A counter-junk-DNA summary

A list of bullet-points with very high-level argumentation against the junk DNA can be found in comment 30 by JoeCoder here.

There is also a very good book on it by Jonathan Wells entitled "The Myth of Junk DNA". This book is highly recommendable to laymen in biology like myself who have a scientific background though. 

The teaching of St Maximus and design detection

St Maximus the Confessor († AD 662)

The teaching of St Maximus the Confessor about the divine logoi of creation (for a summary in Russian, see here) can serve as a philosophical foundation for Intelligent Design. In short, according to St Maximus, each created thing, alive or not, has the corresponding divine idea (logos) of its existence. Each divine idea is then realized in a certain way called a tropos (plural — tropoi) of the respective created thing. The tropos of a thing is the mode of its existence. For example, the Fall of Man resulted in the change of the tropos of the existence of humans.

"Primordial Prescription": a new book by David Abel

The book "Primordial Prescription: The most plaguing problem of Life Origin science" is free to access and download from here.

Subject matter: life origin, cybernetics and biosemiotics. Highly recommendable.

The future of biology: the emphasis on semiotics

Here is a very interesting book devoted to viewing living organisms as semiotic state systems.

Semiotics is central to understanding life

The problem of sign and sign systems (semiotic systems, symbol systems) is key to understanding what is life from a scientific point of view.