A person on Twitter reached out to me. I’m copying their response below:
Hello, I’m not on Lesswrong, but this is in response to your comment on “Why Are Bacteria So Simple?” I’m also not on Twitter much.
AlphaandOmega has it right, it’s random mutation/losses + evolutionary pressure. With plasmids loss is more common since if during division sometimes one cell ends up with no copies of the plasmid, and if the plasmid is costly then the one without the plasmid reproduces more quickly, and they can outcompete the bacteria with plasmids in hours.
(This is why many plasmids evolve partitioning systems or addiction modules to either make it more likely that both daughter cells have the plasmid, or to kill any daughters without plasmids. Plasmids are selfish, too!)
With resistance on the chromosome it gets a bit more complicated. New gene mutations (like mutating the target of the antibiotic) usually stick around, and the bacteria often evolves compensatory mutations to compensate for the reduced efficiency, though the mutation can still be “lost” if an unmutated bacteria still exists and can outcompete.
However, transposon and recombination can also be used to transfer resistance genes between cell chromosomes. Recombination and transposons often occur at specific sites due to having targeting sites for transposases, or higher AT content leading to weaker DNA bonds. But since these sites are hotspots of recombination, it’s also easier for DNA to be deleted from these regions as well.
There is a way to determine if a part of a genome is more “alien” than the rest, and that’s by looking at what’s called the GC content (percent of DNA that is G or C instead of A or T). If a region with otherwise similar GC content is interrupted by a region with a drastically different GC content, this can be evidence of a DNA insertion from a different species. It is unlikely that bacteria can detect this change and respond, but is interesting anyways.
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The details are sound, but I’m not a big fan of the framing of the article; bacteria are far from simple, and undergo extremely complex regulation for survival under multiple environments (A single bacterium contains the energy metabolism contained in all eukaryotes, as well being able to use light to eat rocks, DMSO, and carbon monoxide, in addition to nitrogen fixation).
Bacteria also contain membrane-bound organelles (magnetosomes, for example), but membranes aren’t the only method of segregation, as you can have protein complexes or phase-separation boundaries to increase efficiency.
Bacteria also have “duplication and divergence”, in fact, probably moreso than eukaryotes. It has been shown that bacteria can duplicate copies of heavily-used genes, then delete them when they’re no longer required. But if the duplicates mutate before they’re deleted, they can diverge.
I’m not sure how accurate the section on modularity is; I know of bacterial systems which are controlled by three or four different regulators so that its levels can be precisely tuned for the environment it’s in. Not all bacterial genes are in operons, and even in operons there’s additional levels of regulation, including some not found in eukaryotes (like antitermination).
Bacteria also have their own high-level regulators, but since they generally lack multicellularity, it is often in response to specific states, like kinds of stress.
I will concede that bacteria have generally failed to evolve multicellularity and thus have not been able to achieve the specialization tradeoffs for things like body plans, though I think this issue is due to having a extra cell wall/lack of nucleus.
Why are bacteria so simple? They’re not. And given that we can only study the bacteria we know how to grow, I’d guess they’re even more complex than we thought.
A person on Twitter reached out to me. I’m copying their response below:
Hello, I’m not on Lesswrong, but this is in response to your comment on “Why Are Bacteria So Simple?” I’m also not on Twitter much.
AlphaandOmega has it right, it’s random mutation/losses + evolutionary pressure. With plasmids loss is more common since if during division sometimes one cell ends up with no copies of the plasmid, and if the plasmid is costly then the one without the plasmid reproduces more quickly, and they can outcompete the bacteria with plasmids in hours.
(This is why many plasmids evolve partitioning systems or addiction modules to either make it more likely that both daughter cells have the plasmid, or to kill any daughters without plasmids. Plasmids are selfish, too!)
With resistance on the chromosome it gets a bit more complicated. New gene mutations (like mutating the target of the antibiotic) usually stick around, and the bacteria often evolves compensatory mutations to compensate for the reduced efficiency, though the mutation can still be “lost” if an unmutated bacteria still exists and can outcompete.
However, transposon and recombination can also be used to transfer resistance genes between cell chromosomes. Recombination and transposons often occur at specific sites due to having targeting sites for transposases, or higher AT content leading to weaker DNA bonds. But since these sites are hotspots of recombination, it’s also easier for DNA to be deleted from these regions as well.
There is a way to determine if a part of a genome is more “alien” than the rest, and that’s by looking at what’s called the GC content (percent of DNA that is G or C instead of A or T). If a region with otherwise similar GC content is interrupted by a region with a drastically different GC content, this can be evidence of a DNA insertion from a different species. It is unlikely that bacteria can detect this change and respond, but is interesting anyways.
--
The details are sound, but I’m not a big fan of the framing of the article; bacteria are far from simple, and undergo extremely complex regulation for survival under multiple environments (A single bacterium contains the energy metabolism contained in all eukaryotes, as well being able to use light to eat rocks, DMSO, and carbon monoxide, in addition to nitrogen fixation).
Bacteria also contain membrane-bound organelles (magnetosomes, for example), but membranes aren’t the only method of segregation, as you can have protein complexes or phase-separation boundaries to increase efficiency.
Bacteria also have “duplication and divergence”, in fact, probably moreso than eukaryotes. It has been shown that bacteria can duplicate copies of heavily-used genes, then delete them when they’re no longer required. But if the duplicates mutate before they’re deleted, they can diverge.
I’m not sure how accurate the section on modularity is; I know of bacterial systems which are controlled by three or four different regulators so that its levels can be precisely tuned for the environment it’s in. Not all bacterial genes are in operons, and even in operons there’s additional levels of regulation, including some not found in eukaryotes (like antitermination).
Bacteria also have their own high-level regulators, but since they generally lack multicellularity, it is often in response to specific states, like kinds of stress.
I will concede that bacteria have generally failed to evolve multicellularity and thus have not been able to achieve the specialization tradeoffs for things like body plans, though I think this issue is due to having a extra cell wall/lack of nucleus.
Why are bacteria so simple? They’re not. And given that we can only study the bacteria we know how to grow, I’d guess they’re even more complex than we thought.