Fulvio Mazzocchi

Bio: Fulvio Mazzocchi is an academic researcher. The author has contributed to research in topics: Systems biology & Reductionism. The author has an hindex of 1, co-authored 1 publications receiving 63 citations.

Complexity and the reductionism–holism debate in systems biology

Abstract: Reductionism has largely influenced the development of science, culminating in its application to molecular biology. An increasing number of novel research findings have, however, shattered this view, showing how the molecular-reductionist approach cannot entirely handle the complexity of biological systems. Within this framework, the advent of systems biology as a new and more integrative field of research is described, along with the form which has taken on the debate of reductionism versus holism. Such an issue occupies a central position in systems biology, and nonetheless it is not always clearly delineated. This partly occurs because different dimensions (ontological, epistemological, methodological) are involved, and yet the concerned ones often remain unspecified. Besides, within systems biology different streams can be distinguished depending on the degree of commitment to embrace genuine systemic principles. Some useful insights into the future development of this discipline might be gained from the tradition of complexity and self-organization. This is especially true with regards the idea of self-reference, which incorporated into the organizational scheme is able to generate autonomy as an emergent property of the biological whole.

The Century of the Gene. Evelyn Fox Keller. Harvard University Press, Cambridge, MA. 2000. pp. 186. Price £15.95, hardback. ISBN 0 674 00372 1.

Abstract: As a recent convenor for a genetics MSc. course, I was amazed how many students graduating with a degree in genetics lack practical laboratory experience and possess limited knowledge of classical genetics. A good foundation of laboratory investigations is important to complement the theoretical information given in lectures and tutorials, but has been adversely a€ected by the need to keep costs down in many academic institutions in recent years. Genetics Ð Laboratory Investigations, the twelfth edition of a book that has enjoyed success since its initial publication in 1952, addresses this problem. It is a compilation of practical exercises that form a strong foundation in both classical genetics and more recent molecular genetic techniques for students at degree level. Many of the investigations are fairly low budget, while for those that include more expensive elements, cheaper options or sample data sets are given as an alternative. For example, the exercise on PCR gives a manual procedure using dishes of heated oil as an alternative where no PCR machine is available. I was pleasantly surprised how much I enjoyed reading this book! Although the investigations do form a logical progression through the book, it is clearly not designed to be read from cover to cover. However, for myself it was a short nostalgic trip through much of my own undergraduate degree in genetics, and I was left wondering whether earlier editions of this book had had any in ̄uence on the classical genetics practical classes I attended in the 1980s, such as using Drosophila stocks with curly wings and plum eye colour to locate an unknown mutant on a particular chromosome, or counting grey and black ascospores of Sordaria to investigate linkage and crossing-over during meiosis. This edition brings the content right up-to-date within a ®eld that is presently changing rapidly. The 26 exercises cover the range from classical Mendelian inheritance to molecular techniques such as PCR, RFLPs and DNA ®ngerprinting. Much of the human content is discussed in relation to the Human Genome Project where relevant, and also incorporated are new ideas, photographs, data sets and updated references and source material. All students' tastes are catered for with a wide variety of experimental organisms representing microbes, animals, plants and fungi. In particular the several humanbased investigations should appeal to most. The exercises on analysing ®ngerprint ridge numbers and patterns, and whether your urine smells foul after eating asparagus, are particularly intriguing. I was very impressed with the organisation and layout of this book. The text is written for degree-level students and is accompanied by an Instructors Manual that includes hints, sources of materials, and answers to the many questions posed. Each investigation is completely individual, independent and designed for use with no necessary modi®cations. All relevant references, notes and appendices are included in each exercise. Indeed the pages are perforated and hole-punched for easy removal and ®ling. Each exercise has a relevant introduction to the investigation, very clearly stated objectives, and all other information required for the exercise. Suitable data sheets for recording results, and relevant analyses are given, together with questions to test the understanding of the investigator. I was disappointed that the book makes so little use of online web resources. With so many students having both an interest in the Internet and also access to online computing facilities, I feel this is a weakness that should be addressed for the next edition. Another shortcoming is that the book is so clearly aimed at an American readership with all data sets provided based on American examples. Again, online resources could overcome this. I would certainly recommend the use of this book to anyone engaged in formulating or revising a degree-level genetics course.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Abstract: Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Promise of personalized omics to precision medicine.

Abstract: The rapid development of high-throughput technologies and computational frameworks enables the examination of biological systems in unprecedented detail. The ability to study biological phenomena at omics levels in turn is expected to lead to significant advances in personalized and precision medicine. Patients can be treated according to their own molecular characteristics. Individual omes as well as the integrated profiles of multiple omes, such as the genome, the epigenome, the transcriptome, the proteome, the metabolome, the antibodyome, and other omics information are expected to be valuable for health monitoring, preventative measures, and precision medicine. Moreover, omics technologies have the potential to transform medicine from traditional symptom-oriented diagnosis and treatment of diseases toward disease prevention and early diagnostics. We discuss here the advances and challenges in systems biology-powered personalized medicine at its current stage, as well as a prospective view of future personalized health care at the end of this review.

Systematic Reviews of Animal Models: Methodology versus Epistemology

Abstract: Systematic reviews are currently favored methods of evaluating research in order to reach conclusions regarding medical practice. The need for such reviews is necessitated by the fact that no research is perfect and experts are prone to bias. By combining many studies that fulfill specific criteria, one hopes that the strengths can be multiplied and thus reliable conclusions attained. Potential flaws in this process include the assumptions that underlie the research under examination. If the assumptions, or axioms, upon which the research studies are based, are untenable either scientifically or logically, then the results must be highly suspect regardless of the otherwise high quality of the studies or the systematic reviews. We outline recent criticisms of animal-based research, namely that animal models are failing to predict human responses. It is this failure that is purportedly being corrected via systematic reviews. We then examine the assumption that animal models can predict human outcomes to perturbations such as disease or drugs, even under the best of circumstances. We examine the use of animal models in light of empirical evidence comparing human outcomes to those from animal models, complexity theory, and evolutionary biology. We conclude that even if legitimate criticisms of animal models were addressed, through standardization of protocols and systematic reviews, the animal model would still fail as a predictive modality for human response to drugs and disease. Therefore, systematic reviews and meta-analyses of animal-based research are poor tools for attempting to reach conclusions regarding human interventions.