I think instead of trying to make completely new design, let’s try to recreate some of the nature’s RNA.
At the end of a lab challenge you reveal how the nature solved the puzzle. This will be of great help and new hypothesis will rise.
I like it!
How do we prevent people from looking up the “right” answer and circulating the link to it?
The challenge puzzles all come from known sequences, so in a sense you are already doing this!! you just haven’t been shown the naturally occurring answer.
But I think the goal of the game is to go beyond the information that has already been mined from existing sequences and structures as that has only gotten us so far. There’s a danger that if people think the goal is to get the naturally occurring answer when in fact its to find better ones, the creativity in proposed solutions will go down.
Lastly, I’ll point out that most RNA’s have day jobs which requires them to have certain conserved sequences at certain places to regulate our cell’s biochemistry, restraints we don’t have when we are just designing them to hold a certain target shape.
Simultaneously, it also means that seeing how nature designed some of these sequences may not be as helpful as you hope. On one end of the spectrum, there are some protein mRNA’s in the puzzles. Nature can’t mess with those sequences if it will affect the function of the protein it codes for in a bad way, and in those cases it’s the protein shape, not the RNA shape that is being selected for naturally, Whatever shape the RNA happens to take when its just a dumb information carrier is just serendiptous. On the other end there are viral RNA’s whose only job is just to hold a very particular shape to act as a scaffold for something else to hold on to, and in those cases the naturally occurring answers could indeed be interesting to compare to like you imagine.
I totally agree with you on protein coding mRNA, but when i wrote this i had in mind functional RNAs such as tRNA or MicroRNA where the structure gives it’s functionality.
This idea only applies for the lab, where you are struggling to design a molecule that best performs in therm of nature’s rules. Many discussions from the Lab are on theories about what it is the best metric for a lab design. Thus by trying to copy a nature structure you are faced with the same challenges nature had had to solve. At the end of a Lab challenge (after all the round) when the nature structure is revealed, you can see then what tricks nature had to pull to stabilize the structure.
I think that by using a structure that is not easy to find on the internet or by using an unpublished structure.