Something New(ton)?

Question

Recognized as one of the most brilliant scientists of all time, Sir Isaac Newton was always ahead of his time.
On the cusp of something brilliant, late in 1704, he had the idea to send you a coded question.
You might wonder how Newton could send you a message 300-plus years into the future?
Good question.
But let me explain: he was a genius.
I cannot give you all the details, but I can point you in the right direction.
Verified for me, by a Newton scholar, I present to you the coded question Newton intended for you to answer.

P.S. - Oh good, I did not inhibit. Ever get near a rabid otter?

Checksum thing: 6F,35,09,43,04,0D,5D,55,5D,07,04,3D,0F,04,2D,67,04,66,3E,06,47,15,17,7A

 

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Cryptic Clue:
An encoding scheme is a container ends like a yellow bird

Hint:

Edited the introductory paragraph to put the starting point out in the open though I doubt that's what is holding someone back.

Bigger Hint:

Newton holds the key once you've converted his color bar message to the correct format. PS - Don't forget.

One More:

Newton had to take a bite a bit smaller than you normally might. It seems it was a little tight to try and transmit it through the light.

Answer 1

The question Newton is asking is

What color is at 490 THz?

And the the answer is

Orange

I arrived at this answer by applying the following rules to transform the binary for each hex color value:

1) The first digit is always zero. 2) The eighth digit becomes the second. 3) The third digit is always one. 4) The seventh digit becomes the fourth. 5) The fourth digit becomes the fifth. 6) The second digit becomes the sixth. 7) The third digit becomes the seventh, in reverse order from top to bottom. 8) The fifth digit becomes the eighth. This transformation scheme was derived from the transformation from ROYGBIV -> BIGVOYR (comparing the original illustration to the one included in this puzzle). Apply ASCII encoding to the new binary stream to produce the final text.

Here's a screenshot of the transformation:

Answer 2

Partial Attempt. Hope it helps others working on this one...

Findings

Taking first letter of each line of the first paragraph gives - ROYGBIV


Recognized as one of the most brilliant scientists of all time, Sir Isaac Newton was always ahead of his time.
On the cusp of something brilliant, late in 1704, he had the idea to send you a coded question.
You might wonder how Newton could send you a message 300-plus years into the future?
Good question.
But let me explain: he was a genius.
I cannot give you all the details, but I can point you in the right direction.
Verified for me, by a Newton scholar, I present to you the coded question Newton intended for you to answer.

Taking the first letters of the P.S gives - reversed ORANGE INDIGO
Oh good, I did not inhibit. Ever get near a rabid otter?

Cryptic Clue:

An encoding scheme is a container ends like a yellow bird - Container(Bin) ends like a yellow bird(canary-ARY) gives - > BINARY
So, this may indicate that the hex codes need to be translated to binary. And then may be binary to decimal which will reveal the letters to be used.

Hence,

We need to take the Hex string and convert it into binary. Doing it, we get
6F - 1101111
35 - 0110101
09 - 0001001
43 - 1000011
04 - 0000100
0D - 0001101
5D - 1011101
55 - 1010101
5D - 1011101
07 - 0000111
04 - 0000100
3D - 0111101
0F - 0001111
04 - 0000100
2D - 0101101
67 - 1100111
04 - 0000100
66 - 1100110
3E - 0111110
06 - 0000110
47 - 1000111
15 - 0010101
17 - 0010111
7A - 1111010

So, going with the hint we get -

Removing one bit from the start i.e. 0 we get ->
6F - 01101111 -> o
35 - 00110101 -> 5
09 - 00001001
43 - 01000011 -> C
04 - 00000100
0D - 00001101
5D - 01011101 -> ]
55 - 01010101 -> U
5D - 01011101 -> ]
07 - 00000111
04 - 00000100
3D - 00111101 -> =
0F - 00001111
04 - 00000100
2D - 00101101 -> -
67 - 01100111 -> g
04 - 00000100
66 - 01100110 -> f
3E - 00111110 -> >
06 - 00000110
47 - 01000111 -> G
15 - 00010101
17 - 00010111
7A - 01111010 -> z

Hence we get ->

o5C]U]=-gf>Gz This might be an encrypted text which needs to be decoded using the key as NEWTON. Or may be the colors have something to do with this.

Answer 3

Not an answer, but a wrap-up from the OP

Here's my explanation for the entire puzzle:

I first envisioned this puzzle a couple years ago, but didn't really have a place to post it, until I stumbled upon this section of SE.

The idea was that Sir Isaac Newton would send you a message through his optics experiment, but when passing 7-bit binary through the prism, he could have various columnar transpositions of the encryption space.

To add to the challenge, I didn't simply want to create a columnar transposition, but also alter two of the "channels" of the transmission.

Newton "held" the key to the transposition arrangement (ROYGBIV -> BIGVOYR). Since I wasn't sure anyone would interpret Indigo as a color I made sure to reference his 1704 work (Opticks), as well as started each sentence with the letters ROYGBIV to define the transposition space.
To reinforce the fact that the transmission took place through the 7 colors, I also explicitly used INDIGO in one of the twists found in the odd-reading PS - along with ORANGE.

From the encryption standpoint, I took the 7-bit binary encoding, and transposed it according to my key (BIGVOYR), and then also reversed the ORANGE and INDIGO bit streams before re-interpreting the output on the other side of the prism as a stream of colors. The checksum was added both to clarify which colors were in play and thus their binary interpretations. It also served to show that groups of two hex values would be used together.