Huber, Marper and Others: Throwing new light on the shadows of suspicion. INEX Policy Brief No. 8, June 2010

The proliferation of large-scale databases containing personal information, and the multiple uses to which they can be put, can be highly problematic from the perspective of fundamental rights and freedoms. This paper discusses two landmark decisions that illustrate some of the risks linked to these developments and point to a better framing of such practices: the Heinz Huber v. Germany judgement, from the European Court of Justice, and the S. and Marper v. United Kingdom ruling, from the European Court of Human Rights. The paper synthesises the lessons to be learnt from such decisions. Additionally, it questions the impact of the logic of pure prevention that is being combined with other rationales in the design and management of databases. This Policy Brief is published in the context of the INEX project, which looks at converging and conflicting ethical values in the internal/external security continuum in Europe, and is funded by the Security Programme of DG Enterprise of the European Commission’s Seventh Framework Research Programme. For more information visit: www.inexproject.e

Atomic Scale Memory at a Silicon Surface

The limits of pushing storage density to the atomic scale are explored with a memory that stores a bit by the presence or absence of one silicon atom. These atoms are positioned at lattice sites along self-assembled tracks with a pitch of 5 atom rows. The writing process involves removal of Si atoms with the tip of a scanning tunneling microscope. The memory can be reformatted by controlled deposition of silicon. The constraints on speed and reliability are compared with data storage in magnetic hard disks and DNA.Comment: 13 pages, 5 figures, accepted by Nanotechnolog

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

Erwin Schroedinger, Francis Crick and epigenetic stability

Schroedinger's book 'What is Life?' is widely credited for having played a crucial role in development of molecular and cellular biology. My essay revisits the issues raised by this book from the modern perspective of epigenetics and systems biology. I contrast two classes of potential mechanisms of epigenetic stability: 'epigenetic templating' and 'systems biology' approaches, and consider them from the point of view expressed by Schroedinger. I also discuss how quantum entanglement, a nonclassical feature of quantum mechanics, can help to address the 'problem of small numbers' that lead Schroedinger to promote the idea of molecular code-script for explanation of stability of biological order.Comment: New and improved version of the essay, now published in the online journal 'Biology Direct'. Contains more expanded discussion on entanglement. 18 pages, 2 figures. The file includes open reviews by E.Koonin, V.Vedral and E.Karsent

The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA.

In the early 'RNA world' stage of life, RNA stored genetic information and catalyzed chemical reactions. However, the RNA world eventually gave rise to the DNA-RNA-protein world, and this transition included the 'genetic takeover' of information storage by DNA. We investigated evolutionary advantages for using DNA as the genetic material. The error rate of replication imposes a fundamental limit on the amount of information that can be stored in the genome, as mutations degrade information. We compared misincorporation rates of RNA and DNA in experimental non-enzymatic polymerization and calculated the lowest possible error rates from a thermodynamic model. Both analyses found that RNA replication was intrinsically error-prone compared to DNA, suggesting that total genomic information could increase after the transition to DNA. Analysis of the transitional RNA/DNA hybrid duplexes showed that copying RNA into DNA had similar fidelity to RNA replication, so information could be maintained during the genetic takeover. However, copying DNA into RNA was very error-prone, suggesting that attempts to return to the RNA world would result in a considerable loss of information. Therefore, the genetic takeover may have been driven by a combination of increased chemical stability, increased genome size and irreversibility

Self assembled three-dimensional nonvolatile memories

A promising strategy for for the realisation of three-dimensional memories could be the self assembly of articial sub-micron elements (smarticles). Such elements can be realised by combining edge-lithography techniques and anisotropic etching. The first experiments into this direction are encouraging