JCVI-syn3B by Ciro Santilli 37 Updated 2025-07-16
www.biorxiv.org/content/10.1101/2022.09.19.508583v1.full
CVI-syn3B strains differ from JCVI-syn3.0 by the presence of 19 additional non-essential genes that result in a more easily manipulated cell. JCVI-syn3B additionally includes a dual loxP landing pad that enables easy Cre recombinase mediated insertion of genes
It is also interesting to see how they are interested in co-culture with HeLa cells, presumably to enable infectious bacterial disease studies.
At biology.indiana.edu/news-events/news/2023/lennon-minimal-cells.html (2023) they let it re-evove to it it would regain some fitness, and it did.
Arkarya by Ciro Santilli 37 Updated 2025-07-16
Name of the clade of archaea plus eukarya proposed at: www.frontiersin.org/articles/10.3389/fmicb.2015.00717/full. Much better term than prokaryote as that is not a clade. Let's hope it catches on!
Cloaca by Ciro Santilli 37 Updated 2025-07-16
A single hole that is used for shit, pee and fucking. Amazing.
Homeothermy by Ciro Santilli 37 Updated 2025-07-16
It is quite mind blowing that this is polyphyletic on mammals and birds, what can't parallel evolution achieve??
Figure 1.
Phylogenetic tree of the vertebrates
. Source. Highlights how birds should obviously be classified as reptiles.
Placozoan by Ciro Santilli 37 Updated 2025-07-16
Now that's some basal shit! It's basically a fucking blob!!! Except that it is flat. No nervous system. Not even tissues. It is basically a multicellular
Chordate by Ciro Santilli 37 Updated 2025-07-16
Chordate is a sad clade.
You read the name and think: hmm, neural cords!
But then you see that his is one of its members:
Yup. That's your cousin. And it's a much closer cousin than something like arthropods, which at least have heads eyes and legs like you.
Vertebrate by Ciro Santilli 37 Updated 2025-07-16
The big breakthrough of the vertebrates appears to be the ability to swim around in a straight line and eat smaller species that are floating about.
Bones appear to help that a lot!
It is likely the most efficient design to travel long distances. Be thin and wiggle your tail around.
Perhaps smaller animals can skip the bone thing. Maybe a notable example are the lancelets, which look a bit like small fish. But they only go up to 8 cm.
Fish by Ciro Santilli 37 Updated 2025-07-16
This paraphyletic subgroup is easy to form the "acquatic only" (fishes) vs "things that come out of water" (tetrapods). Though mudfishes make that distinction harder.
Which kind of makes sense, why would you want for limbs unless you are going to stay out of water!

Pinned article: Introduction to the OurBigBook Project

Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
We have two killer features:
  1. topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculus
    Articles of different users are sorted by upvote within each article page. This feature is a bit like:
    • a Wikipedia where each user can have their own version of each article
    • a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
    This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
    Figure 1.
    Screenshot of the "Derivative" topic page
    . View it live at: ourbigbook.com/go/topic/derivative
  2. local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:
    This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
    Figure 2.
    You can publish local OurBigBook lightweight markup files to either https://OurBigBook.com or as a static website
    .
    Figure 3.
    Visual Studio Code extension installation
    .
    Figure 4.
    Visual Studio Code extension tree navigation
    .
    Figure 5.
    Web editor
    . You can also edit articles on the Web editor without installing anything locally.
    Video 3.
    Edit locally and publish demo
    . Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.
    Video 4.
    OurBigBook Visual Studio Code extension editing and navigation demo
    . Source.
  3. https://raw.githubusercontent.com/ourbigbook/ourbigbook-media/master/feature/x/hilbert-space-arrow.png
  4. Infinitely deep tables of contents:
    Figure 6.
    Dynamic article tree with infinitely deep table of contents
    .
    Descendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact