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Another Missing Link Demoted 11/12/2003
The microscopic protozoan Giardia may be the bane of hikers who like to drink creek water, but it has been the boon to evolutionists as their missing link between prokaryotes and eukaryotes – until now. New findings “mark a turning point for views of early eukaryotic and mitochondrial evolution,” report Katrin Henze and William Martin in the Nov. 13 issue of Nature¹, summarizing work by Tovar et al.² in the same issue: “Giardia’s place as an intermediate stage in standard schemes of eukaryotic evolutionary history is no longer tenable.” They comment that this paper “will surprise many people.”
What happened? Central to the missing-link idea was the belief that Giardia lacked mitochondria, the ATP-energy factories common to eukaryotes (cells with nuclei, as opposed to prokaryotes, which lack them). Lo and behold, the researchers found tiny mitochondria, dubbed mitosomes, had been present in the little germs all along. And they are not just shriveled up versions of the big ones. They have a unique biochemical path that produces ATP without oxygen, required for their anaerobic environment. They build iron and sulfur clusters and then organize them into oxidation-reduction transport machinery.
So it seems evolutionists have to start over in their search for a new candidate to bridge the gap between the two kingdoms. But all is not lost by the finding; it helps shed light on alternative mitochondria, ones that don’t need oxygen:

We know [sic] that mitochondria arose [sic] as intracellular symbionts [sic] in the evolutionary past. But in what sort of host? That question still has biologists dumbfounded. In the most popular theories, Giardia is seen as a direct descendant of a hypothetical eukaryotic host lineage that existed [sic] before mitochondria did. But Tovar and colleagues’ findings show that Giardia cannot have descended directly from such a host, because Giardia has mitosomes. So our understanding [sic] of the original [sic] mitochondrial host is not improved by these new findings, but our understanding of mitochondria certainly is. In its role as a living fossil from the time of prokaryote-to-eukaryote transition, Giardia is now retired. But it assumes a new place in the textbooks as an exemplary eukaryote with tiny mitochondria that have a tenacious grip on an essential — and anaerobic — biochemical pathway. (Emphasis added in all quotes.)

¹Katrin Henze and William Martin, “Evolutionary biology: Essence of mitochondria,” Nature 426, 127 - 128 (13 November 2003); doi:10.1038/426127a.
²Tovar et al., “Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation,” Nature 426, 172 - 176 (13 November 2003); doi:10.1038/nature01945

Also of interest in this report is Henze and Martin’s admission that the whole story of eukaryote evolution is slightly less than watertight: “The prokaryotes came first [sic]; eukaryotes (all plants, animals, fungi and protists) evolved from them [sic], and to this day biologists hotly debate how this transition took place, with about 20 different theories on the go.” Hate to break it to them on an already bad day, but the endosymbiont theory is not as watertight as they assume, either (see a rebuttal by Don Batten.)
Even assuming their assumption, Tovar et al. admit that whatever this endosymbiont was, it was not a simple clod: “Thus, the original endosymbiont must have possessed the capacity to synthesize Fe–S clusters and to assemble them into functional redox and electron transport proteins.” If you don’t know how to do that, don’t expect that a germ figured it out millions of years ago.

Also of interest in this report is Henze and Martin’s admission that the whole story of eukaryote evolution is slightly less than watertight:

All scientific theories are "slightly less than watertight" they are just theories, and subject to change with new data coming in. How many times do I have to say this?

There is, by the way, also nothing particularly new here, Karl Woese was demonstrating back in 1999 that the Eukariote/prokariote relationship was far more complex then parent/sibling, and the base of the tree of life was re-ordered to show that there is no single commmon ancester at the base root. Eukariotes, Prokariots, and Archia, were, by some interpretations, evolved together by a pre-DNA form of life as various answers to the dilemma of diminishing resources in a cooling world. Mitocondria, like chloroplasts (which they most disturbingly resemble as to apparent origin, function and relationship within their hosts), were, by this thesis, implanted by a non-DNA based form of life that was experimenting with DNA, much as meat machines nowadays are experiments by DNA.

The case remains as I stated it: evolution is painfully obvious when you look at the overall record, revision of details as better data comes to light is the nature of science. Your inclination to view every detail of science's struggle for understanding as a refutation of the science involved, is understandable, since you are trying to make science compete with an alternative explanation of the universe that comes to you perfected by God. Understandable, but not very pursuasive.