Does the Darwinian theory require modification or replacement?

I propose that we are now entering into a new era of the theory of Evolution. This may be called the Information driven theory, the Bio-Communicative theory, the Cell Intelligence theory of Evolution, or whatever appropriate name fits the theory.The History of evolution began with Darwin and his theory of descent with modification, the origins of hereditary variation or random mutations, and natural selection.Darwin’s theory was based upon gradual change and positive natural selection.Next came the Neo-Darwinism or the Modern Synthesis in the 20th century which basically combined Darwinian gradualism with genetics. Again the theory was basically random mutation and natural selection.Both of these theories rely on mechanical forces, Physical and Chemical, and reductionism.In a post in the Forum Biological Evolution I introduced James A. Shapiro’s 21 st Century Natural Genetic Engineering writings in the potential falsifications of the theory of evolutionthread.
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Shapiro’s work is based upon discoveries from genome sequencing such as genome alterations in key places in evolutionary history, horizontal transfers of DNA segments, Whole Genome Doublings etc.He states that the cellular information in the genome is a Read-Write memory system, which is different from the modern synthesis view of the genome as a Read only memory system subject only to accidental change.Shapiro is of the opinion that Mobile DNA movements rather than replication errors serve as the primary engines of protein evolution. Shapiro is not alone in advocating a change in evolutionary theory from the modern synthesis as now expressed, to one of Natural Genetic Engineering.My purpose in this post is to discuss whether the Modern synthesis as it is know today should be modified? Replaced? With A theory based upon adaptations that are directed, modified, regulated and controlled by information exchanges in the cell rather than by mechanical physical, chemical driven adapations driven by random mutations and natural selection.

jar writes; Shapiro in a paper "Revisiting the Central Dogma in the 21st century" published in Annals of the New York Academy of Sciences: 1178: 6-28 (2009) (which for some reason my link won't completely copy out on this page), but can be found by googling the paper in pdf form, wrote when discussing the molecular
analysis of fundamental biochemical processes in living cells wrote: Although he is careful to use the term natural genetic engineering he does say that genetic changes are not by accident. He also states that we expect to see changes operating nonrandomly...
This appears to me that he is talking about non random changes that are different from the theory as set forth today.

Dr Adequate writes; The difference is that these are driven by information in the cell, not by purely mechanical processes.

taq writes; Here is where I have a hard time with Shapiro. In the following quote from Mobile DNA and evolution in the 21st century | Mobile DNA | Full Text he writes : It appears to me that he is saying that the suddent abrupt changes are nonrandom and performed by natural genetic engineering. Once that is finished then micro evolution, ie Darwinian evolution takes over.Note he says "a distinctively 21st century scenario for evolutionary change."

jar writes; He is talking about natural genetic engineering that is nonrandom as I point out in reply to message 8 by taq.If in fact the theory does change in accord with Shapiro and others who are researching about a 21st century theory of evolution that does not rely on random mutation, but rather information in the cell that engineers change then Special Creation will become something that Science will have to deal with.

NoNukes writes; When he talks about system architecture and read write memory systems this is not random and is as close to deterministic as you can get without using the word.

taq writes; If you will recall in the thread "potential falsifications " I e-mailed Shaprio and his whole answer is on that thread.
In my first question to him I asked:Has Natural Genetic Engineering, changed the modern Darwinian theory of evolution as we know it today?He answered. Shapiro seem to be very specific in his choice of words and is a highly regarded professional. When he uses the phrase "going from random accidents to regulated biochemical systems" and "heuristic guidance", which to me means they may be discovering or learning something for themselves., leads me to the conclusion that the whole process is nonrandom.He was also asked "When you use the term sentient do you mean that the cells are capable of making decisions that affect their evolution?"He replied; So I am of the opinion that he is proposing a system of decision making in the cells that go beyond nonrandom mutation.

jar wrote; If you will recall Shapiro told me in his reply to me e-mail, "You have understood my position pretty well..." So perhaps you can enlighten me on what I am missing.
I assume your comment on Special Creation is based upon some scientific finding, and I don't believe all who do have faith in Special Creation, in my case as per the theology of the Roman Catholic Church, are all "con" men.

Dr Adequate writes; I agreeThe changes are made to an actual physical sequence of DNA in accordance wtih the laws of chemistry.What Shapiro and others are trying to determine is what is causing the changes to be made and how does that system of engineering or information sharing work.It is interesting that Darwin knew nothing of Genetics, and that Ernst Mayr in his 2001 book "What is Evolution" said it was difficult to understand the great amount of non-coding DNA that was thought to be 95% and he found it difficult to belive that selection would not have been able to get rid of it if it was totally useless.Mayr was correct, it was not totally useless, and today scientists today such as John Mattick are saying that genomic non-proteincoding sequences are contolling gene expression at many levels.
So the more that is being discovered about information in the cell, the more probable is that the cells have information coded properties that are playing a major role in evolution.

jar writes; That is a distrubing message. Is it your view that anyone who belives in God, that God has a hand in creation, is getting conned?As for any evidence of non-natural influence or guidance, of course it cannot be proven under a microscope, but one only need look at the Universe, and the wonder of life, and deduce how did this happen?I would hope you would meditate on these issues and at least consider that there may be an influence that science cannot prove by physical evidence.I know this message is off post.That is my last sermon and I truely don't want to argue religion or faith with you.

No Nukes writes; That is the probably the question that will never be answered by physical evidence. One will have to meditate on the question and decide for him or herself.All I am saying right now in this post is that Scientists are questioning the modern theory of evolution. That there is more to it than mechanical physical, chemical events that have made evolution as we know it today.Where the information and sentience came from may never be known unless we can find out the Origin of Life.

No Nukes writes; I don't know if I am overstating Shaprio's position.
What I am saying is that the chemical/mechanical functions are known, but how and why the information, that Shapiro calls natural genetic engineering, works to have the cell perform those functions is where the new, modified, replaced theory will be discovered.NoNukes writes; Not sure what you mean by that statment.

Wounded King writes; All I was trying to point out is that Darwin's theory has changed substantially since Darwin published it, as has the modern synthesis theory.When the modern synthesis was declared the leaders of that revision of the theory were very certain that they were correct.
I am now saying that perhaps a whole new look has to be taken to determine what, if any impact, the information, communciation discoveries will take evolution in the future.NoNukes wriites; I agree, and that is why I think all should keep an open mind as to where the Information, communciation, sentience in the cell theories may take us.I have my opinions as to what we are going to find out, but those are my opinons are of course are not fact.When I practiced trial law it was important to learn every word each witness would say at trial, what all the evidence would be, and to then try to lead the jury to the truth as to what the evicence showed.In my cases it was always "what caused the serious injury or death of this person". Was it negligence by the Dr. or was it merely a bad outcome. We relied on experts to tell the jury their opinions based on all the medicine involved in the case.That is what I am trying to do here.I have been reading and trying to digest what all the papers are revealing and then trying to reach an opinion as to where they are leading in re evolution.
Obvioulsy I have a bias, as do all of us on this board, but I try to look at the evidence objectively, as I hope all will also do.

jar writes; What can I say? Could you please defineyour meaning of "Special Creation?"

Wounded King writes; What I am saying is that the information, communciation, sentience research is different from the modern synthesis in that there is direction rather then random mutation, and Shapiro says he defines "selection" as "purfiying" selection.
The definition I found for purfying or negative selection is the selective removal of alleles thar are deleterious.If that is so, how can one define that type of selection as anything but directed or purpose caused?So this is more than a revision of the modern synthesis, it is an invalidation of the theory.Wounded King continues; The evidence I am providing is the work of experts in the field. I as a non scientist cannot provide the nutsl and bolts of the workings of the cell, but rather provide the evidence of the experts in the field.
I have no doubt that Shapiro, based upon his CV, would qualify as an expert in microbiology.
So the quotes from Mary, Mattick and Shaprio are indeed very strong evidence, that I have provided.