"I haven’t been tracking the latest efforts on the part of computer virus writers, but if there was a computer analogy to this RNA-shuffling model, it would be a virus that distributes itself in the form of unlinked object code files plus a small helper program that, upon infection in a host, would first re-link its files in a random order before copying and redistributing itself. In addition to doing this, it would search for similar viruses that may already be infecting that computer, and it would on occasion link in object code with matching function templates from the other viruses. This re-arrangement and novel re-linking of the code itself would work to foil certain classes of anti-virus software that searches for virus signatures based on fixed code patterns. It would also cause a proliferation of a diverse set of viruses in the wild, with less predictable properties."
I was looking at the translation table provided in https://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Gene_expression_and_biochemistry.
I noticed that there are actually 66 codons of the form "UAG". While there should only have been 64, since 6 bit depth(3 * 2 bits per base pair. Sure enough starting working on finding the duplicates among those 66.
Cleaning up the table gave:
GCU
GCC
GCA
GCG
UGU
UGC
GAU
GAC
GAA
GAG
UUU
UUC
GGU
GGC
GGA
GGG
CAU
CAC
AUU
AUC
AUA
AAA
AAG
UUA
UUG
CUU
CUC
CUA
CUG
AUG
AAU
AAC
UAG
CCU
CCC
CCA
CCG
CAA
CAG
CGU
CGC
CGA
CGG
AGA
AGG
UCU
UCC
UCA
UCG
AGU
AGC
ACU
ACC
ACA
ACG
UGA
GUU
GUC
GUA
GUG
UGG
UAU
UAC
UAA
UAG
UGA
alb_d@XPS-13-9370:~$ cat temp | sort | uniq > list2
alb_d@XPS-13-9370:~$ cat temp | sort > list1
alb_d@XPS-13-9370:~$
alb_d@XPS-13-9370:~$
alb_d@XPS-13-9370:~$ diff list1 list2
52d51
< UAG
58d56
< UGA
Looking back at the table, both of them are marked asterisk with notes below saying:
- UAG is normally the amber stop codon, but in organisms containing the biological machinery encoded by the pylTSBCD cluster of genes the amino acid pyrrolysine will be incorporated.[8]
** UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a SECIS element is present.
🤦
Apparently we only discovered this multiplexing for the first time in 2009.
highly recommended!
Great Read!
Awesome read!
How weird is it that we have to understand our own machinery using analogies to something we have created. You would have expected it to be the other way round.
It is weird but it makes sense. We only understand the things we create and we (our conscious minds) didn't create ourselves. But we (our conscious minds) did create computers
"These genes are fundamental to the actual storage of the genome and are thus of paramount importance. Any failure in this code rapidly leads to a non-functioning organism.
So it is to be expected that this code isn’t tinkered with and that turns out the case. The H3 an H4 genes have a zero effective mutation rate in humans. But it goes far beyond that. You share almost the exact same code with anything from chickens to grass or molds."
"If we were to destroy all existing C compilers on the planet and leave only the code for one, we would be in great trouble. Yes, we have the C code to a C compiler, but we need a C compiler to compile it!
In actual fact, this was solved by not writing the first C compiler in C (duh), but in a language that was available already: B. See here for details about ‘bootstrapping’.
The same holds for the genome. To create a new ‘binary’ of a specimen, a living copy is required. The genome needs an elaborate toolchain in order to deliver a living thing. The code itself is impotent. This toolchain is commonly called ‘your parents’."
"It appears that RNA, which is an intermediate code between DNA and a protein, may have been the ‘B’ for DNA. Which begs the question where RNA came from. It is very interesting to note that extra-terrestrial objects often contain amino acids!"