A new paper in Science Advances cites an “incomplete” or “insufficient” enzymatic metabolism of the proposed last universal common ancestor (LUCA) as evidence for “independent origins of unrelated enzymes for the same reaction” in two of the basic domains of life, Archaea and Bacteria. The breadth of genomic evidence surveyed in this study is impressive, and their finding is striking because, when properly understood, it strongly contradicts the expectations of universal common ancestry.
The basic idea is that certain enzymes common to all members of Bacteria perform the same basic functions as enzymes in Archaea. However, those enzymes are so fundamentally different (i.e., non-homologous) that they could not be derived from some common ancestor enzyme that was present in LUCA. These enzymes aren’t trivial — they perform fundamental functions in both domains of life. As the paper puts it, they are “required for the synthesis of amino acids, cofactors, and nucleobases.”
A Very Profound Finding
To get to some of the specific numbers, according to the data in the paper, 89 enzymes in Bacteria that perform these basic functions were not homologous to any enzymes in Archaea. Likewise, 38 enzymes in Archaea that perform basic functions were not homologous to any enzymes in Bacteria. That’s a very profound finding — and it contradicts key predictions of the theory of universal common ancestry (UCA).
But the paper doesn’t put it that way. As impressive as their study was, the authors of the paper were not interested in allowing UCA to be truly testable or falsifiable. Here’s what they say:
Plotting the phylogenetic distributions of core biosynthetic enzymes across bacteria and archaea reveals that enzymatic metabolism in LUCA was incomplete. It expanded via origins of novel enzymes in the lineages leading to LACA [last archaeal common ancestor] and LBCA [last bacterial common ancestor], closely mirroring lineage-specific assembly of the ribosome. In the present sample, 166 enzymes of core metabolism trace to LUCA, yet 89 enzymes required for the synthesis of amino acids, cofactors, and nucleobases arose on the lineage to LBCA, while 38 arose on the lineage to LACA. An additional 37 enzymes were too sparsely distributed for unequivocal lineage attribution. These post-LUCA bacterial and archaeal enzyme innovations reveal that the insufficiency of enzymatic metabolism in LUCA was severe and provide insights into an extremely early phase of biochemical evolution. The metabolic reactions of LUCA capture a time in which the ribosome, the genetic code, and translation were functional because enzymes existed and were arising de novo. However, enzymes were evolving without the support of a complete enzymatic supply of precursors for protein synthesis: Amino acid synthesis, cofactor synthesis, and intermediate carbon metabolism were incomplete in LUCA. How could an incomplete enzymatic metabolism support protein evolution at the ribosome?
The paper thus speculates that there must be “more ancient homologies among proteins than sequence comparisons alone” can reveal, suggesting that indeed these totally distinct enzymes truly do share a form of common ancestry. However, we can’t detect any of that homology in the amino acid sequences.
“Two Origins of Life”
Under the theory of universal common ancestry, or UCA, one would expect that all such fundamental enzymes performing common functions in these various domains would have a somewhat similar sequence and could therefore be confirmed as “homologous.” The fact that in this case their sequences are completely different shows a major failure of a fundamental prediction of UCA and its correlate that all life is descended from LUCA. The paper, again, doesn’t directly acknowledge this — but an article in Smithsonian Magazine interprets the study correctly to say it must imply “two origins of life.” Or, as one of the lead researchers says in the Smithsonian article, “The simplest interpretation is that there were two independent transitions from LUCA to free-living cells.”
That’s a fair comment, but it’s a big admission to say the evidence indicates that there were “two origins of life” or “two independent transitions from LUCA to free-living cells.” Yet the paper and the Smithsonian article refuse to admit that this presents any challenge to UCA or LUCA. Like so many evolutionary biologists, they simply will not treat UCA as a testable scientific hypothesis. When the evidence contradicts predictions of UCA, they just invent auxiliary hypotheses to save the theory.
Insulating Common Descent
The paper tries to explain why totally dissimilar enzymes could perform more-or-less identical functions by arguing there are “more ancient homologies among proteins than sequence comparisons alone” could detect. In other words, the homology is so deep and “ancient” that it predates the advent of amino-acid-based enzymes which performed these functions. Therefore the “homology” cannot be detected by comparing amino acid sequences.
So how were these reactions accomplished in LUCA? Their proposed solution is that somehow abiotic chemical reactions in hydrothermal vents helped synthesize these amino acids, cofactors, and nucleobases in some form of pre-cellular life. Eventually, they propose, enzymes took over — different ones in each lineage. Don’t expect many details about what this looked like or how it happened. It’s highly speculative and the thesis is principally designed to insulate UCA from available evidence.
And here’s where it gets even more difficult for them: We DO find homology between some other core enzymes in Bacteria and Archaea, particularly those required for building ribosomes and fostering translation, and even for some other enzymes required for synthesizing amino acids, cofactors, and nucleobases. For these similar enzymes the authors go the standard route and infer they were present in LUCA. (This means LUCA made heavy use of enzymes after all, apparently producing them in ribosomes.) That’s pretty standard thinking about LUCA. But then how do they explain the complete lack of homology for other core enzymes in Bacteria and Archaea that perform the same basic functions?
Because they must infer totally independent sequence evolution, they propose that in LUCA these functions weren’t performed by enzymes — they were performed by abiotic chemical reactions in the environment. This wasn’t happening inside a “cellular organism” as we understand that today. It was a non-free-living (or only partially cellular) system still confined to compartments in a hydrothermal vent. Don’t get distracted by wondering how the extreme heat near a vent (a toasty 750° F or more inside the vent) wouldn’t quickly break down organic molecules.
A Convoluted Tale
In the end, this is a fantastic study in comparative genomics between Archaea and Bacteria. Literally fantastic, as their interpretation relies on directly contradictory methods of reasoning. In any other area of scholarship, the contradiction would be recognized as unacceptable.
Not so when it comes to the origin of life. When common descent fits the sequence data, you infer that the enzymes were present in LUCA. When common descent doesn’t fit the sequence data, you don’t question LUCA but instead invent a very complex and detail-poor story about how metal catalysts from the environment performed those functions in LUCA, and then totally distinct enzymes replaced the abiotic reactions to perform the exact same roles in later lineages. The lineages led to Archaea and Bacteria respectively.
This convoluted tale seems motivated by one purpose only: to insulate universal common descent from any data that might contradict it, whatever the cost to coherent scientific reasoning. As we’ve seen in many other cases in the literature, this is standard practice among evolutionary biologists.