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ScienceWeek
SCIENCEWEEK
January 5, 2007
Vol. 11 - Number 1
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For the real amazement, if you wish to be amazed, is this process: You start out as a single cell derived from the coupling of a sperm and an egg; this divides in two, then four, then eight, and so on, and at a certain stage there emerges a single cell which has as all its progeny the human brain. The mere existence of such a cell should be one of the great astonishments of the Earth. People ought to be walking around all day, all through their waking hours calling to each other in endless wonderment, talking of nothing except that cell.
-- Lewis Thomas (1913-1993)
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Contents (full text below):
1. Science Policy: On Journals and Fabricated Data 2. Human Evolution: On Neanderthal DNA 3. Climatology: On Shrinking Ice 4. Paleontology: A New Fossil Fish 5. Applied Physics: On Microwave Invisibility 6. Medical Biology: On the Complex Biology of Ageing 7. Neurobiology: On Auditory Fidelity
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Also Noted:
Complex Engineered Systems. Science Meets Technology. D. Braha, A. A. Minai, and Y. Bar-Yam, Eds. Springer, Berlin, 2006. Hardback: 395 pp., illus. ISBN 3540328319. More information at:
http://www.amazon.com/exec/obidos/ASIN/3540328319/scienceweek
Digital Communications Using Chaos and Nonlinear Dynamics. Lawrence E. Larson, Jia-Ming Liu, and Lev S. Tsimring, Eds. Springer, New York, 2006. Hardback: 396 pp., illus. ISBN 0387297871. More information at:
http://www.amazon.com/exec/obidos/ASIN/0387297871/scienceweek
Information and Self-Organization. A Macroscopic Approach to Complex Systems. Hermann Haken. Springer, Berlin, 2006. Hardback: 271 pp., illus. ISBN 3540330216. More information at:
http://www.amazon.com/exec/obidos/ASIN/3540330216/scienceweek
Dark Side of the Moon. The Magnificent Madness of the American Lunar Quest. Gerard J. DeGroot. New York University Press, New York, 2006. Hardback: 335 pp. ISBN 0814719953. More information at:
http://www.amazon.com/exec/obidos/ASIN/0814719953/scienceweek
Meals to Come. A History of the Future of Food. Warren Belasco. University of California Press, Berkeley, 2006. Paperback: 373 pp., illus. $15. ISBN 0520250354. More information at:
http://www.amazon.com/exec/obidos/ASIN/0520250354/scienceweek
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Search or browse thousands of ScienceWeek reports at the ScienceWeek website:
http://scienceweek.com
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1. SCIENCE POLICY: ON JOURNALS AND FABRICATED DATA
The following points are made by Jennifer Couzin (Science 2006 314:1853):
1) One year ago, as the journal SCIENCE was assembling its 2005 Breakthrough of the Year issue, the need for a last-minute change became uncomfortably clear. A shadow was creeping across one of this journal's landmark papers, in which a team of South Korean and American researchers, led by Woo Suk Hwang at Seoul National University, claimed to have created the first-ever human embryonic stem cell lines that matched the DNA of patients. After anonymous allegations of irregularities in that paper appeared on a Korean Web site, South Korean authorities launched an investigation. As the story unfolded, SCIENCE'S news editors hastily pulled an item about the Hwang achievements from the issue's roster of runners-up.
2) Today, the fallout from the Hwang case is plain. Multiple inquiries discredited two papers Hwang published in SCIENCE in 2004 and 2005, which claimed some of the greatest accomplishments to date with human embryonic stem cells. The papers were retracted. But the scientific fraud, one of the most audacious ever committed, shattered the trust of many researchers and members of the public in scientific journals' ability to catch instances of deliberate deception.
3) As it turned out, the Hwang debacle marked the beginning of a bad year for honest science. Incidents of publication fraud, if not on the rise, are garnering more attention, and the review process is under scrutiny. In June, European investigators reported that the bulk of papers by Jon Sudboe, formerly a cancer researcher at the Norwegian Radium Hospital in Oslo, contained bogus data. Those included two articles in THE NEW ENGLAND JOURNAL OF MEDICINE that described a new way of identifying people at high risk of oral cancer, a strategy that many clinicians were keen to apply to patients. In another case, Eric Poehlman, formerly a menopause and obesity researcher at the University of Vermont in Burlington, garnered perhaps the most dubious distinction of all: He became the first researcher in the United States to go to jail for scientific misconduct unrelated to patient deaths.
4) The Hwang case, however, was unique for its combustible mix of startling achievements in a high-profile field and publication in a high-visibility journal. Manipulated images, purportedly of distinct stem cells matched to patients but in fact showing cells drawn from fertilized embryos, handily fooled outside reviewers and Science's own editors. "The reporting of scientific results is based on trust," wrote Editor-in-Chief Donald Kennedy in a January 2006 editorial explaining why journals are not designed to catch fraud. It's a comment echoed often by journal editors facing the nightmare of faked data in their own pages. But the shock of the Hwang deception, along with other recent fraud cases, is jolting journals into a new reality. Five scientists and a top editor of Nature examined Science's handling of the Hwang papers, at the journal's request. Their report, published on Science's Web site earlier this month (www.sciencemag.org/sciext/hwang2005), concluded that operating in an atmosphere of trust is no longer sufficient. "Science must institutionalize a healthy level of concern in dealing with papers," the group wrote. It recommended "substantially stricter" requirements for reporting primary data and a risk assessment for accepted papers. Science and some other journals are also beginning to scrutinize images in certain papers, in an effort to catch any that have been manipulated.
Science http://www.sciencemag.org
ScienceWeek http://scienceweek.com
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2. HUMAN EVOLUTION: ON NEANDERTHAL DNA
The following points are made by SCIENCE News Staff (Science 2006 314:1850):
1) This year (2006), on the 150th anniversary of the discovery of the Neandertal type specimen, researchers in Europe and the United States transformed the study of this ancient human by sequencing more than 1 million bases of Neandertal DNA. In November, two groups, one decoding 65,000 Neandertal bases and the other a million bases, showed that researchers can now find sequence changes between modern and ancient humans, differences that may reveal key steps in our evolution. The studies concluded that Neandertals diverged from our own ancestors at least 450,000 years ago -- approximately the time suggested by fossil and mitochondrial DNA studies. One group's data also suggest that Neandertals and modern humans may have interbred. In the works are a very rough draft of the complete Neandertal genome sequence and, as more fossils become available to sequencers, the development of bacterial libraries containing DNA from several Neandertals.
2) This breakthrough owes a large debt to earlier sequencing feats that demonstrated the potential of a new approach called "metagenomics" for deciphering ancient DNA, both human and nonhuman, and of faster sequencing technologies. For metagenomics, a technique developed for assessing microbial diversity, all the DNA in a sample is sequenced, and then sophisticated computer programs pull out only the target DNA based on its similarity to the sequence of a closely related extant organism. In January 2006, researchers combined metagenomics with a new rapid sequencing technique called "pyrosequencing", which uses pulses of light to read the sequence of thousands of bases at once, to get a whopping 13 million bases from a 27,000-year-old mammoth. The same sample also yielded another 15 million bases from bacteria, fungi, viruses, soil microbes, and plants -- DNA that will provide clues about this giant mammal's environment. With those two advances, ancient DNA sequencing is off and running.
Science http://www.sciencemag.org
ScienceWeek http://scienceweek.com
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3. CLIMATOLOGY: ON SHRINKING ICE
The following points are made by SCIENCE News Staff (Science 2006 314:1850):
1) Glaciologists nailed down an unsettling observation this year: The world's two great ice sheets--covering Greenland and Antarctica -- are indeed losing ice to the oceans, and losing it at an accelerating pace. Researchers don't understand why the massive ice sheets are proving so sensitive to an as-yet-modest warming of air and ocean water. The future of the ice sheets is still rife with uncertainty, but if the unexpectedly rapid shrinkage continues, low-lying coasts around the world --including New Orleans, South Florida, and much of Bangladesh --could face inundation within a couple of centuries rather than millennia.
2) This disturbing breakthrough rests on decades of measurements by airborne laser altimeters and orbiting radars, and more recently by a pair of satellites that measure ice mass directly by its gravitational pull. Different techniques and even different analyses of the same data disagree about just how much ice volume is changing. All of them, however, now show that both Greenland and Antarctica have been losing ice over the past 5 to 10 years. In the north, Greenland is shedding at least 100 gigatons each year. In the south, the figure is less certain but lies in the range of tens of gigatons per year or more.
3) Current ice sheet losses aren't raising sea level faster than 0.1 meter per century, but researchers fear that the rate could rise to a meter per century or more in the near future. As recently as 5 years ago, they assumed that global warming would simply melt more and more ice from the ice sheets, as it is melting mountain glaciers. But it turns out the ice isn't just melting faster, it is moving faster. Radar mapping shows that in recent years, glaciers carrying ice away from the sheets have sped up by as much as 100%. In West Antarctica, warming ocean waters seem to have attacked the floating tongues of ice that hold back the ice sheet's outlet glaciers. Around southern Greenland, something else seems to be quickening the pace of outlet glaciers, perhaps lubrication by increasing amounts of surface meltwater seeping to a glacier's base. Now glaciologists are wondering how the next chapter will play out. Will the relatively strong warming around the ice continue, or will it be weakened by natural variations of climate? Will the ice sheets adjust to the new warmth by eventually slowing their ice loss? And will more glaciers succumb to the spreading warmth?
Science http://www.sciencemag.org
ScienceWeek http://scienceweek.com
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4. PALEONTOLOGY: A NEW FOSSIL FISH
The following points are made by SCIENCE News Staff (Science 2006 314:1850):
1) Paleontologists made a major splash this year (2006) with the debut of a fossil fish that long ago took a deep breath and made some tentative but ultimately far-reaching steps onto land. With its sturdy, jointed fins, the 375-million-year-old specimen fills an evolutionary gap and provides a glimpse of the features that helped later creatures conquer the continents.
2) All limbed vertebrates, known as tetrapods, evolved from lobe-finned fishes some 370 million to 360 million years ago. Many of these sophisticated fishes had skeletons with modifications, such as enlarged bones in their fins, that would ultimately prove useful for weight-bearing limbs. The new species is the most tetrapodlike fish yet discovered.
3) Three specimens were found during a 2004 field expedition to Ellesmere Island in the far north of Nunavut, Canada. They were named Tiktaalik roseae for "large freshwater fish" in the Inuktitut language and a donor who helped fund the expedition, respectively. With fins and scales, the 3-meter-long Tiktaalik is clearly a fish. It had a flat head with eyes on top and lived in shallow streams. What makes Tiktaalik unique among fish is that each of the front fins has a wrist and elbow, providing flexible motion. Also unlike other fish, Tiktaalik sported a neck -- the oldest one known in the fossil record -- and could move its head. Achieving that flexibility required losing a bone called the operculum, which modern fish use to pump water over their gills. Tiktaalik still had well-developed gills, and it probably used its neck and stout limbs to push its head above water to inhale.
4) Another feature that makes Tiktaalik close kin to tetrapods is its robust, overlapping ribs. Although their function isn't completely clear, researchers think they could have helped support its body out of water and aided in breathing. Forays onto land would have offered an escape from sharks and other predators, as well as insects to eat. Tiktaalik isn't a perfect tetrapod, of course -- among other traits, it lacks fingers and toes -- but it was certainly a big step in the right direction.
Science http://www.sciencemag.org
ScienceWeek http://scienceweek.com
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5. APPLIED PHYSICS: ON MICROWAVE INVISIBILITY
The following points are made by SCIENCE News Staff (Science 2006 314:1850):
1) Science veered toward science fiction this year (2006) as physicists cobbled together the first rudimentary invisibility cloak. Although far from perfect -- the ring-shaped cloak is invisible only when viewed in microwaves of a certain wavelength traveling parallel to the plane of the ring -- the device could usher in a potentially revolutionary approach to manipulating electromagnetic waves.
2) The disappearing act began in May, when two independent analyses predicted that it should be possible to ferry electromagnetic waves around an object to hide it. All that was needed was a properly designed shell of "metamaterial", an assemblage of tiny metallic rods and c-shaped rings. The waves churn the electrons in the rods and rings, and the sloshing affects the propagation of the waves. Both analyses specified how to sculpt the properties of the metamaterial and left it to experimenters to design the materials to meet those specs.
3) In October, the team that made one of the predictions did just that -- almost. Physicists at Duke University built a ring instead of an all-concealing sphere. They made some approximations that rendered the cloak slightly reflective. Still, the thing whisked microwaves around a plug of copper, proving that the method works. Cloaks for visible light are likely years off, as researchers must figure out how to make metamaterials that work at such short wavelengths. Even then, the cloak would be a bust for spying because it would be impossible to see out of it.
4) The real breakthrough may lie in the theoretical tools used to make the cloak. In such "transformation optics", researchers imagine warping empty space to bend the path of electromagnetic waves. A mathematical transformation then tells them how to mimic the bending by filling unwarped space with a material whose optical properties vary from point to point. The technique could be used to design antennas, shields, and myriad other devices.
Science http://www.sciencemag.org
ScienceWeek http://scienceweek.com
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6. MEDICAL BIOLOGY: ON THE COMPLEX BIOLOGY OF AGEING
The following points are made by Tom Kirkwood (Nature 2006 444:1015):
1) Contrary to general expectation, human life expectancy in developed countries has not bumped into a ceiling, but continues to increase by around two years per decade (1) -- or five hours per day. The reason previous forecasts proved wrong is simple. It used to be assumed that the ageing process was programmed, that some inner clock set a limit to life. But advances in the understanding of evolutionary mechanisms, and the experimental dissection of the genetics of ageing and longevity, reveal that this is not so (2). Instead, the genetic control of longevity comes through regulation of the body's survival mechanisms --those essential maintenance and repair processes that slow the build-up of the molecular and cellular faults that will eventually undo us.
2) The indirect nature of this genetic control probably explains why the heritability of human longevity -- the capacity for long life to run in families -- is only modest (3). More importantly, it explains the apparent malleability of the ageing process, revealed by the ongoing increase in life expectancy. If we can slow the onslaught of damage, or boost repair capacity, we can aspire to live longer, healthier lives without altering our genetic make-up. New work (4) reports a new genetic disorder in humans that causes accelerated ageing, and the analysis of a mouse model of this condition, yielding valuable insights into ageing.
3) The condition was initially observed in a 15-year-old boy who had unusual sensitivity to sunburn and an array of clinical signs of accelerated ageing in many organ systems. The spectrum of symptoms differed from previously recognized skin-sensitivity disorders such as xeroderma pigmentosum, although there was some overlap. For example, ultraviolet light normally induces a DNA repair process, called nucleotide-excision repair, to deal with any damage caused by this radiation, but in both these ageing disorders this response is almost completely absent. It turned out that the mutation responsible for the new condition severely affected an enzyme called XPF–ERCC1 endonuclease. This endonuclease is necessary for the repair of damage that distorts the DNA helix or the crosslinks between DNA strands. The disorder adds to a growing list of inherited "progeroid" syndromes -- many linked to DNA-repair defects -- that resemble, but do not exactly equate with, an accelerated process of normal ageing (5).
4) So what, if anything, does this tell us about the biology of normal ageing? In the human disorder, the XPF subunit of the XPF–ERCC1 endonuclease is mutated. But to probe this question, Niedernhofer et al (4) exploited already available mice that lack the ERCC1 subunit (Ercc1-/- mice). These animals show a pattern of accelerated degenerative changes very similar to those seen in the human patient, not only at the molecular and cellular level, but also in terms of organ and system functions. Comprehensive analysis of gene expression in the Ercc1-/- mice compared with normal controls revealed a broad spectrum of changes, with 1,675 genes showing significantly different expression in the mutant mice. These changes included a general decrease in the activity of hormonal pathways involved in the regulation of metabolism, such as growth hormone/IGF1 signalling, and increased activity in antioxidant and DNA repair pathways.
References (abridged):
1. Oeppen, J. & Vaupel, J. W. Science 296, 1029–1031 (2002).
2. Kirkwood, T. B. L. Cell 120, 437–447 (2005).
3. Finch, C. E. & Tanzi, R. E. Science 278, 407–411 (1997).
4. Niedernhofer, L. J. et al. Nature 444, 1038–1043 (2006).
5. Hasty, P., Campisi, J., Hoeijmakers, J., van Steeg, H. & Vijg, J. Science 299, 1355–1359 (2003).
Nature http://www.nature.com/nature
ScienceWeek http://scienceweek.com
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7. NEUROBIOLOGY: ON AUDITORY FIDELITY
The following points are made by Thomas D. Parsons (Nature 2006 444:1013):
1) Mammals react to sounds with exquisite temporal fidelity, a feat that is initiated by precise calcium-dependent signalling in the hair cells of the inner ear. Calcium is a common signalling molecule in the nervous system and elsewhere. New work (1) describes how researchers have identified an unexpected player in the auditory system. That player is a molecule called otoferlin, which has not previously been implicated as a calcium sensor for neurotransmitter release in nerve function.
2) A sensitive auditory system confers a tremendous evolutionary advantage, as it protects us from the things we fear most --those we cannot see. The ability to localize these potential dangers or communicate these possible threats depends on the precise timing of signals in the neural code that the brain ultimately perceives as sound. The basis of this temporal fidelity lies in the control of communication between the mechanosensory cell of the cochlea, the inner hair cell, and its downstream partner, the auditory nerve. The mechanical energy of acoustic waves causes minute displacements of sensory hair bundles extending from the cell. These deflections result in rapidly oscillating electrical potentials, which trigger calcium influx from outside the cell; that in turn prompts tiny subcellular organelles filled with a chemical messenger to dump their contents into a well-defined extracellular compartment, the synaptic cleft. This messenger, or neurotransmitter, excites a nearby, afferent nerve fibre, which elicits an all-or-none electrical response that propagates details of the acoustic stimulus to the brain.
3) The capacity of the auditory system to follow acoustic waves oscillating at several thousand times per second suggests that this calcium-dependent regulatory event may need to be as much as ten times more precise than signalling between most types of neuron. So how does the inner hair cell achieve such exquisite temporal fidelity in its release of neurotransmitter? Roux et al (1) suggest that the hair cell has evolved a unique calcium-sensing molecule, otoferlin, for controlling neurotransmitter release. The action of otoferlin allows a hair cell's specialized synapses -- ribbon synapses, a specific class of afferent synapse common to sensory systems -- to meet the requirements of hearing.
4) Both mice and humans suffer from an inherited form of deafness called DFNB9. Defects in otoferlin are responsible, and Roux and colleagues hypothesized that otoferlin might be involved in the correct operation of the synapse between the hair cell and the afferent nerve fibre. They found that, in mice, not only is otoferlin localized to the synaptic vesicles of inner hair cells, but that it also undergoes developmental changes in expression concurrent with the formation of ribbon synapses. Otoferlin also binds in a calcium-dependent manner to SNARE proteins, highly conserved molecules thought to be essential for the release of neurotransmitters and for other events requiring fusion of membranes.(2-5)
References (abridged):
1. Roux, I. et al. Cell 127, 277–289 (2006).
2. Chapman, E. R. Nature Rev. Mol. Cell Biol. 3, 498–508 (2002).
3. Sudhof, T. C. Annu. Rev. Neurosci. 27, 509–547 (2004).
4. Fernandez-Chacon, R. et al. Nature 410, 41–49 (2001).
5. Rhee, J. S. et al. Proc. Natl Acad. Sci. USA 102, 18664–18669 (2005).
Nature http://www.nature.com/nature
ScienceWeek http://scienceweek.com
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