DNA sequence analysis linguistic tools: contrast vocabularies, compositional spectra and linguistic complexity

This is a review of the methods based on counting oligomers in nucleotide and amino acid sequences. Such methods are analogous to the formal linguistic analysis of human texts. This review includes methods based on the calculation of observed occurrences (frequencies) of oligomers and their distribution, as well as those based on deviations between the observed and the expected occurrences (contrast words, genome signatures) in biological sequences. Both types of methods have a wide range of sensitivity and can identify homologous as well as functionally and taxonomically related sequences.     

适合度的相对性与路径依赖的自然选择

自然选择理论认为生物个体或者种群在进化的过程中, 其基因或者性状、行为策略的选择一定是能够提高其适合度或者达到某个可期的“目标”。然而, 随着某个突变基因或者性状特征、行为策略在种群中扩散, 其期望收益将随着其在种群中分布的密度变化或环境改变而发生改变, 这就是适合度景观的悖论, 即静态的、固定可期望的收益可能因此而不存在。基于动态而非静态适合度景观的概念, 我们提出路径依赖的自然选择概念。路径依赖的自然选择过程中, 一个突变的基因或表型在某种环境下随机产生, 但是该基因或表型在某些特定环境下会产生正反馈。尤其是在正反馈与随机漂变的共同作用下, 多条路径的演化就可能发生, 并且其路径的形成将同时受到其种群进化历史过程和空间特征分布等因素的强烈影响。而在不同路径下, 由于观测维度、角度和尺度的不同, 适合度意义将因此而存在不同。在此意义下, 自然选择更可能选择路径频率而不是适合度大小。基于上述概念, 我们借鉴现代物理学中复函数的方法, 来描述多重动力对物种形成或者生物特征、种群进化等路径依赖的演化过程, 以期为同域物种、隐存种形成以及生物多样性演化提供解释机制。     

Multi-dimensional linguistic complexity

Linguistic complexity is a simple and elegant way of calculating complexity of strings of data. It is based on the concept that the greater the vocabulary one uses, the more complex the data. Until now, it has been used only on one-dimensional data, such as DNA and protein sequences and various human language texts. The basic definition can be extended to higher dimensions, thus allowing a practical and simple calculation of linguistic complexity of images, 3D objects and other multi-dimensional data. A simple extension of linguistic complexity is introduced, followed by 2D presentations and a discussion of parametric considerations. An example of linguistic complexity calculations, demonstrating its image processing and medical diagnostic power is presented. The subjects of this paper are patent application pending.     

Isolation by distance, linguistic similarity, and the genetic structure on Bougainville Island

Previous research has revealed extensive genetic variation among villages on Bougainville, in the Solomon Islands. Using previously published gene frequency data for seven loci, the role of isolation by distance in structuring genetic variation on Bougainville was reanalyzed. Newer methods of kinship estimation show that earlier estimates of the isolation by distance parameters were low. The fit of the model is highly significant (R2 = 0.409; P less than 0.001), and the parameter estimates indicate high isolation: a = 0.0538, b = 0.1978, L = -0.0057. Several methods of residual analysis were applied in order to determine factors affecting the fit of the model. Linguistic similarity has a significant effect on genetic variation once the effects of geographic distance are taken into account. Population-specific deviations from the expected model may be explained, in part, in terms of population history. Compared to other human populations, Bougainville Island shows an even greater among-group variation than has been suggested previously.     

Bacterial linguistic communication and social intelligence

Bacteria have developed intricate communication capabilities (e.g. quorum-sensing, chemotactic signaling and plasmid exchange) to cooperatively self-organize into highly structured colonies with elevated environmental adaptability. We propose that bacteria use their intracellular flexibility, involving signal transduction networks and genomic plasticity, to collectively maintain linguistic communication: self and shared interpretations of chemical cues, exchange of chemical messages (semantic) and dialogues (pragmatic). Meaning-based communication permits colonial identity, intentional behavior (e.g. pheromone-based courtship for mating), purposeful alteration of colony structure (e.g. formation of fruiting bodies), decision-making (e.g. to sporulate) and the recognition and identification of other colonies - features we might begin to associate with a bacterial social intelligence. Such a social intelligence, should it exist, would require going beyond communication to encompass unknown additional intracellular processes to generate inheritable colonial memory and commonly shared genomic context.     

Temporal information in speech: acoustic, auditory and linguistic aspects.

The temporal properties of speech appear to play a more important role in linguistic contrasts than has hitherto been appreciated. Therefore, a new framework for describing the acoustic structure of speech based purely on temporal aspects has been developed. From this point of view, speech can be said to be comprised of three main temporal features, based on dominant fluctuation rates: envelope, periodicity, and fine-structure. Each feature has distinct acoustic manifestations, auditory and perceptual correlates, and roles in linguistic contrasts. The applicability of this three-featured temporal system is discussed in relation to hearing-impaired and normal listeners.     

Motor mechanisms in speech ontogeny: phylogenetic, neurobiological and linguistic implications

The rhythmic mandible-generated close-open alternations of the mouth, responsible for the series of consonant-vowel alternations characteristic of babbling and of languages, is receiving increased attention as a possible manifestation of an ontogenetic and phylogenetic 'frame' underlying the serial organization of speech. The supplementary motor area appears important for production of this consonant-vowel frame in adults.     

Allozymic, morphological, phenological, linguistic, plant use, and nutritional data ofBenincasa Hispida (Cucurbitaceae)

Benincasa hispida, from tropical Asia, is cultivated primarily for its edible fruit. To explore its domestication and ethnobotany, we made collections from two regions where it may have been domesticated: (1) Southern China/Southeast Asia, represented by southern Yunnan Province (China) and northern Laos; and (2) the Indian subcontinent, represented by southeastern Nepal. Domestication has resulted in diverse fruit sizes, shapes, and colors; seed sizes and shapes; and, in some accessions, the loss of tendrils. Modern cultivars have larger fruit, earlier flowers, and lower nutritional content than traditional cultivars. Allozyme diversity was low, divergence between these two regions was low, and these results do not clarify the place of domestication. The greater morphological diversity of plants from Yunnan and Laos, as compared to Nepal, suggests domestication in the former region. In all accessions, male flowers precede females.Benincasa hispida is prominent in some traditional stories and rituals.     

Genetic,historical and linguistic perspectives on the origin of the Kelantanese Malays

The Kelantanese Malays who resided in the remote northeastern regions of the Malay Peninsula in the Kelantan state are believed to have a unique genetic signature. The objective of this review is to analyze the populational sub-structure of the Kelantanese Malays from historical, genetic and linguistic perspectives. Historical data suggest that the Semang were composed of the Jahai, Bateq and Kensiu sub-tribes, whereas the Senoi were composed of only the Temiar sub-tribe. The Mendriq sub-tribe is believed to be the first group of aborigines to land in Kelantan. Subsequently, genetic analysis showed that the Kelantanese Malays are an independent clade at the base of the phylogenetic tree and contain genetic material similar to that of the Semang, specifically the Jahai and the Kensiu sub-tribes. The genetic data are supported by the fact that the Aslian language, a branch of the Austroasiatic languages that is widely spoken by the Semang, was potentially transmitted through agricultural activities. However, the potential limitation of this mini-review is the lack of primary reliable sources covering the historical, linguistic and genetic features of the Kelantanese Malays.