I made a dreadful mistake. Before embarking on my trip to Germany, with those long transatlantic flights, I stocked up my Kindle with a couple of books to keep me entertained. One of them was Nessa Carey’s Junk DNA: A Journey Through the Dark Matter of the Genome. It was a poor investment. I could not finish it. I got maybe a half hour worth of reading out of it before I was too exasperated to continue, and instead watched a ghastly Night at the Museum sequel being shown on the plane’s entertainment system. It was a terrible movie, but better than this book.
Actually, it didn’t take me a half hour to become peevish. The very first page after the acknowledgments, in a section called “Notes on Nomenclature,” contained this abomination.
Anything that doesn’t code for protein will be described as junk, as it originaly 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 would probably get four different answers. So there’s merit in starting with something straightforward.
It’s not purists who will scream, but anyone with even a passing awareness of the history of molecular biology and a concern for accuracy will be howling. Zamecnik and Hoagland worked out the chemistry of tRNA in 1954 (discovery of tRNA genes would come later); Jacob and Monod were publishing on genes of regulation in 1959. Given that the structure of DNA was only worked out in 1953, awareness that not everything in the genome coded for proteins came along very quickly.
Yes, there are different criteria used by different scientists to define ‘junk DNA’. I don’t know anyone who claims that any stretch of DNA that doesn’t code for a protein is junk. So Nessa Carey managed to pick one of the few definitions that essentially all scientists would recognize as wrong.
She’s also fond of infuriatingly bad analogies.
There are other ways of envisaging this. Let’s imagine we visit a car factory, perhaps for something high-end like a Ferrari. We would be pretty surprised if for every two people who were building a shiny red sports car, there were another 98 who were sitting around doing nothing. This would be ridiculous, so why would it be reasonable in our genomes? While it’s a very fair point that it’s the imperfections in organisms that are often the strongest evidence for descent from common ancestors — we humans really don’t need an appendix — this seems like taking imperfection too far.
A much more likely scenario in our car factory would be that for every two people assembling a car, there are 98 others doing all the things that keep a business moving. Raising finance, keeping accounts, publicising the product, processing the pensions, cleaning the toilets, selling the cars etc. This is probably a much better model for the role of junk in our genome. We can think of proteins as the final end products required for live, but they will never be properly produced and coordinated without the junk.
Let’s just be clear on one flaw here: my body is not like a sports car. It is especially nothing like a Ferrari. Comparing a process reliant on chance and selection to one contrived by design is not valid.
But it fails in another way. Science did not begin its investigation of what is going on inside the cell with the preconception that the only function that counts is the assembly line of protein synthesis; we are entirely open to including energy production, waste disposal, processing, etc., etc., etc. as functions essential for the operation of the cellular factory. We have mapped many of those functions to gene products, and still we’re only talking about a few percent of the genome. The rest is repetitive or nonsense sequences, stuff like LINEs and SINEs, structural sequences like those found in centromeres and telomeres, and regulatory sequences that take up another few percent (and which were never classified as junk).
This is an incredibly bad argument. She’s relying on an appeal to our perception of what is common sense in human activities to inappropriately claim similarity in molecular/cellular activities. It’s just like Michael Behe declaring that there are literally
little trucks and busses that run around the cell that take supplies from one end of the cell to the other.
It just gets worse and worse. Here are two revealing sentences:
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.
That’s flatly wrong. It it were true, we’d have to crown ferns and salamanders as the most sophisticated organisms in creation, and there are unicellular protists that have an order of magnitude more DNA than human cells do.
OK, one moe horrible, awful, no good analogy before I give up on this worthless book. What possible use could junk DNA have? Carey invokes the insulation theory of junk DNA.
Imagine you own a watch. Not just any old watch, but a phenomenally expensive watch such as a vintage Patek Philippe of the type that sells for a couple of million dollars. Now imagine there is a large and very angry baboon in the vicinity, carrying a really heavy stick. You have to put your watch in a room and you are given a choice. You can’t stop the baboon going into any of the rooms, but you can decide on the room where you want to leave the watch. The choices are:
A. A small room with nothing else in it but a table, on which you have to leave the watch.
B. A large room containing 50 rolls of loft insulation, each roll being 5m in length and 20 cm deep, and you can hide the watch deep in any one of the 50 rolls.
I don’t understand why she has to use Ferraris and overpriced vintage watches in her examples; I think she’s trying to make the reader draw an unsubtle comparison to their own self-worth. Humans are Ferraris! Fruit flies are mere Ford Pintos!
But anyway, the analogy does not work. Mutation rates are measured per nucleotide, not per genome. The baboon does not have a quota of one whack per room, it’s one whack per unit volume, so hiding the watch in a larger room does not reduce the risk to the watch at all. The gene is also not swaddled at all by the presence of nearby junk.
Here’s a better analogy. You have a room with the floor marked off by watch-sized squares, and you have a baboon on a platform above it with an M16, loaded with a number of bullets proportional to the number of squares below it. It doesn’t matter how big the room is; if it contains 100 squares, the baboon gets 5 bullets, if it contains 1000 squares, the gun is loaded with 50 bullets.* You place your watch in any of the squares. If you want, you can place a fluffy little cotton ball in any of the other squares, or in all of them if you insist. The baboon then empties the magazine into the floor, firing wildly.
I think you can see that the cotton balls, the ‘insulating’ junk DNA, make no difference at all, and increasing the size of the room also doesn’t spare your watch, because that also just scales up the number of bullets. It’s a nonsensical argument for functional junk DNA.
That’s where I gave up. I skimmed ahead; there’s a part where she mentions that the high variability o repetitive DNA makes it useful for paternity testing and forensics — hey, it’s a function! See, junk DNA is useful! Then she starts babbling about Hox genes, and I could go no further. It’s a disgraceful book demonstrating a painful ignorance of the subject. I looked at the acknowledgments, curious to see who let this book sail through without scientific criticism, and no scientists are mentioned. Her reviewers were the publisher and Carey’s family. Ouch.
One last thing that drove me nuts throughout that part of the book I read: she keeps comparing “junk DNA” to “Dark Matter”. It’s in the title! I wanted to ask what the heck those two scientific concepts have to do with each other, because they don’t.
My recommendation: if you want to learn anything about molecular biology or genomics, flee if you see this book on a shelf. It will make you stupider and wronger and ignorantic.
*My model is also imperfect, because the relationship between the number of squares and the likelihood of a bullet striking the one square with the watch is not linear. But I’ll let you work that out for yourself.