[Paleopsych] Re: From Eshel--A Glitch in Genetic-centrism
shovland at mindspring.com
Fri Apr 1 05:23:28 UTC 2005
At this point in time we think we are doing well
if we can sequence genes.
What will we find as we begin to analyze the
patterns? Will the whole be holographically
encoded in the part?
From: HowlBloom at aol.com [SMTP:HowlBloom at aol.com]
Sent: Thursday, March 31, 2005 7:31 PM
To: paleopsych at paleopsych.org; kurakin1970 at yandex.ru; ursus at earthlink.net;
paul.werbos at verizon.net
Subject: [Paleopsych] Re: From Eshel--A Glitch in Genetic-centrism
A mechanism central to Jeff Hawkins' analysis of the way brains work in
On Intelligence may provide a clue to the manner in which plants with
of a damaged gene from both their father and their mother manage to
"recover" or reconstruct something they never had-- a flawless copy of the
they've received only in damaged form.
Hawkins brings up a neural network trick called auto-associative memory.
Here's his description of how it works:
"Instead of only passing information forward...auto-associative memories
fed the output of each neuron back into the input.... When a pattern of
activity was imposed on the artificial neurons, they formed a memory of
pattern. ...To retrieve a pattern stored in such a memory, you must
pattern you want to retrieve. ....The most important property is that you
don't have to have the entire pattern you want to retrieve in order to
it. You might have only part of the pattern, or you might have a somewhat
messed-up pattern. The auto-associative memory can retrieve the correct
pattern, as it was originally stored, even though you start with a messy
it. It would be like going to the grocer with half eaten brown bananas
getting whole green bananas in return. ...Second, unlike mist neural
networks, an auto-associative memory can be designed to store sequences of
or temporal patterns. This feature is accomplished by adding time delay
the feedback. ...I might feed in the first few notes of 'Twinkle, Twinkle
Little Star' and the memory returns the whole song. When presented with
the sequence, the memory can recall the rest." (Jeff Hawkins, Sandra
Blakeslee. On Intelligence. New York: Times Books, 2004: pp 46-47.)
Where would such auto-associative circuits exist in a plant cell? Here
some wild guesses:
* In the entire cell, including its membrane, its cytoplasm, its
organelles, its metabolic processes, and its genome;
* Or in the entire cell and its context within the plant, including
the sort of input and output it gets from the cells around it, the signals
tell it where and want it is supposed to be in the plant's development and
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene
By _NICHOLAS WADE_
n a startling discovery, geneticists at Purdue University say they have
found plants that possess a corrected version of a defective gene
both their parents, as if some handy backup copy with the right version
been made in the grandparents' generation or earlier.
The finding implies that some organisms may contain a cryptic backup copy
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
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
organism rather than being put right by a backup system.
"It looks like a marvelous discovery," said Dr. Elliott Meyerowitz, a
geneticist at the California Institute of Technology. Dr. David Haig, an
evolutionary biologist at Harvard, described the finding as "a really
and unexpected result," which would be important if the observation holds
and applies widely in nature.
The result, reported online yesterday in the journal Nature by Dr. Robert
Pruitt, Dr. Susan J. Lolle and colleagues at Purdue, has been found in a
single species, the mustardlike plant called arabidopsis that is the
laboratory organism of plant geneticists. But there are hints that the
mechanism may occur in people, according to a commentary by Dr. Detlef
of the Max-Planck Institute for Developmental Biology in Tubingen,
Dr. Weigel describes the Purdue work as "a spectacular discovery."
The finding grew out of a research project started three years ago in
Dr. Pruitt and Dr. Lolle were trying to understand the genes that control
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
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
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
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
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,
because it is not in the form of DNA, it probably exists as RNA, DNA's
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
has been regarded as unsuitable for preserving the genetic information of
Dr. Pruitt said he favored the idea that there is an RNA backup copy for
entire genome, not just the hothead gene, and that it might be set in
when the plant was under stress, as is the case with those having mutated
He and other experts said it was possible that an entire RNA backup copy
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
receiving it. Dr. Christopher Surridge, a biology editor at Nature, said
the finding had been discussed at scientific conferences for quite a
with people saying it was impossible and proposing alternative
the authors had checked all these out and disposed of them, Dr. Surridge
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
Dr. Haig, the evolutionary biologist, said that the finding was
but that it was too early to try to interpret it. He noted that if there
a cryptic template, it ought to be more resistant to mutation than the DNA
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
Imprinting, an odd feature of inheritance of which Dr. Haig is a leading
student, involves inherited changes to the way certain genes are
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.
said he did not see this posing any problem for evolution because it seems
happen only rarely. "What keeps Darwinian evolution intact is that this
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
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
away many bad mutations. Dr. Pruitt said the backup genome could be
particularly useful for self-fertilizing plants, as arabidopsis is, since
help avoid the adverse effects of inbreeding. It might also operate in the
curious organisms known as bdelloid rotifers that are renowned for not
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
could possess the backup system. Colleagues had been quite receptive to
idea because "biologists have gotten used to the unexpected," he said,
referring to a spate of novel mechanisms that have recently come to light,
Author of The Lucifer Principle: A Scientific Expedition Into the Forces
History and Global Brain: The Evolution of Mass Mind From The Big Bang to
Visiting Scholar-Graduate Psychology Department, New York University; Core
Faculty Member, The Graduate Institute
Founder: International Paleopsychology Project; founding board member:
of Evolution Society; founding board member, The Darwin Project; founder:
Big Bang Tango Media Lab; member: New York Academy of Sciences, American
Association for the Advancement of Science, American Psychological
Academy of Political Science, Human Behavior and Evolution Society,
Society for Human Ethology; advisory board member: Youthactivism.org;
executive editor -- New Paradigm book series.
For information on The International Paleopsychology Project, see:
for two chapters from
The Lucifer Principle: A Scientific Expedition Into the Forces of History,
For information on Global Brain: The Evolution of Mass Mind from the Big
Bang to the 21st Century, see www.howardbloom.net
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