Discussion of all aspects of cellular structure, physiology and communication.
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I'm new to the forum and joined for a particular reason. I've gotten to know of a Biology Graduate who also happens to be an ardent creationist. I'm an atheist and a science groupee but not a trained biologist. I'd like to be able to point out the flaws in some of his web postings. I've reprinted his most recent post below, please can you pick through it and tell me where he's gone wrong?
<BEGINNING OF POST>
<The first paragraph is about the death of Lynn Margulis>
Lynn Margulis took a controversial view on how evolution works, stressing the importance of symbiotic and co-operative relationships over competition. This concept of evolution inspired what is now recognized as her most notable idea, the notion that the eukaryotic mitochondrion -- the power plant of the cell -- was acquired by virtue of an endosymbiotic event. Endosymbiotic theory essentially maintains that mitochondria arose by virtue of a symbiotic union of prokaryote cells. The nearest living relative to the mitochondrion is thought to be the alpha-proteobacteria Rickettsia (Emelyanov, 2000; Andersson et al., 1998). Chloroplasts are also thought to have arisen in a similar manner from the photosynthetic cyanobacteria.
In November 2010, I drew attention to a paper in Nature by Nick Lane and Bill Martin, who showed that the prokaryote-to-eukaryote transition was effectively impossible without the energy demands, pertinent to the biggest event of gene manufacture in the history of life on earth, being met by the mitochondrial processes of oxidative phosphorylation and the electron transport chain. The bacterial cell alone could not meet these energy demands.
The evidence that is typically offered for endosymbiotic theory includes the following:
Mitochondria divide and replicate independently of host cell division and do so in a manner akin to binary fission, possessing homologues of the bacterial division protein FtsZ (Kiefel et al., 2004).
They are enclosed by a double-membrane.
Mitochondria and bacteria are of a similar size and shape.
Circular Mitochondrial Genome
As noted, one of the core arguments for endosymbiosis points to its circular genome. What is often not noted, however, are the cases where eukaryotic mitochondria have linear genomes with eukaryotic telomeres (Rycovska et al., 2004; Nosek et al., 1998; Fukuhara et al., 1993). Indeed, two strains of the same species of yeast differ with respect to the linearity or circularity of their mitochondrial genome (Fukuhara et al., 1993; Drissi et al., 1994).
In the case of linear chromosomes, the DNA polymerase enzymes are unable to replicate right to the end of the chromosome. This is because the enzymes are unable to replace the lagging strand's terminal RNA primer. Unless there is a mechanism for circumventing this, it will result in the chromosomes shortening after each round of replication (in eukaryotes, the enzyme telomerase attaches extra DNA to the chromosomal ends). This means that the transition from genome circularity to linearity -- a fete in itself given the changes that have to be made to the mode of replication -- must happen in concert with the evolution of a mechanism to prevent progressive chromosomal shortening. Such an evolutionary transition is far from trivial. Biologist Albert de Roos writes,
Furthermore, mitochondrial genes often do possess introns (Lang et al., 2007). These are particularly prevalent in the mtDNA of fungi and plants. The mitochondrial genetic code may also be slightly different from that of bacteria (Jukes and Osawa, 1990).
Mitochondrial DNA Replication
The claim one often hears is that circular mitochondrial DNA replication resembles bacterial binary fission. While this is true, in at least some respects, there are also important differences. For example, many of the key components are of eukaryotic origin and replication beginning at the Displacement (D-) loop (Fish et al., 2004; Clayton, 1996) is not the same as bacterial DNA replication.
It is frequently asserted that the double membrane of mitochondria provides evidence for its endosymbiotic origin. There are, however, important differences between bacterial and mitochondrial membranes. Albert de Roos observes,
The Size and Shape of Mitochondria
The argument based on the size and shape of mitochondria is one that has been turned on its head in recent years, being transformed from an argument for endosymbiosis to one against it. These organelles are now acknowledged in the literature to be better understood as dynamic reticular structures (see this link for references).
Electron micrographs displaying cross-sections of mitochondria portrayed the mitochondrion as a sphere. However, when one looks at 3D models of the organelle, the reality is somewhat different. You can take a look at some of these images by going here, here, here, or here.
The Lack of a Mechanism
By far the most potent challenge to the endosymbiotic origin of eukaryotic mitochondria is the lack of a viable mechanism, perhaps most particularly with respect to the transfer of genes from the mitochondrion to the nucleus.
For one thing, there are the variants on the conventional genetic code. This means that, over the course of their transfer to the nucleus, the genes would need to be "recoded" so as to comply with the conventional genetic code. For example, recognizing UGA as a stop codon instead of the codon for Tryptophan (or vice versa) would cause cellular mayhem.
Secondly, mitochondrial proteins made at the ribosomes in the eukaryote cytoplasm need to be identified as such to ensure that they are properly dispatched (this is normally done by attaching a "label" in the form of an extra length of polypeptide to the protein). This would require a coincidental modification of the correct structural gene (which seems unlikely). Biologist Timothy G. Standish notes,
<I've given the original link above but it's a Google search (I think) to hide the fact it comes from circle.adventist.org a Christian Education website.>
Albert de Roos explains,
Furthermore, this gene transfer must have taken place at a time extremely early in the history of eukaryotes, substantially reducing the window of time in which gene transfer could have occurred.
Summary and Conclusion
While we find examples of similarity between eukaryotic mitochondria and bacterial cells, other cases also reveal stark differences. In addition, the sheer lack of a mechanistic basis for mitochondrial endosymbiotic assimilation ought to -- at the very least -- give us reason for caution and the expectation of some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist -- and justifiably gives one cause for skepticism.
<END OF POST>
Thanks in advance. I'm happy to see that the papers supporting Endosymbiosis are from peer reviewed journals, those disagreeing with it are either Albert De Roos - an ex Biologist, now IT consultant and a ppt from a Christian Education website..
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