Does the Darwinian theory require modification or replacement?

Your "I cannot accept that these functions are randomly performed" still does not affect reality.The information in the paper you linked to appears to me to be reality. It is not anything that challenges the modern synthesis, or that is evidence of directed mutation or directed evolution.

I subscribe your deductions. But I would like to make some comments on the last note.In Barbara Wright's mini review I read : "The existence of such mechanisms has been predicted by mathematicians (6) who argue that, if every mutation were really random can accelerate the process of evolution in specific directions. and had to be tested against the environment for selection or rejection, there would not have been enough time to evolve the extremely complex biochemical networks and regulatory mechanisms found in organisms today. Dobzhansky (21) expressed similar views by stating "The most serious objection to the modern theory of evolution is that since mutations occur by `chance' and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye."Also: "...In fact, Darwin shared some of these same views, and even Weismann (106), the father of neo-Darwinism, decided late in his career that directed variation must be invoked to understand some phenomena, as random variation and selection alone are not a sufficient explanation "These of of course are not proofs that there is directed evolution driven by information,not only by random mutations and natural selection.
But i think they pose seriously the relative question. What is your opinion ?--------------------------------------------------------------------------------

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Information: It is time its undeservedly neglectet powerful role to evolution to be restored.

The modern synthesis combines evolutionary theory with genetics. If in fact the causes of species change over time actually include an intelligent designer who plans and implements genomic changes then the modern synthesis would need to be either expanded or replaced.Shapiro does not claim to have identified an intelligent designer. I earlier said that I thought you had a fair grasp of Shapiro's claims, and I chose that characterization carefully. I would have instead said you had an excellent grasp of Shapiro's claims if you didn't see an intelligent designer in his claims of directedness and non-randomness. As my Message 660 makes clear by interpreting that CRISPR paper for you, the "dedicated, nonrandom, beneficial" processes Shapiro calls attention to are not an intelligent designer at work, but are merely the operation of genetic and cellular processes that were produced by evolution. If you doubt this then send Shapiro another email with this exact question: --PercyEdited by Percy, : Typo.

Hi Zi Ko,I would be glad to provide my opinion but instead find that my attention is fully taken up by your odd juxtaposition of quotes. Why on Earth did you quote Wright in such a way as to make it seem she was stating that Darwin shared Dobzhansky's views about eye evolution, when what she actually said was that Darwin shared some of Lamarck's views about the inheritance of acquired characteristics?AbE: For reference for anyone reading this, here's the paper Zi Ko is quoting from: A Biochemical Mechanism for Nonrandom Mutations and Evolution--PercyEdited by Percy, : Provide reference.

Re: Natural Engineering
-------------------------------------------------------------------------------- Sorry. What i wanted was to stress the fact even Darwin didn't exlude the possibility and therefore the mechanism,, in some cases, where environmental or inernal information plays a role in evolution. I don't mean 'environment role'what it comes from natural selection, as Lamarck didn't know anything about natural selection. so anything Darwin was sharing with Lamarck was out of natural selection. I hope i cleared up the misunderstandjng. Edited by Admin, : Fix quote.

Hi Zi Ko,Thanks for the clarification, that helps a little. Here's your original question: If by directed evolution you mean an outside agency that plans and implements genomic changes then I see no evidence of it myself, nor any evidence that Larmarck, Darwin or Dobzhansky subscribed to such ideas.But if by directed evolution you mean mechanisms that evolve to facilitate more rapid adaptation, that possibility was recognized long before examples were ever identified.--Percy

It would also seem that Wright was quote mining Dobzhansky: This article is not the same as the one cited by Wright, but is a reappraisal of the 1950 Scientific American Article. Note the bolded section that was omitted by Wright which makes it clear that Dobzhansky was arguing against the idea of the human eye appearing fully formed from an eyeless precursor.

Hi Percy,I think you've done a pretty good job of summarising what the review paper says about the CRISPR system in terms of anti-viral defence. One bit that I thought was a bit unclear was when you were discussing the non-random selection of sequences. The actual non-randomness is due to the preference for elements of the CRISPR system to target specific nucleotide sequences, these sequences are termed proto-spacer adjacent motifs (PAMS). These PAMS are not actually part of the proto-spacer sequence but rather appear to be the sites targeted by whatever mechanism incorporates the viral sequence into the CRISPR locus. These aren't highly specific sequences, one recognition motif is NNAGAAW (where N represents any nucleotide and W represents an A or T) another is NGGNG. These different recognition sites seem to be associated with distinct CRISPR loci.I'm not sure from your description if you were saying that the viral sequences had any specific function in the virus, there doesn't seem to be anything suggesting that in the paper.So the sequences are non-random in that they are both targeted to specific motifs for picking up proto-spacer sequences and also in as much as the sequences are reincorporated into the appropriate CRISPR locus on the bacterial genome.This all seems to suggest that there must be something in the CRISPR associated genes around a specific CRISPR locus or in the leader sequence which provides both the motif template for PAM recognition and also identifies that CRISPR locus as the point of insertion for newly incorporated spacer sequences. Mutation of PAM sites shows that they are also required to be present in the phage for the resistance mechanism to operate.The selection of the sequences itself is much less interesting in terms of non-randomness, since it is simply based on not very rare recurrent sequence motifs, than the way the system inserts the corresponding spacer sequences back into the right CRISPR loci.TTFN,WK

Do you disagree that the CRISPR System they discuss in the paper, are in the authors opinion dedicated, nonrandom, and beneficial?

I think that it is totally irrelevant whether they hold that opinion or not.In addition, the authors opinions are not relevant to the topic itself.As I pointed out in Message 3: If you look at your OP you will see that you are discussing "directed evolution", and dedicated, nonrandom and beneficial have nothing to do with some directed or drive evolutionary system.You are quite simply, trying to palm the pea, misdirect the audience, con the rubes. create an attractive rabbit hole.And you also refused to answer the question.Does the phrase "dedicated, nonrandom, and beneficial" appear in either the abstract or the article?

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Anyone so limited that they can only spell a word one way is severely handicapped!

I read the other paper I linked in my message. I understand what they are saying about the highly adaptive resistance mechanisms that recognize and destroy the invader. I understand they are saying they are nonrandom and beneficial.
So I assumed Shapiro would not misrepresent the other paper he cited. Do you disagree with the findings that the CRISPR System they discuss is a dedicated, nonrandom and beneficial system?I have read all or most of Shapiro's papers and his new book. I understand his biological findings, even though if I were to look at them microscopically I would not know what I was looking at. I am not a biologist, but I can read and understand what the authors are saying about their findings.I read many papers and books about the theory of evolution by all the major supporters of their particular interpretation. After all my reading I concluded that evolution could not be an accidental, random process guided by natural selection as per Dawkins, Coyne et. al.I read the IDs papers and didn't accept the fact that it was a Science that should be taught in the schools, but their philosphy made sense to me.I then read Shapiro and, by the way, he is not an Idealogue, not an ID proponent. He sets out his findings, explains what they mean w/o resorting to teleology.I am of the opinion that Shaprio is a very qualifed expert in this field and his findings make sense to me. So from his papers and book it is my opinion that Evolution is a planned created process, just as an atheist such as Dawkins finds it is a accidental process which happens to agree with his Atheism.
Could Dawkins ever find or believe that evolultion was planned? So he doing what you say I am doing. Intrepreting his findngs to agree with his belief. I do understand his findings as he told me in the e-mail answers I posted.
Many people on this board will never accept the findings of the CRISPR papers and other findings that lead to dedicated, nonrandom, beneficial changes.
That does not conform to their belief. This was also my intrepretation after I read Shapiro's book, read the Karginov and Hannon paper and looked at the Abstract I linked.That the process developed over time through descent, modification and selection I have no problem with.After accepting these findings I believe we should think about how this could happen.
Is it totally accidental and random?
Is it planned?
Does it operate like an Engineered system as Shapiro states?Which is more logical?
I go with planned, am I wrong ,and if so ,what is the basis for the opinion I am wrong?

The authors believe it is directed mutation.

Dedicated and Directed are not synonymous.

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Anyone so limited that they can only spell a word one way is severely handicapped!

Hi Shadow,First you say: Then you say: Descent, modification and selection are natural processes. Planned and implemented by some entity is not a natural process. You seem to be trying to have it both ways. All people of science at this forum provisionally accept any legitimate scientific finding. The resistance to your arguments isn't about the evolution of processes that aid adaptation. I'm sure very few people here have any problem with the CRISPR papers. The problems stem from your interpretation of Shapiro's comments as supporting direction and planning.--Percy

Thank you for the answer. now i would like to make a most crucial question:What science seems to accept as most propable:
Are these mechanisms that evolve to facilitate more rapid adaptation in bacteria the result of
a) random mutations and natural selection only.
b) innate orders put by Supernatural being in order life to be preserved.
c) innate orders passed to bacteria from the Information system which rules over Substance in life's substance-information dipole.In my opinion b) is the less scientific approach, although Supernatural becomes a logical proposition when we face the question how life has started and how universe was created.
a) faces serious difficulties in accomomodating all new findings in genetic biology.
c) seems to me the most propable of all.
To make things clearer Iquote from my work: (http://www.sleepgadgetabs.com)
" Matter.
If we make a bold jump of thought, we can say the four interactive forces, by which the simplest particles in the universe interact with one another, eg gravity, electromagnetism, weak and strong nuclear forces are all, in other words, expression of communication between them.So communication, eg information transfer is taking place even between non living matter staff and is essential to universe development. Of course this must happen on a more wide and complicated scale on living organisms and especially as regards to life development and evolution. It seems there is in nature, and it is logical to be, a continuum relating communication from simple matter to higher living beings, as I have mentioned in previous chapters.So, material and information, existence’s basic dipole, are the cornerstones of universe, life and consequently of evolution. Both are equally important. Information, it seems, has the potency of a universal law."I should add that information as being perpetual is self perpetuating life.--------------------------------------------------------------------------------

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Information: It is time its undeservedly neglectet powerful role to evolution to be restored.