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

Fri Apr 1 03:31:11 UTC 2005

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
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  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

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