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

Fault diversity among off-the-shelf SQL database servers

Fault tolerance is often the only viable way of obtaining the required system dependability from systems built out of "off-the-shelf" (OTS) products. We have studied a sample of bug reports from four off-the-shelf SQL servers so as to estimate the possible advantages of software fault tolerance - in the form of modular redundancy with diversity - in complex off-the-shelf software. We checked whether these bugs would cause coincident failures in more than one of the servers. We found that very few bugs affected two of the four servers, and none caused failures in more than two. We also found that only four of these bugs would cause identical, undetectable failures in two servers. Therefore, a fault-tolerant server, built with diverse off-the-shelf servers, seems to have a good chance of delivering improvements in availability and failure rates compared with the individual off-the-shelf servers or their replicated, nondiverse configurations

Fault tolerance via diversity for off-the-shelf products: A study with SQL database servers

If an off-the-shelf software product exhibits poor dependability due to design faults, then software fault tolerance is often the only way available to users and system integrators to alleviate the problem. Thanks to low acquisition costs, even using multiple versions of software in a parallel architecture, which is a scheme formerly reserved for few and highly critical applications, may become viable for many applications. We have studied the potential dependability gains from these solutions for off-the-shelf database servers. We based the study on the bug reports available for four off-the-shelf SQL servers plus later releases of two of them. We found that many of these faults cause systematic noncrash failures, which is a category ignored by most studies and standard implementations of fault tolerance for databases. Our observations suggest that diverse redundancy would be effective for tolerating design faults in this category of products. Only in very few cases would demands that triggered a bug in one server cause failures in another one, and there were no coincident failures in more than two of the servers. Use of different releases of the same product would also tolerate a significant fraction of the faults. We report our results and discuss their implications, the architectural options available for exploiting them, and the difficulties that they may present

Conservation evo-devo: preserving biodiversity by understanding its origins

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields

Locality-Adaptive Parallel Hash Joins Using Hardware Transactional Memory

Previous work [1] has claimed that the best performing implementation of in-memory hash joins is based on (radix-)partitioning of the build-side input. Indeed, despite the overhead of partitioning, the benefits from increased cache-locality and synchronization free parallelism in the build-phase outweigh the costs when the input data is randomly ordered. However, many datasets already exhibit significant spatial locality (i.e., non-randomness) due to the way data items enter the database: through periodic ETL or trickle loaded in the form of transactions. In such cases, the first benefit of partitioning — increased locality — is largely irrelevant. In this paper, we demonstrate how hardware transactional memory (HTM) can render the other benefit, freedom from synchronization, irrelevant as well. Specifically, using careful analysis and engineering, we develop an adaptive hash join implementation that outperforms parallel radix-partitioned hash joins as well as sort-merge joins on data with high spatial locality. In addition, we show how, through lightweight (less than 1% overhead) runtime monitoring of the transaction abort rate, our implementation can detect inputs with low spatial locality and dynamically fall back to radix-partitioning of the build-side input. The result is a hash join implementation that is more than 3 times faster than the state-of-the-art on high-locality data and never more than 1% slower