Richard Lenski claims that his experiment provides “one of the most direct demonstrations of Darwinian adaptations by natural selection you can imagine.”
Perhaps the biggest evolutionary development in the course of the experiment involved some bacteria beginning to feed on citric acid.
For my part, I think it’s better to approach the data without assumptions and to let the evidence speak for itself.
If lateral gene transfer is rampant throughout life, the universal tree of life becomes a matter of philosophical preference, not empirical demonstration.
Mathematics has been at the foundation of modern challenges to neo-Darwinism, while those challenges are met mostly with handwaving.