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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&
DE082349 is a juvenile binary brown dwarf at 20.7 pc
Astrometric monitoring of the nearby early-L dwarf DE082349 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
K and 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 and
with a mass ratio of .
Multi-epoch radial velocity measurements unambiguously establish the
three-dimensional orbit of the system and allow us to investigate its kinematic
properties. DE082349 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&
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