Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

I placed an order for the book and noticed that you can browse the first few pages.

How bad is it? ... Really bad. She starts out explaining what she means by "junk" DNA.

There's a bit of linguistic difficulty in writing a book on junk DNA, because it is a constantly shifting term. This is partly because new data change our perception all the time. Consequently, as soon as a piece of junk DNA is shown to have a function, some scientists will say (logically enough) that it's not junk. But that approach runs the risk of losing perspective on how radically our understanding of the genome has changed in recent years.

Rather than spend time trying to knit a sweater with this ball of fog, I have adopted the most hard-line approach. Anything that doesn't code for protein will be described as junk, as it originally was in the old days (second half of the twentieth century). Purists will scream, and that's OK. Ask three different scientists what they mean by the term 'junk', and we would probably get four different answers. So there's merit in starting with something straightforward.

There are so many errors crammed into these two paragraphs that it would take another book to correct them. Let me just point out that knowledgeable scientists define junk DNA as DNA that doesn't have a function. No other definition is worth the paper it's written on.

There was never a time when knowledgeable scientists said that all noncoding DNA was junk. Not in the last century, and certainly not in this century. Nessa Carey is not speaking the truth here. I don't think she's lying—although I don't rule out that possibility—but I do think she is seriously mistaken. How in the world could she write a book on junk DNA without learning how the term is defined?

I also don't think it's correct to say that our understanding of the genome has changed radically in recent years. Mine certainly hasn't and I'm pretty sure that most knowledgeable scientists had a good understanding of genomes 30 years ago. The only exception might be that there are more genes making functional RNAs than we realized back in the 1980s.

On the other hand, the views of some other scientists have changed a lot. They have learned, to their surprise, that most of our genome is junk and that natural selection has not eliminated all nonfunctional DNA. I don't think that's what Nessa Carey is referring to.

The debate over junk DNA is not about the existence of junk—that fact cannot be contested. The debate is over the relative amount of junk DNA in various genomes. There's plenty of real, positive, evidence that the human genome has lots of junk DNA (non-functional DNA) but there are still legitimate scientific discussions about the details and there are even debates about possible structural roles for nonconserved DNA (bulk DNA hypotheses). If a journalist is going to write about this stuff, they have to do a lot of homework. This is no place for amateurs.

For years scientists had no explanation for why so much of our DNA doesn't code for proteins. These non-coding parts were dismissed with the term 'junk DNA'.

Nassa Carey should read Five Things You Should Know if You Want to Participate in the Junk DNA Debate. Back in the 1970s, scientists had two kinds of explanations for noncoding DNA. The first explanation was that some of it was known to be functional. Scientists knew about regulatory sequences, origins of replication, centromeres, telomeres, and various genes for RNA. Later on we learned about introns.

The second explanation was that a lot of the DNA in eukaryotic genomes didn't have a function. Much of the human genome, for example, consisted of repetitive sequences that seemed to be dispensable. We knew that only a small percentage of the genome could be functional because of genetic load arguments. By the 1980s we knew about pseudogenes and we knew that most of the transposons in the human genome were defective bits and pieces. It was easy to explain this as junk because it certainly looked like junk.

But gradually this position has begun to look less tenable, for a whole host of reasons.

Perhaps the most fundamental reason for this shift in emphasis is the sheer volume of junk DNA that our cells contain. One of the biggest shocks when the human genome sequence was completed in 2001 was the discovery that over 98 per cent of the DNA in a human cell is junk. It doesn't code for any proteins.

We had an accurate measure of the size of the human genome back in the 1960s. We knew back then that there were probably fewer than 30,000 genes and that only a small fraction of the genome was complementary to mRNA.

When the decision to sequence the human genome was being discussed in the late 1980s, there were many scientists who said that it would be a waste of money because so little of it coded for proteins. There were no surprises, among knowledgeable scientists, when the draft sequence was published. Most of the genome appeared to be junk, just as expected.

If you were surprised then it was only because you hadn't been keeping up with the literature.

The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans.

Anything found to be true of E. coli must also be true of elephants.

-Jacques Monod (1954)Knowledgeable scientists already knew that humans had about the same number of genes as other animals. Knowledgeable scientists read the papers on the molecular biology of development—mostly in Drosophia—that were published in the 1980s. They realized that the differences between fruit flies, nematodes, and mammals were due largely to small changes in regulatory sequences. That's what evo-devo was all about. The concept was developed over the preceding 50 years.

Apparently, that concept is foreign to Nessa Carey. One wonders what sort of molecular biology she taught to students at Imperial College.

Knowledgeable scientists were not "shocked" to learn that humans had about the same number of genes as other animals and that all animals had similar genes. Stupid scientists might have been shocked but you don't write books about the misconceptions of stupid scientists—unless you are one.

As researchers deepened their analysis of what differentiates humans from other organisms at the DNA level, it became apparent that genes could not provide the explanation.

Genes plus regulatory sequences provide the explanation. That was known 40 years ago and it's still true today.

In fact, only one genetic factor generally scaled with complexity. The only genomic features that increased in number as animals became more complicated were the regions of junk DNA. The more sophisticated an organism, the higher the percentage of junk DNA it contains. Only now are scientists really exploring the controversial idea that junk DNA may old the key to evolutionary complexity.

I'm not making this up. A science writer with a Ph.D. actually wrote this in a book published in 2015!
... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.

Stephen Jay Gould
Ontogeny and Phylogeny (1977)

Researchers are only just beginning to unravel the subtleties and interconnections in the vast networks of junk DNA. The field is controversial. At one extreme we have scientists claiming experimental proof is lacking to support sometimes sweeping claims. At the other are those who feel that there is a whole generation of scientists unable to see or understand the new world order.

I'm in the second category. There's a whole generation of scientists who seem to be completely ignorant of the history of their field so they make up stories that are out of touch with reality. They don't understand the major conceptual advances of the second half of the 20th century, especially evolution (population genetics), the molecular biology of development, and genomics.

They don't see or understand the new world order because they, and their teachers, missed the revolution that took place 30 years ago. It will take them a few more years to realize that most of our genome is, indeed, junk and that this is supported by lots of evidence. Eventually they will realize that a genome full of junk is compatible with evolution. Meanwhile we will probably have to put up with more nonsense like the nonsense in this new book.

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