John Parrington and the C-value paradox

We are discussing John Parrington's book The Deeper Genome: Why there is more to the human genome than meets the eye. This is the second of five posts on: Five Things You Should Know if You Want to Participate in the Junk DNA Debate

1. Genetic load

John Parrington and the genetic load argument

2. C-Value paradox (this post)

John Parrington and the c-value paradox

3. Modern evolutionary theory

John Parrington and modern evolutionary theory

4. Pseudogenes and broken genes are junk

John Parrington discusses pseudogenes and broken genes

5. Most of the genome is not conserved

John Parrington discusses genome sequence conservation

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2. C-Value paradox

Parrington addresses this issue on page 63 by describing experiments from the late 1960s showing that there was a great deal of noncoding DNA in our genome and that only a few percent of the genome was devoted to encoding proteins. He also notes that the differences in genome sizes of similar species gave rise to the possibility that most of our genome was junk. Five pages later (page 69) he reports that scientists were surprised to find only 30,000 protein-coding genes when the sequence of the human genome was published—"... the other big surprise was how little of our genomes are devoted to protein-coding sequence."

Contradictory stuff like that makes it every hard to follow his argument. On the one hand, he recognizes that scientists have known for 50 years that only 2% of our genome encodes proteins but, on the other hand, they were "surprised" to find this confirmed when the human genome sequence was published.

He spends a great deal of Chapter 4 explaining the existence of introns and claims that "over 90 per cent of our genes are alternatively spliced" (page 66). This seems to be offered as an explanation for all the excess noncoding DNA but he isn't explicit.

In spite of the fact that genome comparisons are a very important part of this debate, Parrington doesn't return to this point until Chapter 10 ("Code, Non-code, Garbage, and Junk").

We know that the C-Value Paradox isn't really a paradox because most of the excess DNA in various genomes is junk. There isn't any other explanation that makes sense of the data. I don't think Parrington appreciates the significance of this explanation.

The examples quoted in Chapter 10 are the lungfish, with a huge genome, and the pufferfish (Fugu), with a genome much smaller than ours. This requires an explanation if you are going to argue that most of the human genome is functional. Here's Parrington's explanation ...

Yet, despite having a genome only one eighth the size of ours, Fugu possesses a similar number of genes. This disparity raises questions about the wisdom of assigning functionality to the vast majority of the human genome, since, by the same token, this could imply that lungfish are far more complex than us from a genomic perspective, while the smaller amount of non-protein-coding DNA in the Fugu genome suggests the loss of such DNA is perfectly compatible with life in a multicellular organism.

Not everyone is convinced about the value of these examples though, John Mattick, for instance, believes that organisms with a much greater amount of DNA than humans can be dismissed as exceptions because they are 'polyploid', that is, their cells have far more than the normal two copies of each gene, or their genomes contain an unusually high proportion of inactive transposons.

In other words, organisms with larger genomes seem to be perfectly happy carrying around a lot of junk DNA! What kind of an argument is that?

Mattick is also not convinced that Fugu provides a good example of a complex organism with no non-coding DNA. Instead, he points out that 89% of this pufferfish's DNA is still non-protein-coding, so the often-made claim that this is an example of a multicellular organism without such DNA is misleading.

[Mattick has been] a true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.

Hugo Award Committee Seriously? That's the best argument he has? He and Mattick misrepresent what scientists say about the pufferfish genome—nobody claims that the entire genome encodes proteins—then they ignore the main point; namely, why do humans need so much more DNA? Is it because we are polyploid?

It's safe to say that John Parrington doesn't understand the C-value argument. We already know that Mattick doesn't understand it and neither does Jonathan Wells, who also wrote a book on junk DNA [John Mattick vs. Jonathan Wells]. I suppose John Parrington prefers to quote Mattick instead of Jonathan Wells—even though they use the same arguments—because Mattick has received an award from the Human Genome Organization (HUGO) for his ideas and Wells hasn't [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research].

For further proof that Parrington has not done his homework, I note that the Onion Test [The Case for Junk DNA: The onion test ] isn't mentioned anywhere in his book. When people dismiss or ignore the Onion Test, it usually means they don't understand it. (For a spectacular example of such misunderstanding, see: Why the "Onion Test" Fails as an Argument for "Junk DNA").

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