Darwin Proven Wrong?

[Chas]

Evolution of Life
Despite the lack of concrete evidence with regard to the nature and origin of the universe, for the sake of further exploring truth, we can assume the absolute nature of material reality as a given in order to delve deeper. From here, we will explore the truth about what has been called “life”, or the “origin of species”. Darwin’s “theory of evolution” is based on the fact that all species that exist (at least on planet earth) are genetically similar. This “truth” assumes that all forms of life have a common ancestor and that differentiation has occurred due to “natural selection”. There seems to be little as to theory of how non-living matter and energy originally became that first life form, however, again, for the sake of delving deeper, we will accept it as a given. “Natural selection” assumes that over great lengths of time genetic mutations, or changes to the genetic code, happened as a natural aspect of evolution, as expressed through the first organism’s subsequent offspring. It is claimed that the mutations that were beneficial to the organism in it’s environment allowed the organism to be fruitful in reproduction, whereby encouraging the transmission of that mutation in that environment. It is further claimed that the mutations that were harmful to the organism in it’s environment interfered with reproduction, preventing the transmission of that mutation in that environment. This is referred to as “survival of the fittest” and is said to explain how very small differences in genetic code resulted in the extreme diversity of species. This seems to be the public opinion with regard to evolution that has existed over the past hundred years. It seems to be widely accepted because of it’s simplicity.

This is not really the 'public opinion'. Most either deny evolution or utterly misunderstand it.

But is it actually true?

The massive amount of evidence shows that it is true beyond any reasonable doubt.

The new science of Epigenetics

There is no new science of Epigenetics. There is genetics.

now has researchers digging deeper into the mechanisms of genetic expression and inheritance than was previously possible. What they report finding seems to imply that the truth of evolution may not be so simple.

The problem here is that you are mixing up levels of explanation.
There is no doubt that all organisms have a common ancestor, that natural selection and sexual selection are the sieves through which pass genetic change, and that it is a mindless algorithm.

Epigenetics is the study of detailed processes of genetic expression.

While it is observed that the genetic codes of all earth’s species are similarly structured, it is said that the actual expression of genes are observed to be very different between species and even among members of the same species.

That is quite inaccurate. The genetic code is identical for all life forms. The same base pairs, the same three-pair coding for the same 20 amino acids.

There are homologous genes across many species, some of which do exactly the same things, some of which do slightly different things, and some of which are unexpressed in some species.

This suggests that it is not simply mutations that result in differentiation, but the dynamic nature of the expression of each gene in the code sequence.

Again, you are confusing levels.

For example, a comparative analysis of gene expression between humans and primates found that there were more than 800 genes that varied in their methylation patterns among orangutans, gorillas, chimpanzees, and bonobos. Despite these apes having the same genes, methylation differences are said to account for their phenotypic variation. Further, although humans and the great apes share 99% of their DNA, so far, there are known to be 171 genes that are uniquely methylated in humans which have directly correlated with advanced cognitive abilities. This evidence suggests that similar gene sequences can actually be expressed in very different ways. Further, the evidence suggests that gene mutations can either be expressed to some degree or silenced based on the specific circumstances of each individual organism. This evidence, therefore, seems to negate the assumed “truth” that gene mutations are responsible for evolution of life and the differentiation of species on earth.

This looks like copy/paste. Do you even understand 'methylation patterns'?.

Further, epigeneticists are now reporting evidence that gene expression is dynamic and influenced by all aspects of the environment. The expression markers are said to change regularly within a single lifetime as a result of environmental stimuli. Additionally, the epigenetic markers are said to be transmitted between generations. This new evidence now leaves open to question every possible variable imaginable as being influential in the development and life of the organism, even those mysterious unknowns (“dark matter”, “dark energy”, “god”, “chi”, “cosmic rays”, etc).

There are no 'epigeneticists'. There are geneticists studying the mechanisms.

I warned you what I had to say about truth was likely to make you uncomfortable.

No, it doesn't make me uncomfortable, largely because it is not "The Truth".