Help Me Understand

[RoadRunner79]

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Well, I'll start with your Darwin quote. The fact that you listed that tells me you have not read his book. Creationists are fond of quoting Darwin's "this is a problem for my theory" statements, found in On the Origin of Species  and elsewhere in his writings, but it's just the way he wrote. He would start with the objections he expected to hear, from those to whom he was showing his radical new idea, and then continue on to explain why it was not a valid objection. For some reason, there are entire organizations that delight in quoting his opening line, and then ignoring everything he says after it. Secondly, there are lots of things which were not known to Charles Darwin in the mid-1800s, when he was writing his ideas down, compared to our knowledge today. Not one scientist on earth uses Darwin as the basis for his understanding of biology, except for the law of Natural Selection, one of the four major mechanisms by which the percentages of genes expressed in a population are altered from generation to generation (the other "reducing" element being genetic drift, while mutation and recombination increase the variety of genotypes/phenotypes available for NS to operate upon).

I'm not really sure what you mean by "how they came to be". We know how species come to be; it's not a really complex question... though defining a "bright line" of what exactly constitutes speciation and/or a distinctive species can be problematic, depending on how one defines several factors in considering it so. Populations expand and fragment, and if behavioral changes or territorial separation cause two groups of the same population to cease exchanging genes within the gene pool of that species, then Group A and Group B will begin to diverge from one another with each generation, until at some point they are no longer able to interbreed and produce fertile offspring. As we know with mules and ligers, there can be quite a distinct difference between recently-related species before they cease to at least have the ability to produce viable offspring. Perhaps the easiest analogy for understanding species "creation" is to think of a family tree, and with isolated species groups as sharing a grandparent. "Cousin" species are distinct from one another, yet share a common ancestral population (the grandfather, in this analogy). Go back far enough, and every species on earth is a distant cousin.

The objection that species once thought extinct sometimes show back up isn't really an objection against evolution, but against zoology.

Seriously, though, it's a common misconception that things are trying to "evolve upward", or "toward" something. Older types which experienced insufficient selection pressure (being already well-adapted to their environments to the point that very few things caused them to lose members due to fitness problems), like sharks or alligators or turtles, stick around just fine as they were, as long as their environment does not change radically enough to place them under pressure, while other species may be under such selection pressure that they change fairly radically through each generation (though still by incremental degrees; even punctuated equilibria is slow, only appearing fast on a geological timescale). Humans are not any "more evolved" than a worm, or a monkey.

Think of a sperical-shaped tree full of branches, ever expanding outward and branching new offshoots, but only having leaves (existing species) on the very tips. Some branches are thick and some are thin, depending on how populous that species is, but all are "expressed" only at the tip. Some branches dwindle and die out, no longer reaching the surface. Some split off in directions so radical it takes an expert to find the branch from which they originated, especially if the central vein of that old branch no longer reaches the surface. Pick any leaf on that tree to look at, and another from the far side of the tree, and you find two "equally-evolved" species. The old view of climbing a great ladder toward compexity, as described by Aristotle, is almost entirely mistaken, yet continues to inform our common view of how species evolve.

I'm curious to know exactly what your questions are about the fossil record, because I'm unfamiliar with any major problems with it. Sure, there are gaps, but one of the biggest finds in evolutionary biology's history, Tiktaalik roseae, was found as a direct result of our understanding of the fossil record and its geological stratification, because of another (descendant) species that was found that suggested it should have an ancestor like Tiktaalik.

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Sorry for the delayed response.  I have been meaning to get back to this thread, and have been side tracked.  I have not read "The Origin of the Species" (I have downloaded it, and would like to, but since the theory has changed much since, it's hasn't been a priority).
First, the comment on extinct species being found alive and kicking, wasn't an argument against common descent, just that I find it interesting, and is evidence that the fossil record has large gaps by nature.  As I had said I do consider myself skeptical in regards to common descent, and consistent with that I'm not really make claims against it.  
As to evolving upwards or towards something, I have seen studies which may indicate that this may be the case.  I'm going to try and find some links, as my current search didn't produce the results I was looking for.
I am familiar with the tree or bush comparisons to evolution.  However the part that I question is the branches.  I do not see these in the fossil record.  

Part of the reason, that I did take a while to respond is; because I was re-researching Tiktaalik Rosea.  It does seem that this is no longer believed to be a common ancestor to tetrapod’s, but a relation (according to some evolutionist).  There is also a claim of tetrapod tracks prior to Tiktaalik Rosea.  However when searching for walking fish, it seems that there where a number of animals found in the fossil record which share some traits with tetrapods, but they are all different features.  Science shows that the hox gene for tetrapod development of hands and feet are present in paddlefish.  

There are gaps in the fossil record, and I don’t see the connection made in the fossil record.  It is more of this feature in an animal is similar to this feature in another, and it is assumed that common descent is the cause (I don’t think this has been shown).  I would love to see a chart that shows common descent similar to the tetrapod features I found in fish. Something similar to this graph I found on walking fish, but showing more of a progression towards the claims of common descent.  https://en.wikipedia.org/wiki/Walking_fish
I also question some of the claims of broad speciation made from the fossil record.   And in the context of this discussion, I don’t think that the definition of speciation in regards to reproduction is adequate.  

A large problem I believe is that I do not believe that similar features necessitates common descent, and I have not seen the evidence presented in a way which connects the dots across the timeline.  In regards to Tiktaalik Rosea, I had seen on image, in which the fin of a whale was remarkably similar (or more so) than the link to tetrapod's.