September 14 2020, 00:45

Check out this fantastic lecture on viruses by Evgeniya Lazareva @[1040949013:2048:Lazareva Evgenya]

If you don’t feel like watching the whole thing and just want to see the part related to what I write below, then check out

– about how the virus manages to encode 4 genes on a super short circular DNA. Programmers will find this especially interesting.

For this Hepatitis B virus, one of the strands (in the ring) is even shorter than the other (1700-2800 nucleotides) – just 3200 nucleotides long. And this “program” encodes four genes (which encode 4 proteins: HBsAg, HBcAg, polymerase, and the gene expression regulatory protein). So, it seemingly does not fit the information for 4 genes at first glance. And you know how they solve this? The same sequence is read in six different configurations of a “floating reading window.” Roughly speaking, the same “bit” participates in six “bytes” simultaneously.

Sapolsky stated in his lectures that the interpretation of this program gives different results depending on the cell’s state. I then started actively googling and stumbled upon an interesting thread on Reddit, describing how an organism understands which cells to make for different tissues using the same program:

https://www.reddit.com/r/askscience/comments/irxncu/how_does_a_cell_know_what_to_become_if_they_all/

There are enzymes that suppress or otherwise activate genes by their presence during the polymerase’s operation, i.e., during the “program’s” reading and interpretation. These enzymes can appear from the external environment (e.g., from the mother in an unborn child) or be produced by the body itself, or they might be the product of the same program. But overall, the real mind-blower is that a program controlled by these enzymes can create enzymes that will control the mechanism in the next cycle, which will also create an enzyme that will control the next cycle where a protein is then created. This part of the process is called “epistasis,” and such genes – suppressor genes or inhibitor genes. If you’re interested in examples, read https://en.wikipedia.org/wiki/Epistasis (in English), where there are many examples.

The mechanism that creates different isoforms of a protein from the same “program” is called alternative splicing. For example, the human body synthesizes no less than 100,000 different proteins, while the number of genes encoding them is approximately 20,000. Thus, inhibiting one of the components in the presence of a hundred others already results in a new protein.

Sapolsky also mentioned in his lectures that these inhibitor enzymes need to be present in progeny cells in their previous concentrations when a cell divides, which is a probabilistic process. If the number of enzymes in the progeny cell is insufficient to suppress some gene during its expression, it begins to produce what it shouldn’t, and some serious problem develops. But this usually does not happen because there are error-correcting mechanisms – cells where something has gone wrong are destroyed.

Imagine what a single mistake in an unfortunate place in the genome could lead to? Thus, a system largely based on probabilities and a “suitcase balance on a needle point” turns out to be very reliable if there’s plenty of time for debugging and clear environmental fluctuations. Again, programmers will find this interesting.

Clearly, designing all this on purpose as we currently envisage, by “trial and error”: once created by chance (at its first level of complexity), and then simply survived in some conducive conditions and perished in 99.9999(9)% unfavorable ones, and 99.9999(9)% did not find any favorable conditions and died off as “species” never achieving the “goal”, and we now think that it was a mechanism specifically created by evolution for such conditions. No, it’s just because there are very, very many organisms, even more conditions, the simplest organisms have fast generation turnovers, and there were 3-4 billion years to work with. Basically, trial-and-error programming works excellently when you are not in a hurry and have infinite resources at your disposal.

But it looks like magic, I swear.

P.S. What else to write on FB first thing in the morning, 5 minutes after waking up.