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Delphi or DNA?


2008-01-04 01:19:07 AM
delphi158
ds9a.nl/amazing-dna/index.html
<q>
Furthermore, 97% of your DNA is commented out. DNA is linear and read
from start to end. The parts that should not be decoded are marked very
clearly, much like C comments. The 3% that is used directly form the so
called 'exons'. The comments, that come 'inbetween' are called 'introns'.
</q>
-ioan
 
 

Re:Delphi or DNA?

"e1">ds9a.nl/amazing-dna/index.html
Quote

<q>
Furthermore, 97% of your DNA is commented out. DNA is linear and read
from start to end. The parts that should not be decoded are marked very
clearly, much like C comments. The 3% that is used directly form the so
called 'exons'. The comments, that come 'inbetween' are called 'introns'.
</q>
As he notes later, there are indications "that the comments are doing
something important." The notion that most DNA is inactive is tending to be
replaced by the view that we simply don't understand how these sections work
yet.
bobD
 

Re:Delphi or DNA?

e1 writes:
Quote
ds9a.nl/amazing-dna/index.html

<q>
Furthermore, 97% of your DNA is commented out. DNA is linear and read
from start to end. The parts that should not be decoded are marked very
clearly, much like C comments. The 3% that is used directly form the so
called 'exons'. The comments, that come 'inbetween' are called 'introns'.
</q>
I read one paper which speculated that the junk DNA serves as an
important structural component - whether to govern the shape of the
strand of DNA itself or maybe to introduce a time delay while decoding.
Cheers,
Nicholas Sherlock
 

Re:Delphi or DNA?

Bob Dawson writes:
Quote
"e1">ds9a.nl/amazing-dna/index.html
><q>
>Furthermore, 97% of your DNA is commented out. DNA is linear and read
>from start to end. The parts that should not be decoded are marked very
>clearly, much like C comments. The 3% that is used directly form the so
>called 'exons'. The comments, that come 'inbetween' are called 'introns'.
></q>

As he notes later, there are indications "that the comments are doing
something important." The notion that most DNA is inactive is tending to be
replaced by the view that we simply don't understand how these sections work
yet.
We already do have a clue about what the "junk-DNA" is; it is meta
information. And its *very* active and crucial for correct
interpretation of the "old" protein coding DNA.
In 2007 the ENCODE project (analyzing ~1% of all DNA) published
results indicating that some 93% of the genome seems to be /very/
active (Nature 447: 799?16, 2007)
So, what was formerly thought to be "junk-DNA" is in reality even
more active than the old "regular" (3%) 'exon' DNA.
The new findings indicate that the "junk-DNA" is actually
*Meta Information* determining how the ribosomes (cell "factory")
should interpret the "regular" (3%) protein coding DNA.
That junk-DNA is actually curcial meta information is indicated by DNA
transcripts (mRNA, the intermediate "message" format, or "marshalling
format" between "storage" and "factory") being multiple times the size
of the DNA which codes for a protein. The huge amount of intermediate
mRNA doesn't match the amount of the source data and the end result.
Here a short summary of what they found out about this so called
"junk-DNA":
<quote>
* About 93% of the genome is transcribed (not 3%, as expected).
Further study with more wide-ranging methods may raise this figure to
100%. Because much energy and coordination is required for
transcription this means that probably the whole genome is used by the
cell and there is no such thing as ‘junk DNA?
* Exons are not gene-specific but are modules that can be joined
to many different RNA transcripts. One exon (i.e. one part of one
gene) can be used in combination with up to 33 different genes located
on 14 different chromosomes. This means that one exon can specify one
part shared in common by many different proteins.
* There is no ‘beads on a string?linear arrangement of genes, but
rather an interleaved structure of overlapping segments, with
typically 5, 7, 9 or more transcripts coming from the one ‘gene?
* Not just one strand, but both strands (sense and anti-sense) of
the DNA are fully transcribed.
* Transcription proceeds not just one way but both backwards and
forwards.
* Transcription factors can be tens or hundreds of thousands of
base-pairs away from the gene that they control, even on different
chromosomes.
* There is not just one START site, but many, in each particular
gene region.
* There is not just one transcription triggering (switching)
system for each region, but many.
</quote>
www.creationontheweb.com/content/view/5158
Regards,
// Rolf Lampa
 

Re:Delphi or DNA?

Farshad skrev:
Quote
The part of not-coding DNA is called Junk-DNA. Recently, there are studies
that show that this portion of DNA actually serves important functions which
are yet to be discovered. From a programming point of view it can be
speculated that Coding part of DNA is "Code Segment" and the rest of is some
kind of "Data Segment".
Meta information is a better name.
Since this additional info evidently is very active in the
transcripts (the intermediate language, "IML", of cell biology) it
seems to be a form of very advanced biological RT(M) info.
Meta information is a threat to the evolution paradigm though.
Nature simply don't come up with such.
One concrete thing to consider now is how DNA information could
emerge naturally when one sequence of information is reused in many
other places, or, in several different proteins for example.
Reusable information, just like reusable classes and generic
functions in software, defies step-for-step evolution of new novel
genetic information, since now we understand that one piece of
information is used in many places, and it needs to be beneficial
(or at least neutral) in multiple context simultaneously.
Regards,
// Rolf Lampa
 

Re:Delphi or DNA?

"Rolf Lampa [RIL]" <XXXX@XXXXX.COM>writes
Quote
We already do have a clue about what the "junk-DNA" is; it is meta
information. And its *very* active and crucial for correct
interpretation of the "old" protein coding DNA.
LOL. What a load of {*word*99}.
 

Re:Delphi or DNA?

Bob Dawson writes:
Quote
"e1">ds9a.nl/amazing-dna/index.html
>
><q>
>Furthermore, 97% of your DNA is commented out. DNA is linear and
>read from start to end. The parts that should not be decoded are
>marked very clearly, much like C comments. The 3% that is used
>directly form the so called 'exons'. The comments, that come
>'inbetween' are called 'introns'. </q>

As he notes later, there are indications "that the comments are doing
something important."
Compiler directives? Documentation for the Creator? <g>
--
Rudy Velthuis [TeamB] www.teamb.com
"I have come to believe that the whole world is an enigma, a
harmless enigma that is made terrible by our own mad attempt to
interpret it as though it had an underlying truth."
-- Umberto Eco
 

Re:Delphi or DNA?

"Rolf Lampa [RIL]"
Quote
Meta information is a better name.
Maybe.
Quote
Since this additional info evidently is very active in the
transcripts (the intermediate language, "IML", of cell biology) it
seems to be a form of very advanced biological RT(M) info.
The distribution graph of junk-DNA shows fractal correlations but the
coding section shows no such correlation. It suggests that non-coding
section mostly follows the structure of a language (or a data library).
Quote
Meta information is a threat to the evolution paradigm though.
Nature simply don't come up with such.
Indeed. I bet Dawkins et al. are not happy with these new findings.
 

Re:Delphi or DNA?

"Farshad" <XXXX@XXXXX.COM>writes
Quote

"Rolf Lampa [RIL]"
>Meta information is a better name.

Maybe.

>Since this additional info evidently is very active in the
>transcripts (the intermediate language, "IML", of cell biology) it
>seems to be a form of very advanced biological RT(M) info.

The distribution graph of junk-DNA shows fractal correlations but the
coding section shows no such correlation. It suggests that non-coding
section mostly follows the structure of a language (or a data library).
Languages don't have fractal correlations.
Quote

>Meta information is a threat to the evolution paradigm though.
>Nature simply don't come up with such.

Indeed. I bet Dawkins et al. are not happy with these new findings.
They'd have to read the "findings" in a respectable scientific journal, not
some crackpot creationist tract to form much of an opinion on it.
 

Re:Delphi or DNA?

"Farshad" <XXXX@XXXXX.COM>writes
Quote
The part of not-coding DNA is called Junk-DNA. Recently, there are studies
that show that this portion of DNA actually serves important functions
which are yet to be discovered.
How can a study show that something does a function that is completely
unknown? That doesn't even make sense.
We know there are large sections of unused DNA because they mutate at rates
that are several times faster than the parts that do something. If these
sections really did contain "metadata" then these rapid mutations would
quickly yield an unviable organism, because the effects of changes in
metadata would be far greater than the effects of changes in mere data.
Logic tells you that if a section of DNA contains metadata, it ought to
mutate at a very slow rate. That is not the case for these large sections of
junk DNA.
One of the regions of DNA that contain a lot of "junk" are the ends of the
DNA strands, which are long stretches of the same small sequence of amino
acids over and over again. These stretches vary in length as the DNA is
replicated, because replication tends to lose pieces at the ends, but the
enzyme telerase (sp?) puts pieces on the end to try and replace this junk.
As long as telerase can do this, the loss from the messy imperfect
replication process never reaches into the live code and there is no
generational degradation caused by this loss at the end of the DNA strands.
But when telerase stops doing this replacement, the cumulative losses at the
end of the DNA strands reaches into the active code and bad things start
happening to the elderly organism.
Those large sections of junk at the ends of DNA strands do not have any
metadata in them, they are just filler. This is one of many reasons why
programming computers and DNA have far less in common than some would like
us to believe. Put a bunch of junk filler in your program and you will simply
look like a fool. But in DNA, this filler is the evolutionary accommodation
of the messy replication process.
Programming is in no way similar to the protein folding and protein
generation that occurs along DNA strands of living organisms. Introduce even
the slightest mutation randomly into a program and it quickly crashes or
operates incorrectly, but introduce slight mutations in random sections of
DNA and the results are usually that nothing observable has been altered in
the living organism. This is because programs are concise and efficient
means of replicating and implementing information, whereas DNA is not
concise and not efficient.
In programming, you design the program to perform its tasks with the least
amount of code possible, if you are good programmer. Tight, efficient code
is the mark of a good programmer. Imagine what you would think of a peer if
his code was filled with thousands of lines of NOOP and JMP instructions
that went to other NOOP or JMP instructions.
"Hey, Nimesh, I noticed that you have huge sections of junk in your code."
"That's not junk, it is part of the program."
"But it doesn't do anything."
"Yes it does. It contains metadata. You just don't understand it, that's
all."
"So what does it do?"
"Important stuff, but you wouldn't understand it even if I told you."
"It can not be too important. I took it all out and ran the program and it
ran the same as it did before."
"D'oh!"
Before you continue on this, you ought to explain how it is possible for
those sections of DNA to contain "metadata" when molecular biologists have
written stuff over it without any effect on the following generations.
 

Re:Delphi or DNA?

"Rudy Velthuis [TeamB]" wrote
Quote
>
>As he notes later, there are indications "that the comments are doing
>something important."

Compiler directives? Documentation for the Creator? <g>
Safest statement at the moment would be that encoding amino acids (-->
proteins) is not the only function of DNA. that is simply its most understood
process.
A very open question is how timing works: how are genes turned on and off
(become active/inactive in the production of amino acids) through the
lifecycle of the cell and/or organism.
bobD
 

Re:Delphi or DNA?

"John Jacobson" wrote
Quote
Logic tells you that if a section of DNA contains metadata, it ought to
mutate at a very slow rate. That is not the case for these large sections
of junk DNA.
But it is the case for others
news.bbc.co.uk/2/hi/science/nature/3703935.stm
see also
www.sciencedaily.com/releases/2006/11/061113180029.htm
news.bbc.co.uk/2/hi/science/nature/4940654.stm
www.sciencedaily.com/releases/2007/04/070423185538.htm
The term "junk DNA" is actually tending to fall out of the literature.
bobD
 

Re:Delphi or DNA?

"Rolf Lampa [RIL]" wrote
Quote

Here a short summary of what they found out about this so called
"junk-DNA":
[...]
www.creationontheweb.com/content/view/5158
Reading science from an evangelical website is no way to learn science, I'm
afraid.
bobD
 

Re:Delphi or DNA?

John Jacobson skrev:
Quote
"Farshad" wrote
>"Rolf Lampa [RIL]"
>>Meta information is a threat to the evolution paradigm though.
>>Nature simply don't come up with such.
>Indeed. I bet Dawkins et al. are not happy with these new findings.

They'd have to read the "findings" in a respectable scientific journal,
not some crackpot creationist tract to form much of an opinion on it.
The "findings" were reported in the following references (and more):
# Birney, E., et. al., Identification and analysis of functional
elements in 1% of the human genome by the ENCODE pilot project,
Nature 447: 799?16, 2007.
# Philipp Kapranov, P., Willingham, A.T. and Gingeras, T.R.,
Genome-wide transcription and the implications for genomic
organization, Nature Reviews Genetics 8: 413?23, 2007.
# Akhtar, A. and Gasser, S.M., The nuclear envelope and
transcriptional control, Nature Genetics 8:507-517.
# Latent memory of cells comes to life, 17 May 2007,
<www.physorg.com/news98623491.html>
# Mikkelsen, T.S. et al., Genome-wide maps of chromatin state in
pluripotent anbd lineage-committed cells, Nature 448:553-560, 2007.
# Aladjem, M.I., Replication in context: dynamic regulation of DNA
replication patterns in metazoans, Nature Reviews Genetics 8:588-60,
2007.
Etc., etc.
John, guess what the problem is with this meta information?
The short version is that meta-information is inextricably dependent
upon the information it refers to. This means that an independent
origin is impossible.
Or, do you have a "non-crackpot" solution to it? Or perhaps there
were no "findings" at all by the "crackpots" listed above?
Regards,
// Rolf Lampa
 

Re:Delphi or DNA?

John Jacobson skrev:
Quote
"Farshad" <XXXX@XXXXX.COM>writes
news:XXXX@XXXXX.COM...
>The part of not-coding DNA is called Junk-DNA. Recently, there are studies
>that show that this portion of DNA actually serves important functions
>which are yet to be discovered.

How can a study show that something does a function that is completely
unknown? That doesn't even make sense.
It HAS been shown to have funtion. That "junk-DNA" which isn't really
'junk-DNA' has been shown to be
1. very
2. active
in transcription. (DNA-->mRNA-->(protein, for example)).
Still don't get it?
A. DNA
|
v
B. mRNA (DNA x "100" kinda, collected from "junk"(!))
|
v
C. Protein
Now you got it?
Regards,
// Rolf Lampa