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I mostly agree with what you have said here. Obviously there are multiple mechanisms by which new gene rise and doubtless many new ways by which genes arise and evolve new functionality will be discovered. The link you quoted refers to the exciting research of de-novo gene formation where non-functional segments of DNA, through mutations, acquires new functionality in protein transcription and hence become a new "gene". What this shows is that
1)Not every gene need evolve from a previous gene. Mutations can spontaneously create new genes that are then fixed by selection. That means that, while venerable gene families with long family history exist, there are new kids on the block too who join the gene population and contribute to the organism. This once for all answers the question of whether the mutations-selection process can create new information in the organism. The answer is an unambiguous yes. Notice what the article says:-
The Odds of Becoming a Gene
Scientists are testing computational approaches to determine how often random DNA sequences can be mutated into functional genes. Victor Luria, a researcher at Harvard, created a model using common estimates of the rates of mutation, recombination (another way of mixing up DNA) and natural selection. After subjecting a stretch of DNA as long as the human genome to mutation and recombination for 100 million generations, some random stretches of DNA evolved into active genes. If he were to add in natural selection, a genome of that size could generate hundreds or even thousands of new genes.
At the Society for Molecular Biology and Evolution conference last month, Albà and collaborators identified hundreds of putative de novo genes in humans and chimps — ten-fold more than previous studies — using powerful new techniques for analyzing RNA. Of the 600 human-specific genes that Albà’s team found, 80 percent are entirely new, having never been identified before....
Evidence suggests that a portion of de novogenes quickly become essential. About 20 percent of new genes in fruit flies appear to be required for survival. And many others show signs of natural selection, evidence that they are doing something useful for the organism.
In humans, at least one de novo gene is active in the brain, leading some scientists to speculate such genes may have helped drive the brain’s evolution. Others are linked to cancer when mutated, suggesting they have an important function in the cell. “The fact that being misregulated can have such devastating consequences implies that the normal function is important or powerful,” said Aoife McLysaght, a geneticist at Trinity College in Dublin who identified the first human de novo genes.
Genes code for proteins which are 100—1000 chain sequence of the 21 amino acid molecules. Each amino acid is coded by 3 letters in the DNA. So if a single mutation occurs flipping one of the letters, this only changes one amino acid in that protein composed of 1000 such units. The activity of a protein depends on its three-dimensional shape, and in most (but not all) cases, alteration of one amino only slightly alters this shape. Such moderate shape change only has moderate effects (positive or negative) on the protein's function. And it is these small (usually) variations in protein activity that are selected for or against in as far as it effects the survival and reproductive fitness of the organism. Thus permanent alterations in DNA usually results in slight alterations in protein activity and it is this activity variation that is selected for or against.
The number of positive mutations that are seen to arise are numerous. Positive mutations are not rare at all, and this also an exciting find made in the last decade. Put an organism in an environment of high stress, and the number of mutations with positive effect skyrocket. The reason is simple. The proteins perform certain functions. If the organism is in an environment where it's well adapted, most proteins are acting at optimized peak performance. But if the environment is stressful, then this implies that the proteins created by the organism's genes are not optimized to this new environment, and hence moderate mutation induced protein structure variations become more likely to improve its functions than decrease it by the logic of probability itself. In fact the frequency of beneficial mutations is so large that the same set of 6-7 mutations optimizing the fitness of yeast emerged in 40 different independently cultured yeast strains over a 1000 generation period, though in different order and at different times for each strain.
https://www.sciencedaily.com/releases/2013/07/130722203041.htm
Paper
Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations
I meant that natural selection aids in preserving and increasing the frequency of the new gene with fitness benefits among the population to which the organism having that new gene belongs. I explained the process (which a light sprinkling of algebra) in the post below. Please also the quoted post for the background. Hopefully it would be clear.
What is Evolution?
Yes. Reproductive isolation will cause genetic divergence. The post I wrote was based on the studies that shows how an old gene can create a new gene with a new function without requiring reproductive isolation. There are many well studied mechanism for generating reproductive isolation. I described a particularly fascinating mechanism in the thread below (see the opening post of the thread as well).
How Speciation Happens (yes it does)
Hope these are informative. If you have other questions or concerns about evolutionary biology, please let me know.
You will have to say more than this for me to understand what precisely you are suggesting and for me to assess if your suggestion if even possible.
