Does the Darwinian theory require modification or replacement?

Why does it need modification or replacement? Your reply was not clear at all.

This is perfect. This is the exception that proves the rule.The paper you cited was not available for free, so I would direct your attention to this paper:http://www.biochemj.org/bj/imps/pdf/BJ20110901.pdfIt is the same system you are pointing to, and it details the molecular mechanisms that produce the mutations.In this case, we have an entire operon devoted to inserting phage DNA into a specific area of the genome. I will gladly accept this example as directed mutations.The problem, however, is that an entire set of proteins is devoted to specifically mutating this section of DNA, and it is very specialized. What you have pointed out is the very reason that random mutations are so prevalent in evolving organisms. How large would the bacterial genome need to be in order to guide mutations for the entire genome? For each protein devoted to guiding mutations you also need another set of proteins devoted to mutating that protein, and so forth.Also, is the CRISPR system important for anything other than phage resistance? Nope. This system does not guide mutations for the evolution of new enzymes involved in metabolism, for example. On top of that, this system is not seen in eukaryotes.Edited by Taq, : No reason given.

If which mutations are nonrandom? If 99.999% of mutations are random with a few examples of specialized systems that insert viral DNA into palindromic sequences would the entire theory need to be rewritten, or would a footnote do?

Isn't that what a scientist should do? No serious scientist would claim that empathy guides mutations. So you admit that you have no mechanism, not testable hypotheses, and no theory. Why should we take you seriously? Weismann died in 1914. Work since then has shown that he was wrong.If you want to argue against the theory of evolution as it existed at the turn of the 20th century then you are more delusional than I thought. Please join us in the present.

I didn't change the meaning of your answer. You are complaining that I keep asking for evidence and mechanisms to back your claims. I am asking why a scientist should not do this. Can you answer the question or not? Or are you saying that scientists should accept something as fact simply because someone claims it? And those are . . . ? How?

I would agree.Would you also agree that the mechanisms which produce mutations in the CRISPR genes do not cause mutations throughout the rest of the genome? I can look back, but I would hazard a guess that the CRISPR region takes up less than 10k bases. This is less than 1% of the genome, and much less than that if we only include the features within the CRISPR regions that are actually mutated by these mechanisms. So we are still seeing more than 99% of the genome mutated by random mutations. Wouldn't you agree?

Do you disagree that the CRISPR system only produces mutations within the CRISPR DNA? Do you also agree that eukaryotes like ourselves lack CRISPR regions?

You are blinded to the larger picture. Why are E. coli different than Salmonella enterica? It isn't due to differences in CRISPR insertions. It is due to the differences in the rest of the genome, differences that are produced through the processes of random mutation followed by selection. Remember, the theory of evolution is trying to explain why species are different from each other.

How do you think a symbiotic relationship is created other than through random mutation and natural selection? How is this a problem for the modern theory? Last I checked, the modern theory happily accepts hybridization. Darwin cited embryonic development as one of the strongest evidences of evolution, and the evo in evo-devo is in reference to the modern theory of evolution. Epigenesis is not responsible for the differences seen between species, the thing that theory of evolution is trying to explain. The differences between humans and chimps is not due to epigenetics. You mean the plasticity made possible by the random mutations that have been filtered through natural selection? What about it?

So you admit that there is no known mechanism for directed mutations outside of CRISPR domains?

You mean discoveries that have not been made yet?If I was a prosecuting attorney, could I convict someone on the claim that I will find evidence in the future? And I have already addressed this multiple times. Retroviral insertions will produce neutral, beneficial, and detrimental mutations. Inserting upstream of genes, even with a slight bias, does not guarantee that they will be beneficial. Therefore, retroviral insertions are random with respect to fitness in line with the Modern Synthesis. And I have discussed one of Wright's papers with you where I demonstrated that the mutations Wright references are in fact random with respect to fitness. I believe it was this paper. I would be happy to go through this paper again with both you and zi ko if you would like.

Not without reading more of the book to understand what he is getting at. Does Mayr deal with transposons, retrotransposons, or the process of mutagenesis at all in the book?

From Mayr's essay 80 Years of Watching the Evolutionary Scenery (2004):

quote:

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By the end of the 1940s the work of the evolutionists was considered to be largely completed, as indicated by the robustness of the Evolutionary Synthesis. But in the ensuing decades, all sorts of things happened that might have had a major impact on the Darwinian paradigm. First came Avery's demonstration that nucleic acids and not proteins are the genetic material. Then in 1953, the discovery of the double helix by Watson and Crick increased the analytical capacity of the geneticists by at least an order of magnitude. Unexpectedly, however, none of these molecular findings necessitated a revision of the Darwinian paradigmnor did the even more drastic genomic revolution that has permitted the analysis of genes down to the last base pair.

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From that quote, do you think Mayr is happy with the current Modern Synthesis?

Using your argument from authority, it doesn't matter. Mayr is an authority. Period. Therefore, anything he says is gospel, right? Or are you saying that you have a firm enough grasp on the biology to challenge Mayr on this subject? Of course this is just rhetorical given the fact that Mayr passed away a few years back.Edited by Taq, : No reason given.

The Modern Synthesis is made up of two major pillars:1. Variation is produce by mutations that are random with respect to fitness.2. The probability that a mutation will be passed on to future generations is determined by the interaction of the population with the environment.No one in this thread has presented data that challenges these two pillars. Shadow has quoted Shapiro saying that mutations are not random with respect to "biological utility", but never did Shapiro state that mutations are not random with respect to fitness. Wright claims that mutations are not random with respect to fitness, but a closer look at the data from Wright's papers demonstrate that they are indeed random with respect to fitness. What we see is a lot of smoke and mirrors from the likes of Wright and Shapiro. When those mirrors are broken and when that smoke clears the same observation is made: the mechanisms that produce mutations are blind to the effects that those mutations will have on the fitness of the organism.Let's look at two examples. First, Shapiro cites transposon mutagenesis as a "non-random" mechanism. This is wrong. The effects of transposon mutagenesis on fitness can be detrimental, neutral, or beneficial. They are random with respect to fitness. Further reading of Shapiro's work indicates that non-random in Shapiro-ese is defined as mutations that are not replication errors. Second, Wright points to the increase of specific mutants in a given environment. As it turns out, this is due to an increase in the random mutation rate, not a specific mutation of a specific base in response to an environmental stimuli.Each time that an example is given for non-random mutations it turns out to be random. The only exception I have seen that breaks this pattern are CRISPR domains. I will gladly admit that these are perfect examples of non-random mutations. However, CRISPR domains are a tiny portion of some bacterial genomes. They can not be used to explain the evolution of the rest of the genome, much less the rest of the species on Earth that do not have CRISPR domains. CRISPR domains are a very limited mechanism with very limited evolutionary reach.