Genetics, Statistics, Quantitative Linguistics

Mainstream model-theoretic works for institutionalized organized funded scientific research: uite contrary to the explosion of deploying Chomskyan syntactic structure to read sequential order of DNA, it seems that Chomsky himself is totally skeptic about the metaphorical displacement of linguistic structure in the DNA-structure. The immediate question, which arises in our mind, is: why should we depend on linguistic structure to decipher DNA-code?It is not at all a new phenomenon to borrow formal structure from Linguistics and to deploy it in other fields to understand the nature of objects. In the mid 60s, it was termed as “linguistic turn”, when different social scientific disciplines were borrowing techniques from structural linguistics. In case of Genome, Monod(1972) predicted that the sequential order of codons follows the Chomskyan syntactic structure. However, Chomskyan syntactic structure is regularly changing, Now, the question is, which model of Chomsky is used so far in case of DNA? No satisfactory answer is possible until we would explore the preliminaries of linguistic analysis. This basic knowledge of Linguistics is necessary before deploying such structure in the sequential order of triplets. However, it is found that the mainstream DNA-research ignores 2. THE GOAL AND PRELIMINARIES OF LINGUISTICS The goal of Linguistics is to explore the formal structure of language to understand the structure of Language Acquisition Device, a hypothetical physical organ, from which infinite sets of sentences are created/generated out of finite sets of words. Chomskyan syntax is meant for such investigation: to know the syntactic pattern means to know the partial structure of cognitive domain. How these words are distributed in the sentence? Not only that, how phones are also distributed in words? What is the formal construction pattern of infinite sets of sentences? [ Please note that in language, there are hierarchical levels: from smallest phonemes to largest sentence or discourse] To answer such questions, let us move to some basic notions of Linguistics before Chomsky. 2.1 LEVELS OF LINGUISTIC ANALYSIS (The following excerpts are borrowed from Lyons, 1968) By virtue of potentiality of occurrence in a certain context, a linguistic unit (like phoneme [smallest meaningless unit; A, G, T, C may be metaphorically considered as such smallest units], Morpheme[smallest meaningful unit], lexeme [culturally defined words; all the triplets are metaphorically considered as words], sentence) enters into two types of interdependent relation: syntagmatic and paradigmatic relations. In case of syntagmatic (or horizontal relation), a unit co-occurs with the other units in the same level with which it occurs and which constitutes the context. In case of paradigmatic (or vertical or substitutable) relation, a unit enters into the relations with all the other units which can also occur in the same context. Examples: /p/, /e/, /t/ in English “pet” occur in a syntagmatic relation. We can also say that /p/ syntagmaticaly co-occurs with /–et/ in English. Any sequence of A, T, G, C is a syntagm. Their relationship is, thus syntagmatic relation. Triplets, again occur syntagmatically. Each triplet occurs syntagmatically with each other, e.g., ATG syntagmatically co-occurs with TTT or TGC…. This /p/ in ‘pet’ can be substituted by /b/ or /s/ in English (as in ‘bet’ or ‘set’). The unit /p/ stands in paradigmatic relationship with /b/ and /s/. One can also say that if some triplets are producing same amino acid is said to be in a paradigmatic relationship( in case of one can be substituted by the other). They are considered as synonymous. B. In a given syntagm, how the units are distributed? Is there any selectional restriction for any occurrences? For example, “Colorless green ideas sleep furiously” is unacceptable(due to their selectional restriction) syntagmatic combination. In case of an incomplete sentence like “A bottle of….”, a native speaker can easily fill up the blank space with his/her paradigmatic choice: milk, wine, water, oil etc. All these units (milk, wine, water, oil but not cow) are forming a paradigm. C. In Linguistics, it is necessary to find out the construction-type of syntagms on the basis of distribution of units. There are two types of construction: Endocentric and Exocentric constructions. An Endocentric construction is one whose distribution is identical with that of one or more of its constituents. Example: “tall boy” is an endocentric construction as in any English sentence in which boy occurs can generally be matched with another sentence in which “tall” occurs in a same position. Please note that “tall boy” has the same distribution as its constituent “boy”; any English sentence in which boy occurs can generally be matched with another sentence in which tall boy occurs in the same position; and since boy is a noun, tall boy is described as a Noun Phrase (NP). On the other hand, in Mysore is exocentric, since its distribution is different from either the preposition in or the noun Mysore. The phrase in Mysore has much the same distribution as there and other adverbs of place; here preposition C(onstituent)-commands the noun; therefore this is a prepositional phrase. Endocentric construction fall into two main types: Co-ordinating and Sub-ordinating. Co-ordinative construction have the same distribution as each of their constituents taken separately; thus old man and old woman and coffee or tea are co-ordinative constructions. The constituents whose distribution is the same as that of the resultant construction is called the head; the other constituents is the modifier. In sub-ordinating construction one modifier may be recursively “nested” within another, e.g, the man on the top of the bus, there are two constituents, the man (head) and on the top of the bus (modifier);on the top of the bus is an exocentric prepositional phrase consisting of preposition on and the endocentric noun phrase the top of the bus. This (inter)dependency relation may be summarized as follows: CONSTRUCTION TYPE OMMISSION CHARACTERISTICS OF CONSTITUENTS RELATION BETWEEN CONSTITUENTS Exocentric Both constituents obligatory, i.e.,AB Interdependence (=mutual dependence) Subordinative One obligatory constituents (=the center), i.e., A(B) or (A)B Dependence (of modifier on center) Co-ordinative Neither constituents obligatory (A)(B) Independence This preliminary dependency-relation is crucial for deploying the complexities of Chomskyan Syntax. Frankly speaking, we do not have enough evidences for such dependency relation for a particular coding region in DNA. (in case of AGC, ATC, CCC etc.). 3. WHAT IS TO BE DONE? Keeping in mind above-mentioned constraints, we may look into the following aspects of DNA-Structure with an ultimate goal to discover dependency-relation: A. Rank-Frequency distribution of triplets. B. Selectional restrictions of triplets or Distributional pattern of triplets C. String-length of a coding region (Cf. sentence length ) D. In connection with B, probability of occurrences of triplets can be investigated to achieve the predictability. E. This is the last crucial task: is there any (inter)dependency relationship among triplets? A has already been explored. We may now concentrate on B, C, D. All the claims regarding the deployment of Chomskyan syntax is fallacious, unless one can substantiate E. 4. MODEL-THEORETIC APPROACH: THE PROBLEMS Here we shall discuss the problem of Model-theoretic approach with a view to understand the adoption of particular model for analyzing particular object. The model imposes particular taxonomy to an object for better understanding of that object or to attain objectivity. The question is: Does such practice of taxonomizing (imposing certain order of things on some selected object) yield objectivity? Or is it a subjective cultural practice? (Searle mentioned loosely the term “Post-Modern” at the end of his paper in the Nature. These questions are of course Post-modern questions, however, I will try to answer these questions from classical perspective.) To doso, let us now try to understand the following excerpts from Russell: “We all start from ‘naïve realism,’ i.e., the doctrine the things are what they seem. We think that grass is green, that stones are hard and snow is cold. But physics assures us that the greenness of grass, the hardness of stones, and coldness of snow are not the greenness, hardness and coldness that we know in our own experience, but something very different. The observer, when he (sic) seems to himself (sic) to be observing a stone, is really, if physics is to be believed, observing the effects of the stone upon himself (sic). Thus science seems to be at war with itself: when it most means to be objective, it finds itself plunged into subjectivity against its will. Naïve realism leads to physics, and physics, if true, shows that naïve realism is false. Therefore naïve realism, if true, is false; therefore it is false.” In course of reviewing this book Einstein quoted this paragraph and remarked, “Apart from their masterful formulation these lines say something which had never previously occurred to me.” (1954: 20, emphasis added). Whatever it may be, what is important here is the (subjective) imposition of certain order of things upon some objects to meet the alleged objectivity. Despite such constraints, we can adopt certain model to achieve enough explanatory adequacy that may also serve some practical purpose.