Atrás da Árvore da Vida só não vai quem já morreu...

Assim como na música de Caetano Veloso Atrás do trio elétrico só não vai quem já morreu.... de 1969, desde 1869 que os cientistas estão atrás dessa tal de Árvore da Vida de Darwin:

I. INTRODUCTION

Darwin's vision of the "great Tree of Life ... with its everbranching and beautiful ramifications" has challenged scientists and others for generations. Darwin's use of tree imagery inspired efforts to classify all the major groups of organisms, and to reveal the pattern of historical relationships that would explain the similarities and differences among them. Phylogenetic knowledge, by virtue of its explanatory power, has proven useful in many fields, such as choosing experimental systems for biological research, tracking the origin and spread of emerging diseases and their vectors, bioprospecting for pharmaceutical and agrochemical products, preserving germplasm, targeting biological control of invasive species, and evaluating risk factors for species conservation and ecosystem restoration. At the same time, progress in many disciplines from genomics to evolution and development is currently hampered by the lack of a rigorous phylogenetic framework to guide research.

The features of life's genealogy at the broadest scales have been captured in the three-domain model of Archaea, Bacteria, and Eukaryota, but relationships among many groups of organisms remain unanalyzed and unresolved. Patterns of phylogeny among the domains and among most phyla, the extent of web-like reticulate connections among lineages, and the tempo and mode of evolutionary change remain unknown for most lineages on earth. Despite the enormity of the task, with 1.7 million described species and the likelihood of vastly more yet to be discovered, now is the time to reconstruct the tree of life: the conceptual, computational and technological tools are available to resolve most, if not all major branches of the tree of life.

Researchers in biological and computational fields have recognized both the need and the potential for success and have called for a national and international effort to Assemble the Tree of Life. There are currently five general goals:

1. To increase the numbers of taxa and data sets beyond current practice for extant and extinct organisms in order to resolve phylogenetic relationships among major taxonomic groups (such as classes, phyla and even kingdoms);

2. A strong focus at present is on major taxonomic groups not yet addressed by current or previous AToL projects. This list includes, but is not limited to, major groups of prokaryotes, protists, protostomes, and viruses. Renewals of projects will not be considered in this year's competition in order to focus on large groups not yet addressed by the AToL program.

3. Research on and development of tools for computational phylogenetics and phyloinformatics. These projects might include the archiving and managing of phylogenetic data, matrices, trees and networks; collaborative work environments for large scale systematics; automated alignment and analysis workflows that integrate search and dataset assembly methods; software development to improve construction, visualization and navigation of the Tree of Life; assessment of empirical support and uncertainty in trees and networks; and exploration of the predictive capabilities of hierarchical structure in the Tree of Life;

4. A critical need at this point is to integrate across all major taxonomic groups and to produce the promised phylogenetic framework for the Tree of Life. We therefore invite proposals directed toward: 1) integrating and synthesizing all previous Tree of Life projects and all available data for critical major lineages; and 2) establishing a framework for integration of future AToL projects into a single, robust Tree of Life. Examples include coordination and collaboration across all AToL projects, including data sharing, incorporation of available data for major lineages, identification of ‘core' genes conserved across major groups that can be used in analyses across all major lineages of the Tree of Life, identification of mechanisms that ensure a coordinated approach to data collection and data access across previous, current and future AToL projects, and integration with other projects working toward understanding of the tree of life, such as iPToL and ToLWeb;

5. Outreach and education in comparative phylogenetic biology and paleontology, emphasizing new training activities, informal science education, and Internet resources and dissemination.

II. PROGRAM DESCRIPTION

Projects for Assembling the Tree of Life are expected to be ambitious and large scale, and to include training, outreach, and dissemination components. When appropriate to the question under study, projects should include multiple investigators from multiple disciplines and multiple organizations. Tree of Life projects that are taxon-oriented will focus on phylogenetic resolution of large lineages or clades. This taxon focus is not intended to deflect interest in or attention to theoretical or analytical issues, particularly when the clade under study raises critical questions about the suitability or power of current phylogenetic methods of analysis, such as complexities caused by reticulate evolution and lateral gene transfer. Major taxonomic groups that have not yet been addressed by current or previous AToL projects are now an emphasis of this program. In addition to hypothesis-driven work, Tree of Life projects may also be method or theory-oriented, in which case they will address major analytical or computational problems in phylogenetic research and phyloinformatics. Tree of Life projects may also synthesis-oriented, in which case they will address integration of current and future knowledge pertaining to the Tree of Life, and accessibility to that knowledge.

Tree of Life projects that are taxon-oriented should address the following issues:

• the broad taxonomic scope of research, with justification for the proposed large-scale approach beyond the scope of current single-investigator or small-team projects, as well as summaries of current classification (including identification of specialists in the taxa) and current phylogenetic knowledge of the group and closest relatives, fossil record and its concordance with patterns of evolutionary divergence, major collections or stocks or cultures and their availability for the study, and Internet resources relevant to these organisms;

• comprehensive plans for sampling and data collection, including choice of taxa and samples, rationale for chosen genes (i.e., how these genes will be available and useful for larger integration across broader taxonomic ranges),, retrospective data capture, procedures for acquisition and quality control of new data, especially automated or high-throughput data, curation and vouchering of specimens and cultures (and extracts, images, etc.), and databasing of observations and associated specimens and cultures with appropriate annotation and Internet access; and

• description and justification of data analyses, with specific plans for dissemination of results, and including attention to tree-search criteria, data combinability and congruence, strategies for handling large data sets and for concatenating trees (if necessary), evaluation of tree robustness and of alternative topologies or networks, and archiving of datasets (specimens, characters, nomenclature, trees, character-by-taxon matrices), along with description of computer and software resources and expertise available to the project. Knowledge of, contribution to, and explicit coordination with appropriate major global database and portal efforts to disseminate taxonomic data are expected.

Tree of Life projects that are method or theory-oriented should address the following issues:

• description and justification of research in computational phylogenetics and phyloinformatics, on problems such as data acquisition and management, alignment and analysis of gene order, combinability of data whether genomic or morphological or both, tree-search or network strategies with very large datasets, measures of robustness and support, methods for linking or concatenating trees ("supertrees"), evaluating molecular clock estimates, integrating fossil evidence, and assessing empirical support and alternative topologies; hardware and software resources required for the project should be described, with plans for dissemination of products developed from the project;

• description and plans for archiving and managing data, trees, networks and associated character matrices and analytical methods from completed or ongoing phylogenetic projects, including development of efficient Internet tools for data submission from researchers in the community or other sponsors of phylogenetic research results; current NSF awardees conducting phylogenetic research are identifiable from the FastLane award abstracts posted on the NSF website (http://www.nsf.gov/awardsearch/);

• development of software for phylogenetic reconstruction, navigation, visualization, and query throughout the hierarchy of the Tree of Life and for data mining of associated character-by-taxon matrices developed as part of the project or available in other biological databases; and

• development of databases of taxonomic or clade-based names, including names at upper ranks of the formal hierarchies, with associated taxonomic synonyms and vernacular equivalents in the major international languages, to facilitate sophisticated query and data mining functions; this activity should be closely coordinated with global efforts in this area and should include the use of globally recognized data standards, with appropriate metadata, and service, or update to, at least one major electronic database or portal. Broad coordination with multiple providers is strongly encouraged.

Tree of Life projects that are synthesis-oriented should address the following issues:

• comprehensive plans for the completed taxonomic projects that will be included, as well as summaries of phylogenetic knowledge to date for those groups;

• strategy for integration of results, including choice of genetic markers and analytical methods, that will facilitate synthesis;

• description and justification for long-term synthetic activities to coordinate and integrate all Tree of Life projects and results;

• development of tools for archiving, managing, and querying the synthetic Tree of Life.

Regardless of approach taken, whether taxon-oriented or method-oriented, a mix or otherwise, all proposals for Assembling the Tree of Life should address the following issues including submission of a Management Plan:

• training and outreach activities, including field, laboratory, and/or museum experience for trainees, as well as communication among team members and expansion of the group if justified, integration with colleagues not formally part of the group whether national or international, and efforts to disseminate results to the public as well as to scientific communities. Hosting of workshops and other service activities are encouraged, to disseminate best-practices resulting from the project, new software, and other products. Activities designed to encourage participation of investigators at small institutions, minority serving institutions, community colleges, and secondary school teachers are encouraged; and

• a Management Plan should identify personnel responsible for all major tasks with time-scheduling across all members of the team for the duration of the project, with annual milestones for judging productivity and progress; describe curatorial, computational, sequencing, and informatics facilities and resources; describe plan for long-term preservation and research accessibility of collected samples; describe the database schema, if databases are being created as part of the project, including database design and metadata standards, interface for Internet query, and plans for maintenance beyond the duration of the grant, with identification of personnel charged with technical design and implementation; and describe plans for coordination with foreign-based projects on the same or related organisms. The Management Plan may be up to 5 pages in length and is in addition to the 15-page Project Description, and should be submitted in the Supplementary Documentation section of FastLane. For Grants.gov users, supplementary documents should be attached in Field 11 of the R&R Other Project Information Form.

III. AWARD INFORMATION

Estimated program budget, number of awards and average award size/duration are subject to the availability of funds. Three to six awards are anticipated in FY 2010, made as standard or continuing grants, from the anticipated $12 million in FY 2009 available to the program. Each award, whether single-institution or collaborative project, may range up to $3 million total, for durations up to five years.

IV. ELIGIBILITY INFORMATION

The categories of proposers eligible to submit proposals to the National Science Foundation are identified in the Grant Proposal Guide, Chapter I, Section E.

Organization Limit:
None Specified

PI Limit:
None Specified

Limit on Number of Proposals per Organization:
None Specified

Limit on Number of Proposals per PI:
None Specified

V. PROPOSAL PREPARATION AND SUBMISSION INSTRUCTIONS

A. Proposal Preparation Instructions

Full Proposal Preparation Instructions: Proposers may opt to submit proposals in response to this Program Solicitation via Grants.gov or via the NSF FastLane system.

• Full proposals submitted via FastLane: Proposals submitted in response to this program solicitation should be prepared and submitted in accordance with the general guidelines contained in the NSF Grant Proposal Guide (GPG). The complete text of the GPG is available electronically on the NSF website at: http://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg. Paper copies of the GPG may be obtained from the NSF Publications Clearinghouse, telephone (703) 292-7827 or by e-mail from nsfpubs@nsf.gov. Proposers are reminded to identify this program solicitation number in the program solicitation block on the NSF Cover Sheet For Proposal to the National Science Foundation. Compliance with this requirement is critical to determining the relevant proposal processing guidelines. Failure to submit this information may delay processing.

• Full proposals submitted via Grants.gov: Proposals submitted in response to this program solicitation via Grants.gov should be prepared and submitted in accordance with the NSF Grants.gov Application Guide: A Guide for the Preparation and Submission of NSF Applications via Grants.gov. The complete text of the NSF Grants.gov Application Guide is available on the Grants.gov website and on the NSF website at: (http://www.nsf.gov/publications/pub_summ.jsp?ods_key=grantsgovguide). To obtain copies of the Application Guide and Application Forms Package, click on the Apply tab on the Grants.gov site, then click on the Apply Step 1: Download a Grant Application Package and Application Instructions link and enter the funding opportunity number, (the program solicitation number without the NSF prefix) and press the Download Package button. Paper copies of the Grants.gov Application Guide also may be obtained from the NSF Publications Clearinghouse, telephone (703) 292-7827 or by e-mail fromnsfpubs@nsf.gov.

In determining which method to utilize in the electronic preparation and submission of the proposal, please note the following:

Collaborative Proposals. All collaborative proposals submitted as separate submissions from multiple organizations must be submitted via the NSF FastLane system. Chapter II, Section D.3 of the Grant Proposal Guide provides additional information on collaborative proposals.

The following instructions supplement GPG or NSF Grants.gov Application Guide guidelines.

Results from Prior NSF Support:

Be aware that if any PI or co-PI on the project has received NSF funding in the past five years, information on the prior award(s) is required. Each PI and co-PI who has received more than one prior award (excluding amendments) must report on the award most closely related to the proposal. The information required is described in the GPG and the NSF Grants.gov Application Guide. Reviewers will be asked to comment on the quality of the prior work described in this section of the proposal. Please note that the proposal may devote up to five pages to describe the results, within the maximum 15 pages of Project Description. Results may be summarized in fewer than five pages, which would leave the balance of the 15 pages for the Project Description.
Management Plan for Assembling the Tree of Life:

A Management Plan, up to 5 pages maximum, as described in the Program Description, should be included in the Supplementary Documentation section of the FastLane proposal. For Grants.gov users, supplementary documents should be attached in Field 11 of the R&R Other Project Information Form. This section, therefore, is in addition to the 15 pages of Project Description in the proposal, and should be coordinated with the research and education activities therein described.

Coordination among Projects for Assembling the Tree of Life:

If phylogenetic research on the chosen group of organisms is already funded by another NSF award (check the NSF FastLane website for award listings), the PI will be asked to provide a plan for coordinating activities with the funded project. If two or more proposals with substantially overlapping goals and scope remain in consideration for funding after initial merit review, the PIs of those proposals may be asked to collaborate, and to submit a coordination plan prior to the final funding decision.

International Opportunity:

The Tree of Life activity encourages laboratory-to-laboratory interactions between U.S. and foreign organizations to address Tree of Life goals. NSF funds may be requested to support foreign investigators and students to work in U.S. laboratories, and for U.S. investigators and students to work in international laboratories. However, foreign counterparts should secure support for their projects from their own national programs.

A "Conflicts of Interest" Document:

A "Conflicts of Interest" document must be included in the "Additional Single Copy Documents" section of the proposal. Include a table, in the format shown below, that lists the names of persons with conflicts of interest for all senior personnel (PI and co-PIs) and any named personnel whose salary is requested in the project budgets. Conflicts to be identified are: (1) Ph.D. thesis advisor or advisee; (2) postdoctoral adviser or advisee for the previous 48 months; (3) collaborators or co-authors for the past 48 months; and (4) any other individual or organization with which the investigator has financial ties (please specify). Organize the information as shown in the sample table here; list full names in each column in alphabetical order.

Source/Fonte.

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NOTA DESTE BLOGGER:

Cientistas brazucas podem participar destes esforços científicos de finalmente corroborar as especulações transformisas de Darwin por meio de uma Árvore da Vida. Não se esqueçam do que foi 'prometido' e nunca atingido, e que o ATOL se propõe:

"A critical need at this point is to integrate across all major taxonomic groups and to produce the promised phylogenetic framework for the Tree of Life"

E o que tínhamos antes? Era apenas uma nota promissória sem fundos de evidências encontradas na natureza corroborando a robustez das especulações transformistas de Darwin no contexto de justificação teórica??? E o fato, Fato, FATO da evolução ser tão cientificamente certo como a lei da gravidade???

Afinal de contas, atrás da Árvore da Vida só não vai quem já morreu...

Os itálicos são para chamar a atenção de que a Árvore da Vida continua sendo uma miragem epistêmica que foi mascateada nos livros didáticos como sendo uma verdade científica comprovada. Nada mais falso!

Que venga la nueva teoría de evolución que não deve e nem pode ser selecionista. Y esta nueva Árvore da Vida será monofilética ou polifilética? Gradualista ou de equilíbrio pontuado? E se o registro fóssil não corroborar este empreendimento milionário, nós ficaremos sabendo?Através da NSF??? Pela Grande Mídia? Em 2020???

Alô MEC/SEMTEC/PNLEM, em 2010 nós teremos livros didáticos abordando esta insuficiência epistêmica fundamental da teoria geral da evolução ou os alunos do ensino médio continuarão sendo engabelados pela Nomenklatura científica???

Este blogger está de olho, e vai de novo a Brasília se for preciso: agir politicamente como sugeriu a Folha de São Paulo em editorial em 2009 sobre o direito à informação. [Requer assinatura da FSP ou do UOL]