Just a note before I get to googling all of your unattributed Shapiro quotes.
It is common courtesy to provide cites and links to your sources.
For example, when I google your assertion that Shapiro thinks "Mobile DNA movements rather than replication errors serve as the primary engines of protein evolution.", I find this:
shapiro.bsd.uchicago.edu/Shapiro.2010.MobileDNA.pdf
In the future, please provide your cites.
That said.
What is with the laundry list? Reverse transcription? Ribozymes? DNA repair? Shapiro says in the introduction that he is going to review:
technical advances in our views about genome organization and the mechanisms of genetic change
That's all that is, shadow. A list of a some mechanisms.
And then we come to your summary of what Shapiro means:
He accepts descent with modification, but does not accept natural selection and random mutation to the degree that the modern evoluntionists believe.
.I believe he is formulating a theory that does not rely on Random Mutation as a primary player in the evolving of organisms.
That's where you go off the rails.
NOWHERE does Shapiro assert the above.
In fact, here's Shapiro addressing that question directly:
The following text was published in The New York Times, November 10, 1996.
To the Editor: I find myself quoted in Michael J. Behe's Op-Ed article questioning Darwinian explanations for cellular evolution (Oct. 29), leaving the impression that I share his call for a return to religious explanations. This is not my position.
Darwinism and creationism are not the only ways to think about sources of biological function and diversity. The virtue of science is its ability to evolve concepts that render ''miraculous'' aspects of the world comprehensible.
Molecular biology has uncovered complexity in genome structure and cellular function. It has also revealed biochemical systems that cells use to restructure DNA molecules in ways that resemble our own genetic engineering. These systems introduce potentials for rapid genome reorganization and biological feedback into the evolutionary process.
Scientists have the task of exploring how far the operation of natural genetic engineering systems can provide novel ways to account for biological adaptations not explained by random mutation and selection.
James A. Shapiro
Professor of Microbiology
at the University of Chicago.
Chicago, Nov. 5, 1996
http://www.stephenjaygould.org/...e/design/shapiro_behe.html
Take a close look at that last sentence:
Scientists have the task of exploring how far the operation of natural genetic engineering systems can provide novel ways to account for biological adaptations
not explained by random mutation and selection.
Let me translate that for you:
There are lots of things that we can explain with random mutation and selection. However, if there is something that we can't explain, I bet we will find the answer in natural genetic engineering.
As a reminder. Shapiro's definition of natural genetic engineering (aka nonrandom changes):
www.shapiro.bsd.uchicago.edu/...evisitingCentral%20Dogma.pdf
Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations106 or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.107—110 Genetic change is almost always the result of cellular action on the genome.
And from the ISCID chat:
Masciarelli
I'm curious about "their non-random operations." Does 'non-random' suggest that the very instructions for all possible morphological changes are front loaded or pre-programmed into living things, needing only a given catalyst to get things going?
James Shapiro
No. Non-random means that they operate under certain conditions (e.g. after genome damage or viral infection) and that these systems make characteristic kinds of changes ... These phenomena show us that cells are capable of altering their genomes in non-random but not rigidly specified or pre-determined ways.
Is that clear, shadow?
And when Shapiro says:
Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cell.
He is absolutely NOT saying we CANNOT know but that we DO NOT know. For now.
Remember?
Shapiro writes:
The possibility that computational control of natural genetic engineering functions can provide an answer to the problems of irreducible complexity and intelligent design deserves to be explored fully. Contrary to the claims of some Creationists, these issues are not scientifically intractable. They require an application of lessons from the fields of artificial intellligence, self-adapting complex systems, and molecular cell biology.
Let me translate that for you:
"ID and irreducible complexity are bullshit. We will figure it out."
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