February 10, 2008

A Supporter of the Han and Warda Mitochondria Review: There Had To Be One Somewhere

Out of sheer curiosity and a slow morning spent largely on studying phylogenetic analysis methods long enough to make my eyeballs hurt, I decided to run a blog search to find out if there was anyone out there who was in support of the recent review by Han and Warda. I'm referring, of course, to the deservedly infamous Mitochondria, the missing link between body and soul: Proteomic prospective evidence in Proteomics ahead of publication. The paper has been thoroughly torn to shreds on the basis of bad reasoning and outright plagiarism, but still — there had to be someone out there daft enough to come out in support of it, right?

Well, here he is! A DrMC in a blog called AcademicFreedomBlog faults not the plagiarizing authors or the editors asleep at the wheel. Note that the editor-in-chief of the journal has even stated unequivocally that the publication of this paper in any form points to a problem with their review process (his words). But no, this blogger goes after the scientists who went after the paper itself:

Another Darwin-Doubter Criminalized

...Consider the following article which may not see the printed page next month. It is entitled "Mitochondria, the Missing Link Between Body and Soul: Proteomic Prospective Evidence," and passed review for Proteomics, "a well-regarded molecular-biology publication..."
Did it pass review? The scientist heading the journal seems to think it points to a problem in the review process, intimating that it didn't go through what he would consider a proper review at all.
...make no mistake about the real objection- -the one that led to all the
search for other problems. Take for instance, Pharyngula, a blog which leads into its attack of the editors by saying
plagiarism get past them. It gives one sentence as an example of this flaw, but then dedicates most of the article to restating and discussing whole paragraphs that leak words like "wisdom" into the discussion of mitochondrial workings. This particular blog sees no logical connection between the description of the ubiquitous mitochondria and the possibility of a creator, but buys whole heartedly the theory that this source of power for the cell holds its place as the result of having been swallowed by a more primitive cell form in the primordial sea...
That theory was itself controversial until not too long ago and only gained acceptance because of increasing evidence coming from numerous independent lines of inquiry. At one time, endosymbiotic mitochondrial origin was cited as an example of a weakness in evolutionary theory by its critics. Now we have critics citing acceptance of the theory by evolutionary biologists as a weakness of evolutionary theory. Make up your minds, people!
...No incredulity is wasted on the fact that the cell form without mitochondria has never been found in fossil or living form, and that no one can even explain how such a cell could survive without the oxygen-processing provided by mitochondria...
Wrong, wrong, wrong. I know of at least two taxa of single-celled eukaryotic organisms that lack mitochondria.

First, there is the phylum Microsporidia. Most likely a group of ultra-reduced fungi, they have been shown to have one or more nuclear genes that we normally find in mitochondrial genomes. They retain what may be a vestigial mitochondrion in the form of a body called the mitosome which itself has no genome, unlike true mitochondria. Thus, it is possible that this taxon primitively contained mitochondria but reduced them drastically as the result of gene transfer to the nucleus.

Secondly, there are the Trichomonads, a group of anaerobic, parasitic flagellates that lack mitochondria and have organelles called hydrogenosomes. These latter organelles are responsible for generating energy in the cells in a manner similar to mitochondria, but they are at best something like the mitosomes. That's at least two cells that lack mitochondria, though they likely once have had them.

Of course, the decision as to whether or not they had them rests entirely upon principles of evolutionary biology, and therein lies the problem for DrMC and those like him (her? I don't know). It is impossible to say whether or not all primitive eukaryotes had, or did not have, mitochondria without invoking evolution in the first place, since it is patently impossible to make that judgment without first positing some organized line of changes between them, also known as phylogeny. Without evolution, phylogeny is absolutely meaningless. Of course, we shouldn't criticize too harshly for this someone who thinks that we could ever find intact membrane-bound organelles in cells fossilized a billion years ago and more! I'm not aware of the fossil record of the earliest eukaryotic cells, or indeed if there is one, but we can't peer down a microscope and see the fine cell structure of much more recent fossils, either. If not for evolutionary principles in the first place, why should we even expect that they were made of cells at all? Perhaps trilobites were actually silicon-based life forms! Has anyone ever seen an individual cell from a trilobite?

How do we know that trilobite cells has membrane-bound organelles? Maybe they were huge prokaryotes! Without the organization provided by evolutionary biology, there'd be no reason for this idea to sound as daft as it does.
...Forget the hype over plagiarism and grammar. The Chronicle of Higher Education’s "Daily Report" for Feb 7, 2008 introduced its link to the article in question by saying, "’Proteomics’ has made available online a paper on mitochondria that includes language in opposition to the theory of evolution." That is the real crime.
I wasn't aware that the Chronicle of Higher Education had reported on the paper and I hadn't seen others make reference to that fact, either. There are two "crimes" here.

The first is plagiarism. That isn't hype; that's an ethical disgrace falling squarely on the shoulders of the authors. The plagiarism has been documented.

The second is the poor logical quality of the review. It makes unsupported leaps in reasoning, going from a review of published literature about mitochondria to the conclusion that our lack of total understanding is somehow evidence for divine intervention. It's nonsense, and the "crime" is that it very nearly got published in a peer-reviewed journal. The fact that it was caught by others who took the time to read the paper, report their complaint to the editor, and received acknowledgment from that editor that the paper represents a defect in the journal's processes speaks to the vigilance of the scientific community, not to some defect in its character.

No matter how thin the straw, we see, there will be some science-denier somewhere who will grasp at it. That he is blissfully unaware of or must choose to ignore evidence that contradicts his/her claim will never get in the way of an opportunity to spout off propaganda.

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