“Evolution's Best Argument Has Become Its Worst Nightmare” by Brian Thomas of the “Institute for Creation Research” - a Critique by Barry Desborough.

When presenting my FAQ on endogenous retroviruses (ERVs), creationists often proffer a link to creationist material such as can be found at sites like the “Institute for Creationist Research” or “Answers in Genesis”, as if  holding up a crucifix to the dreadful Count Dracula of Truth. These articles are invariably misleading and often plain wrong. I’ll indent and render in red Thomas’ remarks and offer a critique with a special emphasis on ERVs. Thomas begins…

How Functional Transposons Refute "Junk DNA" and Human Evolution

Broad-scale evolution holds that a single-cell organism can eventually develop into a human through natural processes. Unique genetic features called transposons have been introduced as knock-down evidence that this progression actually occurred in humans, but a closer look at new data shows that they strongly argue against evolution.

So we start with a straw-man - a dishonestly distorted version of an argument to be attacked, rather than the real argument. The argument is that large numbers of transposons in common chromosomal DNA locations in different species testify to their common ancestry, not that we evolved from a single-celled organism. A brief explanation of the real argument can be found here, What is the "case for common descent" from ERVs?

Genome Expansion through Transposon Activity

Transposons include several classes of DNA that appear to have been copied, spliced, and reinserted into the genome. Sometimes referred to as jumping genes, these are found in all plants and animals. While some transposons are inactive, many are functional. They have an affinity for transposition into certain areas of the genome.

Regarding transposons that integrate into host DNA using an enzyme called integrase: While it is true that certain retroviruses, for example, can be seen to integrate into certain types of areas more often than others, just like road traffic accidents tend to happen more often in accident “black spots”, the integration sites are not nearly specific enough to account for huge numbers of integrations into precisely corresponding (down to base-pair resolution) locations.

Scientists have observed transposons copying and splicing rapidly, which contradicts evolution's traditional scenario of slow and gradual change.1 Rapid transposon activity appears to be controlled by specific cellular programs and thus is not a product of mutation plus selection, nor is it part of evolution as it has been described.

This is just silly. Mutations and integrations happen in individual DNA molecules. How can these happen “slowly and gradually”?

In a short time--corresponding to fewer than a dozen or so generations--transposons can add more DNA to a population, inflating the total volume of DNA without adding new genes. Some species appear to have large volumes of DNA that were assembled this way. About 44 percent of human DNA consists of repetitive elements, much of which came from transposons.

These vast sequences are repeated blocks of identical DNA. Many evolutionists believed them to be random sequences, conveniently useful for evolutionary processes to tinker with and develop into new genetic features. However, they are now known to be quite useful. Therefore, if evolution were to mutate them randomly, rather than leading to genetic improvements, it could actually kill the host.

Certain sequences have been found to be useful. It is dishonest to imply that they have all been found to be useful. And their utility or otherwise is irrelevant to the real argument, the one not made of straw.

Transposons in Chimps--Leftovers from the Evolutionary Past?

Intriguingly, chimpanzees and humans share some almost identical transposons that are found on similar-looking chromosomes. How did they get there? Evolutionists have insisted that "ancient retroviruses slipped bits of their DNA into the primate genome millions of years ago."2 Though often asserted as fact, it is only speculation that today's transposons came from yesterday's viruses.

Standard dishonest creationist ploy: Pretend that a conclusion reached by gathering and examining the evidence, then trying and failing to test that conclusion to destruction, is a mere “speculation”. Here is why virologists and geneticists conclude that ERVs derive from retroviruses.

Some transposons supposedly entered chimps and humans by a viral infection when both were part of one ancestral species. Later, humans and chimpanzees "diverged" from that primate ancestor. Thus, the same transposon sequence in both species is used as evidence that humans and chimps came from a common ancestor. And if humans transmutated from some earlier primate, then big-picture evolution is true. This has been one of evolution's best arguments.

Transposons are also thought to have provided "junk DNA" for ages of mutations to have organized into new features, forming today's diverse living forms. But science has shown that these long, repeated transposon sequences are useful on their own and even necessary. The arguments that transposons demonstrate common ancestry between chimps and humans, and that they provide scrap material for evolutionary progression, only have merit if transposons are largely useless.

This is very muddled. ERVs are not thought to be “junk”, but inherited remnants of retroviral integrations. Some components (never a complete ERV!) of some ERVs serve a purpose. How could they produce evolutionary “progression”* if they are useless?

*The use of the term “evolutionary progression”, by the way, is a bit of a giveaway showing that Thomas’ grasp of evolutionary science is somewhat feeble. Evolution is not a “progression” in the sense of the medieval pre-evolutionary conception of “The Great Chain of Being”. It is the process by which organisms adapt to changing circumstances, where the only (metaphorical) “directive” is to reproduce successfully.

Some scientists, open to the possibility that transposons were purposefully created and therefore functional, predicted at least a decade ago that important functions for transposons would be discovered. When nobody knew if these repetitive sequences had a useful genetic role, evolutionary biologists assumed that they did not, since they don't code for proteins. However, new genomic technologies have revealed more about what transposons actually do.

ERVs are transposons. They code for proteins and also for promoters (without which, the proteins would not get transcribed.)  The statement that scientists assumed that no components of ERVs had any useful role is incorrect. It is also irrelevant.

Transposons with Functions

The last decade has provided a growing list of examples of transposon functions, including the 2006 discovery of one that regulates a nerve cell development gene common to all mammals and even the "living fossil" coelacanth.  Transposons that regulate the expression rates of plant gene products have also been found.

Transposons in a single-cell ciliate were determined in 2009 to be critical to the tiny organism's development. The study's authors wrote, "These transposons might not merely be parasitic invaders that reduce host fitness or have little phenotypic effect but instead mutualists directly contributing a useful function for the organism, such as genomic DNA processing." They found that these transposons "spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow." So, if transposons have functions in these organisms, could they also play important roles in chimps or humans?

Publishing in Nature Genetics, an international team of researchers led by geneticist Geoff Faulkner found that in mammal tissue between 6 and 30 percent of RNA transcripts come from retrotransposons, not genes. Retrotransposons are a class of transposon.

RNA transcripts begin as single-strand copies of small sections of a DNA sequence. Some transcripts specify the information to make a protein, but most RNA transcripts help regulate the speed and amounts of important cellular processes and products. Also, information inside transposons provides alternate places for the transcription machinery to latch onto and begin transcribing the DNA. With transcription beginning at these various start sites and proceeding forward and backward on both strands of DNA, the necessary varieties of RNA are generated.

Faulkner stated in a University of Queensland press release, "Our results showed that retrotransposons that can no longer move around the genome may still be expressed in a broad range of cells, and thereby regulate the expression of nearby genes." Transposon-derived transcripts are very important for cells.

Parasitic DNA sequences from some ancient virus should yield useless junk, not important information-carrying material. The idea that transposons came from viral infections but somehow later learned uses within their new hosts has been baptized into evolution with the name "exaptation." But this conclusion is speculative, unobserved, and irrational. Without proper gene regulation provided by transposons that are already intact and fully integrated into the genome, the organism may die.

This conclusion of Thomas is speculative, unobserved, and irrational. It is a mere argument from personal incredulity, and asserts that evolution is impossible because evolution is impossible. For a discussion of why we think that bits and bobs from ERVs have been scavenged by evolution, see
ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?

ERVs promote the transcription of host DNA. Doesn't this prove they are designed?

ERVs are essential in reproduction (syncytin and the formation of the placenta). How can this be?

Isn’t it odd that all of these exaptated ERV components have been found by real working scientists, rather than creation “researchers” who do no research, but merely try to spin the work of others?  How many of them had some crisis leading them to the conclusion that evolution must be all wrong? They do not suffer the personal incredulity of Thomas at all. And what about the creationist conspiracy theory - that scientists hide or distort research so as to fool the rest of the world about evolution? There is no hiding going on here!

By analogy, copies of a computer virus on a hard drive do not improve software or performance, but rather harm it. Useful software comes only by planning and effort. Science has shown that transposons are useful biological software. But this means that they did not come from viruses, despite contradictory popular press. Instead, they appear to have come from a pre-designed system of integrated genetic elements that mobilize under strict regulation, and which in turn regulate other systems.

This is an extremely poor analogy. But we know already that Thomas has no clue as to what he is writing about. See Aren't the same ERV genetics in the same places in different species because they have to do the same job?

The Entire Genome Is Information-Rich

The reason why both chimpanzees and men have such similar-looking transposons in similar chromosomes could be because the sequences were programmed to serve similar biological functions. Or, they could have followed similar biologically significant patterns when they were being copied and inserted, for reasons that are no longer discernible.

See above.

Since transposons did not come from ancient viruses, but are instead essential parts of genomes, they can no longer be used to support the belief that chimpanzees and humans evolved from a common ancestor. And this means that one of evolution's best arguments has failed, just like the debunked parade of prior "best" arguments.

I have shown that Thomas’ “argument” is an attack on a straw man. What Thomas miserably fails to do is to address the compelling evidence that ERVs are the inherited remnants of retroviral integrations - the evidence for which I link to above. I note that there is no attempt to support the assertion that there is a ‘debunked parade of prior "best" arguments’. I think we can apply Hitchens’ Razor here.

The demotion of transposons as an evolutionary "proof" is reminiscent of the old, discredited "vestigial organ" argument. One hundred-eighty organs in the human body had been cited as useless leftovers from an evolutionary past, but each has been found to have an important function, including the appendix and tonsils.14 Now that these vast expanses of genetic material are known to be information-rich, the concept of "junk DNA" has to be junked. And with no spare genetic material for it to mutate, what mechanism is left that broad-scale evolution could have used to produce the variety of life observed today?

Yet another straw-man, and another unsupported assertion. Vestigial organs are not necessarily useless. Reduced or altered function is enough to qualify a feature as vestigial. I have survived 61 years without an appendix, with no noticeable problems. And before then, my placenta was built with the help of an exaptated retroviral envelope gene.

It is difficult, if not impossible, to imagine how evolution could tinker with transposons without disrupting their precise coordination, which is vital to life forms. But it is easier now to see that the original people--like the first chimpanzees, plants, and even single-cell life forms  --were expertly fashioned, through and through, by a brilliant Engineer.

Yes, Brian. We know that your imagination is severely hampered by your religious presuppositions. Evolution is impossible because it is unthinkable that it is not.