Two competing
teams of scientists have released the first spectacular set of
discoveries from the new catalog of the human genome, findings
that promise to begin reshaping our view of who we are and
where we came from.
Hundreds of researchers reporting Monday in the scientific
journals Nature and Science have just scratched the surface of
what the genome will eventually reveal. Even these early
results, though, herald a sea change in thought about modern
medicine and humanity's earliest roots.
We are genetically less
complex than anyone dreamed--the entire set of genetic
instructions for making a human is not much larger than that
for a fruit fly or a roundworm.
We are more closely related to other organisms than anyone
knew and even received some genes directly from bacteria,
providing essential biological machinery that still ticks
within us.
And we contain a sort of fossil record in our DNA of our
evolutionary past.
Genes, the researchers learned, are far more lively,
complicated, adaptable, universal and inventive than anyone
ever thought.
The historic articles mark the first attempt to take the
measure of the monumental genetic sequence since scientists
announced its completion in June. But the new information in
Monday's publications makes them more scientifically
significant than last summer's milestone.
Scientists are looking both into the past and into the
future, finding a family tree that goes back 500 million
years, as well as discovering genes that predict how long a
person is likely to live, what he or she may die from, and how
that fate may be changed.
"This is for the first time having in front of us the human
book of life and realizing that it's actually three books,"
said Dr. Francis Collins, director of the National Human
Genome Research Center and mastermind of an international
consortium of public investigators that is one of two major
groups to publish its findings this week.
"It's a history book that tells us about where we came
from, looking back hundreds of millions of years. It's a shop
manual that contains within it a list of the parts that we're
made of. And it's a textbook of medicine that contains within
it clues to the causes of diabetes, heart disease, cancer and
a variety of other disorders that we only at the moment barely
glimpse."
Perhaps most surprisingly, the new estimate that each
person carries about 30,000 distinct genes is far lower than
expected--hardly greater than the figure for mustard weed or a
worm.
The startlingly low gene number has some experts mystified
at how nature can create a complete person with such minimal
instructions.
"I'm hoping that historically, this change in our thinking
will be somewhat equivalent in magnitude to Copernicus and
Galileo proving that the Earth is not the center of the
universe," said J. Craig Venter, CEO of the other research
group, a private genomics company called Celera. "This is
helping to show that humanity is not the center of the
biological world."
The furious race to decode the human genome, which so far
has cost more than $2 billion, is being run by scientists from
the international public sector under Collins and those
working for Celera.
Collins' group is reporting its results in Nature; Celera
in Science. The findings were to be made public Monday, but
the two journals ended their embargoes on the information when
a London newspaper published the story early.
The treasures being uncovered inspired a moment of awe for
the researchers writing in Nature. "We find it humbling to
gaze upon the human sequence now coming into focus," they
said. "In principle, the string of genetic bits holds
long-sought secrets of human development, physiology and
medicine."
Only 30,000 genes
Up to now, most scientists had guessed that the human
genome contained 100,000 genes or more.
The research being published this week puts the long-sought
figure at a paltry 30,000.
"Boy, that's an affront to our pride," said Eric Lander,
director of the Whitehead Institute Center for Genome Research
at the Massachusetts Institute of Technology and a main author
of the public genome paper.
Active genes--little booklets of DNA code that, through the
proteins they produce, shape everything from individual cells
to major organs--comprise just a tiny fraction of the human
genome's 3 billion DNA components.
Before the whole genome was sequenced, there was no way to
know how many genes existed, leaving a yawning gap in
knowledge about the complexity of human biology.
As recently as 1999, a paper in Nature by researchers from
Incyte Pharmaceuticals put the gene figure at a whopping
142,634.
To get a more accurate estimate, researchers plugged the
genome's huge sequence into sophisticated computer programs
designed to look for anything resembling genes found in other
organisms.
The scientists also looked at sequences of RNA, a chemical
cousin of DNA that helps bring out the proteins encoded in
genes. By matching known RNA sequences with DNA found in the
genome, the teams isolated thousands of likely genes.
Having surveyed virtually the entire genome, scientists can
tell where previous calculations went wrong.
It turns out that unlike bacteria or yeast, human genes are
thrown in with a huge amount of inactive DNA that does not
code for proteins. Some erroneous gene estimates in the past
focused on two chromosomes that are unusually chock full of
genes.
"Those are two of the most gene-dense regions of the
genome," Venter said.
Although Celera and the public project used some different
human samples and computer algorithms, their estimates are
strikingly similar. Each group found rock-solid support for
about 24,000 to 26,000 genes, with partial evidence raising
the likely number to around 30,000.
"If we'd said there were 32,000 genes and they'd said there
were 200,000, this would be a very different conversation,"
Collins said.
Beyond its implications for human biology, evolution and
inheritance, determining the number of genes may affect the
bottom line of biotechnology companies.
Many firms have bet huge fortunes on finding and patenting
genes with medical uses; some believe the more genes there
are, the more potential for profit.
Proteins solve puzzle
So if we have only 30,000 genes, a mustard weed has 25,706
and a fruit fly 13,338--and all the genes are pretty much
alike--what is it that makes us human?
That's been a huge puzzle in biology, but now the answer is
in--it's the proteins.
One of the biggest revelations to come out of decoding the
human genome is that each of our genes can make three to 10
proteins, and possibly more, while the genes of simpler
organisms average only one protein per gene.
Before, it was thought that one gene could make only one
protein. So firm was the idea that the two scientists who
first proposed it won a Nobel Prize.
But though a fruit fly essentially makes a little more than
13,000 proteins, humans make up to 250,000. What's more, those
can be combined in different ways to produce millions of
different potential proteins.
That is what accounts for the complexity of higher
organisms.
Collins explains, "If an organism is going to develop a
larger number of organ systems and tissues and functions, like
an immune system and nervous system--all the things that are
not present or present in a rudimentary form in worms and
flies--you have a way of adding that additional potential for
complexity."
The food we eat contains basic elements called amino acids
that genes use to make instructions for building proteins.
Those proteins then perform all the roles needed to build and
maintain a body.
Some of them serve as construction workers that cut, join
and move other proteins, which serve as the building blocks
for everything from cell membranes to bones.
Take, for example, a protease protein that cuts other
proteins. In worms and fruit flies it simply acts like a
paring knife. It just cuts. But in humans, that same protein
can be modified to perform like a Cuisinart. It can cut, chop
and dice at different speeds.
The insulin gene, for instance, makes proinsulin, which
gets cut into four parts to make insulin and two other
proteins.
"If you look at how we're different from worms and flies,
part of it seems to be this ability to add new functions to
old proteins," Collins said. "Over the course of evolution,
that may have been responsible for us becoming what we are.
Without it we might still be in the roundworm stage."
Bacteria break the rules
One finding was so unexpected and unsettling that the
researchers had trouble believing it: 223 of our genes appear
to have come directly from bacteria.
In the Nature paper, Collins and Lander surmise that
ancient bacteria passed DNA to our remote ancestors, perhaps
fish swimming in primordial seas.
Those sequences are not present in more primitive organisms
such as worms and insects, which should have inherited the
genes if they had been passed along through normal evolution.
More remarkably, most of those genes now play central roles
in the human body's basic metabolism and early development.
Some have been connected to depression and other mental
illness.
Several researchers were convinced that their samples had
been contaminated by bacteria in the lab, said project leader
Robert Waterston of Washington University in St. Louis.
"People basically didn't accept it--they wanted to just
throw these sequences out," Waterston said. "It wasn't until
we looked hard that we realized these weren't contaminants.
They were actually human DNA."
No one knows exactly how or when the bacterial genes hopped
across species. But the importance of those sequences for our
survival probably means it was well over 200 million years
ago.
Bacteria routinely exchange genes among themselves--a
process biologists call horizontal transfer. But no one had
thought that it could happen between bacteria and complex
animals.
"This breaks all the rules," Collins said.
The bacterial genes play numerous essential roles in
people, from the metabolism of nitrogen to the maintenance of
mitochondria--the tiny power plants that supply energy to
muscles and other tissues.
One of the genes produces an enzyme linked to depression
and mental illness. Drugs that inhibit the enzyme, called
monoamine oxidase, are used as antidepressants. And
researchers in the early 1990s tied a defect in the gene to a
disorder they dubbed Brunner syndrome, which is marked by
aggressive behavior and exhibitionism.
"All of this should make us humble in a way, because it
connects us with the rest of nature," Lander said. "We see
within our own DNA our intimate connections with everything
from chimpanzees to fish, to fruit flies, to baker's yeast. I
don't think most people think of the chromosomes as being a
paleontological dig. It's pretty amazing."
Men, women and heat
The Y chromosome, carried only by men, plays a unique role
in evolution, researchers have found.
The Y is the littlest chromosome we have, carrying only a
hundredth the genetic information of the female X chromosome
and just a third the size.
It is the only part of the genome that is specific to one
sex. And it is something of a genetic junkyard.
Only the Y does not recombine and swap DNA with its partner
when eggs and sperm are made. Because 95 percent of the Y
chromosome never swaps genes with a female X chromosome, it
preserves the genes that allow it to determine gender.
But over time it also has degenerated, losing most of its
active genetic material, and accumulating mutations. The
public project shows that the Y chromosome contributes twice
as many mutations as the X.
That, the genome researchers have determined, is good news
and bad.
The bad: Men cause two-thirds of genetic diseases. The
good: They also are responsible for two-thirds of evolution,
because beneficial mutations are a driving force behind it.
Researcher David Page calls the Y chromosome "the Rodney
Dangerfield of the genome--it has gotten no respect from
scientists, and in fact, may have something of an attitude."
Page, of the Whitehead Institute at M.I.T., and Bruce Lahn,
of the University of Chicago, have compared the DNA sequences
of the sex chromosomes back to the time they were exactly the
same, about 300 million years ago.
"In our reptilian ancestors, gender was most likely
determined by the temperature of incubating eggs, like in
today's turtles or crocodiles," Page said. Thus sex predated
the sex chromosome.
"Then about the time mammals parted company with birds, a
mutation occurred on one member of the chromosomal pair,
creating a gene that when present always produced a male, no
matter what the temperature was. That put sex in our DNA."
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