No, that's "non-coding DNA". The Ars Technica article has a very nice Venn diagram. In short, we infer that most non-coding DNA is junk DNA because it shows signs of neutral drift (i.e. it doesn't matter to reproductive fitness), but non-coding DNA is different from junk DNA, and regulatory DNA is always non-coding but can be either junk or non-junk.

Some concrete examples (with Venn diagram colors in parens):

• Coding DNA that isn't junk (white): a gene.
• Coding DNA that is junk (blue): an endogenous retrovirus.
• Regulatory non-coding DNA that isn't junk (orange/yellow): a promoter for a gene.
• Regulatory non-coding DNA that is junk (orange/yellow/blue): a promoter for a pseudogene.
• Non-regulatory non-coding DNA that isn't junk (yellow): hmm... an intron, I guess.
• Non-regulatory non-coding DNA that is junk (yellow/blue): the letters "CGG" 30 times in a row on the X chromosome. (See aside below for more info.)

(Terminology: a "pseudogene" is a gene damaged so badly by frame shifts or early stop codons that it can't code for protein anymore. Before they break and become pseudogenes, they're often duplicates of some existing gene, which is why breaking them can be fitness-neutral. DNA transposons and sloppy cross-overs in meiosis make gene duplication reasonably common. Gene duplication is important for evolution as well: duplicated genes are free to mutate in random directions until they stumble on a new useful function, with the original free to keep the old one. For instance, the vertebrate blood clotting cascade was clearly formed from several rounds of dupe-then-mutate, and similarly with the huge family of myosin muscle proteins.)

(Terminology: an "intron" is a stretch of DNA that gets snipped out of the resulting RNA before the RNA can code for protein. It's not quite junk: an intron has recognition signals that say "please cut RNA here", and IIRC the intron needs to have roughly the correct length, but most of the intron is arbitrary nonsense. Some genes have alternative splices, where the same gene can code for different proteins by swapping in different coding regions -- "exons" -- like lego bricks. Alternative splices are important in the immune system, for instance: they're how antibodies work. And the alternative splicing stuff wouldn't be possible without introns, including the nonsense filler that helpfully spaces out the exons so the splice enzymes can operate correctly.)

(Aside: long sequences of repetitive DNA can trip up the DNA polymerase enzyme that copies DNA, causing the stretch of DNA to lengthen itself in the next generation... and the longer it gets, the better the chance is that DNA polymerase will screw up and make it longer still. The ...CGG-CGG-CGG... sequence I mentioned has about 30 repeats in healthy individuals; but if the number of repeats climbs high enough, it causes Fragile X syndrome. Apparently the nucleus tries to silence the repeat by attaching methyl groups (CH3), which is standard procedure in the nucleus for turning off misbehaving DNA, but methylation isn't terribly precise and a nearby promoter happens to live nearby. This promoter is responsible for a nearby gene that's important in brain development; if the promoter is silenced by methylation, the reduced gene expression causes a form of severe autism.)

Agreed

I think most people, both in and out of the United States, see a result like this as absurd.

That's the issue all right. And I think the Court's decision is absurd.

Apple's greatest strength and most damning faults laid bare in one comment.
It just works, you know what you're getting, your old stuff keeps working.
Evolutionary, not revolutionary. Does not play well with others.

Er... I stand corrected: http://www.ssa.gov/history/hfaq.html Q20.

SSNs are recycled. They're only unique among the living.

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?

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...)

Yes, we HAVE confirmed that most DNA is junk. See this talk by biologist PZ Myers. (Money quote starts at 35:20.) Cyberax's figures are an exaggeration, but... roughly 5% is functional (protein-coding, rRNA, tRNA, microRNA), 10% is structural (centromeres and telomeres), 45% of the human genome is known parasitic DNA (LINEs, SINEs, endogenous retroviruses, transposons), and only 40% is unexplained. As PZ Myers asks, if the remaining 40% is all functional... why do onions need ten times as much as humans need, and why can the fugu pufferfish thrive without any of it?

If I recall correctly from Jared Diamond's Collapse, the non-tonal Polynesian languages originated in South Asia but were pushed out by tonal ones, e.g. Vietnamese, who were themselves pushed out by Han expansion from China.

I noticed some pro-RIAA posts saying that defendant was liable for distributing, not just downloading. This is simply not so. Distribution, within the meaning of the Copyright Act, requires a sale or other transfer of ownership, or a rental, lease or lending.... none of which occurred here. 17 USC 106(3)

No, constitutional due process... the principle that statutory damage awards are supposed to bear some reasonable relation to the actual damages sustained.

After the jury's verdict, if the judge finds the verdict for punitive or statutory damages to be out of all reasonable proportion to the actual economic harm sustained, it is supposed to reduce the verdict to a number that bears a reasonable proportion to the harm sustained. The Supreme Court noted that it will rarely be a number higher than 10x the actual damages. In finding the magic number, the court weighs various factors, such as the outrageousness of the defendant's conduct, etc. Regular copyright law also requires that copyright statutory damages bear some reasonable relationship to actual damages. In non-RIAA cases the courts usually sustained multiples of 2 to 4 times the actual damages.