Collado-Vides J
Departamento de Neurociencias, Universidad Nacional Autónoma de Mexico, México D.F.
J Theor Biol. 1989 Feb 22;136(4):403-25. doi: 10.1016/s0022-5193(89)80156-0.
An important problem in biology is the lack of a set of common principles unifying biological knowledge. We propose generative grammar for constructing an integrative paradigm for the understanding of genome organization and the regulation of gene expression. Linguistic terms in molecular biology are defined. A genetic syntactic structure is defined as being equivalent to a sentence. The hypotheses for the grammar of genome structure are: (i) the "grammaticality" of the linguistic approach studies the "regulability" of genome structures; (ii) the "regulability" of genetic structures is independent from their specific biochemical meaning and (iii) the dynamics of regulation is implicit in the genome structure. A general structure is presented for the grammar; the application of phase-structure rules is justified by the existence of lexical categories. Transformational rules are utilized to represent loops of regulation. Negative inducible, positive repressible, positive inducible and negative repressible alternative mechanisms of regulation are represented, by four transformational rules, and the application of these rules is established by two principles. Finally, this approach is compared to other linguistic applications in molecular biology.
生物学中的一个重要问题是缺乏一套统一生物学知识的通用原则。我们提出了生成语法，用于构建一个综合范式，以理解基因组组织和基因表达调控。定义了分子生物学中的语言学术语。将遗传句法结构定义为等同于一个句子。基因组结构语法的假设如下：（i）语言学方法的“语法性”研究基因组结构的“可调控性”；（ii）遗传结构的“可调控性”独立于其特定的生化意义；（iii）调控动力学隐含在基因组结构中。给出了该语法的一般结构；通过词汇类别的存在证明了相结构规则的应用合理性。利用转换规则来表示调控回路。通过四条转换规则表示负诱导、正阻遏、正诱导和负阻遏等不同的调控机制，并且通过两条原则确立了这些规则的应用。最后，将这种方法与分子生物学中其他语言学应用进行了比较。
