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PostPosted: Thu Jul 09, 2009 2:41 am 
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OK, let's begin ladies and gents... welcome to Mr Green Gene's Zappa Forum DNA lesson...

Here we will try to exhaust MGGs limited knowledge about the DNA molecule and its implications and influences in todays rapidly changing world (you will have to excuse me, I love to cite my idols, this will come up a few times).

Please feel free to step in anytime and come forward with your doubts, corrections, suggestions, random and casual comments, well suited jokes and etc. Don't be shy to ask... Flaming and trolling is not welcome, but since it is very likely this won't be avoided, any contribution is welcome. At some point, our specialist friends could step in and make some cool contributions of their own, for example, about Placoderm fishes living in the upper Devonian being attacked by religious kind of sharks and stuff... OK grab your shoes and socks, also your pencils and paper [whatever substance you need coffee, etc], fast your seat belts and let's go:

1 - Why do I need to know about DNA?

That question is central to understanding anything you study, DNA being no different. I can think of several alternative reasons that might or might not apply specifically to yourself: you might be a natural nerd, you might be just plain curious, you might want to catch up with the latest technologies, you might want to see what this crazy bastard has come up with this time, I don't know, you should state that yourself, since you came here! But the fact is you might have seen DNA being crammed down your throat in the media all the time now for the last 10 years... You might have heard of famous people who had to admit paternity and pay what is due to whom it may concern, you might have heard of people being falsely accused gain liberty after years of injustice, you might have heard of genetic engineering, crimes being solved, diseases being approached with alternative means and such, genes for being gay, for being smart, for being and genes for this and genes for that... I have to forward to you that there is tons of bullshit on the media about genetics and we will try to demystify that along the way as well... You might yourself had been tested for some DNA health of parental tests and etc... And fact is DNA technologies are the cutting edge tools literally dessicate, understand, heal and mess up with living systems and evolution...

To understand the ultimate, far most, extreme, Huxleyrian scenario conceivable about Eugenocracies (think of the Nazis), I recommend the Hollywood movie GATTACA. Even although the scientifically conceivable consequences of such practises could be even more bizarre (as the human species splitting in two with a socially dominating species), it is a nice reflection about the subject...

Image

Meditate on this, I will... Complimentary read:
http://en.wikipedia.org/wiki/Genetic_engineering

That's right folks, don't touch that dial. Stay tuned...

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PostPosted: Thu Jul 09, 2009 4:24 am 
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This presents a problem to someone I know who when in a pinch asserts the Bible is right on everything and says humans have been here only a few thousands of years. He believes genetic evidence is rock solid, so when confronting him on his little factual delimma, it's no problem-he just talks over you. (Lol, he says he's anti-war too, he's an Obama voter).

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PostPosted: Thu Jul 09, 2009 7:12 am 
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My 4 year old is obsessed with DNA, talks about it all the time, his deepest understanding seems to be that protein makes DNA. He can sit and watch videos about DNA all day. Me hopes this portends biggish things!!!!!

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PostPosted: Thu Jul 09, 2009 7:17 am 
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baddy wrote:
This presents a problem to someone I know who when in a pinch asserts the Bible is right on everything and says humans have been here only a few thousands of years. He believes genetic evidence is rock solid, so when confronting him on his little factual delimma, it's no problem-he just talks over you. (Lol, he says he's anti-war too, he's an Obama voter).

I always had a problem with fundementalists railing against evolution and the amount of time humans have been on the Earth. There are Christians who have weighed the evidence, and wisely assert, that biblically, it states "a thousand years is as a day to God" or some such thing, at any rate, it makes the whole "God created the earth in seven days" REALLY subjective. I don't feel evolution is incongruent with the religion, you simply have to understand a parable isn't entirely literal. Oh well.

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PostPosted: Fri Jul 10, 2009 2:02 pm 
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2 - What the fuck is DNA?

That's right folks, you heard right... As a matter of fact, DNA matters as fuck in a fuck... After all, sex is nothing more than attempting to transmit DNA to offspring (at least originally).

DNA is a long filamentary molecule from a class of molecules first described as being Nucleic Acids (as in acid substances in the nucleus of a cell) in the late 19th century. There are other nucleic acids apart from DNA, notably RNA, which I am sure we will get the chance to discuss sometime in the future... Nucleic acids in general are heteropolymers [Hetero=different, poly=many, meros=parts], meaning they are composed of basic repetitive variable bricks. In the case of DNA those building bricks are called nucleotides. There are four common bricks, or nucleotides, that make up DNA. We will name them ahead. Each nucleotide is a molecule sharing a common basic plan, composed of the following basic elements: Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorus... those atoms are ensebled together in three groups of fundamental molecules that make up a nucleotide: 1) nucleobase, more commonly called a nitrogenous base, which is the variable part of the four different DNA nucleotides, 2) a five carbon cyclical sugar molecule called the deoxyribose and 3) a phosphate group (one in the DNA per nucleotide, but up to three in the cellular free swimming form found inside the cell [monomers - free bricks floating around in the cellular inner environment, see ATP for example...] (fig 1):

Image
Deoxyribose sugar (notice the Carbon atoms are all the vertices of the pentagon except for the Oxygen on the top)

Image
The phosphate, note the disposition of the ionized oxygen atoms...

and the variable part, the four different Nitrogen Bases:

Image
(same thing, the carbon atoms are not shown on the hexagonal cyclic molecule...

So those three fundamental blocks come together to make one nucleotide (DNA's building bricks). The only variable part is the nucleobase and it makes each one of the four different nucleotides have different molecular shapes, so you can easily imagine 'em as lego bricks with a basic design but slight different shapes. Note by looking at the nucleobases above called Guanine (G), Adenine (A), Cytosine (C) and Thymine (T) that they group in two different overal shapes : A and G are called the Purines and C and T are called the Pyrimidines.

So the four nucleotides are:
Image

SO if anything, learn this, life is acid!

Ok boys and girls, that is enough for you to meditate on for now... Next we will discuss how those nucleotides stack together to form half-filament of DNA (a strand) and against each other in a opposing half (the opposite strand) to for the marvellous of DNA, the double helix...

;-(~

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PostPosted: Sat Jul 11, 2009 1:54 pm 
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our big prize tonite is fifty american dollars to the 1st person to identify this dna:

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PostPosted: Sat Jul 11, 2009 5:33 pm 
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slime.oofytv.set wrote:
our big prize tonite is fifty american dollars to the 1st person to identify this dna:

Image

That's easy:
Image

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PostPosted: Sun Jul 12, 2009 9:09 am 
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Location: A holographic construct outside of linear time
i believe that dna was sent here from another star system. not necessarily on purpose, but they were searching for appealing conditions that were suitable for the dna to thrive and develop. i believe that in the junk dna, we'll find the entire history of our species catalogued like a hard drive and one day we'll have the awareness to tap into it.

and never one to shy away from a bit of spam, i did an ambient/drone album based on this very subject last year. That's available for free download from archive.org :mrgreen:

http://www.archive.org/details/Ch.pm-AlienGenomeProject

01 Source Of Light
02 Junk Code
03 Transference
04 Replicate
05 Mystic Structure
06 Source Of Light (Reprise)
07 Alien Genome Project
08 Hybrid

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PostPosted: Mon Jul 13, 2009 8:23 am 
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Image / Image wrote:
That's easy .../i believe that dna was sent here from another star system...
sorry guys, sorry better try it again



hint: 3rd dna ever

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PostPosted: Mon Jul 13, 2009 2:45 pm 
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slime.oofytv.set wrote:
our big prize tonite is fifty american dollars to the 1st person to identify this dna:

Image


Jeopardy: What is Poodle's DNA?

Image

Image

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Last edited by Mr_Green_Genes on Mon Jul 13, 2009 4:25 pm, edited 2 times in total.

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PostPosted: Mon Jul 13, 2009 4:23 pm 
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mr_green_genes wrote:
Jeopardy: What is Poodle's DNA? ...
we have a winner ... totally committed to the fifty bucks






3rd party check's in the mail
please allow 90 days for delivery

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Last edited by slime.oofytv.set on Mon Jul 13, 2009 7:34 pm, edited 1 time in total.

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PostPosted: Mon Jul 13, 2009 4:25 pm 
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slime.oofytv.set wrote:
mr_green_genes wrote:
Jeopardy: What is Poodle's DNA? ...
we have a winner ... totally committed to the fifty bucks


Make your checks payable to 'Mr Green Genes, Second Greatest Living Philostopher Known to Mankind'! :wink:

Your tip gave it away.... :mrgreen:

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PostPosted: Mon Jul 13, 2009 8:50 pm 
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HAHAHHAH! Slime, that was awesome, especially the hint!
And also awesome green GENES got it in his thread about deoxyribonucleic acid. Sort of validifies your expertise a little!!!

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PostPosted: Tue Jul 14, 2009 1:41 pm 
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slime.oofytv.set wrote:
Image


3 - What keeps both strands of DNA together

To answer that question we will use Slime's Poodle DNA as a perfect example, because it shows the individual nucleotides grouped together in a chain-like fashion. Also you will notice a 69-ish nature to DNA's structure, for there are two chains one heading up and one heading down...

You can figure out buy looking at the diagrams in the #2 exposition, that the phosphate groups make the connections among the pentagonal ciclyc sugar molecule(deoxyribose), each of which carry one of the four possible nitrogenous base (C or T or G or A or C or A in the example above).

You can also notice the VERY IMPORTANT principle that in the opposite strand, the nucleotides correspond to a fix pattern of BASE PAIRING (A mates with T, C mates with G and vice versa)...

And finally you also check that there are bonds between each base pair... those are invisible bonds called Hydrogen Bonds a force created by electric polarization charges in atoms such as Oxygen, Nitrogen and Hydrogen... A and T form two hydrogen bonds between them and C and G form three hydrogen bonds, meaning it takes around 50% more energy to spoil a pairing of G and C than A and T. Those bonds are called week forces, but together each pairing between both complementary single strands acts as a the teeth in a zipper, which keeps DNA double helix structure together along the whole filament... To generate enough energy to break all bonds in a whole genome in solution you need in average to reach a temperature of 94°C (at 100°C the waters turns black, heh, I mean, excuse me, it turns to vapour)...

Image Image

What keeps each nuclotide tied together as a chain in each single single strand is a very important strong force (the phosphodiester bond) which will explore further next time, along with the double spiral structure features of life...

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PostPosted: Mon Jul 20, 2009 7:57 pm 
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PostPosted: Tue Jul 21, 2009 2:33 pm 
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Actually, I already knew this. I have an excellent 3 disc teaching CD called The Biology Of Life.

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PostPosted: Sat Jul 25, 2009 1:31 pm 
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I don't know if you heard about this : http://www.genomeweb.com/sequencing/snp ... tudy-finds
This means the DNA sequence in the human body might not be unique and identical.


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PostPosted: Sun Jul 26, 2009 12:04 am 
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Maroual wrote:
I don't know if you heard about this : http://www.genomeweb.com/sequencing/snp ... tudy-finds
This means the DNA sequence in the human body might not be unique and identical.

Yes I had heard about this! Once again we are but babies in our knowledge of the universe.

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PostPosted: Mon Jul 27, 2009 7:09 am 
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Very interesting article, thanks. Genetics is a very complex filed, and yes we are still leaving the crawling stage and beginning to give our first firm steps in the molecular field...

There are a few factors which are well established about what are called somatic mutations, which take place in body cellular lineages that spread specific mutations to daughter cells and that, when ever it occurs during early embrionary stages, can lead to clearly alternative phenotipic (i.e. the bodily/biochemichal/behaviourial physical appearance) differences and are deeply involved with the cancer phenomena, for instance... This article shows alternative additional possibilities that have some important implications. We need to develop the general theory in this thread before proceeding to this area, which is really important and interesting, though...

But the article states:
Quote:
So far, Schweitzer said it's unclear whether these BAK1 differences in the blood and aortic tissue are the consequence of RNA editing, which changes the messenger RNA but not the gene, or DNA editing, which involves differences in the gene itself.

Which is a major possibility since he sequenced cDNA (complementary DNA, made from asingle strand RNA, thorugh a process called reverse transcription) which involves the possibility of RNA editing (changes in the arrangement of the set of expression products (mRNAs) from exonic coding regions - we should define all this jazz later on...). And in the end someone in article states:
Quote:
"It is much more likely that the missing heritability that we are all searching for will be accounted for by rare DNA variants, copy number variants, and heritable epigenetic modifications than by this mechanism."

which I agree also

A very nice find with some important possible theoretical impact and some precautionary practical advise implications for people who works with DNA extraction...

I intend to develop on all this through this channel as we go along... The serious lay reader should be capable of taking a clear deep look at the implications and beauty of our genetic nature in the tapestry of the universe...

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PostPosted: Thu Apr 29, 2010 5:40 pm 
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After a long recess, let's get on with this:

Why is DNA so important as a molecule?

Because it has two basic properties to play the role of heredity's molecule: it can hold information (represented by the nucleotide sequence on either of the double-helix strands) and it can be precisely replicated and give rise to new copies of itself (one molecule can make 2 molecules). Information in this case means all the instructions the cell needs to know in order to build a full new organism. And to replicate is to reproduce (to pass the instructions to new generations ahead).

Remember, [genetic] information is not knowledge and 'they need to reproduce'...

The replication of DNA, the way one molecule can generate exact copies of itself happens in a process called semi-conservative replication. It means that from one double-helix (two strands), two new complete molecules will be generated, each containing one old strand (which will act as a template) and one new strand, newly synthesized according to instructions on the template strand (the base pairing rules, discussed above).

The catch here is that nature only knows how to polymerize (build) a new DNA strand in one single direction (called 5'->3') [please, check the diagram on my first 14 Jul 2009 entry]. New building blocks (each nucleotide) can only be added to a nucleotide chain (strand) exhibiting a free 3'-OH [hydroxyl] group on one end. This chemical group is necessary to make a new [strong] chemical bond to attach the entering nucleotide to the forming chain. In order to make this possible, 1) the twisted molecule needs to be unwinded and rest 'flat'; 2) both strands (running on opposite directions, the 69 configuration), being held by relatively weak hydrogen bonds formed by the opposite strands base pairs need to be separated (as in an opening zipper), so the new strands can be constructed over the two old strands...

Animation:
Image

Notice that all this process are mediated by a host of Enzymes (functional proteins that can foster chemical reactions to take place). Also notice that because of the strict direction limitation in the making of a new strand, as the replication fork advances (the direction of the separation of the two original strands), one new strand can be constructed in a direct continuous fashion, following the direction of the DNA's unzipping, while the other new nascent strand needs to be made discontinuously, as the unzipping takes place. The old strand acts as a template for the new strand being created, in a way that if in a particular position, an A is found on the old strand, a T will be incorporated in the new strand. If a G is found on the old strand, a C will be placed in the new strand and vice-versa [A always pairs with a T, and vice versa; and a G always pairs with a C, and vice-versa]

Illustration:
Image

Legend:
Helicase=Enzime responsible to unzip the double strand and bring each strand apart (an enzyme called Girase, untwist the double helix before that)
SSB=Single strand Binding Proteins (stabilizes the single strands, preventing them to renaturate - to conform to their stable complimentary double strand configuration)
Primase= Adds a short primer (a temporary RNA which pairs with the template DNA) to supply a 3'-OH group necessary to the further addition of each new nucleotide used to build the new forming strand)
DNA Pol. III or DNA Polymerase III (the marvellous enzyme which adds the free nucleotides floating inside the cell to for the new chain of linked nucleotides) - It not only does that, as it can proofread it's work done to avoid errors in the sequence, also known as mutations)
DNA Pol I = Replaces the RNA primers with DNA filling
Ligase = Form the lacking [phosohodiester] bonds among adjacent nucleotides, left behind by primers, among DNA segments (called Okazaki Fragments) in the newly formed discontinuous lagging strand (lower chain in the animation)...

One image is worth more that a thousand words:
Image

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PostPosted: Sun May 02, 2010 4:13 pm 
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Let's briefly move to:

The World of the RNA

Later I will make some comment on the RNA World hypothesis, which is about the abiotic origin of life scenario that might interest some of the readers. But first...

The RNA - Ribonucleic Acid - molecule:

RNA is DNA's older cousin, also pertaining to the class of Nucleic Acids, nanometric filamentary (rope-like) structures build up from nucleotides (variable building bricks) as in wagons on a train or links in a chain...

The main difference among the nucleotides used by DNA and RNA is the sugar used on their backbone (remember, nucleotides are made of a phosphate group, bonded to a sugar [pentagonal cyclic ring=pentose] and a nitrogenous base): DNA uses deoxynucleotides which lack an hydroxyl group on the so called 2' position of the cyclic ring:

Image
Carbon positions on the sugar ring

Image Image
Deoxyribose <<<<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>> Ribose.

Also RNA uses another base in the place of Thymine. This other base, called Uracil (U) also pairs with Adenine (A).

Image

Just as like DNA, RNA backbones is made of alternating phosphate-sugar molecules linked specifically from their 5' -> 3' carbons (giving the chain a polarity, an up and down, directional quality):

Image.

Unlike DNA, RNA is usually single stranded (as opposed to DNA's double-helix pair of complementary strands). This allows several different classes of RNAs to form complex base pairing interactions from different portions of a same single strand, as it is the case with a special RNA called tRNA and which confers complex spatial molecular structure to RNAs and enzymatic properties (capable of catalysing biochemical reactions) to this molecule.

Image
(for some reason Ts are in the places of Us in this animations, note the base pairs forming on the same strand of a single stranded molecule.)

As DNA RNA can carry a genetic message, throughout its nucleotide sequence.

As my pizza is waiting we will get back on that latter...

Remember: Eat your greens!

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PostPosted: Sun Jun 06, 2010 11:13 am 
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ah-yup, each and every day. You could naturally catch a rainbow on a rainy day, say.

A fortnight ago there was a documentally, me following the whole lot. More than twenty years after the disaster of that ukrainian reactor, a few, all scientists there, sampling the data of relevance, stress from the makers on the big and useful chance etc. Now, the results be, radiation can be useful, so an american profi also, who has been sent mice and stuff, first was almost the talk of the specialists, then got it right. They now think it could be a cure with far less side-effects. So, the body, and do ask what is this marvellous, trillions of cells co-functioning together via wonder, creates more of its natural defense system, all info from Earth' history, and fight the antioxydans, which may be there. In so doing the helix, which could be damaged, will get more co-fighters. Like I said, the complete .. humanity knows in effect quite a little.

Could be that it's not accurate ... what happens when the strings copy, a force is pulling them in a way, that makes me raise my hands up to the sky. Heh, guess nobody has understood this. Anyway, you got the know now. What luck say, ..not yet spoken of our incredible place in space. I'll wrightey blog ...a book. Wager all that it's goose-skin on the go then... for solely a certain Tick, Trick and Track. - One would need fantasy, you know ..where we're trembling about, overdreamenduous, when one relishes in thinking of it all.

Spinach's the very thing, best frozen, and then with lots of salt, some nutmeg and bit of pepper. Broccenroly isn't too difficult either .. sort of.


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PostPosted: Sun Jun 06, 2010 12:43 pm 
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well understood without saying: dutch sauce (roasted meal, with milk added - simpler to dissolve the flour in the milk and then try to make it bubble without creating a mess) and the helix is healing itself. Life and its force ... you would like an explanation? have found a stupid allegory. Me hates lame photons.

Sirius Lee the Wossname, the speech of light is so dim, it takes more than a second to the Moon etc. ... 4 years to the very next sun-system, some 1oo ooo to fly across our galaxy. 3ooMm/s is actually ..stunning or gig-a-what? nighty-flighty.


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PostPosted: Sun Jun 06, 2010 1:00 pm 
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..and do not start us startling up with what we not already feel poppin' up in that great, better than cosmos' tumulti-ultimately, matter of yours,

http://www.world-science.net/othernews/080415_brain.htm

all dreams have already been slipped through, now a few years later reality becomes ya-super. Toodle-hooh


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PostPosted: Sun Sep 26, 2010 9:04 am 
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That's a very cool graphic.

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