I've never seen any reason why natural selection couldn't explain the origin of our species (unless your talking about life itself, the origins of which have nothing to do with evolution).
I'm actually talking about the idea that single cell organisms eventually changed over a long period of time to become the species we know today, including humans - and yes, mutations are required for this.
DNA differs greatly between the organisms we know of today - and it varies all over the place, including different numbers and lengths of chromosomes. When reproduction occurs within a single species, the DNA does takes the half of the information from the mother and half of the information from the father and combines them - the result is that the amount and length of the information is unchanged.
In addition, it is found that the information often follows certain rules, as found in Punnett squares:
http://en.wikipedia.org/wiki/Punnett_square
In this case, there are certain dominant and recessive alleles that are combined in a finite number of ways, and the only way to go beyond the finite number of combinations possible is to use mutations. In addition, since the number and length of chromosomes generally does not vary within a species, mutations are required to achieve the variety of chromosome structure we see today.
Natural selection is not by itself a form of mutation - it's simply selecting traits from an existing gene pool. Only mutation really allows for creation of new traits, so yes, it's required for the "molecules to man" explanation of life found in most textbooks.
the more an organism makes use of certain traits or abilities, the more they develop and alter over time.
This is called "Lamarckism" and is an old theory that has since been replaced with the "natural selection + mutation" theory I referred to.
The problem is, there is little genetic basis for Lamarckism - it's known that DNA has four bases of A, C, G, and T, and that one base doesn't slowly change into another. As far as we know, DNA does not record events over an organism's lifetime, and the traits the organism received when it began its life are the traits it will pass to its offspring.
IIRC the initial instruction is two of every animal, then the seven and two, then back to the two. Now it could be God decided that he wanted more of the clean animals, then realised the plans he'd furnished Noah with didn't take this into account.
OR it could be brevity, as I had mentioned. I don't think it's uncommon for a person to give the big picture, then explain it in detail, then to use a shorter version later to keep things simple. In fact, most of my college essays use that style, with the body having the most detail, and the introduction and conclusions having less detail.
Here's what I see (Genesis):
6:19 - Basic generalized explanation. Establishes the basic idea of bringing a pair of most animals to the ark.
7:2 - More detail. 7 (or 7 pairs) of every clean animal and birds "of the air" (
shamayim Strong's H8064) would be bought in. Note that other types of birds (probably flightless or "unclean" birds) would be bought in as a single pair, as indicated by 6:20.
7:8 - refers everything as "pairs," reinforcing the idea of 7 pairs of clean animals entering the ark rather than 7 animals.
Frankly, all I see are differences in detail, not necessarily contradictions. There's a small squabble about the number of birds, but the more detailed verse includes a qualifier not found in other verses - something that was missed in my NIV translation

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http://www.blueletterbible.org/cgi-bin/c.pl?book=Gen&chapter=7&verse=3&version=KJV#3
On Day 6, God creates the animals. We then have the "God saw that it was good", but there is no night. Instead, he creates Adam before calling it a night.
Odd. The Blueletter Bible claims that both day and night were in the Hebrew:
http://www.blueletterbible.org/cgi-bin/c.pl?book=Gen&chapter=1&verse=31&version=KJV#31
(which is strange in itself. Why would God require a day off?, furthermore, it appears to be the only Holiday the poor bloke gets in the entire Bible.).
We humans need an occasional rest - and what better way of showing this than by example?
And oh, yeah - later during the Exodus God also gets the passover as a holiday

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Flooding (even on a global scale) was quite popular in the early period (in many ways they were the classical version of a disaster movie).
If there was in fact a large scale flood, it would only make sense that everybody would be talking about it!
The basic structure of the story is almost identical to that found in other contemporary or even earlier texts, for example the Sumerian Gilgamesh Epic (circa 2100BC). . . . A similar story exists in both Persian and Roman legend too (right down to the birds
. . . which would make sense if they were based off of the same event . . .
Hard to do without knowing more about how your current studies are based, and whether you have any background in history or anthropology.
My studies are based primarily off of the education I had at the Christian school, some websites I've found, and some books I've read. Sorry, no background in history or anthropology, just computer science, although logic and information theory can often be applied to other practices.
"#2: Isn't time rather convenient here? I see this as 'given enough time, anything is possible.'"
If the universe is actually infinite then that would be true
Interesting assertion. How do you know if this is true?
I fail to see why the time would be convenient.
Lemme put it simply:
Frog -> Prince = fairy tale
Frog + millions of years -> Prince = "science"
In other words, time is a type of "god in the gaps" for naturalists. It's the convenient catch-all explanation given when other explanations fail.
Unless you're a believer in the young Earth theory, which the church itself disproved in the late 19th century.
I've heard of a lot of possible disproof from the scientific community, but not much from the church. AFAIK, the Bible never mentions creation as a long period of time, with only anecdotal evidence from passages that don't discuss the creation event. 18th century sounds about right, though: This is the period of time when people started to use their own hypotheses about the workings of the universe to interpret scripture.