Why Do the IDiots Have So Much Trouble Understanding Introns?

Most eukaryotic genes have introns. Introns make up about 18% of the DNA sequences in our genome. Most of these sequences are junk but introns are functional and up to 80bp of each intron is required for proper splicing. The essential sequences contain the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). The branch site and the splice sites are where specific proteins bind to the mRNA precursor [Junk in Your Genome: Protein-Encoding Genes]. It turns out that within introns about 0.37% of the genome is essential and about 17% is junk.


The primary transcripts of some genes are alternatively spliced. In other words, there are at least two different versions of mRNA produced from the same primary transcript. We've been teaching alternative splicing for thirty years—it's been in the textbooks for decades. The inclusion or exclusion of an exon during splicing is controlled by regulatory proteins that bind to specific sites within the intron—often near or at the 5′ splice site or the 3′ splice site. The binding sites are, at most, 10bp in size. Even if there were five of them per intron this would only mean an additional 50bp of essential sequence and it would only apply to a small percentage of all introns. Not enough to worry about when calculating the total amount of junk DNA in our genome.

Casey Luskin worries about such things [Yet Another Blow to "Junk DNA": Paper Shows How Introns Are Key to the Splicing Code]. He found a recently published paper by Wang et al. (2013) that identified a handful of new splicing regulatory factors and binding sites. This leads Casey Luskin to conclude that ...

Studies like this one add to the weight of evidence showing introns are vital -- in this case, for splicing of RNA to create important protein-coding transcripts. The "junk" in the genome turns out, once again, to be very much otherwise.

It seems as though poor Casey has just learned for the first time that there are RNA binding sites in introns. It's apparent that he does not have the knowledge to calculate how much of an effect this might have on the total amount of junk DNA in our genome.

THEME

Genomes & Junk DNA

Alternative splicing has been a problem not only for Casey Luskin but also for Richard Sternberg, who actually has some training in biology (i.e. fewer excuses). A few years ago (June 2010) he published an article in Evolution News & Views (sic) where he claimed that 171,000 introns in the human genome participate in alternative splicing pathways. He believes (incorrectly) that 90% of human genes are alternatively spliced. There are about 190,000 introns in 20,500 protein-encoding genes for an average of about 9 introns per gene.² According to Sternberg, since 90% of 190,000 = 171,000 it means that there are a lot of "functional" introns. They can't be junk [Creationists, Introns, and Fairly Tales]. Sternberg made a serious error in his calculation—one that could not be made by anyone who understands alternative splicing.¹

When the error in his calculations was pointed out to him he repeated the mistake in another post [IDiots Do Arithmetic a Second Time - Same Result].

Jonathan McLatchie [Alternative Splicing and Why IDiots Don't Understand How Science Works] and Jonathan Wells [Jonathan Wells Weighs in on Alternative Splicing] have also demonstrated an inability to understand splicing and alternative splicing even though they write about it on creationist blogs.

This is why I gave a talk recently on Science vs IDiots where I pointed out that most creationists don't know enough about biochemistry, molecular biology, and evolution to pass an undergraduate course. Yet that doesn't prevent them from criticizing papers on all three topics. And no matter how often you point out their lack of knowledge, it doesn't seem to stop them from making the same mistakes over, and over, and over again. Isn't that strange?

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1. Even if 90% of our genes are alternatively sliced—they aren't—that only means that at least one intron is involved in alternative splicing events. The best you can say is that 90% ×: 23,000 genes = 21,000 genes are alternatively spiced and as few as 21,000 introns participate in alternative splicing.

2. A better average is 7.2 introns per gene [Junk in Your Genome: Intron Size and Distribution].

Wang, Y., Xiao, X., Zhang, J., Choudhury, R., Robertson, A., Li, K., Ma, M., Burge, C.B., and Wang, Z. (2013) A complex network of factors with overlapping affinities represses splicing through intronic elements. Nature Structural & Molecular Biology 20:36-45. [doi:10.1038/nsmb.2459]