Thanks for sharing the links and your thoughts.
You're right that the bacterial flagellum and the injectisome both use a shared core system called the Type III Secretion System (T3SS). That’s interesting and shows they have some parts in common.
It's more than interesting. It shows that these parts were recruited for different functions over time. Remember, there are lots of different kinds of bacterial flagella, and that alone torpedoes Behe's belief that "the bacterial flagellum" is irreducibly complex. They are of varying degrees of complexity.
I respect Todd Wood’s attempt to be fair to the scientific community, but I fundamentally disagree that evolution is a viable model, even within naturalistic assumptions.
Wood and other YECs in the sciences disagree with you, and they actually know the evidence. As Dr. Wood points out, evolutionary theory works and it works well.
Bottom Line:
-These fossils show variation over time, expected within lineages.
Sorry, that's wrong. For example, we see the evolution of the mammalian ear out of things like reptilian jaw joint and other parts. It's well-demonstrated in the fossil record. One of the major misconceptions YECs have about evolution is that they suppose it requires entirely new structures to evolve ex nihilo. If you think about it, I'm sure you see how absurd that it. Evolution never creates anything entirely new; it modifies things already present. Would you like some more examples?
-They do not demonstrate fully documented, functional intermediate forms working at each stage to build complex systems.
And that's also wrong. The transition from the multibone reptilian lower jaw to the single-bone mammalian jaw is well-documented. Would you like to learn about that? It's interesting that some modern mammals demonstrate that transition in utero, showing that the reptilian genes remain, but in a modified form.
The claim that evolution “works” doesn’t answer the deeper problems: it still fails to explain the origin of information
Perhaps you don't know how information is produced in populations. Would you like me to show you the math for a simple case wherein information increases or decreases in a population? It's no mystery how new information happens in evolution. BTW, evolution can also decrease information. Fixation, for example. In biology, we use Shannon information theory. And we know it works because it's used to accurately transmit information from low-powered transmitters over billions of kilometers of space.
, irreducibly complex systems,
As you have seen, irreducible complexity evolves. It's even been observed directly to evolve.
and the sudden appearance of fully formed body plans.
Can you give us an example?
A model isn’t vindicated just because it fits a framework; it must match reality. And evolution doesn’t.
You've confused models and theories here. Evolutionary theory is accepted by almost all biologists, because its predictions have been repeatedly confirmed by subsequent evidence. That's mating reality. It's like gravity; an observed phenomenon. Once again, you've confused common descent with evolution.
Thus an entire system of lactose utilization had evolved, consisting of changes in enzyme structure enabling hydrolysis of the substrate; alteration of a regulatory gene so that the enzyme can be synthesized in response to the substrate; and the evolution of an enzyme reaction that induces the permease needed for the entry of the substrate. One could not wish for a batter demonstration of the neoDarwinian principle that mutation and natural selection in concert are the source of complex adaptations.
[ DJ Futuyma , Evolution, ©1986, Sinauer Associates, Sunderland, MA. pp. 477-478.]
That example actually proves the point of intelligent systems within organisms. It shows bacteria can adapt by reusing and modifying existing genetic machinery.
That's what evolution does. Thought you knew. It is true that new genes can come from mutations to non-coding DNA as well, but that's really the same process, isn't it? And of course, the process was shown to have been by random mutations, sorted out by natural selection. No intelligence required, other than a Creator who made a world in which such things happen by the natural processes He created.
But it doesn’t explain the origin of that machinery in the first place.
That's another YEC misconception. Evolutionary theory isn't about the origin of life. It assumes life appeared, and describes how it changes.
The components used (enzymes, regulatory genes, permeases) were already functional and present in the genome.
No. Neither the new enzyme nor the regulator existed in the initial population. These were produced by mutations and natural selection.
Tinkering with existing parts is not the same as building irreducibly complex systems from scratch.
You were apparently unaware that evolution works by tinkering with existing parts. That's (for example) how legs evolved. Would you like to learn how we know this?
Evolution explaining small tweaks is not the same as explaining the origin of entire systems where no part functions on its own.
In biology, everything is tied to everything else. But as you have seen, irreducible complexity can easily evolve by a number of means. Would you like to see more examples?