Does the Darwinian theory require modification or replacement?

shadow71 writes:Obviously I cannot prove that, nor can you disprove it.

Throwing spacers at random in and around the proximal point of gene loci is better than completely random mutations of any type anywhere

Al-Attar et al. writes:Investigating the spacer content of the genomes of more than 13 crenarchaeal acidothermophiles and the genome of S. thermophilus suggested that proto-spacers are integrated into the CRISPR array randomly and irrespective of strand polarity (Shah et al., 2009; Mills et al., 2010). Similar findings were also made in Escherichia and Salmonella (Touchon and Rocha, 2010). These findings contrast with early S. thermophilus results, which suggested that proto-spacers are not randomly selected (Deveau et al., 2008) and that PAMs mark potential proto-spacers. The presence of PAMs appears to be a general phenomenon among the CRISPR/Cas systems (Mojica et al., 2009). However, spacer uptake could still be a random process but only spacers corresponding to compatible PAMs are maintained in a population due to increased fitness of the host.

Wounded King writes: Just to clarify, I don't think the insertion site into the bacterial genome is as non-specific as you seem to be making out here...

The paper uses the word "proximal" a lot, and I interpreted that to mean that insertion is not at a very specific point, but at a point near a very specific point, i.e., the leader.

Shah et al. writes:The results demonstrate that CRISPR spacer matches are uniformly distributed throughout the virus/plasmid genomes, regardless of both gene location and degree of gene conservation. Moreover, there is no significant bias to either sense or antisense strands of genes (with the exception of STIV): both strands are targeted to an equal degree.

life itself as a messy and error-prone process

jar writes: quote:
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The CRISPR system is an elegant, effective, and fluid mechanism of defense against foreign genetic elements (Fig. 4). It is rightly described as an adaptive immune system, which evolved long before its famed namesake. Interestingly, CRISPR's ability to acquire a resistance phenotype and pass it to progeny could be construed an example of a soft, or Lamarckian, mode of inheritance. One could also view this from a conventional Darwinian perspective, where pressure exerted by the environment simply selects the fittest. However, armed with knowledge of the molecular basis of this response, CRISPR-cas does seem to fit more firmly with a Lamarckian paradigm, in essence because increases in fitness do not rely on random mutations but on a much more specific acquisition of genetic information from environmental sources.
--------------------------------------------------------------------------------mentions "dedicated, nonrandom, beneficial change"?

Perez et. al. writes:Though widely accepted as the official scientific explanation for evolution, exerting great influence on both our interpretation of biodiversity and our understanding of the world, modern synthesis lacks some major elements, to wit: endosymbiosis, reticulate evolution, the modern synthesis of embryonic development and evolution (evo-devo), epigenesis, phenotypic plasticity, evolvability; which involve several evolutionary mechanisms such as: fusion of genomes and gene fragments, methylation of DNA, tool kits, regulatiory cis-elements, hybridization and polyploidy. It is also necessary to include different sources of genetic variation, not only mutations. All this knowledge underscores the necessity to develop a new evolutionary theory, a coherent alternative to modern synthesis.Evolution can occur incrementally through small changes (genetic drift and natural selection) or abruptly through hybridization, endosymbiosis, and changes in gene regulation. The environment plays an important role in the evolution of organisms, through epigenesis. Current knowledge allows for the rejection of the central dogma of biology. Although it seems that the study of macroevolution is not an extrapolation and magnification of the events that occur within populations and species, these events cannot be decoupled, since the population in which macroevolution occurs is the same population that evolves at the microevolutionary level.Evolutionary innovations do not seem to arise at random; on the contrary, they seem to have originated from non-random processes based on the epigenetic system. As a consequence of these developments, especially that of epigenetic inheritance, a new and wider definition of evolution seems necessary, one that would be the result of several mechanisms that change both the genetic and epigenetic compositions of populations.The integration of evo-devo with the synthetic theory seems difficult or impossible. The synthetic theory is based mainly on population dynamics, on the correlation of phenotypic variation with statistical gene frequencies in populations, whereas evo-devo explains phenotypic change through alterations in developmental mechanisms, whether they are adaptive or not.As a final conclusion, we think that a new evolutionary theory is needed.

Or does the theory of evolution need a modficaton, a new paradigm, that includes and explains:
Endosymbiosis
Reticulate evolution
Embryonic devopment and evo-devo
epigenesis
Phenotypic plasticity
Evolvability etc.?

I said everything has its time. Do you thing it is clever to change the meaning of my answers?

Isaid that the mechanisms are the same that are accepted by
Darwin and Weismann.

My hypothesis is testable.

But he says that... CRISPR is inherited to progeny.....and seems to fit with Lamarckian paradigm...not relying on random mutations... but on genetic information from environment sources.Do you agree with these?

Do you disagree with the findings that the CRISPR System they discuss is a dedicated, nonrandom and beneficial system?

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.

Or does the theory of evolution need a modficaton, a new paradigm, that includes and explains:
Endosymbiosis

Reticulate evolution

Embryonic devopment and evo-devo

epigenesis

Phenotypic plasticity

Evolvability etc.?

Taq writes: 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?