Genome Project

The “Encyclopedia of DNA Elements” (ENCODE) project was launched by the US National Human Genome Research Institute in the aftermath of the Human Genome Project (HGP). It aimed to systematically map the human transcriptome, and held the promise that identifying potential regulatory regions and transcription factor binding sites would help address some of the perplexing results of the HGP. Its initial results published in 2012 produced a flurry of high-impact publications as well as criticisms. Here we put the results of (...) ENCODE and the work on epigenomics that followed in a broad theoretical and historical context, focusing on three strands of research. The first is the history of thinking about the organization of genomes, both physical and regulatory. The second is the history of ideas about gene regulation, primarily in eukaryotes. Finally, and connecting these two issues, we suggest how to think about the role of genetic material in physiology and development. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological (...) research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

This year’s topic is “Genomics and Philosophy of Race.” Different researchers might work on distinct subsets of the six thematic clusters below, which are neither mutually exclusive nor collectively exhaustive: (1) Concepts of ‘Race’; (2) Mathematical Modeling of Human History and Population Structure; (3) Data and Technologies of Human Genomics; (4) Biological Reality of Race; (5) Racialized Selves in a Global Context; (6) Pragmatic Consequences of ‘Race Talk’ among Biologists.

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

With notable exceptions, specialist museums have generally failed to collect an adequate record of the material culture of post-war science and technology. Some reasons for this failure are identified, and some suggestions for remedying this situation are made with the help of a specific example: genomic science and medicine. Genomics is a quintessentially 21st-century science: data-rich, digital, and technique-and technology-driven. As such, it presents particular challenges and opportunities to museums wishing to improve their performance in collecting recent and contemporary science (...) and technology. The paper explores different dimensions of this challenge through the attempt to establish a Museum Genomics Initiative, an international group of museum professionals who are committed to collaborating around the documentation of genomic science and medicine. (shrink)

In this article, I argue that genomic programs are not substitutes for multi-causal molecular mechanistic explanations of inheritance, but abstract representations of the same sort as mechanism schemas already described in the philosophical literature. On this account, the program analogy is not reductionistic and does not ignore or underestimate the active contribution of epigenetic elements to phenotypes and development. Rather, genomic program representations specifically highlight the genomic determinants of inheritance and their organizational features at work in the wider context of (...) the mechanisms of genome expression. (shrink)

In recent years, the selective flow of knowledge has emerged as an important topic in historical and social studies of science. Related questions about the production of ignorance have also captured attention under the rubric of agnotology. This paper focuses on information control in interaction, examining how actors seek to control the flow of scientific knowledge as they interact with others, either in face-to-face encounters or in modes of communication involving circulating documents, data, materials and other entities containing knowledge. The (...) analysis uses an ethnographic approach to study how actors work to control which knowledge becomes available to whom, when, under what terms and conditions, and with what residual encumbrances. Secrecy, for example, is not framed as an isolated,sui generisphenomenon, nor as one side of a secrecy/openness dichotomy, nor even as a pole on a secrecy/openness continuum. Instead, the analysis explores how actors manage a dialectic of revelation and concealment through which knowledge is selectively made available and unavailable to others, often in the same act. The emphasis on selective revelation highlights partial transfers of knowledge, targeted distribution, matters of timing, and the rights and encumbrances that attach to knowledge at different points in its transit. Examples are drawn from genome research, a field marked by ongoing disputes about modes of information control. (shrink)

The Baldwin effect is a process by which learnt traits become gradually incorporated into the genome through a Darwinian mechanism. From its inception, the Baldwin effect has been regarded with skepticism. The objective of this paper is to relativize this assessment. Our contribution is two-fold. To begin with, we provide a taxonomy of the different arguments that have been advocated in its defense, and distinguish between three justificatory dimensions—feasibility, explanatory relevance and likelihood—that have been unduly conflated. Second, we sharpen the (...) debate by providing an evolutionary game theoretic perspective that is able to generalize previous results. The upshot of this paper is that the mechanism envisaged by Baldwin is less puzzling than commonly thought. (shrink)

Recent data show that catastrophic events during one cell cycle can cause massive genome damage producing viable clones with unstable genomes. This is in contrast with the traditional view that tumorigenesis requires a long‐term process in which mutations gradually accumulate over decades. These sudden events are likely to result in a large increase in genomic diversity within a relatively short time, providing the opportunity for selective advantages to be gained by a subset of cells within a population. This genetic diversity (...) amplification, arising from a single aberrant cell cycle, may drive a population conversion from benign to malignant. However, there is likely a period of relative genome stability during the clonal expansion of tumors – this may provide an opportunity for therapeutic intervention, especially if mechanisms that limit tolerance of aneuploidy are exploited. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

This paper presents the case study of the Estonian Genome Project during its initial phase from 2001 to 2007. In these years, the EGP was an independent foundation established by the Estonian government and almost fully financed by foreign and local private venture capital. In essence, it was a public-private partnership in science, research and development. At the end of 2004, this governance structure broke down and private funding was pulled from the project. The paper discusses what went wrong with (...) the EGP and what the main policy lessons are, namely that particularly developing and transition countries like Estonia with low administrative and policy implementation capacity should approach public-private partnerships in high-tech research and development with high caution as conflicts of interests and loss of accountability seem likely; this is particularly the case in biotechnology because of the high scientific and business uncertainty characteristic of the field. (shrink)

Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...

Systems biology is largely tributary to genomics and other “omic” disciplines that generate vast amounts of structural data. “Omics”, however, lack a theoretical framework that would allow using these data sets as such (rather than just tiny bits that are extracted by advanced data-mining techniques) to build explanatory models that help understand physiological processes. Systems biology provides such a framework by adding a dynamic dimension to merely structural “omics”. It makes use of bottom-up and top-down models. The former are based (...) on data about systems components, the latter on systems-level data. We trace back both modeling strategies (which are often used to delineate two branches of the field) to the modeling of metabolic and signaling pathways in the bottom-up case, and to biological cybernetics and systems theory in the top-down case. We then argue that three roots of systems biology must be discerned to account adequately for the structure of the field: pathway modeling, biological cybernetics, and “omics”. We regard systems biology as merging modeling strategies (supplemented by new mathematical procedures) from data-poor fields with data supply from a field that is quite deficient in explanatory modeling. After characterizing the structure of the field, we address some epistemological and ontological issues regarding concepts on which the top-down approach relies and that seem to us to require clarification. This includes the consequences of identifying modules in large networks without relying on functional considerations, the question of the “holism” of systems biology, and the epistemic value of the “systeome” project that aspires to become the cutting edge of the field. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

In this paper we discuss the scientific value of the human genome project. To what extent is the data obtained by sequencing the entire human genome useful in the gene dicovery process? Responding to Alex Rosenberg' skepticism about the value of such data, we maintain that brute sequence data is much more useful than he suggests.

Through an examination of the actual research strategies and assumptions underlying the Human Genome Project (HGP), it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models (CAMs). In order to answer a series of questions about what is being modeled and what claims about the models are warranted, a descriptive epistemological method is employed that uses historical techniques to develop detailed accounts which, in turn, help to reveal (...) forms of reasoning that are explicit, or more often implicit, in the practice of a particular field of scientific study. It is suggested that a more valid characterization of the reasoning structure at work here is a form of case-based reasoning. This conceptualization of the role of model organisms can guide our understanding and assessment of these research programs, their knowledge claims and progress, and their limitations, as well as how we educate the public about this type of biomedical research. (shrink)

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in the (...) regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

"Written with passionate conviction about the ethical uses of science, The Sun, the Genome, and the Internet is both a brilliant reinterpretation of the scientific process and a challenge to use new technologies to close, rather than widen, the gap between rich and poor."--BOOK JACKET.

In lieu of an abstract, here is a brief excerpt of the content:The Environmental Genome Project and BioethicsRichard R. Sharp (bio) and J. Carl Barrett (bio)Eight years ago, the Kennedy Institute of Ethics Journal published a brief selection by Eric Juengst (1991) entitled “The Human Genome Project and Bioethics.” That essay introduced and described the Ethical, Legal, and Social Implications (ELSI) Program at the National Center for Human Genome Research. 1 Since that time, the ELSI program has grown to become (...) one of the largest and most well regarded bioethics programs in the country, sponsoring the work of hundreds of researchers and coordinating bioethics activities both nationally and internationally (Marshall 1996; Meslin, Thomson, and Boyer 1997). In 1991, however, Juengst, the first director of the ELSI program, had no way of anticipating these developments. Juengst’s goal in his essay was simply to highlight some of the moral and social issues that were emerging as focal points for the ELSI program. Looking back, the issues he outlined may seem vague and overly broad. At the time, however, the essay served an important purpose, to identify areas requiring additional study and thereby to serve as a guide to others interested in joining in these discussions.In many ways, Juengst’s article serves as an inspiration to those of us working on a new bioethics project. The National Institute of Environmental Health Sciences (NIEHS) recently launched a multi-year project aimed at better understanding genetic influences on environmentally associated diseases (Albers 1997; Brown and Hartwell 1998; Cannon 1997; Kaiser 1997). This project, known as the Environmental Genome Project (EGP), plans to identify and study a number of common genetic variants that may play an important role in determining how individuals respond to environmental exposures. NIEHS hopes that the information learned through the EGP will be instrumental in developing more effective disease-prevention strategies and intervention programs. Following the precedent developed in connection with the Human Genome Project, NIEHS also plans to address the moral and social implications of the EGP. Efforts in this regard include sponsoring workshops and conferences to address such issues, as well as supporting research on the ethical, legal, and social implications of the EGP. Through this work, NIEHS hopes to anticipate potential problems before [End Page 175] they arise and to develop policies that maximize the benefits of the research while avoiding potential misuses of the information learned.In exploring the social implications of the EGP, we at NIEHS are very fortunate to be able to draw upon the work being done by the ELSI program at the National Human Genome Research Institute (NHGRI), as well as the ever-expanding bioethics literature that has been sparked by the ELSI program. Still, there is much to be done and this is an exciting time for those of us involved with the EGP. Many of the ethical, legal, and social implications of the project are only beginning to become clearer, and several of these issues appear quite different from the sorts of concerns that have previously been discussed in connection with other types of genetic research.This essay highlights some of the ethical, legal, and social implications that are emerging as important focal points for the Environmental Genome Project. Like Juengst’s 1991 paper, the goal of this article is to provide an overview of current areas of interest and to encourage others to join us in thinking about these difficult issues.The Environmental Genome ProjectIndividuals differ greatly in their responses to chemicals, drugs, radiation, smoking, alcohol, and other environmental exposures. These differential responses are the result of complex interactions between many factors, including an individual’s genetic make-up, age, sex, nutritional status, and overall health. The EGP aims to better understand the genetic basis of differential responses to environmental exposures. The vast majority of diseases, many forms of cancer, for example, are the consequence of both environmental and genetic contributions (Perera 1997). Hence, understanding the relationships between genetic variation and response to environmental exposure is important for understanding the causes of human disease and is crucial for the development of effective disease-prevention strategies.The EGP and projects like it represent a new stage of genomic research. It is expected that the Human Genome Project will complete... (shrink)

The current German criticism of HUGO centers around the term ‘human dignity’; consenquentialist and autonomy-based arguments are used. The debate culminates in questioning the integrity of bioethics as a scholarly discipline and has created a heterogeneous coalition of disparate political and social groups that oppose any research that would facilitate genetic pre-selection of human characteristics.

The Human Genome Project (HGP) represents a massive merging of science and technology in the name of all humanity. While the disease aspects of HGP-generated data have received the greatest publicity and are the strongest rationale for the project, it should be remembered that the HGP has, as its goal the sequencing of all 100,000 human genes and the accurate depiction of the ancestral and functional relationships among these genes. The HGP will thus be constructing the molecular taxonomic norm for (...) humanity. Currently the HGP genomic baseline is almost exclusively skewed toward North Atlantic European lineages through the extensive use of the Centre d’Études du Polymorphisme Humaine (CEPH) data set. More recently, the HGP has shifted to the use of volunteer donors since adequate informed consent had not been secured from the CEPH families. No evidence exists that either the CEPH families or the current volunteers are the most appropriate demographic or evolutionary lineages for the functional genomic studies that will guide production of new DNA based drugs, targeted therapeutics and gene-based diagnostics. The lack of scientific representativeness of the HGP is a serious impediment to its broad applicability. Yet this can be remedied, and five alternative sampling strategies are presented. In response to the current exclusionary design of the HGP, there is noteworthy caution and skepticism in the African American community concerning genetic studies. The Manifesto on Genomic Studies Among African Americans reflects both a desire to be systematically included in federally funded genomic studies and a desire to maintain some control over the interpretation and application of research results. Representative sampling in the HGP is seen as an international human rights issue with domestic ethical implications. (shrink)

We are living through one of the greatest scientific revolutions in history: the “information revolution” in genetics. The revolution is leading to a deep understanding of biological processes and is uncovering the molecular basis of many human diseases and susceptibilities. It is also confronting society with a vast array of choices, and presenting each individual with the question of what knowledge to seek and how to act on that knowledge, My purpose is to discuss the scientific foundations of this revolution (...) and to foreshadow its consequences.The current scientific revolution has perhaps one appropriate historical precedent: the chemical revolution that followed Dmitri Mendeleev's key insight in 1869 that the elements could be organized in a simple periodic table. (shrink)

On October 1, 1988, thirty-five years after co-discovering the structure of the DNA molecule, Dr. James Watson launched an unprecedented experiment in American science policy. In response to a reporter's question at a press conference, he unilaterally set aside 3 to 5 percent of the budget of the newly launched Human Genome Project to support studies of the ethical, legal, and social implications of new advances in human genetics. The Human Genome Project (HGP), by providing geneticists with the molecular maps (...) of the human chromosomes that they use to identify specific human genes, will speed the proliferation of a class of DNA-based diagnostic and risk-assessment tests that already create professional ethical and health-policy challenges for clinicians. “The problems are with us now, independent of the genome program, but they will be associated with it,” Watson said. “We should devote real money to discussing these issues.” By 1994, the “ELSI program” (short for “Ethical, Legal, and Social Implications”) had spent almost $20 million in pursuit of its mission, and gained both praise and criticism for its accomplishments. (shrink)

In the Museum of Science and Technology in San Jose, California, there is a display dedicated to advances in biotechnology. Most prominent in the display is a double helix of telephone books stacked in two staggered spirals from the floor to the ceiling twenty-five feet above. The books are said to represent the current state of our knowledge of the eukaryotic genome: the primary sequences of DNA polynucleotides for the gene products which have been discovered so far in the twenty (...) years since cloning and sequencing the genome became possible. (shrink)

The Human Genome Project has raised many issues regarding the contributions of genetics to a variety of diseases and societal conditions. With genetic testing now easily conducted with lowered costs in nonmedical domains, a variety of privacy issues must be considered. Such testing will result in the loss of significant privacy rights for the individual. Society must now consider such issues as the ownership of genetic data, confidentiality rights to such information, limits placed on genetic screening, and legislation to control (...) genetic testing and its applications. There is often a conflict between individual rights to privacy and the need for societal protection. (shrink)

The economic costs to the insurers of complementary routine genetic testing would outweigh the benefits. However, should testing technology in future be refined so as to produce a cheap and reliable test, there is no reason why insurers might not take up predictive testing as part of the normal underwriting process. It is this possibility which justifies formulating a pre-emptive policy. At the very least, there are reasons for promoting and protecting the welfare of the proposer so as to redress (...) the bargaining positions between him or her as a consumer of a service and the insurer as a commercial concern. Further considerations relate to the social purpose of insurance as a social mechanism, and the need to find ways of avoiding undermining this in light of Human Genome Project. (shrink)

Scientists of the Human Genome Project tend to rely on three metaphors to describe their work, each of which implicitly tells much the same story. Whether they claim to interpret the ultimate "book," to fix a flawed "machine," or to map a mysterious "wilderness," they invariably cast the researcher as one who dominates and exploits the Other. This essay, which explores the ways such a story conflicts with feminist values, proposes an alternative.

Popular and scientific accounts of the U.S. Human Genome Project often express concern about the implications of the project for the philosophic question of free will and responsibility. However, on its standard construal within philosophy, the question of free will versus determinism poses no special problems in relation to genetic research. The paper identifies a variant version of the free will question, free will versus internal constraint, that might well pose a threat to notions of individual autonomy and virtue in (...) connection with genetic research. Whether it does depends on the extent to which the genetic basis for behavior turns on behavioral incapacities. (shrink)

For the first time in history, genetics will enable science to completely identify each human as genetically unique. Will this knowledge reinforce the trend for more individual liberties or will it create a ‘brave new world’? A law policy approach to the problems raised by the human genome project shows how far our democratic institutions are from being the proper forum to discuss such issues. Because of the fears and anxiety raised in the population, and also because of its wide (...) implications on the everyday life, the human genome analysis more than any other project needs to succeed in setting up such a social assessment. Keywords: human genome project, judiciary law policy, legislative activity, new ethics institutions, methodology in law reform, public debate, social consensus CiteULike Connotea Del.icio.us What's this? (shrink)

In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the project. (...) The second section distinguishes among four kinds of issues relevant to an evaluation of the HGP: those economic and organizational issues related to the feasibility of the project; the ethical questions arising in the development of the project and the application of the data gathered; the empirical issues relevant to the scientific value of the project; and conceptual issues like reductionism and determinism relevant to understand the nature and scope of the project. In a third section, I analyze in detail whether the HGP and, more generally, molecular biology is reductionistic. (shrink)