Transposable element (TE), Transposon, “Jumping Genes”

A DNA sequence that can change its position in a genome, and in so doing, sometimes alters the expression of other genes, is called a transposon. Such genes are also useful in inserting foreign sequences into a genome (GMO research).

Barbara McClintock (1902-1992) working with corn, saw some strange changes in pure breeding corn. She thus came to discover “jumping genes”. She presented her work in 1951 but no one would believe her observations or conclusions. Her work was ignored until the 1960s-1970s when the same phenomenon was observed in bacteria. She received the Nobel Prize for Physiology and Medicine in 1983.

TEs are used now used in some evolutionary explanations often in combination with horizontal gene transfer.

The HGT stories grow ever more fantastic. When one’s sole criterion for evaluating evidence is that it had to come about through unguided processes, then no naturalistic situation seems too improbable if evolution-based explanations are scarce.

Consider the case of some marine fish, herring (Clupea harengus) and rainbow smelt (Osmerus mordax) and Japanese smelt (Hypomesus nipponensis). These fish exhibit the unusual antifreeze protein AFP II. Some other fish also exhibit this protein (specifically sea raven Hemitripterus americanus and longsnout poacher Brachyopsis rostratus.) Herring, rainbow and Japanese smelts however produce type II AFPs that require calcium ions for their antifreeze activity, whereas the type II version in sea raven and longsnout poacher does not. This suggests that the action of the two antifreeze proteins is different and that their molecular details are also somewhat different.

Scientists have proposed three different evolutionary mechanisms which could foster the AFP II protein in herring and smelt, which are considered to be distantly related. Why do we see it in just these two kinds of fish? The proposed explanations are horizontal gene transfer, convergence, or common descent. If convergent evolution were correct, then this situation would have involved three independent evolutionary events. If common descent had occurred, then the ability to synthesize this protein would have been lost independently at least three different times. [Ulf Sorhannus. 2012. Evolutionary Bioinformatics 8: 535-544 see p. 536] None of these scenarios looks realistic. Also, if one adopts an HGT explanation, that also could potentially involve a number of lateral transfer events according to the author of the 2012 paper.

In the summer of 2021, there has been renewed interest in HGT as an explanation for this situation. Apparently, the protein in the herring and smelt is nearly identical, with no other fish exhibiting this exact molecule. (Five different antifreeze proteins have been described in fish, but they differ in action and molecular structure.) In addition, the taxonomic relationship of the herring and smelt are considered to be “distant” and they do not interbreed. To this point, the thinking among molecular biologists as to the possibility of a HGT was that it was “wildly unlikely” with “insurmountable barriers” to success. [Christie Wilcox. 2021. Quanta Magazine  June 9 pp. 1-13 See p. 5]

The new study however called upon another explanatory tool in addition to HGT. Transposable elements (TEs) are mobile chunks of DNA that can copy and paste themselves into a genome. There are a number of sequences around the AFP gene in herring that may (or may not) be transposable elements. [p. 5] These TEs are not found in other fish except that three of them are adjacent to the AFP gene in the smelt (and in the same order as in herring). As far as the current research team is concerned, this situation with the TEs is “definitive proof” that HGT has occurred. They declare that it is “indisputable that a chunk of herring chromosome made its way into smelt.” [p. 5]

The article then provides another example of a presumed TE event, this one between a few mammals, a reptile and an amphibian. A genome biologist, Cedric Feschotte from Cornell University, summarizes the implications with the remark: “Anything you want, I can give you an example of what a transposon [TE] can do and has done. Bringing in new genes, new regulatory sequences, rearranging chromosomes – you name it.” Indeed TEs can be used as the magic that makes improbable events look possible.

We must realize however that HGT and TEs have not explained where this unusual antifreeze protein came from nor how (or if) the gene was moved between totally unrelated fish not only into the fish, but into the germ line. (See diagrams in Wilcox p. 4 for imaginative proposals on how this could take place.)  Other even more fantastic stories are used to prop up the “it must have happened” story. These molecular biologists are not willing to consider that common design is a lot more parsimonious and logical than wildly unlikely evolutionary scenarios!