From Morse code to Hellschreiber human eyes and ears have shown to perform as good or better than algorythms and faster.
To show what I mean here are two examples of musically interpreting the HBV.
5.4 MB May 8 12:07 plain-mRNA.mp3
plain-mRNA.mp3
1 (0) AUU (C F F) (1) AAA (C C C)
6 Intron 980 -1 (c) 29895
12 (0) AUA (C F C) (0) CCU (D D F) (1) UCC (F D D) (1) CAG (D C E)
22 Intron 80 232 (a) 29879
28 (1) CAA (D C C) (0) ACC (C D D) (1) AAC (C C D) (1) CAA (D C C)
40 (0) CUU (D F F) (1) UCG (F D E) (0) AUC (C F D)
48 Riboswitch (c) 31 ACCAA CCAAC UUUCG AUCUC UUGUA GAUCU
49 (1) UCU (F D F) (1) UGU (F E F) (0) AGA (C E C) (1) UCU (F D F)
61 (0) GUU (E F F)
64 Riboswitch (a) 51 UUGUA GAUCU GUUCU CUAAA CGAAC UUUAA
64 (0) CUC (D F D)
67 STOP (a)
67 (1) UAA (F C C) (0) ACG (C D E) (1) AAC (C C D) (0) UUU (F F F)
79 (1) AAA (C C C) (0) AUC (C F D) (1) UGU (F E F) (0) GUG (E F E)
91 (0) GCU (E D F) (0) GUC (E F D) (0) ACU (C D F) (0) CGG (D E E)
103 (0) CUG (D F E) (1) CAU (D C F)
107 START (b)
107 (0) AUG (C F E) (0) CUU (D F F) (0) AGU (C E F) (0) GCA (E D C)
119 (0) CUC (D F D) (0) ACG (C D E) (1) CAG (D C E) (1) UAU (F C F)
131 (1) AAU (C C F)
134 STOP (b)
134 (1) UAA (F C C) (1) UAA (F C C) (0) CUA (D F C) (0) AUU (C F F)
146 (0) ACU (C D F) (0) GUC (E F D) (0) GUU (E F F) (3) GAC (E C D)
158 (0) AGG (C E E) (0) ACA (C D C) (0) CGA (D E C) (0) GUA (E F C)
170 (0) ACU (C D F) (0) CGU (D E F) (0) CUA (D F C) (1) UCU (F D F)
182 (1) UCU (F D F) (0) GCA (E D C) (0) GGC (E E D) (1) UGC (F E D)
194 (0) UUA (F F C) (0) CGG (D E E) (0) UUU (F F F) (0) CGU (D E F)
206 (0) CCG (D D E) (1) UGU (F E F) (1) UGC (F E D) (0) AGC (C E D)
218 (0) CGA (D E C) (1) UCA (F D C) (1) UCA (F D C) (0) GCA (E D C)
230 (1) CAU (D C F) (0) CUA (D F C)
235 Intron 663 878 (a) 29666
241 (0) CGU (D E F) (0) CCG (D D E) (0) GGU (E E F) (0) GUG (E F E)
253 (0) ACC (C D D) (3) GAA (E C C)
259 Intron 555 286 (a) 29642
2.3 MB May 9 20:31 Amino-Acid.mp3
Amino-Acid.mp3 Amino-Acid-Rev.mp3 created with rna-nuc.c
468 START (c)
468 (34) AUG (C F E) (46) UGU (F#6:C#6:A#6) (41) UCA (F#5:D5::B5) (41) UCA (F#5:D5::B5)
480 (45) AAC (D6::A5::F#6) (35) GUU (E F F) (53) CGG (E6..G#6.C#6) (34) AUG (C F E)
492 (32) CUC (D F D) (62) GAA (E6,,A5,,C#6) (32) CUG (D F E) (51) CAC (A5..D6..F#5)
504 (32) CUC (D F D) (34) AUG (C F E) (35) GUC (E F D) (34) AUG (C F E)
516 (32) UUA (F F C) (46) UGG (F#6:C#6:A#6) (32) UUG (F F E) (41) AGC (F#5:D5::B5)
528 (46) UGG (F#6:C#6:A#6)
531 STOP (c)
594 START (c)
594 (34) AUG (C F E) (46) UGG (F#6:C#6:A#6) (37) GCG (E D E) (52) AAA (C6..F6..A5)
606 (43) UAC (D6::B5::G6) (44) CAG (B5::F#5:D#6) (46) UGG (F#6:C#6:A#6) (32) CUU (D F F)
618 (42) ACC (A#5:F#5:D#6) (37) GCA (E D C)
624 Intron 637 526 (c) 29277
630 (31) UUC (F F D) (31) UUC (F F D) (35) GUA (E F C) (53) AGA (E6..G#6.C#6)
642 (42) ACG (A#5:F#5:D#6) (35) GUA (E F C) (33) AUA (C F C) (52) AAG (C6..F6..A5)
654 (81) GAG (E C E) (32) CUG (D F E) (35) GUG (E F E) (37) GCC (E D D)
666 (33) AUA (C F C) (35) GUU (E F F) (42) ACG (A#5:F#5:D#6) (37) GCG (E D E)
678 (36) CCG (D D E) (33) AUC (C F D)
684 STOP (c)
901 START (a)
901 (34) AUG (C F E) (51) CAC (A5..D6..F#5) (31) UUU (F F F) (35) GUC (E F D)
913 (53) CGA (E6..G#6.C#6) (42) ACA (A#5:F#5:D#6) (42) ACU (A#5:F#5:D#6) (81) GGA (E E C)
925 (32) CUU (D F F) (43) UAU (D6::B5::G6) (38) UGA (F E C) (51) CAC (A5..D6..F#5)
937 STOP (a)
RNA is our memory but RNA is our ALU as well and how do I unmix them? or should I?
Assembly Language is not the right way to go, or is it? The trouble with many modern languages is the puristic separation of code from data. Microcontrollers even keep them apart from each other and the result is a beast that cannot have a debugger but is crippled by bugs.
Back to the roots languages like Lisp and Prolog go the other way. Code looks like data and of coarse you can compile your database and run it as a programme. How to read and process RNA? How does biology do it?
Does it happen or does it exist?
It is interesting to see two distinct names for the Virus and for the Desease. This is no mistake. People who made the distinction must have known Srong btsan Gampo.
RNA is it hardware or is it software? Taken RNA apart I see exons and I see introns. It looks like exons form the programme and introns build the processing hardware.
Exons look easy enough if it was not for slippery sequences were RNA decides with a free will how it wants to be decoded by ribosomes. But introns can be real bastards. Seeing the code for an intron can mean the end of this intron or the beginning of another one.
The most importang thing for HBV is to make a working copy of itself. But how does it do that?
With some 30 k bases or some 300 Lakh bases as they might say in Asia, this is a monster. It is bigger than DNA people like humans say it could be. What is the secreet. There are some proteins known to be able to copy a few snippets of RNA but 300 Lakh, no way.
Although a Touring machine might not need it I am looking for something like a loop structure or goto. Quantum computers do have a maybe and slippery sequence comes really close. With introns we can see something like a squirrel cage where a ribosom might be engaged to make an endless RNA.
Most important HBV needs to make a copy of itself. I do not know how biology does it but I guess making a negative by completing the RNA to form a double helix is a concept proven to work. Taking a lot of short cuts
does that. Read in an ".rna" file and write it from tail to head. The result is yet another ".rna" file and repeating the process results in the original again.
How does a ribosome know to skip over an intron and how does it know the next intron is the end of the code to skip or another intron included in the first one?
NC045512.fna: 1558 Intron 59 1004 (a) -28343
NC045512.fna.REV: -6905 Intron 878 59 (b) 22996
NC045512.fna.REV: -27676 Intron 139 878 (a) 2225
NC045512.fna: 15759 Intron 909 139 (c) -14142
NC045512.fna: 1573 Intron 958 718 (a) -28328
NC045512.fna.REV: -11246 Intron 870 958 (b) 18655
NC045512.fna: 14493 Intron 958 472 (c) -15408
One example how introns somehow seem to relate to introns in their mirrored copy. Here is how even more amzing the RNA looks at this location.
1431 START (c) AUG (C F E)
1431 (0) AUG (C F E) (1) AAU (C C F) (0) CUG (D F E) (0) GCU (E D F)
1443 (1) UGA (F E C) (1) AAA (C C C) (0) CCA (D D C) (0) UUC (F F D)
1455 (0) UUC (F F D) (0) GUA (E F C) (0) AGG (C E E) (0) GUG (E F E)
1467 (0) GUC (E F D) (0) GCA (E D C) (0) CUA (D F C) (0) UUG (F F E)
1479 (0) CCU (D D F) (0) UUG (F F E) (3) GAG (E C E) (0) GCU (E D F)
1491 (0) GUG (E F E) (1) UGU (F E F) (1) UCU (F D F)
1498 Riboswitch (a)
1481 UUUGG AGGCU GUGUG UUC-UC UUAUG UUGGU
1500 (0) CUU (D F F) (0) AUG (C F E) (0) UUG (F F E) (0) GUU (E F F)
1512 (0) GCC (E D D) (0) AUA (C F C) (0) ACA (C D C) (0) AGU (C E F)
1524 (0) GUG (E F E) (0) CCU (D D F) (0) AUU (C F F) (0) GGG (E E E)
1536 (0) UUC (F F D) (1) CAC (D C D) (0) GUG (E F E) (0) CUA (D F C)
1548 (0) GCG (E D E) (0) CUA (D F C) (0) ACA (C D C)
1557 STOP (c) UAG (F C E)
1558 Intron 59 1004 (a) 28343
1560 (0) GUU (E F F) (0) GUA (E F C) (0) ACC (C D D) (0) AUA (C F C)
1572 (1) CAG (D C E)
1573 Intron 958 718 (a) 28328
1575 (0) GUG (E F E) (0) UUG (F F E) (0) UUG (F F E) (3) GAG (E C E)
1587 (1) AAG (C C E)
1588 Intron 151 375 (a) 28313
1590 (0) GUU (E F F) (0) CCG (D D E) (1) AAG (C C E)
1597 Intron 61 167 (a) 28304
1599 (0) GUC (E F D) (0) UUA (F F C)
1605 START (c) AUG (C F E)
1605 (0) AUG (C F E) (0) ACA (C D C) (0) ACC (C D D) (0) UUC (F F D)
1617 (0) UUG (F F E) (1) AAA (C C C) (1) UAC (F C D) (1) UCC (F D D)
1629 (1) AAA (C C C) (1) AAG (C C E) (0) AGA (C E C) (1) AAG (C C E)
1641 (1) UCA (F D C) (0) ACA (C D C) (1) UCA (F D C) (0) AUA (C F C)
1653 (0) UUG (F F E) (0) UUG (F F E) (0) GUG (E F E) (0) ACU (C D F)
1651 UAUUG UUGGU GAC-UU UAAAC UUAAU GAAGA
1664 slip (b)
1665 (0) UUA (F F C) (1) AAC (C C D) (0) UUA (F F C) (0) AUG (C F E)
1677 (1) AAG (C C E) (0) AGA (C E C) (1) UCG (F D E) (0) CCA (D D C)
1689 (0) UUA (F F C) (0) UUU (F F F) (1) UGG (F E E) (1) CAU (D C F)
1701 (0) CUU (D F F) (0) UUU (F F F) (0) CUG (D F E) (0) CUU (D F F)
1713 (0) CCA (D D C) (1) CAA (D C C) (0) GUG (E F E) (0) CUU (D F F)
1725 (0) UUG (F F E) (1) UGG (F E E) (1) AAA (C C C) (0) CUG (D F E)
1737 (1) UGA (F E C) (1) AAG (C C E)
1664 (0) UUU (F F F) (1) AAA (C C C) (0) CUU (D F F) (1) AAU (C C F)
1676 (3) GAA (E C C) (3) GAG (E C E) (0) AUC (C F D) (0) GCC (E D D)
1688 (0) AUU (C F F) (0) AUU (C F F) (0) UUG (F F E) (0) GCA (E D C)
1700 (1) UCU (F D F) (0) UUU (F F F) (1) UCU (F D F) (0) GCU (E D F)
1712 (1) UCC (F D D) (0) ACA (C D C) (0) AGU (C E F) (0) GCU (E D F)
1724 (0) UUU (F F F) (0) GUG (E F E) (3) GAA (E C C) (0) ACU (C D F)
1736 (0) GUG (E F E) (1) AAA (C C C)
If I could touch the mRNA how would it feel like? Could I make it sound and how would that sound? Getting some ideas from J. S. Bach