This post will likely reveal the limitations on my intelligence for the first time, but I'm glad to post it
Stephen R. Covey is a man who takes principles in the Book of Mormon and passes them off very successfully to the secular world who don't know that they aren't his ideas. Stephen C. Moyer's is the guy who wrote this paper and now lives at a Christian University which doesn't exactly woo scientists.
Here are the major observations I would make of the fossil record. Feel free to edit or add.
1. It is always in increasing order of complexity
2. Identical fossils exist at similar times in differing places.
3. Differences in time, space, features, and equilibrium of fossils are found in the record.
4. Progressions in microevolution are exhibited spatially.
Now we make hypotheses of at least one mind and tests it. Best to start out with the simplest hypothesis first... could our minds themselves explain this. We would still need a mechanism for how minds like ours could do it, but lets answer the question first. Increasing in complexity is just what humans do in inventing. The computers we've used to chat on message boards is the answer right in front of us. A mind could make breakthroughs in genetic engineering, just like there was a recent huge breakthrough in transistors.
Would our minds make the fossil record this way? I took the first example to mind, amphibians and reptiles. A 3-chambered heart is probably no harder to make then a 2-chambered heart, and the skin is nothing new. But the nervous system is much more advanced and could have been beyond current science beforehand. In the equilibrium of fossils there are a few missing links which could have been prototypes to ensure for a desired equilibrium (we desire equilibrium in companies). This is all testable once you allow for hypotheses from both.
How about the geological time scale? This is exactly what Meyer's starts off with - the Cambrian explosion. Our knowledge of how complete the fossil record should be, along with a sudden explosion in many species preceeded by and followed by a long lull, is what to test. I believe this is better explained by a mind, as our nature is to make sudden rapid changes sometimes, and it could be a new mind on the scene reverse engineering existing organisms, than by chance, as when we use computer code evolution there's nothing drastic ever because its not allowed for.
Microevolution vs. Macroevolution. Small changes like a foot adapting to different climate can be built into the organism. Yet for macroevolution, you need to explain the evolution of novel genes. This is clearly the most important part of the debate, as both papers I showed you go to great lengths to exaggerate. Meyer's would have the lazy person believe that any change in a sequence immediately kills the organism and the organism would have to die countless times before a desired change can have an effect on whether the organism can be more fit. The other paper's authors give the impression that all the relevant nucleotides are side by side and one change of any of them will produce a brand new species. The truth is in the middle which is exactly why I made the third link to the 180+ papers (and 600 scientists rejecting evolution at the start of this paper is more than these 180 papers) where proposals to how novel useful genes evolve are attempted. In all the papers I didn't have to pay for and hence all the papers I looked at, there was not a single mutational method with a greater probability of making a novel useful gene than the simple one nucleotide mutating at the time. No mathematical calculation has ever been done in support of evolution of new genes, except by Meyer's against it. This is where evolution breaks apart and intelligent design must be given full attention. This is where I draw the line in the sand and say, "Who's with me and who's against me (and who doesn't have a clue)?" The fact novel genes are found is eons away from accounting for it with a probability calculation on known ways genes get wrecked. You may say, hey, we haven't yet learned the mutational technique. The more randomness you rule out, the more directed it is and the more a mind was likely at play in designing how the mutation would occur. Novel genes are more easily explained by a mind just taking an organism when nobody's watching to a laboratory and tweaking it.
I've drawn the line to where I think evolution breaks down. However Meyer's won't stop there, and the counter-paper doesn't even cover any of it. He points out that no matter how simple it would be to turn one DNA strand into a very different strand, DNA itself is quite limited. DNA does not change the cellular skeleton when cells reproduce, making an interspecies explanation impossible from anything Darwin suggested. Not only can you not change cell types from DNA changes, but egg cells are rigid as well in dictating what types of organism can develop no matter what the DNA says. Moyer's goes on and on, pointing to the absurdity of changing ever higher structures like tissues, organs, and finally organism.
I still have to answer your particular questions. Common line of descent is just what we do. In our stories, philosophies, sciences, and models and versions of inventions and software, there is a common line of descent. The change in mitochondrial mutation has been used without a yardstick except the geological time scale to date these descensions. However modern species' measured mitochondrial mutation rates are totally incompatible with long term predictions. I will back this up with a paper if you challenge it. Hence this is another thing explained by intelligent design and not rigorously explained in evolution.
Germ Theory and Genetics require posts of their own.
Now to unviel the mechanism for intelligent design. Alien life is the simplest. Although the common alien encounter story can be discredited legitimately, the real question is again probability. I refer to the Drake equation and Fermi paradox. Yes, they calculate that it's too improbable for aliens to visit us out of how many planets can have alien life. But I think one of the coefficients in the product isn't write... how many planets are inhabitable. There's no refutation that aliens could have the technology to modify planets to make them inhabitable, hence a much smaller conceivable limit to how many planets could not be inhabited, and alien life on earth is completely plausible. I also think its the simplest explanation. You may say, hey, there is a difference between the sophistication to make a planet inhabitable and genetic engineering. But I could shrug this away by one group creating and allowing another group to do the genetic engineering, especially as the climate might still be more suitable to one group. The only problem I see in any of this is why did it take 3.5 billion years? That bothers me, and the best explanation I can give is that time is not constant. People extrapolated their view to say the earth was flat. Why should we extrapolate 3.5 billion years to say that time is constant? Again, this is why I say time is irrelevant to either side.
That's about the same quality as my original post.
