What research is uncovering is that most evolution is NOT taking place “vertically” through inheritance from ancestors. Genes are also transferred “horizontally” between organisms near each other – even to other species. In other words – evolution from those we spend time with. (laughs)
Darwinian evolution is only prominent in more recent history and in more complex species. The dominant mode historically and in the present is the transfer of improvements to neighbors.
As the article observes, this overwhelming evidence was missed due to assumptions. Also, the Darwinian model does not predict how the remarkable reliability of genes could have evolved. Nor why the same code base is universal, something that would be both created and supported with horizontal transfer.
“It’s natural to wonder if the very concept of an organism in isolation is still valid at this level”
It also directly implies that evolution occurs as a result of the self-organizing potential of living systems. This, not survival of the fittest, is the dominant mode of evolution. In fact the survival mode leads to evolutionary dead-ends.
“The actual genetic code stands out like a sore thumb as being the best possible.”
As a commenter notes, it also provides a mechanism for Lamarkian evolution – passing traits on to our offspring, after birth.
This illustrates a weakness Science is prone to. The more you look into the details, the greater the tendency to forget the bigger picture. When you start simplifying rules by implying a closed system, you can forget there are no closed systems. There is no separate anything.