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Common Sense Design Principles and the Real World

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A recent paper in PLOS Genetics considers the origins of new "genes" in humans and chimps. By comparing RNA sequences, researchers identified over 600 transcriptionally active "genes" that appear to be present only in humans and not in chimps or the other mammal species tested. They claimed that these "genes" were the product of evolution from previously non-coding, untranscribed DNA. They argued that some of the "genes" are made into proteins and perhaps may be subject to selection, meaning that they are evolving.

I put genes in quote because this is not what the term gene typically means. It used to be that a gene was a stretch of DNA that coded for a protein, meaning it was a stretch of DNA that was copied into RNA (transcribed), and then translated into protein.

These researchers are using "gene" to signify any stretch of DNA that is copied (transcribed) into RNA and that meets certain criteria (size, the frequency with which they found it, etc.). They do not require that the RNA be turned into protein. In fact most of the time it probably isn't. But still they call them genes. Only in some cases do they find evidence that these genes actually make protein, protein that may be evolving new functions, they say.

Something to bear in mind -- all these conclusions are based only on the comparison of DNA sequences among species. They are conclusions based on the assumption that the differences reflect some sort of genetic history based on common descent -- the conclusions are not based on any experiments or observations of real events happening in real time.

As to their claims: I believe them when they say there are more than 600 regions of the genome that are transcribed in a manner unique to humans. After all, humans are different from chimps and can reasonably be expected to have genetic differences. Second, they may even be genes, if they produce a functional RNA, which is possible. I suspect they will be functional as RNAs. Third, these genes are in parts of the genome that used to be thought of as junk. Well, that's no surprise either. ID proponents have always expected most DNA to have a function and not be junk.

What I doubt is the claim that these genes evolved from untranscribed random sequences that somehow acquired promoter sequences, became transcribed, and even further, sometimes became translated and then became functional. The reason I doubt this? Douglas Axe's and my work on the evolution of enzymes, and a dose of common sense.

First of all, it is no trivial thing to "acquire" the promoter sequences that turn on a gene's transcription, and the signals that say when to stop. That one little undemonstrated word hides a multitude of requirements, and probably signifies a designer's action. Second, the words "became translated" hide all sorts of complex signals and activities, and likely require a designer as well. But the biggest problem of all is the business of taking non-functional protein and turning it into functional protein.

This scenario is what we tested in our most recent paper in BIO-Complexity. First, how hard is it to take a piece of junk protein and turn it into a brand new functional enzyme -- without a designer -- even if the junk protein already has a small amount of the new function to start? The answer -- it's not possible. We tested it in silico (using a computer program called Stylus, available online), and in the lab with a real protein. We were unable to improve the "junk" protein's function much at all, even after multiple rounds of mutation and selection.

Second, it's not possible to take a weakly functional, but already structured enzyme and change it to a new function at wild-type levels, even when the protein's not junk to start, and already has a small amount of the new function. If it has the wrong shape, the function can't be improved much at all -- nowhere near the levels normal wild-type enzymes have.

Third, if you are only a few selectable mutations away from a new function, it is possible to get there -- as long as each step is an improvement. That means in order for evolution to be able to make a wild-type enzyme, it has to begin with something that is most of the way there -- it's already pretty much the enzyme that's needed. New proteins have to be essentially of the right design in order to be improved to wild-type function.

Why bother with these experiments on proteins in the first place, you may ask. The answer is this -- what is true in the microscopic world about evolution is also true in the macroscopic world. What works (or doesn't work) with enzyme evolution demonstrates what evolution can or can't accomplish on a large scale.

If it's not possible to evolve new proteins from any starting point, evolving buttercups or cows won't work either. That is, unless the buttercups and cows pretty much already are buttercups and cows.

Evolution can't build something new from scratch. And it can't reconfigure something that already exists into something different. That's why I doubt the story of evolving new human genes from random non-coding sequences. I don't doubt that the genes are there -- they are. It's just that I think they were designed, not evolved.

Now for the dose of common sense. Let's turn the microscopic to macroscopic analogy on its head and use what we already know of design in the macroscopic world.

We all know you can't take a pile of scrap metal and turn it into a washing machine. You'd have to start from scratch, even though they are both made mostly of metal. What about turning a washing machine into a dishwasher? There's more similarity there -- after all, they both wash things. Still, neither process will happen without a designer or without considerable refashioning. Now what if a washing machine was merely broken? What if it had a few loose bolts and a torn gasket on the door? A blindfolded repairman might be able to fix that. That would be harder but not impossible. But even this analogy breaks down because the repairman is intelligent.

These are not perfect comparisons to biological processes -- the examples used all require intelligence and are man-made. But these things are simpler than enzymes, so perhaps our design intuitions do transfer to the biological realm.

Don't just take my word for it, though. For the real experimental data, read the paper and see for yourself. Check out the experiments that demonstrate in real time what really can and can't be accomplished.

Image: Buttercups, by Kate Jewell [CC BY-SA 2.0], via Wikimedia Commons.