Recently a correspondent of mine raised the issue of whether we should assume that there is 100 percent continuity throughout the tree of life — what is often called “universal common ancestry” (UCA) — until demonstrated otherwise. In the debate over UCA, such a framing would shift the burden of proof to those who claim that there are discontinuities. I get the feeling that UCA-proponents want to put UCA-skeptics into an “extraordinary claims require extraordinary evidence” box, and the idea that there is discontinuity in biology is being implicitly classed as an “extraordinary claim.” 

For my part, I think it’s better to approach the data without assumptions and to let the evidence speak for itself. No claim about whether discontinuities exist in the tree of life should be handicapped as “extraordinary,” although I think a good case could be made that UCA is the more “extraordinary” claim. Why? Because all we directly observe today are discrete groups that don’t interbreed (these are like leaves on a tree), while common ancestry (like the branches of the tree) is inferred based upon various methodological justifications. Those methodologies often are inconsistent, contradictory, or exclude non-tree-like data. But I can leave that alone for now. I would say that no viewpoint should be handicapped and both pro-UCA and anti-UCA views should be treated equally. Thus, I reject attempts to frame the issue or shift burdens of proof. Let’s just follow the evidence where it leads. 

And What Is That Evidence?

The core postulate of evolutionary biology is “descent with modification.” Crucial to assessing this postulate is the adequacy of evolutionary mechanisms. ID proponents have raised many reasonable mathematical and biological challenges to the adequacy of these mechanisms to account for transitions that are claimed to have occurred in the history of life. 

For example, consider ID’s inquiry into waiting times: whale fossils are supposed to provide some of the best examples of “transitional forms” in the fossil record, demonstrating common descent between whales and land mammals. Whale intermediates have become a favorite argument for common descent. I distinctly recall one of my professors teaching us that the evolution of whales happened “incredibly fast” — at an almost unbelievably rapid pace. ID researchers are looking at the genetic changes necessary to transform a land mammal into a whale, and when you apply the mathematics of population genetics to the time available from the fossil record, there simply is not enough time for standard evolutionary mechanisms to produce those genetic changes. 

So what ID theorists are doing is showing that standard evolutionary mechanisms are incapable of producing the descent and modifications that are claimed to have taken place. If such an argument would not constitute a mathematically demonstrated discontinuity in the tree of life, I don’t know what would. Our critiques of the mechanisms of evolution give very adequate evidence-based reasons to be skeptical of the tree of life, and to suspect that discontinuities exist. 

Koonin and Company

Some leading biologists agree that there is evidence for discontinuity:

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution. 

Eugene V. Koonin, “The Biological Big Bang model for the major transitions in evolution,” Biology Direct, 2:21 (August 20, 2007)

Koonin sees a lot of evidence for “discontinuity” (his word) in the tree of life. Here’s what he writes:

Below I list the most conspicuous instances of this pattern of discontinuity in the biological and pre-biological domains, and outline the central aspects of the respective evolutionary transitions.

1. Origin of protein folds

There seem to exist ~1,000 or, by other estimates, a few thousand distinct structural folds the relationships between which (if existent) are unclear.

2. Origin of viruses

For several major classes of viruses, notably, positive strand RNA viruses and nucleo-cytoplasmic large DNA viruses (NCLDV) of eukaryotes, substantial evidence of monophyletic origin has been obtained. However, there is no evidence of a common ancestry for all viruses.

3. Origin of cells 

The two principal cell types (the two prokaryotic domains of life), archaea and bacteria, have chemically distinct membranes, largely, non-homologous enzymes of membrane biogenesis, and also, non-homologous core DNA replication enzymes. This severely complicates the reconstruction of a cellular ancestor of archaea and bacteria and suggests alternative solutions.

4. Origin of the major branches (phyla) of bacteria and archaea

Although both bacteria and archaea show a much greater degree of molecular coherence within a domain than is seen between the domains (in particular, the membranes and the replication machineries are homologous throughout each domain), the topology of the deep branches in the archaeal and, especially, bacterial phylogenetic trees remains elusive. The trees conspicuously lack robustness with respect to the gene(s) analyzed and methods employed, and despite the considerable effort to delineate higher taxa of bacteria, a consensus is not even on the horizon. The division of the archaea into two branches, euryarchaeota and crenarchaeota is better established but even this split is not necessarily reproduced in trees, and further divisions in the archaeal domain remain murky.

5. Origin of the major branches (supergroups) of eukaryotes

Despite many ingenious attempts to decipher the branching order near the root of the phylogenetic tree of eukaryotes, there has been little progress, and an objective depiction of the state of affairs seems to be a “star” phylogeny, with the 5 or 6 supergroups established with reasonable confidence but the relationship between them remaining unresolved.

6. Origin of the animal phyla

The Cambrian explosion in animal evolution during which all the diverse body plans appear to have emerged almost in a geological instant is a highly publicized enigma. Although molecular clock analysis has been invoked to propose that the Cambrian explosion is an artifact of the fossil record whereas the actual divergence occurred much earlier, the reliability of these estimates appears to be questionable. In an already familiar pattern, the relationship between the animal phyla remains controversial and elusive.”

Koonin, “The Biological Big Bang model for the major transitions in evolution,” emphases added; citations omitted

Multiple Independent Converging Lines 

Koonin ultimately adopts a fairly orthodox evolutionary position, but he certainly shows that those who see discontinuity aren’t unjustified in doing so. I could cite additional evidence for discontinuity between groups. In the 2017 volume Theistic Evolution, I contributed a chapter critiquing UCA by looking at five common lines of evidence. The chapter critiques UCA in a manner that responds to the precise form of the argument that evolutionary biologists make: an argument from multiple independent converging lines of evidence. For example, in a 2010 Nature article, Douglas Theobald writes:

UCA [universal common ancestry] is now supported by a wealth of evidence from many independent sources, including: (1) the agreement between phylogeny and biogeography; (2) the correspondence between phylogeny and the palaeontological record; (3) the existence of numerous predicted transitional fossils; (4) the hierarchical classification of morphological characteristics; (5) the marked similarities of biological structures with different functions (that is, homologies); and (6) the congruence of morphological and molecular phylogenies.

Douglas L. Theobald, “A formal test of the theory of universal common ancestry,” Nature 465 (May 13, 2010): 219-222; emphasis added

A Comprehensive Critique

This is a form of argument found not just in the technical literature but also in many biology textbooks. So in my chapter in Theistic Evolution,titled “Universal Common Descent: A Comprehensive Critique,” I framed a critique of UCA by looking at “evidence from many independent sources” — specifically, biogeography, paleontology, molecular and morphological phylogenies, and embryology. Here’s what I found:

• In biogeography, evolutionists appeal to unlikely and speculative explanations where species must raft across vast oceans in order for common descent to account for their unexpected locations.
• Paleontology fails to reveal the continuous branching pattern predicted by common ancestry, and the fossil record is dominated by abrupt explosions of new life forms. 
• Regarding molecular and morphology-based trees, conflicting phylogenies have left the “tree of life” in tatters. Inconsistent phylogenetic methods predict that shared similarity indicates common inheritance, except for when it doesn’t.
• Similar inconsistent methodological problems exist in embryology, where significant differences exist between embryos in their early stages, leading evolutionary biologists to predict that similarities will exist between vertebrate embryos, except for when we find differences, and then it predicts those too.

The collective evidence cited above shows that those who believe the tree of life is not 100 percent continuous across all organisms aren’t crazy. Whatever burdens of proof need to be met to have our view taken seriously, we’ve far exceeded them. 

At the very least, I think that the framing where the default assumption should be “total continuity” among organisms (UCA) until some “extraordinary evidence” comes along to show otherwise, is not appropriate framing. There’s plenty of evidence of discontinuity in biology, and this alone should allow us to have a real conversation about the data, where both viewpoints can converse on equal footing. 

Scientific arguments should be based upon a rhetorical symmetry. If a piece of evidence counts as evidence for a theory, then the opposite should count against it. So if one finds evidence for common descent, then it is necessary that when we find the opposite evidence, then that should count against common descent. And indeed we find much evidence opposite to the predictions of UCA. Those who believe discontinuities have plenty of evidence to back their view. They should not be rhetorically handicapped as they participate in this conversation.