Ontological realism, concepts and classification in molecular biology: Development and application of the gene ontology

Purpose – The purpose of this article is to evaluate the development and use of the gene ontology (GO), a scientific vocabulary widely used in molecular biology databases, with particular reference to the relation between the theoretical basis of the GO, and the pragmatics of its application. Design/methodology/approach – The study uses a combination of bibliometric analysis, content analysis and discourse analysis. These analyses focus on details of the ways in which the terms of the ontology are amended and deleted, and in which they are applied by users. Findings – Although the GO is explicitly based on an objective realist epistemology, a considerable extent of subjectivity and social factors are evident in its development and use. It is concluded that bio-ontologies could beneficially be extended to be pluralist, while remaining objective, taking a view of concepts closer to that of more traditional controlled vocabularies. Originality/value – This is one of very few studies which evaluate the development of a formal ontology in relation to its conceptual foundations, and the first to consider the GO in this way

No planet for HD 166435

The G0V star HD166435 has been observed by the fiber-fed spectrograph ELODIE as one of the targets in the large extra-solar planet survey that we are conducting at the Observatory of Haute-Provence. We detected coherent, low-amplitude, radial-velocity variations with a period of 3.7987days, suggesting a possible close-in planetary companion. Subsequently, we initiated a series of high-precision photometric observations to search for possible planetary transits and an additional series of CaII H and K observations to measure the level of surface magnetic activity and to look for possible rotational modulation. Surprisingly, we found the star to be photometrically variable and magnetically active. A detailed study of the phase stability of the radial-velocity signal revealed that the radial-velocity variability remains coherent only for durations of about 30days. Analysis of the time variation of the spectroscopic line profiles using line bisectors revealed a correlation between radial velocity and line-bisector orientation. All of these observations, along with a one-quarter cycle phase shift between the photometric and the radial-velocity variationss, are well explained by the presence of dark photospheric spots on HD166435. We conclude that the radial-velocity variations are not due to gravitational interaction with an orbiting planet but, instead, originate from line-profile changes stemming from star spots on the surface of the star. The quasi-coherence of the radial-velocity signal over more than two years, which allowed a fair fit with a binary model, makes the stability of this star unusual among other active stars. It suggests a stable magnetic field orientation where spots are always generated at about the same location on the surface of the star.Comment: 9 pages, 8 figures, Accepted for publication in A&

Hubble Space Telescope times-series photometry of the planetary transit of HD189733: no moon, no rings, starspots

We monitored three transits of the giant gas planet around the nearby K dwarf HD 189733 with the ACS camera on the Hubble Space Telescope. The resulting very-high accuracy lightcurve (signal-to-noise ratio near 15000 on individual measurements, 35000 on 10-minute averages) allows a direct geometric measurement of the orbital inclination, radius ratio and scale of the system: i = 85.68 +- 0.04, Rpl/R*=0.1572 +- 0.0004, a/R*=8.92 +- 0.09. We derive improved values for the stellar and planetary radius, R*=0.755+- 0.011 Rsol, Rpl=1.154 +- 0.017 RJ, and the transit ephemerides, Ttr=2453931.12048 +- 0.00002 + n 2.218581 +- 0.000002$. The HST data also reveal clear evidence of the planet occulting spots on the surface of the star. At least one large spot complex (>80000 km) is required to explain the observed flux residuals and their colour evolution. This feature is compatible in amplitude and phase with the variability observed simultaneously from the ground. No evidence for satellites or rings around HD 189733b is seen in the HST lightcurve. This allows us to exlude with a high probability the presence of Earth-sized moons and Saturn-type debris rings around this planet. The timing of the three transits sampled is stable to the level of a few seconds, excluding a massive second planet in outer 2:1 resonance.Comment: revised version. Significant updates and new figures; to appear in Astronomy and Astrophysic

The HARPS search for southern extra-solar planets. XXIV. Companions to HD 85390, HD 90156 and HD 103197: A Neptune analogue and two intermediate mass planets

We report the detection of three new extrasolar planets orbiting the solar type stars HD 85390, HD 90156 and HD 103197 with the HARPS spectrograph mounted on the ESO 3.6-m telescope at La Silla observatory. HD 85390 has a planetary companion with a projected intermediate mass (42.0 Earth masses) on a 788-day orbit (a=1.52 AU) with an eccentricity of 0.41, for which there is no analogue in the solar system. A drift in the data indicates the presence of another companion on a long period orbit, which is however not covered by our measurements. HD 90156 is orbited by a warm Neptune analogue with a minimum mass of 17.98 Earth masses (1.05 Neptune masses), a period of 49.8 days (a=0.25 AU) and an eccentricity of 0.31. HD 103197 has an intermediate mass planet on a circular orbit (P=47.8 d, Msini=31.2 Earth masses). We discuss the formation of planets of intermediate mass (about 30-100 Earth masses) which should be rare inside a few AU according to core accretion formation models.Comment: 9 pages, 5 figures. Accepted to A&

DE0823−-49 is a juvenile binary brown dwarf at 20.7 pc

Astrometric monitoring of the nearby early-L dwarf DE0823$-$49 has revealed a low-mass companion in a 248-day orbit that was announced in an earlier work. Here, we present new astrometric and spectroscopic observations that allow us to characterise the system in detail. The optical spectrum shows LiI-absorption indicative of a young age and/or substellar mass for the primary component. The near-infrared spectrum is best reproduced by a binary system of brown dwarfs with spectral types of L1.5 $+$ L5.5 and effective temperatures of $2150\pm100$ K and $1670\pm140$ K. To conform with the photocentric orbit size measured with astrometry and the current understanding of substellar evolution, the system must have an age in the 80--500 Myr range. Evolutionary models predict component masses in the ranges of $M_1\simeq0.028-0.063\,M_\odot$ and $M_2\simeq0.018-0.045\,M_\odot$ with a mass ratio of $q\simeq0.64-0.74$. Multi-epoch radial velocity measurements unambiguously establish the three-dimensional orbit of the system and allow us to investigate its kinematic properties. DE0823$-$49 emerges as a rare example of a nearby brown dwarf binary with orbit, component properties, and age that are characterised well. It is a juvenile resident of the solar neighbourhood, but does not appear to belong to a known young association or moving group.Comment: 9 pages, 11 figures. Accepted for publication in A&

The HARPS search for southern extra-solar planets. XXVII. Up to seven planets orbiting HD 10180: probing the architecture of low-mass planetary systems

Context. Low-mass extrasolar planets are presently being discovered at an increased pace by radial velocity and transit surveys, opening a new window on planetary systems. Aims. We are conducting a high-precision radial velocity survey with the HARPS spectrograph which aims at characterizing the population of ice giants and super-Earths around nearby solar-type stars. This will lead to a better understanding of their formation and evolution, and yield a global picture of planetary systems from gas giants down to telluric planets. Methods. Progress has been possible in this field thanks in particular to the sub-m/s radial velocity precision achieved by HARPS. We present here new high-quality measurements from this instrument. Results. We report the discovery of a planetary system comprising at least five Neptune-like planets with minimum masses ranging from 12 to 25 M_Earth, orbiting the solar-type star HD 10180 at separations between 0.06 and 1.4 AU. A sixth radial velocity signal is present at a longer period, probably due to a 65-M_Earth object. Moreover, another body with a minimum mass as low as 1.4 M_Earth may be present at 0.02 AU from the star. This is the most populated exoplanetary system known to date. The planets are in a dense but still well-separated configuration, with significant secular interactions. Some of the orbital period ratios are fairly close to integer or half-integer values, but the system does not exhibit any mean-motion resonances. General relativity effects and tidal dissipation play an important role to stabilize the innermost planet and the system as a whole. Numerical integrations show long-term dynamical stability provided true masses are within a factor ~3 from minimum masses. We further note that several low-mass planetary systems exhibit a rather "packed" orbital architecture with little or no space left for additional planets. (Abridged)Comment: 20 pages, 15 figures, accepted for publication in A&

The HARPS search for southern extra-solar planets. VI. A Neptune-mass planet around the nearby M dwarf Gl 581

We report the discovery of a Neptune-mass planet around Gl 581 (M3V, M = 0.31 Msol), based on precise Doppler measurements with the HARPS spectrograph at La Silla Observatory. The radial velocities reveal a circular orbit of period P = 5.366 days and semi-amplitude K1 = 13.2 m/s. The resulting minimum mass of the planet (m2 sin i) is only 0.052 Mjup = 0.97 Mnep = 16.6 Mearth making Gl 581b one of the lightest extra-solar planet known to date. The Gl 581 planetary system is only the third centered on an M dwarf, joining the Gl 876 three-planet system and the lone planet around Gl 436. Its discovery reinforces the emerging tendency of such planets to be of low mass, and found at short orbital periods. The statistical properties of the planets orbiting M dwarfs do not seem to match a simple mass scaling of their counterparts around solar-type stars.Comment: letter submitted to A&