In recent years a great host of orphans has descended on the camp of the Darwinists -- not a human army but an army of genetic code known colloquially as orphan genes, or more technically as taxonomically restricted genes (TRGs). Evolutionary theory led evolutionists to expect such genes to be rare. As it turns out, they aren't.

Genes are strings of DNA, many of which code for different kinds of proteins. Proteins come in thousands of different shapes and sizes and comprise a diverse kit of micro-miniature machines and other tools essential for life. DNA is "written" using a four-character alphabet (analogous to the way English text is written using a 26-letter alphabet). Some genes, if written out in the four chemical "letters" of DNA -- adenine (A), thymine (T), cytosine (C), and guanine (G) -- would be only a sentence long. Most genes would be at least a paragraph long. Many others would be chapter length. A few genes would dwarf War and Peace.

Orphan Genes

An orphan gene is a gene whose DNA sequence is so bracingly different from any other known gene in any other plant, animal, or microbe that evolutionists label it an orphan. That's because evolutionists typically use genetic similarity between genes as a marker of relatedness between the organisms possessing the genes. Find two genes with highly similar DNA sequences, and perhaps one gene evolved from the other, with the very few differences put down to random genetic mutations to the DNA during reproduction somewhere in the chain of generations. But an orphan gene doesn't resemble any known gene in any other species or group. It's as if the gene, like the biblical Melchizedek, had appeared on the scene "without father or mother or genealogy."

To the evolutionists, that can't be right! According to modern Darwinism, all life evolved through a series of small genetic mutations from a universal common ancestor, spreading and diversifying like the branches of a great tree. As biologist Ann Gauger explains, "The working assumption had been that, given common descent and the fact that most housekeeping genes are shared among living things, and the assumption hitherto that evolution occurs by incremental small changes, orphan genes (protein-coding sequences without known protein-coding antecedents) should be rare if not non-existent."

When molecular biologists began sequencing the DNA of various species, and these unexpected orphan genes started popping up, evolutionists didn't panic, however. Philosopher of biology Paul Nelson tells of a lecture he gave at Dartmouth in 2005 on the challenge orphan genes pose for Darwinism. Someone in the audience objected that only 122 bacterial species had been sequenced; surely biologists would find the families of these taxonomically restricted genes once additional sequencing had been completed. But that's not how things played out.

As Nelson pointed out recently, fully 18 years after his Dartmouth talk, a Polish research team surveyed the genomes of more than 80,000 bacterial species and some 250 million bacterial proteins. They uncovered 10.7 million taxonomically restricted proteins. And the numbers keep growing.

The same thing is happening with the genes of plants and animals. It's a California Gold Rush, and the orphan genes are the gold. The action is so lively that a prominent science journal, PLOS ONE, recently published a peer-reviewed paper reporting on "ORFanID: A Web-Based Search Engine for the Discovery and Identification of Orphan and Taxonomically Restricted Genes." The term "ID" in the search engine name refers to the engine's ability to help investigators identify previously undiscovered orphan genes. But, as it so happens, the engine's development was funded by a grant from Discovery Institute's Center for Science and Culture, the leading institutional hub for work on the theory of intelligent design (ID), where I serve as a Senior Fellow.

It Gets Worse

Writing in Salvo, I have noted that this orphan-gene gold rush clashes with Darwinian expectations but fits neatly with the intelligent design perspective. As I explained, if an organism has a feature shared with another species, then we might expect the designer of life to repurpose an already existing stretch of DNA for programming that feature; but if the feature is unique to the species or lineage, then we tend to expect the designer to have written new DNA code for the new feature (like software engineers do), resulting in a lot of unique code across the biosphere, much as we're finding. My earlier description is true in broad outline, but it actually understates the problem for the Darwinists.

Researchers are discovering that oftentimes even a shared feature across a group of "sister" species is programmed in each species by its own unique orphan genes. Nelson offers a for-instance. "In many species of mollusks, the way that they construct their mantle and their shell ... is mediated by species-specific proteins -- [and] of course, species-specific genes coding for those proteins -- which one would not expect on the view that all mollusks share a common ancestor."

Undaunted

Undeterred by this burgeoning host of orphan genes, evolutionists have grown increasingly creative in explaining away this onslaught of uncooperative evidence.

One such explanation is to say that these orphans will turn out to be functionless junk. But no, more and more it's turning out that orphan genes do important work for the organisms.

Okay, then maybe the pattern is due to what is known as horizontal gene transfer, or perhaps to gene loss. "The hypothesis was that what appeared to be unique was so because it was the result of some rare transfer between species, and we hadn't identified the source," writes Gauger. "Or what once was widespread had been lost over evolutionary time." But no, she adds, such explanations have not been borne out by subsequent investigation.

Okay, then perhaps the orphans are related to other genes, but their DNA sequences diverged so dramatically as to be unrecognizable. On this view, Gauger explains, "only their protein structures might reveal relatedness," but "this also has not been borne out by studies that have determined structures of orphan proteins."

So, how do evolutionists rescue their theory? Some have taken to claiming that, as it so happens, it's actually really easy to get brand new genes from random (non-coding) DNA and the like. Sure, this flies in the face of decades of evolutionary thinking based on probability calculations in population genetics. But because for them evolution must be true (and intelligent design rejected), and because it now appears that evolutionary theory absolutely requires easy-peasy de novo gene evolution to account for all these orphan genes, therefore such presto-chango evolution must be the case.

"Their method of determining how orphan genes originated is simple," writes biochemist Emily Reeves:

Here it is: they counted them. Since they exist, it must have been a cinch for evolution to create them.... From the junkpile of non-coding DNA, strands with "potential" to be functional exist, waiting for their moment in the light. Once they show some function, natural selection is fully capable of amplifying them into genes from scratch.... Evolution is a fact, remember? It's the Darwin skeptics' fault if they can't see the logic.

Defying the Evidence

This solution from the Darwinian faithful doesn't just defy the hard-won findings of population genetics. It also butts up against research by Douglas Axe and others showing that, if anything, it's far more difficult to evolve new proteins (and by extension, the new genes that code for them) than previously assumed.

The results of such research, conducted at laboratories in Cambridge, England, and elsewhere, should not come as a surprise. Our uniform and repeated experience tells us that generating significant amounts of novel, functional information doesn't happen by chance. It requires a mind. Our uniform experience tells us this, and probability calculations applied to everything from English text and software code to DNA confirm it.

What of this army of orphan genes, growing year by year? The Darwinists are partially right. There is a sense in which none of these orphan genes are true orphans. They each have a father. A maker. As do we all.

Notes

Editor's note: This article is republished from Salvo 72 with permission of the author.