| Topic: |
Religions > Atheism |
| User: |
"MrPepper11" |
| Date: |
23 Mar 2005 06:55:41 AM |
| Object: |
Startling Scientists, Plant Fixes Its Flawed Gene |
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene
By NICHOLAS WADE
In a startling discovery, geneticists at Purdue University say they
have found plants that possess a corrected version of a defective gene
inherited from both their parents, as if some handy backup copy with
the right version had been made in the grandparents' generation or
earlier.
The finding implies that some organisms may contain a cryptic backup
copy of their genome that bypasses the usual mechanisms of heredity. If
confirmed, it would represent an unprecedented exception to the laws of
inheritance discovered by Gregor Mendel in the 19th century. Equally
surprising, the cryptic genome appears not to be made of DNA, the
standard hereditary material.
The discovery also raises interesting biological questions - including
whether it gets in the way of evolution, which depends on mutations
changing an organism rather than being put right by a backup system.
"It looks like a marvelous discovery," said Dr. Elliott Meyerowitz, a
plant geneticist at the California Institute of Technology. Dr. David
Haig, an evolutionary biologist at Harvard, described the finding as "a
really strange and unexpected result," which would be important if the
observation holds up and applies widely in nature.
The result, reported online yesterday in the journal Nature by Dr.
Robert E. Pruitt, Dr. Susan J. Lolle and colleagues at Purdue, has been
found in a single species, the mustardlike plant called arabidopsis
that is the standard laboratory organism of plant geneticists. But
there are hints that the same mechanism may occur in people, according
to a commentary by Dr. Detlef Weigel of the Max-Planck Institute for
Developmental Biology in T=FCbingen, Germany. Dr. Weigel describes the
Purdue work as "a spectacular discovery."
The finding grew out of a research project started three years ago in
which Dr. Pruitt and Dr. Lolle were trying to understand the genes that
control the plant's outer skin, or cuticle. As part of the project,
they were studying plants with a mutated gene that made the plant's
petals and other floral organs clump together. Because each of the
plant's two copies of the gene were in mutated form, they had virtually
no chance of having normal offspring.
But up to 10 percent of the plants' offspring kept reverting to normal.
Various rare events can make this happen, but none involve altering the
actual sequence of DNA units in the gene. Yet when the researchers
analyzed the mutated gene, known as hothead, they found it had changed,
with the mutated DNA units being changed back to normal form.
"That was the moment when it was a complete shock," Dr. Pruitt said.
A mutated gene can be put right by various mechanisms that are already
known, but all require a correct copy of the gene to be available to
serve as the template. The Purdue team scanned the DNA of the entire
arabidopsis genome for a second, cryptic copy of the hothead gene but
could find none.
Dr. Pruitt and his colleagues argue that a correct template must exist,
but because it is not in the form of DNA, it probably exists as RNA,
DNA's close chemical cousin. RNA performs many important roles in the
cell, and is the hereditary material of some viruses. But it is less
stable than DNA, and so has been regarded as unsuitable for preserving
the genetic information of higher organisms.
Dr. Pruitt said he favored the idea that there is an RNA backup copy
for the entire genome, not just the hothead gene, and that it might be
set in motion when the plant was under stress, as is the case with
those having mutated hothead genes.
He and other experts said it was possible that an entire RNA backup
copy of the genome could exist without being detected, especially since
there has been no reason until now to look for it.
Scientific journals often take months or years to get comfortable with
articles presenting novel ideas. But Nature accepted the paper within
six weeks of receiving it. Dr. Christopher Surridge, a biology editor
at Nature, said the finding had been discussed at scientific
conferences for quite a while, with people saying it was impossible and
proposing alternative explanations. But the authors had checked all
these out and disposed of them, Dr. Surridge said.
As for their proposal of a backup RNA genome, "that is very much a
hypothesis, and basically the least mad hypothesis for how this might
be working," Dr. Surridge said.
Dr. Haig, the evolutionary biologist, said that the finding was
fascinating but that it was too early to try to interpret it. He noted
that if there was a cryptic template, it ought to be more resistant to
mutation than the DNA it helps correct. Yet it is hard to make this
case for RNA, which accumulates many more errors than DNA when it is
copied by the cell.
He said that the mechanism, if confirmed, would be an unprecedented
exception to Mendel's laws of inheritance, since the DNA sequence
itself is changed. Imprinting, an odd feature of inheritance of which
Dr. Haig is a leading student, involves inherited changes to the way
certain genes are activated, not to the genes themselves.
The finding poses a puzzle for evolutionary theory because it corrects
mutations, which evolution depends on as generators of novelty. Dr.
Meyerowitz said he did not see this posing any problem for evolution
because it seems to happen only rarely. "What keeps Darwinian evolution
intact is that this only happens when there is something wrong," Dr.
Surridge said.
The finding could undercut a leading theory of why sex is necessary.
Some biologists say sex is needed to discard the mutations, almost all
of them bad, that steadily accumulate on the genome. People inherit
half of their genes from each parent, which allows the half left on the
cutting room floor to carry away many bad mutations. Dr. Pruitt said
the backup genome could be particularly useful for self-fertilizing
plants, as arabidopsis is, since it could help avoid the adverse
effects of inbreeding. It might also operate in the curious organisms
known as bdelloid rotifers that are renowned for not having had sex for
millions of years, an abstinence that would be expected to seriously
threaten their Darwinian fitness.
Dr. Pruitt said it was not yet known if other organisms besides
arabidopsis could possess the backup system. Colleagues had been quite
receptive to the idea because "biologists have gotten used to the
unexpected," he said, referring to a spate of novel mechanisms that
have recently come to light, several involving RNA.
.
|
|
| User: "Mike Painter" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 08:06:55 AM |
|
|
MrPepper11 wrote:
<snip >
A mutated gene can be put right by various mechanisms that are already
known, but all require a correct copy of the gene to be available to
serve as the template. The Purdue team scanned the DNA of the entire
arabidopsis genome for a second, cryptic copy of the hothead gene but
could find none.
Maybe they should start looking for RAID like ability (or technology if you
are an IDiot) in the plants.
Such a technique could fix minor errors without need of a backup.
<snip>
.
|
|
|
| User: "JPG" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 08:22:17 AM |
|
|
On Wed, 23 Mar 2005 08:06:55 GMT, "Mike Painter" <mddotpainter@sbcglobal.net>
wrote:
MrPepper11 wrote:
<snip >
A mutated gene can be put right by various mechanisms that are already
known, but all require a correct copy of the gene to be available to
serve as the template. The Purdue team scanned the DNA of the entire
arabidopsis genome for a second, cryptic copy of the hothead gene but
could find none.
Maybe they should start looking for RAID like ability (or technology if you
are an IDiot) in the plants.
Such a technique could fix minor errors without need of a backup.
Like a Hamming code?
<snip>
.
|
|
|
| User: "Mike Painter" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 07:31:56 PM |
|
|
JPG wrote:
On Wed, 23 Mar 2005 08:06:55 GMT, "Mike Painter"
<mddotpainter@sbcglobal.net> wrote:
MrPepper11 wrote:
<snip >
A mutated gene can be put right by various mechanisms that are
already known, but all require a correct copy of the gene to be
available to serve as the template. The Purdue team scanned the DNA
of the entire arabidopsis genome for a second, cryptic copy of the
hothead gene but could find none.
Maybe they should start looking for RAID like ability (or technology
if you are an IDiot) in the plants.
Such a technique could fix minor errors without need of a backup.
Like a Hamming code?
Why not. It would give a reason for "junk" DNA to exist.
<snip>
.
|
|
|
|
|
| User: "Tukla Ratte" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 07:47:17 PM |
|
|
On Wednesday 23 March 2005 02:06 am, Mike Painter wrote:
MrPepper11 wrote:
<snip >
A mutated gene can be put right by various mechanisms that are
already known, but all require a correct copy of the gene to be
available to serve as the template. The Purdue team scanned the DNA
of the entire arabidopsis genome for a second, cryptic copy of the
hothead gene but could find none.
Maybe they should start looking for RAID like ability (or technology
if you
are an IDiot) in the plants.
Such a technique could fix minor errors without need of a backup.
There *is* all that "junk" DNA....
--
Tukla, Eater of Theists, Squeaker of Chew Toys
a.a. #1347, Official Mascot of Alt.Atheism
.
|
|
|
| User: "wcb" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 10:23:59 PM |
|
|
Tukla Ratte wrote:
On Wednesday 23 March 2005 02:06 am, Mike Painter wrote:
MrPepper11 wrote:
<snip >
A mutated gene can be put right by various mechanisms that are
already known, but all require a correct copy of the gene to be
available to serve as the template. The Purdue team scanned the DNA
of the entire arabidopsis genome for a second, cryptic copy of the
hothead gene but could find none.
Maybe they should start looking for RAID like ability (or technology
if you
are an IDiot) in the plants.
Such a technique could fix minor errors without need of a backup.
There *is* all that "junk" DNA....
It probably isn't. The reason Arabdopsis is used
for plant studies is, it got rid of all its junk DNA
in the fairly recent past.
Its genome count is one of the smallest for flowering plants.
Recently it has been realized much human DNA does
not code for proteins, but for RNA. For example small
forms of RNA have a lot to do with our immune system's
functioning.
These RNA forms are known as iRNA.
It might be that some form of RNA is repairing the damage.
--
When I shake my killfile, I can hear them buzzing!
Cheerful Charlie
.
|
|
|
|
|
|
| User: "Cedric Knight" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 03:19:30 PM |
|
|
MrPepper11 wrote:
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene
By NICHOLAS WADE
In a startling discovery, geneticists at Purdue University say they
have found plants that possess a corrected version of a defective gene
inherited from both their parents, as if some handy backup copy with
the right version had been made in the grandparents' generation or
earlier.
....
Scientific journals often take months or years to get comfortable with
articles presenting novel ideas. But Nature accepted the paper within
six weeks of receiving it. Dr. Christopher Surridge, a biology editor
at Nature, said the finding had been discussed at scientific
conferences for quite a while, with people saying it was impossible
and proposing alternative explanations. But the authors had checked
all these out and disposed of them, Dr. Surridge said.
It would at first seem most likely that the plants they were looking at
were partly heterozygous, with one unmutated copy of the gene, and I
wouldn't be surprised if the whole thing later turned out to be a huge
methodological mistake. But I hope not.
....
Dr. Pruitt said he favored the idea that there is an RNA backup copy
for the entire genome, not just the hothead gene, and that it might be
set in motion when the plant was under stress, as is the case with
those having mutated hothead genes.
That may be the case, but there would have to be some way of the genetic
machinery responding to the stress.
....
He said that the mechanism, if confirmed, would be an unprecedented
exception to Mendel's laws of inheritance, since the DNA sequence
itself is changed. Imprinting, an odd feature of inheritance of which
Dr. Haig is a leading student, involves inherited changes to the way
certain genes are activated, not to the genes themselves.
This is now standard 'epigenetics', if anything in such a new science
could be described as standard. Maybe what we have here is some
inherited recording of the position of an uncorrected mutation, rather
than a complete 'backup'.
The finding poses a puzzle for evolutionary theory because it corrects
mutations, which evolution depends on as generators of novelty. Dr.
Meyerowitz said he did not see this posing any problem for evolution
because it seems to happen only rarely. "What keeps Darwinian
evolution intact is that this only happens when there is something
wrong," Dr. Surridge said.
I'm not sure how he knows that. Presumably the effect could also
reverse a beneficial mutation, unless there is some way of deciding
after a generation or two whether the organism is doing well.
Could not this kind of mechanism be a huge advantage for DNA-based life,
not just asexual or self-fertilising species? If germ cells could
safely 'test out' a mutation in a phenotype and yet be able to revert if
it detectably threatened survival and reproduction, then the energy that
had gone into producing mutated offspring would not be completely lost,
but successful adaptation could occur at a much greater rate.
The reasons why such a technique would not have evolved would be the
difficulty of an individual organism's genome 'knowing' if it was in a
precarious ecological niche or changing environment where 'tentative
mutations' might be useful; and then the difficulty in assessing their
own success, and preventing the genetic reversion if the mutation turned
out to be successful.
CK
.
|
|
|
|
| User: "MarkA" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
24 Mar 2005 04:21:47 PM |
|
|
On Tue, 22 Mar 2005 22:55:41 -0800, MrPepper11 wrote:
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene By NICHOLAS WADE
In a startling discovery, geneticists at Purdue University say they have
found plants that possess a corrected version of a defective gene
inherited from both their parents, as if some handy backup copy with the
right version had been made in the grandparents' generation or earlier.
Those plants had better hope that Bill Gates didn't already patent the
concept of "restoring from backup."
--
MarkA
(still caught in the maze of twisty little passages, all different)
.
|
|
|
| User: "Ed Earl Ross" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
24 Mar 2005 06:10:09 PM |
|
|
MarkA wrote:
On Tue, 22 Mar 2005 22:55:41 -0800, MrPepper11 wrote:
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene By NICHOLAS WADE
In a startling discovery, geneticists at Purdue University say they have
found plants that possess a corrected version of a defective gene
inherited from both their parents, as if some handy backup copy with the
right version had been made in the grandparents' generation or earlier.
Those plants had better hope that Bill Gates didn't already patent the
concept of "restoring from backup."
IBM mainframes were doing backups about the time Bill Gates entered
grade school. How many patents did Bill have by the age of six?
--
Humbly--Ed
Mark Twain
"There is something fascinating about science.
One gets such wholesale returns of conjecture
out of such a trifling investment of fact."
.
|
|
|
| User: "MarkA" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
24 Mar 2005 08:48:31 PM |
|
|
On Thu, 24 Mar 2005 18:10:09 +0000, Ed Earl Ross wrote:
MarkA wrote:
On Tue, 22 Mar 2005 22:55:41 -0800, MrPepper11 wrote:
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene By NICHOLAS WADE
In a startling discovery, geneticists at Purdue University say they have
found plants that possess a corrected version of a defective gene
inherited from both their parents, as if some handy backup copy with the
right version had been made in the grandparents' generation or earlier.
Those plants had better hope that Bill Gates didn't already patent the
concept of "restoring from backup."
IBM mainframes were doing backups about the time Bill Gates entered grade
school. How many patents did Bill have by the age of six?
Yes, but I doubt if they thought to patent the idea. Gates has been very
big on the concept of "intellectual property" for the last several years,
to the point of getting patents on the most trivial concepts.
--
MarkA
(still caught in the maze of twisty little passages, all different)
.
|
|
|
|
| User: "Tukla Ratte" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
25 Mar 2005 02:37:08 AM |
|
|
On Thursday 24 March 2005 12:10 pm, Ed Earl Ross wrote:
MarkA wrote:
< snip >
Those plants had better hope that Bill Gates didn't already patent
the concept of "restoring from backup."
IBM mainframes were doing backups about the time Bill Gates entered
grade school. How many patents did Bill have by the age of six?
You must not be familiar with the US Patent Office.
--
Tukla, Eater of Theists, Squeaker of Chew Toys
a.a. #1347, Official Mascot of Alt.Atheism
.
|
|
|
|
|
|
| User: "Tukla Ratte" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 07:49:25 PM |
|
|
On Wednesday 23 March 2005 12:55 am, MrPepper11 wrote:
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene
By NICHOLAS WADE
In a startling discovery, geneticists at Purdue University say they
have found plants that possess a corrected version of a defective gene
inherited from both their parents, as if some handy backup copy with
the right version had been made in the grandparents' generation or
earlier.
Goddidit.
< snip >
--
Tukla, Eater of Theists, Squeaker of Chew Toys
a.a. #1347, Official Mascot of Alt.Atheism
.
|
|
|
|
| User: "MrPepper11" |
|
| Title: Re: Startling Scientists, Plant Fixes Its Flawed Gene |
23 Mar 2005 07:18:21 AM |
|
|
Washington Post
March 23, 2005
Plants Fix Genes With Copies From Ancestors
By Rick Weiss
Washington Post Staff Writer
Plants inherit secret stashes of genetic information from their
long-dead ancestors and can use them to correct errors in their own
genes -- a startling capacity for DNA editing and self-repair wholly
unanticipated by modern genetics, researchers said yesterday.
The newly discovered phenomenon, which resembles the caching of early
versions of a computer document for viewing later, allows plants to
archive copies of genes from generations ago, long assumed to be lost
forever.
Then, in a move akin to choosing their parents, plants can apparently
retrieve selected bits of code from that archive and use them to
overwrite the genes they have inherited directly. The process could
offer survival advantages to plants suddenly burdened with new
mutations or facing environmental threats for which the older genes
were better adapted.
Scientists predicted that by harnessing the still-mysterious mechanism
they would be able to control plant diseases and create novel varieties
of crops. If the mechanism can be invoked in animals -- as some
tantalized scientists venture may be possible -- it could also offer a
revolutionary way to correct the genetic flaws that lead to cancer and
other diseases.
"We think this demonstrates that there's this parallel path of
inheritance that we've overlooked for 100 years, and that's pretty
cool," said Robert E. Pruitt, a professor of botany and plant pathology
at Purdue University in West Lafayette, Ind., who oversaw the studies
with co-worker Susan Lolle.
The finding represents a "spectacular discovery," wrote German
molecular biologists Detlef Weigel and Gerd Jurgens in a commentary
accompanying the research in tomorrow's issue of the journal Nature,
released yesterday. The existence of an unorthodox inheritance system
does not overturn the basic rules of genetics worked out by Austrian
monk Gregor Mendel in the 1800s, they noted. But like a newly
discovered room in a mansion of treasures, it opens up a mind-boggling
world of possibilities and proves that genetics is still a young
science.
"It adds a level of biological complexity and flexibility we hadn't
appreciated," said Lolle, who is on a leave from Purdue to serve at the
National Science Foundation, which funded the work.
The Purdue team began to suspect that something strange was afoot while
studying a mutation in the mustard family weed Arabidopsis thaliana, a
popular workhorse of plant genetics.
The mutation was in a gene known as hothead -- one of many related
genes, including fiddlehead, airhead, pothead and deadhead, that when
mutated cause abnormalities in stems and flowers.
Arabidopsis plants typically self-fertilize. So when both copies of a
gene are mutated in a plant, its offspring is bound to be similarly
flawed -- in hothead's case, exhibiting the parent's mutant flowers.
Yet in the Pruitt-Lolle lab, a small but steady percentage of hothead
offspring had normal flowers, like their grandparents'. Somehow the
mutation -- a single misspelled "letter" of genetic code in a gene made
of 1,782 molecular letters -- was being repaired.
"At first, we assumed there had to be a simple explanation," Pruitt
said. But a series of tests over more than a year eliminated every easy
explanation, such as known DNA repair mechanisms or windblown pollen
from normal plants.
Instead, molecular studies indicated that the plants harbored molecular
"memories" of versions of their genetic code going back at least four
generations -- versions that the plant can somehow use as templates to
correct the spelling of mutated stretches of DNA.
The team has not found the templates, but evidence suggests they are
pieces of RNA, a molecular cousin of DNA that can be inherited
separately from the chromosomes that carry the primary genetic code in
cells.
Pruitt said others have occasionally noted the appearance of
"revertant" plants but ignored them, assuming they were the result of
sloppy technique or other errors. By contrast, Pruitt and Lolle took
the observation seriously, said Elliot Meyerowitz, a pioneering
arabidopsis researcher at California Institute of Technology.
"There are different sorts of scientists. Some like to ignore the
exceptions, and others like to concentrate on them," Meyerowitz said,
adding that he suspects the novel gene-fixing mechanism is present in a
wide variety of organisms, including animals. He suspects the trick has
been overlooked because it operates only some of the time and because
scientists have been predisposed to write off the evidence as random
events.
The discovery, he said, seems on par with a few others that have
significantly modified scientists' understanding of genetics since
Mendel. Studies in corn led to the discovery of an important
gene-shuffling mechanism that has since been found in other plants and
animals, including people. Studies in insects found a new mechanism for
gene regulation that has since been found throughout the biological
world. And a mechanism for turning off genes, first identified in
soil-dwelling roundworms and since found in humans, too, is now one of
the hottest topics in medical genetics because of its potential to shut
down disease-causing genes.
"I won't be surprised," Meyerowitz said, if the new DNA editing
mechanism is present in people, too.
Gerald Fink, a professor of genetics at the Whitehead Institute for
Biomedical Research in Cambridge, Mass., said it would be important to
identify exactly how the mechanism operates and whether it works in all
kinds of genes. But he said he was convinced that "something weird is
definitely going on." The work serves as a good reminder, he added,
that the central genetic code by itself is only part of the mystery of
how inheritance works.
"This gives the lie to the idea that you know everything once you
sequence the genome. You don't."
Lolle said the trick is probably a lifesaver for plants, which cannot
run away from radiation, environmental extremes and other insults to
their DNA. It is probably especially important for self-pollinating
plants such as arabidopsis, she said, which are constantly at risk of
becoming seriously mutated as a result of inbreeding.
She described the mechanism as one that allows a plant to reach back in
time for a version of a gene "that's already been road-tested."
Lolle said she foresees medical benefits as scientists learn to control
the molecular counterpart she suspects is in humans.
"I'm very optimistic," she said. "Once the scientific community takes
hold of this, it's going to work forward at a very rapid pace."
----------------------------------------------------------
.
|
|
|
|
|
Related Articles |
|
|
