Tuesday, March 6, 2012

astro picture for the day

Image Credit & Copyright: Leonardo Julio & Carlos Milovic


  1. I've not posted any number of astronomical images like this(made possible by ever more capable ccd devices . . . instead of the photographic plates that revolutionized astronomy in the 1800s, and makes digital cameras possible today!). I thought I'd post it and post some science/technological news. I also havn't posted any number of big, medium, and small science and technological news . . . just because there's so much. But, I just feel that I should post this one somewhere! So, why not post it as a reply to a great astronmy picture?!

    "One of the more exciting discoveries in biology in the last few years is the role that quantum effects seem to play in many living systems.

    The two most famous examples are in bird navigation, where the quantum zeno effect seems to help determine the direction of the Earth's magnetic field, and in photosynthesis, where the way energy passes across giant protein matrices seems to depend on long-lasting quantum coherence.

    Despite the growing evidence in these cases, many physicists are uneasy, however. The problem is the issue of decoherence, how quickly quantum states can survive before they are overwhelmed by the hot, wet environment inside living things.

    According to conventional quantum calculations, these states should decay in the blink of an eye, so fast that they should not be able to play any role in biology.

    That's led many physicists to assume something is wrong: either the measurements are faulty in some way or there is some undiscovered mechanism that prevents decoherence.

    Today, Gabor Vattay and Stuart Kau man at the University of Vermont in the US and Samuli Niiranen at the Tampere Institute of Technology in Finland say its the latter.

    These guys have worked out that in certain special circumstances, quantum systems can remain coherent over much greater timescales and distances than conventional quantum thinking gives credit for. And they argue that biology exploits this process in a way that explains the recent observations from quantum biologists.

    Their discussion focuses on the weird phenomenon, even by quantum standards, of quantum chaos, in which small changes to a quantum system can have a huge influence on its evolution, just as in classical chaotic systems.

    When a systems changes from being merely quantum to being quantum chaotic, it passes through a kind of phase transition. The new thinking focuses on this transition.

    Physicists have known for many years that when a system is finely balanced between two phases, all kinds of strange behaviour can occur. For example, water changes from a gas to a liquid to a solid at certain temperatures and pressures. These states all have well defined properties.

  2. However, there is a certain temperature and pressure at which all three states of water can co-exist. At this so-called critical transition, the distinction between gas, liquid and solid essentially disappears.

    Kauffman and co say a similar kind of critical transition occurs as quantum systems switch to a chaotic regime. Here the distinction between chaotic behaviour and ordinary quantum behaviour disappears. And in these conditions, quantum coherence suddenly changes from the fragile, blink-and-you-miss-it regime to a much more robust long-lived phenomenon.

    It is in this state, say Kauffman and co, that the observed processes of quantum biology must take place. They even demonstrate this by simulating the improved coherence of the light harvesting complexes involved in photosynthesis. "It is very likely that biological systems use this mechanism," they say.

    That's an interesting mechanism that, if verified experimentally, could have an important impact on quantum engineering.

    The critical transition that Kauffman and co talk about is also known as the the metal-to-insulator transition, which allows the transport of quantum information and energy. If that can be made to work at room temperature, as Kauffman and co suggest, all kinds of new quantum devices may be possible.

    "The results may open up new possibilities to design low loss energy and information transport systems," they say.

    Worth keeping an eye on"

    Why not indeed! I remember like maybe five years ago physicists made or proved quantum chaos; nobody knew what it was good for! Metamaterials(large molecules formed in sheets that can do weird things like cloaking devices) have been doing great things recently like cloaking energy; they could cloak earthquakes; i've thought they could be usefull for cloaking the energy of meteorite impacts for O'Neill colonies. They've done much else also! The immediate future is going to be star trekkish!

    We're talking dna/rna nanomanufacturing is going to come of age this year.

  3. Dna nanotechnology allows for more self-assembling ability. Rna brings the ability to make robust nanomechanical parts and chemical reactions possible. Rna nanotechnology has recently made much progress.

    "As we pointed out recently, a unique advantage of RNA nanotechnology compared to DNA nanotechnology is that the more complex rules of base pairing involved in RNA folding allow the formation of a variety of compact, complex three-dimensional shapes. Although one principal function of RNA molecules in cells is as messenger RNA, carrying a copy of the information in a DNA gene to the ribosomes where that message is translated to make a protein, a large number of other RNA molecules, including those comprising the ribosomes themselves, have complex three-dimensional shapes and embody various functional properties dependent on those shapes, as do proteins.

    Taking advantage of the rapid increase in available high resolution, three-dimensional structures for various non-coding RNA molecules, a new computational method has uncovered many new RNA structural motifs, revealing the tool kit of RNA nanotechnology to be even more diverse than thought. A hat tip to Science Daily for reprinting this news release from the University of Central Florida “Computer Sleuthing Helps Unravel RNA’s Role in Cellular Function“:

    … University of Central Florida Engineering Assistant Professor Shaojie Zhang used a complex computer program to analyze RNA motifs – the subunits that make up RNA (ribonucleic acid). …

    The units that make up RNA fold like a long accordion and vary in structure. Many have been identified in the past, but finding a quick automatic way to determine patterns in the varying types of units has been elusive until now.
    “We have discovered many new RNA structural motifs using our new computational method,” Zhang said. “This breakthrough can largely increase our current knowledge of RNA structural motifs. And newly discovered motifs may also help us develop possible treatment of certain diseases.”

    Zhang’s work is this month’s cover story in Nucleic Acids Research [abstract, Open Access Full Text], an academic journal.

    Using computers, Zhang and his team have been able to view these RNA accordion-like structures and how they fold in a 3-D scale. The program can quickly go through many RNA samples and discover units that are distinct and form patterns. That information gives researchers clues about their function. …

    The newly identified structural motifs contain variations in base-pairing rules. As the authors conclude:

    These new motifs may lead to the discovery of unknown structure–function relationships and define new building blocks for the RNA architecture, significantly improving our understanding of the RNA structural motifs. …

    The next test will be to see if these new insights into RNA structure will enable the design of new RNA machines with novel functions, and eventually artificial RNA molecular machines.
    —James Lewis"

  4. "New computer assisted design (CAD) tools for engineering RNA components have been developed for the growing field of synthetic biology. The knowledge of RNA folding and RNA catalytic and binding functions incorporated into these CAD tools may also prove useful for RNA nanotechnology. A hat tip to Science Daily for reprinting this news release from the Lawrence Berkeley National Laboratory (Berkeley Lab) “CAD for RNA“:

    The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences. Researchers at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or “RNA devices” for controlling genetic expression in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals.

    “Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs,” says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. “Our work establishes a foundation for developing CAD platforms to engineer complex RNA-based control systems that can process cellular information and program the expression of very large numbers of genes. Perhaps even more importantly, we have provided a framework for studying RNA functions and demonstrated the potential of using biochemical and biophysical modeling to develop rigorous design-driven engineering strategies for biology.” …

    The ressearch was published in Science [abstract]. To test their CAD tools, the researchers engineered 28 molecular devices to regulate metabolic pathways in bacteria via RNA-controlled gene expression, and verified that expected levels of expression were obtained. From the abstract, “… More broadly, we provide a framework for studying RNA functions and illustrate the potential for the use of biochemical and biophysical modeling to develop biological design methods.”

  5. The news release continues:

    … As with other engineering disciplines, CAD tools for simulating and designing global functions based upon local component behaviors are essential for constructing complex biological devices and systems. However, until this work, CAD-type models and simulation tools for biology have been very limited.

    Identifying the relevant design parameters and defining the domains over which expected component behaviors are exerted have been key steps in the development of CAD tools for other engineering disciplines,” says Carothers, a bioengineer and lead author of the Science paper who is a member of Keasling’s research groups with both JBEI and the California Institute for Quantitative Biosciences. “We’ve applied generalizable engineering strategies for managing functional complexity to develop CAD-type simulation and modeling tools for designing RNA-based genetic control systems. Ultimately we’d like to develop CAD platforms for synthetic biology that rival the tools found in more established engineering disciplines, and we see this work as an important technical and conceptual step in that direction.” …

    RNA nanotechnology has a unique set of advantages as a pathway technology toward atomically precise productive nanosystems that reflect its central role in biological systems. Unlike the simple Watson-Crick base-pair molecular recognition code that underlies DNA nanotechnology, the more complex rules of base-pairing involved in RNA folding allow RNA to fold into compact complex three-dimensional shapes. These shapes are somewhat reminiscent of the complex folds of protein structures, yet the folding rules are considerably simpler than those of proteins. These RNA CAD tools may be an important step toward powerful design tools for folded polymer paths toward molecular machine systems."

  6. With the recent advances of cad/cam for dna and rna nanotechnology(and even more advances shown here and those not shown . . . there's so many dna nanotechnology advances, I can't even remember them all!), dna/rna nanotechnology will mature before this year is out!

    With this basic nano-manufacturing ability, all these quantum technologies will be made practical beyond our wildest imaginations! The Star-trekkish future is happening this year! I'm not sure how to express my feelings about this!

    It should be pointed out that when a nano-manufacturing ability gets started, nano-computers can be built on a mass scale. And from there, a.i. can be made much more than say the expert systems we've had since the 1970s(i'm not sure about this date; the history of a.i. might surprise you; it sure did me when I read Kurzweil's "Age of Spiritual Machines."). With all that computing power, science and technology will really accellerate.

  7. Mankind has been technologically dependent for ~4 million years now. Around ten to thirty thousand years ago, the cave paintings and sophisticated wood tools were being developed(well, maybe a lot earlier than that; see my recent post about the possibility of boats made and used by Homo Erectus for almost a million years!); then, 10,000 years ago, agriculture happened; this accellerated science and technology a good bit! But, it wasn't till 3 to 4 thousand years ago that the Babylonians came up with so much mathematics(intuitive kind) and then the Classical Greeks discovered reasoning in mathematics(and the implications for culture in general; although not fully understood even by Plato! And, it didn't stick; see the dark ages of Europe!). After the dark ages, came the industrial revolution, and science/technology took off; i've remarked before, that the years around 1790 was when mankind experienced a great scientific/technological breakthrough each year. Now!(lol!), mankind's awakening is about to really go through the roof! 2012 folks! Mark it down!

    I can't describe what this means for me folks; the life struggles I've had are amazing to say the least! Those things will be revealed to humanity in due course! With mindreaders made practical in the coming year or two, I'll be a happy man! Evil will be swept away! Most likely though! I'll just walk into the future and take it like taking candy from a baby!

    I think I've posted before about how astronomically greater astronomy alone will be in a nanofuture. That time will come sooner than some realize!

  8. http://www.nanowerk.com/news/newsid=24524.php

    The above article linked to has a picture of 600 molecules patterned by peptide linking. The work was first published . . . drumroll . . . three months ago. Who knows how much further they are with this; combined with rna - nanotechnology, we are definitelly going to start seeing molecular assembly happen long before this year is out!

    "We could unambiguously demonstrate that molecular arrangements can be assembled one by one with a precision much better than the resolution limit of the light microscope", Gaub says.(one of the researchers who did the work . . . three months ago.