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I look at the same facts that he does. We both believe that homology points to a relationship. Matzke assumes that this relationship comes about by fortuitous changes being selected.I believe that the changes are more directed and that the plasticity of protein structure is being used in a creative manner.

The difference is, Matzke has evidence on his side. We have observed foruitous mutations happen in the laboratory and get selected for.
The E.coli long term evolution experiment is one such instance. I believe Calilasseia has a considerable list of papers that demonstrate this abtly both in the lab and in the wild.

Additionally, your claims are unfalsifiable and therefore unscientific. You can fit your explanation to any observed fact. "I believe what we see here is the product of intentional design" Well how do you know? "Because it looks like what the designer would want it to look".

I would say that the evidence points more towards the assumptions that I am making.

In which case you are making an unsupported bare assertion. we don't see any designers running around tweaking lifeforms today and there is no evidence around that this happened in the past.

If you propose that two functional proteins are the unplanned "offspring" of a single protein, you need to look at the search space needed to be sampled, the regulatory changes that need to accompany the new function, the various connections that need to be considered in order for the proteins to be installed in their new roles.

Uhh what? No, I don't need to do all those things. That's ludicrous. Why would that be a requirement?
The hypothesis is that the hook and filament are build by proteins secreted by a secretory system. Therefore the hook and filament proteins should be homologous to the ancestral secreted protein. They are.

Where in the organisms of the earth are all the functionless proteins or proteins with an inefficient function waiting to slot into a new system that evolution has brought forth?

What? This is a specious question when I have already told you about geneshufflings and duplications. A gene coding an existing protein can be duplicated, leaving one of them open for mutations resulting in alternate or superior function. Or two, three or more existing genes can be shuffled together into a new and highly functional protein.

Additionally, any given protein has the potential for superior function, depending on the environment. Take hemoglobin in humans for blood oxygen transport. You may argue that this protein is highly functional, but If I move to an area of extreme cold, it's ability to extract and transport oxygen is no longer adequate and it get's difficult to breathe. This leaves hemoglobin open to mutations which can undergo selection for improved function in extreme cold.
There are no "functionless" proteins waiting in a que somewhere. When the environmental and selective pressures change, the already existing and highly functional proteins undergo selection for improved function in their NEW environment.

Has anyone observed a biological system becoming more efficient over time as natural selection working on changes makes the necessary tweeks.

Yes. I'll dig something up later when I get home from work but to get you started, the observed evolution of increasingly effective camouflage in multiple species are some excellent examples.

And if the hook protein FlgE had no functionless precursors what was the path in the diversification between it and its homologs?

This question assumes the precursor must be functionless. Which is ludicrous and flatly wrong. Whatever the precursor proteins function was, as the entire precursor system started serving a motility function, the hook-precursor protein was under selection for increased functionality, in this case successful transfer of torque without breaking. Those that failed, died, those that succeeded didn't.

If you try to make a hook out of proteins that don't have the specific properties of FlgE and you will no doubt end up breaking the flagellar drive.

Big surprise?

And there is no evidence whatsoever of a pre-existing universal joint being co-opted and slotted into place in the drive train.

Which is not the proposed model and therefore a strawman.

Goal directed development is something we see all the time. We see it every time an individual organism grows from an egg or a seed.

Yes, that goal being the construction of bodies from genes evolved through succesive generaitons over hundreds of millions of years, to successfully construct bodies that enhanced their chances of successful replication. Which Is why we have so many vestigial traits and organs and share so many attributes and oddly constructed imperfections with related species. And why ours and every other organism's DNA fits so well in a hirearchial tree of life. Why comparative anatomy, biogeography, embryology, the fossil record and everything else fits so well with the darwinian evolutionary explanation.

The fact that self-aware creative beings have appeared on the earth is no accident

Baseless blind assertion.

CharlieM:
I was talking about natural selection on its own. I know things are different when mutations are taken into account. My point was that natural selection cannot create novelty it only removes or lets through what is already there.

PhiloKGB:
This is pure bullshit, an assertion which can only be made by those merely Google-educated who nonetheless consider themselves experts.

I don't know why you think I consider myself an expert. I came here to learn and I think the best way to learn is to share your opinions with those who you know are going to disagree with them and to see what they come back with.

If you think what I said is bullshit can you explain to me how natural selection on its own can create anything that was not already there waiting to be selected?

Red herring.
We are under no obligation to explain how natural selection can create novel information, when none of us claim it does. Natural selection selects, mutations, gene duplications and geneshufflings CREATE. Please try and grasp this fundamental concept.