JAX/XLA does offer some really nice tools for doing automated sharding of models across devices, but for really large performance-optimized models we often handle the comms stuff manually, similar in spirit to MPI.

The odd set of claims is that somehow biology has 1) figured out how to preserve long-range entanglement and coherent states at 300K in a solvated environment when we struggle to do so in cold vacuum for quantum computing and 2) somehow still manages to selectively couple this to the -known- neuronal computational processes that are experimentally proven to be essential to thought and consciousness.

This more or less amounts to assertions that "biology is magic" without any substantive experimental evidence over the last thirty years that any of the above is actually happening. That's why most biophysicists and neuroscientists don't take it at all seriously.

It's hard to buy that their proposed stories are the simplest explanation for these few measurements. Much more boring phenomena can influence QY. e.g. simply occluding fluorophores from the bulk solvent can have a huge influence on QY and spectra. (I used to design biological fluorescent reporter reagents...)

It's hard to buy that their proposed stories are the simplest explanation for these few measurements. Much more boring phenomena can influence QY. e.g. simply occluding fluorophores from the bulk solvent can have a huge influence on QY.

Fold prediction is an incredibly useful tool for scientists and genetic engineers to help design new proteins, but it doesn't magically solve molecular or cell biology. Designing new functions and mechanisms is still going to involve a huge amount of labor and brute-force experimentation.

I certainly don't think it will help at all with stability. Things like Q/K layernorm are better tricks for softmax stability when scaling: https://arxiv.org/pdf/2302.05442.pdf

As a 2-decade genetic engineer: there are no genetic "markers" pointing to a lab leak, there's really no sign of unnatural manipulation in the sequence.

What I've tried repeatedly to impress upon people here is that most routine cloning strategies leave pretty clear signatures, and the idea that a lab would go so far as to eliminate these signatures for such mundane virology work is tantamount to a much more elaborate conspiracy theory.

What they're observing is homologous recombination between strains - all the sites they're claiming are found in nature.

Again - there would be a genetic signal the strength of the noonday sun burning your eyes out if sars-cov-2 was made by cut-and-paste at these sites. You wouldn't need this ridiculous circular argumentation to prove that point.

If we're linking to tweets, these two go into great depth about how ridiculous this paper is: https://twitter.com/Friedemann1/status/1583519970902048768 https://twitter.com/acritschristoph/status/15834864034169692...

This paper posits a completely crazy cloning strategy that makes no sense (ie doing something far more convoluted than typical bsaI/bsmbi seamless cloning workflows that breaks the whole point of "seamless" workflows), and then tries to use that to make a case for a genomic signature that we could look for. They then look at a handpicked set of viral genomes, but leave a bunch out and duplicate others (I think WIV04 and WHu are the same), and largely seem to be observing without realizing it that yes, recombination occurs among these viral lineages.

This isn't even getting into the fact that a restriction-ligation based cloning strategy would leave glaringly obvious fingerprints behind in the form of the hundreds of nucleotide differences that are present outside the cutsites across the lineages... it would be blindingly obvious if someone just cut-and-pasted sars-cov-2 from other studied genomes.

Comments URL: https://news.ycombinator.com/item?id=32946389

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A lot of people weren't even on this site back then... but this is exactly like watching the "ClimateGate" scandal play out here on HN over a decade ago, and in fact even involves some of the key players like Matt Ridley! Now, over a decade later, it turns out some messy dendrochronological paleoclimatology did not in fact represent a conspiracy invalidating the entirety of climate research and global warming is an even clearer threat.

In another decade we're going to have a much better understanding of horseshoe bats, asian animal markets, and coronavirus evolution... and not a single one of the breathless accusers involved in these screeds will ever apologize for flogging conspiracy.

Yeah, science is messy, scientists are flawed humans, desperate for money and generally terrified of bad PR and the mob. But the entirety of viral reverse genetics can't be thrown into an ill-defined "GOF" bucket. What constitutes acceptable risk and GOF in these areas has been an active debate in virology for as long as I can remember, and the quality of this dialogue is not going to be aided by this circus.

Of course it's possible to describe a physically possible route to sampling, lab accident, and infection. Anyone can come up with these just-so stories. Professors too! Making a chimera of random isolates is crazy story. It's incredibly annoying to mess with 30kb RNA viruses. You have no idea. That's just not how a skilled practitioner would go about asking these questions. There's a reason most work on these things are in characterized strains.

These stories remain ludicrous when compared with the unambiguous epidemiological evidence for zoonosis that we have in hand. You're simultaneously alleging this tight collaboration between western scientists and WIV, but positing that somehow all these western scientists were in the dark about a conspiracy to do this massive amount of work without our knowledge, or an active conspiracy on the part of a significant percentage of western virology to hide it. All in a field that before the pandemic was a completely undramatic backwater of science!

The power of "lab-leak" isn't its strength as an evidence-backed scientific hypothesis, it's its power as a compelling work of fiction, and I doubt any amount of hard evidence will kill it.

The damage it does is distracting us from the unregulated wild-meat and fur industries that were the overwhelmingly likely cauldron for evolving these strains (as in SARS-1!). If we yet again fail to shut down those sources, we risk another pandemic just like this happening again in a few decades. That's where international attention and pressure should be applied, not this cockamamie distraction.