# A puzzle inspired by "Cryptobiology? Biocryptology?"

This puzzle is a "look-alike" of the puzzle Cryptobiology? Biocryptology? but is different at its core. I was convinced that the other puzzle was trying to go in one direction, but after fruitlessly trying solutions targeted in that direction on that puzzle I threw my hands up and rewrote the puzzle as if it were. The setting of the puzzle and the hint provided are both shamelessly stolen.

Find the hidden message:

4413441•4421322442344414441433141•1141431211 || 431424434214•3422134142214111•113324311121422411241144431

The message is the answer to "What is the name of a long-ago-established (contested at the time) theory in biology?"

Also, 1 < 2 < 3 < 4, but figuring out what to do with this information is a weighty task.

The person who came up with this puzzle is a mediocre biologist, but they are a better biologist than they are a cryptologist!

Hint:

This hint is not required to solve the puzzle, it may help put you on the right direction.

They told me "You silly biochemist, to get you started, consider the amino acids and apply their strategy in your strategy. Or consider the behavior of those nucleobases you're talking about."

Another hint:

The message is hidden in the department of transportations

• I lied. I'm finding things. May 5, 2016 at 13:25
• Sounds like you are close. May 5, 2016 at 16:05

Building from SendersReagent:

You can basically use the part of the sequence after "||" as a complement to the first part, where 1 pairs with 4 and 2 pairs with 3:

If you treat the dots as:

missing bits of sequence, you can fill them in based on the complementary strand where 1 pairs with 4 and 2 pairs with 3. Then you unfold the entire strand again, and take just the numbers that were dots to begin with.

And based on the hint:

I think we probably have to assume that the numbers 1-4 stand for DNA or RNA bases in order of weight, which means:

C=1, T=2, A=3, G=4

So converting the numbers gives:

AAC GAG TGA ACT CGG GCC CTA

And then using the Amino Acid code gives:

N E * T R A L

So the controversial-at-the-time theory in biology is the idea of:

Neutral evolution which posits that much of the change in species over time comes from random mutations and genetic drift, rather than natural selection.

• Getting warmer. Perhaps it would be good at this step to try to figure out what the dots mean? May 10, 2016 at 3:16
• How do you know it's not {1=A, 2=C, 3=G, 4=T} or {1=T, 2=G, 3=C, 4=A}, etc? What do you mean "in order of weight"? May 10, 2016 at 7:04
• I originally assumed that it was alphabetical, A < C < G < T, but OP changed the wording of the hint to point towards weight, and different nucleotides have slightly different molecular weights. May 10, 2016 at 15:08
• While not needed to guess the message, the * can code for en.wikipedia.org/wiki/Selenocysteine May 13, 2016 at 20:32
• Oh, atypical proteinogenic amino acids! Silly gooses. May 14, 2016 at 20:29

These are essentially just my notes for now. On Android, needed to save them anyway, and figured this way, everyone else could see what what I was thinking. I'm laying down, so I needed to save them somehow.

4413441•4421322442344414441433141•1141431211 || 431424434214•3422134142214111•113324311121422411241144431

Working through using RNAi?

4413441• 1142114

442132244
113423311

234441

4441433141•
1114122414

•114

1431211
•4124344

43142

•342213
121422
44431

234441, •114, 43142, •342213, 121422, 44431
TAG GGC •CC GGA CGT •AG TTC ACT CGT TGG GAC

Or maybe

T ≈ U
GCAAAT TTA ACTAG CAG TC TGTAGG AAACT

Or maybe it's one of the other strings...

4113441•; 442132244; 4441433141•; 1431211

Or

1142114; 113423311•; 1114122414; •4124344

Or one of the things backwards.

I'm having a hard time getting any of these to mean anything, though.

• Definitely on the right track. May 5, 2016 at 19:10
• I'll say some more: So far, you haven't used the "1 < 2 < 3 < 4" bit. Finally, one hint: Your next step may require thinking backwards. May 5, 2016 at 19:35
• The question as posed expected you to try a few possible interpretations for "1 < 2 < 3 < 4" I've decided this is a bit mean. Question updated to give you a direct way to resolve this. May 10, 2016 at 0:50
• Hmmm... I was afraid you were going to make it too east with that, but I like it. I'll give'r a shot, I thought you just meant A=1, C=2, etc. i.e. 1 is the earlier number, making it "less" than 4, which is the latest letter in the alphabet. Still working. Just wanted to make my notes thus far look a bit nicer. May 10, 2016 at 0:56

Building on @DanRussels work, still no solution:

The dots

Assume the dots are missing pieces. Then, we can reconstruct almost everything, except the part that has 312243 in the bottom part, and 114 in the top part. Which means there might be something missing from both parts here, which could explain why the length (64) isn't divisible by 3. So, the complete string is probably
134 441 142 114 224 121 113 423 311 321 114 111 412 241 431 224 3* 441 412 434 424 134.

Matching numbers to bases

Next, note that the string begins and ends in 134. This might be a start/stop codon. From https://en.wikipedia.org/wiki/Genetic_code, this should be either UGA or UAG. So we want U to be 1, but the base with the lowest molar mass is C. (Replacing U with T doesn't change this fact; C has 111, U has 112, T has 126; next is A with 135 and G with 151). However, when checking the densities, U/T is actually lower than C - T has 1.230, U 1.320, C 1.550, A 1.600, G 2.200. So let's assume 1 is U, 2 is C, 3 is A, 4 is G. Now we get
UAG GGU UGC UUG CCG UCU UUA GCA AUU ACU UUG UUU GUC CGU GAU CCG A* GGU GUC GAG GCG UAG.

Bases to letters

Every triplet has an amino acid it encodes; these acids have letters as abbreviations. So let's replace the triplets with letters. Unfortunately, this results in
_ G C L P S L A I T L F V R D P ? G V E A _

So, let's discount the idea of a start/stop codon for a moment, and swap U with C, using molecular weights instead of densities. Now we get
134 441 142 114 224 121 113 423 311 321 114 111 412 241 431 224 3* 441 412 434 424 134
CAG GGC CGU CCG UUG CUC CCA GUA ACC AUC CCG CCC GCU UGC GAC UUG A* GGC GCU GAG GUG CAG
Q G R P L L P V T I P P A C D L G A E V Q