Search

The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.

The Municipal Limits of Slavery Freedom National: The Destruction of Slavery in the United States, 1861-1865. By James Oakes. (New York: W. W. Norton & Company, 2013. Pp. xxviii, 595, illustrations, notes, index. Cloth, $27.95.)Freedom National offers a sweeping synthesis of what historians have come to call the abolitionist narrative of the American Civil War.1 James Oakes takes the title for his book from a speech delivered on the floor of the United States Senate in August 1852 by Massachusetts Senator Charles Sumner. Sumner sought the repeal of the federal Fugitive Slave Act that had been passed by Congress as part of the Compromise of 1850. His "Freedom National" speech expressed at length what had emerged over the previous decade as an antislavery historical analysis of the constitutional relationship between slavery in the Southern states and the authority of the federal government. It is the central thesis of Oakes' work that the Freedom National doctrine insured a wartime progression toward universal emancipation and citizenship rights for former slaves.Oakes'thesis is particularly important as it relates to Lincoln's decision to issue the Emancipation Proclamation and to recruit black troops. "Like most historians," writes Oakes," I have always believed that the purpose of the war shifted 'from Union to emancipation,' but over the course of my research that familiar transition vanished like dust in the wind, and I have been unable to recover it"(p. xxiii). War Democrats experienced a profound shift as their willingness to support a war to preserve the Union advanced a Republican war to free the slaves. But for Republicans, Oakes insists, the pursuit of emancipation and citizenship rights directly fulfilled the promise of the Freedom National doctrine.Oakes draws on an extensive secondary literature and on published primary sources to locate the origins and trace the antebellum development of the Freedom National doctrine. By the time Sumner delivered his 1852 speech, the doctrine had been elaborated upon by antislavery politicians for more than a decade. Its principal architect was Salmon P. Chase, a leading figure in antislaveiy politics who served as Lincoln's Treasury Secretary during the Civil War and replaced Roger B. Taney as Chief Justice of the United States Supreme Court in 1864. Chase presented his first extended exposition of the Freedom National doctrine in his 1837 defense of a fugitive slave named Matilda. At the time, Chase was a young lawyer who had moved west from his native New Hampshire, to settle in Cincinnati, Ohio. In the Matilda Case, Chase defended the fugitive and her abolitionist benefactor, James G. Bimey. Bimey had been a slave owner in Alabama before embracing the abolitionist cause and moving to Cincinnati during the first wave of antislavery agitation following the formation of the American Antislavery Society in 1833. When Birney gave Matilda employment in his home he did so as the prominent editor of the Cincinnati Philanthropist. Chase defended Matilda and Birney: the former from being returned to slavery and the latter from charges that he harbored a fugitive in violation of Ohio's fugitive slave law.At the core of Chase's defense of Matilda and Bimey was the insistence that the federal Constitution neither sanctioned slavery nor recognized the right to hold properly in persons. Chase conceded that the fugitive clause of the Constitution dealt with the relationship between master and servants, but it had nothing to do with property in persons. The fugitive clause referred to a "Person held to Service or Labour," not to property in slaves. Chase conceded as well that the Constitution did not prohibit slavery in the original states. But, by offering slavery no specific recognition, the national compact left the institution as the drafters found it, confined to the existing slave states where municipal laws enforced the right to hold property in persons. …

The Billion Oyster Project and Curriculum and Community Enterprise for the Restoration of New York Harbor withNew York City Public Schools (BOP-CCERS)(NSF DRL 1440869/PI Lauren Birney) program is a National ScienceFoundation (NSF) supported initiative through collaboration by multiple institutions and organizations led by PaceUniversity. Partners on this initiatitve include Columbia Lamont Doherty, the New York Aquairum, the New YorkHarbor Foundation, the New York Academy of Sciences, the River Project, Good Shepher Services, SmartstartEvaluation and Research, the University Maryland Center for Environmental Science and Fearless Solutions. Inthis study, teachers from one cohort were paired with teachers from a succeeding cohort in order to facilitate amentoring process between the two cohorts. This allows for teacher ambassardors to have a support structurethroughout the program, seek integral feedback, modify teaching techniques, integrate project research and establishlong term partnerships within the project team.

The deaths of Earle Birney and Robertson Davies late in 1995 reminded readers of Canadian literature that the old order—those writers born before the First World War—was quickly passing. Of the major figures born in the early years of this century (Birney, Davies, Callaghan, MacLennan, Ross), only Ross was still living at the beginning of 1996, albeit in very poor health in a nursing home in Vancouver. http://dx.doi.org/10.5007/2175-8026.2003n45p31The deaths of Earle Birney and Robertson Davies late in 1995 reminded readers of Canadian literature that the old order—those writers born before the First World War—was quickly passing. Of the major figures born in the early years of this century (Birney, Davies, Callaghan, MacLennan, Ross), only Ross was still living at the beginning of 1996, albeit in very poor health in a nursing home in Vancouver.

To be successful, consortia need clear management, codes of conduct and participants who are committed to working for the common good, says ENCODE lead analysis coordinator Ewan Birney.

This paper is about “Mappemounde,” a beautiful but difficult poem composed in 1945 by the esteemed Canadian poet Earle Birney. While exploring the reasons for its composition, we examine the poem’s debts to Old and Middle English poetry as well as to medieval world maps known as mappaemundi, especially those made in England prior to 1400. But Birney took only so much from these maps. In search of more elusive inspirations, both cartographic and otherwise, we uncover other sources: Anglo-Saxon poems never before associated with “Mappemounde,” maps from the Age of Discovery and beyond, concealed details of Birney’s personal life. Then we trace Birney’s long-standing interest in geography and exploration to show how he used maps, especially mappaemundi, as visual metaphors for his intellectual, spiritual, and personal life.

This paper elicits a twentieth-century American story that is deeply rooted in the legacy of American philosophical pragmatism, its impact on a particular school, and its reconstruction of American theology. The paper focuses on three generations of American theologians, and it centers on how these theologians reconstruct theology in light of the science of their day and how they maintain a true plurality of insights about human life in the world. The pragmatic theologian regards the creative exchange between theology and natural science as an opportunity for renewing our understanding of religious life and appreciating the various commitments of scientists and theologians as they meet at the juncture of human interests. The first voice is that of the early Chicago School of Theology represented by Shailer Mathews, Gerald Birney Smith, and George Burman Foster. The second voice is that of Henry Nelson Wieman, a second-generation theologian at Chicago. The final theologian discussed is James M. Gustafson, former Professor of Theological Ethics at Chicago.

On 11 June 2000, Dr. Elmer C. Birney unexpectedly passed away from cardiac arrest suffered while outside caring for his cattle at his home in Blaine, Minnesota. One of his former students, Robert Timm, probably best expressed the immediate reaction of his family and many friends: “He was too young and in too good of health to be gone so soon.” At the time of his death, Elmer was Professor in the Department of Ecology, Evolution and Behavior, the Curator of Mammals at the Bell Museum of Natural History, and Director of Graduate Studies of the program in Ecology, Evolution and Behavior at the Twin Cities campus of the University of Minnesota. Dr. Birney was born 26 March 1940 in Satanta, Haskell County, Kansas, to Russell and Esther Birney. He had 2 sisters—Letty Gay and Lorna Ann. Elmer married Marcia F. McVey on 5 August 1961 in Culver City, California. They had 2 children, Amy and Clayton, and 2 grandchildren, Aaron and Danielle. Elmer's family described its feeling about him in the obituary that appeared in Minneapolis Star-Tribune: “He was a great husband, father, grandfather, friend, University of Minnesota Professor, and hobby farmer who loved his life.” Dr. Birney attended the public schools of Sublette and Satanta, Kansas, and he graduated from Satanta Rural High School in May 1958. Elmer enjoyed athletics and played both football and basketball throughout high school as well as participating in the junior class play. His high school graduation motto really did set the tone for the remainder of his life: “The men who roll up their sleeves never lose their shirts.” Although he was never truly passionate about professional sports, he still knowledgeably followed his favorite teams, and he and his wife played in an adult volleyball league. Elmer had a competitive streak that …

DAVIES, M. B., J. AUSTIN, AND D. A. PARTRIDGE. 1991. Vitamin C: Its chemistry and biochemistry. Royal Society of Chemistry, Cambridge, United Kingdom. DIAMOND, J. M. 1986. Why do disused proteins become genetically lost or repressed? Nature 351: 565-566. ELLIOT, O., N. J. YESS, AND D. M. HEGSTED. 1966. Biosynthesis of ascorbic acid in the tree shrew and the slow loris. Nature 212:739-740. ENGLARD, S., AND S. SEIFTER. 1986. The biochemical functions of ascorbic acid. Annual Review of Nutrition 6:365-406. FITCH, W. M. 1971. Towards defining the course of evolution: minimal change for a specific tree topology. Systematic Zoology 20:406-416. HANSSEN, K., H. J. GRAV, J. B. STEEN, AND H. LYSNES. 1979. Vitamin C deficiency in growing Willow Ptarmigan (Lagopus lagopus lagopus). Journal of Nutrition 109:2260-2278. HORNIG, D. 1975. Distribution of ascorbic acid, metabolites and analogues in man and animals. Annals of the New York Academy of Science 258: 103-118. JACOB, R. A. 1994. Vitamin C. Pages 432-448 in Modern nutrition in health and disease, vol. 1 (M. E. Shils, J. A. Olson, and M. Shike, Eds.). Lea and Febinger, New York. JENNESS, R., E. C. BIRNEY, AND K. L. AYAZ. 1980. Variation of L-gulonolactone oxidase activity in placental mammals. Comparative Biochemistry and Physiology 67B:195-204. MADDISON, W. P., AND D. R. MADDISON. 1992. MacClade (version 3): Analysis of phylogeny and character evolution. Sinauer Associates, Boston. PAULING, L. 1970. Vitamin C and the common cold. W. H. Freeman and Company, San Francisco. PIANKA, E. R. 1994. Evolutionary ecology. Harper Collins, New York. POLLOCK, J. I., AND R. J. MULLIN. 1987. Vitamin C biosynthesis in prosimians: Evidence for the anthropoid affinity of Tarsius. American Journal of Physical Anthropology 73:65-70. ROBBINS, C. T. 1993. Wildlife feeding and nutrition. Academic Press, San Diego, California. SIBLEY, C. G., AND J. E. AHLQUIST. 1990. Phylogeny and classification of birds: A study in molecular evolution. Yale University Press, New Haven, Connecticut. SIBLEY, C. G., AND B. L. MONROE, JR. 1990. Distribution and taxonomy of birds of the world. Yale University Press, New Haven, Connecticut.

We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust ‘Genome Informatics’ Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later.

S tudent lab research projects, even when unsuccessful in a conventional sense, can provide a valuable window into how real-world research science works. Here, I discuss five general observations, made while conducting my own independent research project, that might be helpful to prospective student researchers. I was extremely fortunate to have the opportunity to conduct an independent research project with my microbiology professor at Montgomery College, Dr. Margaret Birney, from June 2011 through May 2012. This project sought to combine a few fundamental ideas: since bacteria use chemical messages to coordinate simple behaviors, since a number of organisms have evolved anti-predator chemical warning systems, and since bacteriophages (viral predators of bacteria) have been shaping bacterial evolution for billions of years, I wanted to see if bacteria might be able to utilize an anti-phage warning system to collectively defend against phage attack. For most of the project, it seemed that such a warning system did indeed exist. We found that bacterial populations pre-treated with an ‘‘infected filtrate’’ (molecules fromother bacteria exposed to phage) survived better against phage attack than did control populations pre-treated with an ‘‘uninfected filtrate,’’ or molecules from normal bacteria not exposed to phage. After exploring further aspects of this antiphage warning system, I prepared a manuscript for submission to a peer-reviewed journal, but on the advice of a mentor, I decided to run a few more controls before sending it in. It soon became clear that we had missed something from almost the very beginning: an overlooked control snatched defeat from the jaws of victory, rendering our conclusions unsupportable and my manuscript unpublishable. Even though the project didn’t ultimately succeed in a conventional sense, my time in the lab was far from unproductive. To the contrary, working on this project gave me a year-long window into how real-world science works and the planning, diligence, critical thinking, and people skills that are required for successful research. The goal of this piece, then, is to share with the readers of BIOS some of the most important things I learned during my year as a student researcher.

The evening bat, Nycticeius humeralis, is an austral species (Armstrong, Choate, and Jones 1986) that ranges from the southeastern United States north to the southern Great Lakes region and west to the central Great Plains (Watkins 1972). In Kansas, the species was known from just four counties (Clay, Douglas, Jewell, and Johnson) in the northeast when Jones, Fleharty, and Dunnigan (1967) reviewed the distributional status of bats in the state. Birney and Rising (1968) subsequently reported specimens of the evening bat from Franklin and Ford counties, the latter in southwestern Kansas, and Kunz, Choate, and George (1980) reported specimens from Barber and Comanche counties in south-central Kansas. Sparks and Choate (2000) added more than a dozen counties, most in north-central Kansas, to the known range of the species in the state and opined that this tree-dwelling species, which previously was rare at the western limit of its range, was becoming increasingly common in riparian corridors. They concluded that the lack of forested habitats in much of western Kansas in the past possibly restricted the range of the evening bat to the eastern twothirds of the state (Sparks and Choate 2000), but that growth of forested habitats along watercourses was enabling this species to expand westward.

A bioinformatician’s career benefits from good timing, hard work and trust in his colleagues.

"HOW CAN MOTHERS be educated and the na tion made to recognize the supreme importance of the child?" 1* This is a question from the note book of Mrs. Alice McLellan Birney, under whose leadership the first Congress of Mothers was called. The date was February 17, 1897, but the problem was far from new, for there is arresting evidence that the germ of the idea was alive in the 1830's, and grew steadily through the next several decades. It appears repeatedly in the proceedings and reports of educational meetings and institutes, in contemporary journals and in the writings and speeches of such outstanding educators as Emma Willard and Henry Barnard. It is patent that there was widespread preoccupation with such perplexi ties as parental understanding of school problems and home-school relationships many years before the Parent Teacher movement became an organ ized activity in the late nineties. Henry Barnard in 1839, when he called the first meeting in Connecticut to "further the cause of common schools, " ^ held as part of his program a course of evening lectures to interest parents and the public, and later in 1847 planned discus sion of "reciprocal duties of parent and teacher. "3 This idea of an evening meeting for the public per sisted. It reappears in 1844 in New York when Monticello citizens at the Sullivan County Teachers' Institute held a public gathering to express their interest in the Institute and its workings. 4 The following year a Chatauqua County Institute asked itself "what is the best method of interesting par ents?" The answer seems to have been one entire evening given over to a discussion of how to "awaken the spirit of inquiry in children. " Could this be aided by teachers visiting parents or par ents visiting schools? 5 jn 1845 Madame Emma Willard, ever mindful of the cause of women, of fered some resolutions at the Oneida County Insti tute which were debated and passed. Included were the forthright statements that women must

CONTINUED EFFORTS have been made to de termine the relative effectiveness of different teach ing methods upon achievement of college students. Among these are studies by Birney and McKeachie (1), Guetzkow (2), Lyle (3), and Stovall (7). For the most part, such studies reveal that the method of presentation tends to have little or no bearing upon academic achievement. When other types of outcomes are considered, however, student-centered approaches often tend to be favored slightly. Through student-centered instructional programs, such as those of Birney and McKeachie (1), Patton (5), Wispe (8), and Wispe (9), students apparently develop more tolerant attitudes, gain a greater sense of initiative and independence, improve in certain emotional and social skills, and enjoy the student-centered sessions more. The present study was an attempt to determine the relative in fluence of teacher-centered, pupil-centered, and group-centered instruction upon attitudes toward both the instructor and the course involved.

The National Coal Resources Data System (NCRDS) of the U.S. Geological Survey has the capability through spatial data bases and computer software to depict coal geology and calculate coal resources by computer. The Birney 1:100,000 map in southeastern Montana and the Canyon coal bed were selected to demonstrate this capability. The Birney quadrangle includes parts of Big Horn, Rosebud, and Powder River Counties. Other political entities are the Northern Cheyenne Indian Reservation and the Custer National Forest. The Canyon coal bed locally splits into an upper and lower unit, whose thicknesses range from 1/3 to 33 ft (0.1 to 10 m). The desired data subset retrieved from the stratigraphic (USTRAT) data base consists of more than 300 drill-hole and 100 outcrop locations and their respective Canyon coal stratigraphic sections. Required digitized information included: X-Y locations (lat. and long.) for each point, township-range intersections, county, and national forest boundaries from the base map, the Indian reservation boundary, the Canyon bed outcrop, and the 200, 400, and 1,000 ft (61, 122, and 305 m) overburden isolines as drafted by the geologist. GARNET, a NCRDS interactive graphics program, produces isopachs and structure maps, does trend analysis, and allows the user to edit data points, expand areas of interest, and calculate coal-resource areas and tonnages for any defined area. The USGS methodology for calculating and reporting coal resources requires that computations be delimited by criteria of coal thickness, overburden thickness, rank, and distance from points of observation as related to land classification and political subdivisions. GARNET allows interactive graphic combination of digitized and computer-derived lines to produce boundaries of these categories. End_of_Article - Last_Page 605

n/a