As PZ Myers asks, if the remaining 40% is all functional... why do onions need ten times as much as humans need,
When you question them, this is all the "Junk DNA" proponents' arguments ever boil down to: "I don't understand it, therefore it's junk."
We DO understand what 60% of the genome is doing. 45% of it is parasitic. Do you really think that LINEs, parasitic DNA strands that make copies of themselves over and over again, are NOT junk?
and why can the fugu pufferfish thrive without any of it?
Thrive....under what conditions? And what is your definition of "thrive"? Have you subjected the animal to every possible condition it could ever experience in life, to completely ensure that the DNA in question can never be triggered under any circumstances?
Of course you haven't--because you haven't the foggiest clue how it all even works. "Junk DNA", like many other idiocies in the long history of science, is the legacy of morons.
Fugu "thrive" in the sense that they're alive and reproducing. Fugu are not dying off. Fugu are not endangered. Fugu are not at an evolutionary dead end suffering under a genetic legacy that's handicapping them, like pandas or the various all-female species of parthenogenic whiptail lizard are. Like I said, thriving. The only thing that threatens them at all: their tasty lip-numbing tetrodotoxin convinces humans to turn them into sushi.
Why do fugu (390 megabases) get by with 3.5 times less DNA than zebrafish (1.4 gigabases)? Why do fruit flies eliminate non-coding "junk" DNA from their genome 40 times faster than crickets do? (And, for that matter, why do both fruit flies AND crickets AND most eukaryotes excise DNA from their genome at all?) Why does the common onion, Allium cepa (15876 megabases), need 2.3 times more DNA than its close relative the Blue Spear chive, Allium altyncolicum (6860 megabases)? Does bear's garlic, Allium ursinum (30870 megabases), have extra DNA stashed away in preparation for a future alien invasion that will sap the precious bodily fluids from lesser garlics? No. If two closely related Allium species both live in the same area, and look similar, and taste similar, and their cells have a similar appearance under a microscope, and they are equally prolific in their environment... but one has twice as much DNA as the other... then by definition at least half of the larger wad of DNA must be redundant. Maybe not inert, but "junk" in the sense of duplicate or obsolete functionality that doesn't need to be there to grow a successful, sexually mature plant that can compete in the real world.
In short, "junk DNA" is basically a shorthand for "DNA that could be deleted from all individuals in a species without harming the reproductive fitness of those individuals". By this standard, LOTS of DNA is junk -- at least the part that's known to be parasitic (45% of the human genome), and probably a lot more.
Are there regions of non-coding DNA, in the 40% of the human genome as yet not understood by humanity, that confer a benefit to their hosts? Almost certainly. But as a percentage of the genome, the 80% claim in the ENCODE press release is f***ing ridiculous. As best as I can tell, the ENCODE papers are using a shotgun approach that would categorize known parasites like LINEs, ERVs, and transposons as "functional". In one sense, such DNA is not passively sitting there, so it's not "junk" in the sense of being "inert". But for all the spinning of its little wheels, it's doing nothing to help you survive. Sure sounds like junk to me.
Beyond that... fine, call me a moron if you like, but PZ Myers is a Ph.D. professor of biology who studies genetics. This is his area of expertise, and his day job is to teach this stuff to people. If you don't have a Ph.D. in biology, maybe you shouldn't dismiss him as a moron; instead, shut up and watch his video. You might learn something, instead of emotionally flipping out and calling people names, as if "nuh uh, you're a poopy-head" were a valid form of argument. (Hmm... are you sure you're not a Creationist? Flipping out and calling people names is a rather Creationist style of "debate". Although there's such a high background level of it on Slashdot I'm not sure my priors are sound on the matter...)