See Also:

Wells: Homology in Biology” A Problem for Naturalistic Science

Wells: Critical Perspectives on Homology

Michael Denton in Bio-Complexity

Design of Life- General Notes

Membrane Patterns Carry Ontogenetic Information

Utah Law review 2000

The Music of Life Sourcebook

Evolution: A View from the 21st Century , Signature in the Cell: DNA and the Evidence for Intelligent Design 

Design of Life



The genetic code is a highly complicated flow of information that often resides outside the physical sequence of DNA base pairs and older models such as the one gene – one protein hypothesis cannot account for the multilayered, multidirectional nature of gene expression.

The Human Genome Project, completed in 2003, carried a great sense of expectancy in its endeavor to sequence the DNA that comprises the entire human genome. With the nucleotide base pairs of every gene identified and mapped, the functionality of each would be elucidated holding tremendous promise for the understanding and treatment of disease. The international team of researchers initially expected to find about 100,000 genes (protein coding sequences of DNA) but at the conclusion of the project, the number dropped precipitously to only about 25,000 protein coding genes, a number significantly less than some plants. Additionally, many unexpected findings emerged over years since the discovery of the structure of DNA in 1953 by Watson, Crick, and Franklin. Most notably, the same gene or genes will give rise to vastly different structures in different animals. For example, a gene in fruit flies that controls the development of legs is also found in mice where the gene affects the development of the hindbrain. Conversely, very different genes will give rise to the same structures as in the case of the genetic programming of limbs, the gut, and spinal chord in different animals. That is, very different genes will often control the development of these “homologous” structures thought to have the same evolutionary origin and as such “the inheritance of homologous structures from a common ancestor … cannot be ascribed to identity of genes.” (Wells, 1996, de Beer, 1971) Wells further comments that “If similar genes can “determine” such radically different structures, then those genes aren’t really determining structure at all. Instead, they appear to be functioning as binary switches between alternate developmental fates, with the information for the resulting structures residing elsewhere.” (Wells, 1996) Moreover, since “advanced structure developments involve the orchestrated expression of many different loci.” and these “mutations are nonrandom, large scale, and uncoupled to natural selection, conventional explanations that randomly generated advantageous changes in complex characters accumulate one locus at a time are unconvincing on both functional and probabilistic grounds, because there is too much interconnectivity and too many degrees of mutational freedom.” (Shapiro, J.A, 1999) The picture that is emerging is that the genome, is essentially a logical switch-board with a “system architecture”. What makes one organism different from another, then, is not so much its proteins or genes, but the “logic” in which all this material/text (common to all life forms) is expressed and this in turn is partially a function of the manner in which the “junk DNA” is arranged. (Gene, M., 2004) Hence while we originally thought of the genome in terms of the “One Gene, One Protein Hypothesis”, we are now, however, viewing the genome as a vast network of the flow of information. Pictured below for visual enhancement is a computer logic board alongside a schematic of the genomic “switchboard” found in the first 30 hours of the life of sea urchin elucidated by Davidson in 2006:


de Beer, Gavin, Homology: An Unsolved Problem. London: Oxford University Press (1971)

Gene, M. (a pseudonym), Personal Correspondence (2004) Mike Gene wishes to remain anonymous due to the controversial nature of his work in molecular biology and is the author of The Design Matrix.

Shapiro, J.A., Genome system architecture and natural genetic engineering in evolution. Ann N Y Acad Sci 1999 May 18;870:23-35

Wells, J., Nelson, P., Homology: A Concept in Crisis, Critical Perspective, Origins & Design 1996 18:2 http://www.arn.org/docs/odesign/od182/hobi182.htm

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