[Paleopsych] Re: From Eshel--A Glitch in Genetic-centrism

[Steve Hovland]

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?

Steve Hovland
www.stevehovland.net


-----Original Message-----
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

re:

(http://www.nytimes.com/adx/bin/adx_click.html?type=goto&page=www.nytime  
s.com/printer-friendly&pos=Position1&camp=foxsearch-emailtools09-nyt5&ad  
=pf_million
s.gif&goto=http://www.foxsearchlight.com/millions/index_nyt.html%20)
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  Tubingen, 
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

 << File: ATT00000.html >>  << File: clip_image001.gif >>  << File: 
clip_image002.gif >>  << File: clip_image003.gif >>  << File: ATT00001.txt 
>>