93 research outputs found
Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science
The INBIOSA project brings together a group of experts across many disciplines
who believe that science requires a revolutionary transformative
step in order to address many of the vexing challenges presented by the
world. It is INBIOSAâs purpose to enable the focused collaboration of an
interdisciplinary community of original thinkers.
This paper sets out the case for support for this effort. The focus of the
transformative research program proposal is biology-centric. We admit
that biology to date has been more fact-oriented and less theoretical than
physics. However, the key leverageable idea is that careful extension of the
science of living systems can be more effectively applied to some of our
most vexing modern problems than the prevailing scheme, derived from
abstractions in physics. While these have some universal application and
demonstrate computational advantages, they are not theoretically mandated
for the living. A new set of mathematical abstractions derived from biology
can now be similarly extended. This is made possible by leveraging
new formal tools to understand abstraction and enable computability. [The
latter has a much expanded meaning in our context from the one known
and used in computer science and biology today, that is "by rote algorithmic
means", since it is not known if a living system is computable in this
sense (Mossio et al., 2009).] Two major challenges constitute the effort.
The first challenge is to design an original general system of abstractions
within the biological domain. The initial issue is descriptive leading to the
explanatory. There has not yet been a serious formal examination of the
abstractions of the biological domain. What is used today is an amalgam;
much is inherited from physics (via the bridging abstractions of chemistry)
and there are many new abstractions from advances in mathematics (incentivized
by the need for more capable computational analyses). Interspersed
are abstractions, concepts and underlying assumptions ânativeâ to biology
and distinct from the mechanical language of physics and computation as
we know them. A pressing agenda should be to single out the most concrete
and at the same time the most fundamental process-units in biology
and to recruit them into the descriptive domain. Therefore, the first challenge
is to build a coherent formal system of abstractions and operations
that is truly native to living systems.
Nothing will be thrown away, but many common methods will be philosophically
recast, just as in physics relativity subsumed and reinterpreted
Newtonian mechanics.
This step is required because we need a comprehensible, formal system to
apply in many domains. Emphasis should be placed on the distinction between
multi-perspective analysis and synthesis and on what could be the
basic terms or tools needed.
The second challenge is relatively simple: the actual application of this set
of biology-centric ways and means to cross-disciplinary problems. In its
early stages, this will seem to be a ânew scienceâ.
This White Paper sets out the case of continuing support of Information
and Communication Technology (ICT) for transformative research in biology
and information processing centered on paradigm changes in the epistemological,
ontological, mathematical and computational bases of the science
of living systems. Today, curiously, living systems cannot be said to
be anything more than dissipative structures organized internally by genetic
information. There is not anything substantially different from abiotic
systems other than the empirical nature of their robustness. We believe that
there are other new and unique properties and patterns comprehensible at
this bio-logical level. The report lays out a fundamental set of approaches
to articulate these properties and patterns, and is composed as follows.
Sections 1 through 4 (preamble, introduction, motivation and major biomathematical
problems) are incipient. Section 5 describes the issues affecting
Integral Biomathics and Section 6 -- the aspects of the Grand Challenge
we face with this project. Section 7 contemplates the effort to
formalize a General Theory of Living Systems (GTLS) from what we have
today. The goal is to have a formal system, equivalent to that which exists
in the physics community. Here we define how to perceive the role of time
in biology. Section 8 describes the initial efforts to apply this general theory
of living systems in many domains, with special emphasis on crossdisciplinary
problems and multiple domains spanning both âhardâ and
âsoftâ sciences. The expected result is a coherent collection of integrated
mathematical techniques. Section 9 discusses the first two test cases, project
proposals, of our approach. They are designed to demonstrate the ability
of our approach to address âwicked problemsâ which span across physics,
chemistry, biology, societies and societal dynamics. The solutions
require integrated measurable results at multiple levels known as âgrand
challengesâ to existing methods. Finally, Section 10 adheres to an appeal
for action, advocating the necessity for further long-term support of the
INBIOSA program.
The report is concluded with preliminary non-exclusive list of challenging
research themes to address, as well as required administrative actions. The
efforts described in the ten sections of this White Paper will proceed concurrently.
Collectively, they describe a program that can be managed and
measured as it progresses
Accommodating Ontologies to Biological RealityâTop-Level Categories of Cumulative-Constitutively Organized Material Entities
BACKGROUND: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. âobjectâ, âfiat object partâ, âobject aggregateâ) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. METHODOLOGY/PRINCIPAL FINDINGS: Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for âportion of matterâ as another material building block. This implies the necessity for further extending BFO by âportion of matterâ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. CONCLUSIONS/SIGNIFICANCE: We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle
Spatio-structural granularity of biological material entities
<p>Abstract</p> <p>Background</p> <p>With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.</p> <p>Results</p> <p>The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the <it>compositional object perspective </it>as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities.</p> <p>Conclusions</p> <p>The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different <it>views </it>on its content (i.e. data, knowledge), each organized into different levels of detail.</p
Terrestrialization, Miniaturization and Rates of Diversification in African Puddle Frogs (Anura: Phrynobatrachidae)
Terrestrialization, the evolution of non-aquatic oviposition, and miniaturization, the evolution of tiny adult body size, are recurring trends in amphibian evolution, but the relationships among the traits that characterize these phenomena are not well understood. Furthermore, these traits have been identified as possible âkey innovationsâ that are predicted to increase rates of speciation in those lineages in which they evolve. We examine terrestrialization and miniaturization in sub-Saharan puddle frogs (Phrynobatrachidae) in a phylogenetic context to investigate the relationship between adaptation and diversification through time. We use relative dating techniques to ascertain if character trait shifts are associated with increased diversification rates, and we evaluate the likelihood that a single temporal event can explain the evolution of those traits. Results indicate alternate reproductive modes evolved independently in Phrynobatrachus at least seven times, including terrestrial deposition of eggs and terrestrial, non-feeding larvae. These shifts towards alternate reproductive modes are not linked to a common temporal event. Contrary to the âkey innovationsâ hypothesis, clades that exhibit alternate reproductive modes have lower diversification rates than those that deposit eggs aquatically. Adult habitat, pedal webbing and body size have no effect on diversification rates. Though these traits putatively identified as key innovations for Phrynobatrachus do not seem to be associated with increased speciation rates, they may still provide opportunities to extend into new niches, thus increasing overall diversity
The Development of a Conceptual Framework and Tools to Assess Undergraduates' Principled Use of Models in Cellular Biology
Recent science education reform has been marked by a shift away from a focus on facts toward deep, rich, conceptual understanding. This requires assessment that also focuses on conceptual understanding rather than recall of facts. This study outlines our development of a new assessment framework and toolâa taxonomyâ which, unlike existing frameworks and tools, is grounded firmly in a framework that considers the critical role that models play in science. It also provides instructors a resource for assessing students' ability to reason about models that are central to the organization of key scientific concepts. We describe preliminary data arising from the application of our tool to exam questions used by instructors of a large-enrollment cell and molecular biology course over a 5-yr period during which time our framework and the assessment tool were increasingly used. Students were increasingly able to describe and manipulate models of the processes and systems being studied in this course as measured by assessment items. However, their ability to apply these models in new contexts did not improve. Finally, we discuss the implications of our results and the future directions for our research
Genetic variation and evolution in the red cell carbonic anhydrase isozymes of macaque monkeys
The electrophoretic phenotypes of the two isozymes of red cell carbonic anhydrase, CA I and CA II, are described in nine species of macaque monkeys from southeast Asia and Japan. Twelve phenotypes of CA I, apparently under the control of seven alleles, and five phenotypes of CA II, under the control of three alleles, were found in the different macaque populations studied. Extensive electrophoretic polymorphisms of CA I were found in three species (Macaca nemestrina, Macaca speciosa , and Macaca fuscata) , and polymorphisms at the CA II locus were found in Macaca irus, Macaca mulatta , and M. nemestrina . In addition to the electrophoretic polymorphisms at the CA I locus in M. nemestrina , an inherited deficiency of CA I was also discovered in which approximately 30% of the individuals in all populations of M. nemestrina tested showed the deficient phenotype. Although the recessive gene controlling this deficiency appears to be an allele of the CA I locus, it is postulated that the CA I deficiency could also be under the control of a closely linked gene. The comparative data on the extent of genetic variation observed in the two isozymes of red cell carbonic anhydrase in macaques appear to support the concept that CA I has evolved more rapidly than CA II in mammals.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44171/1/10528_2004_Article_BF00485644.pd
Bioacoustic analysis of advertisement call in Hyla nana and Hyla sanborni (Anura, Hylidae) in Botucatu, SĂŁo Paulo, Brazil
Meaning and Function in the Theory of Consumer Choice: Dual Selves in Evolving Networks
- âŚ