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all things organic and algebraic

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  • September 5, 2013
  • 05:20 PM

Wonderous Stories

by csoeder in Topologic Oceans

Science is sometimes criticized as draining the meaning and beauty out of existence, when in reality it has the opposite problem. Because it allows one to acquire knowledge otherwise inaccessible to common perception, science gives us access to a whole other landscape, with terrifying and beautiful scenery. It is hard to discuss the history of […]... Read more »

  • August 21, 2013
  • 06:46 PM


by csoeder in Topologic Oceans

One of my hobbies is sacred geometry‭ ‬-‭ ‬loosely defined,‭ ‬it’s the study and use of mathematical archetypes in nature and culture,‭ ‬often with a focus on traditional compass and straightedge constructions.‭ Don’t worry‭; ‬I’m not about to go off into numerology,‭ ‬telling you that you can derive the groovy cosmic secrets of the ancients […]... Read more »

Luca Bindi, John M. Eiler, Yunbin Guan, Lincoln S. Hollister, Glenn MacPherson, Paul J. Steinhardt, & Nan Yao. (2012) Evidence for the extraterrestrial origin of a natural quasicrystal. Proceedings of the National Academy of Sciences of the United States of America, 109(5), 1396-1401. DOI: 10.1073/pnas.1111115109  

Schülli TU, Daudin R, Renaud G, Vaysset A, Geaymond O, & Pasturel A. (2010) Substrate-enhanced supercooling in AuSi eutectic droplets. Nature, 464(7292), 1174-7. PMID: 20414305  

  • August 13, 2013
  • 09:23 PM

What’s Up with the Bad Chemistry?

by csoeder in Topologic Oceans

Watts Up With That is a very, very silly website. Here’s what I mean: In a recent article at WUWT, chemical engineering graduate Steve Burnette tries to dismiss concerns about ocean acidification, but his claims are outright wrong when they are coherent. The centerpiece of the article is a calculation meant to estimate the change […]... Read more »

Albright R, Mason B, Miller M, & Langdon C. (2010) Ocean acidification compromises recruitment success of the threatened Caribbean coral Acropora palmata. Proceedings of the National Academy of Sciences of the United States of America, 107(47), 20400-4. PMID: 21059900  

Anthony KR, Kline DI, Diaz-Pulido G, Dove S, & Hoegh-Guldberg O. (2008) Ocean acidification causes bleaching and productivity loss in coral reef builders. Proceedings of the National Academy of Sciences of the United States of America, 105(45), 17442-6. PMID: 18988740  

Caldeira, Ken, & Wickett, Michael. (2003) Anthropogenic carbon and ocean pH. Nature. DOI: 10.1038/425365a  

Gazeau, Frédéric, Quiblier, Christophe, Jansen, Jeroen M., Gattuso, Jean-Pierre, Middelburg, Jack J., & Heip, Carlo H. R. (2007) Impact of elevated CO2 on shellfish calcification. Geophysical Research Letters, 34(7). info:/

Hinojosa, J. L., Brown, S. T., Chen, J., DePaolo, D. J., Paytan, A., Shen, S.-z., & Payne, J. L. (2012) Evidence for end-Permian ocean acidification from calcium isotopes in biogenic apatite. Geology, 40(8), 743-746. DOI: 10.1130/G33048.1  

Kump, Lee, Bralower, Timothy, & Ridgwell, Andy. (2008) Ocean Acidification in Deep Time. Oceanography, 22(4), 94-107. DOI: 10.5670/oceanog.2009.100  

Wood, Hannah L, Spicer, John I, & Widdicombe, Stephen. (2008) Ocean acidification may increase calcification rates, but at a cost. Proceedings of the Royal Society B, 1767-1773. DOI: 10.1098/rspb.2008.0343  

  • January 29, 2013
  • 08:22 PM

LabLulz: densitometry of hydrogen purr-oxide

by csoeder in Topologic Oceans

Today in LabLulz, I’m going to walk through a recent preparation I did in my chemistry lab: increasing and measuring the concentration of hydrogen peroxide. WARNING: This procedure involves heat and the end product is a powerful oxidizer. Don’t get burned and don’t get it on yourself – wear gloves, splash-resistant goggles, and an apron. […]... Read more »

  • January 20, 2013
  • 12:34 PM

ThermoPoker Dot Viz: using pygame animations to understand iterated games

by csoeder in Topologic Oceans

I’m revisiting some older research of mine, so that I can talk a little bit about some data visualization I did along the way. If you frequent TriZPUG or the SplatSpace, you might have seen my original presentation, but In Case You Missed It… You might remember a while back I got interested in researching [...]... Read more »

Annila, A., & Salthe, S. (2009) Economies Evolve by Energy Dispersal. Entropy, 11(4), 606-633. DOI: 10.3390/e11040606  

Anttila, J., & Annila, A. (2011) Natural games. Physics Letters A, 375(43), 3755-3761. DOI: 10.1016/j.physleta.2011.08.056  

  • December 15, 2012
  • 12:14 PM

Light and Noise in the Anthropocene

by csoeder in Topologic Oceans

There is a companion article exploring the issue from the perspective of environmental monitoring over at ArkFab. Human influence on the environment has increased dramatically over the last 10,000 years, to the point that some geologists have argued that human reworking of the earth defines a new geologic age, The Anthropocene. (Zalasiewicz et al, 2008) [...]... Read more »

José Alicea-Pou, Olga Viñas-Curiel, Wanda Cruz-Vizcarrondo, & Osvaldo Alomar. (2005) Monitoring of the Environmental Noise Level in San Juan, Puerto Rico. Environmental Quality Board. info:/

David Dunn, & James P. Crutchfield. (2006) Insects, Trees, and Climate: The Bioacoustic Ecology of Deforestation and Entomogenic Climate Change. Santa Fe Institute Working Paper. arXiv: q-bio/0612019v1

Fuller, R., Warren, P., & Gaston, K. (2007) Daytime noise predicts nocturnal singing in urban robins. Biology Letters, 3(4), 368-370. DOI: 10.1098/rsbl.2007.0134  

Longcore, T., & Rich, C. (2004) Ecological Light Pollution. Frontiers in Ecology and the Environment, 2(4), 191. DOI: 10.2307/3868314  

Zalasiewicz, J., Williams, M., Smith, A., Barry, T., Coe, A., Bown, P., Brenchley, P., Cantrill, D., Gale, A., Gibbard, P.... (2008) Are we now living in the Anthropocene. GSA Today, 18(2), 4. DOI: 10.1130/GSAT01802A.1  

  • November 19, 2012
  • 01:27 AM

Airbag Saved My Life: the Carolina Review’s Clinical Derpitude Continues

by csoeder in Topologic Oceans

I had thought that once I graduated college, annoying student publications would quit being so… annoying. Alas, this isn’t the case. A previous article examined the quality of analysis at the Carolina Review, UNC’s ‘journal of conservative thought and opinion’; let’s see if things have approved any in the handful of years that I’ve been [...]... Read more »

Wenzel, T., & Ross, M. (2008) Safer Vehicles for People and the Planet. American Scientist, 96(2), 122. DOI: 10.1511/2008.70.3638  

  • July 24, 2012
  • 04:22 AM

Global Warming Killed My Friend’s Dog

by csoeder in Topologic Oceans

I sit at the Carrboro Really Free Market, on the first caturday in July. I sit in the shade and the banners are blowing lazily in the breeze; still it’s nearly 100 degrees; the humidity jacks it up to 103, and the breeze is welcome but ineffectual. Air quality is ‘Orange’: ozone levels ‘may approach [...]... Read more »

John A. Church, & Neil J. White. (2006) A 20th century acceleration in global sea-level rise. Geophysical Research Letters. DOI: 10.1029/2005GL024826  

Andrew C. Kemp, Benjamin P. Horton, Jeffrey P. Donnelly, Michael E. Mann, Martin Vermeer, & Stefan Rahmstorff. (2011) Climate related sea-level variations over the past two millennia . PNAS. DOI: 10.1073/pnas.1015619108  

Le Conte Y, & Navajas M. (2008) Climate change: impact on honey bee populations and diseases. Revue scientifique et technique (International Office of Epizootics), 27(2), 485. PMID: 18819674  

Jesse A. Logan, & James A. Powell. (2001) Ghost Forests, Global Warming . AMERICAN ENTOMOLOGIST , 47(3), 160-172. info:/

E. Zorita, T. F. Stocker, & H. von Storch1. (2008) How unusual is the recent series of warm years?. Geophysical Research Letters. DOI: 10.1029/2008GL036228  

  • April 28, 2012
  • 03:05 AM

Graphing Out Loud: ups and downs

by csoeder in Topologic Oceans

A while back, we started looking at a poorly thought-out article from the website C3Headlines. C3 is starting to make a name for itself as a goldmine of climate comedy- their claims have recently been addressed at Tamino and SkepticalScience. We’re going to keep digging into C3‘s claim that carbon dioxide concentrations have been increasing linearly over [...]... Read more »

Long, S., Elizabeth A. Ainsworth, Andrew D. B. Leakey, Josef Nosberger, & Donald R. Ort. (2006) Food for Thought: Lower-Than-Expected Crop Yield Stimulation with Rising CO2 Concentrations. Science, 312(5782), 1918-1921. DOI: 10.1126/science.1114722  

  • April 9, 2012
  • 12:53 AM

Mycology Symposium, Poster Session

by csoeder in Topologic Oceans

It is a lovely spring day and I am absorbing some sunlight, hanging out in the tail end of the Carrboro Really Free Market while I type up my notes on the Duke Mycology Symposium. There were a couple of posters which really caught my eye. One thing that I think is very interesting about [...]... Read more »

Randolph Nesse, & George Williams. (1994) Why We Get Sick: The New Science of Darwinian Medicine. Vintage Books: New York. info:/

  • April 6, 2012
  • 09:42 PM

Mycology Symposium, Day 2

by csoeder in Topologic Oceans

Day 2 of the Duke Mycology Symposium has wound to a close, [DAY 1 HERE] and I am sitting on my porch contemplating the afternoon’s lectures: “Pathogen recombination during the amphibian Chytridiomycosis pandemic: Why change what’s working?” A genetics perspective on Bd, a fungus responsible for widespread amphibian mortality. Apparently one of the factors in [...]... Read more »

  • April 5, 2012
  • 11:53 PM

Mycology Symposium, Day 1

by csoeder in Topologic Oceans

When I’m not too busy raging at skuptaloids online, I enjoy molecular biology and mycology, the study of fungi. Towards those ends, I’m visiting the Duke Symposium in Celebration of Mycology and Mycologists. I was only able to attend a few afternoon lectures on the first day of this conference, but am enjoying it greatly! [...]... Read more »

Randolph Nesse, & George Williams. (1994) Why We Get Sick: The New Science of Darwinian Medicine. Vintage Books: New York. info:/

Trick, C., Bill, B., Cochlan, W., Wells, M., Trainer, V., & Pickell, L. (2010) From the Cover: Iron enrichment stimulates toxic diatom production in high-nitrate, low-chlorophyll areas. Proceedings of the National Academy of Sciences, 107(13), 5887-5892. DOI: 10.1073/pnas.0910579107  

Turnbull, J., & Field, R. (2007) Emerging glycomics technologies. Nature Chemical Biology, 3(2), 74-77. DOI: 10.1038/nchembio0207-74  

  • April 4, 2012
  • 04:26 PM

Graphing Out Loud: curves and lines

by csoeder in Topologic Oceans

I love graphs – my eyes quickly glaze over at a table of numeric data, but a graph, used correctly, can quickly and easily tell the whole story. ‘Used correctly’ is the key phrase – for all their power, graphs are infamously easy to bungle, and when used incorrectly they can misinform – or lie [...]... Read more »

Andreas D. Hüsler, & Didier Sornette. (2011) Evidence for super-exponentially accelerating atmospheric carbon dioxide growth. arXiv. arXiv: 1101.2832v3

  • January 24, 2012
  • 02:08 AM

temperature aNOMalies

by csoeder in Topologic Oceans

If you are new to climate science, you might be wondering what, exactly, this ‘temperature anomaly’ thing is that you keep hearing about. I know I was a bit confused at first! This post explains the concept, using a real-world example. Cities tend to be warmer than their surrounding countrysides, a fact known as the [...]... Read more »

  • October 5, 2011
  • 07:22 PM

cnfusin rained and chas

by csoeder in Topologic Oceans

Last time, we looked at a very simple atmospheric model known as the Lorenz equations, and saw it exhibit the ‘Butterfly Effect,’ in which even very small changes in initial conditions can dramatically effect which path the system takes. However, we also saw that the initial condition had a relatively small impact on the statistical [...]... Read more »

Lorenz, Edward N. (1963) Deterministic Nonperiodic Flow. Journal of the Atmospheric Sciences, 20(2). info:/

  • August 29, 2011
  • 11:17 PM

Did chaos theory kill the climatology star?

by csoeder in Topologic Oceans

Last time, we saw that some mathematical systems are so sensitive to initial conditions that even very small uncertainties in their initial state can snowball, causing even very similar states to evolve very differently. The equations describing fluid turbulence are examples of such a system; Lorenz’s discovery of extreme sensitivity to initial conditions ended hopes [...]... Read more »

Easterling, D., & Wehner, M. (2009) Is the climate warming or cooling?. Geophysical Research Letters, 36(8). DOI: 10.1029/2009GL037810  

Lorenz, Edward N. (1963) Deterministic Nonperiodic Flow. Journal of the Atmospheric Sciences, 20(2). info:/

  • July 1, 2011
  • 11:38 PM

Thermodynamics and Poker

by csoeder in Topologic Oceans

There is a comapnion article which discusses this project’s role in decentralized community and citizen science at ArkFab. You can find the current paper here. A while back, I got the idea to investigate how the entropy of a poker tournament evolves with time. In thermodynamics, entropy is a measure of how ‘spread out’ energy [...]... Read more »

Clément Sire. (2007) Universal statistical properties of poker tournaments. J. Stat. Mech. (2007) P08013. arXiv: physics/0703122v3

Annila, Arto. (2009) Economies Evolve by Energy Dispersal. Entropy, 11(4), 606-633. DOI: 10.3390/e11040606  

  • May 10, 2011
  • 12:56 PM

A quick video about the environmental chemistry of carbon dioxide

by csoeder in Topologic Oceans

I find some dry ice and hilarity ensues. Veron JE, Hoegh-Guldberg O, Lenton TM, Lough JM, Obura DO, Pearce-Kelly P, Sheppard CR, Spalding M, Stafford-Smith MG, & Rogers AD (2009). The coral reef crisis: the critical importance of Marine pollution bulletin, 58 (10), 1428-36 PMID: 19782832... Read more »

Veron JE, Hoegh-Guldberg O, Lenton TM, Lough JM, Obura DO, Pearce-Kelly P, Sheppard CR, Spalding M, Stafford-Smith MG, & Rogers AD. (2009) The coral reef crisis: the critical importance of. Marine pollution bulletin, 58(10), 1428-36. PMID: 19782832  

  • March 28, 2011
  • 04:17 PM

unknowns, uncertainties, and obsolesence

by csoeder in Topologic Oceans

Antiscience campaigns often share the characteristic that they complain about the open questions, anomalies, and experimental limitations inscience. Scientists, on the other hand, work hard to resolve these issues. Creationists complain about uncertainties on the chemical origins of life; biochemists generate and test hypotheses, developing useful technology and techniques in the process. (Bullard et al. [...]... Read more »

  • March 2, 2011
  • 11:55 AM

John Everett, Part VIII: The Conch Loosens

by csoeder in Topologic Oceans

The last part of Dr. Everett’s testimony presents his conclusions. Much of it is simply reiteration ofclaims he has already made, but he also takes the opportunity to thicken the smoke screen just a little bit more. Some parts are mundane: ‘The most important approach [...] is to examine what happened during past times.’ I completely [...]... Read more »

Fabry, V., Seibel, B., Feely, R., & Orr, J. (2008) Impacts of ocean acidification on marine fauna and ecosystem processes. ICES Journal of Marine Science, 65(3), 414-432. DOI: 10.1093/icesjms/fsn048  

Ken Caldeira. (2007) What Corals are Dying to Tell Us About CO2 and Ocean Acidification. Oceanography, 20(2), 188-195. info:/

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