Why? Alternative A appears to be the correct one. But i reasoned that it is impossible to tell if i haven’t read anything about the specific genes i question. Some of them could have been subject to horizontal gene transfer, thus obstuficated the the direct homology. Then i read the Introduction in the paper, and what did i read? “we will conclude that there was lateral gene transfer when the enzyme is only present in some members of the domain and branches within another domain in phylogenetic trees.”

I feel so smart;)

If there is this type of discontinuity in genetics then the burden of proof is on the evolutionist. They must give a reason why. In this article they give the reason why as “lateral transfer” of genetics through a certain type of virus. The job now is to disprove this hypothosis. One way is to examine the local genetic environment and detect problems with this theory. If the virus is inserted randomly into a genome, then we should see this type of pattern in the genomes. On the other hand if we see a continuity of topoisomerases between genomes then we should discount the “lateral transfer” theory.

“An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists. The reality turned out to be quite different, and more interesting.”

To the authors: “Your Intelligent Designer is too small”.

Compare the chimpanzee and giraffe, shrew and whale, ant and rhinoceros.
Would not this lead to the following hypotheses?
One design principle of an Intelligent Designer is:

“Provide for high complexity using combinations of components.”

The authors have clearly never played “Hide and Seek” either themselves or with their children. Otherwise they would recognize the value of progressively harder challenges towards maturing children while making it enjoyable. (Or would never admit to it.)

This experience could be summarized in another Design Principle:
“Provide enough simple systems to encourage biologists, and provide numerous complex systems to challenge them.”

Applying these to topoisomerases raises the following hypotheses for design regarding topoisomerases:

1) “Form topoisomerases with sufficient complexity to form a wide variety of systems.”

2) “Form topoisomerases with enough simplicity to encourage biologists in their discovery, and with enough of diversity to challenge them.”

Design hypothesis 1) could be disproved by showing that all systems could be formed from two ubiquitous Topo I and Topo II topoisomerases.

Design hypothesis 2) Could be disproved by showing that topoisomerases are too simple to provide a challenge. i.e. that they fit into Darwin’s neat “tree of life.”

Objection 2 appears to be dismissed by:

“the distribution of topoisomerases families and sub-families among modern organisms is not congruent with the universal tree of life based on 16S rRNA sequence comparison (with the trinity Archaea, Bacteria and Eukarya).”

PS curious use of “trinity”.

From the growing evidence of highly specified complexity in biochemical systems, a third Design Principle might be hypothesized:
“

Provide sufficient complexity to refute all theories that life could have occurred without an Intelligent Designer.”

Don’t miss the authors’ comment 12 lines down, in the right-hand column…

This confused me for a while… I believe it should say “on the right-hand side of the column”? In my browsers there is only one column…

Anyway, thanks Paul for giving us the heads-up — a valuable service from one who reads the literature to those who don’t.

An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists.

That is the secret handshake that is required to remain in good standing with the scientific community when you publish a paper that ID supporters are going to love. It is also an admission of insecurity. It is always the papers that are the most damaging to Darwinism that get an explicit disclaimer of intelligent design. It reminds me of the the classic “nothing to see here” scene in Naked Gun.

Here is a link to a 30 second clip if you don’t know what I am talking about.
http://www.youtube.com/watch?v=rSjK2Oqrgic

The remarkable thing, though, is that this peer-reviewed, Darwinist paper asserts that the designer hypothesis makes a testable prediction!

And then of course, it’s a prediction that’s abundantly confirmed (and sometimes disconfirmed) — homology. If these authors would follow their reasoning to its conclusion, there is an awful lot of homology out there supporting the conclusion that there is a designer.

So let’s add this to the list of peer-reviewed publications supporting ID… :-p

Too bad it’s baloney.

I can’t count the number of times I’ve looked at some computer code (even my own that I had not visited in quite a while) and thought: “That’s a dumb way to do it! There’s a much simpler, easier, and more efficient way to do it.” I modify the code, and when I run it the program goes down in flames and leaves a big smoking hole in the ground.

Upon further reflection I discover that the original code really was the best, or even the only way to do it. Biologists who speculate about how an intelligent designer would have done something should do it their way and see how it works, as proof that their speculation is valid. They might be in for some big surprises.

Counter-question: How does the “science” of ID determine what an intelligent designer would and would not do?

Straight ID theory does not provide those answers since it’s about design detection. But I’m presuming you’re asking about mechanisms or “how did the actor act” which is the realm of ID-compatible hypotheses.