According to evolutionary theory, positive changes contributing to organogenesis mostly evolve independently of one another and then develop relationships after they are already there. That creates two criteria:

1.) The changes are viable on their own, and
2.) The changes are viable in the context of the entire body

What about the development of mammalian stomachs? The stomach is filled with hydrochloric acid, which has ten times the acidity of lemon juice, and pepsin, which breaks down the organic materials (flesh, whether of animals or plants) that are put into it. Epithelial cells secrete mucus that forms a protective barrier between the stomach wall's cells and the stomach's acids.

According to you, glands secreting hydrochloric acid and pepsin developed independently of the epithelial cells which protect the body's tissue from the acids. However, any organism with acids being secreted internally could not survive without some sort of protection measure that is 1.) already there and 2.) geographically located in such a place that they actually contain and inactivate those acids. I find it very hard to believe that body changes which come about unintelligently would have the foresight to accomplish such a task.

So, what am I missing?  How could mammalian stomachs have come about through evolutionary gradualism?

Plug in the Numbers

So, life on earth originated about 3.9 billion years ago...

Homo sapiens came around 200,000 years ago...

The smallest genome we see in existence today has 159,662 base-pairs of DNA...

The human genome today has 3 billion nucleotide base-pairs of DNA.

Even assuming that the very first bacteria were as complex as the smallest genomes of the modern day...

The first strain of life would have to add 2,999,840,338 nucleotide base-pairs to its genome in 3.8998 billion years just to evolve from itself to Homo sapiens...

Thus meaning that approximately .76 new nucleotides would show up every year on average (rounding down).

Or a new nucleotide would, on average, show up every 1.31 years (rounding up).

Do we see species adding novel base-pair nucleotides, on average, every 1.31 years?  1.5 years?  2 years?

No?

Keep in mind, I tilted the numbers toward the more plausible Darwinian timeline throughout the whole process.  I've been told the first bacterium would be way less simple than modern bacteria, yet I used a much more complex modern bacterium, I went with the upper boundary of the estimate of life's origins and the lowest boundary of human origins I could find, and I rounded up the time to get to where we are today, and I rounded down the number of new pair-base nucleotides that would have to be added. 

If I went the opposite way, putting an estimate of 100,000 pair-base nucleotides in the first bacterium, there would have to be .85  novel pair-base nucleotides ever year (rounding down), or a new additive evolutionary stage once every 1.18 years (rounding up).

Why aren't there an average of .76-.85 novel pair-base nucleotides every two years or so?

Any examples of macroevolution beyond genus that have been observed? 

I've seen plenty of "this plant became a different kind of plant that can't pollinate with the parent species," but are there any instances of "this plant became something other than a plant"; "this dog became something other than a dog", etc., etc.?

How could sex have come about through natural selection?

Let's say that...

-The very first organism reproduced asexually.  Otherwise, there would be no subsequent organisms.

-The offspring of this organism reproduced asexually, as they were pretty much the same genetic material, being exact copies of the original (slight variations, yes, I'll get to that).

When the very first organism with polarized sex came about, wouldn't it be eliminated through natural selection?  Unless there another organism of a species similar enough to reproduce with this sexual being and this other organism had a polarized sexuality opposite to the organism we mentioned first, then the sexual organism would not be able to reproduce and that strain of genetic data would die out. 

Now, as evolution is a gradual process without a goal, I am inclined to believe that that scenario of another opposite sexual organism existing at the time would not happen.  Are there any possible explanations for this that I am not considering?

I know that there are organisms that are hermaphroditic that exist today.  However, wouldn't hermaphrodite organisms be favored by natural selection, and wouldn't that mean that evolving into organisms with opposite sexes in individuals would be regressive evolution?  The added competition for finding a mate in the animal kingdom would be disadvantageous to the organisms, as other hermaphroditic organisms do not have to find mates but are self-replicating.  Polarized sex in organisms distorts natural selection itself, adding more factors by which their species can become extinct (instead of just natural hazards and predators, now lack of a mate can prevent reproduction), so natural selection favors asexual organisms rather than sexual organisms. 

On the other side of things, why only two sexes?  Have any third sexes come about by evolution?  If not, why so?  Is it not a possibility?  Wouldn't it be advantageous to be able to reproduce with more than one group of organisms?  I ask this to give an understanding of just how precise the development of sex had to be and actually is- not too little, not too much.  How is this?

Or, for those who don't like to read the boring stuff,

How did sexual organisms come into being if natural selection is against them more than asexual organisms, and is it possible for two organisms to independently develop compatible sexes in the same generation?

In the course of my research, I frequently physically disrupt cells by grinding them in liquid nitrogen. Sometimes I do this to obtain functional proteins, but more often to get the nucleic acids RNA or DNA. In any case, I have yet to find that the protein or nucleic acid I was working on was not functional after being removed from the cell, and yet, even though all the cell components were present and functional following disruption, I have never observed a single cell start to function again as a living organism, or even part of a living organism. For natural selection to occur, all proteins on which it is to act must be part of a living organism composed of a host of other functional protein machines. In other words, the entire system must exist prior to selection occurring, not just a single protein.

-Timothy G. Standish.  Dr. Standish is associate professor of biology at Andrews University in Berrien Springs, Michigan. He holds a B.S. in zoology from Andrews University, an M.S. in biology from Andrews University, and a Ph.D. in environmental biology and public policy from George Mason University, Fairfax, Virginia. He teaches genetics at Andrews University and is currently researching the genetics of cricket (Achita domesticus) behavior.

Now, I used a quote here, but I am going to explain it in laymen's terms, as I encourage all of you to do if you feel it is appropriate to use a quote or source.  All I ask is that you prove you understand your sources rather than just toss them around like a child with a gun.

This passage, taken from a critique of Richard Dawkins's The Blind Watchmaker, explains why Dawkins's "Methinks it is a Weasel" analogy does not present an acceptable explanation against the argument of the impossibility of complex functions arising from natural selection.  Dr. Standish's actual observable experimentation shows that cells, minus even one nucleic acid or protein, simply do not function as a living organism.

My question is, what does this mean for the belief in abiogenesis?  If we can see that the basic building block of life (Behe's "black box") is not alive unless every component it needs is present and arranged correctly, then how can we explain the origin of cells? 

Natural selection? 
They'd have to be alive for natural selection to occur. 

Random chance?
Please argue by science, not neo-Darwinism.