The Evolutionary Tree Continues to Fall: Falsified Predictions, Backpedaling, HGTs and Serendipity Squared

Charles Darwin’s theory of evolution states that the species arose from earlier species. Slight changes accumulating over long time periods resulted in one species giving rise to a new species, over and over.

Prediction

In this evolutionary process new species sometimes branch off from older ones and the history of life forms a tree-like pattern—an evolutionary tree. Indeed, the one figure in Darwin’s book, shown below, was that of such a pattern.

As evolutionists further elaborated on Darwin’s idea in the twentieth century the concept of an evolutionary tree became increasingly foundational to the theory. This figure below from a leading textbook [George Johnson, Jonathan Losos, The Living World, Fifth Edition, McGraw Hill, 2008.] is typical.

As the textbook explains:

Today scientists can decipher each of all the thousands of genes (the genome) of an organism. By comparing genomes of different organisms, researchers can literally reconstruct the tree of life. The organisms at the base of the tree are more ancient life-forms, having evolved earlier in the history of life on earth. The higher branches indicate other organisms that evolved later.

Evolutionists have even developed a Tree of Life Web Project, shown below, that provides information for each species and how the different species are related in the evolutionary tree:

And as more genome data have become increasingly available evolutionists naturally assumed it would be feasible to derive a comprehensive evolutionary tree:

Once universal characters were available for all organisms, the Darwinian vision of a universal representation of all life and its evolutionary history suddenly became a realistic possibility. Increasing reference was made to this universal, molecule-based phylogeny as the “comprehensive” tree of the “entire spectrum of life” [13, 14, 15, 16, 17].

A key corollary of this evolutionary tree concept is that the different traits of the species agree and point to the same tree. Various evolutionary effects may cause occasional differences between the trees, but roughly speaking, if different traits are used to reconstruct the evolutionary tree, they should produce similar trees. There may be some evolutionary “noise,” but different traits should mostly agree.

In the early twentieth century blood immunity studies provided just such confirmation. The results provided a new trait that could be used to judge the similarity and difference between different species. When the results were found to agree with the previously established evolutionary tree based on visible traits, evolutionists hailed the findings as new proofs of evolution.

Similarly, evolutionists hailed similar confirmations in the molecular sequence data that were discovered later in the century. Here is evolutionist Jerry Coyne’s summary from his recent book Why Evolution Is True:

Creatures with recent common ancestors share many traits, while those whose common ancestors lay in the distant past are more dissimilar. The “natural” classification is itself strong evidence for evolution. [p. 9]

Strong evidence indeed. Evolutionist David Penny made the point that this evidence provides a means to falsify evolution. The philosopher Karl Popper had argued evolution is not falsifiable, but for Penny this evidence proved Popper wrong. Penny showed how different proteins, compared across different species, lead to similar evolutionary trees. If they hadn’t, Penny argued, evolution would be false.

Falsification

Now, thirty years after Penny cited the congruence of different evolutionary trees as a prediction that could falsify evolution, it is not controversial even amongst evolutionists that the prediction is false. The plethora of new DNA and protein sequence data have provided a steady stream of incongruent evolutionary trees. These trees strongly conflict with the trees based on other sequence data, or with the consensus evolutionary tree. And the disagreement is far beyond evolutionary “noise.” As one evolution wrote:

Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.

Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”

Or as one evolutionist succinctly put it, “Life is not a tree.” Here is how other evolutionists explain the evidence:

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.

Evolutionists are not sure just what the data mean, but even they agree that different traits, across different species, often do not produce congruent evolutionary trees. And the difference is not mere “noise.”

Reaction

How do evolutionists deal with this falsification? David Penny, the evolutionist who cited the congruence of different evolutionary trees as a prediction that could falsify evolution now has a different story. Penny now reveals that congruent trees never really were a prediction of evolution. After all, Darwin was not nearly so keen on promoting the evolutionary tree concept as he was descent with modification. In fact, according to Penny, the new evidence “enriches our understanding of evolution.”

Likewise, another paper argues that perhaps the evolutionary tree was more of a heuristic than a prediction.

And as usual evolutionists appeal to a spectrum of explanatory devices to correct the narrative. The most prevalent of these epicycles is the horizontal gene transfer (HGT), a term that encompasses several known mechanisms by which genes can transfer between organisms such as bacteria.

In fact, if evolution is true then HGT must have been one of its key players. As one paper explained, HGT “has emerged as a central force in the evolution of many different prokaryotes.”

But under evolution, HGT must also have been important in the evolution of eukaryotes:

and now cases of HGT in eukaryotes are emerging at an increasing rate and account for many adaptively important traits

So HGT is now a key mechanism of the evolutionary process. It can do what the old mechanisms could not. In fact, one must wonder how this powerful mechanism knows when to send which genes where. For the various versions of HGT are incredibly intelligent.

For instance, consider the HGT process of transformation in which DNA from the extracellular environment is imported into the cell via what one paper describes as “a complex process” involving a small army of protein machines.

Then there is the HGT process of conjugation in which the DNA is transferred via cell-to-cell contact. A bridge-like connection is constructed between the two cells through which helpful DNA is transferred. And the donor cell has the molecular machinery to verify that the receiving cell does not already possess the donated DNA. And the DNA includes genes critical in the conjugation process. The DNA to be sent over is nicked and unwound so a single strand can be threaded through the bridge connection.

Serendipity squared

Gone are the days of simple mutations creating so much of the biological world. They were reminiscent of those swerving atoms of the Epicureans. And like those swerving atoms, they are prima facie incapable of creating biology’s wonders.

Beyond this obvious failure, much more than mutations are required to explain biology’s patterns. The evolutionary tree is out and networks, or webs, or some such, are in. And a new set of mechanisms, such as HGTs, are the brains behind the creation.

But epicycles are not free. In this case, the marshalling of HGTs as the explanation for biology’s patterns and success raises the question of where these complex mechanisms came from in the first place. According to evolutionary theory, evolution created the incredibly complex HGTs which then facilitated, yes, evolution.

Do they seriously expect us to believe this? Religion drives science, and it matters.