Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth

Although overwhelming circumstantial evidence supports the existence of the universal common ancestor of all extant life on Earth, it is still an open question whether the universal common ancestor existed or not. Theobald (Nature 465, 219–222 (2010)) recently challenged this problem with a formal statistical test applied to aligned sequences of conservative proteins sampled from all domains of life and concluded that the universal common ancestor hypothesis holds. However, we point out that there is a fundamental flaw in Theobald's method which used aligned sequences. We show that the alignment gives a strong bias for the common ancestor hypothesis, and we provide an example that Theobald's method supports a common ancestor hypothesis for two apparently unrelated families of protein-encoding sequences (cytb and nd2 of mitochondria). This arouses suspicion about the effectiveness of the “formal” test

Schr\"odinger's cat in an optical sideband

We propose a method to subtract a photon from a double sideband mode of continuous-wave light. The central idea is to use phase modulation as a frequency sideband beamsplitter in the heralding photon subtraction scheme, where a small portion of the sideband mode is downconverted to the carrier frequency to provide a trigger photon. An optical Schr\"odinger's cat state is created by applying the propesed method to a squeezed state at 500MHz sideband, which is generated by an optical parametric oscillator. The Wigner function of the cat state reconstructed from a direct homodyne measurement of the 500MHz sideband modes shows the negativity of $W(0,0) = -0.088\pm0.001$ without any loss corrections.Comment: 11 pages, 9 figure

(2,7-Dimeth­oxy­naphthalen-1-yl)(3-nitro­phen­yl)methanone

The title compound, C19H15NO5, has an intra­molecular C—H⋯O=C hydrogen bond between a naphthalene H atom and the O atom of the carbonyl group. The inter­planar angle between the naphthalene ring system and the benzene ring is 69.59 (5)°. The dihedral angle between the bridging carbonyl C—C(=O)—C plane and the naphthalene ring system is 61.02 (6)°, which is far larger than that between the bridging carbonyl plane and the benzene ring [12.68 (7)°]. The nitro group is slightly out of the plane of the benzene ring [O—N—C—C torsion angle = 4.97 (17)°]. In the crystal, the packing is mainly stabilized by C—H⋯O inter­actions between an H atom of the benzene ring and an O atom of the nitro group

1,8-Bis(4-amino­benzo­yl)-2,7-dimeth­oxy­naphthalene

The title compound {systematic name: [8-(4-aminobenzoyl)-2,7-dimethoxynaphthalen-1-yl](4-aminophenyl)methanone}, C26H22O4N2, possesses crystallographically imposed twofold symmetry, with two C atoms lying on the rotation axis. In the crystal, the mol­ecules inter­act through inter­molecular N—H⋯O hydrogen bonds between the amino and meth­oxy groups on the naphthalene ring systems and N—H⋯π inter­actions between the amino groups and the naphthalene rings. Furthermore, weak C—H⋯O hydrogen bonds and π–π stacking inter­actions between the benzene rings are observed. The centroid–centroid and inter­planar distances between the benzene rings of the aroyl group and the naphthalene ring systems of adjacent mol­ecules are 3.6954 (8) and 3.2375 (5) Å, respectively. The dihedral angle between the mean planes of the benzene ring and the naphthalene ring system is 83.59 (5)°. The benzene ring and the carbonyl group in the benzoyl unit are almost coplanar [C—C—C—O torsion angle = 175.91 (10)°]

Characterization of entangling properties of quantum measurement via two-mode quantum detector tomography using coherent state probes

Entangled measurement is a crucial tool in quantum technology. We propose a new entanglement measure of multi-mode detection, which estimates the amount of entanglement that can be created in a measurement. To illustrate the proposed measure, we perform quantum tomography of a two-mode detector that is comprised of two superconducting nanowire single photon detectors. Our method utilizes coherent states as probe states, which can be easily prepared with accuracy. Our work shows that a separable state such as a coherent state is enough to characterize a potentially entangled detector. We investigate the entangling capability of the detector in various settings. Our proposed measure verifies that the detector makes an entangled measurement under certain conditions, and reveals the nature of the entangling properties of the detector. Since the precise characterization of a detector is essential for applications in quantum information technology, the experimental reconstruction of detector properties along with the proposed measure will be key features in future quantum information processing.Comment: 18 pages, 6 figure

Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA.

The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene, and it supports our new evolutionary hypothesis of the Japanese black bear

Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages.

Little is known about how mammalian biogeography on islands was affected by sea-level fluctuations. In the Japanese Archipelago, brown bears (Ursus arctos) currently inhabit only Hokkaido, the northern island, but Pleistocene fossils indicate a past distribution throughout Honshu, Japan's largest island. However, the difficulty of recovering ancient DNA from fossils in temperate East Asia has limited our understanding of their evolutionary history. Here, we analysed mitochondrial DNA from a 32 500-year-old brown bear fossil from Honshu. Our results show that this individual belonged to a previously unknown lineage that split approximately 160 Ka from its sister lineage, the southern Hokkaido clade. This divergence time and fossil record suggest that brown bears migrated from the Eurasian continent to Honshu at least twice; the first population was an early-diverging lineage (greater than 340 Ka), and the second migrated via Hokkaido after approximately 160 Ka, during the ice age. Thus, glacial-age sea-level falls might have facilitated migrations of large mammals more frequently than previously thought, which may have had a substantial impact on ecosystem dynamics in these isolated islands