Suppose that a microorganism with a collection of unique genetic information somehow transfers one gene or a suite of its specialized genes into an unrelated organism. This could involve a process such as conjugation, where two prokaryote cells become linked by a tiny tube, and genetic material passes from one organism into the other. And suppose that the foreign gene(s) somehow become incorporated into the new host chromosome. This does not normally happen. As s result of such an event however, two very different organisms could both contain the specialized gene, but not as a result of common descent. This process is called horizontal gene transfer (or lateral gene transfer). Some specialists propose that this happened often early in life history among prokaryotes.
This is the currently popular explanation for why the DNA sequences (and their resulting biomolecules) from many different organisms, fail to demonstrate evolutionary lines of descent (in other words an evolutionary tree). The difficulty of detecting any kind of pattern in similar gene sequences between organisms, has made life very difficult for supporters of Darwinian evolution. Instead, what we see are design choices that in many cases display an unexpected mosaic pattern which cannot be explained by spontaneous processes. But mainstream biologists do not see the issue this way.
About 1990 Carl Woese and colleagues proposed a radical new interpretation of the tree of life (evolutionary tree they called it). These scientists instead proposed three domains: eukaryotes, bacteria and archaea.
Woese’s system was based on ribosomal RNA (part of the smaller subunit in a ribosome which pieces together proteins based on the information found in DNA). This molecule was called 16SrRNA. Woese believed that he had found a system to reliably identify lines of descent for all creatures. These molecules were used to trace an evolutionary tree, but it was different from the previous trees based on shape and function of each organism. However, this radical new system did not last. The problem was that it did not work. When people looked at other molecules in the cell, they often traced out entirely different evolutionary trees!
According to a highly influential paper by W. For Doolittle in 1999: [In the past] “From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a ‘universal tree of life,’ taking it as a basis for a ‘natural’ hierarchical classification of all living things…. [But] more challenging evidence [has been discovered] that archaeal and bacterial genomes …. Contain genes from multiple sources.” [W. Ford Doolittle.June 25, 1999. Phylogenetic Classification and the Universal Tree. Science vol. 284pp. 2124-2128. See p. 2124]
The significance of this is, declared Dr. Doolittle that “then no hierarchical universal classification can be taken as natural ……… because the history of life cannot be represented as a tree.” [p. 2124] This was the end of the Darwinian system of tracing descent with modification, the evolutionary tree of life. Enter the new era of Horizontal Gene Transfer explanations for the pattern in DNA sequences that we see among organisms.
Explanations involving HGT between bacteria and archaea and even some simple eukaryotes have substantially taken over studies comparing genome sequences of various organisms. In general, it was expected that multicellular organisms are exempt from such explanations. The germ lines (eggs and sperm) of animals are greatly protected by ovaries and testes and microbes do not readily cross that barrier. However, some exceptions to that rule have been identified. The point is however that any gene in one organism that is found to be similar to a gene in another, very different kind of organism, is now typically attributed to HGT. Rather than admitting that such an observation contradicts ideas of evolutionary relationship, scientists now attribute the situation to HGT, suggesting that this is just a different evolutionary process. As a commentary in Nature declared: “The evolutionary significance of horizontal gene transfer (HGT) is widely recognized for prokaryotes, but it is now becoming evident that it is an important driving force for the adaptive evolution of eukaryotes.” (April 1, 2021 p. 13)
Example: “First known gene transfer from plant to insect identified” from Nature commentary on-line March 25. The article in Cell (Xia et al. 2021 184: 1-13) declares that a whitefly (cosmopolitan agricultural pest) has acquired a plant-derived gene through a plant-to-insect horizontal gene transfer event. The commentary admits that “The results were surprising but convincing.” Apparently, this was the “most parsimonious explanation,” but it is not really an explanation at all because, the scientists admit, “how the whitefly managed to swipe a plant gene is unclear.” In fact, the technical article admits: “Although we showed that [genes] BtPMaT1 and BtPMaT2 were horizontally acquired from plants, we were not able to precisely identify the plant donor species….” [p. 11]
The bottom line is that HGT is an attempt to rescue evolution theory from its failure to predict and explain the pattern of biomolecules in living organisms. This pattern is supposed to demonstrate the action of evolution, but it does not. And nobody even knows how HGT might take place.