April 17, 2020 | David F. Coppedge

Common Method for Evolutionary Inference Collapses

Evolutionists are going to be very upset over what this paper claims: phylogenetic trees of living animals are meaningless.

A recent post here (15 April 2020) referred to a philosophical constraint on scientific theories called “underdetermination of theory by data” (see Stanford Encyclopedia of Philosophy). It basically means that data cannot prove a theory, because there are always other theories that can explain the data equally well.

Initial sketch of a branching tree of life from Darwin’s notebook

A classic example of this problem surfaced in a recent paper in Nature on 15 April, 2020. The article concerns the practice of building ‘phylogenetic trees’ from observations of living species – i.e., looking at a group of species and deciding which ones evolved first and are related to what other species. We’ll let the authors, Stilianos Louca from the University of Oregon and Matthew W. Pennell from the University of British Columbia explain the problem. First, they say that tree-building is a widespread practice in evolutionary research:

Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics. However, there has been considerable debate surrounding the reliability of these inferences and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation.

Then, they pull the rug out from under this whole practice:

We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence.

“Diversification” is essentially synonymous with Darwin’s “Origin of Species” concept of speciation by natural selection. They’re touching a raw nerve.

Louca and Pennell go on to say that this ambiguity in congruent models cannot be eliminated by appeals to Ockham’s Razor or by thinking that the most ‘likely’ models will eventually converge on the true phylogeny. No; this is an inherent limitation in the method. Why has this not been noticed before?

Because any given true diversification history (even a relatively simple one) is unlikely to exactly match the particular functional form considered, fitting the latter may not even approximately yield the true diversification history. The existence of congruent scenarios can thus seriously alter macroevolutionary conclusions—for example, when assessing the influence of environmental factors on diversification dynamics.

Speaking of environmental factors, look what evolutionists at McGill University said a couple of months ago (25 Feb 2020): “Adaptation: Competition and predation may not be the driving force scientists thought.” They examined 125 papers that claimed the environment drives plants and animals to evolve and adapt. They found support that temperature affects species (e.g., cold-climate species tend to have longer fur), but not predator-prey relationships, which have long been considered driving forces for evolution.

Surprisingly, they found that although the interactions strongly affected how well species grew, survived, or reproduced, interactions did not necessarily spur adaptation. “We expected experiments to show us stronger local adaptation when stressful interactions were left intact. But we found that it wasn’t stronger or common in these cases—except perhaps in the tropics,” says Hargreaves.

How about a little overkill? The other paper already said that the problem of congruent trees can “seriously alter macroevolutionary conclusions” when assessing the influence of environmental factors on origin of species. Well, the environmental factors were weak to begin with!

Shedding Doubt

Many evolutionists like to smile and claim that their work is “shedding light” on evolution. Look what Louca and Pennell say their paper sheds:

Our findings thus shed doubt over previous work on diversification dynamics that is based solely on extant timetrees, including some of the conclusions from work that we have coauthored. Previous studies have underestimated this issue because they typically consider only a limited set of candidate models at a time, both when analysing real datasets and when assessing parameter identifiability via simulations; as a result, previous studies have been (un)lucky enough to not compare two models in the same congruence class….

Evolutionary biologists have known enough math to produce phylogenetic trees that scored high on ‘likelihood’ compared to other models, but they “severely underestimated” the problem of congruent trees. That has major implications for “macroevolutionary inference,” these two authors prove mathematically.

A Sad Amen

In a commentary on this paper in the same issue of Nature, Mark Pagel reluctantly agrees that these two have uncovered a serious problem in evolutionary theory. In his article, “Evolutionary trees can’t reveal speciation and extinction rates,” his subtitle adds that the new work “casts doubt” on the “widely used” approach  for estimating the rates at which branching relationships between species occur. He says that “Louca and Pennell challenge a major aspect of that enterprise.” His commentary has no good news. “Even worse for those who want to use the rates of speciation and extinction to study evolution, the possible alternative scenarios of time-varying speciation and extinction rates that are consistent with the deterministic lineage-through-time model often differ qualitatively.


Humpty Darwin sits on a wall of foam bricks held together by decayed mortar. Identify the crumbling bricks discussed in this article. (Cartoon by Brett Miller commissioned for CEH. All rights reserved.)


Big Problems

Their paper makes it clear that this is a big problem for evolutionary theory. It concerns not just small, microevolutionary inferences; no; it concerns large macroevolutionary conclusions made from the data.

Using simulated and real timetrees as examples, we demonstrate how failing to recognize this issue can seriously mislead our inferences about past diversification dynamics.

If what Louca and Pennell say is true, it appears a lot of evolutionists have wasted their time and possibly their careers trying to prove the unproveable, and have misled their readers by insinuating that phylogenetic trees show that evolution is true.

Another ramification is that immeasurable piles of scientific papers are now rendered meaningless. Will journals go back through every publication about extant timetrees and retract them?

The authors attempt to apply salve to the problem by offering a little bit of hope:

We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.

So what are these variables? They offer some terms in the differential equations that “can be interpreted” this way or that to add some confidence. However, the best way forward is to look at fossils, they think. Whoops; there’s a problem with fossils, too!

Fossil data could help to resolve the ambiguities highlighted here, and biological knowledge could, in principle, also help to reduce ambiguities. For example, if ρ and μ are somehow known from other sources, the congruence class collapses to a unique diversification scenario…. Nevertheless, for many taxa the fossil record remains scarce and ambiguous, and our general understanding of what constitutes a plausible diversification scenario is poorly developed.

This is like telling Charlie, “Mr. Darwin, I have bad news and bad news.”

Without further information or biologically well-justified constraints, in general extant timetrees alone cannot be used to reliably infer speciation rates (except for the present day), extinction rates or net diversification rates. Consequently, correlations between λ, μ or r and fluctuating environmental factors (such as temperature) also cannot be reliably inferred, neither when λ, μ or r are first estimated and then related to the environmental factors nor if λ, μ and r are expressed as parameterized functions of the environmental factors and then fitted to the timetree (Supplementary Information section S.5), because different parameterizations can lead to completely different inferences.

As paleontologist Stephen Jay Gould famously said, the “trade secret of paleontology” is that fossils do not show evolution, but instead illustrate abrupt appearance, stasis and extinction.

Do you remember how many times that phylogenetic trees made from molecular clocks have contradicted the fossil record? Well, now the authors think they know why. Not only that: other problems with tree-building could be lurking in the shadows.

Our findings could explain why diversification dynamics observed in the fossil record often contradict inferences based on phylogenetics, although other explanations have also been proposed. It is possible that similar major identifiability issues may also be hiding in other evolutionary reconstruction methods based on extant organisms alone, but this remains to be examined.

What is the upshot of the “epistemological carnage” wrought by Louca and Pennell, regarding what can be known? Pagel pours salt in the wound, saying that

Louca and Pennell’s conclusions will be dispiriting to evolutionary scientists who are looking for a link between past levels of speciation and extinction and historical climate change or other environmental events, or who want to test ideas about what features of a species — such as diet, mating system or the length of a generation — might be used to predict speciation and extinction rates. The limitations that Louca and Pennell have identified for estimating speciation and extinction rates do not go away as the size of the phylogenetic tree increases. Nor do other common features of trees provide much help: for example, if a group of species has never suffered any extinctions, estimating their speciation rate would be straightforward. But this is rare, and unlikely to be known in advance. Having abundant fossils could help, because they provide evidence needed to estimate extinction rates; however, fossils are seldom abundant. We can make assumptions about how speciation and extinction might vary with each other, through time, or with the number of species, but these assumptions are being made about the things that we would like to estimate.

It’s a very sorry situation for poor Mr Darwin and his band of disciples.

Without fossils, all evolutionary scientists, whether studying speciation and extinction or attempting to reconstruct the features of distant ancestors, need to be aware that the evolutionary processes they identify are those that operated in the species that would survive and eventually leave descendants in the present. We can’t be sure what was going on in those that went extinct. It is the evolutionary version of the observation that history is written by the victors. The supreme irony of this predicament is that Charles Darwin’s idea about the survival of the fittest, the story that we want to understand, by its very nature renders elusive some of the key components needed to study it.

Louca and Pennell are not going to leave Charlie weeping over his stomach-ache, are they?

On a more positive note, we have resolved a long-standing debate and precisely clarified what information can be extracted from extant timetrees alone, formulated in terms of easily interpretable and identifiable variables.

This is like adding, ‘But, Mr Darwin, the good news is that we understand the huge implications of your problem better now.’

Tom Bethell, Darwin's House of Cards (2017)

Bethell’s book blows down the castle Darwin built.


It’s kind of fun watching Darwin’s house of cards collapse, when you weren’t living in it anyway.


Recommended Resource: Watch this short video on why homology is a logically faulty argument for Darwinism.


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