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The Darwinian Basis of the Prokaryote-to-Eukaryote Transition Collapses

Jonathan McLatchie

The question of the evolution of eukaryotic cells from prokaryotic ones has long been a topic of heated discussion in the scientific literature. It is generally thought that eukaryotes arose by some prokaryotic cells being engulfed and assimilated by other prokaryotic cells. Called endosymbiotic theory, there is some empirical basis for this. For example, 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.

Despite such evidence, however, when assessing the causal sufficiency of unguided processes, they — predictably — come up short. After all, it is all-too-easy to lapse into a long-discredited Lamarckian “inheritance-of-acquired-characteristics” mentality. It is important to bear in mind that, even if a cooperative assemblage of prokaryotes did by some fluke of luck arise, such an arrangement is of no evolutionary significance unless there is a genetic basis to ensure its propagation.

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 on their way to the nucleus. 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. 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.

A few weeks ago, a review paper was published in the prestiguous journal, Nature, by the internationally renowned scientists and authors, Nick Lane and Bill Martin.

The abstract reports as follows:

All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that gave rise to mitochondria restructured the distribution of DNA in relation to bioenergetic membranes, permitting a remarkable 200,000-fold expansion in the number of genes expressed. This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life.

The paper’s chief concern is with regards to the energy costs of what they describe as “the most intense phase of gene invention since the origin of life.” The problem is that bacterial cells are highly unlikely to possess the technology necessary to facilitate such a transition.

How is one to resolve this paradox? The authors explain:

The answer, we posit, resides ultimately in mitochondrial genes. By enabling oxidative phosphorylation across a wide area of internal membranes, mitochondrial genes enabled a roughly 200,000-fold rise in genome size compared with bacteria. Whereas the energetic cost of possessing genes is trivial, the cost of expressing them as protein is not and consumes most of the cell’s energy budget. Mitochondria increased the number of proteins that a cell can evolve, inherit and express by four to six orders of magnitude, but this requires mitochondrial DNA. How so? A few calculations are in order.

The paper’s authors then present a discussion of the energy costs associated with the processing of eukaryotic DNA, and find that this value is far greater than that which can be produced by a bacterial cell. They thus conclude that the ATP required for the processing of eukaryotic DNA necessitates the presence of mitochondria, the powerhouse of eukaryotic cells.

Moreover, this mitochondrion needed to contain just the right set of genes and possess just the right gene density. The mitochondrion also required thousands of copies of the said genes, with each copy located in close enough proximity to the respective machinery such that the required energy could be produced at a fast enough rate.

The authors conclude by saying,

The transition to complex life on Earth was a unique event that hinged on a bioenergetic jump afforded by spatially combinatorial relations between two cells and two genomes (endosymbiosis), rather than natural selection acting on mutations accumulated gradually among physically isolated prokaryotic individuals. Given the energetic nature of these arguments, the same is likely to be true of any complex life elsewhere.

It gets worse, of course. Even if one presumes a sufficient supply of ATP from mitochondrial processes (such as oxidative phosphorylation and the electron transport chain), no traction is given to the causal sufficiency of undirected mechanisms in accounting for the origin of novel genes and proteins which are required for eukaryotic life. One might just as easily say that purchasing a bigger power supply for your computer will cause the computer to magically be programmed to perform more complex calculations and activities! Obviously, such power would be useless without the input of novel programming script — information — to appropriately harness the available power.

The paper describes the invention of new protein folds in eukaryotes as being “the most intense phase of gene invention since the origin of life.” The problems associated with the chance-based origin of novel genes is only accentuated by the bioenergetic dilemma described here. Granting a satisfaction of the energy demands required for those new genes and protein folds, does neo-Darwinism gain any traction? It seems very clear that it does not.