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Location: UFOUpDatesList.Com > 2005 > May > May 29

New Findings About "Junk DNA" May Bring Some

From: UFO UpDates - Toronto <ufoupdates.nul>
Date: Sun, 29 May 2005 17:39:35 -0400
Fwd Date: Sun, 29 May 2005 17:39:35 -0400
Subject: New Findings About "Junk DNA" May Bring Some




Source: http://www.gewo.applet.cz/health/DNA_1e.htm

January 22, 2001

New Findings About "Junk DNA" May Bring Some Surprises

A group of researchers working at the Human Genome Project will
be announcing soon that they made an astonishing scientific
discovery: They believe so-called non-coding sequences (97%) in
human DNA is no less than genetic code of an unknown
extraterrestrial life form.

The non-coding sequences are common to all living organisms on
Earth, from molds to fish to humans. In human DNA, they
constitute larger part of the total genome, says Prof. Sam
Chang, the group leader. Non-coding sequences, also known as
"junk DNA", were discovered years ago, and their function
remains mystery. Unlike normal genes, which carry the
information that intracellular machinery uses to synthesize
proteins, enzymes and other chemicals produced by our bodies,
non-coding sequences are never used for any purpose. They are
never expressed, meaning that the information they carry is
never read, no substance is synthesized and they have no
function at all. We exist on only 3% of our DNA. The junk genes
merely enjoy the ride with hard working active genes, passed
from generation to generation. What are they? How come these
idle genes are in our genome? Those were the question many
scientists posed and failed to answer - until the breakthrough
discovery by Prof. Sam Chang and his group.

Trying to understand the origins and meaning of junk DNA Prof.
Chang realized that he first needs a definition of "junk". Is
junk DNA really junk, (useless and meaningless) or it contains
some information not claimed by the rest of DNA for whatever
reason? He once mentioned the question to an acquaintance, Dr.
Lipshutz, a young theoretical physicist turned Wall Street
derivative securities specialist. "Easy," replied Lipshutz.
"We'll run your sequence through the software I use to analyze
market data, and it will show if your sequences are total
garbage, "white noise", or there is a message in there." This
new breed of analysts with strong background in math, physics
and statistics are getting more and more popular with Wall
Street firms. They sift through gigabytes of market statistics,
trying to uncover useful correlation between the various market
indexes, and individual stocks.

Working evenings and weekends, Lipshutz managed to show that
non-coding sequences are not all junk, they carry information.
Combining massive database of the Human Genome Project with
thousands of data files developed by geneticists all over the
world Lipshutz calculated Kolmogorov entropy of the non-coding
sequences and compared it with the entropy of regular, active
genes. Kolmogorov entropy, introduced by the famous Russian
mathematician half a century ago, was successfully used to
quantify the level of randomness in various sequences, from time
sequences of noise in radio lamps to sequences of letters in
19th century Russian poetry. By and large, the technique allows
researchers to quantitatively compare various sequences and
conclude which one carries more information than the other does.
"To my surprise, the entropy of coding and non-coding DNA
sequences was not that different", continues Lipshutz. "There
was noise in both but it was no junk at all. If the market data
were that orderly, I would have already retired."

After a year of cooperation with Lipshutz, Chang was convinced,
there is a hidden information in junk DNA. However, how could
one understand its meaning if the information is never used?
With active sequences you try to watch the cell and see what
proteins are being made using the information. This wouldn't
work with dormant genes. There will be experiment to test a
hypothesis; one should rely on the power of his thought. Since
there are letters, it should be tested in some old languages,
perhaps Sumerian, Egyptian, Hebrew, and so on. Prof. Sam Chang
solicited help from three specialists in the field, but none of
them managed to find a solution. There were no cultural clues,
no references to other known languages, the field was too alien
for the linguists.

"I asked myself: who else can decipher a hidden message?" Chang
continues. "Of course, cryptographers! In addition, I began
talking with researchers at the National Security Agency. It
took me few months to make them return my calls. Were they
running background checks on me? Alternatively, were they too
busy lobbying senators on retaining and strengthening their
authority to control exports of encryption technologies?
Eventually, a junior fellow was assigned to answer my questions.
He listened, requested my questions in writing and after
another, few months turned me down. His message was polite but
meant, "Go to hell with your crazy ideas. We are a serious
agency, its National Security, dude. We are too busy."

Well, Sam, forget the Government, talk to the private sector.
Therefore, I began approaching computer security consultants.
They were genuinely interested, and a couple of them even began
working on my project, but their enthusiasm always faded after a
month. I kept calling them until one nice fellow told me: "I'd
love to work on your project if I had more time. I am
overbooked. Emissaries of major banks and Fortune 500 companies
are begging me to plumb the holes in their networks. They pay me
$500 an hour. I can give you an educational discount, can you
afford $350?" Scrambling $15/hr for a post doctoral studies is a
big deal in academia, $350 sounded as something extraorbital."
Eventually Prof. Chang was referred to Dr. Adnan Mussaelian, a
talented cryptographer in the former Soviet republic of Armenia.
Poor fellow barely survived on a $15 a month salary and
occasional fees for tutoring children of Armenian nuveau riches.
A $10,000 research grant was a struck of luck, he began working
like a beaver.

Adnan promptly confirmed the findings of his Wall Street
predecessor: The entropy indicated tons of information almost in
the clear, it was not too strong cryptographic system, it didn't
appear to be a tough problem. Adnan began applying differential
cryptoanalysis and similar standard cryptographic techniques.

He was two months in the project when he noticed that all non-
coding sequences are usually preceded by one short DNA sequence.
A very similar sequence usually followed the junk. These
segments, known to biologists as alu sequences, were all over
the whole human genome. Being non-coding, junk sequences
themselves, alu are one of the most common genes of all.

Trained as a cryptographer and computer programmer, and having
no knowledge of microbiology, Adnan approached the genetic code
as of computer code. Dealing with 0, 1, 2, 3 (four bases of
genetic code) instead of 0s and 1s of the binary code was a sort
of nuisance, but the computer code was what he was analyzing and
deciphering all his life. He was on familiar territory. The most
common symbol in the code that causes no action followed by a
chunk of dormant code. What is that? Just playing with the
analogy Adnan grabbed the source code of one his programs and
fed it into the program that calculates the statistics of
symbols and short sequences, a tool often used in decoding
messages. What was the most common symbol? Of course, it was
"/", a symbol of comment! He took a Pascal code, and it were {
and } ! Of course, the code between two slashes in C is never
executed, and is never meant to be executed; it is not the code,
it is the comment to the code!

Being unable to resist the temptation to further play with the
analogy, Adnan began comparing statistical distributions of the
comments in computer and genetic code. There must be a striking
difference. This should show up in statistics. Nevertheless,
statistically, junk DNA was not much different from active,
coding sequences. To be sure, Adnan fed a program into the
analyzer: surprisingly, the statistics of code and comments were
almost the same. He looked into the source code and realized
why: there were very few comments in between the slashes, it was
mostly C code the author decided to exclude from execution, a
common practice among programmers.

Adnan, religiously inclined person, was thinking about the
divine hand - but after analyzing the spaghetti code inside the
sequences he convinced himself that whoever wrote the small code
was not God. Who wrote the active, small coding part of human
genetic code was not very well organized, he was a rather sloppy
programmer. It looked like rather somebody from Microsoft, but
at the time human genetic code was written, there was no
Microsoft on Earth.

On Earth? It was like a lightning... Was the genetic code for
all life on Earth written by an extraterrestrial programmer and
then somehow deposited here, for execution? The idea was mad and
frightening, and Adnan resisted it for days. Then he decided to
proceed. If the non-coding sequences are parts of the program
that were rejected or abandoned by the author, there is a way to
make them work. The only thing one needs to do is to remove the
symbols of comments and if the portion between the /*......*/
symbols is a meaningful routine it may compile and execute!
Following this line of thought, Adnan selected only those non-
coding sequences that had exactly the same frequency
distribution of symbols as the active genes. This procedure
excluded the comments in Marcian or Q, whatever it was. He
selected some 200 non-coding sequences that most closely
resembled real genes, stripped them of /*, //, and similar stuff
and after few days of hesitation sent e-mail to his American
boss, asking him to find a way to put them in E-coli or whatever
host and make them work.

Chang did not replied for two weeks. "I thought I was fired",
confessed Dr. Mussaelian. "With every day of his silence I more
and more realized how crazy my idea was. Chang would conclude I
was a schizophrenic and would terminate the contract. Chang
finally responded and, to my surprise, he did not fire me. He
had not bought my extraterrestrial theory but agreed to try to
make my sequences work."

Biologists have attempted for years to make junk sequences
express, without much success. Sometimes nothing turned out;
sometimes it was junk again. It was not surprising. Grab an
arbitrary portion of the excluded computer code and try to
compile it. Most likely, it will fail. At best, it will produce
bizarre results. Analyze the code carefully, fish out a whole
function from the comments, and you may make it work. Because of
careful Mussaelian's statistical analysis 4 of the 200 sequences
he selected, began working, producing tiny amounts of a chemical
compounds.

"I was anxiously awaiting the response from Chang," says Dr.
Mussaelian. "Would it be a more or less normal protein or
something out of ordinary? The answer was shocking: it was a
substance, known to be produced by several types of leukemia in
men and animals. Surprisingly, three other sequences also
produced cancer-related chemicals. It no longer looked like a
coincidence. When one awakens a viable dormant gene, it produces
cancer-related proteins. Researchers began searching Human
Genome Project databases for the four genes they isolated from
junk DNA. Eventually, three of the four were found there, listed
as active, non-junk genes. This was not a big surprise: since
cancer tissues produce the protein, there must be somewhere a
gene, which codes it! The surprise came later: In the active,
non-junk portion of the code the gene in question (the
researchers called it "jhlg1", for junk human leukemia gene) was
not preceded by the alu sequence, i.e. the /* symbol was
missing. However, the closing */ symbol at the end of "jhlg1"
was there. This explained why "jhlg1" was not expressed in the
depth of the junk DNA but worked fine in the normal, active part
of the genome. The one who wrote the basic genetic code for
humans excluded portion of the big code by embracing them in
/*... */ but missed some of the opening /* symbol. His compiler
seems to be garbage, too: a good compiler, even from terrestrial
Microsoft, would most likely refuse to compile such program at
all.

Prof. Sam Chang with his students began searching for genes
associated with various cancers, and almost in all instances
they discovered that those genes are followed by the alu
sequence (i.e. protein as a comment closing symbol */), but
never preceded by the comment opening /* gene! "This explains
why diseases result in cell damage and their death, whereas
cancers lead to cell reproduction and growth. Because only few
fragments from the big code are expressed, they never lead to
coherent growth. What we get with cancer, is expression of only
few of genes alien to humans and symbiosis with some genes of
bacterial parasites that lead to illogical, bizarre and
apparently meaningless chunks of living cells. The chunks have
its own veins, arteries, and its own immune system that
vigorously resists all our anti-cancer drugs.

"Our hypothesis is that a higher extraterrestrial life form was
engaged in creating new life and planting it on various planets.
Earth is just one of them. Perhaps, after programming, our
creators grow us the same way we grow bacteria in Petri dishes.
We can't know their motives - whether it was a scientific
experiment, or a way of preparing new planets for colonization,
or is it long time ongoing business of seedling life in the
universe. If we think about it in our human terms, the
extraterrestrial programmers were most probably working on one
big code consisting of several projects, and the projects should
have produced various life forms for various planets. They have
been also trying various solutions. They wrote the big code,
executed it, did not like some function, changed them or added
new one, executed again, made more improvements, tried again and
again. Of course, soon or later it was behind schedule. Few
deadlines have already passed. Then the management began
pressing for an immediate release. The programmers were ordered
to cut all their idealistic plans for the future and concentrate
now on one (Earth) project to meet the pressing deadline. Very
likely in a rush, the programmers cut down drastically the big
code and delivered basic program intended for Earth. However, at
that time they were (perhaps) not quite certain which functions
of the big code may be needed later and which not, so they kept
them all there. Instead of cleaning the basic program by
deleting all the lines of the big code, they converted them into
comments, and in the rush they missed few /* symbols in the
comments here or there; thus presenting mankind with illogical
growth of mass of cells we know as cancer."

There are three options to the problem. Either delete all the /*
symbols and comments and clean this way the basic code, or add
all the missing */ and avoid illogical mixing of the basic code
with the big code. Alternatively, in the third option, remove
all the / symbols and let work the basic code with the big code
as a complete program. Unfortunately, none of these options are
within our capacity. If we were able to efficiently insert genes
into the chromosomes of living men, our breakthrough discovery
would mean instant cure for all future cancer cases; at least
from the programmer point of view. Theoretically, we can do it
in a laboratory, but we have no practical means to implant the
repaired DNA into living subjects. The mystery of "junk DNA" and
cancer seems to be solved, but no quick cure shall be expected.
The best thing we can do now is to try nourishing new, cancer-
free line of humans with gradually debugged basic genetic code.
That will take a long time. For us and our children, there is no
hope on the horizon.

"However, from the programmer's point of view, there is also
positive outlook in it. What we see in our DNA is a program
consisting of two versions, a big code and basic code. First
fact is, the complete program was positively not written on
Earth; that is now a verified fact. The second fact is, that
genes by themselves are not enough to explain evolution; there
must be something more in the game. What it is or where it is,
we don't kow. The third fact is, no creator of a new work, be it
a composer, engineer or programmer, from Mars or Microsoft, will
ever leave his work without the option for improvement or
upgrade. Ingenious here is, that the upgrade is already enclosed
- the "junk DNA" is nothing more than hidden and dormant upgrade
of our basic code! We know for some time that certain cosmic
rays have power to modify DNA. With this in mind, plausible
solution is available. The extraterrestrial programmers may use
just one flash of the right energy from somewhere in the
Universe to instruct the basic code to remove all the /*=85*/
symbols, fuse itself with the big code ("junk DNA") and
jumpstart working of our whole DNA. That would change us
forever, some of us within months, some of us within
generations. The change would be not too much physical, (except
no more cancers, diseases and short life), but it will catapult
us intellectually. Suddenly, we will be in time comparable to
coexistence of Neanderthals with Cromagnons. The old will be
replaced giving birth to a new cycle. The complete program is
elegant, very clever self-organizing, auto-executing, auto-
developing and auto-correcting software for a highly advanced
biological computer with build-in connection to the ageless
energy and wisdom of the Universe. Software wise, within us is
either short and diseased life, or potential for a super-
intelligent super-being with a long and healthy life. This
triggers puzzling questions - was the reduction to the basic
code done by sloppy programmers in a rush (as it appears to us),
or was the disabling of the big code purposeful act which can be
cancelled by a "remote control" whenever desired?"

Soon or later, we have to come to grips with the unbelievable
notion that every life on Earth carries genetic code for his
extraterrestrial cousin and that evolution is not what we think
it is. This discovery may well shake the very roots of humanity
- our beliefs in our concept of God and in our own power over
our destiny. With the right paradigm, we may discover one day
that all forms of life and the whole Universe is just one huge
intellectual exercise in thoughts expressed mathematically, by
Design, by Creator.


[Thanks to Stuart Miller of http://www.uforeview.net for the lead]


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