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Scientific Investigations Report 2005-5232 The carbonate-rock aquifer of the Great Basin is named for the thick sequence of Paleozoic limestone and dolomite with lesser amounts of shale, sandstone, and quartzite. It lies primarily in the eastern half of the Great Basin and includes areas of eastern Nevada and western U... |
as well as the Death Valley area of California and small parts of Arizona and Idaho. The carbonate-rock aquifer is contained within the Basin and Range Principal Aquifer, one of 16 principal aquifers selected for study by the U.S. Geological Survey’s National Water- Quality Assessment Program. Water samples from 30 |
ground-water sites (20 in Nevada and 10 in Utah) were collected in the summer of 2003 and analyzed for major anions and cations, nutrients, trace elements, dissolved organic carbon, volatile organic compounds (VOCs), pesticides, radon, and microbiology. Water samples from selected sites also were analyzed for the isoto... |
and tritium to determine recharge sources and the occurrence of water recharged since the early 1950s. Primary drinking-water standards were exceeded for several inorganic constituents in 30 water samples from the carbonate-rock aquifer. The maximum contaminant level was exceeded for concentrations of dissolved antimon... |
mg/L) in three samples, and total dissolved solids (500 mg/L) in seven samples. Six different pesticides or metabolites were detected at very low concentrations in the 30 water samples. The lack of VOC detections in water sampled from most of the sites is evidence thatVOCs are not common in the |
carbonate-rock aquifer. Arsenic values for water range from 0.7 to 45.7 μg/L, with a median value of 9.6 μg/L. Factors affecting arsenic concentration in the carbonate-rock aquifer in addition to geothermal heating are its natural occurrence in the aquifer material and time of travel along the flow path. Most of |
the chemical analyses, especially for VOCs and nutrients, indicate little, if any, effect of overlying land-use patterns on ground-water quality. The water quality in recharge areas for the aquifer where human activities are more intense may be affected by urban and/or agricultural land uses as evidenced by pesticide d... |
proximity of the carbonate-rock aquifer at these sites to the land surface and the potential for local recharge to occur through the fractured rock likely results in the occurrence of these and other land-surface related contaminants in the ground water. Water from sites sampled near outcrops of carbonate-rock aquifer ... |
has a much shorter residence time resulting in a potential for detection of anthropogenic or land-surface related compounds. Sites located in discharge areas of the flow systems or wells that are completed at a great depth below the land surface generally show no effects of land-use activities on water quality. |
Flow times within the carbonate-rock aquifer, away from recharge areas, are on the order of thousands of years, so any contaminants introduced at the land surface that will not degrade along the flow path have not reached the sampled sites in these areas. First posted February, 2006 Part or all |
of this report is presented in Portable Document Format (PDF); the latest version of Adobe Reader or similar software is required to view it. Download the latest version of Adobe Reader, free of charge. Schaefer, D.H., Thiros, S.A., and Rosen, M.R., 2005, Ground-water quality in the carbonate-rock aquifer of the |
Great Basin, Nevada and Utah, 2003: U.S. Geological Survey Scientific Investigations Report 2005-5232, 41 p. Description of Study Area Study Design and Methods Appendix 1. Water-quality constituents analyzed in ground-water samples from wells and springs in the carbonate-rock aquifer, Nevada and Utah |
Coastal and Marine Geology Program The Swinomish Channel in La Conner, Washington. Inset shows U.S. Geological Survey instrument tripod used to measure circulation and water-column properties. (Photographs by E. Grossman |
and A. Stevens, U.S. Geological Survey.) Time-series and spatial measurements of nearshore hydrodynamic processes and water properties were made in the Swinomish Channel to quantify the net direction and rates |
of surface water transport that influence habitat for juvenile Chinook salmon along their primary migratory corridor between the Skagit River and Padilla Bay in northern Puget Sound, Washington. During the |
spring outmigration of Skagit River Chinook between March and June 2007, currents measured with fixed acoustic doppler current profilers (ADCP) at the south and north end of the Swinomish Channel |
and with roving ADCP revealed that the currents are highly asymmetric with a dominant flow to the north (toward Padilla Bay). Maximum surface current velocities reached 1.5 m/s and were |
generally uniform across the channel near McGlinn Island Causeway. Transport times for surface water to travel the 11 km from the southern end of Swinomish Channel at McGlinn Island to |
Padilla Bay ranged from 2.1 hours to 5.5 days. The mean travel time was ~1 day, while 17 percent of the time, transport of water and passive particles occurred within |
3.75 hours. Surface water in the Swinomish Channel during this time was generally very saline 20-27 psu, except south of the Rainbow Bridge in the town of La Conner where |
it ranged 0-15 psu depending on tide and Skagit River discharge. This salinity regime restricts suitable low salinity (<15-20 psu) surface waters for fry Chinook salmon to the southernmost 2 |
km of the channel. The mean change in salinity along the channel was 10-13 psu. The high northward current velocities have the capacity to transport Chinook fry into less suitable, |
high-salinity waters toward Padilla Bay within hours. The rapid transport times of 2.1 to 3.75 hours between McGlinn Island and Padilla Bay that occur 17 percent of the time, are |
considerably less than the time considered adequate for juvenile Chinook to acclimate and produce a temporal salinity gradient for pre-smolt salmon that can exceed 4 psu/hour during high northward current |
flow. Download this report as a 97-page PDF file (sir2007-5120.pdf; 14.2 MB). For questions about the content of this report, contact Eric Grossman Suggested citation and version history Download a |
Ten thousand people were killed and 10 to 15 million left homeless when a cyclone slammed into India's eastern coastal state of Orissa in October 1999. In the aftermath, CARE and the Catholic Relief Society distributed a high-nutrition mixture of corn and soy meal provided by the U.S. Agency for |
International Development to thousands of hungry storm victims. Oddly, this humanitarian act elicited cries of outrage. "We call on the government of India and the state government of Orissa to immediately withdraw the corn-soya blend from distribution," said Vandana Shiva, director of the New Delhi-based Research Foun... |
and Ecology. "The U.S. has been using the Orissa victims as guinea pigs for GM [genetically modified] products which have been rejected by consumers in the North, especially Europe." Shiva's organization had sent a sample of the food to a lab in the U.S. for testing to see if it |
contained any of the genetically improved corn and soy bean varieties grown by tens of thousands of farmers in the United States. Not surprisingly, it did. "Vandana Shiva would rather have her people in India starve than eat bioengineered food," says C.S. Prakash, a professor of plant molecular genetics at |
Tuskegee University in Alabama. Per Pinstrup-Andersen, director general of the International Food Policy Research Institute, observes: "To accuse the U.S. of sending genetically modified food to Orissa in order to use the people there as guinea pigs is not only wrong; it is stupid. Worse than rhetoric, it's false. Afte... |
all, the U.S. doesn't need to use Indians as guinea pigs, since millions of Americans have been eating genetically modified food for years now with no ill effects." Shiva not only opposes the food aid but is also against "golden rice," a crop that could prevent blindness in half a |
million to 3 million poor children a year and alleviate vitamin A deficiency in some 250 million people in the developing world. By inserting three genes, two from daffodils and one from a bacterium, scientists at the Swiss Federal Institute of Technology created a variety of rice that produces the |
nutrient beta-carotene, the precursor to vitamin A. Agronomists at the International Rice Research Institute in the Philippines plan to crossbreed the variety, called "golden rice" because of the color produced by the beta-carotene, with well-adapted local varieties and distribute the resulting plants to farmers all ov... |
June, at a Capitol Hill seminar on biotechnology sponsored by the Congressional Hunger Center, Shiva airily dismissed golden rice by claiming that "just in the state of Bengal 150 greens which are rich in vitamin A are eaten and grown by the women." A visibly angry Martina McGloughlin, director of |
the biotechnology program at the University of California at Davis, said "Dr. Shiva's response reminds me of... Marie Antoinette, [who] suggested the peasants eat cake if they didn't have access to bread." Alexander Avery of the Hudson Institute's Center for Global Food Issues noted that nutritionists at UNICEF doubted... |
was physically possible to get enough vitamin A from the greens Shiva was recommending. Furthermore, it seems unlikely that poor women living in shanties in the heart of Calcutta could grow greens to feed their children. The apparent willingness of biotechnology's opponents to sacrifice people for their cause disturbs ... |
who are trying to help the world's poor. At the annual meeting of the American Association for the Advancement of Science last February, Ismail Serageldin, the director of the Consultative Group on International Agricultural Research, posed a challenge: "I ask opponents of biotechnology, do you want 2 to 3 million |
children a year to go blind and 1 million to die of vitamin A deficiency, just because you object to the way golden rice was created?" Vandana Shiva is not alone in her disdain for biotechnology's potential to help the poor. Mae-Wan Ho, a reader in biology at London's Open |
University who advises another activist group, the Third World Network, also opposes golden rice. And according to a New York Times report on a biotechnology meeting held last March by the Organization for Economic Cooperation and Development, Benedikt Haerlin, head of Greenpeace's European anti-biotech campaign, "dism... |
African and Asian lives at the risk of spreading a new science that he considered untested." Shiva, Ho, and Haerlin are leaders in a growing global war against crop biotechnology, sometimes called "green biotech" (to distinguish it from medical biotechnology, known as "red biotech"). Gangs of anti-biotech vandals with ... |
monikers such as Cropatistas and Seeds of Resistance have ripped up scores of research plots in Europe and the U.S. The so-called Earth Liberation Front burned down a crop biotech lab at Michigan State University on New Year's Eve in 1999, destroying years of work and causing $400,000 in property |
damage. (See "Crop Busters," January.) Anti-biotech lobbying groups have proliferated faster than bacteria in an agar-filled petri dish: In addition to Shiva's organization, the Third World Network, and Greenpeace, they include the Union of Concerned Scientists, the Institute for Agriculture and Trade Policy, the Insti... |
Rural Advancement Foundation International, the Ralph Nader-founded Public Citizen, the Council for Responsible Genetics, the Institute for Food and Development Policy, and that venerable fount of biotech misinformation, Jeremy Rifkin's Foundation on Economic Trends. The left hasn't been this energized since the Vietna... |
successful, its victims will include the downtrodden people on whose behalf it claims to speak. "We're in a war," said an activist at a protesters' gathering during the November 1999 World Trade Organization meeting in Seattle. "We're going to bury this first wave of biotech." He summed up the basic |
strategy pretty clearly: "The first battle is labeling. The second battle is banning it." Later that week, during a standing-room-only "biosafety seminar" in the basement of a Seattle Methodist church, the ubiquitous Mae-Wan Ho declared, "This warfare against nature must end once and for all." Michael Fox, a vegetarian... |
from the Humane Society of the United States, sneered: "We are very clever little simians, aren't we? Manipulating the bases of life and thinking we're little gods." He added, "The only acceptable application of genetic engineering is to develop a genetically engineered form of birth control for our own species." |
This creepy declaration garnered rapturous applause from the assembled activists. Despite its unattractive side, the global campaign against green biotech has had notable successes in recent years. Several leading food companies, including Gerber and Frito-Lay, have been cowed into declaring that they will not use gene... |
their products. Since 1997, the European Union has all but outlawed the growing and importing of biotech crops and food. Last May some 60 countries signed the Biosafety Protocol, which mandates special labels for biotech foods and requires strict notification, documentation, and risk assessment procedures for biotech c... |
launched a "Five-Year Freeze" campaign that calls for a worldwide moratorium on planting genetically enhanced crops. For a while, it looked like the United States might resist the growing hysteria, but in December 1999 the Environmental Protection Agency announced that it was reviewing its approvals of biotech corn cro... |
that it might ban the crops in the future. Last May the Food and Drug Administration, which until now has evaluated biotech foods solely on their objective characteristics, not on the basis of how they were produced, said it would formulate special rules for reviewing and approving products with genetically |
modified ingredients. U.S. Rep. Dennis Kucinich (D-Ohio) has introduced a bill that would require warning labels on all biotech foods. In October, news that a genetically modified corn variety called StarLink that was approved only for animal feed had been inadvertently used in two brands of taco shells prompted recall... |
front-page headlines, and anxious recriminations. Lost in the furor was the fact that there was little reason to believe the corn was unsafe for human consumption-only an implausible, unsubstantiated fear that it might cause allergic reactions. Even Aventis, the company which produced StarLink, agreed that it was a ser... |
to have accepted the EPA's approval for animal use only. Most proponents favor approving biotech crops only if they are determined to be safe for human consumption. To decide whether the uproar over green biotech is justified, you need to know a bit about how it works. Biologists and crop |
breeders can now select a specific useful gene from one species and splice it into an unrelated species. Previously plant breeders were limited to introducing new genes through the time-consuming and inexact art of crossbreeding species that were fairly close relatives. For each cross, thousands of unwanted genes would... |
introduced into a crop species. Years of "backcrossing"-breeding each new generation of hybrids with the original commercial variety over several generations-were needed to eliminate these unwanted genes so that only the useful genes and characteristics remained. The new methods are far more precise and efficient. The ... |
variously described as "transgenic," "genetically modified," or "genetically engineered." Plant breeders using biotechnology have accomplished a great deal in only a few years. For example, they have created a class of highly successful insect-resistant crops by incorporating toxin genes from the soil bacterium Bacillu... |
on crops as an effective insecticide for decades. Now, thanks to some clever biotechnology, breeders have produced varieties of corn, cotton, and potatoes that make their own insecticide. B.t. is toxic largely to destructive caterpillars such as the European corn borer and the cotton bollworm; it is not harmful to |
researchers, science writers, editors, translators, illustrators, publishers Services and support for research-based communication in all languages and media. Join groups to meet people with related interests. Publish science! Thanks to Editage and Medlist International for practical support and advice. Click here for ... |
of geographical information that may help our members locate each other and communicate. The International Organization for Standardization displays a list of 248 official short names for countries, together with short identification codes for each country. The World Gazetteer created by Stefan Helders is a rich source... |
of the world, with a comprehensive destination gazetteer. The AuthaGraph world map shows the true areas of ocean and land in a rectangular layout. Freesurfing.com has assembled a great range of information on postcodes, zipcodes, and postal systems generally, and covers all regions of the world. (Long Bay, NZ) Last upd... |
Microsoft Windows is a series of popular proprietary operating environments and operating systems created by Microsoft for use on personal computers and servers. Microsoft first introduced an operating environment named Windows in November, 1985, as an add-on to MS-DOS. This was in response to Apple Computer's computer... |
eventually came to dominate the world personal computer market with market analysts like IDC estimating that Windows has around 90% of the client operating system market. All recent versions of Windows are fully-fledged operating systems. Tools and Libraries - Curses library - List of C Development enviroments on the G... |
The stated mission of Sage is to be viable free open source alternative to Magma, Maple, Mathematica, and Matlab. Sage’s predecessors, known as HECKE and Manin, came about because William Stein needed to write them as part of his research in number theory. Started by William in 2005 during his time at Harvard Universit... |
mathematics software, packaging and unifying them through a common interface. Many researchers in number theory, including William himself, use this common interface to build upon and extend the functionalities of underlying packages for number theory research. Such software packages include Givaro, MPIR, NTL, Pari/GP,... |
Sage because they require a comprehensive free open source mathematics package that offers symbolic and numerical computation. Most of the time, people are happy with what Sage has to offer. As is common throughout the free open source software (FOSS) world, many people often identify cases where Sage lacks certain mat... |
the underlying source code that comprises Sage in order to extend it for their purposes, or expose functionalities of underlying packages shipped with Sage in order to use their favourite mathematics software packages from within Sage. The Sage-Combinat team is comprised of researchers in algebraic combinatorics. The t... |
voluntary effort of a large international team of students, teachers, professors, researchers, software engineers, and people working in diverse areas of mathematics, science, engineering, software development, and all levels of education. The development of Sage has benefited from the financial support of numerous ins... |
contributors can be found on the Sage Development Map and the history of changes can be found in the high-level changelog. Refer to the acknowledgment page of the Sage website for an up-to-date list of financial and infrastructure supporters, mirror network hosting providers, and indirect contributors. A standard rule ... |
inspection. The Sage project believes that not doing the same for mathematics software is at best a gesture of impoliteness and rudeness, and at worst a violation against standard scientific practices. An underlying philosophical principle of Sage is to apply the system of open exchange and peer review that characteriz... |
Sage project nor the Sage Development Team make any claims to being the original proponents of this principle. The development model of Sage is largely inspired by the free software movement as spearheaded by the Free Software Foundation, and by the open source movement. One source of inspiration from within the mathem... |
paper and in particular the following quotation from his paper: You can read Sylow's Theorem and its proof in Huppert's book in the library without even buying the book and then you can use Sylow's Theorem for the rest of your life free of charge, but...for many computer algebra systems license fees have to be paid reg... |
time of their use. In order to protect what you pay for, you do not get the source, but only an executable, i.e. a black box. You can press buttons and you get answers in the same way as you get the bright pictures from your television set but you cannot control how they were made in either case. With |
this situation two of the most basic rules of conduct in mathematics are violated: In mathematics information is passed on free of charge and everything is laid open for checking. Not applying these rules to computer algebra systems that are made for mathematical research...means moving in a most undesirable direction.... |
of a program that he is not allowed to see? Moreover: Do we really want to charge colleagues in Moldava several years of their salary for a computer algebra system? Similar sentiments were also expressed by Andrei Okounkov as can be found in in particular the following quotation: Computers are no more a threat to mathe... |
a threat to cooks. As mathematics gets more and more complex while the pace of our lives accelerates, we must delegate as much as we can to machines. And I mean both numeric and symbolic work. Some people can manage without dishwashers, but I think proofs come out a lot cleaner when routine work is automated. This brin... |
issues. I am not an expert, but I think we need a symbolic standard to make computer manipulations easier to document and verify. And with all due respect to the free market, perhaps we should not be dependent on commercial software here. An open-source project could, perhaps, find better answers to the obvious problem... |
platform independence, standard libraries, etc. One can learn from the success of TeX and more specialized software like Macaulay2. I do hope that funding agencies are looking into this. Sage was not written from scratch. Most of its underlying mathematics functionalities are made possible through FOSS projects such as... |
standard packages repository. The principle programming languages of Sage are Python and Cython. Python is the primary programming and interfacing language, while Cython is the primary language for optimizing critical functionalities and interfacing with C libraries and C extensions for Python. Sage integrates over 90 ... |
which consists of over 700,000 lines of new Python and Cython code. See ohloh.net for source code analysis of the latest stable Sage release. The following is an incomplete list of institutions and projects that use Sage. If any institution or project is missing, please let us know by reporting to the sage-devel mailin... |
a distribution of over 90 FOSS packages for symbolic, numerical, and scientific computation. In general, the combinatorial explosion of configurations to debug is way too large. It is next to impossible to find any Linux distribution (e.g. Arch, CentOS, Debian, Fedora, Gentoo, Mandriva, Ubuntu) where the version number... |
people who contribute to Sage do so in their free time. These are people who hold day jobs that are not directly related to computer programming or software development. It is next to impossible for anyone to track down the correct versions of packages, configure and compile them on Linux, Mac OS X, Solaris, or Windows... |
could start using Sage or start working on their first contribution to Sage. While the Sage project aims to be useful to as wide an audience as possible, we believe that Sage first needs to be as easy as possible to install by anyone with any level of computer experience. If you want to help Sage realize this goal, ple... |
email the sage-devel mailing list. Any software package contains bug. With something as complex as Sage, neither the Sage community nor the Sage Development Team make any claims that Sage is free of bugs. To do so would be an act of dishonesty. A Sage release cycle usually lasts for about 3 to 4 weeks. Each release cyc... |
chaired by a single release manager who looks after the Sage merge tree for the duration of the release cycle. During that time, the release manager often needs to devote the equivalent of full-time work to quality management and actively interacts with an international community of Sage users, developers, and potentia... |
two Sage contributors paired up to be the release managers for a Sage release cycle. However, it is often the case that few people have the equivalent of 3 weeks’ worth of free time to devote to release management. If you want to help out with release management, please subscribe to the sage-release mailing list. Since... |
Sage project, Sage contributors have tried to listen and think about what would increase the chances that serious potential contributors would actually contribute. What encourages one contributor can discourage another, so tradeoffs need to be made. To decide that a stabilization release would merge patches with bug fi... |
have been told in advance that their positively reviewed patches will not be merged. The Sage community believes in the principle of “release early, release often”. How the Sage project is organized and run differ greatly from that of a commercial software company. Contributors are all volunteers and this changes the d... |
be if Sage were a commercial development effort with all developers being full-time employees. To download the Sage standard documentation in HTML or PDF formats, visit the Help and Support page on the Sage website. Each release of Sage comes with the full documentation that makes up the Sage standard documentation. If... |
Our cells generate most of the energy they need in tiny structures inside them called mitochondria, which can be thought of as the cells' powerhouses. Mitochondria have their own DNA, independent of the cell's nuclear genome, which is compelling similar to the DNA of bacterial genomes. What this suggests is that many t... |
but were in fact unicellular organisms in their own right. According to this hypothesis – the endosymbiotic theory – mitochondria (and possibly some other organelles) originated as free-living bacteria which later became incorporated inside other cells in a symbiotic relationship. Like man-made powerhouses, mitochondri... |
hugely reactive particles which cause damage to all cellular components through oxidative stress. They attack the first thing they come across, which is usually the mitochondrion itself. This hazardous environment has put the genes located in the mitochondrion at risk of mutational damage, and over many years of evolut... |
well-protected from the deleterious effects of free-radicals alongside all of the cell's other DNA. This is called allotopic expression, and it has moved all but thirteen of the mitochondrion's full complement of at least one thousand genetic instructions for proteins into the 'bomb-shelter' of the nucleus. However, th... |
likely to mutate. Mutated mitochondria, as Aubrey de Grey has identified, may indirectly accelerate many aspects of ageing, not least when their mutation causes them to no longer produce the required energy for the cell, in turn impairing the cell's functionality. In order to combat the down-stream ageing damage as a c... |
needs to be repaired or rendered harmless. His characteristically bold solution to this problem is to put the mutations themselves beyond use by creating backup copies of the remaining mitochondrial genetic material and storing them in the safety of the cell's nucleus. Allotopically expressed here, like the rest of the... |
backup master copy, which is much less likely to mutate hidden away from the constant bombardment of free radicals. There are several difficulties to this solution, not least the fact that the remaining proteins are extremely hydrophobic and so don't 'want' to be moved at all, and additionally the code disparity betwee... |
a simple transplantation without translation impossible. Even if this engineered solution to the problem proves impracticable, at the very least the theory is sound. If we can devise a way systematically defend our mitochondria from their own waste products, we will drastically reduce the number of harmful free radical... |
young from the old, extending and improving the quality of our lives as a result. Dr Aubrey de Grey, a gerontologist from Cambridge, believes that ageing is a disease that can be cured. Like man-made machines, de Grey sees the human body as a system which ages as the result of the accumulation of various types of damag... |
that this damage can be periodically repaired, potentially leading to an indefinite extension of the system's functional life. De Grey believes that just as a mechanic doesn't need to understand precisely how the corrosive processes of iron oxidation degrades an exhaust manifold beyond utility in order to successfully ... |
that interact to contribute to our ageing. All we have to do is understand the damage itself. De Grey is confident that he has identified future technologies that can comprehensively remove the molecular and cellular lesions that degrade our health over time, technologies which will one day overcome ageing once and for... |
these technologies, de Grey has made it part of his mission to break the 'pro-ageing trance' that he sees as a widespread barrier to raising the funding and stimulating the research necessary to successfully combat ageing. De Grey defines this trance as a psychological strategy that people use to cope with ageing, fuel... |
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