ARMAN’s Novel Genes and Unique tRNA Editing

As we have explained many times, being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought to create such a wonder. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought. So today’s falsification, though it falsifies one of evolution’s most treasured predictions, will be no different. Once again, evolutionists have great news.

According to evolutionists, one of the most powerful evidences for their notion that the world just happened to arise somehow on its own, is the underlying unity of biology’s fundamental biochemistry. From information storage in the DNA macromolecule to basic metabolism, the same designs are found across biology’s wide spectrum. As Niles Eldredge put it:

The basic notion that life has evolved passes its severest test with flying colors: the underlying chemical uniformity of life, and the myriad patterns of special similarities shared by smaller groups of more closely related organisms, all point to a grand pattern of descent with modification.

Likewise, Christian de Duve triumphantly declared:

Life is one. This fact, implicitly recognized by the use of a single word to encompass objects as different as trees, mushrooms, fish, and humans, has now been established beyond doubt. Each advance in the resolving power of our tools, from the hesitant beginnings of microscopy little more than three centuries ago to the incisive techniques of molecular biology, has further strengthened the view that all extant living organisms are constructed of the same materials, function according to the same principles, and, indeed, are actually related. All are descendants of a single ancestral form of life. This fact is now established thanks to the comparative sequencing of proteins and nucleic acids.

“The essential macromolecules of life,” explained philosopher Michael Ruse, “speak no less eloquently about the past than does any other level of the biological world.”

And exactly why is it that similarities at the molecular level mandate evolution. Why is it that a conserved DNA code must have arisen spontaneously? Evolutionists cannot explain how the DNA code arose on its own, but they are certain that it must have because it is conserved across the species.

Yes we know, such reasoning does not come from science, but we are getting ahead of ourselves. We can only address one fallacy at a time and the fallacy we are addressing here is not evolution’s hypocritical foundation of metaphysics, nor its illogical affirming of the consequent. Here we are addressing evolution’s failure on modus tollens. Or we might say, its denial of denying the consequent.

Simply and classically put, if P Implies Q, then Not Q Implies Not P. Or in plain English, if a theory makes a prediction, and that prediction turns out to be false, then the theory has a problem. It’s that simple.

To be sure, some predictions are soft and of less consequence. They are more like suggestions than predictions, and if they are found to be false then only minor adjustments are required. But if I insist my theory is confirmed by the success of a prediction, then the failure of that prediction spells trouble for my theory. I cannot claim victory if the prediction works while suffering no consequences when the prediction fails. I can’t have my cake and eat it too.

Not so with evolution. As we saw above the universal DNA code and conserved molecular machinery in all life was claimed to be proof texts for evolution. With such high accolades, one might think that counter indications would pose major problems for evolutionists. Not at all, for this is no ordinary theory.

When the DNA replication apparatus—a rather fundamental biochemical process—was found to be significantly different across different species, evolutionists didn’t miss a beat. Those different versions of DNA replication, we were told, probably evolved independently. Or maybe they diverged. Anyway they evolved, that was for certain.

Another interesting example is the archaeal Richmond Mine acidophilic nanoorganism, or ARMAN, found in microbial mats in the drainage of the acidic northern California mine owned by Ted Arman.

Referred to as enigmatic, the ARMAN species are morphologically unique. They are only a few hundred nanometers across—about a third the size of common bacteria—and some are found strangely attached (actually impaled by a protruding needle) to a nearby larger microbe in apparently some sort of symbiotic or parasitic relationship.

On the inside of this example of lineage-specific biology, the ARMAN species have about two orders of magnitude fewer ribosomes than common bacteria. And their genes don’t map nicely to other organisms. About a fifth of their genes are similar to bacterial genes, and a few of these have never been found except in bacteria. Meanwhile about a third of the ARMAN genes appear to be unique, with no known cousin genes in other species.

Some of the ARMAN species also have some unique molecular machinery. Specifically, they have a unique protein enzyme that edits newly transcribed genes that will become tRNA molecules. tRNA molecules have a three nucleotide reader on one end, and when charged have an amino acid attached to the other end. The type of amino acid corresponds to the type of reader at the other end, and the ribosome uses the tRNAs when translating a messenger RNA molecule according to the genetic code, to construct a protein.

The editing of tRNA genes is one of those fundamental molecular processes hailed by the evolutionists above which were supposed to “point to a grand pattern of descent with modification.” But when we look closely, what we actually find are violations of the pattern. A couple of the ARMAN species, for instance, suddenly show up with their own unique solution.

And if confirming evidence proves evolution, then contradictory evidence must harm evolution, right? Wrong. The first rule one learns for evolution is that all observations are supporting evidence. As the evolutionists concluded, the new finding “represents a new example of the coevolution of tRNA and their processing enzymes.”

You see the “underlying chemical uniformity of life,” such as it is, was never a proof text for evolution because it was never required by evolution. Different DNA codes, one off molecular machines, alternate DNA replication architectures, lineage-specific transcription regulation, unique epigenetic codes, and so forth, will never harm evolution. Contradictory scientific evidence does no damage because evolution never was about following the evidence. It was about interpreting the evidence through a particular theological lens. And like any good lens, this theological lens is transparent to those looking through it.

Religion drives science, and it matters.