Origins of introns based on the definition of exon modules and their conserved interfaces

de Roos AD. Origins of introns based on the definition of exon modules and their conserved interfaces. Bioinformatics. 2005. Jan 1;21(1):2-9 (PDF).

From the Abstract:
The design-by-contract methodology of software development offers a modular approach to design that seeks to increase flexibility by focusing on the design of constant interfaces between functional modules.

From the Introduction:

Modern software designs seek to increase flexibility by using a modular approach which allows for the addition, replacement and changing operations within individual modules.

Complex software architectures are based on a methodology in which a software system is viewed as a set of communicating modules whose interaction is based on precisely defined interfaces. The interfaces can be viewed as specifications of the mutual obligations or contracts.

The effect of constant interfaces across modules is a reduction of the interdependences across modules or components and a reduction in the risk that changes within one module will create unanticipated changes in other modules. This methodology is also known as design-by-contract (Meyer,B. (1997) Object-Oriented Software Construction, 2nd ed. Prentice-Hall, NY.).

...it is hypothesized here that genome architecture reflects the paradigms of design-by-contract: definition of functional modules that interact with each other by well-defined interfaces.

From the Full Text:

In our design-by-contract model, the recognition sequence represents the interface for the splicing of the exons and therefore, any mutation in this sequence would be deleterious since it would result in the inactivation of the splice site (Fig. 3B) and resulting loss of function of the encoded protein.

Fig. 3. mRNA intron phase shifts can change the amino acid sequence without changing the ancient splice recognition site.
(A) The sequence at the splice junctions codes for the amino acids glutamine and valine that would result from concatenation of the exons [at the top in this figure].
(B) Mutations in the splice site recognition sequence will disrupt splicing.
(C) Phase shifts can change the splice junction amino acid sequence without disruption of the recognition site. In phase 0, there is only one amino acid sequence possible, glutamine followed by valine. In phase 1 and 2, translation will read through the splice junction in a different way, making various combinations of amino acids possible. Note the conservation of the sequence at the splice junctions (in red).

The application of the design-by-contract methodology by viewing the exon as a module that interacts with its environment by its interface, led to a series of logical steps explaining the intron–exon structure of genes and intron phase differences.

Other works by the same author in PubMed and in Scholar Google , as well as some ARN postings:

Half saved from ARN's broken threads:
"The ribosome is, in fact, a nano-scale computer"

Biology as Technology (synthetic biology)

Double trouble: Cells with duplicate genomes can trigger tumors

The ARN's broken threads:
Topic: Does cell design sacrifice energetic efficiency for conceptual integrity?

Critique of Endosymbiosis

Berlinski vs. Scott (I know where I'm placing my money)

Designed Errors and Deliberately Bad Designs
does ID propose a mechanism?

Evolution of an Arbitrary Sequence

populations vs individuals
Etc.