Sunday, July 17, 2022

Junk DNA R Us - 4

Which one is it?

One long-time controversy in genomics is what has been called "codon usage bias", or CUB (Junk DNA R Us - 3).

When we think of what is meant by the word "bias" our conclusion will be based on various types of analysis.

After all the word has more than one meaning (Meriam-Webster Dictionary). 

Microbes probably don't have dictionaries to look-up the meaning of bias, so their supposed bias is more likely than not scientists playing with the Frankenstein dolls again.

Regular readers will remember that Dredd Blog has focused on some of the characteristics of codons in DNA and RNA in terms of quantum mechanics in previous posts.

For example, in the sense of atom counts per codon type see (Quantum Biology - 5, at Appendix One and Appendix Two).

For another example, there are lists by chromosome (Quantum Biology - 6).

But those do not focus on "bias", so to assist readers with contemplating and focusing on what this "bias" is all about, today I have included two appendices which show codon locations in an Omicron variant (Appendix One) and a non-variant SARS-CoV-2 (Appendix Two).

To get what they are talking about when they mention "bias" notice that some of the codons are located in twice or so more places in the virus genome than other codons are.

They hypothesize that microscopic organisms (microbes) are biased and therefore like voters at the polls, they make biased choices:

"A similar genetic code is used by most organisms on Earth [they have a code book they use like our zip codes?]" ... "different organisms have different preferences for the codons they use [those dolls are sooo choosy aren't they?]" ... "Evolutionary constraints have molded which codons are used preferentially in which organisms - organisms have codon usage bias. [they finger the perpetrator as 'evolutionary constraints' then blame it on the organism itself instead of the perpetrator]" ... "you might think it’s easy to come up with a workable DNA sequence to encode your peptide of interest and produce that peptide in your organism of choice. [when you get ready to make your own frankenstein organism, don't get all puffy about it] Unfortunately, codon preferences make it so you cannot choose among the possible codons at random and expect your sequence to express well in any organism [its hard for human frankenstein makers not to be biased and we don't really know why the microscopic organisms are that way]" ... "The reasons for varied codon preferences among organisms aren’t completely understood [they are smarter than us when it comes to quantum biology and know how to 'bias' better than we do]" ...

(Plasmids 101: Codon usage bias, [my comments in brackets]). We don't know "is an embarrassment" according to the scientist featured in the first video below.

There are many embarrassments that finger biologists as metaphorically playing with dolls while practicing teleology:

"When organic chemists anthropomorphize molecules, they say that moleculeswant to be in their lowest energy conformation”. This means that when they have energy molecules can move into different conformations, but they have a resting position that they come back to."

(On The Origin of Genieology - 2). Got teleology? Got conjuration?  

Plasmid lovers mutating into 'mother nature' ("what could possibly go wrong?")?!

In a future post I plan to discuss the atomic-level application of Löwdin's hypothesis in greater detail because it is non-teleological.

The previous post in this series is here.