Who the hell are these people? I came across this review article today (link to the abstract found here), and it grabbed my attention. Now, without giving too much info about myself - I like to remain mysterious - I work in a proteomics lab, and my thesis is rooted in this field, so I think it's not too forward of me to say that I know something about and think very highly of the field in general. I'm not an expert on mitochondrial biochemistry or anything, but as soon as I saw the title of this article, I nearly shit myself.
Mitochodria, The Missing Link Between Body and Soul: Proteomic Perspective Evidence??????
Seriously, how did this title stand up to peer response, let alone the article itself? (I'll say now that the article was a might difficult to read due to the fact that the authors were clearly not experts in the English language, but I don't think this was a matter of translation errors, for reasons that should become clear).
First, let me explain something about the type of article that this happens to be. A review article differs significantly from a research article. A review is meant to summarize all of the available literature within a particular field, sometimes that which has taken place over a specific period of time. Often the author(s) will go slightly out on a limb and hypothesize about what is the most likely explanation for a particular phenomena, and even propose experiments which would prove or disprove said hypothesis. What a review article should not do is overreach its grasp and try to predict something, when there is not a significant body of evidence to support it. This is exactly what has happened here.
The authors happen to call themselves the Mitochondrial Research Group (so you can imagine how high their pedestal for these admittedly important organelles is), at Inje University in Korea. I've never heard of this place, but that doesn't mean it's not a perfectly good institute. It does make you wonder how someone from a fairly unknown place can get away with stretching things so much, but I guess that's a little unfair, and besides the point.
In the abstract they say:
"These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative."
Wow. That's all I can say. Wow. The hypothesis that mitochondria arose from bacteria that took up residence within other cells is a long-standing one, that has withstood quite a bit of criticism to implant itself in the scientific mindset. Maybe they made that statement in the abstract just to grab our attention... oh, wait. They said it again:
"In accordance with this disciplined performance, the work looks at recent proteomics evidence that disproves previous
lines of thought on mitochondrial evolution in eukaryotic cells."
To be fair, the endosymbiotic theory is still a theory (as plainly stated in its name), but one with mounds of evidence to back it up. You better have some real good data to feel comfortable saying that you have disproved it. Let's see what they've got...
"A recent new interpretation in the proteomics front broadens our scope of understanding toward a better realization of the mitochondrial–cellular integration with the intimate relationship to other organelles. This relationship expands its coverage from the tiny peroxisomes  to the giant ER (Fig. 1). This shared relationship, however, is basically essential rather than complementary for cell survival."
OK, that sounds reasonable, so far. They are basically saying that cells cannot exist without mitochondria. Nothing outrageous there. The thought is that the symbiotic relationship between pre-mitochondrial bacteria and other cells is what allowed multi-cellular life to form. Not that mitochondria are a parasite. Anyway, what else have they got?
"Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life."
Damn children! That's a hell of a leap. I can't quote everything in the paper that lead up to this statement, but I can say that none of it was very convincing. Basically they tried to claim that there was zero evidence for an intermediate between a bacterial endosymbiont and a mitochondria, which is untrue. Then they say that a majority of the mitochodrial proteome is synthesized from nuclear DNA and transported into the mitochondria. Fair enough, but what does this prove? Nothing! The whole idea is that this happened so long ago that things will have changed drastically, and the host cell has adapted its processes to take advantage of the endosymbiont. It doesn't surprise me at all that the mitochodrion is contributing so little to the process, it's the host cell that is taking advantage of a specific mitochondrial function. And to say that it is more likely the fingerprint of a creator? I can say with 100% confidence that there is more evidence for the endosymbiotic theory than for the creator theory, so you have betrayed yourselves. You're a couple of creationists trying to shoe-horn your creation myth into science. Shame on you, and shame on the journal for publishing this.
*Edit (5 minutes later)*
Son of a bitch!!! PZ Meyers totally scooped me. Why is reading Proteomics anyway? It's a middle-tier proteomics journal that I barely read, and I'm a proteomics guy!