Too often reviews on lncRNAs begin with the same old tired trope: “non-coding DNA was long dismissed as useless junk, but now we know better”.
Do you?
And more importantly, do you really understand where the idea of junk DNA came from?
If you want to engage in this debate you really have to understand key concepts that support the idea of junk DNA. If you do not, and simply sidestep all of these issues, then you are not really engaging in debate. You are just being ignorant of the major issues advanced by the field.
So what are the major issues? If you are interested please read The Case for Junk DNA, where Ryan Gregory and I cover these issues in detail. If you happen to have read it, I’ll point out that I have a few extra items & concepts (after all, its been 8 years, and my thinking on junk DNA has evolved - no pun intended) that I plan to cover in future posts.
In this post I’ll discuss the first of these concepts, The Onion Test.
Too often, commentators will point out that non-coding DNA correlates with complexity, and then show the infamous “Dog’s ass plot”. The idea here is that humans have the biggest genome and are the most complex organism that we know of. This is one of the most idiotic arguments out there.
There are many problems with this argument. First, it is a prime example of what Larry Moran dubbed “The Deflated Ego Problem” - humans apparently are the pinnacle of complexity and apparently we must prop up the supposed superiority of Homo sapiens at all costs. But are we really more complex than other animals? Birds can fly and have a whole slew of adaptations that permit them to accomplish this feat. This includes hollow yet mechanically strong bones, altered nitrogen metabolism, efficient air circulation, etc. The fly genome essentially specifies several different organisms and the ability to metamorphose between them. Can you do that? Maybe we are the most complex, but maybe not. This is simply human chauvinism.
The second problem is that the human genome is not the largest genome out there. In fact our genome is quite pedestrian in terms of size when compared to other animals. We can even extend this to other multicellular organisms or even eukaryotes. When T. Ryan Gregory discusses this idea he has a great slide that sums up how certain commentators explain away this diversity - humans have a genome that is obviously larger than all those other simple organisms, but smaller than those silly organisms that are full of junk DNA.
So how should we discuss genome size? How do we make sense all of the diversity in genome size that is present in nature?
If you have an explanation, it is needs to pass The Onion Test. This was originally proposed by Gregory on his blog (the original post is no longer online, but a subsequent one post can be read here).
The test has two parts.
First, if you believe that junk DNA does not exist, then why does the onion, Allium cepa, have a genome that is five times bigger than the human genome? Note that this onion is diploid (meaning that just like you, it only has two copies of each chromosome). This is important as some commentators argue that many plants have duplicated their genome and are thus tetraploid (four copies), or have even higher numbers of chromosome. But this is not the case here.
Now you might think that onions might need all that DNA. After all, they can convert sunlight into ATP. They also have very sophisticated metabolic pathways. Think about all the pharmaceutical compounds that plants make. So maybe they are five times more complicated than us lowly humans.
Of course, the choice of onions and humans is arbitrary. We could have compared any two other organisms. Puffer fish have eight times less DNA in their genome than humans, and lungfish have 25 times more. The obvious question would be, why do lungfish have 400 times more DNA than puffer fish? Not so obvious, eh?
But maybe we are being presumptuous. Maybe lungfish really are complicated creatures, and the problem is our lack of knowledge. This is where the second part of the test comes in.
Part two of The Onion Test. If you believe that junk DNA does not exist, then how would you explain he diversity of genome sizes between closely related onion species. As pointed out by Gregory, DNA content varies tremendously between onions. For example, the genome size for Allium altyncolicum is less than half that of Allium cepa, which in turn has a genome that is half the size of Allium ursinum. Between the smallest and biggest there is a 4.5 fold difference. Again, all of these species are diploid.
So why would such similar organisms have drastically different genome sizes? And why would they vary so much? Again if you believe that all DNA is functional, you must explain all of this.
Needless to say, I have never read or heard anyone explain away junk DNA while addressing The Onion Test.
To be continued …