Here's an example (pp. 34-36). She describes a situation where an angry baboon might smash an expensive watch. If you hide the watch in large rolls of insulation, the baboon is less likely to cause damage.
And the insulation theory of junk DNA was built on the same premise. The genes that code for proteins are incredibly important. They have been subjected to high levels of evolutionary pressure, so that in any given organism, the individual protein sequence is as good as it's likely to get. A mutation in DNA—a change in a base pair—that changes the protein sequence is unlikely to make a protein more effective. It's more likely that a mutation will interfere with a protein's function or activity in a way that has negative consequences.There are two obvious difficulties with the insulation theory of junk DNA. The first is that Nessa Carey believes that a lot of noncoding DNA is functional. If she's correct, that requires a great deal of insulating DNA if it's going to protect the functional parts. You can't have it both ways.
The problem is that our genome is constantly bombarded by potentially damaging stimuli in our environment. We sometimes think of this as a modern phenomenon, especially when we consider radiation from disasters such as those at the Chernobyl or Fukushima nuclear plants. But in reality this has been an issue throughout human existence. From ultraviolet radiation in sunlight to carcinogens in food, or emission of radon gas from granite rocks, we have always been assailed by potential threats to our genomic integrity. Sometimes these don't matter that much. If ultraviolet radiation causes a mutation in a skin cell, and the mutation results in the death of that cell, it's not a big deal. We have lots of skin cells; they die and are replaced all the time, and the loss of one extra is not a problem.
But if the mutation causes a cell to survive better than its neighbours, that's a step towards the development of a potential cancer, and the consequences of that can be a very big deal indeed. For example, over 75,000 new cases of melanoma are diagnosed every year in the United States, and there are nearly 10,000 deaths per year from the condition. Excessive exposure to ultraviolet radiation is a major risk factor. In evolutionary terms, mutations would be even worse if they occurred in eggs or sperm, as they may be passed on to offspring.
If we think of our genome as constantly under assault, the insulation theory of junk DNA has definite attractions. If only one in 50 or our bases is important for protein sequence because the other 49 base pairs are simply junk, then there's only a one in 50 chance that a damaging stimulus that hits a DNA molecule will actually strike an important region.
The second problem is that it doesn't pass the Onion Test. (I don't think the Onion Test is mentioned in the book but I haven't finished it yet.)
I'm sure you can come up with other objections.
Here's how I like to think of this explanation using the field of bullets analogy popularized by David Raup in his book Extinction: Bad Genes or Bad Luck.
Imagine an automatic machine gun in a pillbox firing 10 rounds a second. It swivels from left to right spraying bullets at random across a field. The enemy has only one grenade and in order to silence the machine gun, some soldier has to run across the field avoiding the bullets until he gets within throwing distance of the pillbox.
Will the soldier's chances be increased if he lines up side-by-side with 99 other soldiers (no grenades) and they all charge together? No.
What if all 100 soldiers line up in single file with the man holding the grenade at the back? That will work.
So, the only way that the insulation theory works is if the extra DNA forms a tight shield around the important functional DNA and physically protects it from cosmic rays or UV light. But this DNA is already "shielded" by a plasma membrane, a nuclear membrane, and various histones; not to mention all the other protein molecules, carbohydrates, and water molecules inside the cell. It's difficult to see what advantage DNA molecules have in direct shielding.
None of these problems are discussed in the book.