Help Me Understand

[TheRocketSurgeon]

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.

No problem. I think you still have a mild misunderstanding of what the implications are, when you say "the gene exists in fish", since it's not really the comparison of the features that makes species related in the evolutionary sense, but common gene-pools which differentiated. Whether they look similar is, as you noted, a side-effect of those genetics, and hox genes (also noted) can make things appear to vary quite rapidly, when selection gets hold of them. A better way to look at the "related features" thing, in terms of common descent, is to ask how that feature came to be a feature of that population-- in other words, "did it inherit the DNA for that feature from an ancestor, perhaps one who used the DNA in a different way or perhaps one who had the same set of features, modifying that feature as the population of the descendant species continued to evolve in its environment?"

Similar features does not  indicate common descent... you are quite correct. BUT, and this is an important qualifier, when we find features of similarity, we must ask whether or not that is the result of common descent or simply a coincidence.  As with the eyes of octopi versus those of vertebrates, we note that while the features are highly similar (called convergent evolution, as you know; there are notable differences in basic architecture and genetics to form that architecture, which allow us to make that distinction). 

I do actually recommend that you read that link; it will give you a good idea of the degree of analysis that such convergence claims undergo, which (respectfully) I think you are too-lightly brushing off.

Also, I cannot stress enough how important Neil Shubin's book Your Inner Fish  is for understanding much of the topic you're bringing up. You might be shocked to learn how much of our body-plan genetics goes clear back to those myriad ancestors, and how our plan-form was selected for and modified over millions of generations. Please, if you want to have an in-depth discussion of developmental genetics and its import for describing/understanding the Common Descent model, nothing would please me more. I often strive to use "common language" in here instead of slipping into technical-speak, but I'd relish the opportunity to speak on a more detailed level about it but if and only if  I can feel confident that I won't waste half the conversational effort on filling in "basic" (to me) knowledge which would prevent misconceptions before and misdirection within the discussion.

You should also check out this PDF series of graphics from the book, via the Tiktaalik website at University of Chicago's website:

http://tiktaalik.uchicago.edu/downloads/...re.ppt.pdf