Thursday, May 27, 2010


Existence of RNA 'dark matter' in doubt : Nature News

"The abundance of transcripts from the genome may have been overestimated. RNA 'dark matter' hinted at by previous studies of mammalian genomes may not exist after all. The mysterious matter refers to the large amounts of RNA that are copied from the DNA sequence, or transcribed, but which cannot be accounted for by the genes that have been identified so far." Full news article @ Nature News

Tuesday, May 25, 2010


Top 10 New Species - 2010

"A committee of taxonomists and the International Institute for Species Exploration at Arizona State University have picked the top 10 new species identified in 2009. The list includes a fanged minnow (dubbed Danionella dracula, naturally), which marks the first time scientists have spotted oral teeth in this family, the largest among freshwater fishes. Other picks include a golden orb spider, a carnivorous sponge, a sea slug that eats insects, a worm that releases green bioluminescence when threatened, and a frogfish with a psychedelic pattern." Read more @ The Scientist and Top 10 New Species - 2010 | International Institute for Species Exploration

Monday, May 24, 2010


swarm intelligence for adaptive routing in telecommunications networks

"We identify typical building blocks of swarm intelligence systems and we show how they are used to solve routing problems. Then, we present Ant Colony Routing, a general framework in which most swarm intelligence routing algorithms can be placed. After that, we give an extensive overview of existing algorithms, discussing for each of them their contributions and their relative place in this research area. We conclude with an overview of future research directions that we consider important for the further development of this field." Full paper @ Swarm Intelligence

Wednesday, May 19, 2010


C Library for Simulated Evolution of Biological Networks

". Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the functional space spanned by biochemical networks, studying natural evolution, or designing new synthetic networks. If there was a method for easily performing such studies, it can allow the community to further experiment with simulated evolution and explore all of its uses. As a result, we have developed a library written in the C language that performs all the basic functions needed to carry out simulated evolution of biological networks. " Article @ arXiv


Bacterial foraging algorithm

"a novel nature-inspired heuristic optimization algorithm: bacterial foraging algorithm with varying population (BFAVP), based on a more bacterially-realistic model of bacterial foraging patterns, which incorporates a varying population framework and the underlying mechanisms of bacterial chemotaxis, metabolism, proliferation, elimination and quorum sensing. In order to evaluate its merits, BFAVP has been tested on several benchmark functions and the results show that it performs better than other popularly used EAs, in terms of both accuracy and convergency." Full paper @ Biosystems.

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Testing the common ancestry of life

"The question of whether or not all life on Earth has an ultimate common origin is a subtle one, complicated by the phenomenon of lateral gene transfer. It has now been tackled with a formal statistical analysis. [...]Theobald's work is unlikely to be the last word on common ancestry. It is difficult to exclude all other explanations for correlations, and further work will probably address this problem. In the meantime, there is now strong quantitative support, by a formal test, for the unity of life." Full news article @ Nature


Molecular robots

"Moving robotics to the single-molecule level is possible in principle, but requires facing the limited ability of individual molecules to store complex information and programs. One strategy to overcome this problem is to use systems that can obtain complex behaviour from the interaction of simple robots with their environment. A first step in this direction was the development of DNA walkers, which have developed from being non-autonomous to being capable of directed but brief motion on one-dimensional tracks. [...] Single-molecule microscopy observations confirm that such walkers achieve directional movement by sensing and modifying tracks of substrate molecules laid out on a two-dimensional DNA origami landscape. When using appropriately designed DNA origami, the molecular spiders autonomously carry out sequences of actions such as ‘start’, ‘follow’, ‘turn’ and ‘stop’. We anticipate that this strategy will result in more complex robotic behaviour at the molecular level if additional control mechanisms are incorporated. One example might be interactions between multiple molecular robots leading to collective behaviour; another might be the ability to read and transform secondary cues on the DNA origami landscape as a means of implementing Turing-universal algorithmic behaviour." Full article @ Nature


Comparing genomes to computer operating systems

"The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. [...] The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers’ continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems." Full article @ PNAS

The hierarchical layout of the E. coli transcriptional regulatory network and the Linux call graph.

Tuesday, May 18, 2010


Small RNA Makes Its Move

"It has been known for almost 100 years that when a plant virus infects a leaf, mobile signals are transmitted through vessels in the stem to other leaves to confer resistance to subsequent infection. More recently, the silencing of exogenous transgenes has been shown to involve a mobile signal (1). Although RNA molecules have been implicated in systemic plant cell-to-cell communication, the nature of mobile RNA that silences gene expression has not been clear (2). Now, four studies---including those by Molnar et al. and Dunoyer et al. [...]---report that small interfering RNA (siRNA) and microRNA (miRNA) are mobile signals that control gene expression during plant development." Full perspectve @ Science

Friday, May 14, 2010


The Aliens Among Us

Searching for alternative life on Earth might seem misconceived, because there is excellent evidence that every kind of life so far studied evolved from a common ancestor that lived billions of years ago. Yet most of the life that exists on Earth has never been properly classified. Full article@

Thursday, May 13, 2010


DNA robots

"Scientists are one step closer to creating molecular robots that may eventually perform complex tasks, such as building nanomolecules or delivering drugs to target tissues". Read more: DNA robots get sophisticated - The Scientist

Monday, May 10, 2010


A Turing Machine Overview

"My goal in building this project was to create a machine that embodied the classic look and feel of the machine presented in Turing’s paper. I wanted to build a machine that would be immediately recognizable as a Turing machine to someone familiar with Turing's work.
"A Turing Machine Overview

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