Help Me Understand

[RoadRunner79]

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I have been meaning to respond to your question here, and finally found a moment to do so.  I would start by saying, that I do believe in evolution as in change over time.  A snake with legs does not surprise me, or get me worried. I started out as a theistic evolutionist, and then started to study as questions arose.  As I mentioned to TRS in my introductory posts, I would say that I am skeptical of common descent evolution and think that the arguments against the neo-Darwinian model of devastating (and that it is only held onto, for lack of anything better).  From here on out, I'll shorten common descent evolution to just evolution for simplicity.

First, I see two categories of evidence in regards to evolution, which haven't changed much since Darwin.  There are similarities between creatures, and the appearance and disappearance of creatures in the fossil record.  While the categories of evidence  haven't changed much, we do have more information than Darwin did, and I see some of this as aiding the theory of common descent and some has hurting it.  The discovery and study of DNA has shown us, that the previous assumptions of similarity are at times more than we previously thought.  Sometimes it can be used to correct, and I think that sometimes it hurts the theory.  One of the main assumptions of evolution is that similarities are the result of common descent.  That similar features are the result of similar descent.  This is what I would expect if our understanding of DNA is true.  However when this reasoning doesn't fit the accepted phylogenetic model, then it is said to be convergence and further evidence of evolution (the original assumptions cannot be wrong).  Nature finding a similar method to solve a similar problem.  The reasoning shifts to accommodate the model.  The addition of DNA studies does make this a more convincing argument; however we are also finding that convergence (including at the DNA level) is more common then we thought.  I think that it is reasonable that similar species are more likely to have convergence with a similar starting point, than dis-similar species.  Further and I think that the most convincing evidence for common descent is the presence of retro-virus DNA found along a believed line of evolution.  There is some debate over whether these are really retrovirus's especially when they are found to be functional and necessary.  It is also my understanding that these too, suffer from the problem of convergence.  If this can occur in unrelated species, then I believe that this also weakens the presumption in similar species... again shouldn't similar species be more likely to have a similar retro-virus?

I realize that this could be a fairly long post, so I'm gong to break it up into a couple of posts.   Comments and corrections are welcome; non-constructive criticism will likely be ignored.  There will be three posts for anyone who wishes to wait until I'm done.

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Oh thank goodness, a debater who has some concept of the subject material!! Thank you for that! Seriously. I had become nearly worn out with arguing with Christians just trying to get them to accept the most basic premises of science; rather than arguing about evolution, we ended up arguing about what science even was and why their arguments weren't what science claims at all. So it was a big tension followed by a big relief to read this.

That said, I do have a couple of things I'd like clarified before I begin to answer, here (and I recognize you said you have more coming, so it may be in that, and if so I apologize in advance).

First, what do you mean by DNA "shifts the model" in cases of convergent evolution? Can you give me an example of something we thought was an issue of common descent that DNA later proved to be convergent, and was shifted? I'm unfamiliar with this actually happening. I'm aware of quite a great many examples of convergent evolution, of course, but none that we did not already know were such before the advent of DNA scanning techniques. Then again, I went to college after those techniques were invented, so I may have missed such shifts that occurred before my time. Still, I would be very surprised to learn of any examples of something that is convergent evolution that was thought to be the product of a shared recent ancestry, prior to 1985 (invention of Polymerase Chain Reaction that allowed for sequencing of DNA on any useful scale).

Second, you said, "There is some debate over whether these are really retrovirus's [sic] especially when they are found to be functional and necessary."  That's not really how endogenous retrovirus (ERV) scars work; I'm not even sure how you could mean an endogenous retrovirus being "functional and necessary", since by definition they are not part of the cell's original apparatus. They have been known to trigger useful mutations, but that's not quite the same thing. They are non-functional "scars" of previous infections, and while there are ERVs that infect more than one group of species in a region (meaning ones that cannot be related for other biological or genetic reasons), they're not used as evidence of common descent (though they are sometimes used to look at prehistorical patterns of migration; if they were not in contact regionally, they cannot have been exposed to the same exact virus). To the second part of the ERV question: If the species are similar enough genetically to get the exact same species of retrovirus, as with some that affect chimpanzees and us, or baboons and all other primates, then (depending on the location infected, which may be shared among all groups) it just indicates that they share that heritage because of the exact site of scarring. You may be thinking of germs (such as H1N1) that cross entire genera or even families of animals, but those actually must mutate in a particular way to do so; it is this evolution pattern of the influenza virus that forces us to look at it when it first appears in China in birds and "guess" what mutations will occur to let it jump to us... sometimes we guess wrong. So again, I'm going to need some examples of where this occurs.

You are also leaving out other "gene-scarring" elements that, once they occur, get passed down only in the descendants, and do not cross over to other members of the species (of that generation; in later generations, as they have more descendants, it "spreads out" among the population, and may become "fixed" in the whole species over several generations), let alone other species, such as transposons. Are you aware of these and their significance?

And third, when you say "The discovery and study of DNA has shown us, that the previous assumptions of similarity are at times more than we previously thought.", this is true... sort of. There were some errors, in places where the evidence was "thin on the ground", so to speak, and conjectures had to be made, but scientists are pretty careful to mark conjecture as  conjecture, and not to say "we know what this is!" before they do. Usually, more evidence means we can settle things that were not fully settled before, which is different from how you seem to be phrasing this point. I don't mean to be a jerk by saying so, only that I think you may be reading the significance of those shifts in an inaccurate light. As before, I would need specific instances before I could tell you more about it.

I'm going to go get some food now. Be back in 45 minutes or so, most likely. I feel like having Chinese buffet.

Edit to Add: I am ten years "out of the loop" on the latest science, as I was wrongfully incarcerated for the past 9 years, and only got exonerated (thankfully only 1/3rd of the way through the sentence I would otherwise have had to serve!) and released in late April. Though I have worked hard to catch up on the latest, I recognize that there may be some discoveries in the past ten years of which I am myself not aware. Please feel free to link me to any scholarly articles or good science blogs on the points you wish to offer... you will find me appreciative.

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Thank you for the compliments... I am by no means any type of scholar on the issue, but I do try to follow it and find it interesting.  Upon typing some of this (particularly the second post after which you commented, I am realizing, that I do need to read more of the scholarly articles if I can find the time and I'm able to understand.  I find many of the popular sites and comments to be a bit fishy, and low on actual evidence.  I do visit http://www.uncommondescent.com/   you may not agree with many there, but I think you could enjoy some of the info, and perhaps even contribute. 

To your first question, about convergence; what I mean is that the same reasoning and evidence for common descent doesn't come to the same conclusion when it doesn't fit the model.  I'm either missing something which validates this distinction, or this reasoning is more based on presumptions to the idea, then is normally let on.  I think it at least calls into question the certaintly when applied to common descent.

To the second question, I am by no means an expert, although I do ask questions.  I apologize in advance if I mix up terms.   I welcome any insight you can give me here, or better yet, point me in the right direction to study further.

In your third point, I agree that I need to read more of the scholarly articles.  And I agree that scientist are "pretty careful" in mark conjecture  in these articles, although I have read some which aren't so, and pass peer review with big assumptions especially in regards to evolution.  Some skepticism on peer review is generating into more of a debate lately though I notice.  I also find that many of the popular articles presented to the public far exceed the statements of the scholarly ones.  Would you agree, that in peer review accepted ideas are going to be much easier to pass, than controversial ones?  I did hear an interview of someone who had passed the peer review board, and received notice at the last minute that his article would not be published, because of complaints about it's contents and the implications that could be made.  This was unprecedented for this publisher after passing peer review, and the article was rejected because it was I.D. friendly.  (Not promoting I.D. but could be used by them). 

Do you think that evidence which may be harmful to the theory of evolution should be taught?  I do agree, that the difficulty from both sides is to do so without bias.

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Crap... somehow instead of new post, my second post was combined with my response to you.  I thought it was a copy and paste duplicate, and deleted it.   I guess I'll have to re-write it later.