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An Proposed Explanation of the Bree Solution
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TOSG
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PostPosted: Thu Jul 12, 2007 1:08 am    Post subject: An Proposed Explanation of the Bree Solution Reply with quote

So, there has been a lot of awesome work done deciphering the words that have been water-damaged. What’s missing from a lot of this effort, though, is a cohesive theory making sense of the document. Below, I present a theory, developed in collaboration with marlasinger (lovely diagrams courtesy of her, too!), regarding the meaning and significance of the document’s contents.


So, Bree’s blood contains a ribozyme that has a special activity that is unique only to her (Given Fact #1). The gene coding for this ribozyme (in everyone, not just Bree), has a regulatory element that is prone to hypermutation – that is to say, a regulatory portion of the gene mutates frequently (Given Fact #2). We propose that this regulatory element is controlling the correct synthesis of the RNA strand that is complementary to the active coding strand. Put more simply, the coding strand specifies a RNA molecule that is “active” – it is the functional ribozyme that resides in Bree’s blood. Each Hymn of One girl has this gene (Given Fact #3). HOWEVER, each of them also synthesizes the RNA strand that is complementary to this active molecule. This complementary strand binds to the ribozyme, rendering it inactive.

Figure 1.0 – ribozyme; inactive with complementary RNA strand binding to active RNA strand:

Note – complementary colors indicate where strands bind.

But, what makes Bree special is this – the regulatory element has mutated, such that it prevents the correct synthesis of the complementary RNA strand! Thus, the complementary strand is not made, and cannot bind to the active strand – the active strand remains active. Given the interpretation that Given Fact #4 says “this portion (the active strand) still functions, but you cannot block it because the complementary strand won’t copy,” this makes perfect sense. Without the complementary strand to “occlude the activity” of the active strand (Theoretical Solution #3), Bree’s ribozyme remains active.

Figure 1.1 – active strand: normal gene sequence



Figure 1.2 – complementary strand: gene sequence including regulatory gene portion, inhibiting complementary strand synthesis (note: the regulatory element is likely also located on the coding strand, but it is depicted on the complementary strand to reinforce that is where it has its effect).

Note – complementary colors indicate where strands bind.



So, this explains all of the “Given Facts,” but it goes even further – in this context, the treatment makes perfect sense. A blood sample must be taken from Bree, and the active ribozyme isolated. The ribozyme can then be sequenced – once its sequence is known, the sequence of the complementary strand will also be revealed, as in RNA, base A binds with base U on the complementary strand (and vice versa), and base G binds with base C (and vice versa). This complementary strand can be synthesized, and injected into Bree. Bree’s mutated regulatory element renders her unable to make the complementary strand, but once this strand is injected into her, it will bind to her active ribozyme and inactivate it, just as it does in everyone else who naturally synthesizes the complementary strand in their bodies. Given the text that Kellylen, Marla, myself, and others have decoded, this theory explains the proposed treatment as well!

And, this theory may even suggest a reason for the purity bond. As noted in Given Fact #2, the mutation in the regulatory element changes with every generation – it may be possible that if Bree were to have children, the ribozyme would be further destabilized, perhaps becoming uncontrollably active. Because we do not know the function of the ribozyme, we do not know what the consequences of this would be, but given its importance to the Hymn of One, the danger could be vast.

So, in the context of this theory, the pieces of this puzzle – and its solution – begin to assemble together.
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thoughtssopoetic
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PostPosted: Thu Jul 12, 2007 2:13 am    Post subject: Re: An Proposed Explanation of the Bree Solution Reply with quote

TOSG wrote:
So, there has been a lot of awesome work done deciphering the words that have been water-damaged. What’s missing from a lot of this effort, though, is a cohesive theory making sense of the document. Below, I present a theory, developed in collaboration with marlasinger (lovely diagrams courtesy of her, too!), regarding the meaning and significance of the document’s contents.


So, Bree’s blood contains a ribozyme that has a special activity that is unique only to her (Given Fact #1). The gene coding for this ribozyme (in everyone, not just Bree), has a regulatory element that is prone to hypermutation – that is to say, a regulatory portion of the gene mutates frequently (Given Fact #2). We propose that this regulatory element is controlling the correct synthesis of the RNA strand that is complementary to the active coding strand. Put more simply, the coding strand specifies a RNA molecule that is “active” – it is the functional ribozyme that resides in Bree’s blood. Each Hymn of One girl has this gene (Given Fact #3). HOWEVER, each of them also synthesizes the RNA strand that is complementary to this active molecule. This complementary strand binds to the ribozyme, rendering it inactive.

Figure 1.0 – ribozyme; inactive with complementary RNA strand binding to active RNA strand:

Note – complementary colors indicate where strands bind.

But, what makes Bree special is this – the regulatory element has mutated, such that it prevents the correct synthesis of the complementary RNA strand! Thus, the complementary strand is not made, and cannot bind to the active strand – the active strand remains active. Given the interpretation that Given Fact #4 says “this portion (the active strand) still functions, but you cannot block it because the complementary strand won’t copy,” this makes perfect sense. Without the complementary strand to “occlude the activity” of the active strand (Theoretical Solution #3), Bree’s ribozyme remains active.

Figure 1.1 – active strand: normal gene sequence



Figure 1.2 – complementary strand: gene sequence including regulatory gene portion, inhibiting complementary strand synthesis (note: the regulatory element is likely also located on the coding strand, but it is depicted on the complementary strand to reinforce that is where it has its effect).

Note – complementary colors indicate where strands bind.



So, this explains all of the “Given Facts,” but it goes even further – in this context, the treatment makes perfect sense. A blood sample must be taken from Bree, and the active ribozyme isolated. The ribozyme can then be sequenced – once its sequence is known, the sequence of the complementary strand will also be revealed, as in RNA, base A binds with base U on the complementary strand (and vice versa), and base G binds with base C (and vice versa). This complementary strand can be synthesized, and injected into Bree. Bree’s mutated regulatory element renders her unable to make the complementary strand, but once this strand is injected into her, it will bind to her active ribozyme and inactivate it, just as it does in everyone else who naturally synthesizes the complementary strand in their bodies. Given the text that Kellylen, Marla, myself, and others have decoded, this theory explains the proposed treatment as well!

And, this theory may even suggest a reason for the purity bond. As noted in Given Fact #2, the mutation in the regulatory element changes with every generation – it may be possible that if Bree were to have children, the ribozyme would be further destabilized, perhaps becoming uncontrollably active. Because we do not know the function of the ribozyme, we do not know what the consequences of this would be, but given its importance to the Hymn of One, the danger could be vast.

So, in the context of this theory, the pieces of this puzzle – and its solution – begin to assemble together.

*bows down*
You are amazing, and my hero.
Actually, all of you crazy intense geniuses are my heros.
*coughTOSGmarlasingerkellylencough*
(and whoever else I am forgetting to mention)
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fan
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PostPosted: Thu Jul 12, 2007 6:24 am    Post subject: Reply with quote

I think you're trying to describe RNAi for some sci-fi application.
http://en.wikipedia.org/wiki/RNA_interference
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TOSG
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PostPosted: Thu Jul 12, 2007 7:05 am    Post subject: Reply with quote

fan wrote:
I think you're trying to describe RNAi for some sci-fi application.
http://en.wikipedia.org/wiki/RNA_interference


It's not RNAi. RNAi involves uptake of double-stranded RNA, and the subsequent cellular destruction of the gene that codes for that RNA, as a result.

This simply suggests that the single-stranded complementary strand is being injected, and binding to (and inactivating) the active ribozyme.

I've got to run, but I can elaborate on this later if people are still unclear.
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suze900
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PostPosted: Thu Jul 12, 2007 7:31 am    Post subject: Reply with quote

Awesome! I salute you, Kelly, Marla, and everybody who worked on solving this
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wordfish
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PostPosted: Thu Jul 12, 2007 10:33 am    Post subject: Reply with quote

there was no smiley to accurately express how in awe i am of all you smarty pantses.

i figured this one would have to do.

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Angelheart
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PostPosted: Thu Jul 12, 2007 4:07 pm    Post subject: Almost got it... Reply with quote

TOSG has done a wonderful job on decifering the main message and then putting this scientific problem solving into everyday language for all of us. **Major props 2 U !**

As far as actually solving Isaac's paperwork word for word i've almost got the solution... who knows if there's more patterns or clues hiding within the completed text. Word(s) with ** around them are logical guesses (from my own biology and chemistry background studies) that were not as obvious as say filling in (Bree) on fact 1. Hopefully more people with more sofisticated software than "paint' are able to figure out the really smeared words on the bottom section.

The Bree Solution

Objective:
How to transform Bree from TRAIT: POSITIVE to TRAIT: NEGATIVE

Given Facts:
1) Bree's blood contains a special ribozyme mutated and unique only to her.
2)*The gene* for said ribozyme has a *regulatory* hyper-mutation that changes with every generation.
3)A non-functioning *portion of* ribozyme exists and manifests differently in every Hymn of One girl.
4)This portion still functions, but you cannot *blend it* because the complimentary strand of RNA won't combine.

Theoretical Solution:
1) Block the ribozyme in question by obtaining a sample of that same ribozyme in order *blood* (this could be quite off, there is only smearing to assume the second line finishes underneath THE of the first line)
2)Create a ciomplimentary strand of RNA
3)Q.E.D.: Strand will bind to ribosyme and occlude its *....y*

Practical Solution:
1)Obtain blood sample of Bree's
2)Synthesize complimentary strand of RNA
3)Inject Bree with this complimentary strand
4)Q.E.D.: Ribozymes blocked rendered innefectual

Intended Results:
1)Once synthesized and injected into Bree, she will become TRAIT: NEGATIVE
2) Additional consequences (if any) - TBD (to be discovered)

..... Reference Points:
............................ing Ribozyme Function
...........................ted - tRNA cleavage
......................correlated - Intron/Exon splice
....................................- Telomere synthesis
........ribozyme mutated - fructose-6-phosphate pathway


~*Angelheart*~
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dorothyann07
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PostPosted: Thu Jul 12, 2007 6:09 pm    Post subject: Reply with quote

TOSG wrote:

And, this theory may even suggest a reason for the purity bond. As noted in Given Fact #2, the mutation in the regulatory element changes with every generation – it may be possible that if Bree were to have children, the ribozyme would be further destabilized, perhaps becoming uncontrollably active . Because we do not know the function of the ribozyme, we do not know what the consequences of this would be, but given its importance to the Hymn of One, the danger could be vast.


Okay... so I watched the latest video and when Taylor said maybe she had already made herself trait negative by breaking the purity bond and Spencer said you couldn't change DNA by just performing the act. That had me thinking.... Then I come on here to find the papers and see that they're already figured out. I quoted TOSG because again, something stuck out to me (which is in bold). I am by no means trying to sound like a perv. But I just kinda wanted to throw something out there. All this info is leading to something, obviously.. lol. But maybe Bree isn't completely ignorant to what is going on here. What if she's trying to find more information in the order to break it up, or to find Jonas's parents. But she needs to be in with them to find that out instead of running from them. Okay, my mind is going like crazy on the things that could be happening. I know all of this is a GUESS.. prediction as to what is going on. I could be completely wrong. But I just wanna keep going with my thoughts. You can say I'm crazy.... but the 'events' aren't always that believable. Anyways, back on topic. Maybe Bree is pretending to be "brainwashed" by the order to get inside to find out more information that they couldn't find out on the outside just running. Maybe she's working with the mule. Like I mentioned before, remember how she promised to help find Jonas's parents? Maybe when she talked to Lucy the day she left she realized that she wouldn't be able to find out anything without being on the inside.
And you're thinking, why not tell the guys this?? The answer is why tell them? They pretty much tell us everything through here, which would get back to the order. So she had to keep them out on this so she could do her "secret mission" .. Anyways, so what if time is running out and the ceremony is coming up. Then she knows she has to take quick actions, like breaking her purity bond. What if it was planned by her and another person inside the order helping her to let them know where she was going to be that day for them to come get her. But she has to act like she didn't want to be there so it wouldnt blow her cover. And then she knew she had to break her purity bond with someone.. why not Jonas.. they do have a bond. So maybe in 9 months.. we'll have a little B&J baby Wink I dont know for sure.. it all sounds kinda crazy to me in my head. but still kinda possible to fit the crazy 'events' that have already happened.
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TOSG
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PostPosted: Fri Jul 13, 2007 5:26 pm    Post subject: Reply with quote

Check out the video that Marla made, presenting this theory much more coherently Smile

http://www.youtube.com/watch?v=FaCMKEVh1HY
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stevemedigod
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PostPosted: Sat Jul 14, 2007 3:07 am    Post subject: Reply with quote

Nice job TOSG, Marla, Kelly.

The part I'm unsure of is how will they isolate the ribozyme from the blood? A blood sample will have plenty of RNA molecules unrelated to this ribozyme, so they need to be able to distinguish the correct RNAs from all the other naturally occurring molecules. So we need other information (possibly in the papers from Dr. Gilman?) that gives us either some actual sequence information for the ribozyme, or tells us what its biochemical activity is.
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PostPosted: Sat Jul 14, 2007 8:36 am    Post subject: Reply with quote

Steve - absolutely. We need to find out what exactly the trait IS in order to isolate the ribozyme. Hopefully what information was given last night will be just that.
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kellylen
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PostPosted: Sat Jul 14, 2007 8:38 am    Post subject: Reply with quote

well marla not much info was given in the video. unless danny was told more. or if it is a drop there would be stuff in the box
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PostPosted: Sat Jul 14, 2007 8:57 am    Post subject: Reply with quote

droppppp.
who is in LA?

GO! NOW!
you are commanded.
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PostPosted: Sat Jul 14, 2007 9:10 am    Post subject: Reply with quote

I'll be there in 10 days....err....but i'm NOT going down a dark alleyway. Noooooo way.
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The Bree Solution.
http://one.revver.com/watch/330795

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thoughtssopoetic
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PostPosted: Sat Jul 14, 2007 9:25 am    Post subject: Reply with quote

marlasinger wrote:
I'll be there in 10 days....err....but i'm NOT going down a dark alleyway. Noooooo way.

Haha, I don't blame you, actually I wouldn't either.
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