Monday, November 26, 2012


Architecture Reveals Genome’s Secrets

"Three-dimensional genome maps are leading to a deeper understanding of how the genome’s form influences its function." News piece @ The Scientist Magazine®

Thursday, November 15, 2012


Evolutionary layering and the limits to cellular perfection

"Although observations from biochemistry and cell biology seemingly illustrate hundreds of examples of exquisite molecular adaptations, the fact that experimental manipulation can often result in improvements in cellular infrastructure raises the question as to what ultimately limits the level of molecular perfection achievable by natural selection. Here, it is argued that random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes. Moreover, although substantial improvements in fitness may sometimes be accomplished via the emergence of novel cellular features that improve on previously established mechanisms, such advances are expected to often be transient, with overall fitness eventually returning to the level before incorporation of the genetic novelty. As a consequence of such changes, increased molecular/cellular complexity can arise by Darwinian processes, while yielding no long-term increase in adaptation and imposing increased energetic and mutational costs." Full paper @ PNAS


Biologically inspired LED lens from cuticular nanostructures of firefly lantern

"Cuticular nanostructures found in insects effectively manage light for light polarization, structural color, or optical index matching within an ultrathin natural scale. These nanostructures are mainly dedicated to manage incoming light and recently inspired many imaging and display applications. A bioluminescent organ, such as a firefly lantern, helps to out-couple light from the body in a highly efficient fashion for delivering strong optical signals in sexual communication. Here we report a unique observation of high-transmission nanostructures on a firefly lantern and its biological inspiration for highly efficient LED illumination." Full paper @ PNAS

Wednesday, November 14, 2012


Computer science: Virtually there

"In On Computing, Paul Rosenbloom examines the case for computing to enter the pantheon of great scientific domains alongside the physical, biological and social sciences. The centenary year of computing pioneer Alan Turing's birth seems a fitting moment to put the idea to the test." Full review @ Nature

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Friday, November 09, 2012


Noam Chomsky on Where Artificial Intelligence Went Wrong

Noam Chomsky on Where Artificial Intelligence Went Wrong - Yarden Katz - The Atlantic

A great read is also the reply to Chomsky by Peter Norvig. (thanks Artemy!)



Transposable Elements, Epigenetics, and Genome Evolution

"Transposable genetic elements (TEs) comprise a vast array of DNA sequences, all having the ability to move to new sites in genomes either directly by a cut-and-paste mechanism (transposons) or indirectly through an RNA intermediate (retrotransposons).[...] it is precisely the elaboration of epigenetic mechanisms from their prokaryotic origins as suppressors of genetic exchanges that underlies both the genome expansion and the proliferation of TEs characteristic of higher eukaryotes. This is the inverse of the prevailing view that epigenetic mechanisms evolved to control the disruptive potential of TEs. The evidence that TEs shape eukaryotic genomes is by now incontrovertible. My thesis, then, is that TEs and the transposases they encode underlie the evolvability of higher eukaryotes' massive, messy genomes."Transposable Elements, Epigenetics, and Genome Evolution

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Wednesday, November 07, 2012


Genetic programs constructed from layered logic gates in single cells

"Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics1. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits2, 3, 4, 5, 6, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. [...] Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output." Full article @ Nature

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Tuesday, November 06, 2012


Boolean modeling of gene regulatory networks: Driesch redux

Conducting research on sea urchins at the Naples Zoological Station, 19th century developmental biologist Hans Driesch demonstrated the totipotent nature of early embryonic cells, contributing significantly to the then-nascent field of “developmental mechanics.” [...] As developmental biology moves into its third century of existence as a modern science, we find that major advances are bringing us full-circle to approach central questions posed by early pioneers[...]. In PNAS, Peter et al. (2) describe a quantitative model to describe at a molecular level the processes of cellular differentiation that have fascinated generations of biologists, providing a means to link developmental and systems biology. See full letter @ PNAS. See original reference:

Peter IS, Faure E, Davidson EH (2012) "Predictive computation of genomic logic processing functions in embryonic development". PNAS 109:16434–16442.

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Saturday, November 03, 2012


New Way to Look at Life

"Ever since Charles Darwin, biologists have been building trees to show how organisms are related to one another. Now, computational biologist James Rosindell of Imperial College London and his colleagues have come up with a tree that outdoes all trees. Called OneZoom, the approach works like Google Maps: A user can drill down the tree's trunks, branches, and tips to view ever-finer details, and the structure can incorporate an infinite amount of information." Full news analysis @ Science

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Slime mold uses an externalized spatial “memory” to navigate in complex environments

"Spatial memory enhances an organism’s navigational ability. Memory typically resides within the brain, but what if an organism has no brain? We show that the brainless slime mold Physarum polycephalum constructs a form of spatial memory by avoiding areas it has previously explored. " Full article @ PNAS


Immune Reactions Help Reprogram Cells

"When under threat, it pays to be flexible. That principle may help explain why scientists have been able to use viruses to reprogram differentiated cells into stem cells, an advance that was recognized as part of this year's Nobel Prize in physiology or medicine. In the 26 October issue of Cell, a U.S. research team reports that a cell's defensive reaction to viruses seems to make it more open to expressing genes that are usually shut down—whether they be those that trigger inflammation or those that are active in stem cells. The find could help scientists better understand how cellular reprogramming works, and may also help them develop more efficient and safer ways to reprogram cells." Full news analysis @ Science. Full article:

Lee et al [2012. "Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming". Cell 151 (3):547 - 558.

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Thursday, November 01, 2012


Bacterial survival strategies suggest rethinking cancer cooperativity

"Despite decades of a much improved understanding of cancer biology, we are still baffled by questions regarding the deadliest traits of malignancy: metastatic colonization, dormancy and relapse, and the rapid evolution of multiple drug and immune resistance. New ideas are needed to resolve these critical issues. Relying on finding and demonstrating parallels between collective behavior capabilities of cancer cells and that of bacteria, we suggest communal behaviors of bacteria as a valuable model system for new perspectives and research directions. Understanding the ways in which bacteria thrive in competitive habitats and their cooperative strategies for surviving extreme stress can shed light on cooperativity in tumorigenesis and portray tumors as societies of smart communicating cells. This may translate into progress in fathoming cancer pathogenesis. We outline new experiments to test the cancer cooperativity hypothesis and reason that cancer may be outsmarted through its own ‘social intelligence’." Full paper @ Trends in Microbiology


The Implications of Interactions for Science and Philosophy

"Reductionism has dominated science and philosophy for centuries. Complexity has recently shown that interactions—which reductionism neglects—are relevant for understanding phenomena. When interactions are considered, reductionism becomes limited in several aspects. In this paper, I argue that interactions imply nonreductionism, non-materialism, non-predictability, non-Platonism, and non-Nihilism. As alternatives to each of these, holism, informism, adaptation, contextuality, and meaningfulness are put forward, respectively. A worldview that includes interactions not only describes better our world, but can help to solve many open scientific, philosophical, and social problems caused by implications of reductionism." Full Paper @ Foundations of Science

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