Gradualism in Evolution not supported by genome studies (Agnosticism)

by David Turell , Sunday, October 04, 2020, 15:47 (1510 days ago) @ David Turell

The new studies, as with Behe, show gene losses and new gene gains with gaps in the record that deny Darwin gradualism:

https://inference-review.com/article/the-origin-of-novel-genes

The four studies find that organisms with different morphologies possess different sets of genes. Given that genes provide much of the information encoding the morphology of living organisms, this finding may not seem a surprise. That novel genes do not accumulate with Darwinian gradualism in the phylogeny is perhaps more surprising. The authors describe bursts of innovation: upon the origin of placental mammals, 357 novel genes; upon the origin of the metazoan, 1,189 novel genes; upon the origin of the land plants, 1,167 novel genes; and upon the origin of the flowering plants, 2,525 novel genes.

Equally surprising is evidence that the patterns of presence and absence of many genes in these studies do not form a nested hierarchy congruent with the accepted phylogeny. Particular genes often appear in more than one clade. This leads the authors to infer massive gene losses and frequent horizontal gene transfer in the history of life.

The unexpected nature of these findings was not lost on the authors of the studies. Three of the paper titles emphasize unexpected novelty and one emphasizes unexpected loss. But all four show similar patterns. More is revealed in each than a single title can convey.

IN THIS CONTEXT, the gene does not embody solely unique protein-coding sequences, nor groups of slightly different protein-coding sequences, but larger cohesive clusters that the authors term homology groups...According to the parameters applied by the authors, the homology groups in question are typically larger groupings than a gene family...Of the 87 homology groups examined, 15 exhibited detectable similarity with other homology groups in mammals and 39 with other homology groups in animals. This left 33 of the 87 homology groups with no detectable similarity to any other groups in their study. Even if all proteins that have any detectable similarity with BLASTP were joined together, the resulting sequence space would resemble an archipelago, rather than a continent.

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The largest of these four studies included more than nine million protein-coding sequences from 208 genomes, spanning eukaryotic life from yeast to humans to ash trees.3 Such a sample might be expected to show continuous variation. Instead, these nine million sequences clustered into 661,545 homology groups.

The evolution of novel genes is a subject with a substantial literature all its own, which has recently shifted from the view that all new genes begin as duplicates of pre-existing genes to a view that many genes evolve de novo from non-coding sequences.

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Rather than emerging gradually, a few at a time, the evidence presented in these four papers suggests the occurrence of punctuated bursts. At every major phylogenetic node that was examined, the appearance of hundreds, and in some cases thousands, of novel homology groups was detected.

Evolution by bursts is, of course, not expected if natural selection is the main driver. “[N]atural selection acts only by taking advantage of slight successive variations,” Darwin remarked; “she can never take a great and sudden leap, but must advance by short and sure, through slow steps.” The findings presented in these papers suggest otherwise. It seems that the evolution of life is characterized by leaps involving large numbers of novel homology groups.

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The fossil record depicts the appearance of the first angiosperms as a sudden event, with no clear progenitors. This was known, in part, to Darwin, who famously complained to the Director of Kew Gardens in 1879 that the origin of the dicotyledonous angiosperms was an “abominable mystery.”7 The mystery has since deepened to include all other angiosperms.

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ALL FOUR STUDIES under review found massive gene losses for phylogenetic nodes at the base of the major groups of living organisms. This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones. Such processes would represent a radical overhaul in the genetic composition of organisms. (my bold)

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The authors suggest that horizontal gene transfer could explain the incongruent patterns of gene presence or absence that give rise to some of the apparent losses. Bowles et al. found that 323 homology groups were present in fungal and land plant genomes, but absent from all other taxa. Instead of being lost in the lineages between fungi and land plants, the genes could simply have jumped.

The incongruence between patterns in the absence or presence of homology groups and widely accepted phylogenies raises a broader issue. A single phylogeny is clearly an inadequate model for the history of life, but there is no obvious replacement.

Comment: Genomic studies don't support Darwin. Behe is supported, and the Cambrian gap is not the only major gap to be explained. Certainly fits God in charge.