But how is that even possible?
If UCD or CD had empirical content of their own, it should not be possible to fake them out — i.e., to trick UCD or CD into giving the wrong answer. Compare:
Surgeon (to hospital technician): I used these surgical instruments today. Please sterilize them.
Technician: I’m sorry, sir, but sometimes bacterial cells self-organize on the tray after we put the instruments in the autoclave.
Surgeon: You idiot — the autoclave is broken. Call the repairman.
Theoretical background: spontaneous generation does not occur. Full stop. There are no exceptions to worry about, and the technician needs to re-learn cell biology.
UCD and CD, by contrast, travel around with enormous and ill-defined ceteris paribus clauses attached to them. These clauses are parasitic, and bleed both UCD and CD of their empirical content. Any damn thing can happen along the branches of a phylogenetic tree, and does. For example, from 1966 to 1985, the genetic code looked universal, and this confirmed UCD. From 1985 to 2018, we observed variant (non-universal codes), and, mirabile dictu, that also was consistent with UCD.
So the phylogenetic exercises aren’t fake. UCD and CD rule out nothing, as the phylogenetic exercises demonstrate.
As I said earlier, the phylogenetic exercises merely make vivid what systematic biologists have known for a long time. John Harshman declined to read Vogt 2007, which I provided to him, but this is relevant:
"Neither such background knowledge as for instance 'descent with modification’, nor any specific tree hypothesis prohibits the occurrence of convergent evolution. This allows for both apomorphy (throughout this paper, I will use the term ‘apomorphy’ to mean structural sameness due to shared common origin and not simply observational similarity) and homoplasy as possible explanations for the sameness of character states and their distribution patterns. A given tree hypothesis is logically congruent with any specific observable evidence of character state distribution. In other words, a given tree, in combination with decent with modification as background knowledge, does not prohibit any specific character state distribution pattern (Farris, 1983; Sober, 1983). As there is no deductive link between any tree hypothesis and any specific character state distribution there exists no direct empirical test of hypotheses of monophyly (i.e., clades) sensu Popper (Sober, 1988; Rieppel, 2003)—one cannot think of any observation, which, in case it would represent a true statement, would allow to conclude the falsity of a clade or a given cladogram through modus tollens.” (p. 4, emphasis added)
I hope others will try the exercises, because the bigger the sample of outcomes, the more interesting the moral we can draw. Please contact me at firstname.lastname@example.org or email@example.com, and I will send the form. I will also provide the source publications after you do the exercises.