Besides, none of the terms that are used for evolution, like genes, or alleles, make sense in conjunction with abiogenesis.
This is true. It is an important. Many of the biological words NOW used to discuss evolution are too specific to include abiogenesis. The words that we use NOW are specific to life as it manifests TODAY.
You pointed out that evolution is not specific to biological systems. Much of the specificity that we see in biological processes hypothetically happened in stages. Therefore, the phylogenic precursors of biological processes can't properly be described by words that were coined for a processes that had already evolved to interlock in a very specific way.
Darwin never used the words 'gene', 'allele', or 'mutation' in ANY of his books. He refereed to his theory as 'modification with descent', not 'evolution'.
He used words like 'feature', 'variation' and 'spontaneous chance variation'. The words are still being used now, although they still have a very broad meaning.So a modern discussion of evolution sounds nothing like 'Origin of the Species'.
That was mostly the ignorance of the biochemistry and microbiology of living things. Scientists hadn't identified genes, alleles and specific mutations yet. The words weren't coined until Mendel's work was publicized. The word mutation didn't come about until Morgan did that work with fruit flies. The scientific words that were coined after Darwin died helped scientists avoid ambiguity.
These scientific words now have meaning far too specific to encompass the new discoveries. New research findings and modern technology has found phenomena that see to be on the edge of the so called biological phenomena.
None of the modern words used in biology can be applied to abiogenesis. Suppose that we find on a a crystal made of amino acids that grows and sometimes breaks off small crystals. Is that crystal growth or metabolism? Is that merely breaking or is it reproduction? As in all crystal growth, there are atomic scale defects that spontaneously occur randomly. Is this spontaneous formation of defects or is it mutation? Darwin may have called it spontaneous variation, but no one uses that
So Darwin's vocabulary may be useful! I read articles by scientists trying to describe transgenerational epigenetics, claiming that it may sometimes contribute to evolution. 'Transgeneration epigenetics' involves inheritance that doesn't use the formally defined genes and alleles. Yet, this type of inheritance could easily fall within the description that Darwin himself gave.
The theory of evolution is a metatheory, not a specific theory. Darwin did not know any of the microscopic and atomic scale processes in living things. He came to conclusions that were quite valid on a macroscopic level but had no support on a atomic and molecular level. The biochemistry of reproduction and metabolism as we learn it now are just plain theories. By plain theory, I mean something with a rather unambiguous mechanism on an atomic and molecular level.
The problem with modern words in biology is that their usage has become tied to the specific theories, not the metatheory. A desert locust can change from a solitaire to a swarmer due to hormones in the food it eats. Its children (juveniles) inherit its state of development. A scientist that observes this inheritance may call it a mutation. However, there is no 'gene' associated with the inheritance. There is no cite on the DNA of a chromosome that is specific to the swarming state. There are genes that are turned on and off, but they don't change sequence. Better that the scientist call it a 'spontaneous variation' until he knows more.
I am really amused at the debates that I have heard on 'gene duplication'. It is even misused by scientists in articles. Sometimes it means something very specific. I actually heard a scientist say that gene duplication is not a mutation. However, some other scientist will say that evolution is caused by the natural selection of mutations ONLY. So that means that evolution can't occur through gene duplication. Then someone will say that it must be a mutation because it contributes to evolution. Then someone else will say that gene duplication couldn't be mutation because the methods used in decoding the genome couldn't detect any gene duplications, even if they occurred.
New flash: lots of evolution came about through gene duplication.
I propose that scientists go back to Darwin's vocabulary when studying things at the edge. We should go back to referring to mutation-like phenomenon as 'spontaneous variation'. Instead of allele, we can call it 'an inherited variation'. If a scientist actually discovers the site on a chromosome that changed, we could THEN call it an allele.
You may think this is just semantics. However, misused language often slows down discovery.
The problem becomes really bad when it comes to abiogenesis. Some of our oh so early ancestors could have been rocks. The precursors to cells may have been crystal defects in the minerals.
In those days, the metabolism and the reproduction of crystal defects were not specifically interlocked. What we call a gene may have been monomer nucleic acids adsorbed to the crystal surface. Now, the defect may have reproduced inefficiently without the rest of the cell. Their success rate at making exact duplicates of themselves may have been only 1%. There would be no true metabolism, just unspecific reactions catalyzed at the surface.
I would argue that the evolution of these crystal defects very much followed the metatheory described in 'Origin of the Species'. Yes, it is evolution as Darwin would have seen it. However, referring to the nucleic acid as a gene is a bit much. Referring to the catalysis as metabolism would be much. It is not evolution the way a modern scientist would see it because the organism is too inefficient.
I recommend 'Origin of the Species' to everyone, ESPECIALLY biochemists who work with genes. A lot of biochemists learn all the theories but don't understand the metatheories.
