Dispatches from the Creation Wars

Testability 3.0

In a recent posting, Rusty answers me once again on the issue of testability. He proposes an actual test for both creationism and evolution. This is what he says:

But in the strictest sense of the term testability, a falsifiable prediction must be made in order for a scientific theory to be considered valid. Fair enough. So, although I am not associated with Reasons to Believe, I think I can make the following testable prediction from their model:

Further research will reveal function for so-called Junk-DNA sequences. Although considered by evolutionists to be a closed case, the Creation Model predicts that currently held scientific opinion on this issue will eventually concede that function is inherent in the Junk-DNA sequence. The failure of this test would be a devastating, if not killer, blow to the Creation Model.

This is a very interesting thing to say, for several reasons. He seems to be saying that if a function is not found for every single bit of the genome, creationism is falsified. Okay, I’ll take that bet. Let’s examine so-called “junk DNA” a bit further.

Junk DNA is the term given to that portion of the genome that does not code for proteins, meaning it does not manifest itself in the phenotype. The human genome project has identified about 40,000 active genes, but that is only about 2% of the total amount of genetic material in the human genome. The rest is often referred to as junk DNA. But that doesn’t really tell the full story. Even the junk DNA is divided into different types, and it’s certainly true that a few of the genes that were once thought to be non-coding have been found to have function. Indeed, that is one of the main tasks of the ongoing Human Genome Project, to identify each and every gene and determine whether it is active or inactive. A portion of what is referred to as junk DNA is made up of pseudogenes: sequences of genomic DNA with such similarity to normal genes that they are regarded as non-functional copies or close relatives of genes. There are two types of pseudogenes, processed and unprocessed, produced by two different processes:

duplication – modifications (mutations, insertions, deletions, frame shifts) to the DNA sequence of a gene can occur during duplication. These disablements can result in loss of gene function at the transcription or translation level (or both) since the sequence no longer results in the production of a protein. Copies of genes that are disabled in such a manner are termed non-processed or duplicated pseudogenes.

retrotransposition – reverse transcription of an mRNA transcript with subsequent re-integration of the cDNA into the genome. Such copies of genes are termed processed pseudogenes. These pseudogenes can also accumulate random disablements over the course of evolution.

How do we know that these processes take place? Because they’ve been observed. In microbe populations in the lab, scientists can identify gene duplications as they, identify the specific gene that has been duplicated, and then watch over subsequent generations as mutations build up in the duplicated pseudogene. In other words, this isn’t guesswork, it’s observation. And this not only provides powerful evidence for evolution, it also gives us enormous insight into how evolution took place by comparing pseudogenes in different genomes:

In any study of molecular evolution, it is necessary to compare and contrast genes from a variety of organisms to gauge how the organisms have adapted to ensure their survival. Pseudogenes are vitally important since they provide a record of how the genomic DNA has been changed without such evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome.

That’s one type of “junk DNA”. About 40% of the genome, according to recent estimates, is made up of what are called “transposable elements” – bits of DNA that can transpose themselves into other places in the genome and act as a sort of genetic parasite. Carl Zimmer wrote a fascinating article about them a couple years ago. As he puts it:

Through migration and proliferation, transposable elements have become inordinately successful, and that is how they have come to constitute 40 percent of our DNA, either as active copies or dead ones. Much of the remaining junk DNA in our genome may also turn out to be former transposable elements that have mutated beyond recognition. In certain species the proportions are even more staggering: 99 percent of the lily genome consists of transposable elements.

These transposable elements actually can play a major role in evolution, as Zimmer explains:

Transposable elements also appear to play a crucial role in the evolution of the cell’s “legitimate” genes. Genes can evolve only if they first mutate, and transposable elements create a significant fraction of a genome’s mutations. Like other kinds of mutations, most of those caused by transposable elements are neutral or harmful, but some of them can do an organism good. Sometimes, for instance, these mobile genetic parasites drag a piece of a neighboring gene with them to their new home. In the process, they link two preexisting chunks of genes into a new combination that may quickly take on a new function.

Transposable elements themselves have even become vital parts of genes. About 500 million years ago, for example, a transposable element in the genome of early vertebrates was incorporated into a gene that became part of our immune system. This ex-parasite stopped using its DNA-splicing skills to replicate itself and instead began rearranging the genes that encode pathogen-recognizing proteins. Thanks to this transposable element, our immune cells can quickly generate millions of different-shaped proteins. Through a process much like natural selection, the cells with proteins that allow them to identify pathogens will survive and can then be made to alter their genes again to do an even better job. In other words, it is only thanks to an erstwhile parasite that we can fight off other parasites.

Now, what of the few instances where they’ve found that what was previously thought to be junk DNA turned out to have function? Even here, what they have typically found generally means the opposite of what the folks at Reasons to Believe are claiming. Rusty gave a link to a couple of articles from the Hugh Ross website about scientists finding possible function for specific bits of junk DNA, particularly LINE DNA. Since it was a bit beyond my ability to understand, I turned to a friend with some expertise in the field to evaluate the claims. Paul Myers, a PhD biologist from the University of Minnesota-Morris, said that what they have identified is actually the opposite of what they suspect – it’s evolution adapting bits of junk DNA into ongoing genetic processes:

LINE is a specific kind of repeated element that consists of a reverse transcriptase that has copied itself into the genome. It has just copied itself over and over into the DNA.

They describe two “functions”. One is titration: cells make decisions about
when to divide by measuring the nucleus:cytoplasm ratio. In this case, the junk is filler that is taken into account when determining when to divide. It’s putting everything backwards, though: as clutter accumulated in the genome, the ratio set point for division shifted to compensate.

The other is the discovery of enzymes that recognize a LINE sequence. Again, this is an after-the-fact adaptation. Evolution is a process that will co-opt anything lying around, and so a function was found for a short stretch of junk in one chromosome. It’s like the nylonase gene, which acquired its function by fortuitously acquiring a short piece of random DNA from the junk pile, or like found art, that uses useless, discarded crap for a new purpose.

So what we’re left with is this. A sizable portion of the genome is made up of pseudogenes, which are produced through processes that we’ve observed, and which are explainable only through evolution. A sizable portion of it is made up of transposable elements that help drive evolution by providing mutations that can be preserved through natural selection. And a sizable portion of it is made up of just random repetitive sequences, which Paul Myers says results from the fact that “the polymerase ‘stutters’ as it is making copies of long stretches of repeated stuff.” And all told there is about 49 times more of that stuff than there is of active DNA. If Rusty is willing to base the testability of the creation model on finding function for every single bit of this stuff, I suspect he’s going to be disappointed. But I also suspect that since this is an open-ended prediction, it’s not really a true test. No matter how long it drags on, he can always say, “Well maybe we just haven’t found out what the function is yet.” But in the meantime, I’d say that a powerful case has been made for why the existence of pseudogenes and other types of junk DNA provides strong evidence for evolution.

An answer on the second part of his proposed tests, this one for evolution and dealing with irreducible complexity, is on the way.