Larry Moran has a simple list of the 5 basics you need to understand about junk DNA. It’s short and sweet; I’d like to see a creationist, who are often weirdly antagonistic to the whole idea of junk DNA, deal with these basic facts before they start ranting against the observations and conclusions.
Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.
A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.
Modern Evolutionary Theory
Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome.
Pseudogenes and broken genes are junk
More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk.
Most of the genome is not conserved
Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can’t rule out some unknown function that doesn’t depend on sequence.
I’m also relieved to see that the anti-junk fanatics tend to gravitate towards Larry’s blog and leave the rest of us mostly alone.