The human genome is the body's instruction manual. But, unfortunately, that manual currently in many ways is as mystifying as the instruction manuals, obviously not written by native speakers, that accompany everything from software to some-assembly-required toys.

"It is written in a language that we are still trying to learn," Francis Collins, director of the National Institute for Human Genome Research, told reporters at a press briefing.

At the briefing, the Encyclopedia Of DNA Elements or ENCODE Consortium - comprising 35 groups in 11 nations and lauded by Collins as "a prime example of team science at its best" - introduced the results of a three-year effort to learn more of regulatory elements of the genome.

The lead report was published in the June 24, 2007 issue of Nature, together with a companion issue of nearly 30 papers published in Genome Research.

Michael Snyder of Yale University, one of the consortium's leaders, told reporters at the briefing, "We now have a much better map of all of the RNA, the information that's expressed from the genome, and also where the regulatory sequences lie."

Collins added that "We want to go from statistics to functional understanding - this is the way to do it."

The project has come up with a myriad of individual new facts about how genes are regulated, but two trends already are discernible in the data.

First, there is more to RNA than was dreamed of in the old-school genome philosophy. For one thing, Snyder said, the diversity of messenger RNA is "much, much higher than previously appreciated."

Each gene on average makes five different RNAs via splicing variants. Transcription also makes many RNAs, presumably with regulatory functions, that never get translated into proteins. "There's a lot of transcription that happens across the genome - far more than we thought previously," he said.

Such transcription is one of the functions of DNA that has sometimes been termed "junk" DNA. In fact, the other main point that has emerged from the study is a reconsideration of what's junk and what's not.

Unexpected transcription of regions of the genome that do not code for proteins, as well as regulatory elements, have shown functions for yesteryear's junk DNA. But at the same time, study leader Ewan Birney of the European Bioinformatics Laboratory in Cambridge, UK, pointed out that researchers also found the opposite: a surprisingly large number of regulatory sequences that don't seem to be doing much of anything.

Birney said that in comparative genomics studies, the consortium found that many of the newly discovered regulatory elements "were not conserved across mammals, which went against our expectations." The most obvious explanation is that they are what make humans specifically human, but several other pieces of the puzzle argue against that interpretation.

"There's a lot of them, and that's against our basic understanding of how common mammalian biology is," Birney said. The function of those regulatory elements also appears to argue against a role in making humans human. Birney said many of them "seem to be doing very basic not just mammalian biology, but vertebrate biology things."

Instead, Birney's explanation for why all those elements are there smacks a bit of the fictitious chemical element administratium, which is forever increasing its atomic mass. Created via random evolution, such new elements persist because they might come in handy in the future.

Birney likened them to gate-crashers at a party. "They are basically just hanging around, taking the drinks, not involving themselves too much in the business of taking a meeting or such," he said.

However, both Birney and Collins noted that this does not mean such elements are the new junk DNA. Instead, Collins said, they are likely to have a function over longer timescales.

Regulatory elements that are not regulating much of anything are "sort of like clutter in the attic: it's not the kinds of clutter you'd get rid of without consequences, because you might need it," Collins said. "If natural selection comes along and needs to operate on something, you're much better off if you've got clutter in the attic than if it's spic and span.

"Most of the time the human genome is operating on the first and second floor, but with maybe 5 percent of the genome doing whatever needs to be done in terms of daily activities. But over evolutionary time, a much larger fraction of the genome - the stuff that's up in the attic - becomes important."

The consortium has studied only about 1 percent of the genome to date, but "the success of this now puts us in a position to scale this up," Collins said. Grant applications to investigate regulatory elements of the whole genome currently are being reviewed, and Collins said they will be awarded by the end of September.