Did you know that plants can also tell the time via a special protein (photoreceptor) that responds to a wavelength of light only occurring at dusk — far red light is light that has a longer wavelength than regular red light, but shorter than infrared.

Far red light occurs at dusk because as the Earth rotates, it effectively stretches out the light waves (from the perspective of a place where the sun is setting). It’s basically the same phenomenon as how galaxies that are moving away from us appear to be red (red shift), but on a smaller more subtle scale.

Being able to detect far red light means that a plant can also use mechanisms involving this photoreceptor to perceive the changing of the seasons. For example, if on one day, the sun sets at 6:00pm, and the next day, it sets at 6:05pm, then 6:10pm etc., then the amount of time between each dusk is getting shorter, which means that it’s spring. This is so cool and it blows my mind.

Useful context: I am a biochemist with a passing interest in neuroscience (plus some friends who work in neuroscience research).

A brief minor point is that you should consider uploading the preprint as a pdf instead, as .docx can cause formatting errors if people aren’t using the same word processor as you. Personally, I saw some formatting issues related to this (though nothing too serious).

Onto the content of your work, something I think your paper would benefit from is linking to established research throughout. Academia’s insistence on good citations throughout can feel like it’s mostly just gatekeeping, but it’s pretty valuable for demonstrating that you’re aware of the existing research in the area. This is especially important for research in a topic like this tends to attract a lot of cranks (my friends tell me that they fairly frequently get slightly unhinged emails from people who are adamant that they have solved the theory of consciousness). Citations throughout the body of your research makes it clear what points are your own, and what is the established research.

Making it clear what you’re drawing on is especially important for interdisciplinary research like this, because it helps people who know one part of things really well, but don’t know much about the others. For example, although I am familiar with Friston’s paper, I don’t know what has happened in the field since then. I also know some information theory stuff, but not much. Citations are way of implicitly saying “if you’re not clear on where we’re getting this particular thing from, you can go read more here”.

For example, if you have a bit that’s made up of 2 statements:

• (1): Something that’s either explicitly stated in Friston’s paper, or is a straightforwardly clear consequence of something explicitly stated
• (2): Something that your analysis is adding to Friston’s as a novel insight or angle

Then you can make statement 2 go down far easier if that first statement. I use Friston in this example both because I am familiar with the work, but also because I know that that paper was somewhat controversial in some of its assumptions or conclusions. Making it clear what points are new ones you’re making vs. established stuff that’s already been thoroughly discussed in its field can act sort of like a firebreak against criticism, where you can have the best of both worlds of being able to build on top of existing research while also saying “hey, if you have beef with that original take, go take it up with them, not us”. It also makes it easier for someone to know what’s relevant to them: a neuroscientist studying consciousness who doesn’t vibe with Friston’s approach would not have much to gain from your paper, for instance.

It’s also useful to do some amount of summarising the research you’re building on, because this helps to situate your research. What’s neuroscience’s response to Friston’s paper? Has there been much research building upon it? I know there have been criticisms against it, and that can also be a valid angle to cover, especially if your work helps seal up some holes in that original research (or makes the theory more useful such that it’s easier to overlook the few holes). My understanding is that the neuroscientific answer to “what even is consciousness?” is that we still don’t know, and that there are many competing theories and frameworks. You don’t need to cover all of those, but you do need to justify why you’re building upon this particular approach.

In this case specifically, I suspect that the reason for building upon Friston is because part of the appeal of his work is that it allows for this kind of mathsy approach to things. Because of this, I would expect to see at least some discussion of some of the critiques of the free energy principle as applied to neuroscience, namely that:

• The “Bayesian brain” has been argued as being an oversimplification
• Some argue that the application of physical principles to biological systems in this manner is unjustified (this is linked to the oversimplification charge)
• Maths based models like this are hard to empirically test.

Linked to the empirical testing, when I read the phrase “yielding testable implications for cognitive neuroscience”, I skipped ahead because I was intrigued to see what testable things you were suggesting, but I was disappointed to not see something more concrete on the neuroscience side. Although you state

“The values of dI/dT can be empirically correlated with neuro-metabolic and cognitive markers — for example, the rate of neural integration, changes in neural network entropy, or the energetic cost of predictive error.”

that wasn’t much to go on for learning about current methods used to measure these things. Like I say, I’m very much not a neuroscientist, just someone with an interest in the topic, which is why I was interested to see how you proposed to link this to empirical data.

I know you go more into depth on some parts of this in section 8, but I had my concerns there too. For instance, in section 8.1, I am doubtful of whether varying the temporal rate of novelty as you describe would be able to cause metabolic changes that would be detectable using the experimental methods you propose. Aren’t the energy changes we’re talking about super small? I’d also expect that for a simple visual input, there wouldn’t necessarily be much metabolic impact if the brain were able to make use of prior learning involving visual processing.

I hope this feedback is useful, and hopefully not too demoralising. I think your work looks super interesting and the last thing I want to do is gatekeep people from participating in research. I know a few independent researchers, and indeed, it looks like I might end up on that path myself, so God knows I need to believe that doing independent research that’s taken seriously is possible. Unfortunately, to make one’s research acceptable to the academic community requires jumping through a bunch of hoops like following good citation practice. Some of these requirements are a bit bullshit and gatekeepy, but a lot of them are an essential part of how the research community has learned to interface with the impossible deluge of new work they’re expected to keep up to date on. Interdisciplinary research makes it especially difficult to situate one’s work in the wider context of things. I like your idea though, and think it’s worth developing.

A friend once said that she finds the invasiveness of this legitimately a little triggering, because it so vividly reminds her of the time she spent with an extremely abusive partner, who would similarly restrict her ability to meaningfully say no to something.

Ever since she made this point to me, I realised that I had been thinking of online consent dialogs as being distinct from the general concept of consent that we use in other life contexts (such as sexual consent, medical consent etc.). Since then, I have started to fold the online stuff into the more general notion of consent, which adds a whole bunch of connotations that makes me feel far more icky whenever I see a dialog that doesn’t let you say no.

Good blog post, thanks for sharing. I like the point about companies double dipping by trying to extract both our data and our money; I feel like I’m probably going to use that at some point when I’m on my soapbox and complaining about big tech.

I liked that although Knights of Guinevere was clearly ragging on Disney, it felt like it wasn’t just a cathartic trauma dump from Dana Terrace and crew — it was actually being used to say something meaningful. It’s a good sign when the pilot episode of a show has such a strong sense of themes.

I’d heard a lot of hype when the pilot was released, but didn’t get around to watching it until I randomly thought “I wonder what Dana Terrace is up to nowadays? Hopefully she’s working somewhere better than Disney, because surely there must be someone with power out there who recognised how Disney was squandering her potential”. When I saw that it was her and some of the Owl House team who made Knights of Guinevere, that caused me to immediately go watch it. The only disappointment was that we don’t know when new episodes will be available, but hopefully things will be regular once we do start getting episodes.

“He blew the doors off of something we already knew was happening.”

Usually when an investigation blows the doors off of something, it’s because although many people were aware of what was happening inside, not enough did. Even if the primary gain is bringing awareness to an issue, investigative journalism like this is still important. After all, the doors were closed for a reason

My impression (as someone who is not an economist) is that a lot of it is linked to not-too-distant history: the typical “go-to” strategies for deflation under the prevalent monetarist ideas (i.e. economic school of thought about influencing the economy by controlling the amount of money in circulation) weren’t effective in combatting deflation in a few cases in Japan and the US in the early 1990s and early 2000s.

So perhaps it causes such panic because it exposes the weaknesses in the economic models that we see dominating modern politics. Inflation may be perceived as more manageable because it acts according to what the models say will happen, more or less, which makes it more controllable. It seems that may be less true for deflation.

Your comment fills me with a deep dread that causes me to feel like saying something to discourage you from this path. Alas, it’s not your preparation that is causing that feeling, but the grim circumstances that necessitate this kind of planning.

It’s difficult being on the other side of the world and completely unable to do anything than just watch as America descends deeper into fascism. However, I’m glad that I am not in the impossible position of making the decisions you’re making. I’m sorry that you are.

Good luck, I hope you don’t die. And I hope that people like you are able to claw back democracy from the fascists

This reminds me of an excellent episode of Dark Net Diaries, “Jeremy from Marketing”. https://pca.st/episode/52252c9e-e4a8-42f6-85f5-f162ec3f6b40

Vim has long since won the war. I say that as an emacs user who is familiar with using vim because it’s installed by default on the vast majority of computers I interact with nowadays

I don’t have input on cameras specifically, but I have gone pretty deep into trying to understand how to maximise security and interoperability in smart home stuff, through open source control.

A starting point for the you-in-control app to use for smart devices is Home assistant. I was surprised by how easy it was to set up self hosted smart home stuff, largely because there’s loads of guides that build around home assistant. So whether a particular camera works with home assistant is a good starting search filter

For a while, I was subscribed as a patron to Elisabeth Bik’s Patroeon. She’s a microbiologist turned “Science Integrity Specialist” which means she investigates and exposes scientific fraud. Despite doing work that’s essential to science, she has struggled to get funding because there’s a weird stigma around what she does; It’s not uncommon to hear scientists speak of people like her negatively, because they perceive anti-fraud work as being harmful to public trust in science (which is obviously absurd, because surely recognising that auditing the integrity of research is necessary for building and maintaining trust in science).

Anyway, I mention this because it’s one of the most dystopian things I’ve directly experienced in recent years. A lot of scientists and other academics I know are struggling financially, even though they’re better funded than she is, so I can imagine that it’s even worse for her. How fucked up is it for scientific researchers to have to rely on patrons like me (especially when people like me are also struggling with rising living costs).

It’s from 2024, but some of the best coverage of the use of AI in this genocide is from 972mag, a journalistic outlet whose team includes Israelis and Palestinians. https://www.972mag.com/lavender-ai-israeli-army-gaza/

Thanks for that, I appreciate it.

Noted, thank you

I was talking about this recently with someone (read: ranting as they nodded sympathetically) and I finished up by saying “what’s the point of ‘smart’ tech if the humans who use it are steadily disempowered and ultimately, made less smart?”

I’ve recently been dabbling in HomeAssistant and learning how to set things up properly feels like it’s been making me more smart.

Do you have a link? Because if you tell me you found it but don’t tell me where, then that may put you at risk of being in the same ring of hell as people who comment “nvm, solved it” to their tech forum posts.

That’s incredible, thank you for sharing

As a society, we need to better value the labour that goes into our collective knowledge bases. Non-English Wikipedia is just one example of this, but it highlights the core of the problem: the system relies on a tremendous amount of skilled labour that cannot easily be done by just a few volunteers.

Paying people to contribute would come with problems of its own (in a hypothetical world where this was permitted by Wikipedia, which I don’t believe it is at present), but it would be easier for people to contribute if the time they wanted to volunteer was competing with their need to keep their head above the water financially. Universal basic income, or something similar, seems like one of the more viable ways to improve this tension.

However, a big component of the problem is around the less concrete side of how society values things. I’m a scientist in an area where we are increasingly reliant on scientific databases, such as the Protein Database (pdb), where experimentally determined protein structures are deposited and annotated, as well as countless databases on different genes and their functions. Active curation of these databases is how we’re able to research a gene in one model organism, and then apply those insights to the equivalent gene in other organisms.

For example, the gene CG9536 is a term for a gene found in Drosophila melanogaster — fruit flies, a common model organism for genetic research, due to the ease of working with them in a lab. Much of the research around this particular gene can be found on flybase, a database for D. melanogaster gene research. Despite being super different to humans, there are many fruitfly genes that have equivalents in humans, and CG9536 is no exception; TMEM115 is what we call it in humans. The TL;DR answer of what this gene does is “we don’t know”, because although we have some knowledge of what it does, the tricky part about this kind of research is figuring out how genes or proteins interact as part of a wider system — even if we knew exactly what it does in a healthy person, for example, it’s much harder to understand what kinds of illnesses arise from a faulty version of a gene, or whether a gene or protein could be a target for developing novel drugs. I don’t know much about TMEM115 specifically, but I know someone who was exploring whether it could be relevant in understanding how certain kinds of brain tumours develop. Biological databases are a core component of how we can big to make sense of the bigger picture.

Whilst the data that fill these databases are produced by experimental research that are attached to published papers, there’s a tremendous amount of work that makes all these resources talk to each other. That flybase link above links to the page on TMEM115, and I can use these resources to synthesise research across so many separate fields that would previously have been separate: the folks who work on flies will have a different research culture than those who work in human gene research, or yeast, or plants etc. TMEM115 is also sometimes called TM115, and it would be a nightmare if a scientist reviewing the literature missed some important existing research that referred to the gene under a slightly different name.

Making these biological databases link up properly requires active curation, a process that the philosopher of Science Sabine Leonelli refers to as “data packaging”, a challenging task that includes asking “who else might find this data useful?” ^[1]. The people doing the experiments that produce the data aren’t necessarily the best people for figuring out how to package and label that data for others to use because inherently, this requires thinking in a way that spans many different research subfields. Crucially though, this infrastructure work gives a scientist far fewer opportunities to publish new papers, which means this essential labour is devalued in our current system of doing science.

It’s rather like how some of the people who are adding poor quality articles to non-English Wikipedia feel like they’re contributing because using automated tools allows them to create more new articles than someone with actual specialist knowledge could. It’s the product of a culture of an ever-hungry “more” that fuels the production of slop, devalues the work of curators and is degrading our knowledge ecosystem. The financial incentives that drive this behaviour play a big role, but I see that as a symptom of a wider problem: society’s desire to easily quantify value causing important work that’s harder to quantify to be systematically devalued (a problem that we also see in how reproductive labour (i.e. the labour involved in managing a family or household) has historically been dismissed).

We need to start recognising how tenuous our existing knowledge is. The OP discusses languages with few native speakers, which likely won’t affect many who read the article, but we’re at risk of losing so much more if we don’t learn to recognise how tenuous our collective knowledge is. The more we learn, the more we need to invest into expanding our systems of knowledge infrastructure, as well as maintaining what we already have.

[1]: I am not going to cite the paper in which Sabine Leonelli coined the phrase “data packaging”, but her 2016 book “Data-Centric Biology: A Philosophical Study”. I don’t imagine that many people will read this large comment of mine, but if you’ve made it this far, you might be interested to check out her work. Though it’s not aimed at a general audience, it’s still fairly accessible, if you’re the kind of nerd who is interested in discussing the messy problem of making a database usable by everyone.

If your appetite for learning is larger than your wallet, then I’d suggest that Anna’s Archive or similar is a good shout. Some communities aren’t cool with directly linking to resources like this, so know that you can check the Wikipedia page of shadow library sites to find a reliable link: https://en.wikipedia.org/wiki/Anna’s_Archive

This isn’t useful to me at the moment, but nonetheless, I really appreciate when people like you take the time to share knowledge in this way.

There is a special place in heaven for the people who do this, just as there’s a special place in hell for people who reply to their own forum post about a complex technical problem.

(Side note: I tried the find the xkcd where he is yelling at his computer after finding a forum post from someone who has the exact same computer problem as he does, but the original poster hasn’t updated it. Alas, I couldn’t. If anyone knows which one I mean, I’d appreciate you pointing me to it, because it’ll drive me mad until I remember how to find it)