It is quite cool that photosynthesis works just like cellular respiration by producing a proton potential through chemiosmosis.
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? www.visiblebody.com/blog/phylogenetic-trees-cladograms-and-how-to-read-them:
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.
Coral of life by János Podani (2019)
Source. Fantastic work!!! Some cool things we can easily see:
Mostly data driven.
E.g. monotremes laying eggs did not evolve separately after function loss, it comes directly from reptiles.
Basically mean that parallel evolution happened. Some cool ones:
- homeothermy: mammals and birds
- animal flight: bats, birds and insects
- multicellularity: evolved a bunch of times
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.
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:This mess is because people don't realize that clades are all that really matter.
There's about 60 of them.
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.
Developmental Genetics 1 by Joseph Ross (2020)
Source. Talks about homeobox genes.Some good mentions at: Video "Where is Anatomy Encoded in Living Systems? by Michael Levin (2022)".
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: en.wikipedia.org/wiki/Trichoplax
www.u-tokyo.ac.jp/focus/en/articles/a_00220.html "The simplest multicellular organism unveiled" from 2013 mentions Tetrabaena socialis.
- youtu.be/1v6cgSkiHik?t=513 multicellularity is polyphyletic, e.g. evolved separately on plants, fungi and animals.
- youtu.be/1v6cgSkiHik?t=668 describes how unicellular organism choanoflagellates form colony, and how animals are characterized by certain key types of cellular interaction: adhesion, communication, regulation (cell differentiation) and extra cellular matrix production
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:and:
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.
Anything that is not eukaryote, i.e. archaea and bacteria, see e.g.: Figure "Coral of life by János Podani (2019)".
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:
- genetics
- bibliography:
- www.science.org/doi/10.1126/scitranslmed.abj7521 Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort by Carapito et al. (2021)
- bibliography:
- state of the immune system based on disease history
- age
www.youtube.com/watch?v=6DxlkxA82FM COVID-19 Symposium: Entry of Coronavirus into Cells | Dr. Paul Bates
Some are named after the encoded protein. Others that are not as clean are just orfXXX for open reading frame XXX.
Envelope.
As shown at pubmed.ncbi.nlm.nih.gov/16877062/#&gid=article-figures&pid=fig-3-uid-2 has transmembrane domain.
Membrane.
As shown at pubmed.ncbi.nlm.nih.gov/16877062/#&gid=article-figures&pid=fig-3-uid-2 has transmembrane domain.
Spike.
Nucleocapsid phosphoprotein, sticks to the RNA inside.
www.nature.com/articles/s41467-020-20768-y mentions functions:
These are also required for test tube replication.
Mentioned at: cen.acs.org/biological-chemistry/infectious-disease/know-novel-coronaviruss-29-proteins/98/web/2020/04
Unlike SARS-CoV-2 non-structural protein, these are not needed for test tube reproduction. They must therefore be for host modulation.
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.
Pseudo-fuck.
Notable examples:
Structure of a Gram-negative bacteria
. Source. 
Only present in Gram-negative bacteria.
Structure of a Gram-negative bacteria
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