Extended physics as a theoretical framework for systems biology?

In this essay we examine whether a theoretical and conceptual framework for systems biology could be built from the [Bailly and Longo, 2008] and [Bailly and Longo, 2009] proposal. These authors aim to understand life as a coherent critical structure, and propose to develop an extended physical approach of evolution, as a diffusion of biomass in a space of complexity. Their attempt leads to a simple mathematical reconstruction of Gould’s assumption (1989) concerning the bacterial world as a “left wall of least complexity” that we will examine. Extended physical systems are characterized by their constructive properties. Time is acting and new properties emerge by their history that can open the list of their initial properties. This conceptual and theoretical framework is nothing more than a philosophical assumption, but as such it provides a new and exciting approach concerning the evolution of life, and the transition between physics and biology.     

Technological biology? Things and kinds in synthetic biology

Social scientific and humanistic research on synthetic biology has focused quite narrowly on questions of epistemology and ELSI. I suggest that to understand this discipline in its full scope, researchers must turn to the objects of the field—synthetic biological artifacts—and study them as the objects in the making of a science yet to be made. I consider one fundamentally important question: how should we understand the material products of synthetic biology? Practitioners in the field, employing a consistent technological optic in the study and construction of biological systems, routinely employ the mantra ‘biology is technology’. I explore this categorization. By employing an established definition of technological artifects drawn from the philosophy of technology, I explore the appropriateness of attributing to synthetic biological artifacts the four criteria of materiality, intentional design, functionality, and normativity. I then explore a variety of accounts of natural kinds. I demonstrate that synthetic biological artifacts fit each kind imperfectly, and display a concomitant ontological ‘messiness’. I argue that this classificatory ambivalence is a product of the field’s own nascence, and posit that further work on kinds might help synthetic biology evaluate its existing commitments and practices.     

GDF11 as a friend or an enemy in the cancer biology?

The Growth and Differential Factor 11 (GDF11) is a recently discovered representative of Transforming Growth Factor β superfamily. The highest expression of GDF11 is detected in the nervous system, bladder, seminal vesicles and muscles whereas the lowest in the testis, liver or breast. GDF11 role in physiology is still not clear. GDF11 is a crucial factor in embryogenesis, cell cycle control and apoptosis, inasmuch it mainly targets cell retain stemness features, managing to the cell differentiation and the maturation. GDF11 is entangled in lipid metabolism, inflammatory processes and aging. GDF11 is strongly related to carcinogenesis and its expression in tumors is intruded. GDF11 can promote cancer growth in the colon or inhibit the cell proliferation in breast cancer. The aberrated expression is probably allied with the impaired maturation. In this article we summarized an impact of GDF11 on the tumor cells and review the all attitudes connecting GDF11 with carcinogenesis.     

Xenotransplantation: a tool for reproductive biology and animal conservation?

The transplantation of reproductive organs, including ovaries and ovarian tissue, was pioneered over 100 years ago. In the 1960s, ovarian grafting was used as a tool to investigate ovarian function, but with the recent development of more effective cryopreservation protocols for ovarian tissue, germline preservation and propagation have now become realistic goals. This review describes progress in ovarian banking and ovarian tissue transplantation, with emphasis on how fresh and frozen ovarian tissue can be used in assisted reproduction for both humans and animals. This paper focuses most closely on the potential value of xenotransplantation, the transplantation of gonads from one species to another, to conserve rare and endangered species. Specific attention is drawn to the use of xenotransplantation as a strategy for generating viable gametes that can be used to produce live fertile offspring. Other upcoming xenogeneic technologies that may be of potential significance in animal conservation, such as transplantation of whole ovaries or isolated growing follicles, and even male germ cells, are discussed.     

Is there a special conservation biology?

Conservation biology is special to the extent that it fills useful roles in the scientific and conservation fields that are not being filled by practitioners of other disciplines. The emergence of the “new conservation biology” in the late 1970's and its blossoming in the 1980's and 1990's reflect, to a large degree, a failure of traditional academic ecology and the natural resource disciplines to address modern conservation problems adequately. Yet, to be successful conservation biology, as an interdisciplinary field, must build on the strengths of other disciplines both basic and applied. The new conservation biology grew out of concern over extinction of species, although the field has expanded to include issues about management of several levels of biological organization. I examine four controversial questions of importance to conservation biologists today: 1) are there any robust principles of conservation biology? 2) Is advocacy an appropriate activity of conservation biologists? 3) Are we educating conservation biologists properly? 4) Is conservation biology distinct from other biological and resource management disciplines? I answer three of these questions with a tentative “yes” and one (3) with a regretful “in most cases, no.” I see a need for broader Training for students of conservation biology, more emphasis on collecting basic field data, compelling applications of conservation biology to real problems, increased influence on policy, and expansion of the international scope of the discipline. If all these occur, conservation biology will by truly special.     

Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?

Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits of Daphnia ambigua. We measured the duration of predator-induced transgenerational effects, determined when transgenerational responses are induced, and quantified the cues that activate transgenerational plasticity. We show that predator exposure during embryonic development causes earlier maturation and increased reproductive output. Such effects are detectable two generations removed from predator exposure and are similar in magnitude in response to exposure to cues emitted by injured conspecifics. Moreover, all experimental contexts and traits yielded a negative correlation between within- versus across-generation responses. That is, responses to predator cues within- and across-generations were opposite in sign and magnitude. Although many models address transgenerational plasticity, none of them explain this apparent negative relationship between within- and across-generation plasticities. Our results highlight the need to refine the theory of transgenerational plasticity.     

Histochemistry and cell biology: what’s in a name?

Histochemistry represents an integrative discipline aiming at the in situ detection, localization and functional characterization of cellular and extracellular components in single cells and complex organs. Therefore, the development of new methods and improvement of existing ones continues to be important. This, however, is with the declared intent for their application in the various fields of developmental and cell biology as well as pathology in order to contribute to the solution of open problems. This review summarizes recent advancements in these fields. Accepted: 8 November 1999     

Is there a biology of quantum information?

This paper briefly considers the notion of a biology of quantum information from a number of complementary points of view. We begin with a very brief look at some of the biomolecular systems that are thought to exploit quantum mechanical effects and then turn to the issue of measurement in these systems and the concomitant generation of information. This leads us to look at the internalist stance and the exchange interaction of quantum particles. We suggest that exchange interaction can also be viewed using ecological ideas related to apparatus-object. This can also help develop the important notion of complementarity in biosystems in relation to the nature and generation of information at the microphysical scale.     

A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?

We assess the use to which bioinformatics in the form of bacterial genome sequences, functional gene probes and the protein sequence databases can be applied to hypotheses about obligate autotrophy in eubacteria. Obligate methanotrophy and obligate autotrophy among the chemo- and photo-lithotrophic bacteria lack satisfactory explanation a century or more after their discovery. Various causes of these phenomena have been suggested, which we review in the light of the information currently available. Among these suggestions is the absence in vivo of a functional alpha-ketoglutarate dehydrogenase. The advent of complete and partial genome sequences of diverse autotrophs, methylotrophs and methanotrophs makes it possible to probe the reasons for the absence of activity of this enzyme. We review the role and evolutionary origins of the Krebs cycle in relation to autotrophic metabolism and describe the use of in silico methods to probe the partial and complete genome sequences of a variety of obligate genera for genes encoding the subunits of the alpha-ketoglutarate dehydrogenase complex. Nitrosomonas europaea and Methylococcus capsulatus, which lack the functional enzyme, were found to contain the coding sequences for the E1 and E2 subunits of alpha-ketoglutarate dehydrogenase. Comparing the predicted physicochemical properties of the polypeptides coded by the genes confirmed the putative gene products were similar to the active alpha-ketoglutarate dehydrogenase subunits of heterotrophs. These obligate species are thus genomically competent with respect to this enzyme but are apparently incapable of producing a functional enzyme. Probing of the full and incomplete genomes of some cyanobacterial and methanogenic genera and Aquifex confirms or suggests the absence of the genes for at least one of the three components of the alpha-ketoglutarate dehydrogenase complex in these obligate organisms. It is recognized that absence of a single functional enzyme may not explain obligate autotrophy in all cases and may indeed be only be one of a number of controls that impose obligate metabolism. Availability of more genome sequences from obligate genera will enable assessment of whether obligate autotrophy is due to the absence of genes for a few or many steps in organic compound metabolism. This problem needs the technologies and mindsets of the present generation of molecular microbiologists to resolve it.     

Physiotherapy students’ perceptions of ageing – Playing narratives as a pedagogical innovation

Introduction and objectivesThere is a considerable lack of structure in training health professionals in geriatrics. The narratives can promote a collaborative reflection on different topics and might be used as a pedagogic strategy for undergraduate health students. This study aimed to explore the adoption of new perspectives on ageing after the implementation of dynamic narratives in the first graduate year for physiotherapy students.Materials and methodsAn exploratory qualitative study was performed. Participants were included if they were: ≥18 years old, physiotherapy students and agreed to participate. Physiotherapy students (n = 44) were recruited from the School of Health Sciences, Polytechnic Institute of Leiria. Two gaming sessions were performed to help students, as narrators, express their visions and ways to deal with the geriatrics field. Students’ perspectives about ageing at baseline (T1) and after the narratives experience (T2) were collected by answering the following question: What is your perception regarding ageing? Two evaluators were involved in qualitative data analysis by performing: (i) an individual analysis of themes/subthemes and a discussion meeting to evaluate discrepancies and to reach a consensus.ResultsNegative perceptions about ageing were referred 39 times at T1 (most of them related to restriction; deterioration subthemes). There were no negative perceptions registered at T2. Positive perceptions increased at T2, from n = 39 to n = 52, and three new subthemes emerged (beginning of something, fighting ageism, challenge).ConclusionThis study demonstrated the potential of narrative-based experiences as a desirable pedagogic methodology (board games-oriented) for geriatric education in undergraduate health students.     

Pregnancy as a harm?

Michigan's Appellate Court ruled in 2004 that a pregnancy that resulted from a rape should be considered a bodily injury for sentencing purposes. Interestingly, all three possible outcomes of a pregnancy-abortion, miscarriage, or childbirth-are considered to bring with them significant and substantial physical, psychological, and emotional changes. While the immediate impact of the ruling in People v. Cathey affected only the guilty individual, there are larger implications for this ruling beyond just sentencing guidelines. The ruling can be considered a step forward in prosecuting rapists, but possibly at the expense of reimagining the female body. This article considers the Cathey ruling itself, the potential benefits and consequences of this understanding on feminist discourse, and, crucially, the impact of this decision on abortion discussions. The central question that emerges is, can we both consider pregnancy a harm and believe that this harm is not always wrong-making?     

Understanding drugs and diseases by systems biology?

Systems biology aims to provide a holistic and in many cases dynamic picture of biological function and malfunction, in case of disease. Technology developments in the generation of genome-wide datasets and massive improvements in computer power now allow to obtain new insights into complex biological networks and to copy nature by computing these interactions and their kinetics and by generating in silico models of cells, tissues and organs. The expectations are high that systems biology will pave the way to the identification of novel disease genes, to the selection of successful drug candidates—that do not fail in clinical studies due to toxicity or lack of human efficacy—and finally to a more successful discovery of novel therapeutics. However, further research is necessary to fully unleash the potential of systems biology. Within this review we aim to highlight the most important and promising top-down and bottom-up systems biology applications in drug discovery.