It is quite cool that photosynthesis works just like cellular respiration by producing a proton potential through chemiosmoses.
It is important to note that due to horizontal gene transfer, the early days of life, and still bacteria to this day due to bacterial conjugation, are actually a graph and not a tree, see also: Figure "Graph of life".
Definitely have a look at: coral of life representations.
TODO vs Phylogenetic tree?
Cladograms and phylogenetic trees are functionally very similar, but they show different things. Cladograms do not indicate time or the amount of difference between groups, whereas phylogenetic trees often indicate time spans between branching points.
Figure 1. Coral of life by János Podani (2019) Source. Fantastic work!!! Some cool things we can easily see:
Interesting fractal approach to a phylogenetic tree:
Mostly data driven.
Basically the same as clade.
All non-clade groups are evil. All non-clade terms must be forgotten. Some notable ones:
When a characteristic is basal, it basically means the opposite of it being polyphyletic.
E.g. monotremes laying eggs did not evolve separately after function loss, it comes directly from reptiles.
Kind of the opposite of a basal group.
Basically mean that parallel evolution happened. Some cool ones:
The cool thing about parallel evolution is that it shows how complex phenotype can evolve from very different initial genetic conditions, highlighting the great power of evolution.
We list some cool ones at: polyphyly.
Naming taxonomic ranks like genus, domain, etc. is a fucking waste of time, only useful before we developed molecular biology.
All that matters is the tree of clades with examples of species in each clade, and common characteristics shared by the clade.
And with molecular biology, we can build those trees incredibly well for extant species. When extinct species are involved however, things get more complicated.
There's six to eight in different systems of the end of the 20th century:
There's about 60 of them.
Video 1. Do Bacteria Need Oxygen? by Microscope Project (2022) Source. Shows how (persumed) aerobic bacteria flock towards an air bublle in water.
Video 1. Where is Anatomy Encoded in Living Systems? by Michael Levin (2022) Source.
  • we are very far from full understanding. End game is a design system where you draw the body and it compiles the DNA for you.
  • some cool mentions of regeneration
How genes form bodies.
Video 1. Developmental Genetics 1 by Joseph Ross (2020) Source. Talks about homeobox genes.
This is hot shit, a possible worst case but sure to get there scenario to understand the brain!
It is quite mind blowing when you think about it, that the huge majority of your body's cells is essentially just there to support a tiny ammount of germline, which are the only cells that can actually pass on! It is fun to imagine the cell type tree for this, with a huge branching of somatic cells, and only a few germline going forward.
One of the simplest known seems to be: "The simplest multicellular organism unveiled" from 2013 mentions Tetrabaena socialis.
Then of course: Caenorhabditis elegans is a relatively simple and widely studied model organism.
Video 1. Nicole King (UC Berkeley, HHMI) 1: The origin of animal multicellularity by iBiology (2015) Source.
It is hard to distinguish between colonies of unicellular organism and multicellular organism as there is a continuum between both depending on how well integrated they cells are.
From Wikipedia:
Multicellularity has evolved independently at least 25 times in eukaryotes
Complex multicellular organisms evolved only in six eukaryotic groups: animals, symbiomycotan fungi, brown algae, red algae, green algae, and land plants.
Not a clade, and therefore a term better forgotten!
A clade name for arkarya is a proposed clade name for archaea plus eukarya.
It just has RNA that can be transcribed directly by the host ribosome. mentions that they get their lipid layer from the Golgi complex of the host, where they replicate. The Coronavirus Replication Cycle by Kevin Tokoph (2020)
COVID happens in two stages:
  • viral infection
  • inflammatory phase, where the body takes over, and sometimes harms itself. It seems that people are not generally contagious at this point?
This distinction is one of the reasons why separating the virus name (SARS-CoV-2) from the disease makes sense: the disease is much broader than the viral infection.
Why is it there such a clear separation of phases?
Why do people with mild symptoms go on to die? It is a great mystery.
Ciro Santilli's theory is that COVID is extremely effective at avoiding immune response. Then, in people where this is effective, things reach a point where there is so much virus, that the body notices and moves on to take a more drastic approach. This is compatible with the virus killing older people more, as they have weaker immunes systems. This is however incompatible with the fact that people don't seem to be contagious after the viral phase is over...
There are a few possibilities:
Genes at: TODO protein list on a database?
50-200 nanometers in diameter. COVID-19 Symposium: Entry of Coronavirus into Cells | Dr. Paul Bates
Interaction points:
Video 1. Model of Membrane Fusion by SARS CoV-2 Spike Protein by clarafi (2020) Source.
Some are named after the encoded protein. Others that are not as clean are just orfXXX for open reading frame XXX.
Largest gene, polyprotein that contains SARS-CoV-2 non-structural proteins 1 to 11.
Nucleocapsid phosphoprotein, sticks to the RNA inside. mentions functions:
  • helps pack the viral RNA into the capsule
  • also has a side function in immune suppression
These are also required for test tube replication.
Protease that cuts up ORF1ab. Note that it is also present in ORF1ab.
The RdRp, since this is a Positive-strand RNA virus.
Unlike SARS-CoV-2 non-structural protein, these are not needed for test tube reproduction. They must therefore be for host modulation.
Integrates its RNA genome into the host genome.
Sounds complicated! The advantage is likely as in HIV: once inside the cell, it can remain hidden far away from the cell surface, but still infections.
Converts RNA to DNA, i.e. the inverse of transcription. Found in viruses such as Retrovirus, which includes e.g. HIV.
Notable examples:
Figure 1. Structure of a Gram-negative bacteria. Source.
Only present in Gram-negative bacteria.
Figure 1. Structure of a Gram-negative bacteria. Source.
Space between the inner and bacterial outer membrane in Gram-negative bacteria