BioMan

I am continually amused at people not quite understanding what AlphaFold is actually doing, too.

Yes, a bunch of its performance comes from it learning rules about how proteins fold. But not a majority of its performance. MOST of its performance is it effectively acting as a translator of what evolution knows about protein folding into a form we can understand.

A key part of the system is not just cooking the sequence into a structure. A system running alphafold has a database of terabytes of curated sequence information from all over the tree of life. You put in the sequence you care about, and it first searches that database for anything with homology, and builds a "covariation matrix" - wherever theres anything with even vague sequence relatedness, build a matrix of every position in your sequence and the correlation between variation at position X and variation at position Y. This covariation matrix represents implicit information from the evolutionary process about what parts of a sequence are functionally connected to each other, which has a correlation to positional information, and these correlations are in turn learned by the ML system.

You put in de novo designed proteins or orphan proteins without homologs in the curated dataset and performance does not go away, but it drops precipitously. A bunch of what is going on is finding an evolutionary signal, and translating that evolutionary signal into structural information. So still, evolution knows much much more about protein folding than we do or any machine does, and once again a ML system is revealed to essentially be an information channel that takes in information from an interesting source on one end and turns it into a different form of information on the other.

Depends on what Anthropic wants to do with the poached people.

I am actually in the middle of both trying to advance my career and a project about information theory in evolutionary biology making a bunch of explicit parallels to machine learning. Someone where I work suggested that given the connections I was making I should look to a 'frontier AI lab' as an employer.

He did not see the instant flashbacks to chasing these weirdos across the internet for almost two decades, watching in horror as the religious psychosis gained national prominence and great destructive power. All he got to hear was my instant intonation of "I'm sorry Dave, I'm afraid I can't do that."

Google shut down the AlphaFold team, trying to reassign the people behind the super interesting problem of using ML to predict protein structure from sequence onto chatbot development. A whole bunch left the company.

https://www.engadget.com/2225849/google-shuts-down-alphafold/

The Business Idiots are truly running the asylum.

I truly cannot tell which of them are in religious psychosis and which of them are shameless liars

I kind of read wayyyyy too many preprints and some of that is the result of super briefly summarizing some things I have read recently. Here:

https://www.biorxiv.org/content/10.1101/2024.11.26.625518v2 poor codon optimality for your translation system leads to immunogenicity and activation of innate immune signaling in animal cells

As for length and super optimized proteins, it's mostly about RIG proteins (see https://www.pnas.org/doi/10.1073/pnas.1005077107 for an old bit of a review) and the whole DRIP hypothesis about how short mismanufactured proteins are preferentially the source of presented antigens

Biologist here.

This REALLY reminds me of how jealously cells guard their genomic DNA from interaction with nucleic acids out in the environment.

Most genetic information on Earth is malicious information, selfish replicators in the form of viruses or transposable elements or selfish elements. Things that subvert the signals within a cell for their own propagation and provide nothing productive that the cells care about. So cells jealously guard their own genomic DNA and have all kinds of checks to make sure that nothing other than that sequence gets used, and outside sequence does not get incorporated into it. ANY DNA in your cytplasm gets rapidly destroyed, double stranded RNA sets off your immune system like crazy, even RNA with sequence statistics that are not quite like that of your species can set off an inflammatory reaction, immune system cells seeing RNA inside them that is overly compact and optimized like viral RNA treat them as sources of antigen rather than self.

I cannot help but think we are living through the transformation of our non-brain-information sphere into a state like that of the genetic information sphere. Most material out there being meaningless for our purposes and us needing to jealously guard the provenance of information we use so as to not use bull, or worse, huge amounts of malicious information made to subvert us to the purposes of the powers that be that generate it.

Evolution makes parasites more reliably than anything else. How did we train text-generation systems? Basically, to mimic the written word on the page like a stick bug on a stick. They're like those beetles that live in ant colonies, sending out social signals that make the ants see them as offspring that have to be babied rather than parasites that don't contribute. They replicate the form while not being the thing that they have subverted the signals of being.

EDIT: There is something wrong with the upvote counter

Am I right in understanding that almost all the big name results in LLM-derived math recently come from big publicity projects in which someone spent ungodly amounts of money to have the thing nondeterministically fuzz huge numbers random seeds leading to independent random outputs around a topic, putting out simulacra of ideas which could be then deterministically algorithmically checked? In fields where something like finding one counterexample to a conjecture would be a big deal, or where you just need to try a huge number of possible solutions until you happen to hit on one that works, rather than follow a long train of logic?

You speak as if either he or his audience has a coherent worldview other than awe of the AI god

Comments in FAVOR of billionaires being those who seize control of the entire universe (flksdjflkdfjlsdjfl) at the expense of everyone else (!) are appearing.

Land reform / redistribution is always popular with the populi, but per your other point, unless you somehow forbid them from selling or leasing it, it will inevitably end up in the hands of those better able to use those resources pretty shortly. And I will argue that this is a good thing, at least in a capitalist and non-coercive society - much like people think of heiresses leaving their floofy little dogs mansions and million dollar annual stipends as wasteful, leaving an equal proportion of the cosmic endowment with a bunch of v1.2 murder chimps who were so unsuccessful that they couldn't even buy any of it is a colossal waste of that matter/energy. Much like land today is much more valuable to people / governments who have money, the cosmic endowment will be no different.

Today we waste something like 99. nine 9's percent of our sun's energy. If we're the only conscious and intelligent life in the universe, every other star is wasting 100% of their energy. That energy is going to be similarly wasted in the hands of average people, just like the mansions and stipends are wasted on the dogs.

"Well lease it out and profit share!" I bet you're saying. But what will a base human even DO with that energy? It's like the dog. Most "regular" people who remain human will be eaten by digital Infinite Jests, where they can the be tippy top of made up status hierarchies and live out their wildest, meaningless dreams 24/7. You probably barely need $10k a year to do that in terms of matter energy budgets.

Sure, let's guarantee a really generous UBI, Scotts $1-$2M per year in today's wealth equivalent. That's fair. But the cosmic endowment is many, many orders of magnitude more than that, and allocating it to a bunch of floofy dog equivalents is a huge waste.

Awww, but I like the pure science fiction.

I am most amazed at two aspects... how to put it:

One is just, they don't know what they are and what the universe is. The idea that things downstream of things like us can push around galaxies never ceases to amaze me. I felt the same way watching the movie Interstellar. They were using chemical rockets to navigate around a supermassive black hole. The gravitational potential between places they occupied in that film was a third of their rest mass. Chemistry means nothing there. FUSION means nothing there.

(to say nothing of the fact that if interstellar travel were possible there would already be replicators and an ecology throughout the universe, but that's another story)

The second is, things happen because of ideas and agreements rather than actions. You can speak into existence billion year plans for what happens to whole galaxies, and it happens because that is what you said. Laws exist because a bunch of people continue to agree that it's better for them to act like they do than to do what they CAN do. This is a universe without interactions, without agency of anything but the rich weirdos steering the AI god, without for lack of a better word ecology emerging from the interactions of many agents and resource constraints and capacities.

Oh Yud has DEFINITELY taken advantage of his followers like a cult leader.