Sequence alignment is trying to match a DNA or amino acid sequence, even though the sequences might not be exactly the same, otherwise it would be a straight up string-search algorithm.
This is fundamental in bioinformatics for two reasons:
- when you sequence the DNA of a new species, you can guess what each protein does by comparing it with similar proteins in other species that you have already studied
- when doing DNA sequencing, and specially short-read DNA sequencing, you generally need to align the reads to reference genomes to know where you are inside the entire genome, and then be able to spot mutations, notably single-nucleotide polymorphisms
BLAST is a sequence alignment.
The NCBI free-to-use BLAST server: blast.ncbi.nlm.nih.gov/Blast.cgi. Having a centralized query server is fundamental, because the gain of sequence alignment really comes from having one huge database to link information together, which is best centralized.
Ciro Santilli just always feels that what can be classified as "artificial life" simulators have too much focus on beating more continuous population mechanics, and lack the discrete elements which he feels could be important to AGI: Section "The missing link between continuous and discrete AI".
There is great interest in this direction of research however quite clearly.
Unknown real developer name, claims to be from Canada on YouTube channel about: www.youtube.com/@TheBibitesDigitalLife/about, likely because he's a software developer and wants to keep his employer's claws away from his side project.
Appears to be closed source unfortunately, so not suitable for research.
Video 1. "What will happen after 100h of evolution? by The Bibites (2022)" mentions it was started five years ago, so circa 2017.
Appears to be Unity-based, if you download and extract for Linux you get files named
UnityPlayer.so.Author is named Leo Caussan in game credits at startup: www.linkedin.com/in/l%C3%A9o-caussan-560350136/, a Canadian software engineer.
Was not very Linux compatible: www.reddit.com/r/TheBibites/comments/vqk6ac/program_stalls_at_a_blue_screen/ Trying to run 0.5.0 leads to a blank screen after you click "start simulation".
Creator of Primer
youtube.fandom.com/wiki/Primer gives real identity:Feels exactly the background you'd expect: disilusioned by the educational system, and working to make education better! Great guy! Reminds Ciro Santilli of himself a bit.
- the name is Justin Helps from Minnesota
- dropped out of his PhD that got boring, and used to work at Khan Academy
- LinkedIn gives PhD subject: www.linkedin.com/in/justin-helps/ as materials science
- twitter.com/helpsypoo personal Twitter account
Face reveal at: www.youtube.com/watch?v=QC91Bf8hQVo
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!
Intro to OurBigBook
. Source. We have two killer features:
- 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-calculusArticles 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/derivativeVideo 2. OurBigBook Web topics demo. Source. - 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.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
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. 
- Infinitely deep tables of contents:
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