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Science

Genomes of a Feather

Published Jun 19, 2008• 0 citations
Publisher

Abstract

The zebra finch (Taeniopygia guttata) belongs to the most populous bird order (the perching birds or Passeriformes) and is having its genome sequenced. Stapley et al. have created a linkage map of the zebra finch and compared it to that of the distantly related chicken (Galliformes). There was extensive synteny, or conservation of genes on the same chromosomes, indicative of a low amount of interchromosomal rearrangement between bird orders. However, a number of intrachromosomal differences were found between the zebra finch, reed warbler (another Passerine), and chicken, especially on the five macrochromosomes, suggesting that gene order is not conserved even among close relatives. A comparison of recombination rates reveals that chickens have high rates relative to other birds whereas reed warblers experience less recombination. — LMZ

DOI
10.1126/science.320.5883.1564c

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The zebra finch (Taeniopygia guttata) belongs to the most populous bird order (the perching birds or Passeriformes) and is having its genome sequenced. Stapley et al. have created a linkage map of the zebra finch and compared it to that of the distantly related chicken (Galliformes). There was extensive synteny, or conservation of genes on the same chromosomes, indicative of a low amount of interchromosomal rearrangement between bird orders. However, a number of intrachromosomal differences were found between the zebra finch, reed warbler (another Passerine), and chicken, especially on the five macrochromosomes, suggesting that gene order is not conserved even among close relatives. A comparison of recombination rates reveals that chickens have high rates relative to other birds whereas reed warblers experience less recombination. — LMZ
Micro-PK was explored in zebra finches (Taeniopygia guttata) to test the hypothesis of nondirectional REG randomness reduction during an alarm situation. A 15-s video clip of a crawling snake was presented to 80 participants and a REG's outcome during the presentation of the stimulus was analysed under three conditions: Bird Alone, Bird Plus Observer, and Observer Alone. One 200-bit trial was collected every quarter of a second during die presentation of the stimulus and the 5-min control period before die start of die disturbing stimulus, and the obtained cumulative chi-square deviation scores were analysed. The finding diat die scores during die stimulus period for die diree conditions belonged to the same population, their direction being die same when independently and globally analysed, togetiier with the nonsignificant difference with respect to their controls do not support die proposed hypotiiesis. However, an as yet undifferentiated psi observer effect is suggested by die global scores of die stimulus periods departing from chance while the scores of die corresponding controls did not, by die former's values surpassing die latter, and by die scores of die stimulus periods deviating from chance when die observer was present.
Devices known as random event generators (REGs) depend upon quantum effects, and although they are designed to produce a stream of purely random numbers, when people direct their attention to a single focus (not specifically intending to influence the REGs), a surprising reduction of randomness occurs. This nondirectional effect was demonstrated when the attention of an audience (size from one person to 3 billion people) was concentrated on a single matter, be it a human disaster, a personal growth workshop, a comedy show, a poltergeist event, or a praying service (Bierman, 1996; Blasband, 2000; Mason & Patterson, 2007; Nelson, 2001, 2003; Radin, 1997; Radin, Rebman, & Cross, 1996; Williams, 2010). When individual subjects were tested in an attempt to detect any effect of induced emotions on REG outcome, a reduction of randomness resulted during anger induction (Lumsden-Cook, 2005a), especially during anger and sadness dissipation (Lumsden-Cook, 2005b). One question we may ask ourselves is whether attention or emotional states by nonhumans would also affect the random functioning of REGs. Although the prospect for enhanced experimental manipulation would be higher with nonhuman subjects, work with them is very scant. The only two studies of which I am aware dealing with the potential influence on up-to-date, reliable REG devices used soil nematodes and young chickens in the experiment. The first one explored the role of the presence of different genetic lines of a nematode species on REG output, yielding marginally significant results in relation to output variance (Franklin, Kendall, & Vassilieva, 2005). In the second one, a small self-propelled robot on which chicks had been previously imprinted, and driven by an internal REG to manoeuvre randomly, moved significantly more often than chance toward the chicks' location, denoting a reduction in randomness in the output of the REG and suggesting psychokinesis (PK) by the birds (Peoc'h, 1995). My hypothesis, based on the results of these studies, is that a nondirectional reduction in randomness in REG production will occur specifically during the presentation of a disturbing stimulus to birds. At the same time, an observer manipulation will be introduced into the experiment, in order to explore the existence of a psi observer effect. Method The animal species used was the zebra finch (Taeni-0pygia guttata). This bird is one of the most common subjects of research in many scientific disciplines, both in the wild and in the laboratory (Zann, 1996), serving as a model for investigation in neurology, behavior development, and environmental variables that impact human health, and it also appears to be gifted with the ability for short-term precognition (Alvarez, 2010a). All subjects (80 adult male and female zebra finches) lived in two unisexual adult groups of conspecifics in 3 x 3 x 2 m aviaria near Seville, Spain, where water and food (seeds and vegetables) were supplied ad libitum. The 70 x 35 x 35 cm testing cage was provided with four perches and a TFT screen at one end, where a still background image of red tiles was always on display during the experimental sessions. During the sessions, an Orion REG device was permanently in position on the centre of the cage floor and provided the data relative to output randomness. The laptop computer controlling the presentation of the stimulus on the TFT screen and storing the information from the REG was located in an adjacent compartment and was connected to the devices by two long cables. The same scene was shown at the same time on the TFT screen beside the testing cage and on the screen of the laptop computer in the observer compartment. Three conditions were tested: (a) Bird Alone: the test was applied to 40 birds while the observer had gone away from the experimental area (5 to 25 m from the testing cage) ; (b) Bird Plus Observer: while the tests to 40 other birds were taking place, the observer (who knew in advance the time of stimulus presentation) was continuously receiving the same stimulation as the birds on a laptop screen and was intently waiting for the stimulus to appear; (c) Observer Alone: the same as in b (40 tests), but the testing cage was empty. …
Quantum computing has reintroduced itself as a breakthrough technology for machine learning, especially in the analysis of massive datasets, especially the genomic ones. The present research focuses on using QML, namely QSVM, to parse sequences, discover features relating to multiple genetic alterations, biomarkers, and gene expression patterns. The data type under consideration, namely genomic data, is high-dimensional and complex, which presents some problems to the computational methods originating from traditional mathematics. QSVM is designed to work with the mathematical foundations of quantum mechanics including superposition and entanglement and for this reason, it solves problems associated with large scale genomic data more efficiently and accurately. The application of QSVM in MEPs confirms its superiority over classical counterparts in classifying gene mutations, clustering of expression profiles or prediction of disease susceptibility. In addition, through feature mapping, QSVM offers better insights into biological information contained on genomic data, as compared to linear correlations. Furthermore, the ability of QML frameworks to expand to fit the increasing amount of data produced by next-generation sequencing technologies is assessed. Leveraging on this research QSVM has been recognised to redefine precision medicine by rapidly diagnosing diseases and providing unique therapeutic options. The results re-echo the potential of QML in transforming CG and promoting future innovations in biomedicine and health.