[Paleopsych] Re: From Eshel--A Glitch in Genetic-centrism
HowlBloom at aol.com
HowlBloom at aol.com
Sun Apr 3 03:39:12 UTC 2005
These are good guesses, Greg. Your suggestion that some of the missing
pattern of the gene-that-never-was in the mustard plant with a double set of
mutated genes could be in the cytosol is evocative.
Bear with me while I run a string of thought that even I find difficult to
believe. Eshel and Joel Isaacson feel there's validity to some strange
research on water, research indicating that water is capable to carry "imprints" of
influences as vague as thoughts and as the label on the bottle. Cytosol is
the water and water-soluble components of the cell, the stuff that's left
when you get rid of the cell membrane, the nucleus, the organelles and the
cytoskeleton.
If it's true that water bears layer after layer of memory, layer after layer
of imprints from trace chemicals that have long since been removed and other
such things, then, indeed, the water itself could play a part in the
construction of a "proper", "whole" gene to replace the two mangled genes in the
mutated arabidopsis. I suspect that the reconstruction of a gene the mutated
aradidopsis never possessed isn't a serial process by any stretch of the
imagination. I suspect it's a very orchestral process in which numerous influences
inside of the cell and outside of the cell participate.
A cell is constantly receiving information about what form it should take,
what specialization it should adopt, and what it should be doing at this
precise second from genes around it and, I supsect in a sense, from the entire
plant it's a part of--not to mention the signals an individual plant receives
from the plant community and from the eco-system that plant community has
carved out.
As Jeff Hawkins points out in On Intelligence, this multi-level process of
signal transduction, this process of signal receiving and signal summing, isn't
static. It moves continuously, like music. And like the music of a
symphony, the message may be digested down to a simple sequence in each receiver.
One of those receivers is the genome. Another is the segment of a genome
called a gene.
Like Hawkins' neurons, the input coming to the genome includes delayed
feedback on its previous actions...and on the actions of previous generations of
plants.
So take the mysterious and possibly non-existent ability of water to hold a
"memory". Add it to the smarts in roughly 300 million macromolecules of the
cell and in the grander pattern they form. Add all that in to a hierarchy of
contexts that extend shell by shell like an infinite onion, and you may have a
partial explanation for the counter-Mendelian ability of a mustard plant to
generate a gene it never possessed but one that its neighbors and its
ancestors have had for a long, long time. You may get the ability of the plant to
receive an almost infinite number of signals, sum them, and arrive at the
right conclusion for each bit of space and time. In this case the mustard plant
arrives at the right conclusion about what a corrected version of its
damaged hothead gene should be like.
By the way, Pavel Kurakin suggests that a similar hierarchical summation of
the entire cosmos gets fed into the "decision" of a single quantum particle
when it "picks" which receptor device it should move to. Or at least Pavel
suggests this in the interpretation of his work I've been trying to smuggle into
a paper he and I are working on that compares the decision-making of quantum
particles to the decision-making of bees.
Howard
In a message dated 4/1/2005 8:55:19 A.M. Pacific Standard Time,
ursus at earthlink.net writes:
This fabulous bit of science is very evocative.
My best guess is that such “pattern memory”—while some of it could be
stored in cytosol elements, etc.,--is most likely stored in the vast unexplored
territories of “junk” DNA—perhaps in fragments of genes, pseudogenes, etc.,
with non-gene RNA elements acting as controls, inhibitors, etc.
Could be wrong, but this sort of reconstructive memory does seem essential
to life.
Best!
Greg
____________________________________
From: HowlBloom at aol.com [mailto: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: Re: From Eshel--A Glitch in Genetic-centrism
re:
(http://www.nytimes.com/adx/bin/adx_click.html?type=goto&page=www.nytimes.com/printer-friendly&pos=Position1&camp=foxsearch-emailtools09-nyt5&ad=pf_million
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nter-friendly&pos=Position1&camp=foxsearch-emailtools09-nyt5&ad=pf_millions.gif&got
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A mechanism central to Jeff Hawkins' analysis of the way brains work in his
On Intelligence may provide a clue to the manner in which plants with copies
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 gene
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 this
pattern. ...To retrieve a pattern stored in such a memory, you must provide the
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 retrieve 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 version of
it. It would be like going to the grocer with half eaten brown bananas and
getting whole green bananas in return. ...Second, unlike mist neural networks,
an auto-associative memory can be designed to store sequences of patterns, or
temporal patterns. This feature is accomplished by adding time delay to 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 part of
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 are
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 that
tell it where and want it is supposed to be in the plant's development and
ongoing roles.
Howard
re:
____________________________________
New York Times
March 23, 2005
Startling Scientists, Plant Fixes Its Flawed Gene
By _NICHOLAS WADE_
(http://query.nytimes.com/search/query?ppds=bylL&v1=NICHOLAS%20WADE&fdq=19960101&td=sysdate&sort=newest&ac=NICHOLAS%20WADE&inline=nyt-pe
r)
n 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 Tübingen, 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.
----------
Howard Bloom
Author of The Lucifer Principle: A Scientific Expedition Into the Forces of
History and Global Brain: The Evolution of Mass Mind From The Big Bang to the
21st Century
Visiting Scholar-Graduate Psychology Department, New York University; Core
Faculty Member, The Graduate Institute
www.howardbloom.net
www.bigbangtango.net
Founder: International Paleopsychology Project; founding board member: Epic
of Evolution Society; founding board member, The Darwin Project; founder: The
Big Bang Tango Media Lab; member: New York Academy of Sciences, American
Association for the Advancement of Science, American Psychological Society,
Academy of Political Science, Human Behavior and Evolution Society,
International Society for Human Ethology; advisory board member: Youthactivism.org;
executive editor -- New Paradigm book series.
For information on The International Paleopsychology Project, see:
www.paleopsych.org
for two chapters from
The Lucifer Principle: A Scientific Expedition Into the Forces of History,
see www.howardbloom.net/lucifer
For information on Global Brain: The Evolution of Mass Mind from the Big
Bang to the 21st Century, see www.howardbloom.net
----------
Howard Bloom
Author of The Lucifer Principle: A Scientific Expedition Into the Forces of
History and Global Brain: The Evolution of Mass Mind From The Big Bang to the
21st Century
Visiting Scholar-Graduate Psychology Department, New York University; Core
Faculty Member, The Graduate Institute
www.howardbloom.net
www.bigbangtango.net
Founder: International Paleopsychology Project; founding board member: Epic
of Evolution Society; founding board member, The Darwin Project; founder: The
Big Bang Tango Media Lab; member: New York Academy of Sciences, American
Association for the Advancement of Science, American Psychological Society,
Academy of Political Science, Human Behavior and Evolution Society, International
Society for Human Ethology; advisory board member: Youthactivism.org;
executive editor -- New Paradigm book series.
For information on The International Paleopsychology Project, see:
www.paleopsych.org
for two chapters from
The Lucifer Principle: A Scientific Expedition Into the Forces of History,
see www.howardbloom.net/lucifer
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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