Is early cellular evolution plausible?

Southwestern Greenland from 30,000 feet, where the
conventionally oldest rocks on earth contain the earliest
putative traces of living things.

I have a reader's question this week, and this is going to be extra science-y for those of you who like that sort of thing.  For the rest, well, God bless you.  Bear with us as we explore early cellular evolution.

First, a paraphrase of the question:

If all cells possess similar structures that are supposed to have been inherited from a common ancestor, is that something we would have expected?  After all, we're talking about billions of years of evolution!  That's a long time, and many things could change.  The idea that cells still have similarities inherited from the very beginning of life seems unbelievable or at least unexpected.

I'm not sure "expecting"  is the right question.  The reality is that all cells, from Archaea to Bacteria to Eukarya, have have a common core of metabolism and proteins. They all use DNA/RNA/proteins. They all replicate DNA, transcribe RNA, and synthesize proteins. They all synthesize proteins using ribosomes.  So there is a tiny handful of proteins that are found in just about every living thing.  By tiny handful, I mean around 20-30.  Evolution explains this as functional constraint. The common ancestor must have been a cell with DNA/RNA/proteins and ribosomes, and now all descendants have the same thing. Since those metabolic processes were essential to the ancestor, they were less amenable to alterations than other parts of the ancestral cell's genome.  This seems to me to be a reasonable explanation of the current pattern of similarities and differences present in all cells.

Now, one could claim that these universally common features have a different explanation, for example, common design. In that case, one would need to account for both the similarities and differences, which evolution does with the notion of divergence from a common ancestor (to generate difference) and purifying selection (to maintain the similarity).  It's not clear to me that design accounts of similarity ever progress very far beyond saying, "They're similar because of a common designer."  The differences are also a key part of the pattern, especially the differences that reveal a nested hierarchy of similarity.  That is in need of an adequate explanation.

As to the implicit plausibility of the evolutionary explanation, I am deeply skeptical of any attempts to evaluate it.  I would certainly and enthusiastically agree that abiotic scenarios for the origin of life can be evaluated critically and rejected, but once a cell actually exists, I'm not at all certain we can say how it would or would not behave in an environment about which we can surmise very, very little.  Problems that I see: What was the ancestral population of cells like?  What was their DNA replication and cell division like?  Was it good or prone to error?  What was the environment like?  And what was the environment like over the ~1.5 billion years from the origin of life to the origin of the eukaryotes, and for the 2 billion years from the origin of the eukaryotes to the present?  How well or poorly was purifying selection operating in the vastly different life forms that diverged in early cellular evolution?  How well or poorly was purifying selection operating in those early divergences in cellular evolution?  How does the apparent presence of ubiquitous horizontal transfer operating in early cellular evolution alter this scenario?  The vast number of assumptions that have to be made (even though some of them may be plausibly estimated from other sorts of evidence) to even begin evaluating the plausibility of one particular evolutionary scenario means that any attempt at such an evaluation will be vulnerable to enormous error from making an incorrect assumption.

Ultimately, these sorts of concerns are the same concerns I have with most evolutionary modeling.  Models are great for rejecting very specific models that are insufficient to account for the present data, but life and its interaction with the environment is enormously complex and full of surprises.  To think that a model somehow adequately captures and accounts for all possible scenarios in real life strikes me as hubris.  That goes both for those who think their models adequately account for data (such as those who claim that we can reliably reconstruct ancestral population sizes at the evolutionary emergence of Homo sapiens) and for those who claim that their models invalidate entire classes of explanation (such as those who claim that all possible models of evolution and common ancestry are invalidated by simulation and those who reject all possible design/creation explanations based on a casual, shallow thought experiment).

To quote a particularly annoying chaos-tician, "Life finds a way."

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