Quick is not instantaneous. The Cambrian Explosion did not occur as quickly as some surmise, it took tens of millions of years and most body types were in existence before the fossil record could easily capture the evidence, including Chordates.
"We know that the human brain came into existence from thousands of fast and focused changes across the human genome in a way that "categorically different" from M&NS at large.
This is quite the assertion. Care to back it up?
"We know ecologies are balanced carefully across the planet and introducing foreign species wreak havoc on the local environment.
We also know that the majority of organisms that lived on Earth are extinct.
"We know of creatures that live in symbiotic mutualism. We know of creatures that haven't changed in millions of years.
Care to list a few?
"Yet M&NS can apparently perform miracles."
How are any of the things you listed miracles?
Are you seriously suggesting that mutations and NS can not be falsified or that they cannot be compared to other theories?
"Despite some postings about ways to disprove M&NS, without specifically defining a boundary in biology between what it can and cannot do, these statements fall flat. It is in the same boat as "mini-ID" is in the paper."
Both mutations and NS have recognized limits contingent on their preexisting conditions and state. The state of a mutation is determined by the environment it is found in, it may be immediately beneficial, immediately deleterious or it may be neutral. Any one of those three states can change to another if the environment is modified. That environment includes the other genes/regulators within the same genome. Some mutations are extreme enough that their effect is magnified and so deleterious that the organism does not survive. Those mutations are weeded out. That weeding out is natural selection (or some other form of selection).
The limits of what mutations can and cannot do are determined by the existing genome and the environment that genome is found in. Through work in the lab we have determined there are limits to the size, type, location and frequency of mutations. Within the space of all possible phenotypes derivable from all possible genotypes, there are many phenotypes unavailable to a specific genotype. The aphorism "You can't get there from here" is quite apt in the case of specific mutations.
As far as NS is concerned, it cannot produce anything and everything. It can only work on existing morphologies.
You seem to be upset that so far everything we have found in nature has been explainable by a number of evolutionary aspects, (not just limited to M&NS). Is this really surprising or unexpected given that everything we see is a result of changes to existing plans (descent with modification)? Evolution is nothing more than trial and error limited to using previous working organisms as the basis for new organisms.
Even if we ignore Sober's points about falsification and strictly deal with the falsification of evolution we see it fits Popper's criteria. A theory does not need to remain falsifiable throughout it's life time, it only needs to be falsifiable in principle. The theories of evolution, like many other well tested theories, are no longer falsifiable in practical terms not because evolution is no longer science but because thousands of tests have been constructed, based on falsifying criteria of the time, and the theories have passed all of those tests. These tests range from lab work with insects and microorganisms to domestication of livestock to computer simulations.
If we take Sober's point then both ID and evolution have to be tested against another hypothesis, even if that is the null hypothesis. They can also be tested against each other, which is what IDists are trying to do but without asking questions of ID.
If two hypotheses explain the same data equally well then the only option to determine which is the best explanation is to ask questions where the two hypotheses will give different answers. These questions must be independent of the processes being tested and based on previously verified answers. In ID those questions must be based on some prediction where ID will be verified and the deterministic process of mutation and NS shown wrong. Since ID's claim is that an intelligence is necessary to produce complexity it not only has to show that evolution could not produce that complexity but that ID has the capability of doing so and is the only possible answer. Because a designer could just as easily produce a product that looked undesigned as easily as one that looked designed it becomes necessary to understand the intent of the Designer. If we desire to identify design within the artifacts of that design, in this case a string of DNA, then we need to know the indicators of fabrication - in other words - the designers capabilities and manufacturing limits.
We do know the limits M&NS. We know that we will never see a horse give birth to a cat. We know that most trials do little and many result in dead ends. Evolution can not be used to explain every single possible variation, as you seem to suggest, but it has explained every variation we have so far examined.
Evolution has to continue with what already exists. A designer, depending on its capabilities, has no such restriction (Oops. Looks like we need to know its capabilities). Is this perhaps why the question of transitionals keeps rearing its ugly head? IDists know they have to find something that ID explains but evolution does not. Your statement was not equivalent to Sober's.
"This is quite the assertion. Care to back it up?"
http://chronicle.uchicago.edu/050106/lahn.shtml
"Care to list a few?"
http://www.floridaevergladesalligator.com/
"A theory does not need to remain falsifiable throughout it's life time, it only needs to be falsifiable in principle."
It's a little more nuanced than that. See:
http://spot.colorado.edu/~cleland/articles/Cleland.Geology.pdf
You seem to like vagaries for the rest.
"The limits of what mutations can and cannot do are determined by the existing genome and the environment that genome is found in."
"Through work in the lab we have determined there are limits to the size, type, location and frequency of mutations."
And Haldane's dilemma resulted, and was promptly obscured by later researchers.
"We do know the limits M&NS. We know that we will never see a horse give birth to a cat. We know that most trials do little and many result in dead ends."
But you might given enough time. Evolution doesn't tell you a direction.
"Evolution can not be used to explain every single possible variation, as you seem to suggest, but it has explained every variation we have so far examined."
Do you see how little difference there is between these two statements? Evolution has almost 0 predictability and the same amount of explanatory power. Do you know, given a specific population in a specific environment what will happen to the population? Does evolution predict how the population's DNA will change? No. Evolution only predicts that at some point, the DNA will change and whatever changes will be selected from based on an undetermined fitness ratio.