Introduction - Macroevolution

About once every three months I get linked to this article from talkorigins.org, the "ultimate" atheist resource for all things macroevolution and beyond. It has reached a point that I need to stop rehashing the same material and just get it down, point by point, so I can copy and paste. So, while this is a work in progress, I'll at least have a repository for my thoughts. This introduction may grow, but it will begin as a refutation of their opening arguments.
== Evolution, the overarching concept that unifies the biological sciences, ==
This assertion is nothing more than overreaching bluster. We'll see through the course of these studies that not only is evolution not overarching or unifying for the biological sciences, but macroevolution doesn't have anything at all to contribute to the biological sciences, has no predictive capacity, no practical value, can't be repeated, and doesn't even fit the criteria the evolutionists themselves considered science.
=== [Evolution] in fact embraces a plurality of theories and hypotheses. ===
There is a two-fold issue with this admission.
# If evolution is broad enough to encapsulate multiple theories and hypotheses, then evolution itself is not a theory or even a hypothesis, not in the proper understanding of those terms. See the definitions in the next article. Where this is problematic for the evolutionist is that it shows right off that they do not hold to objective truth at all. We'll show that they don't believe anything can be known for certain and allow for "reasonable confidence" to stand in for truth. This is nothing more than worldly hope akin to what the athlete taking the field feels about winning the game. It's not truth. Biblical science is founded on objective, real, knowable truth.
# The most damning part of the admission is that by saying evolution embraces a plurality of theories and hypotheses, the evolutionist admits that evolution is full of nothing but unproven premises. A hypothesis can be any precisely stated premise whatsoever, not even tested once. To argue that evolution "embraces" these premises is to say that evolution embraces any and all untested premises so long as they support evolution. It's ultimately a circular point that leads nowhere. Biblical origin science embraces no hypothesis whatsoever and only tentatively accepts a premise that has achieved theory status as a working premise to operate from until the theory is proven false or is shown to be objectively true.
== Micro vs. Macro ==
"In evolutionary debates one is apt to hear evolution roughly parceled between the terms "microevolution" and "macroevolution". 
 I cannot stress how important this next point is. Many, many evolutionists will not even admit that there is a distinction. This admission is a devastating admission on the part of the evolutionist because if they admit there is a distinction, then it is no longer necessary to first draw that distinction and require them to admit it exists. Furthermore, it becomes the burden of the evolutionist to show that macroevolution exists as a distinct concept from microevolution, to prove it to actually be true without simply asserting that macro is micro over a long period of time. By allowing that there is a distinction at all, the evolutionist has divorced himself from the one hiding spot they have in this entire debate, the ability to dismiss any arguments against macroevolution by appealing back to micro as evidence for macro. 
More on this point throughout the articles, I'm sure. 
Microevolution, or change beneath the species level, may be thought of as relatively small scale change in the functional and genetic constituencies of populations of organisms. That this occurs and has been observed is generally undisputed by critics of evolution. " 
There are already several problems with this small section. 
The first problem is that the word "species" is ill defined by the evolutionist and can be shown to have no more than a convenient "every day" usage that has no technical value at all, especially not for this discussion. See the definition section for more. 
The second issue with these statements is that they use the term "relatively" without telling us exact frame of reference. You see, Einstein's Relativity models have had a large part to do with marketing subjective truth in the scientific community. I am too young to have met Einstein personally and do not impute to him personally any motives here for good or ill. However, people have glommed onto the idea that "everything is relative" and it has led to the idea that truth cannot be known, only perceived in some limited way from our own point of view. By saying that microevolution is changes "on a relatively small scale", we have no definite line to cross and say we are no longer talking about microevolution. They use these terms so that we can just kind of fade into macroevolution using the ill-defined term "species" and "relatively small changes". 
Me: Relative to what? 
Evo: Macroevolutionary changes. 
Me: What are those? 
Evo: Relatively large changes. 
Me: Relative to what? 
Evo: Microevolution 
Yes, that's right, we're going in circles again already. Hope you don't get dizzy easily because we're going to see them doing that a lot in their arguments. 
What is vigorously challenged, however, is macroevolution. Macroevolution is evolution on the "grand scale" resulting in the origin of higher taxa. In evolutionary theory, macroevolution involves common ancestry, descent with modification, speciation, the genealogical relatedness of all life, transformation of species, and large scale functional and structural changes of populations through time, all at or above the species level.
 Again, this is a huge admission that there is even a distinction. However, the distinction that they make is fuzzy, ill defined, and certainly not precise. They start off with their relativity again. "Macroevolution is evolution on the 'grand scale'." Grand compared to what? Microevolution. Oh, that clears it right up. So macro is just micro but bigger? Nice try. 
When they don't precisely define their terms, which is what most of these arguments get down to anyway, then they have whatever wiggle room they need to get out of any logical trap they may set for themselves. 
Another problem with this introductory section on macroevolution is the word "taxa". Taxonomy is a flawed, ever-shifting, man-made grouping of life forms. It's like my son deciding on a method for sorting his toys. Should he separate by color first, then type (LEGOs, Tinker Toys, Kinects) or should he go with type first. There is a certain amount of practical value to the most widely used taxonomy here in the states, but its flawed, mutable, has a critical level of arbitrariness, and isn't even the only taxonomy out there. We'll talk more about the difference between phenotypical taxonomy and genotypical taxonomy later. 
The last sentence involves a huge assumption that must be started with by the evolutionist before they can take the first step in trying to show that macro evolution is true: the assumption that all the constituent parts of macroevolution are already true. 
== Intro to Universal Common Descent ==
Universal common descent is a general descriptive theory concerning the genetic origins of living organisms (though not the ultimate origin of life).
 First off, its not a theory because it hasn't been tested according to the standard that the evolutionists hold to in order to determine that something is scientific. Please show the experiment where universal common descent was tested. Never happened. Can't happen, in fact. It's not testable, which in the words of the evolutionist means it isn't science. Moving on. 
Since UCD isn't really anything more than an unproven hypothesis (remember, macroevolution embraces these even when they aren't tested) to assert that it describes anything is meaningless. I'm a fiction writer. I describe stuff all the time that isn't real. What they assert that UCD describes is the genetic origins of living organisms. Yet they have no way to show this. They can only assume it and assert it. E.g. "Lucy" (the skeleton of a small male ape found in Ethiopia one day) is an ancestor to man. More on "Lucy" later. 
One final note about this sentence. They admit that UCD and indeed macroevolution says nothing about the ultimate origin of life. it is another assumption, this abiogensis, they must start with in order for macroevolution to have happened. Yet they will do everything in their power to divorce abiogenesis from their "overarching concept that unifies the biological sciences, and in fact embraces a plurality of theories and hypotheses." Apparently the overarching doesn't arch enough because it doesn't cover the very foundational premise of life science...where life came from. So much for embracing all those hypotheses. 
The theory specifically postulates that all of the earth's known biota are genealogically related, much in the same way that siblings or cousins are related to one another. Thus, universal common ancestry entails the transformation of one species into another and, consequently, macroevolutionary history and processes involving the origin of higher taxa.
 Disregarding all the assumptions in here for the moment, since we'll cover these in great detail in later articles, the one point I want to make here is that they have admitted the distinction between microevolution and macroevolution above, yet here they are essentially asserting that they are the same thing. "All of earth's [lifeforms] are related much in the same way that siblings or cousins are related to one another." The hypothesis of UCD postulates that the evolutionist's brother is a fungus? Mkay. 
So they propose that UCD covers the transformation of one species (whatever that means) into another and viola, macroevolution. And yes, that really is about all there is to it. They will, time and time again, show us micro and then wave a magic wand and conclude "thus macro". 
Because it is so well supported scientifically, common descent is often called the "fact of evolution" by biologists. For these reasons, proponents of special creation are especially hostile to the macroevolutionary foundation of the biological sciences.
 Except that its not supported at all. There isn't any evidence of UCD at all. Just assertion. IF it were really a fact, something that is objectively true, then it should be a scientific law. But thanks to relativity and lobbying, the scientific method is all messed up (see Definitions). They can't call it a Law because it isn't proven, so they just assert its a fact and because they are all scientists and anybody who disagrees with them isn't, they can just go on calling it true and it doesn't matter that they haven't actually proved it to be true. This isn't science, its just arrogance.
==Scientists Who Aren't==
This article directly addresses the scientific evidence in favor of common descent and macroevolution. This article is specifically intended for those who are scientifically minded but, for one reason or another, have come to believe that macroevolutionary theory explains little, makes few or no testable predictions, is unfalsifiable, or has not been scientifically demonstrated.
 What I like about this paragraph is that they admit that those who are scientifically minded (that means they think like scientists are supposed to think) can come to the conclusion that macroevolution is not scientific. While they will go about vainly attempting to show that it is, it is important to point out that not-macro is considered, at least in the introduction, to be a possible scientific conclusion. We'll eventually show in the articles to come, that its the only logical conclusion to make.