Darwin's "Adaptation" or Lamarck's "organism" as "agency"

The word "adaptation'' was used 36 times by Darwin in his book, Origin of the Species.

This quote is the closest Darwin came to a full definition:

"The structure of each part of each species, for whatever purpose it may serve, is the sum of many inherited changes through which the species has passed during its successive adaptations to changed habits and conditions of life."-Origin of the Species.

Darwin's "adaptation" is intimately intertwined with the terms "natural selection" and "survival of the fittest." 

Darwin's view of evolution was that organisms would slowly "morph" into a new organism by the process of adaptation. This was, however, disproven by Gregor Mendel's work which caused a crisis amongst Darwinists in the early nineteen hundreds. Mendel showed "genetic" traits that we're "particulate" and that they did not "morph" into each other instead remained separate over generations in direct contrast to Darwin's evolution.

To rescue Darwin's theory, population geneticists combined approaches of "mutation-ism" in populations with Darwin's concept of adaptation.

Instead of calling it Neo-Mendelism, for the first discoverer of genetics (Gregor Mendel), they "borrowed" his theory and added it to Darwin, calling it neo-Darwinism.

One hundred years later, this is essentially the approach scientists use today.

Neo-Darwinism posits that a mutation occurred to a gene, which caused it to "adapt," thus incorporating this "advantage" into the DNA.

Over the last 100 years, techniques for studying DNA continued to improve. Following the neo-Darwinism approach, mutations in genes were thought to support the neo-Darwinism model.

Many scientists believed this model was inconclusive - that something else was going on in the DNA that had yet to be discovered. However, due to a "quasi-religious" commitment to Darwin's original idea, these concerns were largely ignored. 

Even worse were the committees that sat on the journal publications. They would pass through journal articles that merely trumpeted Darwin's ideas. The concept of "agency" of adaptation or natural selection was rarely questioned; they were passed through.

In the last 20 years, emphasizing the previous five years, a new field was discovered called epigenetics. This field had Lamarckian features to it. Jean-Baptiste Lamarck, Darwin's senior by 50 years, ascribed the "agency" of the organism to interact with the environment. Lamarck was the first individual to compose a complete treatise on evolution. 

The "agency" was a property of organisms, not random natural selection or adaptation. Epigenetics is the agency upon which the environmental "milieu" reacts to cause change to the organism.

Life is not one big gladiatorial battle. (That is the exception.) Instead, life is made up of individual organisms with complex machinery, giving them the ability to react to the environment around them. It's teleological, not random chance.

Returning to neo-Darwinism, we have a mutation in the DNA, which causes a new form or phenotype which, by adaptation, changes the DNA. But with epigenetics, no changes in the DNA are made. Instead, tags are placed on the DNA directing its expression. Therefore, epigenetics is non-Darwinian.

A primary difficulty of Neo Darwinism was how the mutation rates in the DNA were so slow compared to the many possible traits one might observe. One of the best examples of this was Darwin's finches on the Galapagos Islands, termed "adaptive radiation."

If you studied the DNA between the different finches, it did not correlate with the varieties thereof. However, recently, scientists compared the genetic changes to the epigenetic modifications of the finches only to discover that the epigenetic changes were far more consistent with the traits observed.

This "fast" change occurs because epigenetic tags are placed almost ten thousand times the speed of mutational changes. Therefore, they can react within one generation, whereas literally thousands of generations are necessary for neo-Darwinism to work.

Not to be outdone, Neo-Darwinists are hoping that there are mutations to be claimed in epigenetics. It is true that in certain circumstances, epigenetics can "change" (not mutate) specific nucleotides to another nucleotide; however, these are not "random" mutations per neo-Darwinism; instead, they are "enzymatically" directed changes. Neo-Darwinism would require modifications over extended periods to form a new gene of each different nucleotide. Epigenetics does not do this. Its changes are on specific nucleotides. Epigenetics turns off and on pre-existing genes to cause change.

Lastly, neo-Darwinism hopes that the new traits shaped by epigenetics will fall under natural selection or adaptation. Once again, for this to happen, the above mechanism would have to occur, and it doesn't.

To summarize, we have the word "adaptation" proposed by Darwin explaining the evolution of life. It envisions agency gladiatorial combat between life forms with the victor changing inheritance, as opposed to Lamarckian epigenetics, which foresees the organism as having agency. Its interaction with its environment causes change.

Lamarckian epigenetics has neo-Darwinism in full retreat. To keep their foot in the door, neo-Darwinists hope to keep their pet theory alive by merging it with a new approach called the extended evolutionary synthesis (EES). 

At least they are dropping the word, Darwin. Perhaps that is a start after 150 years of the illusory use of the word "adaptation."