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On The Non-Evidence For The Endosymbiotic Origin Of The Mitochondria

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Over the past several weeks, I have been reviewing the case presented by Daniel Fairbanks for common ancestry in his 2010 book, Relics of Eden. For my previous articles on this topic, see my discussion of the first three chapters here, here and here. Chapter 4 of Fairbanks’ book is entitled “Solving The Trichotomy”. In this chapter, Fairbanks addresses what he calls the “trichotomy problem”— that is, of humans, chimpanzees, and gorillas, which two of the three are most closely related to each other? In the latter half of his chapter, Fairbanks draws evidence from mitochondrial DNA and nuclear DNA studies in support of the traditional view that humans and chimpanzees are the closest genetically related. Before turning to this question, however, Fairbanks offers an array of evidence in view of confirming the standard evolutionary view that the mitochondrion is derivative of alpha-proteobacteria and became incorporated into the now-eukaryotic cell by virtue of an endosymbiotic event. I am going to divide my discussion of this chapter into two separate articles — in the first (this article), I am going to address the purported case for the endosymbiotic origin of mitochondria. In the second, I will discuss Fairbanks’ comments on the “trichotomy problem”.

When I held my former views on common ancestry, I was greatly compelled by the array of evidence often marshalled in support of the endosymbiotic origin of the eukaryotic mitochondrion. Indeed, if such a claim is true, then the proposition of the common ancestry of all eukaryotic life seems to be close at hand. This, I think, is an important area to discuss, for the argument — if sound — does not only establish the common ancestry of our order, primates. It also serves to support the somewhat grander claim that all extant eukaryotes are derivative of a common ancestral progenitor. But the important and fundamental question must be raised: Is this argument sound? Does the evidence support this claim? It is to this question that I now turn.

Does The Evidence Support The Endosymbiotic Hypothesis?

Fairbanks, in my opinion, does not marshall the strongest possible case in support of this popular hypothesis, instead largely appealing to DNA evidence which seemingly indicates that the Rickettsiae is the closest living relative of the mitochondria. He also tells us,

Modern bacteria species within this group live, grow, and divide naturally within eukaryotic cells, much like mitochondria do. Unlike mitochondria, they can briefly escape from their host cells and infect other cells. They often live within the cells of ticks, mites, chiggers, and fleas. Bites from these pests can transmit Rickettsiae and cause diseases such as Rocky Mountain spotted fever and epidemic typhus.

As I noted here, there is some seemingly confirmatory evidence which, at first brush, appears to corroborate this claim. For example, many eukaryotic mitochondria contain a single circular genome, carry out transcription and translation within its compartment, use bacteria-like enzymes/components, and replicate independently of host cell division and in a manner akin to bacterial binary fission. As with all the other apparent evidences for common ancestry, however, upon closer inspection, the evidence very quickly evaporates.

The Lamarckian Underpinnings Of Endosymbiosis

The first striking thing about this popular claim is its marked Lamarckian underpinnings, an old idea which maintains the concept of the inheritance of acquired characteristics (a view which is now at odds with a modern understanding of genetics). As I noted in the article linked above, unless there is a genetic basis for ensuring the propagation of the incorporated mitochondrial cell, there is no reason to think that it will be passed on in any hereditary fashion. Indeed, most of the mitochondrial genome has now been transitioned to the nucleus. But here’s the thing: the mitochondrial DNA has an extremely limited time to integrate with the DNA of the host cell. Otherwise, there is no reason to think that such an organelle could be passed on to proceeding generations, much less assimilated to undertake many critical energy-generating tasks of eukaryotic cells.

I also noted in the article linked above that a second problem with this scenario is that mitochondria use a slight variation on the conventional genetic code (for example, the codon UGA is a stop codon in the conventional code, but encodes for Tryptophan in mitochondria). This implicates that the genes of the ingested prokaryotes would need to have been recoded during the course of their transfer to the host cell’s DNA. Bear in mind that this is no simple process. Besides the re-coding of the mitochondrion (so as to comply with the conventional code), the genes would be required to be expressed correctly, as well as imported back into the mitochondrion in order to have any function. The situation becomes even worse when one considers that, in eukaryotic cells, a mitochondrial protein is coded with an extra length of polypeptide which acts as a “tag” to ensure that the relevant protein is recognised as being mitochondrial and dispatched accordingly. Moreover, the transfer of mitochondrial DNA to the host cell’s DNA would need to occur without any detriment to the host cell, in order to yield even a viable organism, let alone confer selective utility. The significant number of specific co-ordinated modifications which would be required to facilitate such a transition, therefore, arguably make it exhibitive of irreducible complexity.

I also cited a review paper which appeared in Nature a few months ago by the scientists Nick Lane and Bill Martin, which effectively demonstrated that the prokaryote-to-eukaryote transition was effectively impossible without the energy demands, pertinent to the biggest event of gene manufacture (second only to the origin of life) in the history of life on earth, being met by the mitochondrial processes of oxidative phosphorylation and the electron transport chain. These energy demands cannot be met by the bacterial cell alone.

The Cherry Picked “Evidence” For Endosymbiosis

As noted, one of the core arguments for endosymbiosis is its circular genome. What is often not noted, however, are the cases where eukaryotic mitochondria have linear genomes with eukaryotic telomeres. For example, one paper published in Trends in Genetics in 1998 noted that,

At variance with the earlier belief that mitochondrial genomes are represented by circular DNA molecules, a large number of organisms have been found to carry linear mitochondrial DNA. Studies of linear mitochondrial genomes might provide a novel view on the evolutionary history of organelle genomes and contribute to delineating mechanisms of maintenance and functioning of telomeres. Because linear mitochondrial DNA is present in a number of human pathogens, its replication mechanisms might become a target for drugs that would not interfere with replication of human circular mitochondrial DNA.

For further reading, see also this paper.

Another common argument for the endosymbiotic origin of the mitochondrion is its division by mechanisms akin to binary fission. What is often not noted, however, is that the mechanisms by which mitochondria replicate is not the same as those utilised by bacteria — indeed, it’s really quite different. In fact, many components of uniquely eukaryotic origin are used in this process. For a discussion of mitochondrial replication of a linear genome, see this PNAS paper.

Does Genetic Evidence Support Endosymbiosis?

As Fairbanks notes, genetic studies might reveal the presence of gene homologues in bacterial species. But here we are back to the “similarity = common ancestry” line of argumentation. It is only to be expected that biological systems, designed to carry out similar functions, will possess similar genetic makeup. Moreover, particularly when discussing bacterial phylogenies based on homologous genes, caution is warranted. Processes of lateral gene transfer readily upset classic tree topologies, and bacterial phylogenies are notoriously inconsistent (for why, see here and here).

Conclusion

To conclude, while one can 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 — cause us to raise an eyebrow and expect some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist — and justifiably gives one pause for scepticism.

Comments
Further notes on problems with endosymbiosis:
On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story Jonathan M. - January 10, 2012 Excerpt: 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. http://www.evolutionnews.org/2012/01/on_the_origin_o054891.html Bacteria Too Complex To Be Primitive Eukaryote Ancestors - July 2010 Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified.... There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote. http://www.creationsafaris.com/crev201007.htm#20100712b Bacterial Protein Acetylation: The Dawning of a New Age - July 2012 Excerpt: Bacteria have long been considered simple relatives of eukaryotes. Obviously, this misperception must be modified. From the presence of a cytoskeleton to the packaging of DNA to the existence of multiple post-translational modifications, bacteria clearly implement highly sophisticated mechanisms to regulate diverse cellular processes precisely. http://darwins-god.blogspot.com/2012/07/bacterial-protein-acetylation-dawning.html
Even more problematic for evolutionists, than the unexplained gap between prokaryote and eukaryote cells, is that even within the 'bacterial world' there are found to be enormous unexplained gaps of completely unique genes within each different type of bacteria which has had its DNA sequenced:
ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
and since unguided Darwinian processes are found to be grossly insufficient to account for the orgination of even a single protein (or gene),,,
Evolution vs. Functional Proteins ("Mount Improbable") - Doug Axe and Stephen Meyer – Video https://www.youtube.com/watch?v=7rgainpMXa8 Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. http://www.evolutionnews.org/2010/06/doug_axe_knows_his_work_better035561.html
and since unguided Darwinian processes are also grossly insufficient to account for the orgination of protein binding sites,,
"The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")
Then it is easy to see why people doubt that endosymbiosis ever occurred. Shoot, it is easy to see why people doubt that unguided Darwinian evolution ever did anything at all besides degrade pre-existing information! Darwinists simply have no empirical evidence that it is possible for unguided processes to produce even trivial levels of the unfathomed integrated complety we find in life.bornagain77
September 8, 2014
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A few notes on endosymbiosis:
Did DNA replication evolve twice independently? – Koonin Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus. http://nar.oxfordjournals.org/cgi/content/full/27/17/3389 An enormous gap exists between prokaryote cells and eukaryote cells. - Jerry Bergman Excerpt: A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP. All life produces ATP by three basic chemical methods only: oxidative phosphorylation, photophosphorylation, and substrate-level phosphorylation (Lim, 1998, p. 149). In prokaryotes ATP is produced both in the cell wall and in the cytosol by glycolysis. In eukaryotes most ATP is produced in chloroplasts (for plants), or in mitochondria (for both plants and animals). No means of producing ATP exists that is intermediate between these four basic methods and no transitional forms have ever been found that bridge the gap between these four different forms of ATP production. The machinery required to manufacture ATP is so intricate that viruses are not able to make their own ATP. They require cells to manufacture it and viruses have no source of energy apart from cells. http://www.trueorigin.org/atp.asp ATP Synthase: The power plant of the cell - video https://www.youtube.com/watch?v=XI8m6o0gXDY Mitochondria - Molecular Machine - Powerhouse Of The Cell – video https://www.youtube.com/watch?v=RrS2uROUjK4
Of related interest, is the highly sophisticated, extremely precise, organization of ATP production in mitochondria:
Your Rotary Engines Are Arranged in Factories - August 2011 Excerpt: As if ATP synthase was not amazing enough, a team of scientists in Germany now tells us they are arranged in rows with other equipment to optimize performance. From electron micrographs of intact mitochondria, they were able to detect the rotary engines of ATP synthase and other parts of the respiratory chain. Their diagram in an open-source paper in PNAS looks for all the world like a factory.,,, “We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures optimal conditions for efficient ATP synthesis.” The authors had virtually nothing to say about how this might have evolved, noting only that the structure is “conserved during evolution” in every sample they examined (3 species of fungi including yeast, potato, and mammal). What this means is a lack of evolution over nearly two billion years, in the standard evolutionary timeline. http://crev.info/content/110817-your_rotary_engines_are_arranged_in_factories These Molecular Sorting Machines Cooperate With Each Other in a “Complex Topology” - 2012 Excerpt: Even minute errors in the composition of the inner mitochondrial membrane can lead to severe metabolic derangements, which can have an especially negative impact on the energy-hungry muscle and nerve cells. In order to function, the cellular generators depend on the support of numerous highly specialized membrane proteins in the inner mitochondrial membrane. http://darwins-god.blogspot.com/2012/03/these-molecular-sorting-machines.html
Of related interest to 'factories' in the cell:
Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within (eukaryotic) cells consisting of tightly stacked sheets of membrane studded with the molecules that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm
bornagain77
September 8, 2014
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semi OT: it seems Richard Dawkins himself has just unwillingly helped to clearly illustrate to everybody a primary reason exactly why evolution can't possibly be true: Evolutionists have long argued that genetic code is universal for all life forms and that that is strong evidence for evolution from a common anscestor, yet it appears they were wrong once again: Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal: "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10) OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code). Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two. http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.htmlbornagain77
March 9, 2011
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Thanks again Jonathan, another keeper; a few notes: Did DNA replication evolve twice independently? - Koonin Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus. http://nar.oxfordjournals.org/cgi/content/full/27/17/3389 Problems of the RNA World - Did DNA Evolve Twice? - Dr. Fazale Rana - video http://www.metacafe.com/watch/4564682 Was our oldest ancestor a proton-powered rock? Excerpt: In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,... Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria and the archaea). http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html?page=1 Bacteria Too Complex To Be Primitive Eukaryote Ancestors - July 2010 Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified.... There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote. http://www.creationsafaris.com/crev201007.htm#20100712b A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP (energy). http://www.trueorigin.org/atp.asp Evolution Vs ATP Synthase - Molecular Machine http://www.metacafe.com/watch/4012706/ Mitochondria - Molecular Machine - Powerhouse Of The Cell - video http://www.metacafe.com/watch/5510941/bornagain77
March 9, 2011
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Johnathan: Thanks for the article. I read quite a portion of Lynn Margulis's book on Endosymbiosis---I believe it was "Acquired Geneomes"---but then had to stop because she seemed to extrapolate her theory way beyond reasonable bounds. I just didn't think it was worth the effort to continue. Nevertheless, I also thought that there must be good reason to believe that mitochondria and bacteria were related, or, otherwise, scientists wouldn't be making this claim. Yet, based on your original article in November over at Evolution News, and what you post here, it seems like sheer magic is being invoked to say that bacteria gave rise to eukaryotes via endosymbiosis, and popular consensus appears to be wrong--- development that really shouldn't catch me by surprise anymore. We now have not a single "Tree of Life", but all these various "shoots" sprouting up from the ground. This has really become problematic for Darwinists. As to "common descent", when I think about it critically, I don't see how it can be maintained. In mathematical terms, it must be discrete rather than continuous (the latter being what Darwinists maintain) and should more properly be termed "inheritance of common elements". Yet, for the "shoots" that I make mention of before, one has to wonder if there was anything inherited from one to the other at all. Whatever the case may be with the original "shoots", what you present makes very clear that the prokaryote/eukaryote divide is discontinuous. Thanks again for all the information.PaV
March 9, 2011
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