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(2009-08-05 21:50:58)
[2009/07/24] Nanotech Blurs Line With Biophysics
Nanotech Blurs Line With Biophysics   07/24/2009    
July 24, 2009 — Machines on the molecular scale – in the literature these days, one needs to dig to find whether a news article is talking about man-made machinery or the living cell.  Both employ laws of physics to do work.  Notice how seamless the connection is in the following examples.
  1. Kinesin tightrope walk:  Scientists at Northwestern University are figuring out how kinesin “walking machines” in the cell are able to stay on track.  Writing in PNAS,1 they said, “Kinesin I can walk on a microtubule for distances as long as several micrometers.  However, it is still unclear how this molecular motor can remain attached to the microtubule through the hundreds of mechanochemical cycles necessary to achieve this remarkable degree of processivity.”  They found that these tightrope-walking machines keep two feet (actually dubbed “heads”) on the rope (microtubule) at a time (so to speak), keep one foot tightly bound, move the other foot quickly, and keep the toes dug into the rope.  “These 4 features reduce the likelihood that a kinesin I motor will dissociate and contribute to making this motor so highly processive,” they concluded.
  2. Molecular mass spectrometer:  Caltech scientists are inventing a single-molecule mass spectrometer, Science Daily reported.  Michael Rourkes was quoted in the article saying, “the next generation of instrumentation for the life sciences—especially those for systems biology, which allows us to reverse-engineer biological systems—must enable proteomic analysis with very high throughput.”  (For a recent story on systems biology, see 07/21/2009).
  3. Myosin sober navigation:  Another cell motor that walks is myosin.  Like kinesin, it can travel long distances on its highways of actin without falling off.  Scientists have wondered if the motors employ a random walk, like a drunken pedestrian.  That wouldn’t make sense for a cargo delivery system like the myosin-actin process, so scientists at the Institut Curie in Paris used quantum dots to watch them in real time.  They found that the apparent random walk is the motor checking out each intersection in the cris-cross network of actin tracks.  In a report in Science Daily, Dr. David Warshaw cast Mother Nature in the role of nanotechnology engineer in his explanation: “Cargo delivery in cells can’t totally be a random process, therefore, using the approach described here we can characterize how motors and cargo link up and understand the engineering design principles Mother Nature uses to guarantee efficient and effective delivery of cargo within cells.”
  4. Carbon nanotube scale:  Carbon nanotubes have been all the rage in nanotech for several years now.  They’re stiff and strong for their extreme small size.  Science Daily reported a new use for them: weighing single atoms.  “But the real excitement would be in tracking chemical and biological reactions involving individual atoms and molecules reacting right there on the vibrating nanotube,” the report said.  “That could have applications in molecular biology, allowing scientists to study the basic processes of life in unprecedented detail.”
  5. Purposeful tumbleScience reported this week that the flagella of Chlamydomonas (an alga) may go into tumble mode on purpose: for stealth.2 
    One of the most remarkable and pervasive feats in the microscopic world is the coordination of flagella, the slender, whiplike structures that protrude from many types of cells.  The collective motion of flagella (also known as cilia when they occur in large numbers in eukaryotes) drives fluid transport, and permits individuals to save energy through cooperation.  Because the internal structure of cilia is highly conserved among eukaryotes from algae to humans, free-swimming organisms like Chlamydomonas (see the first figure, panel A) have long been powerful model systems.  On page 487 of this issue, Polin et al. show how synchronization of the flagella in Chlamydomonas reinhardtii governs the movement of this green alga through water, a key determinant of its ecological fitness.
    It turns out that the cells synchronize their flagella for about 11 seconds, performing a kind of breaststroke.  Then, they de-synchronize them and tumble, making sharp turns.  The scientists think this is actually an evasion strategy to escape from predators.
  6. Light control.  The bright colors on a scarab beetle are due to nanotechnology.  In another report in Science,3 Sharma et al figured out that the structures in the scale cells of a scarab beetle “are structurally and optically analogous to the focal conic domains formed spontaneously on the free surface of a cholesteric liquid crystal.  These textures provide the basis for the morphogenesis as well as key insights for emulating the intricate optical response of the exoskeleton of scarab beetles.”  Liquid crystals are prominent structures in many man-made objects, too, like wristwatches.
        In the same issue of Science,4 Pete Vukusic commented on the discovery, saying it adds to the technologies the beetle uses.  The scales also display a helical nanostructure that may provide mechanical strength.  “However, the beetle helical ultrastructure is arguably too complex and too costly to produce without the benefit of a suitable optical selection advantage,” he said, “such as effective signaling.  The strong circularly polarized reflection observed in the beetles may, for example, play a role in intraspecific communication.”  Popular reports on this discovery can be found at Science News and Science Daily and BBC News.
How these technologies came to be, Vukusic had no idea.  “With a few noteworthy exceptions,” he said, “the formation processes of these insect systems are not as well understood as are their photonics.”
1.  Toprak, Yildiz, Hoffman, Rosenfeld and Selvin, “Why kinesin is so processive,” Proceedings of the National Academy of Sciences, published online before print July 15, 2009, doi: 10.1073/pnas.0808396106.
2.  Roman Stocker and William M. Durham, “Microbiology: Tumbling for Stealth?”, Science, 24 July 2009: Vol. 325. no. 5939, pp. 400-402, DOI: 10.1126/science.1177269.
3.  Sharma, Crne, Park and Srinivasarao, “Structural Origin of Circularly Polarized Iridescence in Jeweled Beetles,” Science, 24 July 2009: Vol. 325. no. 5939, pp. 449-451, DOI: 10.1126/science.1172051.
4.  Pete Vukusic, “Evolutionary Photonics with a Twist,” Science, 24 July 2009: Vol. 325. no. 5939, pp. 398-399, DOI: 10.1126/science.1177729.
The discovery that biological systems use the same laws of physics on the molecular scale as do artificial systems has at least two important consequences for philosophy.  One is a continuation of the demise of a form of vitalism that asserted that biological stuff is fundamentally different from non-biological stuff.  A long trend away from that began when Wohler synthesized urea in the lab in 1828, proving that an organic substance could be manufactured with known laws of chemistry.  This consequence might seem antithetical to theism, but the other trumps it: the discovery that life uses coded instructions and manufacturing processes to employ those laws and arrange those materials in purposeful ways.  If we humans employ design principles in our nanotechnology, then detect those same principles at work in biological systems, the inference to the best explanation is that design principles were involved in their origin as well.  That theme is explicated thoroughly in Steven Meyer’s new book Signature in the Cell (see Resource of the Week for July 4).  The conclusion is amplified when our best scientists cannot figure out how “Mother Nature” did it.  Maybe they’ve got the wrong Engineer in mind.

   [2009/08/11] Protein Function: It's All in the Fold


   [2009/07/21] Systems Biology Oddly Silent About Darwin


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