eniteris

Karma: 137

In Search of Lost Time—A Review

eniteris5 Feb 2026 1:46 UTC

17 points

1 comment10 min readLW link

eniteris 13 Dec 2025 20:01 UTC
3 points
0
in reply to: Thomas Kwa’s comment on: Thomas Kwa’s Shortform
Yeah the paper seems more like a material science paper than a biology paper. There was no test/simulations/discussion about biological function; similar to DNA computing/data storage, it’s mostly interested in the properties of the material than how it interfaces with pre-existing biology.
They did optimize for foldability, and did successfully produce the folded protein in (standard bacterial) cells. So it can be produced by biological systems (at least briefly), and more complex proteins had lower yields.
Their application they looked at was hydrogels, and it seems to have improved performance there? But functioning in biological systems introduces more constraints.

eniteris 13 Dec 2025 10:10 UTC
16 points
0
in reply to: Thomas Kwa’s comment on: Thomas Kwa’s Shortform
It’s not really that they made it have more hydrogen bonds, they made it longer and therefore more hydrogen bonds. It’s like having a piece of velcro, and then using a bigger piece of velcro. Yes, the bigger velcro will be stronger. The AI was mostly used to design the scaffolding of the velcro.
They didn’t test whether it’s biologically functional (though that’s not really important if you only care about biomechanics).
Though the tintin protein is already absurdly huge, and I’m pretty sure that the time it takes to translate it is longer than the division time of a(n average) cell. And these scientists made it even bigger (or rather, one domain of it even bigger and didn’t make the rest of the protein).

eniteris 13 Dec 2025 10:01 UTC
1 point
−1
on: Insights into Claude Opus 4.5 from Pokémon
Also, he has a noticeable lack of confusion about key NPCs–Oak is consistently Oak, the player character is never “the red-hatted NPC”, and he can pick out gym leader Erika from a lineup.
I’m a little lost on this front. A person who has never encountered Pokemon before would not recognize the Oak or Erika sprite on-sight; why should the AI vision model? Perhaps one could match the Oak sprite to the full size Oak picture at the beginning of the game, but Erika? Erika can really only be identified by sprite uniqueness and placement in the top center of the gym.
I would instead think the newer models are just trained on more Pokemon, and hence can better identify Pokemon images.

eniteris 27 Nov 2025 7:07 UTC
4 points
0
in reply to: J Bostock’s comment on: Mikhail Samin’s Shortform
Minor correction on genome sizes:
DNA phage genomes have a median size of ~50kb, whereas RNA phage genomes are more around the 4kb mark.
Similarily, mammalian DNA viruses are usually >100kb, but their RNA viruses are usually <20kb.
Oddly enough the smallest known virus, porcine circovirus, is ssDNA, mammalian, and only 1.7kb
But yes, mammalian viruses are generally more difficult to culture, probably downstream of mammalian cells being more difficult to culture. Phages also typically only inject their genetic material into the cells, which bootstraps itself into a replication factory. Mammalian viruses, which generally instead sneak their way in and deliver the payload, often deliver their genetic material alongside proteins required to start the replication.

eniteris 19 Nov 2025 10:38 UTC
3 points
0
in reply to: AnthonyC’s comment on: No One Reads the Original Work
I have heard nothing about Mending Wall, so here’s my impressions as a first time reader:
Mending Wall React Comment
I can’t quite parse “Something there is that doesn’t love a wall”. It’s repeated twice, so it’s obviously important. I’m projecting my ambiguity to whether we should love the wall or not.
Later: oh, “Something there is” is equivalent to “There exists something”, practically, entropy; poetically, ???elves???
Classic ambiguous Frost on whether hunters actually destroy walls or not.
It’s obviously a commentary on “good fences make good neighbors”, the same way Dulce et Decorum Est is a commentary on the Latin phrase. This neighbor appears to be good (annual mutual wall maintenance, out-door game), but his insistence on the wall where it serves no purpose (his father’s saying, thus giving into tradition) gives the author the thought of his neighbor as an “old-stone savage armed”, upon contemplating whether the wall is to keep things in or out.
But these thoughts are “mischief” by the author, so are possibly a problem for the sake of a problem.
Also, I don’t think he tackles my interpretation of the phrase, which is about clear communication about boundaries. Frost focuses on the literal interpretation. Would apple trees outcompete pines, or vice versa? the neighbor’s insistence on a clear boundary could make sense.
Summary:
Walls are victims to entropy and must be maintained. Perhaps actively destroyed by hunters?
The mere existence of a wall can be sufficient to imagine the Other as a threat.
Please question Appeal to Tradition.
--
Good imagery and Frost style, but I still find The Road Not Taken to be more clear and more succinct.

eniteris 15 Nov 2025 10:49 UTC
1 point
0
on: List of great filk songs
Nothing from Savitsky? My personal favorites are Millenium’s Dawn and The Stuff That Dreams are Made Of, but Hacker’s Heaven gets a shout out too.

eniteris 5 Nov 2025 11:30 UTC
2 points
0
on: Suffering is what makes it special
A Casino Odyssey in Cyberspace by localroger (author of Metamorphosis of the Prime Intellect) takes place in the same post-scarcity universe. How do you have a casino under post-scarcity?
Spoilers
“The Bugsy [currency] is backed by human misery. The one thing you can buy with a Bugsy that you can’t simply ask Prime Intellect for is the suffering of another bona fide human being. Not a facsimile or a simulation or a recording, but a real live person who feels as you feel.”

eniteris 28 Oct 2025 7:14 UTC
1 point
0
in reply to: Davidmanheim’s comment on: Maybe Use BioLMs To Mitigate Pre-ASI Biorisk?
It seems they were literally using the nonpathogenic attenuated anthrax strain used for vaccines.

eniteris 17 Oct 2025 15:37 UTC
1 point
0
in reply to: J Bostock’s comment on: Maybe Use BioLMs To Mitigate Pre-ASI Biorisk?
marginal bioterrorist
I’m not sure a marginal bioterrorist can train an AI model to obfuscate a DNA sequence to bypass the sequence scanning, but I concede it’s definitely easier to do than recode an organism. I’m not really sure what the skillset/resources of a marginal bioterrorist are.
But we should watch out for proliferation/commercialization of recoded organisms, since recoded organisms would be easier to recode further (if they introduce a new codon, just modify the synthetase to load a different amnio acid).
A marginal bioterrorist could probably just brew up a vat of anthrax which technically counts. Advanced labs definitely have more capacity for modification, but they still need to source the pathogens.

eniteris 17 Oct 2025 12:05 UTC
4 points
9
on: Maybe Use BioLMs To Mitigate Pre-ASI Biorisk?
I’m not a fan of the phage synthesis paper as there was a lot of post-generation filtering and failures going on and the AI-generated phages were basically the same. There’s a couple interesting new mutations, but a lot of them are noncoding/synonymous/in nonessential genes.
Judging by your writing I think you missed a new paper red-teaming DNA synthesis screening software. They’re using AI to create proteins that function the same but with different amino acids (probably conformation-based) which bypasses the DNA screening, because screening (probably) isn’t translating and throwing it into Alphafold and comparing it to known toxins. Though the paper didn’t test whether the AI-generated toxins are actually toxic, but we can assign that a reasonable probability.
That being said...translating DNA to protein with standard codon table is just one encoding scheme. And we can recode organisms to use a different encoding scheme. And no DNA screening would be able to catch it, since they have no knowledge of the nonstandard codon table you’re using.
Also thanks for bringing up the Germy Paradox; I seemed to have missed that sequence.

eniteris 3 Sep 2025 16:14 UTC
31 points
15
in reply to: Hastings’s comment on: The Cats are On To Something
(a sharp distinction from Sniffles the teacup poodle. I don’t care if you think you’re happy, this would not please the prowling wolves of the stone age.)
I have issues with this: I don’t think you can claim that wildcats of the stone age would be pleased with what we’ve done to domestic cats either, sticking them in tiny territories where they cannot roam, kingdoms of a cage. I’m not sure using human judgement in this matter is very useful as we don’t have a good concept of what other species value.
I don’t think evolutionary pressure is an intelligence; it’s in the name. It’s a pressure, like air pressure or water pressure, not an intelligence. There is no agency. The end results can be marvelous all the same. Evolution appears to make FDT-style trades, but is actually completely myopic. It’s survival of the survivors. If you’re dead, we don’t see you.
Also sociality in spiders has evolved independently at least twenty times, and keeps going extinct. It’s probably an evolutionary dead end due to inbreeding [1]. Evolution is completely myopic.
no one is building rooms full of cats on heroin.
We do, however, build rooms full of cats and catnip.

eniteris 7 Jul 2025 9:41 UTC
17 points
3
in reply to: DanielFilan’s comment on: The Cult of Pain
Actually I think the numbers are comparable.
The WHO issued a statement (August 2024) that ~175k people die per year in Europe due to heat (between 2000-2019, statement with source, based off a 2021 study, for reference, they also estimate ~660k cold-related deaths per year).
For other studies, we have two from Nature (2023, summer 2022), which give estimates of ~50k and ~60k heat-related deaths (I assume most heat related deaths take place during the summer). The Lancet has a study (2024) that finds that between 1991 and 2020, there was a median of ~40k heat-related deaths (and ~360k cold-related deaths) per year.
For gun deaths, the CDC (via Pew) states ~45k gun-related deaths in the USA in 2023, so a comparable number, although slightly less.
Of course, Europe has about twice the population as the USA, so one should make per capita adjustments accordingly.

eniteris 21 Dec 2024 19:47 UTC
4 points
2
in reply to: Ulrik Horn’s comment on: Last Line of Defense: Minimum Viable Shelters for Mirror Bacteria
You cannot completely understand the immune system; that is something you learn early on in immunology.
That being said, the key understanding on mirror bacteria evading the immune system is that the immune system generally relies on binding to identify foreign invaders, and if they cannot bind then they cannot respond. Bacteria generally share a number of molecules on their surface, so the innate immune system has evolved to bind and detect these molecules. If they were mirrored, they would not bind as well, and would be harder to detect and respond to.
That being said, you did find the insight that they are not completely invisible. There are also systems that can detect the damage done by the infection and start a counterattack, even if they can’t see the invaders themselves. But much of the counterattack would not be able to affect the mirror bacteria.
What matters in the report is that the immune system of all animals and plants will likely be (much) less effective against mirror bacteria. This doesn’t mean it’s an untreatable disease, as we have antibiotics that should still be effective against the mirror bacteria. But it does mean that if the mirror bacteria finds its way into the environment it is unlikely that anything can fight back well.

eniteris 21 Dec 2024 19:27 UTC
3 points
0
in reply to: Ulrik Horn’s comment on: Last Line of Defense: Minimum Viable Shelters for Mirror Bacteria
I work with bacterial viruses in liquids, and when we want to separate the bacteria from their viruses, we pass the liquid through a 0.22um filter. A quick search shows that the bacteria I work with are usually 0.5um in diameter, whereas the smallest bacteria can be down to 0.13um in diameter; however, the 0.22um filter is fairly standard for laboratory sterilization so I assume smaller bacteria are relatively rare. The 0.22um filter can also be used for gases.
But as with my usage, they block bacteria and not viruses. I’m working with 50nm-diameter viruses, but viruses of bacteria are generally smaller than those of animals; SARS-CoV2 is somewhere from 50-140nm.
If you use a small enough filter it would still filter out the viruses; but you’ll need to get a pore size smaller than what is sufficient for filtering out bacteria. (and smaller pores requires more pressure, more prone to clogging, etc.)
(though for air, it’s quite rare for bare viruses to be floating around; they’re usually in aerosols (bacteria are often also in aerosols, which may be easier to filter out)

eniteris 21 Dec 2024 11:28 UTC
14 points
4
on: Last Line of Defense: Minimum Viable Shelters for Mirror Bacteria
I think focusing framing against mirror bacteria is harmful for the project, as opposed framing it as protection against any general (synthetic) biology risk. Or even colonization of an alien biosphere.
There are a few classes of commonly-used antibiotics that are achiral and would still work against mirror bacteria (trimethoprim, sulfa drugs). We lose the most commonly used ones, but any human infection could probably be treated with these achiral antibiotics, especially since the growth of mirror bacteria is likely slow due only being able to utilize a small fraction of resources. They could evolve resistance, but they would lack access to horizontal gene transfer from non-mirror bacteria, requiring any resistance mechanisms to evolve de novo.
The main threat of mirror bacteria isn’t direct infection of humans, but how they could reshape the biosphere and impact food security, which hiding in a shelter does not protect you from. Other, more targeted risks, such as bioweapons, pandemics and viral outbreaks would be better served by these shelters (though I’m unsure if your filtration system is designed for viruses).

eniteris 30 Sep 2024 12:52 UTC
2 points
0
on: Of Birds and Bees
Nitpicking at the example, worker bees do not have offspring; the best way for them to spread their genes is to protect the queen and thus, the hive.

Birds can have offspring, so self-preservation instead of risky attacks is optimal for individuals of a flock (of genetically unrelated individuals).

It’s not that the group is less intelligent, rather that the individuals of the group have different goals (self-preservation vs hive preservation, though the end goal of maximizing fitness is the same).

But genetic fitness breaks down as a metric when you add culture to the system, so application to humans is limited.

eniteris 19 Sep 2024 9:58 UTC
5 points
3
in reply to: Dana’s comment on: Pronouns are Annoying
It is important to note that people have a wide range of attachment to their gender identity, ranging from willing to undergo extreme body modification in order to match their gender identity, to those who don’t care in the slightest.
The issue is that cisgender is the default, and if you don’t have a strong attachment to your gender identity, you have no reason to change the label. Hence, cisgendered people have a wide range of attachment to their gender identity, from strongly identifying with it to no attachment at all.
(There is also the group of agender, which includes those who have deeply examined their gender identity and decided that they don’t really care (and probably also want to signal their examination and non-caring of gender identity))
Someone who is transgender obviously has an attachment to their gender identity, and this is obviously from which the Pronoun Discourse stems. They have a strong preference for a gender, and a preference to be referred to with the appropriate pronouns, and thus being misgendered is upsetting, as their preferences are violated.
(Of course, most of this rests on the ability to communicate the preference, and accidental violations when the preference was not communicated are less egregious than deliberate violations.)
Otherwise misgendering can be upsetting if it is tied to stereotypes of masculinity and femininity and attempting an insult based off those stereotypes.

eniteris 17 Jun 2024 10:24 UTC
6 points
3
on: Our Intuitions About The Criminal Justice System Are Screwed Up
Incarceration plays three roles (to varying degrees of success): punishment (and therefore deterrent), rehabilitation and exclusion from society.
One group of people would prefer focusing on rehabilitation rather than punishment, and are likely those who oppose solely serving vegan food to prisoners. Another group of people sees prisoners as no longer human and deserving of moral concern, and think that the cruelty of prison is the point.
The US prison system leans more towards the latter than the former (see: mandatory prison labor), though other places in the world lean differently. How far and in what direction prison systems should lean is a topic for philosophical debate.
Though also note that degree of punishment doesn’t really correlate with deterrence from crime (review Apel and Nagin (2011), tl;dr: more about certainty of getting caught, it’s complicated)

eniteris 10 Apr 2024 0:32 UTC
2 points
0
in reply to: Marco Murgia’s comment on:
I’m getting lost and confused here.
I think Dawkin’s God meme refers to all kinds of religious thought; of all practices ascribing cause to unknown capricious forces beyond control, but it’s been a while since I’ve read it and that might be a generous interpretation.
There is information, and there is context, and information in the right context can self-replicate. This framework applies to both memes and genes. Your analogy framework states that the two are not necessarily identical, and I agree. But this, as you say, does not preclude analogy from having its revelatory function.
I think evolutionary lens to look at memes is an interesting one, even if it does not explain everything. I think it’s most misleading from a competition aspect, as only mutually exclusive ideas compete to extinction (other than vague definitions of attention), and you rightly point out that mutation of ideas is a much less random processes.