Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Volume 465 Issue 7300, 17 June 2010

Scientists today are accustomed to having their performance assessed by numerical yardsticks, but are 'science metrics' as widely used as those being measured seem to think? In a collection of News Features and an Opinion piece we present the findings of a Nature readers' poll and survey of institutions around the world, examine the plethora of techniques now available, and what exactly they measure, and canvass the opinions of six researchers as to how metrics methodology can be improved. Picture credit: David Parkins.

Editorial

  • Editorial |

    Transparency, education and communication are key to ensuring that appropriate metrics are used to measure individual scientific achievement.

  • Editorial |

    Taking personal genetic testing into the classroom brings ethical and legal sensitivities to the fore.

  • Editorial |

    Celebrating the treasures of topological twists.

Research Highlights

Journal Club

News

Correction

News Feature

  • News Feature |

    Many researchers believe that quantitative metrics determine who gets hired and who gets promoted at their institutions. With an exclusive poll and interviews, Nature probes to what extent metrics are really used that way.

    • Alison Abbott
    • David Cyranoski
    • Richard Van Noorden
  • News Feature |

    Scientific performance indicators are proliferating — leading researchers to ask afresh what they are measuring and why. Richard Van Noorden surveys the rapidly evolving ecosystem.

    • Richard Van Noorden

Column

  • Column |

    Without effective public engagement, there will be no synthetic biology in Europe, says Colin Macilwain.

    • Colin Macilwain

Correspondence

Opinion

  • Opinion |

    Since the invention of the science citation index in the 1960s, quantitative measuring of the performance of researchers has become ever more prevalent, controversial and influential. Six commentators tell Nature what changes might ensure that individuals are assessed more fairly.

Books & Arts

  • Books & Arts |

    Frank Close enjoys a journalistic account of the sociology and politics of the search for the elusive particle named after physicist Peter Higgs, but cautions that the idea has deeper roots than its name implies.

    • Frank Close

News & Views

  • News & Views |

    The enzyme co-substrate S-adenosylmethionine is a potential source of two different free radicals, yet only one seemed to occur in nature. The discovery of an unusual enzyme reveals that both radicals can be formed.

    • Joan B. Broderick
  • News & Views |

    The use of stellar occultations to disclose unknown aspects of our Solar System is not new. But the latest such event to be reported involves an object that lies beyond the orbit of Neptune — and is a first.

    • Bruno Sicardy
  • News & Views |

    The groundwork for analysing the human microbiome — sequencing the collective genome of all our resident microorganisms — is now done. This work is of significance for understanding both human health and disease.

    • Liping Zhao
  • News & Views |

    Skyrmions are a special type of particle that has long been predicted to exist in many fields of physics. Direct images of these structures have now been made in a magnetic material.

    • Christian Pfleiderer
    • Achim Rosch
  • News & Views |

    Losses in biodiversity and the emergence of new infectious diseases are among the greatest threats to life on the planet. The declines in amphibian populations lie at the interface between these issues.

    • Andrew R. Blaustein
    • Pieter T. J. Johnson
  • News & Views |

    Toll receptors trigger immune responses through adaptor proteins and kinase enzymes. Structural studies reveal that hierarchical assembly of these proteins into a helical tower initiates downstream signalling events.

    • Steven A. Wasserman

Article

  • Article |

    Toll-like receptors (TLRs) are crucial to innate immunity. Activation of these proteins, and of receptors for the pro-inflammatory cytokines IL-1 and IL-18, leads to the recruitment of adaptor proteins such as MyD88. These in turn interact with further proteins such as IRAK2 and IRAK4. The crystal structure of the MyD88–IRAK2–IRAK4 death domain complex is now reported, explaining how these three proteins cooperate in TLR/IL-1R signalling.

    • Su-Chang Lin
    • Yu-Chih Lo
    • Hao Wu
  • Article |

    Translation elongation factor 2 (EF2) from archaea and eukaryotes contains a unique, post-translationally modified histidine residue called diphthamide, which is the target of diphtheria toxin. The biosynthesis of diphthamide involves three steps; here it is shown that the first step in the archaeon Pyrococcus horikoshii requires an unusual iron–sulphur-cluster enzyme, Dph2. It catalyses unprecedented chemistry.

    • Yang Zhang
    • Xuling Zhu
    • Hening Lin

Letter

  • Letter |

    KBO 55636 (2002 TX300) is one of the Kuiper belt objects — specifically, a member of the water-ice-rich Haumea KBO collisional family. Here, observations are reported of a multi-chord stellar occultation by KBO 55636. Calculations show that KBO 55636 is smaller than previously thought and, like its parent body, is highly reflective. The dynamical age implies either that it has an active resurfacing mechanism, or that fresh water-ice in the outer Solar System can persist for gigayear timescales.

    • J. L. Elliot
    • M. J. Person
    • A. Gilmore
  • Letter |

    Skyrmions are stable topological textures with particle-like properties — a mathematical concept that was originally used to describe nuclear particles but has since turned up at all scales. Last year, the presence of skyrmions in the magnetic compounds MnSi and Fe1−xCoxSi was confirmed with neutron-scattering experiments. Here, real-space images are presented of a two-dimensional skyrmion lattice in a thin film of the latter compound. The observed nanometre-scale spin topology might reveal new magneto-transport effects.

    • X. Z. Yu
    • Y. Onose
    • Y. Tokura
  • Letter |

    Over the past few decades, two techniques in particular have opened up new avenues for probing molecular processes: ultrafast spectroscopy and single-molecule detection. The two approaches have now been combined, enabling not only the observation but also the manipulation of vibrational wave-packet interference at ambient conditions. The technique could help to unravel details of molecular function and dynamics in systems as diverse as light-harvesting complexes, photoactive proteins and conjugated polymers.

    • Daan Brinks
    • Fernando D. Stefani
    • Niek F. van Hulst
  • Letter |

    Volcanic eruptions release a large amount of sulphur dioxide. This is oxidized to sulphate and can then form sulphate aerosol, which can affect the Earth's radiation balance. Here, past volcanic eruptions and atmospheric conditions are investigated by using sulphur and triple oxygen isotope measurements of atmospheric sulphate preserved in the rock record. The results show that seven eruption-related sulphate aerosol deposition events occurred in the mid-Cenozoic era in the northern High Plains of North America.

    • Huiming Bao
    • Shaocai Yu
    • Daniel Q. Tong

    Collection:

  • Letter |

    Rifting and magmatism are fundamental geological processes that shape our planet's surface, but the nature of the relationship between these processes has been controversial. Here a numerical model that explicitly accounts for the effects of earlier episodes of extension has been applied to compare magmatism generated at different locations during continental rifting. The findings show that the volume of rift-related magmatism generated depends not only on the mantle temperature but also on the rift history.

    • John J. Armitage
    • Jenny S. Collier
    • Tim A. Minshull
  • Letter |

    It is expected that closely related organisms are more likely to show similar ecological interactions than less related ones. But this has been tested only for certain types of interaction, and in a restricted set of taxa. Now interaction networks have been constructed for 116 different clades of related organisms, across the entire tree of life, and including all types of interaction. The results reveal significant conservatism across the board, including both specialist and generalist species.

    • José M. Gómez
    • Miguel Verdú
    • Francisco Perfectti
  • Letter |

    The need to maintain the structural and functional integrity of an evolving protein limits the range of acceptable amino-acid substitutions — but to what extent does this constrain how far homologous protein sequences can diverge? Here, sequence divergence data are used to explore the limits of protein evolution, and to conclude that ancient proteins are continuing to diverge from one another, indicating that the protein sequence universe is slowly expanding.

    • Inna S. Povolotskaya
    • Fyodor A. Kondrashov
  • Letter |

    To build a representation of the auditory world, neuronal circuits in neonatal rodents exhibit plasticity, allowing sensitivity to the pattern of sensory inputs. At this time, neurons construct a receptive field, which relies on a balance of excitatory and inhibitory inputs. Here, excitation and inhibition were found to be co-tuned upon hearing onset, but later an adjustment in the excitatory input strength occurred. Thus a fine adjustment in synaptic inputs, rather than more radical changes such as input pruning, may refine mature receptive fields.

    • Yujiao J. Sun
    • Guangying K. Wu
    • Li I. Zhang
  • Letter |

    To build a representation of the auditory world, neuronal circuits in neonatal rodents exhibit plasticity, allowing sensitivity to the pattern of sensory inputs. At this time, neurons construct a receptive field, which relies on a balance of excitatory and inhibitory inputs. Here, excitation and inhibition were found to be co-tuned upon hearing onset, but an experience-dependent refinement of inhibition later occurred. Thus a fine adjustment in synaptic inputs, rather than more radical changes such as input pruning, may refine mature receptive fields.

    • Anja L. Dorrn
    • Kexin Yuan
    • Robert C. Froemke
  • Letter |

    Glucocorticoids are widely used to treat patients with autoimmune diseases such as systemic lupus erythematosus (SLE), but many treatment regimens cannot maintain disease control in SLE patients. Here it is shown that the stimulation of plasmacytoid dendritic cells through toll-like receptors TLR7 and TLR9 can account for the reduced activity of glucocorticoids to inhibit the type I interferon pathway in SLE patients. Thus inhibitors of TLR7 and TLR9 signalling might prove to be effective corticosteroid-sparing drugs.

    • Cristiana Guiducci
    • Mei Gong
    • Franck J. Barrat
  • Letter |

    When cells are starved, the enzyme TOR is inhibited, inducing autophagy. In this process, autophagosomes sequester intracellular components and then fuse with lysosomes, producing autolysosomes in which cargo is degraded to regenerate nutrients. Now, a mechanism is revealed by which lysosomes are re-formed. When starvation conditions are prolonged, mTOR is re-activated; this attenuates autophagy and results in tubules and vesicles extruding from the autolysosome and maturing into functional lysosomes.

    • Li Yu
    • Christina K. McPhee
    • Michael J. Lenardo
  • Letter |

    Stop codons in messenger RNA define when a protein sequence has been completely synthesized; such codons bind release factors (RFs), which cause the newly made protein to be released. Structures of RFs alone and in combination with the ribosome have been reported, but the energetics of the reaction in the presence of codons had not been determined. Here, molecular dynamics simulations of 14 termination complexes are used to define how termination is achieved and how the RFs distinguish different sequences.

    • Johan Sund
    • Martin Andér
    • Johan Åqvist
  • Letter |

    Post-replicative repair (PRR) enables cells to bypass or overcome DNA damage during DNA replication. In eukaryotes, ubiquitylation of the replication clamp PCNA by components of the RAD6 pathway activates damage bypass. When this occurs has been debated. It is now shown that PRR can be postponed until much of the undamaged genome is replicated. Moreover, it seems that PRR occurs mainly by an error-prone process, with error-free bypass playing a minor role.

    • Yasukazu Daigaku
    • Adelina A. Davies
    • Helle D. Ulrich
  • Letter |

    Here, the early steps of activator-dependent transcription in yeast are examined by using cryo-electron microscopy to study the transcription activator Rap1 in complex with the general transcription factors TFIID and TFIIA and with yeast enhancer–promoter DNA. A model is proposed whereby interactions between Rap1 and TFIIA convey activating signals to TFIID. Moreover, a Rap1-dependent DNA loop is visualized between the enhancer and the promoter.

    • Gabor Papai
    • Manish K. Tripathi
    • Patrick Schultz
  • Letter |

    The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme that can phosphorylate or dephosphorylate isocitrate dehydrogenase (ICDH) to either inactivate or activate it in response to environmental changes. Now the structures of AceK and the AceK–ICDH complex have been solved, revealing the conformational changes that occur when AceK changes from a kinase to a phosphatase and vice versa.

    • Jimin Zheng
    • Zongchao Jia

Addendum

Erratum

Corrigendum

Careers Q&A

  • Careers Q&A |

    Pathologist Gustavo Ayala of Baylor College of Medicine in Houston, Texas, won a Creativity Award in May from the Prostate Cancer Foundation, Santa Monica, California, for his work on how nerve toxins affect tumours.

    • Virginia Gewin

Career Brief

Special Report

  • Special Report |

    In Britain, organizations award 'chartered status', which claims to validate a scientist's professional credentials. But what are such designations really worth? Nadya Anscombe reports.

    • Nadya Anscombe

Correction

Futures

  • Futures |

    A helping hand.

    • Julian Tang
Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing

Search

Quick links