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| Some of his best friends are germs. |
I. Background
I have complained to the powers that be at GenBank, to no avail, about bad nomenclature that does not adequately respect the difference between DNA and RNA .
Their position is that the rule that uses only a 'T' in genome sequence data for both DNA and RNA, representing the Thymine in DNA and the Uracil in RNA, was made long ago ("and we have been doing this for so long why change now?").
The following symbolic example shows that over a two and a half million atoms of difference exist in Paramagnetospirillum magneticum when comparing how a DNA count would compare to an RNA count, so, you can see that when a sequence contains only a 'T' for both both RNA and DNA , (instead of a 'T' for DNA and a 'U' for RNA), it is inadequate nomenclature.
But such radical differences do not persuade them, so, today's two examples are designed to underscore that fact:
| Atom Type | DNA Count | RNA Count | Difference |
| carbon | 23,214,275 | 22,350,299 | 863,976 |
| hydrogen | 25,699,551 | 23,971,599 | 1,727,952 |
| nitrogen | 19,001,047 | 19,001,047 | 0 |
| oxygen | 4,961,243 | 4,961,243 | 0 |
| Totals | 72,876,116 | 70,284,188 | 2,591,928 |
| Atom Type | DNA Count | RNA Count | Difference |
| carbon | 55,474 | 52,281 | 3,193 |
| hydrogen | 61,358 | 54,972 | 6,386 |
| nitrogen | 43,204 | 43,204 | 0 |
| oxygen | 11,695 | 11,695 | 0 |
| Totals | 171,731 | 162,152 | 9,579 |
The Paramagnetospirillum magneticum is a DNA genome while the Lariophagus distinguendus is an RNA genome.
The RNA Uracil and the DNA Thymine are both represented by a 'T' in the GenBank sequences linked to.
It would seem that a 2,591,928 or even a 9,579 atomic difference is enough to stimulate a nomenclature change.
II. Serious As A Plague
The situation is not a myth nor is it the only virology situation worthy of criticism:
"Influenza A virus (IAV) is a respiratory pathogen that has caused significant mortality throughout history and remains a global threat to human health. Although much is known about IAV replication, the regulation of IAV replication dynamics is not completely understood.
...
Influenza A virus (IAV) is a segmented negative-sense RNA virus and is the cause of major epidemics and pandemics. "
(Segment-Specific Kinetics of mRNA, cRNA, and vRNA Accumulation during Influenza Virus Infection, cf. Virology Blog, emphasis added). IMO, the gist of the problem is that the atomic structure of both DNA and RNA are not sufficiently taken into either symbolic consideration or actual analytic consideration.
The difference in the number of atoms in DNA and RNA and how that impacts the dynamics that are "not completely understood" is my reason for criticizing the use of 'T' to represent both Thymine and Uracil in ACGT sequences depicting genomes.
Not knowing a virus's atomic structure sufficiently is more serious than what appears to be important to those who only care about commercial enterprise:
"However, in 2024, H5N1 breached a new host barrier with global implications: for the first time, it infected dairy cattle in the United States. This event marked an extraordinary turning point in the history of influenza virology, not only because of the species involved, but also due to the systemic vulnerabilities it exposed.
The virus had been silently circulating in migratory wild birds across North America since at least 2021. These birds follow extensive flyways that intersect with major agricultural and livestock areas, facilitating ecological overlap and spillover risk. Despite having advanced diagnostic capabilities and surveillance programs, the United States relied heavily on passive monitoring and failed to detect early incursions. Once H5N1 entered domestic systems, it infiltrated commercial poultry farms where theoretical biosecurity protocols were inadequately implemented. Workers, vehicles, and shared equipment likely acted as mechanical vectors. Moreover, many facilities resumed production shortly after culling, often without comprehensive environmental decontamination—potentially allowing viral persistence and resurgence."
(An Unprecedented Event in the History of Virology, emphasis added). It's not a game (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35).
III. Closing Comment
There's more to see in today's appendices (APNDX 1, APNDX 2, APNDX 3, and APNDX 4).
The previous post in this series is here.
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