SciTech #ScienceSunday Digest, 37/14.
Bio-membranes on silicon, origin of life, complex gene logic, molecular rectifier, large DNA origami, machine vision, re-running evolution, aging, protocells, graphene production.
1. Integrating Synthetic Biological Membranes onto Silicon.
A new process first evaporates chitosan molecules onto a silicon surface and then evaporates a phospholipid molecule onto the chitosan coating to form a stable synthetic phospholipid bilayer over the surface http://publishing.aip.org/publishing/journal-highlights/artificial-membranes-silicon. These are standard organic molecules and are being used as part of a dry process to fabricate artificial bio-silicon interfaces. While the group quote the desire to develop biological sensor surfaces for integrated circuits, the promise here is for far more effective medical implants and other devices to better reside and interface with various systems within the body.
2. Using Information Theory to Tackle Origin of Life Questions.
An interesting analysis using information theory tackles conventional origin of life questions to develop new mathematical models of self-replicating molecules to show how (in some cases) likely self-replicating molecules can develop and evolve https://medium.com/the-physics-arxiv-blog/information-theory-and-the-origin-of-life-4cf6b93d156c. A proof-of-concept demonstration of the predictive ability of the model was able to account for the rate at which others had found self-replicators in a standard in silico simulation system. The key seems to be the difference between the entropy of a non-living and living system; when small the likelihood of finding self-replicating molecules increases by any dozens of orders of magnitude. This is pure mathematics of course and substrate-independent; I wonder if this analysis might be applied to memes, units of human cultural transmission, and the general stuff of thought – and what insights might result.
3. More Complex Logic from Synthetic Gene Circuits.
Work on genetic logic circuits and programs continues apace, with recent synthetic biology techniques successfully performing complex biological-based logic operations http://www.kurzweilai.net/new-synthetic-gene-circuits-can-perform-complex-bio-logic-tasks. Ultimately aiming for mature technology that allows cells to sense and respond to their environment in programmatic ways, the current demonstration worked by building modular genetic circuits with transcription factors engineered to both sense certain environmental chemicals and bind to certain DNA sequences in order to activate genes of interest – up to four engineered transcription factors worked together to process multiple environmental signals and switch certain genes on or off.
4. A Molecular Rectifier.
A molecule comprising a carbon buckyball joined to a carbon nano-diamond has been demonstrated to behave like a molecular diode or rectifier, allowing electric current to flow in one direction only http://phys.org/news/2014-09-buckyballs-diamondoids-tiny-electronic-gadget.html. The group next plans to investigate the creation of transistors out of the same components as part of driving towards molecular electronics and molecular computers.
5. Largest Ever Self Assembled DNA Origami Molecule.
The largest ever DNA origami molecule has been created, self-assembling and folding into a precisely-defined atomically-precise structure measuring 200nm by 300nm and comprising a total of 51,466 bases http://news.ncsu.edu/2014/09/labean-dna-origami/. The achievement was facilitated by new, cheap DNA synthesis techniques (basically a converted inkjet printer) that enabled the rapid synthesis of the 1,600 staple strands required to fold and knit the DNA structure together; the performance of the technique is acceptable with more than 90% of structures self-assembling into the correct shape. On the topic of self-assembly a new molecular assembly line can controllably produce, via repeated iteration, long-chain hydrocarbons of defined length, orientation, and shape http://phys.org/news/2014-09-chemists-assembly-line-molecules.html.
6. The Rise and Rise of Machine Vision.
Technology Review had an interesting overview of the rise of machine vision, object recognition and the tipping point in performance capabilities that occurred in 2012 http://www.technologyreview.com/view/530561/the-revolutionary-technique-that-quietly-changed-machine-vision-forever/. These systems now routinely involve architectures comprising deep convolutional neural networks with hundreds of thousands of simulated neurons stacked multiple simulated layers that learn to distinguish objects; error rates in machine vision have progressively declined to levels where applications now routinely rival human performance levels. Continual advances in this field should enable automated lip-reading in future, as discussed here http://www.technologyreview.com/view/530641/the-challenges-and-threats-of-automated-lip-reading/ – imagine all those “private” conversations hidden in archived video footage just waiting to be analysed by next-generation machine vision systems.
7. Evidence Suggesting Re-running Evolutionary History would Produce the Same Results.
A large, ambitious study exploring the evolutionary trajectories of 640 different strains of yeast cells over 500 generations sampled every 12 hours and originating from a single parent cell has generated strong evidence that re-running evolution results in organsims arriving at the same end point http://www.simonsfoundation.org/quanta/20140911-evolutions-random-paths-all-lead-to-the-same-place/. This goes against conventional evolutionary thinking. The study shows that, regarding evolutionary trajectories, the initial mutations accounting for genotypic differences invariably leads to convergence rather than divergence at the fitness level. This suggests that if we started life on this planet from scratch we would evolve in a similar fashion and broadly arrive at the same point. The work also suggests a disconnect between evolution at the genetic level and at the level of the whole organism.
8. Much Ado About Aging.
There were a nice bunch of aging-related advances this week. First, boosting AMPK (gene / protein) levels in either the intestine or nervous system resulted in a slowing of the aging process beyond the organ in which it was boosted, leading to flies living 30% longer, and believed mainly to be due to significantly increased autophagy and the breakdown of cellular garbage http://newsroom.ucla.edu/releases/ucla-biologists-delay-the-aging-process-by-remote-control. Second, and related to the first, involves increasing levels of heat shock protein in muscle cells, and which resulted in boosting insulin sensitivity and muscular performance in aged mice https://www.fightaging.org/archives/2014/09/inducing-heat-shock-protein-70-as-a-basis-for-therapies.php. Thrd, a trio of studies demonstrated different approaches to restoring the activity of old muscle stem cells https://www.fightaging.org/archives/2014/09/another-method-of-restoring-activity-in-old-muscle-stem-cells.php.
9. Creating and Studying Artificial Protocells.
By creating basic water-filled vesicles and filling them with microtubule proteins, kinesin motor proteins, and ATP molecules basic protocells can be created that not only change their shape but can also move across a surface http://singularityhub.com/2014/09/08/simple-artificial-cells-created-that-change-shape-and-move-on-their-own/. By uncovering basic principles for controlling the protocell’s behaviour they hope to facilitate the creation of more advanced artificial cell systems in future.
10. New Technique for Efficient Production of Graphene Sheets.
A new, simple technique for separating graphene sheets from bulk graphite (and also sheets of other two dimensional materials like boron nitride) has been discovered http://science.psu.edu/news-and-events/2014-news/Mallouk9-2014. The method simply involves intercalation, whereby ions or other molecules are inserted between the graphene layers to pull them apart, and all without the use of oxidising agents and other chemicals that can damage the sheets. In related work graphene was combined with carbon nanotubes to produce ordered three dimensional structures capable of improved energy storage applications for lithium-sulfur batteries http://www.nanowerk.com/spotlight/spotid=37339.php.
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