samuell

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...

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.

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).

> 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

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

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

I want something like this, but completely terminal based

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.

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 ...

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/

How does it compare to MatterMost [1]?

[1] https://mattermost.com/

Somewhat related:

Show HN: Epiq – Distributed Git based issue tracker TUI

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

I think this is a cool project. I see a lot of use cases for this, for cases where it is preferable to keep issues local to the repo, distributed via git only, and not the least for all kinds of personal task management. Avoiding the context switching to a web based tool is a nice plus.

> “People who go all in on AI agents now are guaranteeing their obsolescence. If you outsource all your thinking to computers, you stop upskilling, learning, and becoming more competent.”

> – Jeremy Howard, creator of fast.ai

This so much summarizes it.

I wrote shortly about it from a slightly different angle (piano playing) just this morning: https://livingsystems.substack.com/p/playing-freely

I think the village would be a healthy model for sure. But that is something that was pretty much killed in the modern society as well as most people, especially lower/mid-income workers in larger cities, are spending exceedingly little time of their day in their local neighborhoods.

It is a bit curious with the Mojo 1.0 beta coincidence, as Pascal was the other langauge with a highly readable and quite simple language combined with performant compiled code without GC.

What it lacked was a modern compiler and stack. There is FreePascal for sure, and Lazarus is impressive, but it for sure has its baggage.

As someone who would have strong reasons to invest time in Modular (simple high performant language for implementing bioinformatics scripts), I would say primarily the worry that development might be too tied to Modular, the startup behind it, which eventually might pivot into other priorities.

One would want to see either a strong community build up around it, or really hard evidence for a long-term commitment to the language from Modular. And the latter will take a long time to be assured of I think.

Also, editing tools need to catch up before very wide adoption of a language with a lot of new syntax.

The communication had me try to run some very simple python code assuming it of course should run (reading files line by line), which didn't work at all.

For me this was a big disappointment, and I wonder how much this has backfired across developers.

Which is probably one of the biggest problem with the outsourcing of parenting for half their awake time that is happening with our established school system.

Not that I claim it is super easy to find an alternative on a large scale, but I think societies need to think hard about how to enable involving parents to be as much involved as possible in the kid's day. (For parents working full time shifts + commuting in a major city, this is very hard).

There is also epiq, which is a bit more bleeding edge but has a more powerful UI story, being a TUI app, providing an issue board in the terminal:

https://github.com/ljtn/epiq

So the execution model is now even more similar to Go's one, with the M:N scheduling, IIUC?

I much like to hear that, as I found Crystal to provide pretty much exactly the same concurrency primitives as Go, but with a much nicer syntax, as I compared here:

https://livesys.se/posts/crystal-concurrency-easier-syntax-t...

Indeed! I generally like awk a lot for simpler CSV/TSV processing, but when it comes to cases where you need things like combining/joining multiple CSV files or aggregating for certain columns, SQL really shines IME.

Did you try https://elicit.org ?

I have been impressed by its results.

I think this fact stems more from its initial search phase than its pure LLM processing power, but to me it seems the approach works really well.

Nice experiment and writeup!

On a tangent, nice to see Plasmidsaurus using Emu [1], which has been shown to work great for 16S ribosomal RNA analysis on ONT by basically everyone I've heard who tried it. It has a nice algorithm for predicting if variants are due to ONT sequencing errors or are true variants, based on an expectation maximization algorithm, and thus working around the somewhat limited accuracy in ONT reads. Pretty clever stuff.

And if you want to run your own analysis on the raw data using Emu, you might want to try out our Trana pipeline built around Emu in Nextflow [2]. Apart from running Emu, it does some of the preprocessing like filtering, as well as exporting as Krona diagrams etc.

We're just putting it through validation at the clinical microbiology lab at Karolinska here in Stockholm right now.

The main caveat worth mentioning is that the choice of database seems to be able to affect results quite a lot in some cases.

[1] https://github.com/treangenlab/emu

[2] https://github.com/genomic-medicine-sweden/TRANA

Curious that this hit the front page.

What kind of projects is this software used for?

I tried this to try to extract some speech from an audio track with heavy noise from wind (filmed out on a windy sea shore without mic windscreen), and the result unfortunately was less intelligible than the original.

I got much better results, though still not perfect, with the voice isolator in ElevenLabs.

I love Prolog, and have seen so many interesting use cases for it.

In the end though, it mostly just feels enough of a separate universe to any other language or ecosystem I'm using for projects that there's a clear threshold for bringing it in.

If there was a really strong prolog implementation with a great community and ecosystem around, in say Python or Go, that would be killer. I know there are some implementations, but the ones I've looked into seem to be either not very full-blown in their Prolog support, or have close to non-existent usage.

Yea, a bit like a cheating student rote memorizing and copying another students technique for solving a type of problem, and failing hard as soon as there's too much variation from the original problem.

I was going to ask about wine support. Anyone tried in Bottles (wine distribution)? I've had better luck with Bottles than plain Wine with other software. Hoping to try soon.

I thought protonmail was the go-to for de-googling.