2024-07-23

an introductory section on computers, followed by five

sections exploring the limitations of computers arising from the structure of

logic gates, from mathematical logic, from the unreliability of their components,

from the thermodynamics of computing and from the physics of semiconductor

technology

^ this seems pretty cool!

Could I understand a Turing machine?

Charles Bennett, Rolf Landauer

Rather, computer science is like engineering - it is all about getting something

to do something, rather than just dealing with abstractions as in pre-Smith

geologyl. Today in computer science we also need to "go down into the mines"

- later we can generalize. It does no harm to look at details first

It has illuminated the nature of language, which we thought we

understood: early attempts at machine translation failed because the old-

fashioned notions about grammar failed to capture all the essentials of language.

It naturally encourages us to ask questions about the limits of computability,

about what we can and cannot know about the world around us. Computer

science people spend a lot of their time talking about whether or not man is

merely a machine, whether his brain is just a powerful computer that might one

day be copied; and the field of 'artificial intelligence' - I prefer the term

'advanced applications' - might have a lot to say about the nature of 'real

What is special about biology? What of biology will continue into the future?

“The reason for this is that once you get down to the guts of

computers you find that, like people, they tend to be more or less alike.”

Why are computers digital and is that important for them being computers?

“Let us get a little abstract for the moment and ask: how do you connect

up which set of elements to do the most things”

^ what is this notion of generality, and what types of things are on the tablet do?

What is the principle of Universality?

“A - the way it works, its "state

transition rules" and what-not. Assume that machine B is capable of merely

describing the state of A. We can then use B to simulate the running of A by

describing its successive transitions; B will, in other words, be mimicking A. It

could take an eternity to do this if B is very crude and A very sophisticated, but

B will be able to do whatever A can, eventually. We will prove this later in the

course by designing such a B computer, known as a Turing machine.”

What is Von Neumann architecture?

“All we would lose by the omission of "parallel processing" is speed, nothing fundamental” <- is this true?

Storing information, doing things with that stored information, changing the information

Breaking things down into their component parts

Layers of abstraction

What does universal computation look like, and to what does it imply? If intelligence is an algorithm, then perhaps it applies to it, if consciousness is or is not - that is a question.

When can you count on emergent phenomena occurring, at what level of simulation?

What are gates? What is logic? Why do computers implement logic? What relation does it have to mathematics?

What does it mean to ‘compute’ something and is that similar to what it means to simulate or create something?

Suppose that these simulated people are conscious (as they would be if the simulations were sufficiently fine-grained and if a certain quite widely accepted position in the philosophy of mind is correct)

^ what is the widely accepted position, and for what reasons should we accept it?

“Bostrom's argument rests on the premise that given sufficiently advanced technology, it is possible to represent the populated surface of the Earth without recourse to digital physics; that the qualia experienced by a simulated consciousness are comparable or equivalent to those of a naturally occurring human consciousness, and that one or more levels of simulation within simulations would be feasible given only a modest expenditure of computational resources in the real world”

What would be the moral arguments against, or for, simulations?

1. "The fraction of human-level civilizations that reach a posthuman stage (that is, one capable of running high-fidelity ancestor simulations) is very close to zero", or

2. "The fraction of posthuman civilizations that are interested in running simulations of their evolutionary history, or variations thereof, is very close to zero", or

3. "The fraction of all people with our kind of experiences that are living in a simulation is very close to one."

How much computing power is a future civilization likely to have? What are the bounds on this?

As a corollary to the trilemma, Bostrom states that "Unless we are now living in a simulation, our descendants will almost certainly never run an ancestor-simulation."

^ does this assume we know a bit too much about

- How much computing power will be available

- How plausible it is that simulated minds will be conscious

hilosopher Barry Dainton modifies Bostrom's trilemma by substituting "neural ancestor simulations"

What are the limits to computation? And what are they imposed by? The laws of physics or…computation?

Why would knowing that you are in a simulation end the simulation?

AI agent dream

How do arguments about the value of knowing whether you are in a simulation or not, and no-self, interact?

“In physics, the view of the universe and its workings as the ebb and flow of information was first observed by Wheeler”

“Indeed, thinking about computing as arising from faulty components, it seems as if the abstraction that uses perfectly operating computers is unlikely to exist as anything but a platonic ideal.”

You could always imagine you were a simpler thing, could you?

In On Certainty, the philosopher Ludwig Wittgenstein has argued that such skeptical hypothesis are unsinnig (i.e. non-sensical), as they doubt knowledge that is required in order to make sense of the hypotheses themselves

^ how does this work?

A state of mastery, of understanding of a topic

“It is nothing more than a moral prejudice that truth is worth more than semblance; it is, in fact, the worst proved supposition in the world.... Why might not the world which concerns us⁠—be a fiction?”

How did McCulloch and Pitts think about the computational theory of mind?

An early, though indirect, criticism of the computational theory of mind comes from philosopher John Searle. In his thought experiment known as the Chinese room, Searle attempts to refute the claims that artificially intelligent agents can be said to have intentionality and understanding and that these systems, because they can be said to be minds themselves, are sufficient for the study of the human mind

2024-07-24

p2p computing

Nodes usually find other nodes through some sort of public broadcast signal

https://nadia.xyz/peer-to-peer-at-scale

Reward systems in peer to peer networks

“A wise man once said:

A distributed system is one in which the failure of a computer you didn’t even know existed can render your own computer unusable.

“

How is, or isn’t, the internet a p2p resource?

How do computers talk to each other?

What is the difference between decentralized and centralized?

Portals into peer to peer networks

With peer to peer vs centralized, in both contexts, aren’t you talking to a computer - I see, in p2p, you don’t necessarily expect to get the full answer from one machine, and the protocol plays a greater role

P2P protocols have to operate in an "environment of unstable connectivity and unpredictable IP addresses"

^ with p2p, there’s just more…uncertainty and entropy?

Do computers continuously loop to monitor? What would analog computers look like? How does noise relate to this? How does noise, and its relation to computing, factor into the future of computing?

How are the peers incentivized?

1. Listen for connections

2. Process received messages

3. Respond to messages

How does code do governance?

Are the smart contracts themselves stored on the blockchain or just the calls?

What is the ethereum virtual machine?

Where is ethereum’s protocol

Ethereum nodes are the ethereum blockchain.

“This includes "gossiping" information (one-to-many communication) over the network as well as swapping requests and responses between specific nodes (one-to-one communication)”

This requires two separate p2p networks: one connecting execution clients for transaction gossip and one connecting consensus clients for block gossip.

“A blockchain is a public database that is updated and shared across many computers in a network.”

Who decides or proposes smart contracts - will the protocols themselves ever do that/

Public games as things to build

How are blocks fundamental to blockchain? What would it look like if they were not?

Obsidian?

Are smart contracts stored in blocks, or not? How are they saved?

What is the most complex NFT - are we limited by storage capacity for these images or videos?

“There is a system of rewards and penalties that strongly incentivize participants to be honest and available online as much as possible.”

What is a blockchain with a computer embedded in it?

Everyone agrees what the ethereum virtual machine state is?

Does the EVM typically split up computations, or keep them all in one place?

What is the computational capacity of the EVM?

“As of my knowledge cutoff in August 2023, the gas limit per block on the Ethereum mainnet was around 30 million gas. This gas limit allows for a certain number of transactions and computational operations to be included in each block.”

^ how much computation is this?

What is the equivalent of ether for bacteria - can they send each other resources?

**

“The amount of ETH paid corresponds to the resources required to do the computation. These bounties also prevent malicious participants from intentionally clogging the network by requesting the execution of infinite computation or other resource-intensive scripts, as these participants must pay for computation resources.”

Does staking ETH mean you have to be $$ to have sway on the network?

Who has the most computation -> can overwhelm a network, what would this look like, how is it limited

What does non-digital computation look like?

“Any developer can create a smart contract and make it public to the network, using the blockchain as its data layer, for a fee paid to the network. Any user can then call the smart contract to execute its code, again for a fee paid to the network.”

^ what does it mean to use the blockchain as its data layer

Blockchain is called that because

How does the EVM work? How complex is its state?

Questions:

- What would an EVM with distributed state look like?

-

2024-07-25

How fast will available blockchain compute increase?

How can the EVM execute arbitrary code?

Universality of computation

What can’t be computed - quail?

What can a Turing machine do that a finite state machine cannot do?

What is the theory of computation?

Moving between states vs…what else, what is the continuum

“In the context of Ethereum, the state is an enormous data structure called a modified Merkle Patricia Trie, which keeps all accounts linked by hashes and reducible to a single root hash stored on the blockchain.”

How are Bitcoin and the social contract related?

What is a cryptographically secure, transaction-based state machine?

What is a trustful object messaging compute framework?

“facilitate transactions between

consenting individuals who would otherwise have no means

to trust one anothe”

lock-

chain with a Turing-complete language and an effectively

unlimited inter-transaction storage capability

allowing a receiver to make a physical assertion without

having to rely upon trust

Transaction-based state machine

“anything

that can currently be represented by a computer is admis-

sible”

What is the Ethereum state transition function?

ETH is a way to incentivize computation

You want to avoid nodes not agreeing with each other

How do nodes in Ethereum decide which shall compute which thing?

The EVM is a quasi–Turing-complete state machine; "quasi" because all execution processes are limited to a finite number of computational steps by the amount of gas available for any given smart contract execution

Halting problem

https://cypherpunks-core.github.io/ethereumbook/13evm.html < this is pretty great

“Ethereum acts like a single-threaded machine, without any scheduler


Do miners compute the whole thing or a part of a thing

How does mining work in Bitcoin - do they do the same thing in parallel

Consensus

In other words, consensus is intended to produce a system of strict rules without rulers

What are the benefits of consensus through one source - not as much time / energy computing?

Arguably, PoW is the most important invention underpinning Bitcoin

the real purpose of mining (and all other consensus models) is to secure the blockchain, while keeping control over the system decentralized and diffused across as many participants

Ethash is dependent on the generation and analysis of a large dataset, known as a directed acyclic graph

The more independent miners there are the more decentralized the mining power is

I see - you can shard computation in proof of stake but not proof of work?

Parallel computing - divide a task you know you have - biology is more of a search process

How would you store data on chain? What drives gas costs?

a Byzantine fault–tolerant consensus algorithm for synchronization of state updates (a proof-of-work blockchain)

ether is intended as a utility currency

What is a gossip protocol in peer to peer networks?

Finding out how to scale communication to larger systems

“anything else needed additional off-chain layers, and that immediately negated many of the advantages of using a public blockchain”

“The world’s computer started serving the world.”

What is the function to be run, and how do we evaluate whether this was run

He proved that there are classes of problems that are uncomputable. Specifically, he proved that the halting problem (whether it is possible, given an arbitrary program and its input, to determine whether the program will eventually stop running) is not solvable.

- Globally accessible singleton state (this is the block?) + virtual machine (this is the protocol or the thing which we all agree to validate (?))

How do new nodes find each other - is this a centralized point (?)

‘Machine level opcodes the same certainty as bitcoin transactions’

EVM has stack based architecture

Nick Szabo social scalability

http://unenumerated.blogspot.com/2017/02/money-blockchains-and-social-scalability.html?source=post_page-----9f821905a73e--------------------------------

Social scalability is the ability of an institution –- a relationship or shared endeavor, in which multiple people repeatedly participate, and featuring customs, rules, or other features which constrain or motivate participants’ behaviors -- to overcome shortcomings in human minds and in the motivating or constraining aspects of said institution that limit who or how many can successfully participate. Social scalability is about the ways and extents to which participants can think about and respond to institutions and fellow participants as the variety and numbers of participants in those institutions or relationships grow.  It's about human limitations, not about technological limitations or physical resource constraints. There are separate engineering disciplines, such as computer science, for assessing the physical limitations of a technology itself, including the resource capacities needed for a technology to handle a greater number of users or a greater rate of use. Those engineering scalability disciplines are not, except by way of contrast with social scalability, the subject of this essay.

“Without institutional and technological innovations of the past, participation in shared human endeavors would usually be limited to at most about 150 people – the famous “Dunbar number”.  In the Internet era, new innovations continue to scale our social capabilities. In this article I will discuss how blockchains, and in particular public blockchains that implement cryptocurrencies, increase social scalability, even at a dreadful reduction in computational efficiency and scalability”

^ huh - that’s very interesting

Increasing the effective size of group which can participate in an institution - what does it mean to participate in an institution

“A wide variety of innovations reduce our vulnerability to fellow participants, intermediaries, and outsiders, and thereby lower our need to spend our scarce cognitive capacities worrying about how an increasingly large number of increasingly diverse people might behave. Another class of improvements motivates the accurate collection and transmission of valuable information between an increasing number and variety of participants. Yet other advances enable a wider number or variety of mutually beneficial participants can discover each other. “

Question: How do bacteria incentivize each other in group communication?

Question: Is there a way to shard computation such that nodes compute things which are not equivalent

2024-07-26

In what ways are computing and biological computing similar or different

“It is not from the benevolence of the butcher, the brewer, or the baker, that we expect our dinner, but from their regard for their own interest.”

^ how is or isn’t this true?

What protcols - and how to coordinate, but this is different at a software level or is it? How do things gatekeep wha protocols they will take up?

Tney will eventually come to love the noise

A new or different world

_

What is the difference between a physical limit and a practical limit?

(w/ quantum memory) Computational algorithms can then be designed that require arbitrarily small amounts of energy/time per one elementary computation step < what

https://web.archive.org/web/20150305173119/http://www.transhumanist.com/volume5/Brains2.pdf

Modern computers use ~10^9 x the Landauer limit to do computation (defined by E >= k_B*T ln 2)

https://arxiv.org/abs/1408.5089 < this is cool! A physical test of Landauer’s limit

https://en.wikipedia.org/wiki/Landauer%27s_principle < does Landauer’s principle actually hold? Curious to understnadther challenge parts

What is reversible computing?

Understanding Maxwell’s demon

Free energy?

“After joining IBM Research in 1972, he built on the work of IBM's Rolf Landauer to show that general-purpose computation can be performed by a logically and thermodynamically reversible apparatus; and in 1982 he proposed a re-interpretation of Maxwell's demon, attributing its inability to break the second law to the thermodynamic cost of destroying, rather than acquiring, information”

What is the justification behind Landauer’s principle?

https://worrydream.com/refs/Landauer_1961_-_Irreversibility_and_Heat_Generation_in_the_Computing_Process.pdf

“This dissipation serves the purpose of standardizing signals and making them independent of their

exactlogical histor” < what does this mean, in the abstract to Landauer’s paper?

"The existence of astoragemediumascompact asthe

genetic one indicates thatonecan go very farinthe

direction of compactness, at least if we are prepared to

make sacrifices in the way of speed and random access.” < how well does genomic storage fair wrt physical limitations of memory?

“we can show, or at least very strongly suggest, that infor-

mation processing is inevitably accompanied by a certain

minimum amount of heat generation”

“The relevant point, however, is that the

dissipation has a real function and is not just an unneces-

sary nuisance” < what is the function of the dissipation?

“physical requirements for logical devices” < what is a logical device?

“Classically a degree of freedom is associated with kT of thermal energy. Any switching signals passing between devices must therefore have this much energy to override the noise” < what does this mean?

Brillouin and earlier authors, as summarized by Brillouin in his book, Science and Information Theory,' tothe effect that the measurement process requires a dissipation of the order of kT

https://archive.org/details/scienceinformati0000bril/page/n8/mode/1up

Why is error detection a big deal in information theory?

“The computing process, where the setting of various elements depends upon the setting of other elements at previous times, is closely akin to a measurement. It is difficult, however, to argue out this connection in a more exact fashion.” < what does this mean?

I see - the claim is kind of, for the particle to be in one of two states, there ought to be some energy barrier between the states so the particle stays in one of the states

I see - the argument that you can’t make a reversible computer that causes the particle to, from either of two states, end up in one, is that then you would don’t know in which state to put it when running in the inverse

Is anything deterministic, in the world? What would be, if it was?

What does it mean for the potential well to be lossy?


In Figure 2, where zero and one states are not separated by a barrier - is this sort of like, you wouldn’t need an activation energy barrier between the two states if you had no random motion? And what would that make possible?

2024-07-29

Veins as connecting topologies

Connect things in a more directed fashion

Transition fro ocean had a big impact even inside ocean, were there directed topologies

p2p computing

Communication through air (from Claude)

- Sound waves

- Chemical signals

- Seed and pollen dispersal

- Scent marking

^ are there nucleic acid communications that happen through air, too small to see as larger objects?


If I were to sequence a patch of air, how much and what kind of nucleic acid would be in it typically?

HGT

What types of physical media are involved in literal transmission of signals in p2p computing?

How much of the internet is mediated by underground wires vs satellites - when one has internet in one’s house, is it physically connected to something else or through a satellite link?

The internet uses the internet protocol suite (TCP/IP) to communicate between networks and devices

For the internet, ICANN maintains IP address space and DNS (how does it do that)

The IETF maintains the core protocols

Who implements ICANN?

What goes into one packet - why are things put into packets instead of continuous streams - what would that mean, and is it at all possible?

How do smartphones access the internet through the cellular carrier network

IP addresses are used by Internet infrastructure to direct Internet packets to their destinations

How do you find an IP address

Domain names are converted by the DNS into IP addresses

What is the definition of replication, variation and selection

s of 2023, roughly 65% of all internet traffic came from video sites,[4] up from 51% in 2016

In 2022, roughly 47% of all traffic was estimated to be from automated bots

Predicted global Internet traffic by year[28]

Year Fixed Internet traffic

(EB/month) Mobile Internet traffic

(EB/month)

2018 107 19

2019 137 29

2020 174 41

2021 219 57

2022 273 77

https://ourworldindata.org/internet

https://www.on.kitp.ucsb.edu/online/hgt24/si-schedule.html

https://www.on.kitp.ucsb.edu/online/hgt24/rocha/oh/07.html

What does it mean for a phage to be a plasmid?

Email organizer of KITP HGT conference to see if I could ask for advice?

Are there things which aren’t phages which also carry nucleic acids between bacteria? What are the diversity of organisms of this form?

In a typical phage population, what is the genetic diversity? Would one measure this through…sequencing? When one sequences many phages, do you have a promoter which binds a known region of the target phage genome?

OH my gosh - what is a phage parasite?

How do phages do quorum sensing?

https://www.nature.com/articles/nature.2017.21313 (?) - is this it?

Is it reasonable to assume the average living thing does quorum sensing?

Phages want to help other phages which are similar to it

How did this thing get to be so widespread? Because, once widespread, it was useful with itself - but, how did it get to be widespread?

How did communication systems evolve? How would they spread?


Woah - is HGT a way to spread something to many players at once without reference to selection (so, i.e. if a trait would not be selected for if not expressed by many members of the population, it could still spread widely enough without being selective at this individual level to eventually, once it was population-wide, show a benefit at that level)

- Huh, that’s super interesting

- So, HGT, is like a meta-trait that allows traits that might not otherwise be selected for because they need population-wide expression to show selective benefit to become widespread enough to see that benefit

Would HGT help something like communication systems evolve? But how did HGT evolve, initially?

Do many things spread via HGT which are not selective individually?

I guess this effect isn’t specific to HGT (although somehow that seems ‘faster’ than neutral evolution to me - I’m curious if it is)

So - things which allow non-advantageous traits to spread across the whole population are good (?) because they allow traits which are helpful if population-wide but not individually to show their advantage

How prevalent is neutral evolution?

In what language are these questions asked? And with what tools are they answered? Wow, sequencing is so powerful, I’m so grateful for it

https://elifesciences.org/articles/41491 - this article claims that 5% of the human genome is evolving neutrally. What does that mean?

Maybe neutral mutations seem to be diffusing slowly and steadily - are we sure this is how they spread?

I guess neutral theory of evolution says that, in smaller populations, selection might be less efficient b/c neutral mutations can take over the population more easily (is this bad for selection, if it is happening?)

Woah, what are hitchers?

Shin Liu and Anastasia Lyutina - have done work to quality recombination and gene flow in populations of human gut bacteria

Jimmy Ferrare

https://www.on.kitp.ucsb.edu/online/hgt24/good/rm/jwvideo.html

^ gut microbiome has ~10^14 cells

Cells in the microbiome are split into as many as ___ species, depending on how you count them (50-100)


The microbiome exchanges nutrients with the host and breaks down certain drugs - does it also secrete things relevant to the brain

I’m curious to read…everything about this

How on earth does the microbiome work if it’s not working through any central plan but rather…through some bottom up process of ecology and evolution? That’s so crazy

Woah - what are phages doing in the microbiome community?

How important are phages for the microbiome?

We know (Benjamin Good says in talk) that in the ocean phages play a large role

The virus to microbe ratio is often abbreviated as ___ Vmr

The Vmr in th ocean is ~10x

Does the Vmr include just free-floating bacteria and viruses - does it include viruses that integrate into the bacterial genome?

Viral shunt - so all these lysed bacteria liberate biomass that play a huge role in nutrient cycling, and all of those phages play a really important role in horizontal gene transfer

(what is going on with horizontal gene transfer?)

https://journals.plos.org/Plosbiology/article?id=10.1371/journal.pbio.3002472

^ this is the cited paper quantifying recombination + gene flow in human gut bacteria

^ I could ask the author about the paper? I’m really curious how they thought about methods for that, and what their methods would be likely to miss

In the microbiome, bacteria decrease due to death, but also due to dilution

What intuitions could I have for differential equations? What would be good texts for this?

What could I do this week for linear algebra and calculus? To solidify work and impressions there? What textbooks could I spend time with? What would it look like to spend time with those textbooks?

I see - so viruses become more available when they burst out of the cell (can they ever just secrete out)

Are any messengers actually viruses that learned how to get out of the cell without lysing?

Huh - what kills viruses? Dilution?

Do things in the stomach chop up viruses or bacteria? How do they stick around in that very acidic environment?

How did bacteria learn to survive in very extreme places? What are the physical limitations on this? Were our expectations of those limits ever violated?

R_0 number - the number of successful viral particles that a single virus produces before it gets diluted out of the system (burst, infection rate, total number of bacteria that sit around in the absence of any phage)

How does solving differential equations help one biology? Where is it most helpful or most predictive? What do the properties of the differential equations have to do with this? What kinds of relationships are really locked in vs just ‘we know this goes up if that goes up’ but not the exact linear or nonlinear function?

The slope of the line past the critical point is (R_0 - 1) * K

VMR graphed against R

Benjamin walks through a model that shows that you might have to a lot of phage per bacteria to get reasonable replication rates

^ I could understand this thought experiment #1

^ thought expt #2 around evolution (kill the winner dynamics)

Temporal heterogeneities over time - oh, super interesting

Cycles of phages coming in, infecting a bunch of bacteria, crashing the population, which then creates selection pressure for a mutant which is not open to phage infection

Huh - do kill the winner dynamics actually show up in evolution?

How do we study processes of evolution? How do we make hypotheses, across so many datapoints?

How does one think about data, generally?

Huh - is the picture we have for the gut microbiome quite different from that in the ocean? Why, if so?

Summarize the talks with nice notes?

Population based vs communities?

What questions are new students most skeptical of, or curious about? What are the most important themes in studying the role of HGT and evolution in populations of bacteria and phages right now?

What is cross resistance?

How do simplifications allow you to deal more simply with modeling communities

Which phages interact with which bacteria?

^ who are Daniel and Aditya mentioned in the talk, who have done work on that kind of problem

Why or how is the gut different from the ocean? A mediated environment

What are the first, general tools one would use to look at data? Between a set of paired datapoints, what can one do, independent how one got them?

If you know how you got them, how does that change what you would do?

There is some statistical correlation between the phage (not explicitly bacterial) population in someone’s gut and some disease state or health indicators

Of course, we don’t know which way the causation an correlation go (and could the phage be correlated to some other physiological thing)

What physiological thing would phage be most likely associated with?


Fecal filtrate transplants - transplant (small things like phages and other elements)

Inoculating fecal filtrates (so, phages, and other small things) from natural born piglets into preterm piglets seems to help the preterm piglets

^ what - why did this make more sense to try than to transplant the microbiome?

- Oh, he answers in talk, it’s possible that if you transplant bacteria some pathogenic bacteria might get in there and so it is hypothetically…safer with just phage?

So - with regard to phages - we have some evidence of correlation in phage abundance and disease state, and some evidence that adding phage filtrate to another organism can affect it, potentially in a positive way

A question about, I think, is there even anything there for the viruses to prey on, if you put them in this new environment?

This experiment didn’t do (killing of the phages) to see if it was other elements (?)

What do population look like *over time*

Benjamin Good says we are not even maybe that sure of what the virus to microbe ratio in the gut is, or the average (fitness burden due to bacteriophage) - what is the average fitness burden?

What does the physical ecosystem of the gut microbiome look like?

Is well mixed a good approximation for the gut microbiome?

Terry and Iona Kramer - how much bacterial biomass could be produced by bacteria growing just in biofilms on walls

^ Benjamin Good argues that, from the work of the above authors, theoretically there might not be enough bacterial biomass possible to grow on the walls of the gut to make up most of the microbiome, so you’d guess that a lot of it is in the lumen and there are mixing procedures there, so it is reasonable to model the microbiome as well-mixed

Estimates for the Vmr I the gut range from 10:1 to 1:100 - holy cow! Where do those different estimates come from?

Fitness burden = alpha*V/mu = R_0-1/R_0

What can we quantitatively say about gut ecology - wow, so cool!

A deep dive into the literature to see what we can quantitatively say

What is absolute abundance - of what? Bacteria or phages?

Density of bacterial cells in feces - ~10^11 bacterial cells / g - nice paper from Ron Milo’s group

Wow, Ron Milo’s group is so cool!

Classical way to countphage is imaging, stain DNA dye, count the # of particles in a microscope

- Hm, this throws out the RNA, and therefore (phages which only have RNA?)

- But people might think that most RNA viruses are actually plant viruses (?) - how do we know which viruses are interacting with the host microbiome?

- Can we sequence the host microbiome to try to get a sense of this?

# of phages / g that come out that way is ~2x10^9/g

How many of these are viable? - hm, it might be quite hard because you’re not sure on what host to grow them (could you grow them on a composite, or fecal sample)

Ron Milo’s group

“Population dynamics of phage in the gut microbiome”


Also a sequencing approach, where you spike in phage.

Where do people study bacteria and phage communities

Colin Hill and Andre Schopperof

If you use sequencing (I”m not sure exactly how this works) you might see closer to ~10^10 phages / g

You have to amplify - bacterial or phage DNA? And the amplification rates might be different between the two?

^ modern methods can help with this

How do these things vary in a person over time?

Don’t really vary more than 1 log unit

Vmr from these is .02 - 0.1

So, 100-1,000 fewer are phage particles than the ocean

Last method is phage matching DNA in bulk genomes

- Phonta, from Amy’s lab

Ways to tell how many phage

- Dye DNA + microscopy (no RNA, as that might mostly be plant viruses)

- Sequence compared to spike in

- Sequence bulk genomes

- Do bulk sequencing and compare to database w ~200,000 phage genomes and ~30,000 prokaryotic genomes from the human gut

- Classifies ~95% of all reads

- ~4% of reads come from phages, normalize total # to length of phage genome in gut

- The effective Vmr if you do that is ~4!

I see - this actually makes sense that, if you write down free viral particles to microbes, vs integrated viruses, the latter might be much higher (so, 4x vs 1:10 or 1:100)

2024-07-30

Many prophages (which are integrated into the genome?)

Wow - so even just measuring how many viruses there are, is hard

Multiple displacement amplification

Viruses that are present in VLP sequencing vs bulk (what does the mean)

You cover some fraction of the viral genome with the Phonta tool?

Useful tools

- Phonta from Amy (?)’s lab

Some particles that are present in the bulk and have ratios of phage genomes to phage particles that are pretty similar in the aggregate

Things there are a mix of things we would traditionally classify as prophage vs things we would traditionally classify as lytic (what is the difference)

Lifestyle prediction tools to predict (where in the cycle the phage is?)

So - ~50% of the phage population seems to be in this part of the graph where the (abundances between the two sequencing studies - of free floating to prophage) seem to match what we’d expect for the overall population (is this true)

Many phages have many more phage genomes than they do phage particles

The lifecycle of the phage

What other things are going on? What is being used to communicate? How do we know?

Estimates from different methods seem to be very helpful

Some phages have more of a plasmid lifestyle, and reproduce as plasmids in bacteria

Could be systematically undercounting phage in bulk sequencing methods because our DNA extraction methods don’t deal that well with things that are encapsulated

How much sequencing, and artifacts fromsequecning protocols, affect results - where or how is a good way to learn more about this?

Maybe some phages get stuck in aggregates and don’t make it through the filter

Benjamin Good then says that if they are stuck to bacteria, they will have a bit of a hard time infecting another host

Add prophage and lyosgens to our basic model (how does this relate to the ocean also?)

Is the conclusion something like prophage and lysogens are much more dominant in the microbiome than in the ocean (guess?)

Why do we lose some viral particles when the prophage conversion process happens?

What is a superinfection mechanism

I see you - keep track of infected vs uninfected bacteria

Growth rate of prophage vs growth rate of susceptible ones, induction rate

Can you ask questions through differential equations by translating your question into some term or ratio of terms

If prophage is induced a lot, it’s actually bad for the prophage state, they will die faster than the susceptible

Region with mostly prophage, region with mostly susceptible and viral particles, and small region with a mix of both

If you assume the growth rate cost if you have a prophage is not large, that the major cost of being a prophage is the fact that you get spontaneously induced

BG makes the claim that the prophage only region might explain the kind of count data that we say earlier in the talk

Can you use the number of viral particles floating aroudnto estimate the induction rate (which is the main fitness cost, that sometimes you induce and get killed - as bacteria or phage?)

Can you measure the induction rate in the absence of this?

Can we use this picture to quantitatively estimate the fitness burdens hat bacteria in the gut microbiome face every day

Thinking about things in a complex community - lots of phage combinations

Change in total viral abundance - Colin Hill and Andreoff - 0.7 log units per 30 days (what does that mean)

Argues that even if we are not literally in steady state, as long as we’re able to think bout at least statistical steady states over time, can we still get kind of a steady state picture

Phage genomes to particles are (20-400?)

Gets a lower bound for induction rate- how

Induction rate for gut guess is ~10^-3, which is related to the fitness benefit you might get from being resistant to induction, you might sweep through the population in ~1000 days so quite slow (how do you go from fitness benefit to time to sweep through population?)

- Like, each day, the bacteria that are lysed are removed and those that aren’t stay, and so you increment by ~1/1000 of the bacteria in the population per day? Does that then take into account the amount of differential replication those bacteria have in that timeframe - of, if everything makes one copy, the same proportions continue

Argues for a semi quantitative way of thinking

Argues that phages are piggybacking on bacterial hosts

BG claims that the model suggests one way phages impact their host is to improve fitness - how would this work, and how does the model suggest it?

Phage genomes can sometimes carry metabolic cargo - how common is this?

How fast do bacteria or other entities spread between peoples’ guts - turns out to be relatively low

Huh - that’s interesting, so a relatively constrained ecosystem (but poop and - what else - could spread you between hosts?)

Most of what BG was talking about was from measurements made from feces

- Could a lot of the induction just be happening in feces, because the entities are now starved and exposed to oxygen?

- Is there not a lot of oxygen in the gut?

- Some exciting work to try to measure counts more in the gut now

Different optimal places to infect depending on whether you care about number of bacterial cells, or growth rate of bacterial cells

Gut - well mixed, but very boom/bust?

This model would suggest

- Phages might positively impact fitness (how does this model suggest that)

- There’s not that much benefit to phage defense systems - in which case, why are there so many phage defense systems around?

- How does spreading or co-evolution occur (if many phages are just traveling with their bacterial hosts)

- What pressure is applied for prophages not to just stay there forever, or for there to be a bunch of prophage per cell?

What are good questions for BG? For each attendee there?

- How much do we know about quantifying the amount of HGT in different populations? What are the major papers, labs or work that have attempted this in the past?

- How could we compare this to different communicating systems

Where was BG trained?

The network communicating vs the entities themselves

- The thing which is communicating is the thing, or the thing which is the communication is the thing - how would this perspective affect questions to ask, or ways to process things

What are evolutionary dynamics

- What do we see?

- How could this be different than what is happening in nature?

What skills do I want?

Questions and papers

Can send some time in an environment with talks

What does it mean to understand a subject well

- To know who the good labs are

- To have a clear understanding of the important papers

- To understand the general questions people ask, and the uncertainties with published results

- To have a sense of interesting areas or directions, and good tools one might build (also)

Professors want to

- Know the grad students in the field

- Know their colleagues

- Keep track of interesting areas

- Have the resources to do what they want to do (both for curiosity and career)

People

- Physicist background

Toy models

- What do we think about toy models? What do we get with them?

- We engage with the problem

Equations

- I would maybe find it easier to understand an equation if

- I have enough time to understand what each symbol means, and check to see if it goes up or down how that effects the equation

- If, when referencing the equation, the symbol were highlighted that I should focus on

What skills are the most useful for these labs?

- Experimentalists

- Mathematicians fluent in a given language

Tools

- Microscopy or sequencing

- Why are these the main readouts? Are there others? Stuff that sticks to stuff specifically, and stuff that can look at that stuff?

Helpful mathematical tools

- Differential equations (for keeping track of populations of things in biology)

- Linear algebra (where does this really come in - for keeping track of data?)

- Topology (networks of graphs)

- Calculus

- Where does this really come in - for differential equations? Could you understand differential equations without really knowing calculus?

Differential equation

- What does it mean to understand it

- See what each term is, and what happens when you take it up or down

- What does it mean for terms to be multiplied by each other - are they somehow more dependent on each other?

- What does it mean for there to be multiple equations?

- What should be my first steps when I see a differential equation

- What does it mean to rescale the parameters of a differential equation to understand it better?

- Do you want to make phase diagrams? What types of graphs do you want to make?

- Parameter space

- Can plot things assuming we were in steady state

- Make assumptions to simplify

- What is a steady state?

- What algebraic manipulations to do?

- How would you know what to do?

To understand

- Differential equation model for lytic phage and bacteria abundance

- Bruce Levin, Josh Whites, Nigel Goldenfeld on this infection model - the classic lytic picture

The advantages of a blackboard talk

- Write down notes on paper

What does it take to construct a nice blackboard talk?

What does good discussion look like?

What is a good way to read papers

- PDF or online?

- Notated or not?

- Notes collected?

- The PDF somewhere to reference?

What does academia really look like as an organism, trying as a collection to figure something out?

Quantitative seminar

A spiral discussion

RM or RP?

KITP person?

Bacteria Bionumbers:

How much does air help things communicate?

https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3000102&type=printable

- What is purifying selection?

- Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency

What is the difference between replacement and evolution?

Why do I hate so many graphs from papers? Perhaps it is harder to analyze a graph if seen once than a graph one has seen many times?

The more I write, the more clear my writing becomes

How do people model specifically natural selection, much the less communication

p2p computing

Ethereum = globally accessible singleton state and virtual machine that applies changes to that state

What does it mean for Ethereum to be open source - a program on Ethereum is called a smart contract

Blockchain synchronizes and stores the systems state changes, ether meters and constrains execution resource costs

How does Ethereum check that a contract has been executed correctly

When the transaction is first submitted to the network, it is first validated by the node that receives it

Miners then collect transactions from the transaction pool and include them in a new block they are attempting to mine, they also validate transactions to make sure they adhere to the consensus rules

Ethreeum has ~8,000 full nodes

When a node join

Is Ethereum inherently limited by having nodes have to verify every previous transaction

https://summerofprotocols.com/wp-content/uploads/2024/04/Dangerous-Protocols-Nadia-Asparouhova.pdf

“Protocols demand not just our compli-

ance, but our loyalty in relinquishing our

decision-making power to a formless entity”

Better writing emerges with doing more of it, and really trying to express something, in a focused manner

What is the point of the Sorcerer’s Apprentice

What is a protocol?

‘Protocols are primarily social, not technological, in nature’

I define protocols as procedural systems

of social control that simplify communication

between actors:

“ Some

blockchain governance enthusiasts like

to point out the ways in which technical

protocols can improve social coordination,

suggesting perhaps that governance could

be enhanced by the inclusion of technol-

ogy such as immutability and verifiability. I

think it is the other way around. We do not

control protocols; but with enough time and

participation, protocols control us.”

“But just as antibacterial products can

lead to the evolution of resistant bacteria,

so do protocols learn to avoid our collective

immune system, emerging in a more power-

ful form that are harder to discern or avoid:

implicit protocols”

“What’s

dangerous are solved conversations about

things that really matter. When people

identify deeply with a political party or

a particular philosophy, it’s not difficult

to predict the outcome of any given

conversation. [emphasis mine”

There on Ethereum is mostly useful as a Utility currency

2024-08-05

Nodes - how do more nodes scale the power o an algorithm

Distributed computing - how does the power of a computation scale with the number of nodes and their individual capacity

What each node can do and its individual capacity

Do we assume anything about each of them - for example, the Internet, it’s doing something, we’re not quite sure what, a variety of nodes interacting over a protocol

Just need to e able to ‘compute in some way’

What are the laws?

More nodes, more compute - what are the constraints

What kind of algorithms are we talking about - algorithms for whom the goal is not known

Biological algorithms - whose goal is not known

What is the difference between biological and non-biological algorithms?

What is a genetic algorithm - an algorithm whose goal is not known

Optimization and search problems - but search for what, what if the algorithm is try8ing to find the goal?

But what is the goal - individual survival vs a pattern that will keep going vs a pattern which is one in a lineage of things which will keep going

Evolution

What does it mean to become more visible - to become more widespread, to continue to be there

The internet generated a dataset which was then used to - hm

What does the internet ‘do’

How has the number of nodes connected to the internet changed over time



Internet bandwidth



What is happening on the internet? It’s trying to do something, but what?

Internet is a technology for facilitating communication, at new scale and bandwidth

Currently constrained by how human brains manage communication and social protocols

Markets as coordination systems?

What is up w Dunbar’s #?

Coordination cost to understand new people?

2024-08-06

P2p computing

What is p2p computing used for?

How do different p2p computing algorithms scale with the number of nodes available?

https://www.cs.uic.edu/~ajayk/Chapter18.pdf

In p2p - is it that the algorithm is ‘boss’ and can’t make arbitrary decisions about what happens?

Distributed Hash Table

• Each node stores a list, you know which node to go to by hash (?)

What is the internet computing?

‘Can the internet dream of itself’

‘whatever you created, you owned’

Do you really own it though - can’t others recreate it, without attribution?

What do licenses mean?

Resources to nodes

Why did the internet centralize to a few platforms?

‘the killer app of the interent is networks’

‘today almost no new startup activity takes place on top of social networks’

‘network design determines outcomes’

‘blockchains are a new class of computer’

What was RSS?

‘I am thinking about computers’

How does the value of a network grow as more nodes join?

The web was a ‘space’ in which information could exist

https://www.eff.org/cyberspace-independence

The Greek word from which we get ‘protocol’ meant ‘first sheet of a volume’, which could be related to table of contents, then ‘diplomatic conventions’, then ‘technical standards for software’

How do you change the protocol? It requires consensus

‘Email and web succeed because of their simplicity, generality and openness’

ICANN - how are fees decided

2024-08-07

p2p computing

Why don’t protocol networks have network fees

What is up with corporate networks becoming so popular?

What is a dynamic website? What is a non-dynamic website?

What is the coordination cost in a group? From a group coming to consensus - even independent of the time to get consensus if that will happen.

What does it mean for a network to increase in value at a compounding rate? What doesn’t increase in value?

How do networks not have some part of the chain that provides them become centralized

Who is not on the internet right now?

“a decentralized network of information nodes that are linked using hypertext”

Blockchains as state machines, virtual computers

What are the chokepoints of the internet

Blockchain - cryptography and game theory

What is up with game theory? How does one ‘know’ anything from it?

Could you make a network where the cost of consensus didn’t scale with the size of the network - where a subset of nodes could reach consensus without all nodes having to?

What computing cost on Ethereum would mean a lot of compute happened on network? 1000x less? 1000000x less? More?

The system’s currency pays to the validators

Who makes protocol changes to blockchain?

The two most common operations in crypto are ____ and ____ which mean ______ and ____ (encryption, authentication, encrypt something so only a given person can decrypt, sign something so they know it came from you)

2024-08-10

Limits on scaling p2p computing - how the communication system provides a limit on scale

How large can those systems scale now?

How is the internet usefully connected to half the population? Is only a subset of that population truly ‘doing a computation’?

How do groups compute things? Do we need to undersatnd how they do it - if we just characterize the process itself?

What is nature’s implicit set goal?

If you are still around and doing well, what values are you likely to have?

What will the universe look like later? Do we have a choice?

Markets are interesting coordination mechanisms

What is a learning Markov game?

2024-08-12

What limits does a communication set on the ability and size of a group computation to scale

Well, in a communication system, you could have different bandwiths or abilities to encode things - I guess the communication system is also defined by the transmitter/receiver

So, if the communication system was set up to say different things, you would need more nodes talking to figure something more complex out - like you could have a few not that powerful computers, vs many only a little powerful computers. I guess you also need some way to split up the algorithm - like, implicitly, the communication system is partitioning the computation between the different nodes, so it needs to be able to do that well. So like how many things can be encoded and - does that all just go into bandwith?

I could watch more KITP talks

What is a communication system defined by? How to translate what you want to say into something that then gets received and turned into something by something else. What is it turned into - action? An internal representation that’s similar to the original transmitter? The communication system as the thing. Foreground / background reversal - nodes vs the thing they are communicating. But how does the pattern that is being communicated change over time? In biology, do the nodes go directly to other nodes, or do they talk to everyone at once? Would there also then be spatial constraints? Sound also goes to everyone, but letters are more particular, and some types of communication are more 1:1 (spatially constrained) - what is the difference between brains where the nodes can continuously re-orient themselves in relation to each other vs ones where the relations are fixed.

Question

• Is there a limit on how large a population can be to evolve effectively?

  • In a large population, perhaps things fix less frequently?

  • In a large population, more diversity?

  • In a large population - is reproduction a kind of communication? No, well, kind of - like you make something new which has some information about the thing that made it.

  • In a large population - you have many messages, each trying to be heard

What is the most complex mathematical model which one can store mentally? Are we just continuously trying to compress things such that we can think about them? What is the opposite of this, and is it ever useful? What does it mean to experience a mathematical object? What does consciousness have to do with it? What are all the qualia one could have? Wow - what an unlimited space. I wonder what constrains that? How did ‘yellow’ come about? Are the qualia associated with something more ‘mathematical’ or ‘true’ particularly special - I’m not sure, but it feels like a good direction to go in - like there are some objects that are more ‘helpful’. What is evolution but ‘what happens next’? Could we have guessed that the universe would evolve complex life? What kind of principle would have predicted that? How do I think about complex systems - how should anyone think about them? As complex systems understanding themselves - as their capacity to understand themselves? What would it feel like to be the world, experiencing itself. What would it feel like to - would one have a ‘larger’ experience? What would that mean?

2024-08-13

What is beautiful about science?

Pattern - a kind of lack of entropy, something that takes order to generate?

Is what I’m interested in a theory of everything - and is there some sense that it could be internally represented? I’m interested in experiencing - or something experiencing - the laws that underpin the universe

Why?

Well, I guess our brains our wired to want to do that, it seems kind of good, I don’t know

What does it mean to be guided by a sense of aesthetics

What does our subconscious know? And what relation does it have to consciousness?

“Beauty is truth, truth beauy”

^ what is correct, and what is not correct about this

“I think we may be more likely to win by the data just forcing us in a direction, as opposed to having some great idea that’s aesthetically motivated that pans out to be true,” she says. In other words, it isn’t a physicist’s job to write mathematical poetry expounding upon the platonic “universeness” of the universe. It’s their job to describe the physical reality that we interact with, that we have concrete experimental data about.


How do we make theories - if not guided by aesthetics? What is the point of a theory? What does I mean to explain something?

What does it mean to be rational?

I see - beauty and science are different?

https://plato.stanford.edu/entries/beauty/

^ this is interesting

Why do we view roses or sunsets as beautiful?

“This is the spirit that Beauty must ever induce: wonderment and a delicious trouble, longing and love and a trembling that is all delight”

What does it mean to read?

Hume - judgements of taste are better when not affected by arbitrary preferences?

“Strong sense, united to delicate sentiment, improved by practice, perfected by comparison, and cleared of all prejudice, can alone entitle critics to this valuable character; and the joint verdict of such, wherever they are to be found, is the true standard of taste and beauty” (“Of the Standard of Taste” 1757, 144)

Is taste or aesthetic criteria like - itself an idea? Like the thing which tells you what is good is itself an idea?

“For I must immediately feel the pleasure in the representation of the object, and of that I can be persuaded by no grounds of proof whatever. Although, as Hume says, all critics can reason more plausibly than cooks, yet the same fate awaits them. They cannot expect the determining ground of their judgment [to be derived] from the force of the proofs, but only from the reflection of the subject upon its own proper state of pleasure or pain.” (Kant 1790, section 34)

“But the claim that something is beautiful has more content merely than that it gives me pleasure. Something might please me for reasons entirely eccentric to myself: I might enjoy a bittersweet experience before a portrait of my grandmother, for example, or the architecture of a house might remind me of where I grew up. “No one cares about that,” says Kant (1790, section 7): no one begrudges me such experiences, but they make no claim to guide or correspond to the experiences of others.”

^ I’m interested in this - are these experiences of beauty somehow…they seem valid or interesting to me, but I’m not sure exactly how

“One must focus on the form of the mental representation of the object for its own sake, as it is in itself. Kant summarizes this as the thought that insofar as one is having an experience of the beauty of something, one is indifferent to its existence. One takes pleasure, rather, in its sheer representation in one’s experience:”

So - I can find a thing beautiful but not care whether it exists? How is this similar to, or different from love?

“One important source of the concept of aesthetic disinterestedness is the Third Earl of Shaftesbury’s dialogue The Moralists, where the argument is framed in terms of a natural landscape: if you are looking at a beautiful valley primarily as a valuable real estate opportunity, you are not seeing it for its own sake, and cannot fully experience its beauty. If you are looking at a lovely woman and considering her as a possible sexual conquest, you are not able to experience her beauty in the fullest or purest sense; you are distracted from the form as represented in your experience. And Shaftesbury, too, localizes beauty to the representational capacity of the mind. (Shaftesbury 1738, 222)”

^ this is interesting - you can’t see beauty in things you are interested for just utilitarian reasons, or being interested in something for utilitarian reasons can blind you to its beauty?

“For Kant, some beauties are dependent—relative to the sort of thing the object is—and others are free or absolute. A beautiful ox would be an ugly horse, but abstract textile designs, for example, may be beautiful without a reference group or “concept,” and flowers please whether or not we connect them to their practical purposes or functions in plant reproduction (Kant 1790, section 16). The idea in particular that free beauty is completely separated from practical use and that the experiencer of it is not concerned with the actual existence of the object leads Kant to conclude that absolute or free beauty is found in the form or design of the object, or as Clive Bell (1914) put it, in the arrangement of lines and colors (in the case of painting).”

“Thus, built into judgments of taste is a ‘universalization’ somewhat analogous to the universalization that Kant associates with ethical judgments. In ethical judgments, however, the universalization is objective: if the judgment is true, then it is objectively the case that everyone ought to act on the maxim according to which one acts. In the case of aesthetic judgments, however, the judgment remains subjective, but necessarily contains the ‘demand’ that everyone should reach the same judgment. The judgment conceptually entails a claim to inter-subjective validity. This accounts for the fact that we do very often argue about judgments of taste, and that we find tastes that are different than our own defective.”

^ is beauty a way of…finding things that are universal? (Does Deutsch talk about this?)

“beauty to which all men were forever indifferent is a contradiction in terms. …”

“Now though Santayana thought the experience of beauty could be profound or could even be the meaning of life, this account appears to make beauty a sort of mistake: one attributes subjective states (indeed, one’s own) to a thing which in many instances is not capable of having subjective states.”

“t is worth saying that Santayana’s treatment of the topic in The Sense of Beauty (1896) was the last major account offered in English for some time, possibly because, once beauty has been admitted to be entirely subjective, much less when it is held to rest on a sort of mistake, there seems little more to be said. What stuck from Hume’s and Kant’s treatments was the subjectivity, not the heroic attempts to temper it.”

“And the twentieth century also abandoned beauty as the dominant goal of the arts, again in part because its trivialization in theory led artists to believe that they ought to pursue more urgent and more serious projects.”

^ oh - that’s interesting

“Several theorists made new attempts to address the antinomy of taste. To some extent, such approaches echo G.E. Moore’s: “To say that a thing is beautiful is to say, not indeed that it is itself good, but that it is a necessary element in something which is: to prove that a thing is truly beautiful is to prove that a whole, to which it bears a particular relation as a part, is truly good” (Moore 1903, 201).”

What is an erotics of art

“Beauty was what made things immediately, somatically desirable—encounters that quickened the pulse—and what people desired, they sought to acquire”

As Hickey writes, “We are always falling in love. That’s why we’re critics.”

https://www.thenation.com/article/culture/dave-hickey-biography/

Is beauty related to the context in which it is experienced?

“Alexander Nehamas, in Only a Promise of Happiness (2007), characterizes beauty as an invitation to further experiences, a way that things invite us in, while also possibly fending us off. The beautiful object invites us to explore and interpret, but it also requires us to explore and interpret: beauty is not to be regarded as an instantaneously apprehensible feature of surface. And Nehamas, like Hume and Kant, though in another register, considers beauty to have an irreducibly social dimension. Beauty is something we share, or something we want to share, and shared experiences of beauty are particularly intense forms of communication. Thus, the experience of beauty is not primarily within the skull of the experiencer, but connects observers and objects such as works of art and literature in communities of appreciation.”

^ these seem quite different, or more complicated notions of beauty than the most simple?

“Aesthetic judgment, I believe, never commands universal agreement, and neither a beautiful object nor a work of art ever engages a catholic community. Beauty creates smaller societies, no less important or serious because they are partial, and, from the point of view of its members, each one is orthodox—orthodox, however, without thinking of all others as heresies. … What is involved is less a matter of understanding and more a matter of hope, of establishing a community that centers around it—a community, to be sure, whose boundaries are constantly shifting and whose edges are never stable. (Nehamas 2007, 80–81)”

Beauty in the context of communities?

2024-08-14

p2p computing

I could watch some KITP videos?

I could reach out to the organizer to ask for advice?

Between organisms (bacteria, humans, computers)

p2p computing algorithm

Random vs not random networks

What is the importance of a client/server relation

Don’t portals complicate things - like, how do nodes know how to join the network? Could the thing that transmits that be biased to direct toward certain nodes/

How do nodes find new nodes? Through other nodes they know, or by going back to the portal?

‘If a node wants to enjoy the services that other nodes provide, that node should also provide services’

How is distributed computing relevant to game theory and/or altruism?

A lot of p2p networks are just kind of - distribute file sharing

But what about distributed computing?

Would ethereum be a good example? In that context, the protocol is king

Timekeeping as an interesting example of a protocol

What is a protocol?

Medieval monasteries were high-tech “machines for thinking”

What about distributed computation where there is no goal to the computation

What is the meaning of computation?

More like distributed evolution? But what does that mean?

Computation - calculation that is well defined

Okay, but what do you call it when a group gets together and talks and then does something cool?

Emergent behavior - okay but that seems really boring, isn’t that just like, this is a group doing something where something surprising then happens (ie does emergent behavior imply interactions between members of the group?)

Has literally anything important ever happened in the history of studying emergent behavior

https://plato.stanford.edu/entries/properties-emergent/

‘One can have a good understanding of how tornadoes work while being entirely ignorant of particle physics’

What is the relationship between biology and physics?

What is “causal closure of the physical”

Weak emergence also affirms physicalism

Etiology is the study of causation or origination

SFI

Is emergent behavior what is meant by ‘a group of interacting parts get together, then something cool happens’?

Does evolution quality as emergent behavior? Is it ever also described as distributed computing? What would qualify it for one or the other category if so?

How do we think about complex systems? Are there literally any good ways?

GH Lewes on emergence - talks about co-operation of things of unlike kinds

Some argument that ‘strong emergence’ cannot be simulated, analyses or reduced

What does that mean?

Oh - that’s interesting, some properties of emergence are scale dependent, meaning you can’t do a reductionist analyses to predict them, you must actually simulate the whole system

So, what communication systems would allow you to have interesting scale dependent behavior - does it matter that they can’t be simulated in smaller systems

Is chaotic behavior, by nature, scale dependent (that is, you need to simulate the whole system to be able to predict what will happen)

What is strong emergence? Direct causal action of high-level system on its components?

Why is it that with strong emergence no simulation can exist - because that would entail a ‘reduction down to parts’

Are there good examples of strong emergence - just that somehow it’s not satisfying to explain the whole in terms of its parts? I suppose, how do you choose which parts to use?

How do strong emergence and physicalism interact?

How do observers play into this?

Is emergence linked to scale?

‘The ability to reduce everything to simple fundamental laws does not imply the ability to start from those laws and reconstruct the universe’

What does self organization mean?

Reductionism - the “explanatory arrows always point downward”

I could read “more is different”

https://www.isnature.org/Files/Anderson_More_is_Different.pdf

^ the reductionist argument does not imply a constructionist one

‘The constructionist hypothesis breaks down when constructed with the twin problems of scale and complexity’

Makes the point that

‘The elementary entities of science X obey the laws of science Y’ - but what about the observer

But this hierarchy does not imply that x is just ‘applied y’

Truly amazing to say ‘what if the matter here obeys the same laws as those larger things’ - what would it feel like to feel this was not obvious?

Oscillators

2024-08-15

I’m so excited - what are the most interesting talks?

https://online.kitp.ucsb.edu/online/hgt24/

What am I confused about?

What am I really working on? What is the structure of this project? How does one structure a project so that one can make good progress on it every day?

‘Communication between organisms is an important part of evolution’

There’s some feeling that - I think it’s not satisfying to say ‘we evolved this way’ as though it explains things, because it’s not clear what that’s saying- and that’s somehow related to communication

What does, and doesn’t natural selection explain?

Evolution is certainly powerful - the idea that living things have replicated and changed over time (why did they need to replicate? Could they not change themselves?)

I think I’m really interested in ‘where emergent behavior comes from’ - and what are the rules that govern it? I’m not sure building up from physics will tell us the answers to those things, because that might not inherently know ‘what is important’ (I don’t yet understand the ‘More is Different’ essay, but it feels related here). I’m curious what the presence of a communication system in each of many individuals implies about what each of those individuals will do. Why am I so curious about the communication system in particular? Aren’t many other things also relevant - like what environmental inputs or other noise they have, who they are. Well, yes, but there’s something about - the fact that they can communicate with each other implies the existence of…them. And how much do different environmental states really matter? Somehow I’m just entirely uninterested in information coming in from the environment - maybe this is a total mistake? Because it’s a huge factor? Because it helps determine what should happen next?

I think I just really still don’t get why replication is important or so prevalent - like, without replication, you couldn’t try out new similar versions of the thing and then it wouldn’t really change over time? But aren’t there different ways to do this - like if I built a universal constructor and programmed it with different things. Couldn’t I creatively make something new? But, maybe we didn’t have the capacity to do that in the past so we had to just kind of flop around fitness space until we found something that worked? Both fitness space and literal space? But how did we get replication in the first place - like what the actual hell? What allow itself to be replicated - I see, DNA is like the minimal thing to replicate to then get all the other things. So, you want to compress it down to the core information when you replicate b/c that’s somehow the minimally complex thing, and you can put it all in one format? But replicating is kind of just like - transmitting a message. Why is transmitting a message interesting in life in replication when things mutate, but when you’re actually talking to someone mutation of message isn’t a huge thing? What’s with the invention of abstraction - that seems so different (well, is it really? We started to make more modular things in biology so they could be combined in more interesting ways). So, if you evolve, you eventually invent abstraction through making more and more modular parts to combine in evolution. But what does this say about language - language feels different, in that it’s - I want to tell you something, I’m not just trying to copy - does language get away from the idea of copying? What then, is it trying to do. Oh! Well - maybe it is trying to copy state. So, I see the world a certain way, and I am transmitting some part of how I see the world or some information I have to you. Right, because it must be inside of me for me to give it to you (what does that mean?) and once transmitted then it may or may not be in you. But what does that really mean - so replication is like a full replication of the whole organism and language is a way to share state. When I want to tell someone something, why do - why do two things talk to each other? Well, do the ideas want to spread - ideas that want to be talked about end up in more places? But what about people trying to figure something out or do something. I see - so there are ideas that kind of just spread inherently, there are ideas that are kind of part of some predetermined computation, there are ides as that are…something emerging, but we’re not really sure what yet? What is up with emergent behavior? How does it emerge from a bunch of interactions, like what the literal hell? What is going on there?

Oh, I see, writing can sharpen thinking.

Why do I feel so divorced from reality, so not interacting with any kind of data? Or clear structures? What is a clear structure, in this case?

Perhaps I feel frustrated that I don’t yet have a framework? And perhaps I’m missing something critically important, which can only be learned or seen in academia?

What is life an emergent behavior of?

What is the difference between strong and weak emergence? What is the most beautiful or insightful work dealing with emergence?

An interesting idea from “More is Different” - you could make a computer from many different types of things and it would still be a computer

What is the correct framework in which to think about this problem? Where is the ‘good’ theoretical framework? And where are the structures? What is this object? What on earth is this object? Can you compress the behavior of a population down to just the communication system held by the inhabitants? Are differences in communication system between inhabitants important? Are environmental factors important? How am I searching this idea space? What am I looking for?

I”m looking for something to ‘explain’ what a population talking to each other is or will do. That might look like - how will the population change? No, not really - how will what it decides to do, or what it can do, or what it’s doing change. What is this emergent behavior that happens. And how did we get that population in the first place is what it is planning to do relevant to that?

What is condensed matter physics, and what does it have to do with a less reductionist viewpoint?

It’s interesting that biology evolved in the context of thermodynamic noise…what does that mean?

Beautiful cards.

If string theory was solved, would I be happy? Hell no! Because it still wouldn’t….tell me things about biology that I could compress down to really understanding them. I see - so in life we’re searching for the most compressed ways to understand things, because that gives us the most leverage on turning the resources we have into an understanding or prediction of the world, and this is kind of a fundamental thing.

What….does it mean for a bigger or more complex thing to be casual I literally don’t understand.

I just feel really frustrated - like discussion in this field doesn’t have the ring of truth or clarity to it that discussion in other fields does. Biology is obviously all about information going from one place to another, but this doesn’t feel like a satisfying place to hang your hat - I do think communication systems and constraints on them are interesting.

Do I outsource too much to google or Poe, not building my own structure or interaction with this area of knowledge.

Maybe I’m just not seeing what’s there? But what are, like, the equivalent of proofs for this field (or thing) - beautiful things.

Some kind of inevitability or clarity

I think bionumbers is an example - some way to go to another world mentally, one I can reason from

But in this case it’s complex because - it’s hard to tell when two things are talking to each other, or how to represent that. Or what to say exactly - because it’s not just the information itself, it’s also how the agent reacts to it. So it doesn’t feel like there’s a standard, canonical way to talk about that - and also the protocol itself is the important thing but it’s kind of like the information flowing through it is a bit more arbitrary. Maybe it’s a bit like ML, in that sense? I just really wish I could be building something, or doing something, to get a sense for these systems a bit more clearly. What would that look like? ML is just not a really good analogy for this literally b/c all nodes are kind of force updated, there’s not really an idea of autonomous nodes. In ML, is there an idea of different players in a game? How can I interact with reality, in this context? Why is it that, even when talking about these things, I wouldn’t want to read my own writing - like, I don’t think it would accurately or succinctly convey how to think about these things. What is writing to yourself anyway? What does it mean? Like talking to yourself? What actually is it? Is it representing things externally or - it’s representing things related to some internal experience externally. It’s so crazy, I actually can’t believe that’s possible (I mean I can, but it’s very surprising). I’d love to just sit inside a group of bacteria and watch them communicate - well, I see that it takes energy for them to communicate. They can talk to their neighbors, but they can’t choose who else outside of that sees their message - and the way their message spreads sometimes is neighbors spread it. They have neighbors if they are sitting down but not if they are flying around. How close are they? I feel like if they are sitting down they are pretty close to their neighbors, but if they are flying around they are pretty far away. What can their neighbors do for them - their neighbors can change the different chemicals in the media. That’s pretty much it I guess? Their neighbors can’t push or pull them. They can all fight wars against viruses together. I wonder how many different kinds of chemicals I can secrete to talk to my neighbors? How many neighbors will I meet, in my lifetime? How much will the chemical environment change, in my lifetime? How many chemicals do I bump into in a given second? What is my natural timescale - what is the natural timescale for a bacteria, on which it thinks? Something to do with the time for a protein to diffuse across the bacteria? Bacteria are very constrained by diffusion - can you active transport a message between two bacteria? Do fields matter at all - how do they fall off, and do they help bacteria talk to each other? What thought experiments are well done here? A model of bacterial communication - for fun, not rigor? What would it get right or wrong? How are we so off on some numbers? Which techniques would most help? Which labs are generating answers to these questions? And what are they saying to each other? Do we have a comprehensive plasmid library? If we did, how would we read it - would we have to know what all the different proteins or elements are? How close or far away from that are we right now? What do we know about different protein elements? How do I read or relate to bacteria talking to each other with HGT? Or DNA, in a normal cell - it’s not so kinetic, like the meaning is hidden because it needs to be interpreted to do things. So, when the message gets to the new cell, what happens? It can make things - like proteins - and those things do things in the new cell. It can - I don’t know, sequester proteins that sit on it. But mostly it makes things - is that right, are there other things it can do? It can be replicated. It can pass on to other organisms. How do you read the plasmid though, and how far away are we from being able to do that easily? What are bacteria saying to each other? What is a framework for what they are saying to each other - like, which parts help the bacteria that get the plasmid and which parts hurt it. Yeah, I feel really stuck on genetic material as ‘how do you visualize that’, like in my head it just becomes the number of bits or something but that’s not super interesting. Amount of information - what is the encoded information, actually? What if you just ignored all of that information and only saw how it impacted the new organism that got it? Well, it needs to have ways to be read into things and by how much and when and then it needs to make things. So you could visualize all of those parts - but I feel like that still doesn’t say what the message is saying. If I were sitting on the message, what would I see? Well, I would be sitting in many places at once. I wouldn’t be just in one place - the message is in many places even if each individual physical instantiation is just in one place. Oh - I see, I would be sitting in many places and they would all have some shared understanding because I’m in each of them. I have many eyes. So when I do something, I can do it much bigger than if I were just in one place, and I can know how other people will do the same thing if we are similar. But how do I know how many other people have the same message? Could or does something like quorum sensing help with that? Like, signal that there is some similarity. But it’s frustrating because if I want to do something or change something, I can’t make everyone else do that at the same time if I the individual see something - you have to communicate with them, there’s some delay, some uncertainty. But I’m sitting everywhere, I have multiple eyes. But we don’t see that because we just see from our eyes, as people, we don’t have the feeling of being a message that is in many places at once. I see, there are some similarities, but there are also some difference, and there are lots of changes - I can coordinate by sending out information, or sending out new operating systems. If the message is widespread enough, then it can do a lot - but how do you know if it is widespread. What information is where? What would you do, if you were in that position? Individuals might matter less, but you’d need to coordinate between them. I also have no idea what the environment is doing or what each individual is doing - so the genome is kind of like a static, fixed term experiment, and communication is different, it’s kind of a way to coordinate or update things more quickly. But communication has some problems, or things associated with it, it takes some time to spread and can get noise along the way. But you can try to quickly update everyone in the population. It’s like they all have some independence and then also some working together.

What do bacteria do together that is so cool, anyway? Do they really coordinate in any meaningful ways, what is interesting emergent behavior - well, I guess biofilm are pretty cool. How did biofilms come about? Where did they come from? Where in history did they originate? Who are the best people in this field?

Why do I feel as though I’ve read so much about biofilms, but not retained much? Would Anki help?

https://www.grc.org/microbial-adhesion-and-signal-transduction-conference/2023/ < I could check this out, if they do it next year?

Kerwyn Huang (Stanford University, United States)

"Physical Aspects of Host-Microbe Interactions"

How widespread are biofilms?

What does a typical biofilm look like/

Woah - do biofilms really have channels that allow waste and nutrients to flow through?

How does the matrix help cells communicate? By keeping them local?

How do microbes attach to a surface, and how do they choose which surface and how to attach to? Are they all related to each other, or are they different?

Oh - Anki was incredibly helpful, actually. What is a good way to get back into that?

What is up with electrical communication and…nanowires?

Things that are not like me help me? How do I reason about that? Grow up with them, or communicate back and forth? How can I figure out whether to trust them?

Boles, B. R., Thoendel, M. & Singh, P. K. Self-

generated diversity produces “insurance effects” in

biofilm communities. Proc. Natl Acad. Sci. USA 101,

16630–16635 (2004).

This paper reports the important finding that,

unlike their planktonic counterparts, individual cells

in the biofilm develop clearly distinct phenotypes

after 1–2 days, even for biofilms that are formed

by monoclonal organism

^ this sounds really interesting!

https://www.pnas.org/doi/10.1073/pnas.0407460101

Biofilms: an emergent form of

bacterial life

Hans-Curt Flemming1, Jost Wingender1, Ulrich Szewzyk2, Peter Steinberg3, Scott A. Rice4

and Staffan Kjelleberg4

^ a very cool review

How can I come to learn a field well, and quickly?

Resources:

- “A Different Universe”

- https://www.pnas.org/doi/10.1073/pnas.0407460101 < sounds like a really cool article on diversity arising in biofilms

Idea: language is a way to share state

Thought experiment: Be a bacteria floating around

Action item: How many labs are generating bionumers questions in bacterial communication? What would help this go faster? Fundraise + deploy grants? Would doing a landscape analysis from a funding perspective - like, I want to know what’s between us and the situation where you can sit down and imagine a bacterial thought experiment beautifully.

Yay!

So, next steps:

- Continue KITP

- Read about biofilms (including diversity being generated)?

- Reach out to KITP organizer for advice

- Get back into Anki (super helpful for retention)

- Understand interaction with academia (how to do this well)

- Representing things externally / clarifying thinking through writing

- More thought experiments!

2024-08-19

Wow, many old KITP workshops look really awesome!

I would like to go to a KITP workshop someday

I wonder if they have things like this at Stanford

Active matter

How are active matter, emergent behavior, and computation related - what is teh relationship between emergent behavior and computation?

I feel a bit unsatisfied by the term emergent behavior because it seems to me to lack quantiative definition - Like computation becasue ai can talk about how muhc computation, or speak about what is being computed with some kindof frwamework, whereeas emergent behavior seems a bit more binary - it’s either tehre or it’s not?

https://en.wikipedia.org/wiki/Active_matter

^active matter is composed of a large number of agents

Can one use the framework of speaking about computation, but to desccribe emergent behavior?

Would ML classify as emergent behavior? Why, or why not? It emerges from - well, would you count nodes as agents?

Why aren’t ML systems ofcomposed of many agents? What is the correct framework for thinking about this?

What woudl be the most fun PhD?
Oh - I see, consciousness as a way to impose a goal function on many components

Where that value function has something to do with qualia? Or an imagined future? Where does the thing one wants then come from - is it not emergent?

Do many agents, by definition, have differing goals?

Oh - I see, consciouness as an integrator to provide feedback on the system (how does it then affect the system)?

At what scale can systems be conscious? Are there any bounds on the largest conscious thing? Why is it such a good integrator - why don’t cancer-like dynamics come into play, where parts try to proliferate or conflict? Are we many or one?

How does consciousness know what it wants to do though? By interacting with qualia?

What if consciousness is to the brain what a value function is to a neural net - that is, provides coherent overall feedback to the system

Why are extremophiles interesting?

What can and can’t we cultivate? How can we we study bacteria in their natural environment?

Where is modularity in biology? How should one study biology?

Wow, so it’s really just all about sequencing technology

What are other ways toextract information about this?

Can we design a new CRSPIR de novo now?

What are tradeoffs between horizontal vs vertical transmission?

Poe says these are SFI breakthroughts

Small world networks, Zipf’s law, scaling in biology, collective computation in Ant colonies, autocatalytic sets

Deborah Gordon - collective behavior is the product of local ainteractions rather than something governed by central control

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949665/

What is ecology?

Deborah Gordon notes costs on collective behavior - patchiness of resources, threat of disruption of resources operating costs of running the network

What is the most complex active matter system, and what complex behavior does it do?

What does cancer tell us about other living systems with multiple agents?

Oh - I see, when things get too large for us to internalize and find patterns

Harvester ants in the forest behave different to harverster ants in the desert

What does leadership mean in a grou pof animals?

Evolution generates order in a process that makes itself

What does it mean for a process to make itself?

https://www.amazon.com/Crystals-Fabrics-Fields-Metaphors-Embryos/dp/155643474X

An ant’s response depends on its relation to other ants

What does it mean to do real research?

‘gave up on talking about parts and wholes’

I’m interested in emergent behavior, particularly in the context of active matter

What is dynamical systems and network science

2024-09-01

How do I keep the objects in mind?

What is a realistic plan?

Work 10x harder (?)

I am happy to have made nonzero progress with the project this year, but I do not think it is enough to make significant progress on the project

To work very hard

What will the next 5 or 10 years look like?

Life is like the Dolomites hike - every moment matters, intensely, and total focus and concentration is required to reach the goal

Familiarity with the objects

Communication

Future

Identity

What is a communication protocol?

What is an agent?

Amount of information flow - ability of the agent

Bio numbers on communication protocols

Emergent phenomena (things which look like natural selection) vs prespecifieda computation

I don’t have model systems / toys

Go see dad -> research

I don’t have good models of emergent behavior in groups

What emergent behavior is interesting to study - biofilms? How do different communication systems enable it or not

Grow the field, framework

What are good toy models of emergent behavior to play with, with links to how the emergent behavior is relevant to communication and scale

Problem book for communication in organisms - what are all the toy models of emergent behavior with communication 

Mathematical objects

• look at examples

• extremes

• symmetry (?)

What are the equivalents of Polya’s rules for this field?

The best mental models

2024-09-04

Emergent behavior

• Ising model

Complexity from simplicity

“Wolfram argues that it is necessary to systematically explore all of these computational systems and document what they do. He further argues that this study should become a new branch of science, like physics or chemistry. The basic goal of this field is to understand and characterize the computational universe using experimental methods.”

“The basis of his argument is that the study of simple programs is the minimal possible form of science, grounded equally in both abstraction and empirical experimentation”

“Wolfram argues that one of his achievements is in providing a coherent system of ideas that justifies computation as an organizing principle of science. For instance, he argues that the concept of computational irreducibility (that some complex computations are not amenable to short-cuts and cannot be "reduced"), is ultimately the reason why computational models of nature must be considered in addition to traditional mathematical models. Likewise, his idea of intrinsic randomness generation—that natural systems can generate their own randomness, rather than using chaos theory or stochastic perturbations—implies that computational models do not need to include explicit randomness.”

2024-09-26

What does a community know that an individual doesn’t?

Why does life work by replicating, then group action?

What’’going on’ at the next level? How woul done thihnk about or see that? Is it important to reduce that to something an individual can comprehend?An infinite design space - how do we explore it?

What's the right way to think about communication? What's the purpose?

What can we infer from this widespread nature of this pattern in biology? Either about why it is so widespread, or about the consequences of such a pattern being so widespread, or the consequences of whatever caused the pattern being also (potentially?) so widespread?

‘Why did biology make so many things, and why are they always talking to each other'?"

What would make it obvious that the property of talking to each other would be so widespread? Coordination in a group? But for what purpose? And what does the existence of this property tell us - is it relevant to non-biological substrate or not?

I mean, neural nets were trained on a lot of people talking to each other. But neural nets aren’t a lot (or are they?), and they’re not talking to each other (but they’re talking to a bunch of people)

LIke, I don’t really understand how to think about agenciy of individuals wrt neural nets.

I do understand a bi tmore now how a notion of sel fis tied to predicting the future and taking agents today that access that - liek self as that which you can influence.

2024-11-09

Emergent properties of mult

agent systemsi=agent syst

When do multi-agent systems become incoherent?

Modularity in LLMs

Started off as an interest in ‘general princples of biology’ - I thiought there would be something likeF = MA, but in biology. I now think this is -f not naive, not necessarily true. Beuaty and simplicty don’t necessarily determine the laws of nature, although they might determine which of them are compressible to form in which they can be understood by humans.

What are my non-work goals?

Rigorous discussion of evolutio / natural selection

Understanding multi-agent systems and collective communication in practice

In principle

Physical constraints on how given communications systems scale computational capacity with population size

2024-11-12

what could i do - finally summarize bionumbers? what to do there? amount of communication? what experiments next?

I think with ML this could be much faster

communication networks

HGT

quorum sensing

electrical signaling

what are good frameworks for thinking abou thgt?

a way to store notes / chat about them / partition off tasks

(like collecting bionumbers)

why does it feel so 'not storable' - what is the range of acceptable possibiliteis?

how to think about HGT in a population, how to think about a population in general

passive diffusion makes things easier, bc same everywhere / same principles eeverywhere

agent-based actions is harder because...there is no theory, we don't know how it works? or it, would require simulation each time?

well, you could then try to explore the space computationally and then compress those representations into a latent space you could comprehend - which would require understanding the latent space to compress to

when agents interact, why does it feel so not important - because the interesting things happen on the emergent layer, or the computation truly is spread across many agents?

I see - whereas in the cell, there are many complicated and particular mechanisms at play between any two interacting entities, for agents, it feels a bit less clear - it's less frequent, and more one-off

maybe, I could have more fun thinking about how a population would evolve to meet a particular challenge? so, the contents of the conversation - right, it might be better to consider what they are saying to each other, in a local context. what information is typically in a plasmid? what is one bacteria typically saying to another?

okay - I think I undrestand a bit more about why it's hard to visualize mutli-agent scenarios, and how both thinking about the content of the message could help (and maybe with the ML models having the power to understand the messages better would also be good?)

also posted

Also remembering I wrote a comic about this way back when.

Notes on getting into a science world:

are you in a state of distress (anxiety or depression)

- if outside range addressable through thought (physiological), give yourself what you need physiologically (prob several hours min)

- water

- lie down

- grounding exercise

- if thoughts, write down, see internal, meditation, talk to others - work through

are you curious about something

- if not, ask yourself gently, what might I be curious about

- hold a state of open awareness, looking around - usually there is something there glimmering

sit in a room with enough space to move around in (1m x 1m) and NO DISTRACTIONS, no possibility of interruption

- you need sound isolation

- put in headphones with music with a beat that moves forward

- close your eyes and believe, ask to enter the world of the problem

when you are in the world

- accept you may only have an hour

- sugar helps

- the more you can dance with the concepts, the more the world might unfold

if the above is hard, try doing in nature, or going on a retreat to your favorite place just focused on this

if nothing comes to mind, study enough that something will come to mind. but practice doing this a bit with whatever comes to mind.

'what's important to think about in your life right now' is not the same as what you might want to think about, accept that in this space

added: accept maybe a ~2 hour lag time, to come back to ‘remembering what your priorities are’ afterward, that’s about the (proper) tail of ‘but the concepts are the most important feeling’ at minimum, important to remember to plan around work

Example notes from a ~30 min world to remind myself what it feels like, things I liked from it in bold (not edited and apologies to any readers for the swearing):

- how do concepts in math map to geometric representations that we explore visuaslly

- I can see my brain trying ot generate them

- how math is sucha vast and infinite world

- the strangeness of the concepts there, unlike anything I"ve ever seen or felt before

- to anthropamporphize them?

- if humans had more senses, would we interact with math in more ways?

- looking at a set (points in a circle)

- why is a set points in a circle? that implies distance between the points, orientation in relation to each other

- in partciular, when I look at a bunch of points in a circle visually, the points are literally unique or different, but in a set they should all be indistiguishable (but they are distiguisnable by position in the visual I'm looking at)

- waht does indistiguishable mean then? I'm presented with a point, and I dion't know 'which one' it is or not? or the set simply has a number associated with it, not pionts? but you have to keep track ofthem somehow for mapping - hmmmm, confusing

- does a set have a notion of order in it? or no - imposed on it? how do you map between sets if points are indisituguishable? oh, so the must be distiguishable somehow, so a set is like an ordered list? each poitn has some identifier?

- what's up with exponentials, why do they go up so fast? or the inverse square law - why is it so striking / counter intuitive when things accelerate as tey get closer to. you? how would we feel if that was our life?

- why do I have like zero experiences of bieng so densely surrounded as I would be in a cell?

- what does anentituy look like when it is receiving or giving information? how does that feel? how to think about that? is it changing the entity, internally?

- looking at bacteria floating around me trying to talk to each other but it feels kind of forced - why?

- they don't want ot be there, that'snot their purpose - what the hell are they doing when they are talkign to each tother

- oh, they are in a biofilm now - that's a bit better, why are they in a biofilm?

- they want to...share roesources, worko together

- they want something they can't get by themselves

- how does the biofilm work, what does it loook like?

- there are channels..I don't really know, how stuff goes in and out is really important, if it's too big then ethey can't get what they need - yeah you kind of **have to re-solve the diffusion problem ina biofilm**, that's a way to think about vascuature like it's res-olving the diffusion problem from when things were fre floating

- why are biofilms a certain size - **are there scaling laws, could they be infinitely big**

- does it matter where you are in it, like is it good to be closer to the outside - I'm curious , are there any advantages to being on the **very most inside of the biofilm**, I feel like that would be kind of a dependent place ot be, you would really be screwed if the other bacteria didn't help you out = what kind of abcteria would end up there? really trusting ones? Idk - that's not quite it - you're saying, maybe you want to be **doing stuff for the biofilm** so the bacteria on the outside ned you too

- are nutrieints the main thing - what about genetics, what are your genetics *fuck this is the part I never understand how does evolution think about this* - like it's so confusing to me that they say evolution is about making copies of yourself, but if you do that without changing who you are you won't evolve to get better and so you want to change. who you are but be similar (?) or preserve some property (?) or just you want to be part of a lineage that produced the lineage that is there today but it's not about siilarity to hte previousgeneration? so evolution is **all just about being part of a lineage** < why the fuck do I not understand this yet this is literally the most confusing thing I have ever thoughta bout

- okay, what do the bacteria want

- there are a certain number of bacteria in the biofilm

- they are happy or not

- they are giving each toher stuff and interacting with each other

- also exchanging DNA which fundamentally changes who they are *??????????* idk how to thikn about this at all what the hell is going on there

- why is the DNA so confusing - because it changes who you are, why would i want to do that? to keep going, but what if I liked who I am? so all the bacteria are kind iof like - they're not even entities, they're just part of one big process? bu tthen why have many of them, why not just one thing - I never understand this, replication?

- god, it's so confusing

- if I were surrounded by bacteria, as I was by stars, flying thorugh the universe, what woudl I feel?

- I would feel more seen and understood - they're talkign to each other, they're trying to do something

- they kow the others exist - do they all?

- why the hell are multi-agent systems so prevalent

- what bothers me about this?

- what do they want?

- it's the connection between them that matters - a web, slowly growing more aware of itself

- how do you visualize multi-agent systems? what's the right perspective? as a bacteria trying to figure out hwere it is? or as the information itslef - let's say you're a plasmid, what would your life feel like? it all depends on how you were made, how far you go

- you're trying to get to everyone

- time constraints around copying and distributing the message - are the thhose the fundamental constraits on communication as a group scales?

- all I see is how far I go, not what happens outside

- I can only go as far as there are things to carry me

- I might meet and co-travel with other plasmids

- it's kind of a boring life, I don't really change?

- do I change though? do bacteria edit plasmids as they move through circulation?

- communication systems can change the dynamics

- previously we just had passive diffusion

- **the move from passive diffusion to direct communication as one of the most important jumps in biology?** < huh think more about this

- direct communication = you can specify a rceipient *you didn't used to be able to do this* or could you?

- what does the informaiton want?

- the information wants to figure something out

- to express the world in a compressed way

- what would help me see this wiorld better? help me, please

- just looking at a 2d plane of abacteria

- it's not their size it's - ***how the communication works, how fast it can happen, if I knew more about that, it might be helpful?***

- ^ coming back to this as a motivation for information gathering

- how does the 'ability' to compute or produce emergent properties change as function of communication, what is this communication doing in unicellular populations and multicellular systems

- ^ okay, back to this as a motivation, feeling curious

- how do we know two things are communicating? what does that mean vs just 'sensing the environment'?

- how much does the communication system vary across the whole population? *if that stays the same, can it tell you something about the whole population dynamics to just know about the communication system? do you need to know something else about the technology, etc?*

- what would a good toy problem here look like - like, what's the most complex thing a group of bacteria could do (but they're not really trying to do it) **I wonder if you could try to evolve a group of bacteria to do something that only a group could do (?) - like, a process that would involve the whole group heterogenously coordinating within itself to achieve the behavior***

- renewed motivation to get numbers on / color on / understand communication in unicellular populations and between cells in a multicellular context

- who understands this best in the world, who would *just know* this? what framework would they use?

- bits exchanged?

- capability...somehow?

- the level or type of complex, emergent behavior?

- look for papers that have tried to evolve groups of bacteria to do (complex?) tasks that require heterogenous coordination within the group (what types of bacteria do well here, what types of bacteria would do best here, how do communication systems constrain this - how, actually, do the capabilities of the individual bacteria constrain this?)

- how many groups can do something like this?

- what is everything we know about biofilms? what are other contexts where groups of bacteria work heterogenously together?

combine single cell perspective (bionumbers) with inferring properties of the group from intuitions from there (are there other ways to look at this - the genome content across a population? what would one analyze there?)

what if they were all just one thing, what would that look or feel like? I'd primarily notice the differences, all the ways I didn't fit with myself

___

Random other notes, generally, on the state of immersive thinking

• curious if it has any relation to ‘see-in’ / ‘feel-in’

• curious what’s the difference between a session with dancing vs one without (the former is almost always better? but might require more ‘belief’ in the world?) might require ‘committing’ to a world for a longer session + a more tangible link between some physical principle or movement and moving through the world

• I still have no idea why a certain kind of music is so important to this, why a few songs so consistently matter so much to exploring this state

• is feeling ‘free’ important for the most immersive experience of this state (corollary - is it ever possible to experience the most immersive version of this state in a cafe vs in a field w/ no one around?)

  • I’m curious how to explore / expand this feeling of being ‘free’ - or is that just, like, it will just be the number of people within sensory distance, that is an absolute limit on how immersed you can get

Okay, I see - can use ML to

• understand what the bacteria are saying to each other

• summarize old notes - both to produce summaries (+ fill in associated research) and to give the bones of a thought experiment (maybe?)

• how well could it help understand what bacteria are saying to eachother? is this hte heart of it? the content of the message?

takeaway - what are bacteria saying to each other

a good way to give an ML system a bunch of notes and ask ‘tell me what I think’, to help with finding numbers and new perspective, to speed up those parts?and then to help undrestand waht bacteria are saying - how fast will that field progress?

run a lab from your computer