ScienceWeek

SCIENCEWEEK

October 13, 2006

Vol. 10 - Number 41

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Books must follow sciences, and not sciences books.

-- Francis Bacon (1561-1626)

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Contents (full reports below):

1. Astronomy: On Galactic Interstellar Molecular Gas. The central region of our Galaxy contains a massive concentration of interstellar molecular gas that has been surveyed many times. The most often used probe of this gas is emission from the most abundant molecule that can easily be observed, carbon monoxide. New work extends earlier surveys of CO to a substantially larger region than had previously been mapped...

2. Chemistry: On Boron Compounds. Boron compounds are widely used in synthetic chemistry, but almost all of them are electrophiles (electron acceptors); the few reactions in which boron behaves as a nucleophile (electron donor) are generally catalyzed by a metal. But this situation is about to change. New work reports the synthesis and characterization of a boron compound in which...

3. Genetics: On Junk DNA and RNA as an Evolutionary Force. Transposable elements (TEs) -- commonly called "jumping genes" --are stretches of DNA that move around the genome of a cell, and the genomes of many higher organisms are cluttered with numerous copies of these enigmatic elements. They were discovered by Barbara McClintock in the 1950s, but it has taken half a century to begin to understand how they act...

4. Atomic physics: On Quantum Teleportation. A decade ago, the idea of teleportation was mere science fiction. But following the pioneering proposal of Bennett et al, quantum teleportation has emerged as an important tool in quantum-information science. Quantum teleportation involves the disembodied transfer of a system's most basic feature -- its quantum state -- from one location to another

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Also Noted:

COGNITIVE DEVELOPMENT IN CHIMPANZEES. T. Matsuzawa, M. Tomonaga, and M. Tanaka, Eds. Springer, Tokyo, 2006. Hardback: 540 pp., illus. $89.95. ISBN 4431302468. More information at: http://www.amazon.com/exec/obidos/ASIN/4431302468/scienceweek

THE COSMOS. A Historical Perspective. Craig G. Fraser. Greenwood, New York, 2006. Hardback: 193 pp., illus. $65. ISBN 0313332185. More information at: http://www.amazon.com/exec/obidos/ASIN/0313332185/scienceweek

GENERATION. The Seventeenth-Century Scientists Who Unraveled the Secrets of Sex, Life, and Growth. Matthew Cobb. Bloomsbury, New York, 2006. Hardback: 349 pp., illus. $24.95. ISBN 1596910364. More information at: http://www.amazon.com/exec/obidos/ASIN/1596910364/scienceweek

QUANTUM ENIGMA. Physics Encounters Consciousness. Bruce Rosenblum and Fred Kuttner. Oxford University Press, New York, 2006. Hardback: 221 pp., illus. $29.95. ISBN 019517559X. More information at: http://www.amazon.com/exec/obidos/ASIN/019517559X/scienceweek

Special Note: A New Book by the Editor of ScienceWeek: ------------------------------------------------------

JUNK SCIENCE. How Politicians, Corporations, and Other Hucksters Betray Us. Dan Agin. Thomas Dunne Books/St. Martin's Press, New York, 2006. Hardback: 336 pp., $24.95. ISBN 0312352417. More information at: http://www.amazon.com/exec/obidos/ASIN/0312352417/scienceweek

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1. ASTRONOMY: ON GALACTIC INTERSTELLAR MOLECULAR GAS

The following points are made by Mark Morris (Science 2006 314:70):

1) The central region of our Galaxy contains a massive concentration of interstellar molecular gas that has been surveyed many times. The most often used probe of this gas is emission from the most abundant molecule that can easily be observed, carbon monoxide. New work (1) extends earlier surveys of CO to a substantially larger region than had previously been mapped. The initial results reveal surprising new structures: giant molecular loops located a few thousand light-years from the galactic center and extending almost a thousand light-years above the galactic plane (2).

2) Interstellar gas in our Galaxy -- or in any equilibrated and undisturbed spiral galaxy -- resides in a relatively thin rotating disk. It is confined to this disk by the gravitational force of the stars, which are at their densest in the central plane of the galactic disk. The thickness of the gas disk is determined by the degree to which it has been stirred by supernovae and galactic shocks (both of which generate large-scale turbulence) and by the Galaxy's magnetic field, which prevents the gas from collapsing into a much thinner layer. The magnetic field in the disk of the Galaxy is predominantly parallel to the disk, supporting the gas against the largely "vertical" gravitational field (here, "vertical" means perpendicular to the disk).

3) In 1966, however, Parker (3) pointed out that this configuration is not stable: Any vertical indentation in the magnetic field on a sufficiently large scale will provide a "pool" into which interstellar gas will sink as it slides down the tipped field lines in response to gravity. As gas is unloaded from the higher lying sections of the field lines, the field becomes increasingly buoyant and thus rises there (4). At the same time, as the pooled section gathers mass, it will sink toward the galactic midplane, deforming the field more, accelerating the flow of gas into it. As the resulting gas concentrations become denser, the gas cools relatively quickly, creating dense molecular clouds or cloud complexes via the Jeans instability (5). Because star formation in our Galaxy takes place primarily in molecular clouds, this combined Parker-Jeans instability might play an important role in fostering much of the star formation.

4) The Parker instability is well established among theorists and operates in the Sun, playing a role in the generation of arches, loops, and prominences, and possibly in the production of sunspots. Yet it has not been definitively observed to be operating on galactic scales for want of a good diagnostic. Fukui et al (1) argue that the giant molecular loops they observe have resulted from the Parker instability. The radial velocity field that they infer from the Doppler shifts of the CO emission indicates that these are indeed loops, rather than shells, and that there is a flow of material along the loops, as is anticipated by the theory. Also, the size of the galactic loops is in the range expected for the Parker instability. This raises the possibility of directly confirming this phenomenon on a galactic scale -- a scale larger by 12 orders of magnitude than the magnetic loops seen on the Sun.

References (abridged):

1. Y. Fukui et al., Science 314, 106 (2006)

2. For comparison, our distance from the galactic center is ~25,000 light-years.

3. E. N. Parker, Astrophys. J. 145, 811 (1966)

4. The buoyancy of the magnetic loop is augmented by the pressure of the "gas" of galactic cosmic rays. These essentially light-speed particles inflate the region encompassed by the loop.

5. B. G. Elmegreen, Astrophys. J. 253, 634 (1982)

Science http://www.sciencemag.org

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2. CHEMISTRY: ON BORON COMPOUNDS

The following points are made by Todd B. Marder (Science 2006 314:69):

1) Boron compounds are widely used in synthetic chemistry, but almost all of them are electrophiles (electron acceptors); the few reactions in which boron behaves as a nucleophile (electron donor) are generally catalyzed by a metal. But this situation is about to change. New work (1) reports the synthesis and characterization of a boron compound in which the boron center is nucleophilic. This compound may find application in many different areas of synthetic chemistry.

2) Synthetic chemistry is dominated by two types of reactions: nucleophilic attack and electrophilic attack. Nucleophiles (Lewis bases) possess a filled molecular orbital (an accessible electron pair), which can be stabilized by bonding to an empty orbital on another molecule, causing them to "attack" the other molecule. In contrast, electrophiles (Lewis acids) possess empty low-energy orbitals, which can accept a pair of electrons from a nucleophile. Nucleophilic attack is used to substitute one group for another in organic synthesis, as well as to synthesize many types of compounds from carbonyl-containing organics such as ketones, aldehydes, and esters. Likewise, many routes for attaching ligands to main-group and transition metals involve nucleophilic attack on the metal by the ligand.

3) Carbon compounds can be either nucleophilic or electrophilic. Examples of the former are organolithium compounds such as methyl lithium (CH3Li or MeLi) (2). Although there is a degree of covalency (and a complex cluster structure) in methyl lithium, it can nevertheless be considered to be a useful form of the carbanion, CH3-. Carbon electrophiles include alkyl halides (RX), electron-deficient, three-coordinate carbonium ions (R3C), which contain six electrons rather than the normal eight, and carbonyl compounds, wherein the carbon is the electrophilic site.

4) Boron is considerably more electropositive than carbon. Because boron is located immediately to the left of carbon in the periodic table, neutral, three-coordinate boranes are typically more stable than their isoelectronic carbonium ion analogs. Boranes are electrophilic and represent an important class of Lewis acids. For example, the boron center in boranes can bind to the oxygen atom (electron pair donor) in carbonyl compounds such as ketones, making the carbon center more susceptible to nucleophilic attack. The chemistry of boron (at least in its three-coordinate compounds), although rich, exciting, and extremely important in organic synthesis (3,4), is thus dominated by its electrophilic character, and there are few cases (often metal-promoted) in which the boron atom serves as a nucleophile. For example, transition metal-catalyzed additions of (RO)2B-B(OR)2 to certain C=C and C=O double bonds (diboration) (5) could be viewed as a process in which one boron is transferred as a nucleophile and the other as an electrophile. The metal (such as rhodium or platinum) cleaves the B-B bond, facilitating the sequential transfer of the two boryl units to the two ends of the double bond.(5)

References (abridged):

1. Y. Segawa, M. Yamashita, K. Nozaki, Science 314, 113 (2006)

2. M. J. Lusch, W. V. Phillips, R. F. Sieloff, G. S. Nomura, H. O. House, Organic Syntheses, Coll. 7, 346 (1990)

3. H. C. Brown, Boranes in Organic Chemistry (Cornell Univ. Press, Ithaca, 1972)

4. M. Zaidlewicz, H. C. Brown, Organic Syntheses via Boranes, Volume 2, Recent Developments (Aldrich Chemical Co., Milwaukee, 2001)

5. N. J. Bell et al., Chem. Commun. 1854 (2004)

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

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3. GENETICS: ON JUNK DNA AND RNA AS AN EVOLUTIONARY FORCE

The following points are made by C. Biémont and C. Vieira (Nature 2006 443:521):

1) Transposable elements (TEs) -- commonly called "jumping genes" -- are stretches of DNA that move around the genome of a cell, and the genomes of many higher organisms are cluttered with numerous copies of these enigmatic elements. They were discovered by Barbara McClintock in the 1950s, but it has taken half a century to begin to understand how they act and the effects they can have. It is emerging that these elements have had a significant influence on the evolution of genomes, particularly by controlling gene activity.

2) The elements contain in their sequence all the instructions needed to cut themselves out of their host DNA and splice themselves into another spot. But they are not always benign "junk" DNA -- they can insert into genes or gene regulatory elements, potentially disrupting the gene's function, and they can trigger chromosome rearrangements. So, even though most copies are selectively neutral and not in themselves damaging, they have long been considered as predominantly harmful to their hosts, as they can contribute to the appearance of mutations, some of which can result in disease.

3) But TEs do not always have adverse effects, and their mutational activities contribute to the genetic diversity of the organism. Indeed, some TEs have been domesticated by their host genome, acting as genes or gene regulatory elements, and as a result constitute a source of genetic innovation for the organism (1,2). Progress in understanding how these elements are regulated is bringing an appreciation of how an individual's environment can affect the expression of their genetic complement to produce their own particular characteristics (phenotypes), such as physical appearance, behavior, susceptibility to disease and even neuronal function.

4) Transposable elements are scattered throughout the genomes of many plants and animals, and can form a large proportion of the genome size. There are two main classes of TE: DNA transposons, which act through a DNA intermediate and multiply by using the host cell's replication machinery, and retrotransposons, which act through an RNA intermediate. Retrotransposons are further subdivided into those that have "long terminal repeats" at their ends (LTR retrotransposons) and those that do not (non-LTR retrotransposons). In addition, TEs with composite structures are continually being discovered, illustrating the enormous flexibility of these elements. For example, DNA transposon-like elements called helitron rolling-circle elements were recently found to be responsible for copying various gene segments into new locations in the maize genome, generating a huge diversity among individual maize plants (3-5).

References (abridged):

1. Brandt, J. et al. Gene 345, 101-111 (2005)

2. Medstrand, P. et al. Cytogenet. Genome Res. 110, 342-352 (2005)

3. Messing, J. & Dooner, H. K. Curr. Opin. Plant Biol. 9, 157-163 (2006)

4. Nishihara, H. et al. Genome Res. 16, 864-874 (2006)

5. Peaston, A. et al. Dev. Cell 7, 597-606 (2004)

Nature http://www.nature.com/nature

ScienceWeek http://scienceweek.com

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4. ATOMIC PHYSICS: ON QUANTUM TELEPORTATION

The following points are made by M. Lukin and M. Eisaman (Nature 2006 443:512):

1) A decade ago, the idea of teleportation was mere science fiction. But following the pioneering proposal of Bennett et al (1), quantum teleportation has emerged as an important tool in quantum-information science. Quantum teleportation involves the disembodied transfer of a system's most basic feature -- its quantum state -- from one location to another. The first experimental demonstration of the phenomenon was the transfer of a quantum state of light onto another beam of light (2). More recently, the teleportation of a state between two single, trapped ions was demonstrated (3,4). New work (5) describes the transfer of a quantum state from a light pulse onto a collection of atoms, thereby achieving teleportation between two objects of different nature for the first time.

2) Quantum states are elusive objects, as they are easily destroyed by measurements. When only one copy of a state exists, only one measurement can be made. This single measurement cannot, even in principle, reveal complete information about the state. For this reason, quantum states cannot be copied, and one cannot transmit a quantum state by performing a direct measurement and then using a classical communication channel.

3) Quantum teleportation circumvents these problems by using correlations between physically separated quantum states -- the phenomenon known as quantum entanglement -- to transmit quantum states between distant locations. To teleport a quantum state between a sender (typically called Alice) and a receiver (typically called Bob), each party must possess half of a pair of entangled states. First, Alice performs a joint measurement, called a Bell measurement, on both the quantum state she intends to send and her half of the entangled pair. She sends the result to Bob over a classical transmission line (a telephone will do). Bob can use his half of the entangled pair to reconstruct an exact copy of the initial state from the classically transmitted information.

4) The interest in quantum teleportation is not purely academic. The technique is a crucial element in so-called quantum repeaters, systems that can be used for long-distance quantum communication and secure quantum cryptography. Teleportation is especially helpful when direct communication between two remote locations is not possible because of losses in the connecting channel. Recently, the phenomenon has been shown to have an important role in fault-tolerant quantum computation, an error-correction mechanism for a noisy quantum computer. Quantum teleportation is, in fact, likely to be an indispensable part of any robust quantum-information system.

References (abridged):

1. Bennett, C. H. et al. Phys. Rev. Lett. 70, 1895-1899 (1993)

2. Bouwmeester, D. et al. Nature 390, 575-579 (1997)

3. Barrett, M. D. et al. Nature 429, 737-739 (2004)

4. Riebe, M. et al. Nature 429, 734-737 (2004)

5. Sherson, J. F. et al. Nature 443, 557-560 (2006)

Nature http://www.nature.com/nature

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