Perspectives on the Phylogenetic Tree

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LOCAL PERSPECTIVES ON THE ENVIRONMENTAL AND SOCIAL IMPACTS OF SHRIMP FARMING IN TAM GIANG LAGOON, VIETNAM. TUONG PHI LAI A Thesis Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science (Management of Natural Resources and Sustainable Agriculture) Submitted to: Norwegian University of Life Sciences Department of International Environment and Development Studies June, 2005 ii The Department of International Environment and Development Studies, Noragric, is the international gateway for the Norwegian University of Life Sciences (UMB). Eight departments, associated research institutions and the Norwegian College of Veterinary Medicine in Oslo. Established in 1986, Noragric’s contribution to international development lies in the interface between research, education (Bachelor, Master and PhD programmes) and assignments. The Noragric Master theses are the final theses submitted by students in order to fulfil the requirements under the Noragric Master programme “Management of Natural Resources and Sustainable Agriculture” (MNRSA), “Development Studies” and other Master programmes. The findings in this thesis do not necessarily reflect the views of Noragric. Extracts from this publication may only be reproduced after prior consultation with the author and on condition that the source is indicated. For rights of reproduction or translation contact Noragric. © Tuong Phi Lai, June 2005 E-mail: tuongphilai@yahoo.com Noragric Department of International Environment and Development Studies P.O. Box 5003 N-1432 Ås Norway Tel.: +47 64 96 52 00 Fax: +47 64 96 52 01 Internet: http://www.umb.no/noragric Formatted: French (France) Formatted: English (U.S.) iii DECLARATION I, Tuong Phi Lai, do hereby declare to the Senate of the Norwegian University of Life Sciences, that this dissertation is entirely the product of my own original research work, unless where it is acknowledged, and that it has not been submitted to any other University or academic institution for award of any degree. ------------------------- ------------------ Perspectives on the Phylogenetic Tree Perspectives on the Phylogenetic Tree Bởi: OpenStaxCollege The concepts of phylogenetic modeling are constantly changing It is one of the most dynamic fields of study in all of biology Over the last several decades, new research has challenged scientists’ ideas about how organisms are related New models of these relationships have been proposed for consideration by the scientific community Many phylogenetic trees have been shown as models of the evolutionary relationship among species Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 ([link]a), which served as a pattern for subsequent studies for more than a century The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak ([link]b) However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community The (a) concept of the “tree of life” goes back to an 1837 sketch by Charles Darwin Like an (b) oak tree, the “tree of life” has a single trunk and many branches (credit b: modification of work by "Amada44"/Wikimedia Commons) 1/12 Perspectives on the Phylogenetic Tree Limitations to the Classic Model Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships The various ways that HGT occurs in prokaryotes is important to understanding phylogenies Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence Horizontal Gene Transfer Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring These transfers allow even distantly related species to share genes, influencing their phenotypes It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress As the phenomenon is investigated more thoroughly, it may be revealed to be more common Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection These transfers may occur between any two species that share an intimate relationship ([link]) 2/12 Perspectives on the Phylogenetic Tree Summary of Mechanisms of Prokaryotic and Eukaryotic HGT Mechanism Prokaryotes Eukaryotes Mode of Example Transmission transformation DNA uptake many prokaryotes transduction bacteriophage bacteria (virus) conjugation pilus many prokaryotes gene transfer agents phage-like particles purple nonsulfur bacteria from food organisms unknown aphid jumping genes transposons rice and millet plants epiphytes/ parasites yew tree fungi unknown from viral infections HGT in Prokaryotes The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed The majority of evolutionary models, such as in the Endosymbiont Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species The fact that genes are transferred among common bacteria is well ...Perspectives on the Pulp and Paper Industry 1 Douglas C. Pryke, P.Eng. Executive Director, AET QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Alliance for Environmental Technology QuickTime™ and a TIF F (Uncompressed) decompressor are needed to see this picture. A Responsible Care® Supporting Association Outline North America Pulp & Paper Industry Printing & Writing Paper Market Manufacturing 2 Source: Canfor Ltd. Manufacturing Fundamentals Environmental Protection Measures of Progress Summary N. American Pulp & Paper Industry Bleached pulp production is ~ 35 million tons Printing and Writing Grades Uncoated Free Sheet Coated Free Sheet Uncoated Groundwood 3 Uncoated Groundwood Coated Groundwood Printing and Writing Grades ~ 25 million tons  50% UFS  25% CFS N. American Pulp & Paper Industry US P&P industry 6% of GDP comparable to automotive and plastics industries US Paper Mill Closures 4 plastics industries $200 Billion Annual Sales 1 Million employees $54 Billion payroll Source: AF&PA International Capacity Change 1998-2008 Significant growth in emerging economies Ave. Annual Change,% 5 North America declining on average 1% per year Manufacturing Fundamentals Basic overview Bleached kraft pulp manufacturing Pulping Bleaching Waste treatment QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. 6 Waste treatment Environmental Protection are needed to see this picture. Debarking Chipping Pulping Pulping Chemicals Logs Sawmill Residue Manufacturing Overview The Paper Mill Flowsheet 7 Washing Screening Bleaching Cleaning Paper Machine or Pulp Dryer Chemicals Recovery Waste Treatment Fresh Water Paper- making BleachingPulpingWood Fiber Land Application Waste Treatment Paper Consumers Pulp and Paper Mill EcoPulp and Paper Mill Eco industrial Parkindustrial Park 8 Coal Mine Reclamation Sludge Stabilization Building Products Power Boilers Chemical Recovery Boiler (Black Liquor) Power Grid Power Generation Causticizing Eco-industrial Park 9 Photo Courtesy of: Celso Foelkel, Celsius Degree A Minimum Impact Mill: Minimizes the number of trees used to make a piece of paper Maximizes energy production Minimum Impact Manufacturing 10 Maximizes energy production Minimizes water consumption, solid waste, and air emissions Make high quality paper that is easily recyclable Treats and disposes of waste optimally Creates sustainable value to society [...]... or end-of-pipe treatment Pollution prevention means stopping pollution before it starts! In the late 80s the international pulp and paper industry voluntarily implemented a pollution prevention strategy to eliminate persistent, bioaccumulative toxic compounds The key component of that successful strategy was ECF! Canadian Bleached Chemical Pulp and Paper Mills: Elimination of Dioxin 300 250 200 150 100... environment; and reduces the hazards to public health and the environment associated with the release of such substances, pollutants, or contaminants Technology that prevents pollution: Equipment or technology modifications, processes or procedure modifications, reformulation or redesign of products, and substitution of raw materials 1 Pollution Prevention Act of 1990 42 USC 18101 Laws of 101st Congress... toxicity The compounds with the Cl in the 2, 3, 7, and 8 positions [...]... permits the systematic gathering of information and the profiling of functions and policy in respect of Australia and New Zealand, the United States, Singapore and Canada Part IV, the final section, reflects on the findings of Part III and considers the implications arising for the future relationship between legal functions and social policy as they relate to charity Entitled ‘Re-configuring the Social Policy. .. relation to particular configurations of social policy and charity law The five chapters comprising this Part together provide an analysis of the main legal functions relating to charity and charitable activity Chapter 3 considers the jurisprudence underpinning the functional approach to the law, giving particular attention to the more salient principles and their contemporary impact The legal functions. .. Social Policy explores contemporary law, policy and practice in a range of modern common law nations It does so from the perspective of how this has evolved in the UK As progenitor of a system bequeathed to its colonies and after centuries of leadership in developing the core principles, policies and precedents, the jurisdiction of England & Wales has been and remains central to charity law as a common law. .. activity The Parties Charity in the common law rests on a transaction that involves the interests of donor, charitable organisation, recipient and the State in an amalgam of private and public law concerns Arbitration on any conflict arising between the interests of these parties has traditionally been left to the courts but in England & Wales that responsibility has now largely passed to the Charity. .. Outcome of the Charity Law Reform Process and Implications for the Future of the Support Function and Social Policy Institutional Change and the Support Function The Inland Revenue and the Charity Commission Strengthening the Support Capacity of the Charity Commission New Legal Structures for Charities Increasing Public Confidence... it relates to charity and charitable activity Their origins, in initiatives by government and judiciary, are traced and their effectiveness and policy significance are considered Part III, International Perspectives , provides case studies depicting use of the legal functions, as they apply to type of need and thereby give effect to policy, in each of the selected common law jurisdictions The Charitable... strands is a prerequisite A Mention-Synchronous Coreference Resolution Algorithm Based on the Bell Tree Xiaoqiang Luo and Abe Ittycheriah Hongyan Jing and Nanda Kambhatla and Salim Roukos 1101 Kitchawan Road Yorktown Heights, NY 10598, U.S.A. {xiaoluo,abei,hjing,nanda,roukos}@us.ibm.com Abstract This paper proposes a new approach for coreference resolution which uses the Bell tree to represent the search space and casts the coreference resolution problemas finding the best path from the root of the Bell tree to the leaf nodes. A Maximum Entropy model is used to rank these paths. The coreference performance on the 2002 and 2003 Auto- matic Content Extraction (ACE) data will be reported. We also train a coreference system using the MUC6 data and competitive results are obtained. 1 Introduction In this paper, we will adopt the terminologies used in the Automatic Content Extraction (ACE) task (NIST, 2003). Coreference resolution in this context is defined as partitioning mentions into entities. A mention is an instance of reference to an object, and the collection of mentions referring to the same object in a document form an entity. For example, in the following sentence, mentions are underlined: “The American Medical Association voted yesterday to install the heir apparent as its president-elect, rejecting a strong, upstart challenge by a District doctor who argued that the nation’s largest physicians’ group needs stronger ethics and new leadership.” “American Medical Association”, “its” and “group” belong to the same entity as they refer to the same ob- ject. Early work of anaphora resolution focuses on find- ing antecedents of pronouns (Hobbs, 1976; Ge et al., 1998; Mitkov, 1998), while recent advances (Soon et al., 2001; Yang et al., 2003; Ng and Cardie, 2002; Itty- cheriah et al., 2003) employ statistical machine learn- ing methods and try to resolve reference among all kinds of noun phrases (NP), be it a name, nominal, or pronominal phrase – which is the scope of this paper as well. One common strategy shared by (Soon et al., 2001; Ng and Cardie, 2002; Ittycheriah et al., 2003) is that a statistical model is trained to measure how likely a pair of mentions corefer; then a greedy procedure is followedto groupmentionsintoentities. While this ap- proach has yielded encouraging results, the way men- tions are linkedis arguably suboptimalinthatan instant decision is made when considering whether two men- tions are linked or not. In this paper, we propose to use the Bell tree to rep- resent the process of forming entities from mentions. The Bell tree represents the search space of the coref- erence resolutionproblem – eachleaf node corresponds to a possible coreference outcome. We choose to model the process from mentions to entities represented in the Bell tree, and the problem of coreference resolution is cast as finding the “best” path from the root node to leaves. A binary maximum entropy model is trained to compute the linkingprobability between a partial entity and a mention. The rest of the paper is organized as follows. In Section 2, we present how the Bell tree can be used to represent the process of creating entities from men- tions and the search space. We use a maximum en- tropy model to rank paths in the Bell tree, which is dis- cussed in Section 3. After presenting the search strat- egy in Section 4, we show the experimental results on the ACE 2002 and 2003 data, and the Message Under- standing Conference (MUC) (MUC, 1995) data in Sec- tion 5. We compare our approach with some recent work in Section 6. 2 Bell Tree: From Mention to Entity Let us consider [...]...Introduction David A Wise This is the ninth in a series of volumes on the economics of aging The previous ones were The Economics of Aging, Issues in the Economics of Aging, Topics in the Economics of Aging, Studies in the Economics of Aging, Advances in the Economics of Aging, Inquiries in the Economics of Aging, Frontiers in the Economics of Aging, and Themes in the Economics of Aging Most of the papers... than a small fraction of the large changes we observe The Transition to Personal Accounts and Increasing Retirement Wealth 25 1.2 Plan Contributions and the Retirement Plan Contribution Rate The accumulation of retirement assets depends on the inflow of contributions, the payout of benefits, and the return on invested assets Panel A of figure 1.5 shows private pension plan contributions, which increased... Massachusetts Institute of Technology, and the director of the Public Economics Research Program at the National Bureau of Economic Research Steven F Venti is the DeWalt Ankeny Professor of Economic Policy at Dartmouth College and a research associate at the National Bureau of Economic Research David A Wise is the John F Stambaugh Professor of Political Economy at the John F Kennedy School of Government, Harvard... areas of research begun in earlier volumes For example, the work in this volume emphasizes the spread of personal retirement accounts and macrodata on the implications of the diffusion of these accounts Prior work emphasized the net saving effects of personal retirement accounts based on microdata Work in this volume also revisits the implications of housing ... Mitochondrial DNA can be regarded as the smallest chromosome Interestingly 5/12 Perspectives on the Phylogenetic Tree enough, mitochondrial DNA is inherited only from the mother The mitochondrial... nucleus-first hypothesis, (b) the mitochondrion-first hypothesis, and (c) the eukaryote-first hypothesis Web and Network Models The recognition of the importance of HGT, especially in the evolution of prokaryotes,... accurate description of phylogenetic relationships of life A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too