https://ganguli-gang.stanford.edu/people.html12-07

 https://www.youtube.com/watch?v=0iCYJCndx0E

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1931526/

12-08

What is the beautiful?

Revisiting NW papers

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473391/pdf/biophysj00753-0057.pdf < this is cool as hell

the energy of thermal fluctuation, kT, is large enough to perturb the cell's motion < lol Berg and Purcell claim this, what the hell, seriously?

Should I read the low Reynolds number paper? I never really got that one.

I would also like to finally understand diffusion, like, finally, at long last, dear goodness.

Would it help to understand Einstein’s paper on Brownian motion?

What’s, like, the core principle at work here?

Something something random walk cancelling stuff out something something

Why….does it move it all? Wouldn’t it all just ‘cancel out’ so it would remain in the same place?

I mean, but that’s not quite right, it’s gotta go somewhere.

https://www.maths.usyd.edu.au/u/UG/SM/MATH3075/r/Einstein_1905.pdf < Einstein Brownian motion paper

Fick’s rule, Stokes-Einstein

12-09

Well, I could try to really understand this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473391/pdf/biophysj00753-0057.pdf, (from last time) which gives a lower bound on concentration detectable by an E. Coli (I think).

Ooooh - question - is E. Coli better at detecting concentrations inside than outside?

Well, what is the difference between diffusion and bulk flow? How would I tell a molecule was moving from one vs the other - does it have something to do with correlation of movement to surrounding molecules?

What does it mean for movement to be resisted by viscosity, not intertia? I don’t understand what that means. What does viscosity mean in a cell?

I like the question ‘what is the physical limit on a cell’s ability to sense and respond to changes in its environment?’

What on earth is the Reynold’s number and why does it being low mean anything?

I mean, seriously now, is the energy of a thermal fluctuation really large enough to perturb a cell’s motion?

What, the hell, on earth, really is the diffusion constant

Why is the diffusion equation the way it is?

12-14

What is up with diffusion?

What is a random walk?

At each time step, you can move to the right or left

Could a random walk be continuous, and what would that mean if so?

Back to the Einstein diffusion paper

What is the molecular kinetic theory of heat?

Why is shear stress proportional to shear strain for Newtonian fluids? Why would that be?

Okay, I read until page 3 of this https://www2.gwu.edu/~phy21bio/Reading/Purcell_life_at_low_reynolds_number.pdf

2023-12-15

What would a list of greatest papers in evolution look like?

What is population biology?

2023-12-21

Rules for this session: only this website, youtube (aesthetic/music videos), book.bionumbers.org and papers

Ugh do I want to read though

2023-12-22

Well, I guess I should keep up with https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473391/pdf/biophysj00753-0057.pdf, to understand the lower bound of molecules detectable by E. Coli.

It’s cool that motion can generate an apparent spatial gradient

https://link.springer.com/article/10.1007/s10955-015-1412-9 - this is a cool paper by a cool author, on single-receptor sensing limit

Maybe I’ll look at this a bit today?

Okay, I don’t understand equation 1 of this paper - what is the derivative of c with respect to, and what is c_0?

c_0 is ligand concentration

Why is c-di-GMP used to coordinate group behaviors in bacteria?

What interesting results are there in cellular computation?

Started reading about absorption by specific receptors in Purcell and Berg

2023-12-23

What does a typical biofilm look like?

What do we know about nanotubes?

I read some of this review https://academic.oup.com/femsec/article/96/5/fiaa031/5766226 on biofilms, which was reasonable to think about them if not the best I have ever read

Read a little bit of Chemical Basis of Morphogensis, which was honestly very inspiring - could a similar be paper be written about communication in simple systems? What do I like about this paper?

2023-12-24

Continue https://www2.gwu.edu/~phy21bio/Reading/Purcell_life_at_low_reynolds_number.pdf

Read some from book.bionumbers.org, ending with half of the section on permeability http://book.bionumbers.org/what-is-the-permeability-of-the-cell-membrane/

I’m interested in the bionumbers of physiology + what is going on with phases inside the cell?

Notes:

Thought experiments:

If I am a bacteria, am I looking at many copies of myself - seeing from many places at once?

From where is the action being directed?

What does the information flow between bacteria look like?

How does information flow through neural nets? Through the brain?

Points of view:

I am a message, what do I see?

In a cube of liquid, what messages are there?

I am a part of a bacteria cell membrane, what do I see?

I am a full bacteria, what am I hearing?

I am a bacteria, what do I want to say?

What fraction of the population has which genes?

What is the communication state that a lot of bacteria have access to?

I could understand developmental biology and signaling networks

How does sex relate to communication? How does locality relate to communication?

Why did things start out spread out and individualistic, instead of in a multicellular community?

How do you tell at what level selection is supposed to be acting?

Signalling theory seems interesting?

2023-12-25

This looks cool - direct visualization of horizontal gene transfer https://www.science.org/doi/10.1126/science.1153498

2023-12-26

Ecological Stoichiometry looks like a really cool book (via book.bionumbers.org).

What does the final form of bionumbers for bacterial communication look like?

Well, I still don’t know how many bits transfer on average for each method.

I could make a syllabus for learning game theory.

This seemed like an interesting review of Vibrio dynamics relevant to HGT - https://www.annualreviews.org/doi/full/10.1146/annurev-micro-090817-062148#_i6

Pankaj Mehta’s work looks interesting?

This seems like a cool review of natural transformation - https://www.annualreviews.org/doi/full/10.1146/annurev-genet-112618-043641

2023-12-28

I’m sorry, but I’m just not thinking about the problem properly at all - using neural nets to understand latent spaces in biology is obviously something I should be thinking about, and taking the high-dimensional nature of the problem seriously is something I should be working backwards from, in searching for Newton’s laws of biology. This also requires an updated understanding of what it means to ‘understand’ a thing, and what the goal is there.

Oh - studying protein folding/protein function. But also, what it means to understand something in this way.

2024-01-02

What do I want to work on today?

Gosh, I’m not totally sure - maybe a bit about latent space in biology?

What would be a good reading list for things of the type ‘latent space of biological data’

MN’s blog post was pretty interesting in this regard! Obviously some interesting structure uncovered wrt to protein function. What would it even mean to characterize this latent space? Why would we care about characterizing it in more simple terms, when we can already use it to predict things? Perhaps this goes into the problem posed by interpretability.

What do I think are interesting problems here?

• Can we figure out what the genome is saying, somehow, using NNs?

• <insert data type> can we figure out some structure here - but how does one figure out the structure? What does a satisfying structure look like?

I guess this gets to a core question that I have, personally - what do I care about? Perhaps in physics there is this heuristic - that the laws of that govern the universe are beautiful and simple - and as an art project, I’d be curious to what degree that continues to hold. What does it mean for a law to be beautiful and simple? That it has symmetry? That it is somehow very ‘simple’ (so, two things we measure are proportional to each other)? To what degree are the laws we’ve found in physics truly simple? To what degree is mathematics simple or beautiful. Something that causes us to go ‘ah, yes’ when we see it. Is our belief in the beauty and simplicity of laws of the universe (as in, the most powerful things also looking beautiful and simple) something old that will change once we find more predictive laws soon? Do we measure the power of a law by it’s ability to predict things?

I’ve been really curious about how seriously to take the Feynman quote ‘Nature has a great simplicity and thus a great beauty’

Is, for example, this also true in biology? Is evolution mostly happenstance, a product of chance, that isn’t beautiful (or is beautiful in a different way)?

What is beautiful in biology?

• Nanorobots running a tiny nanofactory

• The mystery of multicellularity (why do cells work together in groups to do complex things)

What is beauty? To what degree is it implicit in - our programming? Beauty is that which we can comprehend - and therefore that which is simple in some way related to human understanding (I don’t think that’s a good general description of beauty, but I’m still curious).

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

^ this looks pretty cool to read!

What do physicists mean when they say beauty? What do I mean when I say beauty? What do we both mean when we talk about simplicity? What do we mean when we speak about power? Is it weird that we can ‘explain’ (but I guess not predict) much of modern phenomena with simple laws? Is there some constraint on things being simple provided by the universe? Can we explain much of the things we see with simple laws?

Maybe, is it - that there are a few, simple laws which can explain much (everything?) if we had sufficient computational power, but we don’t, so other heuristics are useful - I’m curious, though, if it goes both ways, if with a few higher-level laws one could infer that specific lower-level laws must be (and what determines whether something is higher or lower order if so). Maybe this gets into / is relevant to the question of what causality is?

So, things I could check out next time are (just for kicks)

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

Max Tegmark - Our Mathematical Universe

2024-01-03

Who was Eugene Wigner - what did he propose?

Are some sciences more driven by a pursuit of beauty than others?

What are hallmarks of beauty?

Simplicity?

That the theory has just enough - that it is pared down to its bare elemetns?

Power?

That it points to new things, to interesting perspectives

Do we know anything inherently? Are we like neural nets, constantly trying to interpret ourselves?

Other things to read:

• Sabine on Lost in Math

How does natural selection play into the evolution of the sense of beauty which we have now? Can anything be said about that sense from ‘knowing ‘ that we got here through evolution by natural selection.

From Wigner, invariance also important?

How much does what we find beautiful say about us, as humans? To what degree does it reflect some property of the universe, if it does?

Physics explains what will happen given what is there today, but what explains what is there today - is that biology?

What motivates the use of mathematics in physics when we do use it? What tells us what to ‘do next’? Is it surprising that our minds have independently found different structures which are both - where does mathematics come from in the structure of the universe?

What are human minds good for, when machines are also here?

Tegmark on the Mathematical Universe - https://arxiv.org/pdf/0704.0646.pdf

What is the external physical reality which is independent of us? Do we not just see that which we perceive?

Why can’t you define the laws of physics from how we are?

2024-01-04

Beautiful things in biology

Why are RNA transcripts so often used as a shorthand for cell state? What information would that miss?

To the extent to which we are patterns of information, DNA and one cell lineage have both stuck around for billions of years - this is, fundamentally, the nature of life (the nature of life is to stick around)

2024-01-05

So cool! Two new PIs to follow up on:

Michael Hinczewski -

https://www.biorxiv.org/content/10.1101/2020.10.06.327700v3.abstract

Andrew Mugler - https://www.cell.com/fulltext/S2405-4712(18)30245-X

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.118.078101

What am I interested in?

This looks cool (from Hinczewski) - Theoretical Perspectives on Biological Machines

Cellular Signaling Networks Function as Generalized Wiener-Kolmogorov Filters to Suppress Noise

Noise Filtering and Prediction in Biological Signaling Networks - this seems really cool

The price of a bit: energetic costs and the evolution of cellular signaling

Thermodynamic Properties of Molecular Communication

A molecular motor for cellular delivery and sorting

From Mugler

Signal Percolation within a Bacterial Community

Fundamental Limits to Collective Concentration Sensing in Cell Populations

Fundamental limits to cellular sensing - this looks sooooo cool! Oh my gosh, I can’t wait to read this paper

Membrane clustering and the role of rebinding in biochemical signaling

Limits to the precision of gradient sensing with spatial communication and temporal integration

Optimal prediction by cellular signaling networks

Collective chemotaxis through noisy multicellular gradient sensing

Importance of crowding in signaling, genetic, and metabolic networks - ooooh, this looks really cool!

It could be interesting to read this paper from England - https://pubs.aip.org/aip/bpr/article/3/4/041303/2835540

Sabine Hossenfelder - Lost in Math

Sabine makes a good point - why does some part of us react to the beauty inherent in quantum gravity? But perhaps I would take the opposite perspective - assuming that were true, what would it say about us? Do we find theories, then simplify them with conceptual tools that make them more beautiful (comprehensible) and therefore more straightforward to manipulate? What are all the beautiful things ever found in the history of physics?

What is spacetime? Why do we have the number of particles that we do?

What if understanding what we find beautiful in science, and how to relate to that when it becomes decoupled from progress in discovery is something at the core of interest?

2024-01-08

I could continue with Sabine Hossenfelder - Lost in Math

Is it true that if a thousand people read an equation, they read the same equation? Why are math and language different? Why does math have this property?

Is there a crisis of meaning in physics (or science in general) if naturalness or beauty are no longer (as) helpful guides?

What is the most exciting thing that will happen in biology this decade?

2024-01-09

Papers referenced in the Hinczewski ‘price of a bit’ paper:

[10] Tkaˇcik, G., Callan, C. G. & Bialek, W. Information flow and optimization in transcriptional

regulation. Proc. Natl. Acad. Sci. 105, 12265–12270 (2008). - oh cool, this looks interesting!

[11] Cheong, R., Rhee, A., Wang, C. J., Nemenman, I. & Levchenko, A. Information transduction

capacity of noisy biochemical signaling networks. Science 334, 354–358 (2011).

[12] Uda, S. et al. Robustness and compensation of information transmission of signaling pathways.

Science 341, 558–561 (2013).

[13] Voliotis, M., Perrett, R. M., McWilliams, C., McArdle, C. A. & Bowsher, C. G. Information

transfer by leaky, heterogeneous, protein kinase signaling systems. Proc. Natl. Acad. Sci. 111,

E326–E333 (2014).

[14] Selimkhanov, J. et al. Accurate information transmission through dynamic biochemical sig-

naling networks. Science 346, 1370–1373 (2014). - this seems really interesting!

[15] Potter, G. D., Byrd, T. A., Mugler, A. & Sun, B. Dynamic sampling and information encoding

in biochemical networks. Biophys. J. 112, 795–804 (2017).

.CC-BY-NC 4.0 International licenseavailable under a

was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made

The copyright holder for this preprint (whichthis version posted July 5, 2022.;https://doi.org/10.1101/2020.10.06.327700doi:bioRxiv preprint

23

[16] Suderman, R., Bachman, J. A., Smith, A., Sorger, P. K. & Deeds, E. J. Fundamental trade-

offs between information flow in single cells and cellular populations. Proc. Natl. Acad. Sci. - this seems really interesting!

114, 5755–5760 (2017).

[17] Keshelava, A. et al. High capacity in g protein-coupled receptor signaling. Nat. Commun. 9,

1–8 (2018)

https://www.pnas.org/doi/10.1073/pnas.0806077105 - this paper claims it should be possible to transfer ‘much more’ than ‘just one regulatory bit’

What is mutual information?

When do linear correlations make sense? When do they not make sense?

I think this from Terry Tao would be interesting to read re beauty (or ‘goodness’) in mathematics https://arxiv.org/pdf/math/0702396.pdf

Mutual information

First, one must have the notion of information - in this case, the preambles are

• some set of possibilities

• a notion of the frequency with which one observes members of that set

Mutual information is supposed to tell you how much information one variable has about another variable - so, for example, if one variable always equals the value of the other, the mutual information should be (1)? If the two variables are randomly related, the mutual information value should be (0). Are there other constraints? Maybe that it’s monotonic - the more one variable helps tell you about the other, the higher the mutual information? But what does it mean for one variable to tell you about another? Does it mean something about how correlated their outputs are? Do they need to both be the same kind of variable - continuous or discrete? Does mutual information imply that you are guessing two variables are linearly correlated? What does mutual information tell you - if one variable is high, the other one is likely to be high also? What about inverse relationships - it seems like it should predict those as well. Isn’t it the case that for a given function, mapping one to the other, you could know one variable from the other? Maybe it’s how complex that function is? If two variables are equivalent (each is the same as the other at the same value), is that ‘more mutual information’, vs two variables which are perfectly linearly correlated? It seems like both should be fine, but maybe if there is a nonlinear (but perfectly predictive) relationship, the mutual information should be less? For some transfer function, some set of inputs can perfectly predict some set of outputs. So maybe it’s like - if you were just given a bunch of inputs, how much could you just be like ‘here are the outputs’ vs going and having to learn a really complicated transfer function. Could the complexity of the transfer function (and what does complexity mean - how nonlinear it is?) be related to how (little) mutual information there is between the two variables? Why is the function having more wiggles bad? Well, how much information do you need to specify for a function? I guess it would be nice to just say ‘just go in this direction’ - if it wiggles a lot you have to keep track of when. But, you could just specify that as the number of degree-1 factors in a polynomial that represents it - or, actually that might just be the zeros, so you’d do the number of coefficients of the polynomial that represents that function. An (ordered) list of numbers - is the information required to encode that the relevant information? How does the information required to specify numbers in a set differ from the information required to specify numbers in a list? You could say, how much do I need to write down on a piece of paper to specify this function. But I guess - isn’t that a function of the complexity of our tools (for example, this comes back to GR looking beautiful and simple now, but complex then), and also how much the person who is looking at what you’ve written down knows? Is math the way to transfer information, because it is those patterns which seem to have some structure in the universe, to whatever degree we can mean that, independent of our interpretation? I guess, reading colah’s blogpost on visual information theory, http://colah.github.io/posts/2015-09-Visual-Information/ you could also say mutual information is how much more costly it is to use the other variable’s code for something?

Definitions:

• How much one variable tells you about the other (this is mutual information, and I now realize it is symmetric, which I am confused by)

• How much more costly it is to use the other variable’s code for something (this is actually cross-entropy, and is asymmetric)

I still don’t understand what information is

Correlation is one number, which tells you (how much the dots you’re looking at are explained by a linear relationship?).

Information geometry sounds kind of cool! It seems like studying it requires differential geometry. It represents families of distributions as differentiable manifolds.

Okay, so back to the Bialek paper

I guess they cite Shannon’s paper (he shows that mutual information fulfills certain properties) so…let’s get back to that.

https://people.math.harvard.edu/~ctm/home/text/others/shannon/entropy/entropy.pdf - hello old friend

I still don’t get why the logarithmic measurement makes sense - I guess I get that many engineering qualities will work with this, but I don’t get the intuition about two punched cards should have twice the information carrying capacity (I really don’t get that, at all)

Information

Why is it a logarithm???

Why should two punched cards have twice the information carrying capacity of one?

Does it being a logarithm ever matter? What does it mean for our intuition? The number of bits does not equal the number of things it is possible to store, for example.

It’s probably worth spending a lot of time with Shannon’s paper - what would be some ways to do that?

Beauty in science

2024-01-10

Quantum Field Theory

Do we live at length scales at which things become tractable?

What would it look like to understand linear algebra?

I would like to learn about eigenvectors in linear algebra next

I could watch more videos by Nima Arkani-Hamed

How do matrices and derivatives relate to each other?

What is a derivative operator?

Why is a vector in a different inertial frame equal to a derivative operator acting on and summed over all the components of the vector in the first inertial frame? Why does the derivative operator do the transformation?

What is an inertial frame?

The price of a bit - Hinczewski

What is the price of a bit?

I would still like to understand input signal bandwith

(I think) this paper has to do with how high frequency of external signal fluctuations a cell can detect or respond to - although I’m not sure

Lost in math - what is the anthropic principle? Which conditions support life? What is life? Why is quantum theory so interested in measurement?

Sabine Hossenfelder wonders if we’re stuck at the foundations of physics because we’ve reached the limits of what we can comprehend, and it’s time to pass the torch

How could evolution give insight into, like, quantum field theory? Do we pass and evolve intuition on between generations?

2024-01-11

Might be good philosophers on science - Jeremy Butterfield and Tim Maudlin and David Albert.

2024-01-14

Today, I thought about the difference between cooperation and communication - I’ve partially conflated the two recently, but now I’m really curious

• Is communication a way for cells to find similar cells? By definition?

• If it is, does communication allow for cells to coordinate only with those cells which are genetically similar (have the same communication system) and therefore with those they should plausibly be more likely to cooperate with?

• Is there some physical upper bound on the number of cells it is useful for a communication system to scale to (on the number of cells which can usefully coordinate) - or is it that this scales with the population? Maybe it is smaller for more complex communications? It would be interesting if this is related to diffusion? I’m really curious if that correspondingly is related to the size scales at which more macro structures which assist diffusion should be built - and whether this is related at all to how neurons (uniquely?) focus on getting information to just one other specific cell

• A visual picture of populations of cells which share communication systems in a population (visualize cells colored by which communication systems they have) as also those things which are ‘entities’ or organisms - things which will coordinate to act together

• Do cells use ‘cells which share a communication system with them’ as a way to find cells to cooperate with? Do you see something where cells which share a communication system tend to cooperate, then cells which defect follow along, so cells keep evolving new communication systems?

• How quickly can cells get messages to each other? How does communication relate to cooperation? Do cells tend to cooperate much more with cells they can communicate with? Does this define the boundaries of an organism?

Is it the case that beauty is so referenced by physicists because there is now less experimental data to work with, and therefore beauty implicitly must be a guide?

I could try to understand what about Diract deriving something related to the electron was so beautiful.

What is beauty in mathematics?

2024-01-15

Today I want to dive more into the Hinczewski paper, and better understand the physical limits that diffusion places on communication bandwith between bacteria (and, potentially, how larger-scales structures like vasculature, vesicle transport in neurons, or other multicellular structures change these constraints).

Maybe I’ll actually do Mugler, Signal Percolation in a Bacterial Community - that sounds a bit more relevant to my interests

Oh, that’s pretty interesting - is electricity a way to do long-range, faster signal transduction?

This looks like such a cool paper from Mugler - https://www.cell.com/cell-systems/pdf/S2405-4712(18)30245-X.pdf - so far, it seems to assign a cost to signaling, and to discuss the differences between small-scale and population-wide signaling (I wonder how both of these work?)

Which bacteria electrically signal? How do we know it is only them? How did we find out about this initially?

What is percolation theory?

In this context, what does it mean to be a disconnected vs a fully connected conduit of cells?

How do cells decide which cells signal and which cells don’t, in a population of Bacillus subtilis cells which are propagating an electrochemical signal to the outside (or in general)

What things tend to have tradeoffs to fitness and what things do not?

A quote from the Mugler paper - these papers in other domains seem really interesting, and might be worth checking out next!

“Notably, signal propagation through such inhomogeneous populations is not a

problem exclusive to biological systems, but a general question

that has been deeply explored in fields such as physics, chemis-

try, and materials science (B€ar et al., 1996; Sendin˜ a-Nadal et al.,

1998; Steinbock et al., 1995).”

What’s the best way to learn about percolation theory?

I wonder if there are any beautiful things in percolation theory. I also wonder what beauty is!

Should I read Scale by Geoffrey West, if I’m thinking this much about length scales?

“This claim is often justified by the observation of scale-free behaviors, such as power-law dependencies (Bialek et al., 2014; Dai et al., 2013; Steiner et al., 2016).” - what does this mean, in the discussion of Mugler’s paper, and what are these papers?

https://www.pnas.org/doi/10.1073/pnas.1324045111 - oh, this Bialek paper looks really cool!

What is a critical phase transition in the context of biology?

https://link.springer.com/article/10.1007/s10955-011-0229-4 - oh cool, this paper looks like it works to answer that question!

What does it mean to be poised at a very special point in parameter space?

How does one simulate things well?

https://arxiv.org/pdf/1805.03535.pdf - this seems really cool (from Hinczewski)

https://www.sciencedirect.com/science/article/abs/pii/B9780128000465000126 - I could read this, from Mugler, a bit on the effect of physical limits on signaling, I think? What is crowding?

What is a push-pull network?

When can we learn by doing, in theoretical biology?

What is self-organized criticality?

What would it mean for a biological system to position itself near a critical point?

Finished on the second page of Bialek’s paper ‘Are Biological Systems Poised at Criticality’

What is beauty in biology?

What does beauty mean in art?

What did David Deutsch say about beauty?

What did Noether teach us about beauty?

Wilczek…makes the claim that number is the most ‘pure product of mind’, while mass is a property of matter. I’m not sure what I think about this?

‘Beautiful’ things that were wrong:

• Plato proposing the world is made of platonic solids, although Wilczek notes he was ‘right to look for symmetry’

• Note that Newton’s dynamical laws look ‘different’ than the static beauty praised by Pythagoras and Plato

• Did Maxwell something additional to his equations suggested by symmetry?

Do I believe in Plato’s cave?

Brunelleschi brought on projective. geometry.

What could I read, additionally, of Newton’s on light?

Wilczek quotes Newton saying “’Tis much better to do a little with certainty & leave the

rest for others that come after than to explain all things by conjecture without making sure of any thing.”

In what ways does science interface with reality? What does it mean to do this?

Why do regularities appear at different lengthscales? Why are there laws of physics on a macro level?

What is symmetry?

Deutsch describes something as beautiful that is hard to vary

Deutsch notes that perhaps our arts are merely scratching the surface of what is beautiful

Is elegance a useful heuristic when searching for truth? What is the evidence for this? Do we just like it more?

Is elegance a heuristic guide to the truth?

What did Nagel mean?

Deutsch makes the case that, historically, civilizations were mostly destroyed by not having enough knowledge - but does this argument still apply?

2024-01-16

Why is there something and not nothing? What is a thing, as compared to something else?

What is nonduality, and what does it have to do with math?

https://people.math.osu.edu/cogdell.1/6112-Mazur-www.pdf

Are two things ever equal to each other?

What objects are the same?

When are numbers or objects equal to each other?

Does a number i,ply some things are equivalent?

What is a function?

How do we find new ideas in math? What guides that search?

Kant - how is pure mathematics possible?

If there are objective structures in the world, would we have to share understanding those with new intelligences?

2024-01-17

Timescales of reproduction and HGT when it happens in higher organisms - why does HGT happen so much less in larger multicellular organisms?

What is up with cancer and evolution?

Continuous vs discrete in biology (for example, species as discretely things which can or can’t reproduce w each other vs continuously things which are connected by variation)

If you were a cell in an organism, what would you do?

What was the analysis or observation that the emergence of cancer requires multiple probabilistic events?

Replication as a probabilistic way to get rid of aging damage

What are immune systems and how should one think about them?

2024-01-21

What is beauty? In a natural law? What does it mean, now?

Did the Nima Arkani-Hamed talk on the morality of fundamental physics mean a lot to me?

How does one think about beauty? Is one simply immersed in it, a lot?

What does a pleasing structure look like - for me, it definitely involves a lack of arbitrariness. Arbitrary things drive me crazy - they feel so unsatisfying! So, a beautiful thing is one in which each part of the item has a distinct meaning.

Is that all? Purity and specialness also come to mind - like, a beautiful thing has a certain purpose, where the different facets of it feed into that purpose. There’s some kind of unfolding structure to it - do I find many (or any) concepts in physics beautiful? A beautiful thing has some power to it - you can use it, generally.

I like being able to hold the full concept space in my mind, to go places quickly - do I find social things beautiful?

Simple perspectives that give us a vast power - I just don’t think we need to use all the atoms to figure out what will happen. What do regularities in distributions mean here?

Really, I’m talking about a very personal form of beauty - what do I care about or value?

Something that feels bigger than me, that feels separate from me - what does David Lynch mean when he talks about interacting with those types of ideas? And how does that change when ML models predict most things?

What is creativity?

2024-01-23

Mugler - fundamental limits of collective concentration sensing of cell populations

• Compares limits to cell sensing across short vs long distances

• Finds, counterintuitively, that signaling might be ‘better’ for long distances

• More specifically, that sparsely packed cells can sense things more precisely than densely packed cells

• I’m confused why the Dirac delta term is used in the second term on the right side of equation 1 - shouldn’t there be some area, larger than a point source, where it’s possible to bind a receptor? Why is it just literally one point in space? That seems so weird to me - how does it work in a modeling context?

• Why are noise terms just added to equation 1 and equation 2?

https://www.physics.purdue.edu/mugler/talks.html < these lectures might be good!

Also, the q-bio conference?

https://w-qbio.org/ < this could be really cool!

Yay I’m going!!!

I think understanding this paper will take understanding the terms in equation 1

How does one understand whether to use additive vs multiplicative noise?

Is thermal noise generally additive? For what types of things?

Where does multiplicative noise show up?

How do neural nets think about additive and multiplicative noise?

What will they find beautiful?

Is there some way I could have fun understanding what a neural net understands?

What ‘arbitrary’ qualia will those nets come up with - why did humans come up with qualia? What kinds of sensitive stimuli will they absorb? What will they care about?

https://link.springer.com/article/10.1140/epjb/e2010-00027-4 < lol what

Are energy usage and time always constraints?

How does additive and multiplicative relate to normal and log-normal?

Why are ecology and evolutionary biology so often linked? I’m so curious about this.

https://eeb.yale.edu/ < this could be interesting

Why is thermal noise so often additive? Does this mean things often happen at a specific scale?

I guess ecology provides the environmental context for evolution?

2024-02-27

In water, molecules can travel in all directions (small molecules or DNA) - so diffusion based communication can be really effective (vs on land acoustic signaling takes this place) - wonder what communication status of orgs was when they evolved into land and when acoustic signaling evolved in water - how did the first land based animals talk to each other? Why did visual and acoustic signaling evolve? When did they evolve, relative to other things? Do large animals in water use molecules to communicate with each other?

Water is like one big shared state with diffusion based gradients - similar to the cell environment. Why go to land? Did brains evolve on land or sea? Did land based organisms have more spatial coherence for a while? Did biofilms exist on land first? Why did we need to bring water with us? What is with passive diffusion as the basis of things that happen in a cell - how true is that analogy

Why isn’t life more dense - why are some parts of the planet more densely populated than others?

Are there forms of compression which would be beautiful in an ML-like system vs to a human? Are beautiful things compressed in the ‘same’ way across multiple systems which can internalize, compute or experience them?

What are the limits that I found? What is the characterization of bacterial communication? How do I add it all up?

1) a big diagram with bacteria next to each other, showing all the different methods of communication and associated numbers (possible length/complexity of message, number of bits / second or generation, typical use cases, diversity of message?)

2) a set of associated tables summarizing literature values, with sketched out thought experiments (bionumbers style) describing the derivation from those literature values (which present ranges) of the numbers in the diagram

3) then, a comparison to a group of humans talking to each other

Is there some way to estimate how this contributes to fitness? Make a list of things that these processes contribute to, somehow derive (through total number, or mass) how ‘fit’ those organisms are (or fit relative to each other?) and see if there is any correlation between either communication (its binary presence, or total amount) or the behaviors it enables with those things? Possibly also those things over time (what is increasing)?

Lastly, tabulate this for cells in a multicellular system (how much more do cells in a multicellular organism commnicate than do bacteria with each other in a population? how much more ‘fit’ are these systems’)

Can I do this for every known species? For what else would be relevant to do it? What species have and haven’t we studied? Can I do this comparing species from which language has evolved - is the presence of language at all correlated with fitness?

Can you do knockout experiments hwere you remove language nad look for the impact on fitness?

^Okay, so this, by end of year? Which part to do first, make a first table? For quorum sensing or HGT? And go from there? also list possible (but unconfirmed) methods of communication + their associated bounds? And find some way to cohere the whole in a series of thought experiment explorations -like what would be fun for bacteira to do with each other, what would be the constraints, bacterial relativity etc - like they can’t even say hi without pushing all the way! or, they don’t know who their friends are.

How are the messages bacteria pass each other different from symbolic language? There’s some claim about the infinite variety of expressable ideas - but can’t bacteria present an infinitely long sequence of signals? Describing an infinitely long fluctuation of environmental states? If it is, indeed, possible to talk for that long? If language is intwined with our ability to think, is bacterial communication intwined with their ability to compute?

What is beauty? What is beauty in writing?

These sound like cool papers (although potentially fake, no offense) from GPT-4 on the relationship between language and fitness

"The evolution of language" by W. Tecumseh Fitch, published in "Proceedings of the National Academy of Sciences" in 2010. This paper provides an extensive review of the current understanding of language evolution and its implications for fitness.

1. "The Faculty of Language: What Is It, Who Has It, and How Did It Evolve?" by Marc D. Hauser, Noam Chomsky, and W. Tecumseh Fitch, published in "Science" in 2002. This paper discusses the linguistic abilities that differentiate humans from other animals and considers the evolutionary steps that might have led to these abilities.

2. "Language as shaped by the brain" by Morten H. Christiansen and Nick Chater, published in "Behavioral and Brain Sciences" in 2008. This paper argues that the structure of language has been shaped by the constraints of the human brain, with implications for the fitness of individuals.

3. "The social function of intellect" by Nicholas Humphrey, published in "Growing Points in Ethology" in 1976. This paper is one of the foundational texts for the idea that the primary function of intelligence (and by extension, complex communication like language) is to handle social situations rather than to solve ecological problems.

4. "Language and Species" by Derek Bickerton, published in 1990. Bickerton explores the evolution of language as an adaptive trait and discusses the implications for the fitness of Homo sapiens.

5. "Cultural evolution of language" by Peter J. Richerson and Robert Boyd, published in "Cultural Evolution: Society, Technology, Language, and Religion" in 2013. This paper discusses how language evolves through cultural processes, affecting and being affected by the fitness of human societies.

6. "Animal communication and human language: An evolutionary perspective" by Tecumseh Fitch, published in "Philosophical Transactions of the Royal Society B" in 2011. This paper compares human language with animal communication systems and their respective impacts on species survival and fitness.

7. "Talking to Ourselves: The Science of the Little Voice in Your Head" by Charles Fernyhough, which explores inner speech and its role in human cognition and social interactions.

What is…pressure in water, again, ugh.

What does a bacteria want to do on a given day? Just hang out? Beauty in writing?

“Your inbox will become less of a place for coupons and bullshit than for the thoughts of humans you like.” < this is cool and mildly inspirational

Communication - how much does our tone of voice say about what we’re thinking?

2024-03-05

Mugler paper? or - fundamental limits on energy to transmit a bit?

How can I save information well?

Save things that might be surprising to my future self, in a way that’s comprehensible and where I can build on it, in the future?

A way to write + store documents atomically?

how to capture insight? explain it to my future self
practice writing?

Anki -

Is there a system I like? I like the idea of refining and polishing atoms

Do I want my outputs to be writings or cartoons? Diagrams? dances? sounds?

Programming vs evergreen note-writing?

Where can things go to outlive the day? tabs on my page? under sections there?

thought as words - but what about pictures??? poor little pictures

share information with the world, in understandable form - if someone wanted to dig into roughly what I was thinking about, they could, and it would be pretty and they would like it (joking! joking!!!) - but I do want it to be pretty, nice, to feel thoughtful and good to interact with

and a place to put all my stuff - the projects I can find that I like, a place to personally reference and cross reference my things

what was that? oh yes

Connect with and share ideas with friends

Writing for others is like writing for my future self

Stimuli that would most delight my future self? pretty things?

Merge curiosities + research?

Add edit history?

Add a way to give and play with toys - little videos? Pictures? cartoons?

Some regular quantitative thought expts? How do you do this in a fun way? The concept of sliders? A picture? A derivation? A little written thought experiment with picture? Daily thought experiment?

Little things I could collect over time?

Things that would enjoy, surprise, delight my future self + friends?

What’s up with this collection - synthesize in a series of vignettes?

Little thought experiment adventures?

Pictures? Equations? Calculations? Short videos where I explain something on a board?

What abstractions are you working with and how do you communicate those abstractions?

Man, math is gonna be so good with BCIs - holy shit, I am literally so excited

Writing to others as a way to synethesize insight

Interested in - distilled beautiful things in science

What is beauty?

Ah, of course, it must be that way

Tabs!

2024-03-06

Something beautiful

Structured information

Cyberfeminism?

Gardens

Write down a bunch of thought experiments? Viewpoint? Zoom around a bacterial cell? On infinite canvas?

Beautiful mathematics (e.g. the amazing identities of Ramanujan; results which

are easy (and pretty) to state but not to prove); < from Terrence Tao on good mathematics - do I think this is beautiful? more good mathematical insight, personally, or deep, or good mathematical vision

2024-03-19

I’m really interested in the shape of biological laws - what will we look like? What does the shape of the truth look like in biology?

- Thoughts - something about passive diffusion based computing feels interesting to me, also the many to one vs one to one nature of communication (at least sometimes)

- Something about complexity

- What do we know of biology - of life, this rippling in the fabric of the universe, and what from that can we then infer about ways we can interface with this phenomena to understand it?

- What does it mean to understand a physical phenomenon? To write down a physical law - how does one’s mind interacting with that work?

Yeah

Also, what are the laws of the internet? How does the shape of the internet govern truths about it?

How is a ‘truth’ different from a physical laws - are we biased to find physical laws to make sense to us

Aka the laws of physics are pretty to our brains in a way that might have helped them be discovered, what are ways we then think about all the laws we're not seeing

from I'm really interested in the question of how we find physical laws that are biased to be amenable to human intuition, and how we grapple with that - any suggestions for science epistemology literature that might help?

How do we find the laws we’re not seeing? are these the best laws? they just seem that way because we made them pretty for our brains?

what are all the conceivable ways one could understand something?

What’s the best evidence for the kind of implied belief we have that mathematical or physical laws will be discoverable by other entities, or sort of come first? Won’t…social things, or something like that? Like, wouldn’t they have discovered the concept of love earlier? Maybe not if they’re receiving transmissions, but still.

Is it more likely that other civilizations would have discovered the laws of physics or the concept of love first? Which would it really be more easy to communicate about? Or of language?

What is up with physics being expressible in a certain kind of mathematics? And what kind of mathematics is that? Just, like, mathematics?

Can I use current learning tools to teach myself quantum field theory in a semester

What is up with symmetry???? What the literal is up with it, people use it all the time and I have no idea what they’re talking about or why it’s important

Weyl - symmetry?

What if there’s a really easy way of understanding equations that just makes it a lot easier for everyone (i.e. just visualize it as a first move each time)

Resources for what structure

https://www.maths.ed.ac.uk/~v1ranick/papers/wigner.pdf - unreasonable effectiveness of mathematics

Against Method, Logic of Scientific Discovery

Different claims that feel related to this

• there’s a human experience of mathematics that feels quite related to poetry

• some structures or things to look for are inherently more useful than others

His classmate was a bit incredulous and was not quite sure whether

the statistician was pulling his leg. "How can you know that?" was his query. "And what is this

symbol here?" "Oh," said the statistician, "this is pi." "What is that?" "The ratio of the

circumference of the circle to its diameter." "Well, now you are pushing your joke too far," said the

classmate, "surely the population has nothing to do with the circumference of the circle."

^from the Unreasonable Effectiveness of Mathematics - seems actually really true and interesting that this is the case

When do mathematical techniques turn up unexpected connections?

from the same essay - “Much less will be said on the second point:

the uniqueness of the theories of physics. A proper answer to this question would require elaborate

experimental and theoretical work which has not been undertaken to date” < what is this elaborate experimental and theoretical work?

What is a concept in mathematics?

Does this have anything to do with intuitionism in mathematics?

Is it true that intuitionism views mathematical objects as mental constructs, vs objects with a separate reality?

“This property of the regularity is a recognized invariance property and, as I had occasion to point out some time ago, without invariance principles similar to those implied in the preceding generalization of Galileo’s observation, physics would not be possible.”

“Again, it is true that if there were no phenomena which are independent of all but a manageably small set of conditions, physics would be impossible.” < what does this mean?

“The preceding discussion is intended to remind us, first, that it is not at all natural that "laws of nature" exist, much less that man is able to discover them. [E. Schrodinger, in his What Is Life? (Cambridge: Cambridge University Press, 1945), p. 31, says that this second miracle may well be beyond human understanding.] < what does this mean, should I re-read what is life?

What are layers of laws of nature?

“As regards the present state of the world, such as the existence of the earth on which we live and on which Galileo’s experiments were performed, the existence of the sun and of all our surroundings, the laws of nature are entirely silent” < that is so true, what can say something about that? is the anthropic principle actually pretty deep?

What is up with quantum mechanics like literally

laws of nature written in mathematics - but isn’t mathematics just our interface to the laws, rather than the laws themselves?

this seems a bit true and a bit not true?

“As we saw before, the concepts of mathematics are not chosen for their conceptual simplicity - even sequences of pairs of numbers are far from being the simplest concepts - but for their amenability to clever manipulations and to striking, brilliant arguments.” < this is cool!!!

Wigner keeps saying complex numbers are - there’s something interesting going on there

“uncanny number of cases to an amazingly accurate description of a large class of phenomena” < uncanny, amazingly accurate are interesting

Newton did something truly beautiful

“postulated the universal law of gravitation on the basis of a single, and at that time very approximate, numerical coincidence”

Things which look beautiful in a law

• universally applicable (in many different contexts)

• ‘getting something out of’ equations which we did not put in

“first, the law, particularly since a

second derivative appears in it, is simple only to the mathematician, not to common sense or to

non-mathematically-minded freshmen; second, it is a conditional law of very limited scope. It

explains nothing about the earth which attracts Galileo’s rocks, or about the circular form of the

moon’s orbit, or about the planets of the sun. The explanation of these initial conditions is left to the

geologist and the astronomer, and they have a hard time with them”

Surely in this case we "got something out" of the equations that we did not put in.

Has anyone studied how often beautiful things are actually helpful?

I could ask more?

“It is true, on the other hand, that physics as we know it today would not be possible without a constant recurrence of miracles similar to the one of the helium atom, which is perhaps the most striking miracle that has occurred in the course of the development of elementary quantum mechanics, but by far not the only one”

Physics house? surrounded by suggestions of natural phenomena?

“preceding three examples, which could be multiplied almost indefinitely” < really? what are the other examples? what are all the examples of mathematical theories which, by their structure, got more out than you put in?

“I propose to refer to the observation which these examples illustrate as the empirical law of epistemology. Together with the laws of invariance of physical theories, it is an indispensable foundation of these theories” < what is this?

“encouragement and reassurance which are emotional necessities, without which the "laws of nature" could not have been successfully explore” < makes a claim about the beauty of the laws of nature giving emotional reassurance here

“, called it an article of faith of the theoretical physicist, and it is surely that. However, what he called our article of faith can be well supported by actual examples - many examples in addition to the three which have been mentioned”

Put things on the internet until no more feedback or not already written

“Every empirical law has the disquietire which will be discovered, will fuse into a single consistent unit, or at least asymptotically approach such a fusion. Alternatively, it is possible that there always will be some laws of nature which have nothing in common with each other.” < yeah what’s with the conviction that laws will be unified togehter ultimately? why would that be better than not? what does it mean to be unified?

what context do you carry over?

“It is even possible that some of the laws of nature will be in conflict with each other in their implications, but each convincing enough in its own domain so that we may not be willing to abandon any of them. We may resign ourselves to such a state of affairs or our interest in clearing up the conflict between the various theories may fade out. We may lose interest in the "ultimate truth," that is, in a picture which is a consistent fusion into a single unit of the little pictures, formed on the various aspects of nature”

If you can’t unify the two laws relativity abnd quantum mechanics the universe isn’t computed? Or, does the universe have to be self-consistent enough or something like that to be computed?

What would have to be true of the natural laws if we were in a simulation?

“In order to obtain an indication as to which alternative to expect ultimately, we can pretend to be a

little more ignorant than we are and place ourselves at a lower level of knowledge than we actually

possess. If we can find a fusion of our theories on this lower level of intelligence, we can

confidently expect that we will find a fusion of our theories also at our real level of intelligence. On

the other hand, if we would arrive at mutually contradictory theories at a somewhat lower level of

knowledge, the possibility of the permanence of conflicting theories cannot be excluded for

ourselves either. The level of knowledge and ingenuity is a continuous variable and it is unlikely

that a relatively small variation of this continuous variable changes the attainable picture of the

world from inconsistent to consistent. [This passage was written after a great deal of hesitation.

The writer is convinced that it is useful, in epistemological discussions, to abandon the idealization

that the level of human intelligence has a singular position on an absolute scale. In some cases it

may even be useful to consider the attainment which is possible at the level of the intelligence of

some other species. However, the writer also realizes that his thinking along the lines indicated in

the text was too brief and not subject to sufficient critical appraisal to be reliable.]” < this is super interesting!! from Wigner - Unreasonable Effectiveness of Mathematics

what is he saying - that things that less intelligent species can find might also be true at higher levels?

Interesting on his discussion of false theories

Explains a lot

“Let me end on a more cheerful note. The miracle of the appropriateness of the language of

mathematics for the formulation of the laws of physics is a wonderful gift which we neither

understand nor deserve. We should be grateful for it and hope that it will remain valid in future

research and that it will extend, for better or for worse, to our pleasure, even though perhaps also to

our bafflement, to wide branches of learning.”

So interesting when he talks about consciousness/biology and physics!!!!

“e argued that biology and cognition could be the origin of physical concepts, as we humans perceive them, and that the happy coincidence that mathematics and physics were so well matched, seemed to be "unreasonable" and hard to explain.”

I could try to understand what Tegmark is saying about the universe

A fun, free interaction

Do we need to stare at something to compute - input/output

2024-03-22

What about the Mugler and Hinczewski papers - is there good followup to those?

Point about orgs that communicate being the organism

Some question of what this thing that we call life is, multiple different perspectives

Communication/language as central - the exchange of information as the thing in itself

Invert it - did concepts come with communication?

What is the feeling of beauty? Of excitement, adventure?

Style - Strunk and White

What did Noam Chomsky think?

Wittgenstein

language-game "is meant to bring into prominence the fact that the speaking of language is part of an activity, or of a life-form." - Wittgenstein, PI

Books?

2024-04-08

Carl Boyer

Abstraction

Are we generating the universe?

Not important

Halting problem

David Foster Wallace “Everything and More”

Given limits imposed by basic quantum theory, one H. Bremermann proved in 1962 that "No data processing system, whether artificial or living, can process more than 2 X 1047 bits per second per gram of its mass,"

infinity symbol was introduced to math by John Wallis in his 1655 Arithmetica infinitorum, which was one of the important preliminaries for Newton's brand of calculus.

As it happens, the only thing that kept Wallis from actually inventing differential calculus in A. i. was his ignorance of the Binomial Theorem, which is essential to working with infinitesimals-see esp. §4 below

Here is M. Kline again:

"The philosophical doctrines of the Greeks limited mathematics in another way. Throughout the classical period they believed that man does not create the mathematical facts: they preexist. He is limited to ascertaining and recording them.

Plus here is another quotation from D. Hilbert, the great early champion of Cantor's transfinites: [T]he infinite is nowhere to be found in reality, no matter what experiences, observations, and knowledge are appealed to. Can thought about things be so much different from things? Can thinking processes be so unlike the actual process of things? In short, can thought be so far removed from reality?

There is nothing more abstract than infinity.

Take the single most ubiquitous and oppressive feature of the concrete world-namely that everything ends, is limited, passes away-and then conceive, abstractly, of something without this feature.

Weyl?

Infinite abstraction capability?

Life

That we are mostly water, and water is mostly hydrogen, and hydrogen is flammable, and yet we are not flammable

I 'know' my love for my child is a function of natural selection, but I know I love him, and I feel and act on what I know.

One of the quickest routes to this feeling is (from personal A.M. experience) to try to think hard about

dimension.

There is something I 'know,' which is that spatial dimensions beyond the Big 3 Feel the same fluency, but in unbounded dimensions of thought

Truly understand dimension

Expand the true conscious experience of concept

What are the current limits?

Different latent spaces?

Do computing things need to be conscious to do useful things?

Is mathematics inherently neat and clean?

"The certainty of mathematics," says [A. N.) Whitehead, "depends on its complete abstract generality." When we assert that 2 + 3 = 5, we are asserting a relation between three groups of 'things'; and these 'things' are not apples or pennies, or things of any one particular sort or another, but just things, 'any old things.' The meaning of the statement is entirely independent of the individualities of the members of the groups. All mathematical 'objects' or 'entities' or 'relations,' such as '2,' '3,' '5,' '+,'or'=,' and all mathematical propositions in which they occur, are completely general in the sense of being completely abstract. Indeed one of Whitehead's words is superfluous, since generality, in this sense, is abstractness

The sum of the series (1 + 3 + 5 + 7 + 9) = 52 ' is a factoid, whereas (2) 'For any x, the sum of the first x odd integers =

x 2' is a theorem, i.e. actual math

What are these weird objects?

Energy and capacity to understand something like dimension fully

Euclid does not talk about the infinity of primes

Do what the Greeks did but for other new concepts of on a different layer - invent a new kind of math

Patterns of abstraction

Another world, as objects in another world

Re which, again, please keep in mind that a language is both a map of the world and its own world, with its own shadowlands and crevasses-places where statements that seem to obey all the language's rules are nevertheless impossible to deal with.

radoxical crevasses, involve either self-reference or regressus, two demons that have afflicted language since as far back as we might want to go

Self-reference - Hofstadter?

And of course since mathematics is a totally abstract language, one whose lack of specific real-world referents is supposed to yield maximal hygiene, its paradoxes and conundra are much more of a problem. Meaning math has to really deal with them instead of just putting them in the back of its mind once the alarm goes off.

What about logical uncertainties in math? One reason math texts are so abstruse and technical is because of all the specifications and conditions that have to be put on theorems to keep them out of crevasses. In this sense they're like legal documents, and often about as much fun to read

- the concept behind the legalese

Such a number would involve an infinitesimal, meaning a literally infinitely small mathematical entity.

What is an infinitesimal? You may well however not recall-probably because you were not told-that infinitesimals made the foundations of the calculus extremely shaky and controversial for 200 years, and for much the same reason that Cantor's transfinite math was met with such howling skepticism in the late 1800s: nothing has caused math more problems historically, methodologically, metaphysically-than infinite quantities. In many ways, the history of these co-related problems is the Story of Mathematics itself

__

Able to truly understand dimension, do something similar to what the Greeks did with the independent reality of objects (abstract math)

Are we just better at seeing beautiful things?

2024-04-28

Quantifying communication in bacteria.

How fast do bacteria get better because of HGT?

Antibiotic resistance might be a good example - well studied, bacteria do care a lot about it spreading. Does it spread due to differential bacterial replication or HGT though?

How much free floating DNA (or just, nucleic acid) is there in the ocean? What assays would you do to test this?

General Concentrations: Research has shown that the concentration of eDNA can vary significantly depending on the location, depth, and surrounding biological activity. For example, surface waters might have different concentrations compared to deeper waters or sediments. In general, concentrations might range from a few nanograms to several micrograms per liter of seawater.

1. Study by Dell'Anno et al. (2015): This study quantified the amount of extracellular DNA in deep-sea sediments of the Mediterranean Sea. They found that extracellular DNA concentrations ranged from 0.45 to 5.32 micrograms per gram of dry sediment. While this study focuses on sediments rather than water columns, it highlights the significant presence of eDNA in marine environments.

   Citation: Dell'Anno, A., Carugati, L., Corinaldesi, C., Riccioni, G., & Danovaro, R. (2015). "Unveiling the biodiversity of deep-sea nematodes through metabarcoding: Are we ready to bypass the classical taxonomy?" PLoS ONE, 10(12), e0144928.

2. Study by Boström et al. (2004): This research investigated extracellular DNA in the water column and sediments of the Baltic Sea. They reported that eDNA concentrations in water samples were in the range of tens of nanograms per liter, emphasizing the variability and widespread presence of eDNA across different marine environments.

   Citation: Boström, K. H., Simu, K., Hagström, Å., & Riemann, L. (2004). "Optimization of DNA extraction for quantitative marine bacterioplankton community analysis." Limnology and Oceanography: Methods, 2(11), 365-373.

^ from GPT-4, would want ot check numbers

https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2002.47.3.0899

How much DNA is there floating around the air?

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.2002.47.3.0899

^ from above, I’m not sure if I’m interpreting this right, but looks like oom 10 ug/g HDNA (?) what does this mean or feel like?

What about quantifying communication between cells in a multicellular organism?

https://www.annualreviews.org/content/journals/10.1146/annurev.genet.35.102401.090145 < “Thinking about bacterial populations as multicellular organisms” this seems like a cool paper! I like the title, at least.

https://complexityzoo.net/Complexity_Zoo < I love this so much! I love this so much!

^ I love this so much!!!!!!!

What would be similar?

• communication modalities?

  • using different physical forces?

• communication regimes?

• how do you classify these? across types of thing communicated - molecules or forces. Across context - more individual bacteria, vs biofilms or multicellular organisms. and then what kind of communication - like what is it saying? how complex? what does complexity mean in this context? what does it make the other thing do?

• maybe this is the question I’m interested in (right now, l) - how does one classify communication? what are the ‘correct’ boundaries?

• one thing I haven’t thought too much about is what the different types of communication are in the correct way - like what does it want to be

• what are bacteria typically saying to each other? helping each other survive? (like, helping another individual?) or ‘coordinating’? what does ‘coordinating’ involve? do cells signaling in multicellular organisms do both too? what different types of coordination are there? the cells all doing something together that is bigger than any one cell? what does that mean?

• this is so exciting!

2024-04-29

Revisit Hinczweski?

Theoretical perspectives on biological machines - Mauro L. Mugnai, Changbong Hyeon, Michael Hinczewski, and D. Thirumalaim, 2020

What I like about it: describes a comprehensive framework I can ‘trust’ (biological machines feels like an approachable category - but is that correct?), I like theoretical perspectives because I can manipulate them mentally

• what is a nucleic acid translocase?

• what is mesoscale - literally never think about that

• What are the core physical processes in biology? How did we decide on that?

• What are evolutionary constraints?

• Motors - walkers, twirlers

• What is a motor?

  • What types of movement can motors do?

  • In mechanical - how do we make motors do anything?

    • Alternating current -> push things with electric field

    • Converts energy into mechanical energy

I kind of want to understand the full question ‘what can physics tell us about biology’

• roughly, copying the info in the cell, doing things from that info

I mean, related, I love this book, even though it is not a paper

Biophysics - Searching for Principles, William Bialek, 2011

book.bionumbers.org

Rob Philips book on the cell

Uri Alon - Systems Medicine Physiological Circuits and the Dynamics of Disease

2024-06-07

I still (goshdarnit!) don’t have a good # for how many bits bacteria exchange when they talk to each other in different scenarios.

Information - with respect to what baseline distribution?

https://ganguli-gang.stanford.edu/people.html < could this be an interesting place to do work?

https://sarahharvey.github.io/

Stanislav Fort?

Similarities between computation done by neurons and computation done by groups?

How are neural nets relevant to group computation?

https://ganguli-gang.stanford.edu/pdf/16.PowerPrecisionSpeed.pdf < this seem so cool! ‘A universal tradeoff between power, precision and speed in physical communication’. I gotta read this.

Also, how do I store all the papers I read + notes to keep track of them? Online tool? Research EA?

Wow this seems so cool!!!!!!

Notes:

Information theory and thermodynamics

What is biological computation? What characterizes it? What are all of the different types of biological computers?

“For example the human brain performs myriad

computations, including complex object recognition in

150 ms [1] while consuming less than 20 watts”

Thermodynamics and information theory

what is thermodynamics?

“For example, information theory [3, 4] provides limits on the accuracy of communication under power constraints” < how does this work? “More recent work has elucidated the minimal energy required to perform a physical process in finite time [7, 8]), but does not address accuracy in any computation.” < what do these references say?

“Landauer [9–11] revealed that the erasure of information sets a lower bound on the energy consumed in computation” < I’d really like to understand this paper well enough to describe it

2024-06-08

sprint: understand this paper https://arxiv.org/pdf/1603.07758

break down into learning goals?

questions

• what is power?

  • Is this the power required to do a computation?

• what is precision?

  • How would computation be not precise?

• what is speed?

‘information theory provides limits on the accuracy of communication under power constraints’

I could start by looking at the main results + trying to understand what techniques were used to obtain them?

model

• physical channel in contact with a thermal bath, coupled to a signal

• Figure 1 from the paper

“In summary, by deriving general relations between fric-

tion and information, we have shown that the product of

signal speed and channel precision cannot exceed power

dissipation for an extremely general class of physical com-

munication channels. Intuitively, this three-way tradeoff

arises because any increase in speed at fixed precision

requires the channel state distribution to change more

rapidly, leading to increased power dissipation. Similarly

any increase in precision at fixed speed requires high sig-

nal sensitivity, or a larger signal dependent change in the

channel equilibrium state distribution as measured by the

Fisher information metric, which again leads to greater

power dissipation.”

Do these conclusions hold true in all contexts?

Email the lead author?

“external signal λμ(t) modulates the transition rates of an arbitrary continuous-time Markovian dynamical system” < this is a model of > a physical channel in contact with a heat bath

in this context, “A downstream receiver can construct an estimate ˆλμ of the instantaneous signal by observing the instantaneous microstate of the channel.”

Okay - so, it sounds like the ‘system’ is in microstates (i.e. a Markov dynamical system with the state specified by the transition rates - do the number of nodes remain the same?)

Why is it a Markov dynamical system? Why not just, like, a vector of i.e. the transition rates? What is the Markov dynamics saying about the system? How does one ‘observe’ a Markov dynamical system.

Questions for the lead author:

• Why did you model the channel as a continuous-time Markov dynamical system

getting to know an object very well

<jumped to refs>

P. Sterling and S. Laughlin, Principles of neural design. MIT Press, 2015 < this seems pretty cool!

M. Gastpar, B. Rimoldi, and M. Vetterli, “To code, or not to code: lossy source-channel communication revisited,” < this also looks cool!

these all look cool

[9] R. Landauer, “Irreversibility and Heat Generation in

the Computing Process,” IBM Journal of Research and

Development 5 (July, 1961) 183–191.

[10] C. H. Bennett, “Logical Reversibility of Computation,”

IBM Journal of Research and Development 17 (Nov.,

1973) 525–532.

[11] C. H. Bennett, “The thermodynamics of computation-a

review,” International Journal of Theoretical Physics

21 (Dec., 1982) 905–940.

[12] T. Toffoli, “Reversible computing,” in Automata,

Languages and Programming, J. de Bakker and J. van

Leeuwen, eds., vol. 85 of Lecture Notes in Computer

Science, pp. 632–644. Springer Berlin Heidelberg, 1980.

[13] J. J. Hopfield, “Kinetic Proofreading: A New

Mechanism for Reducing Errors in Biosynthetic

Processes Requiring High Specificity,” Proc. Natl. Acad.

Sci. U.S.A. 71 (Oct., 1974) 4135–4139.

20] H. Qian, “Reducing intrinsic biochemical noise in cells

and its thermodynamic limit.,” Journal of molecular

biology 362 (Sept., 2006) 387–92. < ooh this looks really cool

[23] R. G. Endres and N. S. Wingreen, “Maximum

likelihood and the single receptor,” Phys. Rev. Lett. < what is this?

24] P. Mehta and D. J. Schwab, “Energetic costs of cellular

computation.,” Proc. Natl. Acad. Sci. U.S.A. 109 (Oct.,

2012) 17978–82, arXiv:1203.5426 [q-bio.MN] <this looks so fun

[25] A. H. Lang, C. K. Fisher, T. Mora, and P. Mehta,

“Thermodynamics of statistical inference by cells,”

Phys. Rev. Lett. 113 (May, 2014) 148103,

arXiv:1405.4001 [physics.bio-ph].

[26] A. C. Barato, D. Hartich, and U. Seifert, “Efficiency of

cellular information processing,” New Journal of

Physics 16 (may, 2014) , arXiv:1405.7241.

[27] C. C. Govern and P. R. ten Wolde, “Energy Dissipation

and Noise Correlations in Biochemical Sensing,” Phys.

Rev. Lett. 113 (Dec., 2014) 258102.

[41] M. Skoge, Y. Meir, and N. S. Wingreen, “Dynamics of

cooperativity in chemical sensing among cell-surface

receptors,” Phys. Rev. Lett. 107 (oct, 2011) 1–5,

arXiv:1109.4160 [q-bio.MN]

43] S. Ganguli, D. Huh, and H. Sompolinsky, “Memory

traces in dynamical systems.,” Proc. Natl. Acad. Sci.

U.S.A. 105 (dec, 2008) 18970–5.

<questions>

what is a channel? what is a source? what is information? what is communication?

what is an interconnection network?

What is the Flatiron institute?

Revisit the core question, focus in on the result

Stanford professors interested in evolution

ecology vs evolution?

statistics

https://cremerlab.github.io/

2024-06-09

What is friction?

How does a large coding block relate to speed?

What does accuracy mean?

Accuracy, power, speed

Landauer showed that

Why is communication a prerequisite for more complex computations?

What is a Markovian communication channel?

“ in which the power dissipated

can be described through a thermodynamic friction ten-

sor on a manifold of channel state distributions” < what is this? What is thermodynamic friction?

We derive a lower bound on this friction tensor in terms of

Fisher information, a fundamental quantity in the geom-

etry of information < what is Fisher information?

Concepts for https://arxiv.org/pdf/1603.07758

- Fisher information

2024-06-17

Multiverse, mathematical universe

“Sir Isaac Newton (1643-1727), an English mathematician and physicist, believed that his scientific discoveries were a way of revealing the divine order and harmony in the universe.”

“It is quite clear to me that the religious paradise of youth, which was thus lost, was a first attempt to free myself from the chains of the 'merely personal,' from an existence dominated by wishes, hopes, and primitive feelings. Out yonder there was this huge world, which exists independently of us human beings and which stands before us like a great, eternal riddle, at least partially accessible to our inspection and thinking. The contemplation of this world beckoned as a liberation, and I soon noticed that many a man whom I had learned to esteem and to admire had found inner freedom and security in its pursuit. The mental grasp of this extra-personal world within the frame of our capabilities presented itself to my mind, half consciously, half unconsciously, as a supreme goal. Similarly motivated men of the present and of the past, as well as the insights they had achieved, were the friends who could not be lost. The road to this paradise was not as comfortable and alluring as the road to the religious paradise; but it has shown itself reliable, and I have never regretted having chosen it.”

“If something is in me which can be called religious then it is the unbounded admiration for the structure of the world so far as our science can reveal it.”

“Your question is the most difficult in the world. It is not a question I can answer simply with yes or no. I am not an Atheist. I do not know if I can define myself as a Pantheist. The problem involved is too vast for our limited minds. May I not reply with a parable? The human mind, no matter how highly trained, cannot grasp the universe. We are in the position of a little child, entering a huge library whose walls are covered to the ceiling with books in many different tongues. The child knows that someone must have written those books. It does not know who or how. It does not understand the languages in which they are written. The child notes a definite plan in the arrangement of the books, a mysterious order, which it does not comprehend, but only dimly suspects. That, it seems to me, is the attitude of the human mind, even the greatest and most cultured, toward God. We see a universe marvelously arranged, obeying certain laws, but we understand the laws only dimly. Our limited minds cannot grasp the mysterious force that sways the constellations. I am fascinated by Spinoza's Pantheism. I admire even more his contributions to modern thought. Spinoza is the greatest of modern philosophers, because he is the first philosopher who deals with the soul and the body as one, not as two separate things.”

"My views are near those of Spinoza: admiration for the beauty of and belief in the logical simplicity of the order which we can grasp humbly and only imperfectly. I believe that we have to content ourselves with our imperfect knowledge and understanding and treat values and moral obligations as a purely human problem—the most important of all human problems."

“Scientific research can reduce superstition by encouraging people to think and view things in terms of cause and effect. Certain it is that a conviction, akin to religious feeling, of the rationality and intelligibility of the world lies behind all scientific work of a higher order. [...] This firm belief, a belief bound up with a deep feeling, in a superior mind that reveals itself in the world of experience, represents my conception of God. In common parlance this may be described as "pantheistic" (Spinoza)”

Spinoza, mathematical universe.

Mathematical universe - how do we know there is an external physical reality completely independent of us humans?

What, then is mathematics? That which is comprehensible to humans?

It would be cool if mathematics is made by humans!

Intuitionism

Intuitionists only accept the idea of potential infinity?

Is intuitionism cool in the sense that we are the creators?

“According to Brouwer mathematics is a languageless creation of the mind”

^ what does this mean?

Intuitionism contains a notion of time?

The inherent limitations of the human mind, and what it means to be human

2024-07-10

What will the future look like?

I’d like to get a full-stack understanding of biology, but I feel as though it is necessary to invent or create new concepts in biology to have the kind of understanding I desire. A vision for biology?

What is this similar to? Physics can feel satisfying, presumably, because you can build a large structure in your head with which you can make inferences about and reason about what the world will do, and in the building of which one might become friends with some nice structures. Do we expect this to still be an activity (this kind of understanding, coupled to the uncovering of important laws) in the future? I’d assume it would be, as presumably we’d want to compress predictive power as much as possible (are there any ways in which this is obviously wrong?) and this would be a good way to do that. What, then, is beauty - just the most compressed, the most simple version of a thing? But what about human preference, chaos - Madonna Inn-style delights. What is ‘good’ about arbitrary choice - its existence, and the way in which it is expressed?

Are these two different values - oh, I see, one can compress some predictive model of the world a lot, and this is different from experiencing that compressed predictive model. What do I care about the experiencing though - why is it important for a human to be playing with this compressed predictive model?

Maybe I just personally want to have a lot of fun with biology, and fuck it, that’s all the justification I need?

But it does feel as though - what if the world looks very different, and there are other things to do?

What feels fun or nice or interesting? The cell picture, certainly. Truths or constraints that pop out of biology - like passive diffusion - when you look at it. I wonder how many there are, there. They feel satisfying in a different way than the former - the former feels more akin to literally whirling through a universe, the latter feels like an ‘a-ha’ that is - I’m not sure exactly why it’s satisfying and don’t feel the need to unpack it heremore. What else could be satisfying? Really just loading an object into mind and looking over it, fiddling with it, building a version of it that is play-able. Why don’t I just do a lot of math if that’s what I like? Maybe because those objects feel too abstract - I like physics-y things that bounce around in the real world, I just really like biology in particular. I just feel as though biology is playing by rules I don’t understand and, goddamnit, I want to understand those rules! So I can finally look around and say ‘ah, so that’s why that is’.

I just feel as though it’s so obvious that there are some rules we’re close to understanding. For example, the whole ‘what’s going on with communication as a core principle of life’ thing. Why is this important?

• Communication is pretty widespread throughout life (even bacteria communicate in 3 or more different engineered ways)

• We only recently realized how widespread it was (did we think bacteria talked to each other before we discovered quorum sensing?)

• Something that widespread…needs to be explained? At least, it would be fair to explain it (why does it show up so often when life shows up) if we are going to explain replication

A ‘why’ could be analogous to that for replication - that the property gives rise to a process (evolution by natural selection) which can create the complex things which then wonder about how they got there. So, what process is communication contributing to?

Well, it seems like it’s contributing to the process of figuring things out. But what does that mean?

What feels beautiful and true here?

Communication is possible between entities which can communicate - replication makes lots of those

Communication involves some exchange of information, some concept of bandwith

Something about complexity growing as the group grows due to the increasing number of potential pairwise interactions - I really wish I understood distributed computing well enough to understand if there’s some core principle here I ought to know

In a sense, one could view sexual reproduction (which is not necessary for evolution) as a kind of communication - so, sexual selection as a widespread example of this (two entities sharing information - how adaptive to strands of information were - together and creating something new together). I guess I’m confused if one should care about the creating something new part.

I’m curious what kinds of things distributed systems can do really well - like markets?

What does message passing mean, generally? Where is it in its most abstract form? Could one see everything as some form of message passing (i.e. thinking about special relativity through the lens of two people trying to talk).

Distributed systems - difference between having a shared goal and all working together to serve individual goals

How does topology factor into a distributed system?

How could I play w/ a distributed system?

Is there a form of chaos computing, like parallel computing but chaos with agents that want to do their own thing, or distributed computing a subset thereof

Like peer to peer distributed computing

The protocol is king in peer to peer? So whoever makes the best protocol

What is a protocol? Something that a bunch of agents agree to abide by and communicate with respect to?

The protocol by which a group communicates - how then does the group know ‘what to do’ if there is such a thing

Bio through the lens of protocols

A protocol is not the information itself - its sort of like a program? You can use it again and again and change it, but it’s fundamentally about how something is processing some information? How then do protocols change - that feels tricky and interesting - you can accidentally make new ones but what if - you can use a protocol to communicate protocols to others. Watching a group update - using communication to update norms? So protocols lead to protocol updates - and how do they do that? By building on each other? What is a protocol - is a protocol like a compiled program, like it is compiled…..well, from other protocols? A protocol determines how a set of agents will interact with each other (as in, given an input for each agent, what the output will be) - so, biology as the evolution of these? What kinds of protocols could exist between entities? What rules govern what protocols arise? How does evolution….relate to this? Traditionally it was looking at the individual entities, not the protocols that they were following as a group (or was it also looking at those as properties of individual entities which could be selected for)? The point though is that the fitness benefit of such groups might only arise in the context of a group of agents abiding by such a protocol.

So, perhaps it’s best not to think of fitness benefits from communication as being contradictory to evolution by natural selection, rather though, these are the subset of traits which are beneficial in a group. But aren’t all traits selected for in the context of a group?

What are groups doing - and how does it relate to life?

Are companies, then, like living things - honestly grouping things into what ‘is a living thing’ and what isn’t feels super uninteresting to me, I wonder why - kind of like it’s not the right idea, the right idea is to look at protocols and what they will do. Like what protocols will come next -but is that interesting, like with neurons, is it interesting to talk about what protocols they are following? What is an idea in the context of an neuron? So, living things talk via protocols and then…ideas emerge at a layer above?

I feel mildly worried that this writing will not be comprehensible later, and wonder what I could do differently with it. How could my writing be more clear? Could I define terms better? Structure arguments? I wonder how one structures arguments well.

What the hell is going on with self referential systems and complexity, that’s not quite right, I am very curious though.

Learn to love toys?

Thank you

2024-07-16

Communication allows computations to scale to certain sizes

Scaling laws for communication

…also what is up with the mathematical universe hypothesis

What is a theory of everything?

Is the mathematical universe hypothesis compatible with Godel’s incompleteness theorem?

What is Godel’s incompleteness theorem?

Why is the theory of everything a theory of physics?

What is computable physics?

What are emergent laws?

Emergent behaviors - only arise at the right scale

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

Are emergent things patterns at different levels vs the most underlying pattern - what does a pattern at a given level mean? At a level of scale? What is scale?

What am I confused about?

What is emergence and why is it important?

Does emergence imply a notion of scale?

• ‘how big’

• ‘described in what terms’

With programing languages - which is described in the terms of which other?

What does scale mean? Ability to do more? Ability to create different things with the ability to do more?

Are the scale graphs selected without regard for the diversity of species?

What do scale and complexity have to do with each other?

What does it mean to continue going?

Beautiful answer to all of these questions?

Communication allows computations to scale to certain sizes

Scaling laws for communication

…also what is up with the mathematical universe hypothesis

What is a theory of everything?

Is the mathematical universe hypothesis compatible with Godel’s incompleteness theorem?

What is Godel’s incompleteness theorem?

Why is the theory of everything a theory of physics?

What is computable physics?

What are emergent laws?

Emergent behaviors - only arise at the right scale

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

Are emergent things patterns at different levels vs the most underlying pattern - what does a pattern at a given level mean? At a level of scale? What is scale?

What am I confused about?

What is emergence and why is it important?

Does emergence imply a notion of scale?

• ‘how big’

• ‘described in what terms’

With programing languages - which is described in the terms of which other?

What is scale?

Maybe scale is implicitly defined by the units along which one is scaling

Scale implies some concept of size, and something different happening at a certain size

What is the relationship between scale and complexity?

How would one study how communication scales in different systems?

What communication systems allow what computation to happen at what levels of scale?

Latency at larger scales

What are other core concepts?

How does computation work - you have to like integrate a bunch of things? What on earth is the relationship between computation and communication?

Well - I was thinking about this - they both have thermodynamic bounds (?) i.e. the Ganguli paper on bounds on how well thermodynamic systems can convey information, and the bounds on computational efficiency (?)

What computations are done by many agents talking vs not and how do you tell

Can all computation be inherently viewed as being done by a distributed system or…not, presumably in a computer it’s kind of all just there, is there something special about computers talking to each other vs one computer doing something?

What fraction of all computations done are distributed computations?

What computations are occurring that we…might not be able to see yet

Markets??

Analogies between England paper and neural nets?

What do we mean when we say computation?

Related to ‘well-defined’-ness in mathematics?

What is an analytical engine? How does it relate to biology?

https://www.cs.virginia.edu/~robins/Turing_Paper_1936.pdf

^ought I to read this?

Where did computation come from as a concept?

What does it mean for something to be computable?

“According to my definition, a number is computable if its decimal can be written down by a machine.”

What is the relationship between the Turing machine and Shannon’s information theory? If Turing and Shannon had a conversation, what would they say?

What is up with Turing completeness? And Godel? What is up with that?

2024-07-17

How does communication allow computation to scale?

What are good model systems in which to study this?

Communication in bacteria

• Pros: Possible to get a semi-comprehensive view (we can measure - hypothetically - most of the communication), can almost completely understand the system (??)

• Pros: Pretty straightforward to get data + think through the different modalities

• Cons: What does it ‘mean’?

Is there an interim system?

• Communicaiton between multicellular organisms?

• Communication between trees?

  • Could it be more straightforward to gather data around this, b/c don’t have to run around tracking everything?

  • Communication between fungi?

What could we learn from analyzing traffic patterns?

Communication between people

• AKA the internet

  • Why the internet vs other ways people talk to each other?

• Pros: Feels meaningful

• Cons: Super hard to comprehensively track + understand what the communication means

What are the properties of each system?

• ‘meaningfulness’

• Ease of gathering comprehensive data

• Ease of interpreting the syste, (i.e. what is the message trying to say)

• Scale of emergent behavior (?)

• Number of different ways they communicate

• Communication (bandwith?) of the different ways they communicate

• Peer to peer vs not

• Composed of communicating systems vs not (multicellular vs unicellular, species vs animal)

  • Will that keep going?

• Complexity of the communicating agent

  • Something like - hwo much is it like a Turing machine? No - how complex is it?

Other properties

• Whether members of the species are moving through space or not (spatial change)

  • Bacteria + animals are, trees + fungi are not so much

Different ways to break the problem down

• Communication modalities

  • Chemical

  • Electrical

What is an agent?

• What does it mean to perceive? Do all agents perceive?

• Do all agents act as a kind of API?

Are all communication networks in a species peer to peer? What does it mean to have a centralized communication network?

Will we keep creating networks of communicating agents, which then form agents which then form networks of communicating agents?

How would one figure out how complex the communicating agent is?

Fungi might feel as though they have more scale to them (?)

There is communication between the things that compute, and then there are the things that computer

Interfaces or motors

An API is an abstraction? What is an abstraction?

Is computing like creating new abstractions?

Are all abstractions leaky? What does that mean?

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

“model of computation is a model which describes how an output of a mathematical function is computed given an input”

^ computational complexity as the measure of an agent?

Life, and questions about the future

• What will - will we see groups of agents talking to each other?

• Will we see evolutionary processes (slow, changes over long periods of time)

Oh - computers as ways to compute, how does - what does consciousness look like, why was that eventually involved in the process, in the agent process?

What is the random access machine?

What if computers were organic and conscious?

Oh - the way to scale it is communication protocols across multiple agents, what is good about that?

• Redundancy

  • At large scale, not every part has to work perfectly

  • What are other ways to have redundancy?

• How do you negotiate or set up the communication topology in a large p2p network?

  • What does this look like across multiple networks? What are the constraints on this?

What is bootstrapping, what are ways to think about this concept?

What is abstraction? What is compression?

What is the most abstract thing a human can learn?

Neural networks - learn abstractions?

Plato vs Aristotle (is this similar to intuitionism vs not?)

• Plato - ideas already exist, and have concrete realizations

• Aristotle - mind finds similarities across multiple objects

https://biology.stanford.edu/people/kabir-peay

What is dispersal and how is it meaningful in biology?

what is the wood wide web?

Why is fitness invoked in the definition of biological communication?

what is a hyphae re fungi?

How many relationships in nature are mutualistic?

Do plants really send each other warnings when they are attacked?

“Mycorrhizal Links Between Plants: Their Functioning and Ecological Significance,”

Fungi as a massive underground tree?

How does HGT work in fungi? How does HGT work in general?

‘you look at the network, and it starts to look back at you’

Barro Colorado Island, located in the man-made Gatun Lake, in the Panama Canal. There he joined a community of field scientists, overseen by a grizzled American evolutionary biologist named Egbert Giles Leigh, Jr.

What does it look like to be connected to nature? To do this as a scientist? Do I want that?

How does one make a map of the world wide web?

What is the definition of a fungi?

The line between nature and culture blurred

“what we call “the sciences” and what we call “the arts” are both, in my mind, derived from the faculties of imagination, of curiosity, of wonder, and of a sense of felt relationship both with the living world around us, and also with our own abilities to meaningfully experience that world. We think of these two things as belonging in entirely different departments of human life, and I think that this division is based on a centuries of bifurcation of the world into primary quantities—those things we can measure, those things we can understand through measurement and calculation—and secondary qualities, which are feeling-based things, which aren’t things, of course; feelings, like the flavor of something, the color of something, the sensation of cold water over your skin. The modern sciences arose out of this bifurcation, taking on as its job the primary quantities, those things we could measure, bracketing off the secondary qualities, the things we could feel, not because they didn’t exist or were any less important—although they were called secondary qualities—but because those were things that fell into the realm of the arts, those areas of human life that dealt with the feeling matters, the matters of feeling, knowing, and experiencing. So this bifurcation has created, I think, all sorts of confusing boundaries that we stumble over, mistaking them for natural features of our minds when, in fact, no—as you say, and as I said, I really do feel that scientists are, and have always been, whole and intuitive and imaginative human beings wrestling to make sense of world that was not made to be cataloged or systematized. And so I think we’d have a lot more fun if we could dispel this delusion that the arts and the sciences belong in entirely different departments of human life, because I don’t think that’s true. And I think we all live in what we might call “the sciences” and all live in what we might call “the arts” in different kinds of fluid ways all the time—just to be a living, functioning human”

“I think about the ways that the modern sciences are now talking much more about the relational aspect of the living world; that the world is made up not so much of individuals but of relationships between entities, which themselves are bundles of relationships.”

What is relational in modern science?

“One of the things I spend a lot of time thinking about is, what comes first: the entities doing the relating or the relationship between the entities?”

^ yup, that’s it, that’s exactly it

https://emergencemagazine.org/interview/mycelial-landscapes/ < cool visualization exercise

Quantitative thought experiments in communication next? Where to collect? Which labs? Which datasets? What data do we not have?

What is invisible, what do we see in biology?

Traffic systems - what coudl we learn about analyzing traffic patterns?

“One of my favorites is that of Shiva—the creator and the destroyer, the deity of powerful flux—and Vishnu, the preserver; this was within Hindu philosophies and theologies. And you need the creation, the destruction, to generate novelty and possibility, but without any preservation there could be no stability, no form, and none of the things that we see as things.”

https://emergencemagazine.org/interview/mycelial-landscapes/ < this is super interesting

What is intelligence

Fast vs slow

“And then, back to this mystery point—I think fungi teaches us about the power of what lies beneath, what lies hidden from us. And a lot of what we might call Western scientific and philosophical traditions come from the Enlightenment, and this was very much about shining a light on things, revealing things. This metaphor of light and seeing is very powerful in this whole diaspora of thinking. For me, fungi, in reminding us of the power of what lies hidden, of what lies beneath, what we can’t see—all of the subvisible realms, all of these organisms that create the atmosphere in which we live, that have shaped everything we know about the living world—I think fungi take me to that place as well. I think that sense, that intuition that there are some things that we can’t know by shining light on them; there are things that just are always going to be that mystery place: the myein, the closed, the shut, the hidden—I think fungi can take us to that place, too, and I think that’s something you’d find in many of these traditions around the world.”

“So these are some of the ways that we might partner with fungi moving forwards”

I was thinking about—so stories flavor our reality. They’re like the operating system through which we interpret the world. And when the dominant narrative is one of separation, then there’s a certain way of being that sort of allows you to act in a certain way where you look after number one and your family and those dearest to you. And I think the stories that Merlin’s talking about here are stories of symbiosis and interexistence and interbeing. And so I’m really interested in how you address this sort of myth of separation through an experience of interbeing, especially when a lot of our experiences as humans put us, like we were saying before, inside our skin, looking out. I think you could argue that it feels like I’m separate more than part of the greater whole. So I think, you know, what’s the experience of being mycelium? Given that people can drive or captain these huge oil tankers and they can get round corners without hitting stuff, how far can you expand the boundary of your being? You know, can you embody a forest?

https://fitc.ca/speaker/barney-steel/

https://www.vice.com/en/article/535n8n/exploring-new-canvases-meet-marshmallow-laser-feast

https://marshmallowlaserfeast.com/work/

^ other artists?

One of my favorites is that of Shiva—the creator and the destroyer, the deity of powerful flux—and Vishnu, the preserver; this was within Hindu philosophies and theologies. And you need the creation, the destruction, to generate novelty and possibility, but without any preservation there could be no stability, no form, and none of the things that we see as things.

2024-07-18

Communication systems - quantitative bounds on scaling

Distributed system computing

How common are peer to peer structures in nature?

Would we consider neural nets to be peer to peer networks?

Reposting from above -

Communication in bacteria

• Pros: Possible to get a semi-comprehensive view (we can measure - hypothetically - most of the communication), can almost completely understand the system (??)

• Pros: Pretty straightforward to get data + think through the different modalities

• Cons: What does it ‘mean’?

Is there an interim system?

• Communicaiton between multicellular organisms?

• Communication between trees?

  • Could it be more straightforward to gather data around this, b/c don’t have to run around tracking everything?

  • Communication between fungi?

• Examples of peer to peer netwrosk in biology (?)

  • Neural networks?

  • Swarm intelligence (what does this mean) - such as with birds or ants

• Bitcoin network?

  • Each transaction available, nodes clearly defined, size of transaction defined (?)

What could we learn from analyzing traffic patterns?

Communication between people

• AKA the internet

  • Why the internet vs other ways people talk to each other?

• Pros: Feels meaningful

• Cons: Super hard to comprehensively track + understand what the communication means

Re neural networks as a potential model syste

Speed: Neural networks in the brain operate at a much slower timescale compared to digital peer-to-peer networks. Neurons communicate through electrochemical signals, which are slower than the electronic communication in digital networks.

1. Energy efficiency: The brain's neural networks are highly energy-efficient, consuming only about 20 watts of power, whereas digital peer-to-peer networks can consume significantly more energy.

2. Specialization: Different regions of the brain are specialized for processing specific types of information (e.g., visual, auditory, or motor), whereas nodes in a peer-to-peer network are typically more homogeneous in their processing capabilities.

3. Learning and plasticity: Neural networks in the brain have a remarkable capacity for learning and adaptation through the modification of synaptic connections (plasticity). While peer-to-peer networks can adapt to network conditions, they do not exhibit the same level of learning and plasticity as biological neural networks.

4. Complexity: The human brain contains around 86 billion neurons with trillions of synaptic connections, making it an incredibly complex network. Peer-to-peer networks, while potentially large, are typically less complex than the brain's neural networks.

^ differences between neural networks and p2p systems in computing

What are the constraints on scaling neural networks? How does this relate to the question of how to scalecommunication across large groups? Is it best that each node is as simple as possible, when/how does that change?

Neural networks are different from societies in that neurons aren’t agents (what does that mean?)

What are the constraints on scaling communication and computation across large populations of cells (i.e. neurons in the brain or bacteria in a population doing quorum sensing)

I think communication in bacteria populations, chemically, is constrained by diffusion (i.e. at what radius one would still pick up on an appreciable gradient - or, if gradient is not important, overlal concentration (?) of molecules)

Oh - I see, amplification is then important and is separate from having channels between cells which convey signals in a directed manner

Tools one can use to better spread signals in a population of cells

• Use cells around the original signaling cell to amplify the signal (is it then unclear - what information is lost when doing this? I think the direction relative to the next cell, if there was only one other, although if there are many cells perhaps that information will still be there as all the strongest activated cells are clustered around the original cell?)

  • So, with amplification, if the original cell is surrounded by a homogenous population of cells perhaps its location information will not be erased, however if it only had one neighbor it would at least be unclear which started signaling first, I think in the simplest case, although I’m not sure

• Channels between cells to direct signal to specific other cells

  • Activates specific other cells

  • Cons

    • Might be a bit more fixed - as in, you start to have a built in structure

    • Does this imply the cells are not moving around?

• Can one send long range messages, which are only interpretable by cells that have a certain communication system

  • Is this…like a form of encryption? Where only a particular kind of cell can read a message, even if the message itself is available to everyone?

    • What does having a particular kind of communication system say about the cell?

What are the physical constraints on scaling biological neural networks?

• Not specific to communication

  • Total energy requirements

    • If this weren’t a constraint, how big might the network be?

  • Development

  • Skull size

• Communicaiton

  • Is transmission speed a constraint? How would we know if so?

  • How many connections can a neuron handle?

    • Does this change across species?

      • It seems as though smaller brains have higher connectivity (?)

      • I’m curious how this looks for LLMs

        • Human brain has ~10^15 synaptic connections vs around 10^11 parameters in an LLM

  • Noise (?)

    • How is this a constraint?

Scaling laws for neural networks - how large are networks in nature, normally? What is the average connection topology of these networks? What do the bandwith and latency look like?

Is it the case that one cannot have channels to specific other cells unless the cells are not moving around? Are there ways to get around this (i.e. do cells ever encrypt messages to each other?)

Do cells every encrypt messages to each other? I.e. is there a way for two cells very far away from each other to send each other a message, where the message is specific to the other cell?

• This comes back to what communication system both have - perhaps cells which can read a certain type of message definitionally have a certain type of communication system, which says something about the receiving cell?

Is the question of whether biological neural nets could exhibit power scaling laws analogous to LLMs interesting?

Question: What about Newton’s laws do I like? That they are simple? Is that, in of itself, a virtue? That our brains are somehow created such that we can - are brains better at thinking about Newton’s laws then other things? What other tasks do they do? If I want to find the types of ideas that our brains like to think about, should I think about what tasks our brains normally do?

• How is it that we create abstractions? What types of abstractions do we like to make?

• How is it that we can do math? What is doing math, in a normal brain?

• What is language? What are we doing when we use language? Are we assigning symbols to abstractions? How do we then communicate - we match those symbols with the abstractions other brains have created? How does this work well enough? Should we invent groups with sub-languages, to come up with new things? How similar are the concepts discovered across different languages?

Do we create the reality which we then perceive?

It is nice that branching is a structure in nature.

Has the internet changed the structure of social networks?

What are the physical constraints on scaling computation in biological networks?

• What are ideal communication topologies in biological networks?

• ^ I’m really curious, and don’t yet know how to think about it

https://www.science.org/doi/10.1126/scisignal.2001965 < this seems interesting

What is networks analysis?

• What is going on in social network analysis?

  • What are networks and graph theory as primitives?

    • Is graph theory just linear algebra? How is it different?

  • What does the study of meme spread look like? What about for more complex ideas?

  • What can we do to study communication with technology, now, that we couldn’t do 2 or 3 years ago?

  • The concept of ‘network closure’ seems kind of interesting

What does a network feel like when one is thinking about it in graph theory?

Metrics for analyzing social networks:

ize: The number of network members in a given network.

Connections

Homophily: The extent to which actors form ties with similar versus dissimilar others. Similarity can be defined by gender, race, age, occupation, educational achievement, status, values or any other salient characteristic.[30] Homophily is also referred to as assortativity.

Multiplexity: The number of content-forms contained in a tie.[31] For example, two people who are friends and also work together would have a multiplexity of 2.[32] Multiplexity has been associated with relationship strength and can also comprise overlap of positive and negative network ties.[9]

Mutuality/Reciprocity: The extent to which two actors reciprocate each other's friendship or other interaction.[33]

Network Closure: A measure of the completeness of relational triads. An individual's assumption of network closure (i.e. that their friends are also friends) is called transitivity. Transitivity is an outcome of the individual or situational trait of Need for Cognitive Closure.[34]

Propinquity: The tendency for actors to have more ties with geographically close others.

Distributions

Bridge: An individual whose weak ties fill a structural hole, providing the only link between two individuals or clusters. It also includes the shortest route when a longer one is unfeasible due to a high risk of message distortion or delivery failure.[35]

Centrality: Centrality refers to a group of metrics that aim to quantify the "importance" or "influence" (in a variety of senses) of a particular node (or group) within a network.[36][37][38][39] Examples of common methods of measuring "centrality" include betweenness centrality,[40] closeness centrality, eigenvector centrality, alpha centrality, and degree centrality.[41]

Density: The proportion of direct ties in a network relative to the total number possible.[42][43]

Distance: The minimum number of ties required to connect two particular actors, as popularized by Stanley Milgram's small world experiment and the idea of 'six degrees of separation'.

Structural holes: The absence of ties between two parts of a network. Finding and exploiting a structural hole can give an entrepreneur a competitive advantage. This concept was developed by sociologist Ronald Burt, and is sometimes referred to as an alternate conception of social capital.

Tie Strength: Defined by the linear combination of time, emotional intensity, intimacy and reciprocity (i.e. mutuality).[35] Strong ties are associated with homophily, propinquity and transitivity, while weak ties are associated with bridges.

Segmentation

Groups are identified as 'cliques' if every individual is directly tied to every other individual, 'social circles' if there is less stringency of direct contact, which is imprecise, or as structurally cohesive blocks if precision is wanted.[44]

Clustering coefficient: A measure of the likelihood that two associates of a node are associates. A higher clustering coefficient indicates a greater 'cliquishness'.[45]

Cohesion: The degree to which actors are connected directly to each other by cohesive bonds. Structural cohesion refers to the minimum number of members who, if removed from a group, would disconnect the group.[46][47]

What does it mean for a node to be central?

Distance between two nodes

Closure in groups

Why should visualizations help one analyze a network, and how should one visualize them?

How could one visualize the bitcoin network, for example, and what would that teach you?

• How many bitcoin transactions have happened historically?

  • ~1.043B in total

  • ~43K nodes (?)

  • ~85M wallets, around 1.2M daily active addresses

What % of the world’s energy goes to what, and what does that say?

For the traveling salesman problem - do we constrain the topology of the cities so it is ‘reasonable’?

What are interesting rules or conclusions in sociology?

What does web link analysis tell you?

2024-07-20

What’s up

Different models

Quantitative...stuff

How long will it take to load

What does the form of the book look like?

Past, present, future

What systems - how do I interact with data?

In what systems does communication scale and how?

https://www.nature.com/articles/s42254-019-0040-8

Thermodynamic noise as a fundamental constraint (and helper?)

How will computation eventually deal with thermal noise?

How does computation in the brain work?

What are dynamical systems?

What is up with synchronization of neural firing?

Feedback loops?

What is a SQUID?

Why do you need quantum devices to measure brain activity?

What is a continuum model or mean field theory?

How are the 302 neurons in C. Elegans connected?

2024-07-21

What are the bounds on conscious experience?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104292/

2287 synaptic connections between 279 neurons

small-world network properties: a combination of high local clustering of connections between topologically neighboring neurons and short topological path lengths between any pair of neurons (Watts and Strogatz, 1998)

Do distances matter in wiring networks?

https://wormwiring.org/pages/adjacency.html

What have we learned from the brain’s wiring structure, so far?

~10^11, and 10^15 connections

What is the max population size of bacteria that can talk to each other?

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

https://online.kitp.ucsb.edu/online/plecture/dfisher13/ - Daniel Fisher

Physics of Living Matter

https://www.kitp.ucsb.edu/activities/hgt24 - holy shit this looks so cool

Holy cow this is so cool

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

he summer course is closely linked to the concurrent KITP program Horizontal Gene Transfer and Mobile Elements in Microbial Ecology and Evolution​. Course participants will attend the program's daily research seminars as part of the course curriculum. Students and lecturers will also have frequent opportunities for less formal interactions. Confirmed program participants include Aude Bernheim (Pasteur Inst.), Devaki Bhaya (Carnegie Science/Stanford U.), Allison Carey (U. Utah), Ilana Brito (Cornell U.), Daniel Fisher (Stanford U.) Nandita Garud (Stanford U.), Graham Hatfull (U. Pittsburgh), Daniel Huson (U. Tübingen), Eugene Koonin (NCBI), Michael Laub (MIT), Katie Pollard (Gladstone Inst., UCSF), Martin Polz (U. Vienna), Paul Rainey (MPI-EB), Eduardo Rocha (Inst. Pasteur), Julia Salzman (Stanford U.), and Erik van Nimwegen (U. Basel).

Joanne Emerson (UC Davis), Benjamin Good* (Stanford U.), Roberto Kolter (Harvard Medical School), Honour Mc Cann* (MPI-EB), Richard Neher (U. Basel ), Boris Shraiman (KITP/UCSB), and Paul Turner (Yale U.) 

Benjamin Good - Stanford

https://biox.stanford.edu/people/ben-good

https://scholar.google.com/citations?view_op=view_citation&hl=en&user=QnUU_J0AAAAJ&sortby=pubdate&citation_for_view=QnUU_J0AAAAJ:IWHjjKOFINEC

https://scholar.google.com/citations?view_op=view_citation&hl=en&user=QnUU_J0AAAAJ&cstart=20&pagesize=80&sortby=pubdate&citation_for_view=QnUU_J0AAAAJ:KlAtU1dfN6UC

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599682/pdf/nihms-1024507.pdf

Michael Desai (?)

“Much of this work has focused on questions in

evolutionary dynamics. That is, given a

known genotype-to-fitness map, how does evolution determine which combinations of

mutations ultimately reach observable frequencies, where they could be detected in

sequencing or phenotyping assays.”

One of the best-known effective models in evolutionary biology is the Wright-Fisher process (also known as the single-locus diffusion model), which describes the competition between two genetic variants in a well-mixed population [45]

Of particular relevance to microbial evolution, this domain of attraction includes chemostat growth [47], batch culture [43], and even some scenarios with rapid temporal variation [42] or spatial structure with frequent mixing [48] (Fig. 2a).

For example, convergence to the Wright-Fisher model will eventually break down on short timescales (Fig. 2a), when life-history details and other deviations from the model start to become important.

example is spatial structure, which can be important in crowded [54, 55, 56, 57] or otherwise poorly mixed populations

How would I think about using or working with data?

What happens in these experiments?

For large microbial populations, by contrast, theory and experiment both suggest that clonal interference is likely to be a generic feature of short-term evolution [66].

“At first glance, linkage would seem to make the evolutionary dynamics hopelessly complex. To model the fate of a given mutation, one would need to know the rates and fitness effects of all other mutations across the genome”

Could I do long term evolution experiments at home?

How do MGEs spread in complex communities, across spatially heterogeneous environments? 

• How can we quantify rates of transfer in complex systems?

• How do viruses structure bacterial populations within individual hosts and across broad landscapes?

• What impacts do MGEs have on infection dynamics and pathogen evolution?

• How do microbial interactions impact the transfer and maintenance of mobile elements?

• How can we improve computational methods of MGE prediction, phylogenetic reconstruction and visualization to better understand the evolution of mobile elements and their hosts?

• Can a unifying statistical genomic theory of phage and mobilome identification be developed?

• What are the most rigorous methods of evaluating statistical bioinformatic approaches?

• Can statistical bioinformatics determine what is upstream of the initiation of transfer and downstream of DNA receipt in bacterial genomes?

• How will these predicted mechanisms be tested?

• What general principles are emerging in the study of mobile elements?

https://www.kitp.ucsb.edu/activities/viralimmune24 - this seems really cool also!

2024-07-22

What’s going on with peer to peer computing + communication protocols in that - who do I know that could have good recs there? Presumably any constraints on complexity / size of compute constrained by communication protocol complexity would have been discovered there?

Unless the ‘type of thing’ being computed in a p2p computing setting is fundamentally different from that typically being computed in a biological context? How would they be likely to differ?

Computer computation - something specified by an algorithm? Is biology….not that, ever? What is an algorithm?

Is it that in computation - I kind of already know what I want to compute, and the algorithm is computing it, vs in biology it’s sort of like ‘what do I want to do’ - more of a search for interseting things without really knowing what you will find? More traditional computing is kind of pre-specified, whereas in biology it’s a bit more of a search process?

Claude (from Antrhopic) claims that biological algorithms are ‘much more parallelized’ than computing algorithms. Maybe they just sort of…feel pretty differnet, like one evolved slowly and is pretty parallel/redundant. That doesn’t mean it’s necessarily better - maybe it’s better for search processes / when you’re not quite sure what you want to do.

How does the traditional study of algorithms in computer science interact with neural nets?

What did Turing know about this? If Turing and Shannon were talking what would they say?

Why do we talk with symbols, is it so unbeautiful?

What is the most biological computer algorithm?

The internet…doesn’t know what it wants, and is kind of searching?

What does scalable mean in a peer to peer context?

What are the constraints on scaling peer to peer context?

Bandwith, trust - I see, for top-down stuff, it’s more confusing to do a large peer to peer application but that’s different for searching bottom up, biology about finding the goal, normal computation more about I know what I want to do just implementing it. Biological computation - ‘what should we do’.

There is a concept of distributing compute literally over a bunch of a nodes, if a protocol is followed?

How might computation be, implicitly, doing this?

How are decentralized datastructures in, for example, p2p computing different from the types of computations or systems typically seen in a biological context?

Why are computing structures they way they are? Will we see biological things in the future, or no more? If we are not sure of the goal?

p2p principles

• redundancy - so, data is stored on multiple nodes

• I guess cryoptography is pretty important in a p2p context, does it ever show up in a biological context though?

  • would having or not having a communicatoin system be similari to this? what is the core principle in cryptography? I guess it’s a more individual thing - the switch from many to individual communicators?

• eventual consistency?

I could understand what a distributed hash table is - that might be helpful (?)

What is the fundamental structure of data when it is being computed or communicated?

I think my first question, if I were trying to distribute a computation across a p2p network, would be ‘how should I split this computation up’, but I think that is not biology’s first question - it’s not even sure what it’s trying to do

The Recurse Center

A summer understanding peer to peer computing, and applications to and differences from biological computing (and how communication systems or protocols constrain scaling computation in both contexts)

Why an associative array? Where did they come from?

Ordered - vs not ordered. A search process for what you are looking for vs - do linked lists exist in biology? Does cryptography, in a sense?

Oh - I see, arrays reference the concept of a piece of data having some ordered pair of numbers that says waht it has to be - so, linear algebra?

Arrays store related information together?

In a DHT (distributed hash table), the node that stores a particular key is found by hashing that key

So, in effect, your hash table buckets are independent nodes in a network

A DHT can make a ring of n nodes, such that when a node joins it joins the ring, then takes charge of the keys in that ring space

How do you incentivize individual nodes?

How do nodes know how to talk to each other? Do all nodes in a p2p network on the internet feel equally far away, or generally grouped by geography?

Does some notion of spatial - it’s like, previously, in the ocean, you had diffusion but also swimming so things were local but also moved around with relation to each other, then passing messages across long distances became possible but definitely had some cost associated with it, now with the internet it suddenly feels like everything is quite close - communication

So interesitng that we’re removing all these constraints that used to be there - like, there is this structure on top of nodes, but the strucut ris now - decided by someone and implmeented, and then we get to see how it plays out (like, the nodes being arranged with relation to each other, or in some mathematical structure). It’s so funny - what does that mean?

https://steffikj19.medium.com/dht-demystified-77dd31727ea7

How are DHTs decentralized, scalable and fault tolerant? What characterizes something that is scalable? Scalable until what level? What characterizes things that are not scalable?

https://www.linuxjournal.com/article/6797

From Feynman levels on computation (abstract) - “If you keep proving stuff that others have done, getting confidence, increasing complexities of your solutions-for the fun of it-then one day you’ll turn around and discovers that nobody actually did that one! And that’s the way to become a computer scientist.”

What will the future look like?

• The future of conscious experience

• Does anything matter, outside of that?

For next time:

The Feynman lectures on computation look actually quite good, and I’m curious what similar references for both information theory/communication and p2p computation would look like

References

• On computing, in general

  1. "Structure and Interpretation of Computer Programs" (SICP) by Harold Abelson and Gerald Jay Sussman:

  2. "Feynman Lectures on Computation"

  3. "The Elements of Computing Systems" by Noam Nisan and Shimon Schocken

• On DHTs (to read)

  • https://www.linuxjournal.com/article/6797

Todos:

• I could ask Juan for advice on how to think about this space? What are canonical references or finding in p2p computing? What is p2p computing?

Today:

• I thought about the differences between biological algorithms (potentially, a way to find out what you should do) vs computer algorithms (implementing something you already know to do)

• I read a bit about the background for p2p

• Learned about distributed hash tables

• It’s so funny that we’re re-writing how spatial constraints work - like, now nodes are arranged with relation to each other in some kind of spatial constraint that is human defined, and no longer the same thing as jsut defined by geography or other constraints. What types of computation do these new topologies allow?