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samuell

2,549 karma · joined May 13, 2013

Fascinated by Living Systems | Clin Microbio Bioinfo @ Karolinska | PhD http://pharmb.io | Reproducibility, #SciWorkflows | Curious: Genomic Algos, TEs etc

R&D: https://livingsystems.cc Deep think: https://livingsystems.substack.com

Married. Dad. Sinner saved by grace.

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samuell··on Zig Creator Calls Spade a Spade, Anthropic Blows Smoke
> Anthropic is actively campaigning to end software engineering

While this may be slightly overstated, my take on this is that AI progress should have us upgrade our view of the human brain rather than the opposite.

Wrote about it the other day:

https://livingsystems.substack.com/p/ai-progress-should-upgr...

samuell··on Interview with Mitchell Hashimoto about Ghostty and Zig
As much as I'm put away by the dependency horror I've seen in many Rust projects, this is an interesting observation.
samuell··on TypeScript 7
Steve Francia (author of Hugo and a bunch of other top Go projects) wrote up some thoughts of Go's fit in the agentic era:

https://spf13.com/p/go-the-agentic-language/

samuell··on In Praise of Observational Evidence
Quite thought-provoking, and connecting it to a related field it seems the (relative) success of LLMs and the likes are indications that enough data can at least learn you something without always needing to interfere with the world first(?)
samuell··on How to sequence your own DNA at home
Is this the same guy behind https://iwantosequencemygenomeathome.com/ ?

[Edit: Apparently no. That link is by Seth Howes, who also shared the OP post though: https://x.com/SethSHowes/status/2074231119730430203 ]

samuell··on Open Source Low Tech
As someone who has spent some time in sub-saharan Africa, I can tell you that there is lots that can be done if just seeing the possibilities.

Not everyone everywhere are "engineering oriented", and having people with the skills and eye for practical solutions based on available materials, can help tons, and also open up people's imagination for what can be done.

In fact, this goes for northern Europe too, just that more people can manage without home-built solutions and can "buy away the problem" here.

Also, people where immensely thankful e.g. when my quite clever and crafty father managed to repair a water tank tower that'd been broken for months and years, by sourcing some local material, coming up with a repair design, and having local welders create it, etc etc.

samuell··on Gossamer: a Rust-flavoured language with real goroutines and pause-free memory
Glad to see more languages adopt true goroutines [edit: lightweight threads or fibers] with M:N scheduling. Surprised more haven't. Among compiled language I'm only aware of Go and Crystal off the top of my mind.
samuell··on Qualcomm to Acquire Modular
No, this was pure speculation based on what seems like a popular view on where Mojo ended up, where the initial Python-focus don't seem to help it that much anymore.
samuell··on Qualcomm to Acquire Modular
As a meta comment, I'm surprised such a news is not reaching the frontpage already.
samuell··on Qualcomm to Acquire Modular
Maybe Chris was a little unhappy about where Mojo ended up, and sees this as an opportunity to start anew on a properly designed language from scratch :D
samuell··on Qualcomm to Acquire Modular
I'm actually mostly worried about the future of Mojo at this time.

Though hopefully it will be fully released open source still, but I feel there are question marks around whether it will be a priority to continue to develop by Qualcomm, or if they are mainly interested in the AI compute stack?

Time will tell I guess, but a lot feels to be up in the air.

samuell··on Clojure Hosted on Go
Found this previous thread about Lisette: https://news.ycombinator.com/item?id=47646843
samuell··on DaVinci Resolve 21
I'll second looking at KdenLive.

You might want to stay away from very recent major versions for stability, but it is a very capable editor that is also much more robust and performant than openshot.

I haven't compared with Blender VSE though.

samuell··on DaVinci Resolve 21
Wanted to expand on the animation part, so will check this up for sure, thank you.
samuell··on DaVinci Resolve 21
Great to hear.
samuell··on DaVinci Resolve 21
Stability sounds interesting. While KdenLive has worked OKish for me, certain versions have broken my projects, and there are some long-standing bugs, like subtitles disappearing if I do a specific operation in the wrong moment. While the latter is fixed by a simple Ctrl+Z it is giving me second thoughts about using this for really large projects.
samuell··on DaVinci Resolve 21
For people using Resolve, would you recommend someone already quite well-versed in KDenLive to switch, for some non-profit work on cutting together educational content with some animations, some talks etc?

Will it allow me to drastically improve my workflow (save time for some tedious tasks), increase quality of the outputs etc?

samuell··on Zig: Build System Reworked
My main issue with this is I expect Mojo to become the go to tinkering language for me.
samuell··on Ask HN: When and why did you start believing in God?
I grew up in a christian home, so got my initial belief from there.

Had a kind of pivot moment when I moved out from home though, where I immediately realized my parents will not be there forever, and the inner me needs to reach for my ultimate parent. This got me into a much closer relation with the Lord. I had (and have) many somewhat spectacular answers to prayer, and basically learned to have a really trustful relationship with him.

I know many people's faith is challenged when going to the university and learning about biology as I did (studying biotech and bioinformatics).

I had came into contact with some great apologetics material, especially around evolution etc, in Swedish, which I found super interesting.

Still, I must say my faith was even more reinforced when we started to study macro-molecular machines, and I realized that biology is a whole world of extremely advanced nano-machines, working in an extremely intricate network of interlocking interdependencies.

I've been involved in quite a bit of debates regarding evolutionism and creationism over the years, and one thing I have noticed is that scientific creationism is much closer to modern evolutionary theory than most people realize. Recent secular paradigms such as "The third way of evolution" [1] pretty much perfectly recapitulates what many creationists have said for years; Biology is shock-full of pre-programmed ability to adapt, according to pre-existing modules and adjustable parameters, in an extremely dynamic software system, with tons of generative algorithms for how animals and plants are built up through embryogenesis, which allows for powerful adjustments of a lot of parameters with often surprisingly little change in the genomic "source code".

For people interested in an introduction to what secular science has to say here, I often recommend "The Plausability of Life", by Gerhart and Kirschner [2]. Other great titles are "Evolution: A View from the 21st century" by James Shapiro [3], and a few more (the third way website lists a lot of great books).

In my view, the Genesis story in the Bible matches these findings perfectly, disagreeing mainly in the expected age of things. But these biological mechanisms actually mean that "evolution" can happen extremely fast, without even actual genomic changes just by turning on and off or regulating features, via mechanisms like Epigenetics.

Eventually I've became involved in trying to figure out the more detailed view of how the Biblical narrative could explain the bleeding edge of biology, which led me to co-organize a seminar in Sweden in 2024 with European researchers (mostly), which resulted in both a video series and a book, which is available from this web store among others (not affiliated).

This work, especially the chapters on 1) Mendelian genetics 2) Epigenetics and 3) Transposable elements (think Endogenous Retroviruses, Jumping Genes etc), together in my mind creates an extremely interesting explanatory framework for how life was pre-programmed to be extremely efficient - and fast - mind you - at adapting to varying environments.

Whether you want to call that "evolution" or "pre-programmed adaptive creation" is in my mind very much a question of definitions, and TBF, the term evolution hasn't had a very strict definition for as long as I remember.

Anyways, today I'm more fascinated than ever the more I learn about the extremely complex and ingenuous solutions out there in nature to vastly different problem areas like chemistry, metabolism, mechanics, information processing and general cognition. It fills me with awe and respect for the creator that must be there behind all this.

[1] https://www.thethirdwayofevolution.com/

[2] https://yalebooks.yale.edu/book/9780300119770/the-plausibili...

[3] https://www.goodreads.com/book/show/11004717-evolution

[4] https://www.youtube.com/playlist?list=PLNkVOx7YbWiDABv5nB3Ih...

[5] https://store.answersingenesis.co.uk/product/a-creation-scie...

samuell··on Local-First and Portable CI
Optimizing for local-first checking is 100% the way to go, and should be used much more widely I think.

I have done a similar thing using simple makefiles though, collecting more complex chains of tasks into a "meta rule" in Make and just calling that from whatever CI config we're using.

samuell··on Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
You might try sequencing your DNA at home :)

https://iwantosequencemygenomeathome.com/

(Well, the guy offers to do it for you too, delivering the data on an USB stick).

samuell··on Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
> So it seems "Rosalind" is at least very appropriate as a name for a genomics tool such as this.

Indeed. The only argument against it might be that Rosalind is already a pretty well-known website for doing bioinformatics exercises and have them automatically graded:

https://rosalind.info

samuell··on Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
I shared this since it seems to address a somewhat similar niche that I have had hopes to one day develop, based on FlowBase [1]; A library of streaming processing components based on basic operations, that can be easily stitched together into larger pipelines in a compiled language that can run on smaller hardware too.

FlowBase or I didn't have much of ideas about how to keep data structures compact, as the linked library does, and I was mostly aiming to make it really easy to build streaming pipelines.

I haven't yet got my head around how the composability story is in rosalind though, so would be interested in any pointers or examples on how this would be done using it.

[1] https://github.com/flowbase/flowbase

samuell··on Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
Yeah, there is actually a pretty big shift towards Rust in the comp bio / bioinformatics community.

Nature even wrote a feature article about it a couple years ago:

Why scientists are turning to Rust

https://www.nature.com/articles/d41586-020-03382-2

They mention the Rust-Bio [1] project by well known Snakemake author Johannes Köster & co, and there are some other widely used libraries like needletail [2] and noodles [3].

A cool smaller tool developed by performance wiz Ragnar Groot Koerkamp which was just published is Sassy [4] [5]. He has also been involved in developing some high performance SIMD based stuff (minimizers) [6].

[1] https://github.com/rust-bio/rust-bio

[2] https://github.com/onecodex/needletail

[3] https://github.com/zaeleus/noodles

[4] https://github.com/RagnarGrootKoerkamp/sassy

[5] https://academic.oup.com/bioinformatics/article/42/5/btag244...

[6] https://github.com/rust-seq/simd-minimizers

samuell··on Show HN: Files.md – Open-source alternative to Obsidian
I want something like this, but completely terminal based
samuell··on Mojo 1.0 Beta
I'm really quite divided about Rust vs Mojo for bioinformatics in the future.

The syntax i Mojo really seems to shine a lot ... though I still wonder if the train has already left now that so much bioinfo work is already done in Rust.

samuell··on Radicle: Sovereign {code forge} built on Git
Gotcha! Though that is not for the self-hosted version IIUC?

But yea, rust-chat in a way seems like more of a proper open source project ...

samuell··on Mojo 1.0 Beta
Very cool!

I have been pretty hopeful about Mojo as I find many of the modern compiled languages these days requires an surprisingly excessive amount of ceremony just to open a file and read it line by line. At least this is the case with Go, as I've written about [1].

If Mojo is providing any kind of python like experience in this matter, I will be all into it again (it lacked these features when I last tried).

[1] https://livesys.se/posts/golang-for-bioinformatics/

samuell··on Radicle: Sovereign {code forge} built on Git
How does it compare to MatterMost [1]?

[1] https://mattermost.com/

samuell··on Radicle: Sovereign {code forge} built on Git
Somewhat related:

Show HN: Epiq – Distributed Git based issue tracker TUI

https://news.ycombinator.com/item?id=48155570

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