Is the Origin of New Genes “Basically a Solved Problem”?

De Novo Genes a Done Deal

It is no surprise that proteins—the essential machines of life—are not likely to have evolved. At least, that is, if you believe in science. Even according to evolutionists and the most optimistic assumptions possible, the evolution of proteins is so unlikely it is beyond practical consideration. While this conclusion is intuitive and hardly surprising, there are several reasons for it. One of the reasons is that the scenarios evolutionists typically envision involve the pre existence of proteins. For instance, proteins are needed to create proteins, at least in today’s biological world. Indeed, proteins are also required for life as we know it. So the first proteins would have had to evolved in a very different kind of biological world. Another reason why protein evolution is difficult is that the fitness landscape in protein sequence space is mostly flat and rugged. A few random mutations will quickly degrade protein function and most of the hyper-dimensional sequence space has little or no function and is far from a useful protein. It is extremely difficult for a random sequence to migrate via mutations close enough to a useful protein for natural selection to take over. In fact this challenge makes the protein evolution difficult regardless of whether proteins already exist. But in spite of this problem, evolutionists believe that protein evolution is not a significant problem. Recently an evolutionist commented that it is “basically a solved problem.”

It wasn’t too many years ago that evolutionists ruled out such protein evolution. Because the problem is so difficult, they believed proteins somehow evolved very early in evolutionary history, and have merely undergone various modifications ever since. As one recent paper explains:

In the pre-genomics era it was widely assumed that much of present-day genetic diversity could be traced by common ancestry to a molecular big bang, where all genes evolved at once.

Likewise another recent paper states:

The emergence of new genes has long been thought to be almost exclusively driven by duplication or recombination of existing gene fragments. The possibility of de novo evolution from intergenic non-coding sequences seemed remote.

But that has all changed now. Not because evolutionists have figured out how new proteins can evolve de novo, but because, if evolution is true, new proteins must have evolved de novo. For in this post-genomic era, we now know that the genomes of species are chocked full of unique, one-time, protein-coding genes. They are not found in allied species, which under evolutionary theory means those genes must have evolved relatively recently.

But how?

If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.”

Case closed right?

Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:

Was it not a bit serendipitous that DNA segments could so easily become transcribed?

And once transcribed and translated, the resulting protein would most likely be worthless junk. It would be somewhere in the middle of that rugged protein sequence hyperspace, light years away from a design that would improve fitness.

Yet the protein would continue to be synthesized by the patient organism, waiting forever as mutations randomly sample the rugged hyperspace. If that was the case then such experiments would rapidly accumulate, and the organism would be producing a plethora of junk proteins.

For this evolutionists envision that the rapid rise of these experimental protein-coding genes is offset by their destruction:

This fast rate of gene emergence raises the question why the genomes do not fill up with such genes over time. In spite of huge variation in total genome size, genomes do not show a proportionally large variation in terms of protein-coding repertoires. Hence, the emergence rate of new genes must in some way be balanced with a corresponding loss rate.

So evolutionists must say that mutations halt the progress, for example, by creating stop codons somewhere in the middle of the gene.

But if that was the case, then the incredible problem of searching through the sequence space just became that much more impossible. Not only must we search through an astronomically huge, flat, rugged fitness landscape that makes finding a needle in a haystack seem trivial, but now the searches are routinely interrupted and must start all over again from scratch. It is an evolutionary treadmill where mutations are working furiously and getting nowhere as they are continually creating and destroying genes.

This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence.

So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes are observed over and over. And since evolution must be true, then those solo genes must evolved:

Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.

And what exactly do these studies show? Did they really show that “de novo emerged transcripts and proteins can assume a function within the organism”?

Not exactly.

One study found a gene in a yeast species, but the corresponding genome location in allied species came up blank. Again, it is the belief that evolution must be true that does the heavy lifting. A gene is found in a species, it is not found in allied species, those species must share a common ancestor, that common ancestor must have existed relatively recently because the species are similar, therefore the gene must have evolved recently.

It all hinges on evolution being true.

The same logic applies in the other studies, such as the one which found a gene in the mouse genome that is missing in other mammals.

Two more studies found more of these de novo genes in the fly genome, and upon testing discovered that such genes are often surprisingly essential. That doesn’t help. Now, the genes must not only have somehow evolved rapidly, they must have rapidly become essential. It was another surprise for evolutionists. Other studies have found genes in only some individuals, within a population.

Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.

This de novo gene story parallels the twentieth century evolutionary insistence that species adapt by random biological variation, not geared to help with the current environmental challenges. Those random variations are then subject to natural selection, and the resulting adaptation is the first step toward the large-scale change evolution requires to create the species.

Only recently have evolutionists begun to reckon with the failure of that narrative. I don’t know how genes arose, but once again evolutionists have made unscientific and unsubstantiated claims, and set themselves up for another failure. Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved. So it is yet another false prediction followed by yet another epicycle, making the theory far more complicated and unlikely.