The XOR Collective Challenge

Gameplay and Strategies
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XOR Collective Clarity Challenge

The Question:   Can we collectively see with sharper clarity and create design solutions more efficiently than by ourselves?

This challenge is open to ALL eterna members who have not already resolved The real XOR Challenge.

https://eternagame.org/web/puzzle/6096060/

The Challenge:   Collectively resolve the XOR Challenge using this getsatisfaction discussion site to combine our unique ways of seeing, methods and experiments.

On this board please read and, as clearly as possible, express your questions, views, and approaches to designing The real XOR Challenge solution.

This experiment’s goal is to see if we can solve the XOR Challenge Puzzle more elegantly and with more clarity as a result of our working together rather than apart.

Please do not share the solution if you find one.  This site is meant to strictly focus on process.

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Thanks Gerry, while I had the mutation/submission booster do the finishing touch I believe I have some good advice. while having both olegoes bound in state 4 I used UGGGU to disrupt the ms2 sequence. also i has olego1 on one side, olego 2 on the other and the ms2 in the middle.used mutations on the left side of the ms2 to disrupt.

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Thanks Astro!  

I woke up this AM and was wondering how we could share imagined solutions.  I thought a good first step would be to simply highlight areas that we envision binding…like the below example. 

So I envision in State 4, these two highlighted segments binding together.  At the bottom, I have also highlighted that I have Natural State turned on so I can see when those segments bind.  And also at the top, I have the Delta number highlighted because I imagine how strong that binding is might also be important…

Can you find the solution for this partial?  Fast ways to share our thinking in digestible steps to all keep on the same page is important if we are to move ahead and create as one.

Again, I have no idea how to solve this puzzle.

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I think something you should consider Gerry is that these are constraint driven puzzles, and designing sequences/structures that solve the constraints. For example, state 4 requires that the MS2 hairpin not form, while the two oligos must bind to the RNA. That means that you have two constraints you have to fulfill in state 4, but there is a limitation:

  • Distant sequences in your RNA cannot base pair across an oligo bound to the RNA. 
    This means in state 4 it requires the sequence that turns off the MS2 hairpin to be ‘close’ to the MS2 hairpin. This gives space for your oligos to be bound to the RNA while turning off the MS2 hairpin.

Then, you have to consider the constraints in states 2 and 3. Here, 1 oligo is bound, and the MS2 hairpin is ON. Which means that the sequence that turns OFF the MS2 hairpin has to be turned off in states 2 and 3 to turn ON the MS2 hairpin.

Then, state 1 is an OFF MS2 with no oligos, and that ends up being the state where you need to turn off the MS2 through a different pathway, or turn off the sequence that turns on the off state of the MS2.

Granted, there are other solutions to this XOR architecture, but you are ultimately limited by the position of the MS2 hairpin and the length of the RNA.

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ive been trying to solve this monster for months, this might be helpful.

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also, use the mutation/submission, that is helpful, try doing it on 69-81

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correction, 69-76

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With our goal here being to accelerate eterna community’s ability to innovate, we do not want to tread existing paths.  Nothing unexpected would arise from that.

So immediately taking what collective views have been offered, I have experimented using my fuzzy understanding.  Here is what I have come back with.

I used Broud’s guidance of needing a sequence close to MS2.  I place this and his other guidance high in my thought process given I know he has a deep understanding of the science and this particular design.  Note that he has left a lot of space for me to bring my own approach…and I will use that.

Second, I used a first step that I heard Astromon explaining to another player because I also know he is skilled at this.  He said in State 4 to create a sequence that disrupts the oligo at the top right (110-131) 

And third, will use Jaxon’s idea of using mutation tool selecting 4 NT’s to test to find new interesting patterns to follow.  The initial patterns that looked interesting to me relate to which of the 6 top constraint boxes were resolved.

We start with the first 4 of the 6 constraints resolved.   Using the first three steps above, it is easy to  to resolve 1,4,5,and 6.  So those two resolution patterns are basic.

The two resolution patterns I found more unusual were resolving 1,3,4,5 and resolving 1,2,4, 6.
Additionally, I think selecting 4 NT’s to mutate that cause many constraint fluctuations back and forth between these two more unusual constraint patterns means that I might be closer to creating design resolution.

Here is the lowest delta sequence that resolves 1,3,4,5:
  UCAGGAACUGUCAACGCUUUAAAAAAAAAAAAAACAUGAGGAUCACCCAUGUAUGGUGAAAAAAAAAAAAAAAUUCGAAAAAAAA

Here is closely related sequence that resolves 1,2,4,6:

UCAGGAACUGUCAACGCUUGGGAAAAAAAAAAAACAUGAGGAUCACCCAUGUAUGGUGAAAAAAAAAAAAAAAUUCGAAAAAAAA

Additionally, I have found 4 NT’s that cause many fluctuations back and forth between these two more unusual constraint patterns.

This is currently where I am at.

Employing more immediacy in our interactions by sharing what strikes us in the moment, especially when we don’t know how those views fit in, will expand our community’s ability to innovate.

Please share what strikes you.

  

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Let’s name the two above sequences A and B.

Which one of these has the most single mutation options to change it to the other constraint pattern?

Sequence A has only 1 mutation that can switch it to B’s constraint pattern.  Mutating 17 from C to G.

Sequence B has 4 mutations that can switch it to A’s constraint pattern.  Mutating 14 from A to C, 14 from A to U, 19 from U to G and 75 from U to G.

 

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The main critique I would have right now is that you’re not using both oligos binding to the RNA for your solution. You’re on the right track on thinking about the constraints, but your unfolding of the MS2 hairpin is only for the closing base pair in the second state, which is fine (some of the 31 solutions solve it by doing this. It’s essentially cheating but whatever), but you still need to use both oligos to drive the folding/unfolding of your RNA. You’ll never get anywhere trying to get your RNA to change its structures on its own. To put it in perspective, your RNA has a minima, and its not going to lift itself out of a minima (much like lifting yourself while standing in a bucket). An external force is required to do the lifting, and that external force is the oligos binding to sequences on your RNA.

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What creates and sustains the most energy/momentum for our eterna community is not individual learning.  It is the the rapid interactive firings that occur across groups of us.  We are each an eterna neuron and those interactive firings across our connections/synapses create eterna consciousness.  One firing does little.  But if we can trigger connected awareness and firings across groups of neurons, then we create movement of the whole body.

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I recall being able to highlight a series of bases using the shift drag key. Then pressing the right arrow key while holding shift would shift all the highlighted bases to the right. This is while using the 1 state only.  That does not work for me anymore. Am I doing something wrong?

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whbob - I had exactly the same question and experience. 

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I just went back to the TB Labs and tried it. It doesn’t work there anymore either.
Maybe something changed with the enhancements they are making to the game?

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@Gerry: I just spoke with LFP6 in slack and he is going to look into it. If we can get it back working your collaborations will hopefully get a boost:)