The Onion Test, which ENV referred to last week, has been debated for years. See "Onion Expos�: Carl Zimmer on Why ‘Junk DNA’ Had Better Be Real." There may be some very good reasons for onions to have large genomes.
Let’s start with an analogy. My son tells me the computer game StarCraft will play on just about any old piece of computer hardware in the house. However, he says, when you go to download the game from the website, it takes up 15 gigabytes of space. Evidently, in order to be compatible with older hardware, it has to use less CPU power — since the older machines were not as powerful. Much if not most of the CPU processing is used on graphics, and to get the graphics to work on older machines, it had to be nearly uncompressed, hence the 15 GB of memory required. Newer games render graphics more efficiently, using much less space, but they require fancier graphics boards and more powerful graphics processing, known as Graphical Processing Units or GPUs.
Back to the lowly onion. The DNA is software. The proteins are the video feed. The nucleus is the CPU. Humans have highly complex coding/decoding machinery in the nucleus. When mathematical analysis is performed on human DNA, it is found to have a fractal information dimension greater than 3 — indicating that at least three different codes are simultaneously present. This is a number bigger than with chimpanzees, whose DNA is not so compressed, and if I recall correctly, comes in around 2.5 or so. With onions, I think it is a safe bet that the fractal dimension is < 2.0.
What does this changing dimension mean for DNA size? Well the information in DNA is proportional to the volume of phase space, so if humans have dimension 3.0, then the volume ~ (3.2 GB)^3 = 27 GB. This dwarfs the 15 GB of the onion, but then I don’t know the fractal dimensionality of onions.
Now admittedly, the ENCODE papers don’t do the entire genome — they look at little subsets, so I may be generalizing too much to say that I know the dimension of information packing. But if the genome had junk DNA in it, it would drive the number lower, not higher, because junk DNA is uncorrelated to everything else. This is categorically what is not found, and so even without the ENCODE results, it is manifestly obvious that human DNA is not mostly junk.
But if DNA is compressed and packed so efficiently in humans, why is it not packed that way in onions?
A paper that was published a few years ago suggested that embryonic development from ovum to embryo was driven by a clock. As the transcriptase zipped along the DNA, the cell made proteins successively, and the ordering and timing of the proteins were such as to drive the embryogenesis and development. In other words, the spatial location of the DNA was converted into temporal development of the organism. Then if an organism needed to prolong a stage of embryogenesis, the most direct way would involve adding more DNA. No extra machinery is needed, no added complications and regulators, just another 1 GB of DNA to transcribe and the necessary thirty minutes will be added to the development.
Crude, but why do that at such a high cost to the genome of every cell?
Perhaps there is a plant virus that hijacks the "clock" to crank out tumors. This onion solution would then be impervious to such a virus. It might even give it an "evolutionary advantage."
Then the "Onion Test" is not a Darwinian challenge to intelligent design, but an ID challenge to Darwinian imagination. Why don’t they take their own medicine: If the junk isn’t functional, why doesn’t it get selected out?
I don’t even know why the Onion Test keeps getting mentioned anymore unless it is a red herring to impress the masses, like Carl Zimmer. The idea assumes that DNA does one job and one job only — making protein — with one protein per gene. So if the DNA lacks the start/stop codons needed for making protein, it obviously isn’t doing its job. This was "Central Dogma" gospel thirty years ago or so.
But once the DNA was found to have moonlighting jobs doing other things — development, differentiation, regulation, mechanical attachments, iRNA anti-virals, information compression — then the Onion Test simply makes no sense any more.