Welcome to the Microbiome
L 152: It would be good to say that stars cook up our familiar elements from Hydrogen and Helium, the really first elements, and then disperse those elements as they explode; we are thus star-stuff.
L 243: I think the RNA spelled AUGUUAAGU… should be AUGAGA… instead.
Then protein R would come from codon AGA as claimed later.
L 347:
Given some of the tight associations of viruses with cells, and the fact that some viruses are RNA-based, it is more than likely that viruses are quite old too, perhaps even as old as cells.
I would assume that viruses evolved very nearly as soon as suitable hosts evolved.
I suspect this so because I imagine that niches for possible viruses are rarer than the experiments that discover how to exploit these niches.
As soon as the host evolves the virus design becomes the ‘adjacent possible’.
I grant that this is a dangerous sort of logic.
L 410: How are ‘parasitic bacteria’ distinguished from viruses?
Perhaps parasitic bacteria preserve their reproduction and their ‘nutritious environment’ is merely the cytoplasm of the eukaryote.
L 495: Another trait that may or may not be common is how codons code for amino acids.
L 838: “This meant that the researchers could skip the tedious 16S rDNA identification process.”
I have read the preceding page several times and I do not follow this conclusion.
The next paragraph uses the term “plasmid cloning vectors” without much explanation, perhaps in answer to the previous obvious question.
plasmid cloning vector
plasmid cloning vectors
L 850: Without sex it is unclear to me what counting species of bacteria or archaea means.
I suppose that it is another conformation of 16S rDNA that is functional.
I can imagine, however, two populations of microbes that differ only in their 16S rDNA.
Are they really two species?
Conversely I can imagine bacteria which differ in many ways but happen to have the same 16S rDNA.
The later is unlikely, however.
L 929:
Whereas scientists can characterize microbiomes simply by looking for the microbial genes that code for ribosomal RNAs, the diversity of viruses’ size, shape, structure, and targets and the fact that no single gene is found in all viral genomes make it difficult to devise similar approaches for viral community assessment.
I suppose that you can identify a microbe by its ribosomal RNAs, but I don’t suppose you know much about it.
Perhaps identify the microbes amounts to characterizing the microbiome.
L 1449:
By comparison, an entomologist going into a forest in the eastern United States would know the names of nearly 99 percent of the species of insects she encountered, and would be shocked to see a new species.
It would be good to know how many new species per insect, rather than how many new species per specie.
“paralog rooting”
paralog
16S rDNA
The first chapter has an interesting and accessible review of the biology of our earliest known ancestors in more detail than I have seen before—more recent, I think, than that in “The Ancestor’s Tale”.
The book described why the virus is not considered to be “life”.
I found the explanation OK.
there are several sorts of things:
- Archaea
- Bacteria
- Eukaryotes
- virus
- plasmid
- organelle (mitochondrion, chloroplast)
- chromosome
- gene
Each of these have elements of reproduction in their design.
The virus in excluded because it lacks a mechanism to reproduce; it exploits that of cells to do the job.
“Replicon” tries to carve out some of this space.
In retrospect I was sort of hoping to get an ecological, or even and economic view of the gut.
What sorts of business plans are there there?
How stratified is it?
What goes wrong?
Are there concepts to stand in for ‘species’ which concept is stressed in a world without sex.
I suppose that answers to such questions are not available yet.
Perhaps the book was too soon.