Back to irreducible complexity (Introduction)

by David Turell , Saturday, February 06, 2010, 01:19 (5404 days ago) @ David Turell


> Irreducible complexity appears to be present, with both aspects of the genome needing to arrive at the same time.
> 
> http://www.sciencemag.org/cgi/content/abstract/327/5966/693 -Here is a more complete discussion of the article itself, covering how DNA copying is protected from error:-How were RNA gene repeats, "essential" to DNA repair, formed?
DLH
RNA replications have now been discovered to be "essential" to DNA error correction systems. If they are "essential", how could they arrive by random mutation and "selection"? On what basis does neoDarwinism predict error correction in the first place? 
From Intelligent Design, methodology one expects to see evidence of design in complex biochemical systems. From engineering design, I posit a foundational ID principle to be:
"Design systems to protect their design"
Protection: The first level is to protect the design. e.g. we provide protective coating and protective enclosures to protect hard drives, CDs, and DVDs. We provide transient surge protection to preserve electronic power systems. 
"Repair": The next level of preservation design is to provide systems to repair damage that is likely to occur. e.g. Computer systems use Reed Solomon error correcting codes. Similarly Redundant Array of Inexpensive Disks (RAID) systems are used to provide redundance and error correction in computer systems. 
By inference such design preservation methodology would be expected in designs by other intelligent beings. Thus, ID practitioners expect to see design preservation methods in biochemical systems. e.g., including redundant copies and error correction. 
A fascinating recent discovery is that a certain amount of redundance is essential to DNA repair. See: This Week in Science which reports on:
Protective Abundance
Massively repeated sequences are generally dangerous to genomes because they promote recombination and, potentially, genome instability. Eukaryotic ribosomal RNA genes (rDNA), which are highly transcribed, are organized into large arrays of repeats and have a system that actively maintains these large arrays. In getting to the bottom of this apparent contradiction, Ide et al. (p. 693) found that reducing the number of rDNA repeats in yeast resulted in a marked sensitivity to DNA damage, owing to heavy rDNA transcription preventing repair of compromised DNA replication forks. It appears that the additional copies of rDNA both reduce the ability of transcription to interfere with DNA repair and provide, through the action of condensin, templates for the recombination-based repair of replication-induced damage.
On what foundational principle does neoDarwinism predict such "essential" design repair components and functionality? What detailed step by step method is there to provide any rationally significant probability for such to occur? By contrast, the fact that this specific repetition ... error correction system is "essential" suggests that it is also irreproducibly complex. (See Michael Behe on irreproducible complexity). This fits ideally within an ID perspective.
See the article: Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity Satoru Ide, Takaaki Miyazaki, Hisaji Maki, Takehiko Kobayashi Science 5 February 2010: Vol. 327. no. 5966, pp. 693 ... 696 DOI: 10.1126/science.1179044
Abstract
The ribosomal RNA (rDNA) gene repeats are essential housekeeping genes found in all organisms. A gene amplification system maintains large cluster(s) of tandemly repeated copies in the chromosome, with each species having a specific number of copies. Yeast has many untranscribed rDNA copies (extra copies), and we found that when they are lost, the cells become sensitive to DNA damage induced by mutagens. We show that this sensitivity is dependent on rDNA transcriptional activity, which interferes with cohesion between rDNA loci of sister chromatids. The extra rDNA copies facilitate condensin association and sister-chromatid cohesion, thereby facilitating recombinational repair. These results suggest that high concentrations of heavily transcribed genes are toxic to the cells, and therefore amplified genes, such as rDNA, have evolved. 
Note that Ide et al. further observe "each species having a specific number of copies". Combining species specific rDNA copies with rDNA repeat number being "essential" suggests that this minimum rDNA repeat number forms part of the species barrier. On what basis does neoDarwinism predict such species barriers and the steps to form them?
By contrast, in highly competitive environments, design engineers try to differentiate their systems to prevent use of competitive or generic products. e.g., hardware or software "locks" etc. Thus, from the foundational ID principle of ""Preserving the design", one would expect designs by other intelligent agents to provide methods to preserve designs uniqueness. 
How well are rDNA repeats as essential to DNA error correction predicted by neoDarwinism or ID principles. How can these be tested or differentiated?
(Any corrections to these inferences from reading this news and abstract would also be welcome.)