Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George Ellis (eds.), Cambridge University Pres

Ab Initio Modeling of Ecosystems with Artificial Life

Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling techniques. The Digital Life system Avida is introduced and prospects for experiments with ab initio evolution (evolution "from scratch"), maintenance, as well as stability of ecosystems are discussed.Comment: 13 pages, 2 figure

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

Document generality: its computation for ranking

The increased variety of information makes it critical to retrieve documents which are not only relevant but also broad enough to cover as many different aspects of a certain topic as possible. The increased variety of users also makes it critical to retrieve documents that are jargon free and easy-to-understand rather than the specific technical materials. In this paper, we propose a new concept namely document generality computation. Generality of document is of fundamental importance to information retrieval. Document generality is the state or quality of docu- ment being general. We compute document general- ity based on a domain-ontology method that analyzes scope and semantic cohesion of concepts appeared in the text. For test purposes, our proposed approach is then applied to improving the performance of doc- ument ranking in bio-medical information retrieval. The retrieved documents are re-ranked by a combined score of similarity and the closeness of documents’ generality to that of a query. The experiments have shown that our method can work on a large scale bio-medical text corpus OHSUMED (Hersh, Buckley, Leone & Hickam 1994), which is a subset of MEDLINE collection containing of 348,566 medical journal references and 101 test queries, with an encouraging performance