Does the Darwinian theory require modification or replacement?

Objection your honor: speculation.You are misreading what Shapiro says, and then leaping to unsupported conclusions from there. Not a good way to go.

If you will remember back in that thread, I actually demonstrated that the mutations produced by these specific mechanisms are random with respect to fitness. I can go over the E. coli DinB mutagenesis process again if you like.

In message 19 you said the following:quote:
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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.
--------------------------------------------------------------------------------In message 40, in response to a request to explain a link between Shapiro's ideas and Special Creation, you say the following:quote:
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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.
--------------------------------------------------------------------------------The latter statement is considerably weaker and less interesting than your former statement. I was hoping to hear a defense of some of the connections between the ideas in Shapiro's paper and Special Creation that you have made elsewhere and in message 19. Am I expecting too much

Well how about instead of just saying it you actually cite some research showing the mechanism that produces non-random beneficial mutations? Rather than simply mechanisms that slightly affect mutation rates, or that insert in specific but highly frequent sites in the genome, or that insert very common transposable elements. Show us some evidence in fact that these things are 'directed' in any meaningful way rather than simply being environmentally induced stress responses that may turn up a few beneficial variants but are just as likely to produce deleterious ones.

A Biochemical Mechanism for Nonrandom Mutations and Evolution
Barbara E. Wright*Division of Biological Sciences, The University of Montana, Missoula, MontanaINTRODUCTION
Top
Introduction
Conclusion
ReferencesAs this minireview is concerned with the importance of the environment in directing evolution, it is appropriate to remember that Lamarck was the first to clearly articulate a consistent theory of gradual evolution from the simplest of species to the most complex, culminating in the origin of mankind (71). He published his remarkable and courageous theory in 1809, the year of Darwin's birth. Unfortunately, Lamarck's major contributions have been overshadowed by his views on the inheritance of acquired characters. 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 (71). This minireview will describe mechanisms of mutation that are not random and can accelerate the process of evolution in specific directions. The existence of such mechanisms has been predicted by mathematicians (6) who argue that, if every mutation were really random 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."

blind undirected selection.Thanks for clearing that point up, you do have no idea what you are talking about.

As I see things, Shapiro merely suggests a stimulus generated effect on mutations. How does that make Special Creation more likely? I am not asking you for proof. I just want to understand your reasoning.

He states genetic change can be massive and non-random.
In essence he states that :"...cells have molecular computing networks which process information about internal operations and about the external enviroment to make decisions controlling growth, movement, and differentiation,,,""These inducible DNA damage response systems are sophisticated and include so called 'checkpoint' functions that act to arrest cell division until the repair process has been completed. When the checkpoints do not function, cell division proceeds before repair is completed, and the damaged cells die or produce inviable progeny. One can characterize this survelliance /inducible repair/checkpoint system as a molecular computation network demonstrating biologically useful properties of self-awareness and decision making."(Both quotes from "A Third Way: James Shapiro and the Post-Modern Synthesis" in the Boston Review. That article is cited in the thread "potential falisfications of the Theory of Evolution" and can easily be found by googling James A. Shapiro)

This is a perfect example of the mistake you consistently have made in these discussions. Those alterations are random with respect to fitness. The fact that the rate of random mutation is increased by environmental stimuli does not make them non-random as it is described in the Modern Synthesis.

Do you have an opinion whether mutations are random with respect to fitness per the modern Darwinian Theory?

I gave examples in my 2010 article (e.g. biasing retrovirus insertion upstream of coding regions) where certain changes are non-random with respect to their potential biological utility.

Shadow, please don't lie to us and, more importantly, please don't lie to yourself

of this to me leads to the conclusion that evolution is not random mutations for fitness, and "Natural Selection", but rather a planned process.
To me that leads to God.

shit. That is not how your thought process went and you know it. I don't believe for a second that you were lead to your belief in God as creator by Shapiro's waffle. No-one is going to believe that, since it is transparently false. Here is what I suspect you actually did;

So what does directed mean in Dr. Wright's paper. Is it something mysterious that might mean directed by our Creator?

Wright paper states;This minireview suggests that sensitive, directed feedback mechanisms initiated by different kinds of stress might facilitate and accelerate the adaptation of organisms to new environments.

As this minireview is concerned with the importance of the environment in directing evolution
--------------------------------------------------------------------------------Nope. It means directed by the environment. Hmm.And non-random means what exactly?

Exactly as I described above. You spent two years looking for ways to prop up your pre-existing belief in Catholic dogma. In fact your desire to find ways to pick holes in the ToE has been your primary pre-occupation during your time here. You dig out these little holes and then you inject your little god into them.It's plainly rationalisation.

I suspect that you do this because you know perfectly well that Catholic theology is extremely shaky on the subject of evolution and you are looking for a way to make that problem go away. Well this isn't it my friend. You are wasting your energy.

Oh please do tell! I would sincerely love to hear your scenario. What exactly do you imagine is going on? Does Yaweh meddle in every mutation? Just a few? What exactly is his involvement? How does God fill the alleged gaps in the ToE?

Yes, exactly as I said. You go looking to prop up your belief. You find the work of someone like Shapiro and, no matter how much that work is criticised, no matter how fringe it is, no matter how much it is derided by other scientists, you cling onto that germ of hope. I have seen it many times before. Every single one of your posts here has reeked of rationalisation, of the pursuit of a God of the Gaps argument. That is why I say that you are lying to yourself. My advice is to try and break that bad habit and stop lying to yourself, but you are free to take that as you will.

There's one thing that I'd like to ask. You seem to see ways that genomes themselves can react to environmental stimuli as in some way indicative of teleology. What I was wondering was whether you see the same thing in phenotypic plasticity, which you must have known about before you found out that genomes can be directly effected by environmental factors.Do you see teleology behind phenotypic plasticity, or do you think that it can be produced by variation and natural selection?

What utter crap you post.First, as has been pointed out to you several times, this has absolutely nothing to do with religion or atheism and certainly nothing to do with Christianity

As Dr. Wright makes clear, she would replace neo-Darwinism evolution with a neo-Larmarkian explanation of evolution that is based on completely naturalistic processes. The controversy is in her Lamarkian approach and not in the use of non-naturalistic explanations. There's nothing the least bit mystical in her paper.

So, do you see what I'm getting at? These ways that organisms can adjust themselves to external stimuli could be seen as "self-engineering", just like what we've been discussing in relation to genotypes. That was why I was wondering why you wouldn't latch on to these as indications of teleology in biological systems.What do you think?

You really can't get anything straight can you?YOU inserted religion and even said that you began with the conclusion.YOUR posts are more than enough to prove beyond a shadow of a doubt that Creationism and Intelligent Design are NOT science but only an attempt to palm the pea, con the rube, sell the snake oil.

taq writes: No, it doesn't. Your lack of scientific knowledge is causing you to read things into the conclusions that aren't there. The rate and timing of mutations is non-random, but the mutations themselves are still random with respect to fitness.

/wright writes: A multitude of random mechanisms result in hypermutation under conditions of environmental stress and clearly contribute to the variability essential to evolution. However, since most mutations are deleterious, random mechanisms that increase mutation rates also result in genomewide DNA damage. Among microorganisms, from phage to fungi, the overall mutation rate per genome is remarkably constant (within 2.5-fold), presumably reflecting an obligatory, delicate balance between the need for variation and the need to avoid general genetic damage (24, 45, 57). Thus, mutator strains are not selected in nature but remain at 1 to 2% of the population (35, 52); under certain adverse conditions, they flourish for short periods but are then selected against, apparently because of widespread deleterious effects intrinsic to genomewide hypermutation. In contrast, hypermutation that is the consequence of starvation-induced derepression and transcriptional activation represents a very rapid and specific response to each adverse circumstance. The extent to which normal background mutations in nature are due to derepression mechanisms is difficult to estimate, but the location of most C-to-T transitions on the nontranscribed strand suggest that it may be significant. Regardless, a mechanism that limits an increase in mutation rates to genes that must mutate in order to overcome prevailing conditions of stress would surely be beneficial and therefore selected during evolution.