In several of the Lab challenges, there are illegal loops and/or illegal sequences (5 As, say), where all the bases involved are locked. What is the strategy for dealing with such issues?
The lab is running on an energy model. It is an estimate, but not the exact truth about how the RNA will fold. We are investigating the difference between what the energy model allows versus what nature allows. We got allowed to override some of the constraints that the energy model puts on us, exactly for us to better figure how RNA really behaves. Both the players proposing the labs and those solving them, are to some extent allowed to break the constraints.
We have had labs where we have seen non complementary bases base pair, when we get the lab results back, though the energy model says the area is unstable. Those pairs do also exist in nature, though they are usually much weaker than the base pairs GC and AU, that we know from in game.
For the locked sequences, there is nothing you can do to change them. They are locked because the one proposing the lab has an intent with them. Sometimes you can make changes in the surroundings to make them stable, but this is not always possible.
So the best you can do is to accept that you can’t always make everything stable, but do what you think has a shot of working and you can submit despite the energy model says it is unstable.
We have through the time seen lots of winners that the energy model says is unstable and will not fold correct, but that nature (the test tube version of it) let pass none the less. Testing the limits allows us to get wiser on what really works, so we with time can help the scientists make better models for how RNA behaves.
Thanks, that makes sense. I wonder if it would be good to add this to the FAQ and/or the intro/tutorial to doing Lab puzzles? Maybe it’s there already and I just missed it. Thanks again.
Migdalin, np. Glad it makes sense now and a good question.
There is only a minor note on this in the FAQ. There is a bit about it a lab guide but not enough. I will add some more there. But it is a really good idea getting some more about this into the FAQ.
Also I’m dreaming of us getting some more tutorial making tools, like adding text in the puzzles and highlighting, so it will one day be possible to get some lab tutorials made as well.
Lab tuts are planned (one of the higher things on the list, though postponed ATM), and the use of the Flash tutorial tools has been noted, though they need to find someone available to work on it (as you may well know, our team is tiny).
Good to know that they are planned. I know the team is small, so I’m just dreaming aloud on behalf of the future. With these tools in player hands too, it would widely increase the amount of tutorials at hand.
I’m sure there sits players out there with good ideas for how to make lab tutorials, when we get the tool. Especially when thinking about how many puzzles and tutorial puzzles we have already made.
So hereby I just pass on the idea: Feel free to dream about how you want to make a lab tutorial, in the mean time…