Research on Intelligent Design

To put together scientific advances from the perspective of Intelligent Design.

Thursday, November 17, 2005

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.). 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


Blogger S.R. Deardorff said...

Everyone...don't forget to check out an equally valid theory called

Flying Spaghetti Monsterism over at:

And, don't forget, as a newly converted Pastafarian, yours truly, sean, a.k.a. Fresh Parmesan, has received the first of many divine revelations regarding FSM'ism in the form of "Book One: The Pastafarian Revelations," to be found at:

We are doing the open minds of the world a great disservice if we fail to consider the implications of the above!!!!

peace n whatnot,

aka Al Fraydoe's First Prophet,
Fresh Parmesan

Thursday, November 17, 2005 2:06:00 PM  
Blogger fdocc said...

Dear Sean R. Deardorff,

Here, each one of my readers is very important to me.

Elsewhere I have been able to read your work:

"... according to the faithful, it is God and God alone that has the authority to pass judgment. God... is the only entity that has the capacity to label a thing as truth or falsehood - humans like us fall short due to our inability to hold all knowledge."

"... our founding fathers wrote an entire constitution and bill of rights based on the idea that everyone, being given free will by God, had the right to act according to their individual perception of reality so long as those acts did not infringe upon other individual's right to do the same"

"... above all us humans, God knows we must find Him freely; we cannot be conned into or forced into siding with God, we can only be conned into or forced into siding with evil."

"I've always been willing to admit that the Bible offers profound insight on how to live a good life, I'll not deny that..."

"For my lack of desire to appease anyone, I do apologize; but, that's my most American trait..."

You also questioned the authoritarian "thumb" of a current domineering darwinian evolution in the posting board of some old linguist (MG), while you were debating with Miss. Lady J...

You also wrote:

"In closing... I'm done responding to this childish crap... if you wish to continue about normal relations like an adult... I suggest you grow up."

Can you apply your own words to yourself?

You quoted as well:

"All the Kingdom of heaven rejoices more for the repentance of one sinner than for all the world's righteous men."

While expressing:

"The above scripture is to remind us of the power of forgiveness and should remind us of the power of "leading by example" "

I also have read your durr_T_hip_E free verse work entitled "You Pick It" at

I think that, in general, your writing is mostly full of sadness and of a lonely pain...

You also wrote here, there and elsewhere:

"peace" (SHALOM!)

So, I suggest you to try to start here again and brand new as "a mature adult" by expressing your observations (if any) directly related to this article, published in an indexed Journal by Dr. de Roos.

Feel free to comment your scientific evidence in support or your objections to this or to the more than 40 of my postings including scholarly articles.

You yourself wrote to "be mature" to others at your 25 years of age, now, I post your own words back to you.

But other than that, as I have told you at my greetings to you, and even if I disagree 100 % with the comedy and mockery that you posted here, I am surely glad that you have visited my humble place, that you have been and posted on my "Research on Intelligent Design"!

Friday, November 18, 2005 5:50:00 PM  
Blogger JohnADavison said...

Intelligent design is not a matter for debate. It is a mandatory assumption without which nothing in either ontogeny or phylogeny can ever make sense.

Monday, November 21, 2005 5:05:00 PM  
Blogger answer-man said...

ps I'm having a little trouble sending comments so if I do it twice please excuse me and I apologize.

Wednesday, March 15, 2006 12:39:00 PM  
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