[Paleopsych] Human rDNA: evolutionary patterns within the genes and tandem arrays derived from multiple chromosomes.

Sat Apr 2 01:31:53 UTC 2005

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&lis  
t_uids=11350117&dopt=Abstract

Google search:  http://www.google.com/search?hl=en&q=patterns+within+genes

Gonzalez IL, Sylvester JE.

A. I. DuPont Hospital for Children, Wilmington, Delaware 19899, USA. 
igonzale at nemours.org

Human rDNA forms arrays on five chromosome pairs and is homogenized by 
concerted evolution through recombination and gene conversion (loci RNR1, 
RNR2, RNR3, RNR4, RNR5, OMIM: 180450). Homogenization is not perfect, 
however, so that it becomes possible to study its efficiency within genes, 
within arrays, and between arrays by measuring and comparing DNA sequence 
variation. Previous studies with randomly cloned genomic DNA fragments 
showed that different parts of the gene evolve at different rates but did 
not allow comparison of rDNA sequences derived from specific chromosomes. 
We have now cloned and sequenced rDNA fragments from specific acrocentric 
chromosomes to (1) study homogenization along the rDNA and (2) compare 
homogenization within chromosomes and between homologous and nonhomologous 
chromosomes. Our results show high homogeneity among regulatory and coding 
regions of rDNA on all chromosomes, a surprising homogeneity among adjacent 
distal non-rDNA sequences, and the existence of one to three very divergent 
intergenic spacer classes within each array. Copyright 2001 Academic Press.

Steve Hovland
www.stevehovland.net

-----Original Message-----
From:	Greg Bear [SMTP:ursus at earthlink.net]
Sent:	Friday, April 01, 2005 8:55 AM
To:	HowlBloom at aol.com; paleopsych at paleopsych.org; kurakin1970 at yandex.ru; 
paul.werbos at verizon.net
Subject:	[Paleopsych] RE: From Eshel--A Glitch in Genetic-centrism

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:

The New York Times
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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
<http://query.nytimes.com/search/query?ppds=bylL&v1=NICHOLAS%20WADE&fdq=  
1996
0101&td=sysdate&sort=newest&ac=NICHOLAS%20WADE&inline=nyt-per> 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
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

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