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<DIV>re:
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><IMG SRC="cid:X.MA1.1112326269@aol.com" height=47 alt="The New York Times" width=199 align=left v:shapes="_x0000_s1026" DATASIZE="2614" ID="MA1.1112326269" ><SPAN style="mso-field-code: 'HYPERLINK '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_millions.gif&goto=http%3A%2F%2Fwww%2Efoxsearchlight%2Ecom%2Fmillions%2Findex%5Fnyt%2Ehtml%20't'"><A href="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_millions.gif&goto=http%3A%2F%2Fwww%2Efoxsearchlight%2Ecom%2Fmillions%2Findex%5Fnyt%2Ehtml%20" target=_blank><IMG SRC="cid:X.MA2.1112326269@aol.com" height=31 width=200 align=left vspace=10 border=0 v:shapes="_x0000_s1027" DATASIZE="1968" ID="MA2.1112326269" ></A></SPAN><BR style="mso-special-character: line-break" clear=all></P>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2>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.</FONT></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2></FONT> </DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2>Hawkins
brings up a neural network trick called auto-associative memory.
Here's his description of how it works:</FONT></DIV>
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"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.)</FONT></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2></FONT> </DIV></BLOCKQUOTE>
<DIV class=MsoNormal dir=ltr style="MARGIN: 0in 0in 0pt"><FONT size=2>Where would such auto-associative circuits exist in a plant
cell? Here are some wild guesses:</FONT></DIV>
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<LI>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2>In the
entire cell, including its membrane, its cytoplasm, its
organelles, its metabolic processes, and its
genome;</FONT></DIV></LI>
<LI>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2></FONT> </DIV></LI>
<LI>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2>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.</FONT></DIV></LI></UL>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2>Howard</FONT></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2></FONT> </DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2>re:</FONT></DIV>
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<H5 style="MARGIN: auto 0in"><FONT face="Arial Unicode MS">New York
Times</FONT></H5>
<H5 style="MARGIN: auto 0in"><FONT face="Arial Unicode MS">March 23,
2005</FONT></H5>
<H2 style="MARGIN: auto 0in"><FONT face="Arial Unicode MS">Startling
Scientists, Plant Fixes Its Flawed Gene</FONT></H2>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><STRONG><SPAN style="mso-bidi-font-size: 10.0pt"><FONT face="Times New Roman" size=2>By
</FONT><A title="More Articles by Nicholas Wade" href="http://query.nytimes.com/search/query?ppds=bylL&v1=NICHOLAS%20WADE&fdq=19960101&td=sysdate&sort=newest&ac=NICHOLAS%20WADE&inline=nyt-per"><FONT face="Times New Roman" color=#000066 size=2>NICHOLAS WADE</FONT></A><FONT face="Times New Roman" size=2> </FONT></SPAN></STRONG><BR style="mso-special-character: line-break"><BR style="mso-special-character: line-break"></P>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=2><FONT face="Times New Roman"> <SPAN style="FONT-SIZE: 12pt; FONT-FAMILY: 'Arial Unicode MS'"><o:p></o:p></SPAN></FONT></FONT></P></TD></TR></TBODY></TABLE>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=2><IMG SRC="cid:X.MA3.1112326269@aol.com" height=33 alt=I width=11 align=left v:shapes="_x0000_s1028" DATASIZE="392" ID="MA3.1112326269" ></FONT><FONT face="Arial Unicode MS">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. </FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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. </FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">"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. </FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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."</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">"That was the
moment when it was a complete shock," Dr. Pruitt said.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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. </FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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. </FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P style="MARGIN: 0in 0in 0pt"><FONT face="Arial Unicode MS">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.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: center" align=center><FONT size=2><FONT face="Times New Roman">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.<SPAN style="FONT-SIZE: 12pt; FONT-FAMILY: 'Arial Unicode MS'"><o:p></o:p></SPAN></FONT></FONT></P></TD></TR></TBODY></TABLE>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman"> <o:p></o:p></FONT></P></DIV>
<DIV> </DIV>
<DIV><FONT lang=0 face=Arial FAMILY="SANSSERIF" PTSIZE="10">----------<BR>Howard
Bloom<BR>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<BR>Visiting Scholar-Graduate Psychology Department, New York
University; Core Faculty Member, The Graduate
Institute<BR>www.howardbloom.net<BR>www.bigbangtango.net<BR>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.<BR>For information on The International Paleopsychology
Project, see: www.paleopsych.org<BR>for two chapters from <BR>The Lucifer
Principle: A Scientific Expedition Into the Forces of History, see
www.howardbloom.net/lucifer<BR>For information on Global Brain: The Evolution of
Mass Mind from the Big Bang to the 21st Century, see
www.howardbloom.net<BR></FONT></DIV></FONT></BODY></HTML>