I think people have missed the biggest piece of information from the OP..

Somewhere, there is a Temple of Darwin. I want to know where it is, and how much it costs to join.

Here's a hint:  it used to go by another name...

Temple of Doomarwin

Membership is free, but you have to eat monkey brains instead of turkey at Thanksgiving. 

Crazier things have happened.

I mean have you ever heard of Auguste Comte?

Really important philospher and social scientist.

He was also really crazy and created a secular religion.

http://richarddawkins.net/

From your link

Koonin proposes a mechanism to account for this pattern of changes. He suggests that at certain periods in life’s history extensive genetic “scrambling” (horizontal gene transfer, recombination, fusion, fission, transposition) took place. Most of this genetic chaos proved nonproductive, but on rare occasions—by chance—a stable genetic combination emerged. These robust islands of genetic novelty represent a transition to a new regime of biological complexity.

Koonin points out that his idea merely extends the speculations made by other biologists such as the late Stephen Jay Gould, Niles Eldredge, Lynn Margulis, Carl Woese, and Thomas Cavalier Smith, who have all suggested the identical pattern for aspects of the history of the biosphere.

The primary implication of Koonin’s proposal is that no evolutionary tree of life exists.

Koonin’s proposal is intriguing, and on the surface makes sense, but upon more careful reflection raises a number of questions. Why is this pattern of explosive innovation repeated throughout life’s history? What causes the genetic scrambling to take place? Why doesn’t this process happen continuously throughout the history of life? Why should the mechanism Koonin envisions ever result in coherent changes that lead to stable genetic islands that represent discontinuous increases in biological complexity?

^ Oh no, I've added gas to the fire!

I think a more intriguing question is why god has repeatedly killed all of his creation, and then replaced them with very similar versions of what he made. I mean there have been what, five mass extinction events that resulted in at least 50% of all species being wiped off the earth each time? Not to mention the countless smaller extinction events, and the normal rate of extenction. 99% of all species that have ever lived are now dead. And every time he elimated all of his creation (which he apparently thought was pretty good after he made it according to just about every holy book), he decided to wipe it all out, and make something similar but different. Was his creation good, but he just made a little mistake? Wanted to make it just a bit better? I guess the old addage "measure twice, cut once" only applies to carpenters and not god.

Furthermore why did he make such an openly hostile planet that inevitably would lead to mass extinctions? A planet that is incapable of supporting any one species in a place for an extended period of time? I mean just with continental drift, and cyclical climate changes you gaurantee that nothing will be able to make a home for very long before it's environment changes so much that it can't continue to survive there.

This does not sound like a guy that I would trust to build me a bookshelf let alone and entire planet.

Also, go read a fucking book. Genes don't randomly get "scrambled". Go learn something about genetics and how it applies to evolution. Go read the selfish gene, or at least a high school text book on genetics. There is no scrambling that produces a bunch of flaws, and occasionally a winner.

Also, explosive innovation isn't repeated through out life's history. There is a big slow period of cellular evolution, and after the basics were established, followed the one "explosive" pre-cambrian period that still did not produce any life on land, only a variety of aquatic animals (and certainly no flying fowl as genesis suggests), and even then the aqautic creatures rarely resemble modern aquatic life. After that it moves at a brisk pace (compared to the 3 billion years prior). Mass extinction events sometimes would at times leave lots of niches unfilled, and thusly new species could evolve in various directions more rapidly. These are not "mysteries", these are only questions for uneducated biblical apologists who spend there time complaining about evolution, rather than picking up a book on evolution. If they did the latter then they wouldn't have so many uneducated objections.

Ah, screw it. Why do I bother trying? This sort of thing is never a "debate" it is forced education on the unwilling. If somebody is objecting to an idea without even understanding the basic concept of the idea, then there is little reason to try and force them to understand. The basic concepts are available everywhere, any book store, public school, most private schools, an abundance of helpful websites. Niles eldridge and Stephen J Gould would be mortified if they saw their names and studies being abused like this. In fact Gould was mortified even when he was alive.

"Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists -- whether through design or stupidity, I do not know -- as admitting that the fossil record includes no transitional forms. The punctuations occur at the level of species; directional trends (on the staircase model) are rife at the higher level of transitions within major groups."

So communist hater, if you want to actually discuss this. Go read "Why evolution is true" by Jerry Coyne, go read the Selfish Gene by Richard Dawkins,, and at least brush up on some basic concepts. After you read them, if you have questions then come back. At least then you won't be asking what scrambles genes, and claiming there are a bunch of explosions of perfected life.