(6), 692-720. DOI: 10.1111/j.1574-6976.2007.00085.x
Tikhonovich, I., & Provorov, N. (2007) Cooperation of plants and microorganisms: Getting closer to the genetic construction of sustainable agro-systems. Biotechnology Journal, 2(7), 833-848. DOI: 10.1002/biot.200700014
Towe, K. (1996) Environmental oxygen conditions during the origin and early evolution of life. Advances in Space Research, 18(12), 7-15. DOI: 10.1016/0273-1177(96)00022-1
Tsygankov, A. (2007) Nitrogen-fixing cyanobacteria: A review. Applied Biochemistry and Microbiology, 43(3), 250-259. DOI: 10.1134/S0003683807030040
WILLE, M., KRAMERS, J., NAGLER, T., BEUKES, N., SCHRODER, S., MEISEL, T., LACASSIE, J., & VOEGELIN, A. (2007) Evidence for a gradual rise of oxygen between 2.6 and 2.5Ga from Mo isotopes and Re-PGE signatures in shales. Geochimica et Cosmochimica Acta, 71(10), 2417-2435. DOI: 10.1016/j.gca.2007.02.019
- August 7, 2011
- 12:46 PM
- 714 views
Ghost in the Machine?
by Sean Gibbons in Ars Scientifica
Science is a contemporary rebuttal to metaphysics by which the mysterious elements of the universe are broken into component parts and observed, perturbed, and reassembled in myriad ways in order to seek out some objective, material truth. Religious dogma has melted before the torch of empiricism, as demonstrated by Galileo and Darwin. While humbly recognizing the impossibility of knowing all, scientists hold fast to the assumption that all things are inherently knowable. Admittedly, we are o........ Read more »
Fernández, A., & Lynch, M. (2011) Non-adaptive origins of interactome complexity. Nature, 474(7352), 502-505. DOI: 10.1038/nature09992
- July 30, 2011
- 01:30 PM
- 697 views
Teenage Mutant Ninja Fruit Flies
by Sean Gibbons in Ars Scientifica
The word magnetoreception conjures super-human mutant powers from X-Men comics, but it refers to the subtle ability of birds (and other animals, including sea turtles, salmon, and fruit flies) to perceive magnetic fields...... Read more »
Edmonds, D. (1996) A Sensitive Optically Detected Magnetic Compass for Animals. Proceedings of the Royal Society B: Biological Sciences, 263(1368), 295-298. DOI: 10.1098/rspb.1996.0045
Foley, L., Gegear, R., & Reppert, S. (2011) Human cryptochrome exhibits light-dependent magnetosensitivity. Nature Communications, 356. DOI: 10.1038/ncomms1364
Gauger, E., Rieper, E., Morton, J., Benjamin, S., & Vedral, V. (2011) Sustained Quantum Coherence and Entanglement in the Avian Compass. Physical Review Letters, 106(4). DOI: 10.1103/PhysRevLett.106.040503
Gegear, R., Foley, L., Casselman, A., & Reppert, S. (2010) Animal cryptochromes mediate magnetoreception by an unconventional photochemical mechanism. Nature, 463(7282), 804-807. DOI: 10.1038/nature08719
RITZ, T. (2000) A Model for Photoreceptor-Based Magnetoreception in Birds. Biophysical Journal, 78(2), 707-718. DOI: 10.1016/S0006-3495(00)76629-X
Solov’yov, I., Chandler, D., & Schulten, K. (2007) Magnetic Field Effects in Arabidopsis thaliana Cryptochrome-1. Biophysical Journal, 92(8), 2711-2726. DOI: 10.1529/biophysj.106.097139
- July 18, 2011
- 05:00 PM
- 287 views
Exquisite Machines Part 1: prose
by Sean Gibbons in Ars Scientifica
The synthesis of non-equilibrium thermodynamics and biology, pursued in fits and starts over the years by an eccentric cast of thinkers, has produced a few scientific red herrings, but the overall idea has expanded our biophysical horizons.... Read more »
Brown, J., Gillooly, J., Allen, A., Savage, V., & West, G. (2004) TOWARD A METABOLIC THEORY OF ECOLOGY. Ecology, 85(7), 1771-1789. DOI: 10.1890/03-9000
LOVELOCK, J., & MARGULIS, L. (1974) Atmospheric homeostasis by and for the biosphere: the gaia hypothesis. Tellus, 26(1-2), 2-10. DOI: 10.1111/j.2153-3490.1974.tb01946.x
Toussaint, O.; Schneider, E.D. (1998) The thermodynamics and evolution of complexity in biological systems. Comparative Biochemistry and Physiology - Part A: Molecular , 120(1), 3-9. DOI: 10.1016/S1095-6433(98)10002-8
Schneider, E. (1994) Complexity and thermodynamics Towards a new ecology. Futures, 26(6), 626-647. DOI: 10.1016/0016-3287(94)90034-5
von Stockar, U., & Liu, J. (1999) Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1412(3), 191-211. DOI: 10.1016/S0005-2728(99)00065-1
VONSTOCKAR, U., VOJINOVIC, V., MASKOW, T., & LIU, J. (2008) Can microbial growth yield be estimated using simple thermodynamic analogies to technical processes?. Chemical Engineering and Processing: Process Intensification, 47(6), 980-990. DOI: 10.1016/j.cep.2007.02.016
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