This is an extraordinary achievement and truly begs the question of
how to understand the operating code or software behind it. I stand
in awe.
In the meantime, the notion that much of the DNA was junk has turned
out to be downright silly. It made no sense that a system able to
remove the unnecessary with ease could have much junk at all and this
has proven to be true.
Maybe there is a cognitive language inside all this but that remains
a thought. My first question is what does logic look like?
There has to be a natural logic in place that repeats readily and is
applied across the whole regime. We may have enough data now to
address that.
Massive DNA project
shows human genome far from being just junk
Published on Wednesday
September 05, 2012
Malcolm Ritter
NEW YORK— A colossal
international effort has yielded the first comprehensive look at how
our DNA works, an encyclopedia of information that will rewrite the
textbooks and offer new insights into the biology of disease.
The findings, reported
Wednesday by more than 500 scientists, reveal extraordinarily
complex networks that tell our genes what to do and when, with
millions of on-off switches.
“It’s this
incredible choreography going on, of a modest number of genes and an
immense number of ... switches that are choreographing how those
genes are used,” said Dr. Eric Green, director of the National
Human Genome Research Institute, which organized the project.
The work also shows
that at least 80 per cent of the human genetic code, or genome, is
active. That’s surprisingly high and a sharp contrast to the idea
that the vast majority of our DNA is junk.
Most people know that
DNA contains genes, which hold the instructions for life. But
scientists have long known those genetic blueprints take up only
about 2 per cent of the genome, and their understanding of what’s
going on in the rest has been murky.
Similarly, they have
known that the genome contains regulators that control the activity
of genes, so that one set of genes is active in a liver cell and
another set in a brain cell, for example. But the new work shows how
that happens on a broad scale.
It’s “our first
global view of how the genome functions,” sort of a Google Maps
that allows both bird’s-eye and close-up views of what’s going
on, said Elise Feingold of the genome institute.
While scientists
already knew the detailed chemical makeup of the genome, “we didn’t
really know how to read it,” she said in an interview. “It didn’t
come with an instruction manual to figure out how the DNA actually
works.”
One key participant,
Ewan Birney of the European Molecular Biology Laboratory in Hinxton,
England, compared the new work to a first translation of a very long
book.
“The big surprise is
just how much activity there is,” he said. “It’s a jungle.”
The trove of findings
was released in 30 papers published by three scientific journals,
while related papers appear in some other journals. In all, the 30
papers involved more than 500 authors. The project is called ENCODE,
for Encyclopedia of DNA Elements.
The human genome is
made up of about 3 billion “letters” along strands that make up
the familiar double helix structure of DNA. Particular sequences of
these letters form genes, which tell cells how to make proteins.
People have about 20,000 genes, but the vast majority of DNA lies
outside of genes.
So what is it doing?
In recent years, scientists have uncovered uses for some of that DNA,
so it was clearly not all junk, but overall it has remained a
mystery.
Scientists found that
at least three-quarters of the genome is involved in making RNA, a
chemical cousin of DNA. Within genes, making RNA is a first step
toward creating a protein, but that’s not how it’s used across
most of the genome. Instead, it appears to help regulate gene
activity.
Scientists also mapped
more than 4 million sites where proteins bind to DNA to regulate
genetic function, sort of like a switch. “We are finding way more
switches than we were expecting,” Birney said.
The discovery of so
many switches may help scientists in their search for the biology of
disease.
In recent years,
researchers have scanned the genome and found thousands of particular
DNA sequences that seem to raise the risk of disease. But many of
these lie outside of genes, raising the question of how they could
have any effect.
The new work found
that many of these sequences fall within or near regulatory regions
identified by the ENCODE project, suggesting a way they could meddle
with gene activity.
Another finding raises
questions about just how best to define a gene, researcher Thomas
Gingeras of the Cold Spring Harbor Laboratory in New York and
colleagues suggest in their report in the journal Nature. The common
notion that genes are specific regions of DNA that are separated from
other genes “is simply not true,” he said.
He and colleagues said
it would make more sense to define a gene as a collection of RNA
molecules instead of a particular location on the DNA.
Birney said that with
the finding of widespread activity across a person’s DNA,
scientists will be debating how much of it is really crucial to life.
Still, “it’s worth
reminding ourselves that we are very, very complex machines,”
Birney said. “It shouldn’t be so surprising that the instruction
manual is really pretty fearsomely complicated.”
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