I think people are reacting to the press-release more than the work.
I don't see why this is definitely doomed just because they discuss beta-amyloid plaques. Those exist and are real. They probably don't cause it any more than tombstones cause graveyards; very related, but not in the directly mechanistic way we wish.
> Alzheimer’s disease (AD) is a prevalent neurodegenerative disorder characterized by the accumulation of amyloid-beta (Aβ) peptides in the brain.
This can be true and still not be the specific mechanism.
You can treat a specific waste product or you can repair the waste stream. The issue may be waste, but not a specific product, or the issue may not be the waste stream at all.
This work appears to demonstrate evidence of waste stream repair via a well-known waste-product. That doesn't mean that any specific waste product is or is not the problem or that this particular stream is definitely going to remove enough of the waste (if that was the problem).
Maybe there have been a lot of drugs which have similarly attempted waste-stream repair so there's good reason to doubt it on that alone. But I don't think that mentioning beta-amyloid plaque is enough to discard this out-of-hand.
I'm not aware of any, but it wouldn't be insane to build a seekable deflate implementation by defining offsets in a zip comment. This would leave the zip file backwards compatible to usual decompression while allowing internal seeking within an individual file if the decompressor was aware of this index.
Just kidding, I don't see how the overhead of the directory entry is even remotely enough to warrant removal. Most of the magic can be left to efficient DEFLATE compatible blocks and removing entries not in the central directory in the first place (ZIP files can support concatenation of new data so long as you re-write the central directory at the end of the file).
I'm curious to know what you would rate as the most important features to make this work? It seems like calc+if do a lot of the heavy lifting, but the new function syntax is what makes instruction lookup tractable.
It does seem like the state of the art differs from popular understanding. Not only is mitochondrial DNA straight forward (although not especially useful for forensics as it is maternal), but with specialized extraction it is still possible to recover nuclear DNA, just exceedingly painful to do so.
It is the initial purpose of a microbiome to be at least commensal, in that it is usually prohibitively expensive to maintain a sterile environment so the odds of a true pathogen colonizing a system is greatly reduced if you simply have a crowded space of neutral participants.
Once that's true it does seem there's a lot of host and microbiome interactions we've only begun to explore, but it shouldn't be surprising that co-evolution of the microbiome and host begins to take over as soon as you have one. One great example is short-chain-fatty-acid (SCFA) producing bacteria in the human gut. [1] These seem to be essential, and if there was a general takeaway to improve health, it would be to eat your roughage so they can do their job.
This is also why high alpha-diversity (community richness in particular) is such a dead-ringer for healthy vs diseased states. And frustratingly, is often exactly where the story ends for a lot of observational studies.
Also, in case you are curious, artificially sterile mice (gnotobiotic mice) tend to act differently than other mice, which is pretty odd to be honest, and why the gut-brain axis is a plausible mechanism to research further. [2]
> I wish you luck with tracking down versions of software used when you're writing papers... especially if you're using multiple conda environments.
How would you do this otherwise? I find `conda list` to be terribly helpful.
As a tool developer for bioinformaticians, I can't imagine trying to work with OS package managers, so that would leave vendoring multiple languages and libraries in a home-grown scheme slightly worse and more brittle than conda.
I also don't think it's realistic to imagine that any single language (and thus language-specific build tools or pkg manager) is sufficient. Since we're still using fortran deep in the guts of many higher level libraries (recent tensor stuff is disrupting this a bit, but it's not like openBLAS isn't still there as a default backend).