date/2010/12

some mezoued from tunisia this time. its short range leads to a more rhythmic style of playing. i’d argue these pipes are somewhere between more melodic and more rhythmic instruments.

summarizing, first we saw how thermodynamics and information theory are similar, and how the latter is more abstract, applicable to both elementary particles, letters and numbers. by mixing the two, we have a quantitative metric for arrangements of things. then we defined things using a fractal equation. then, from the ground up, we visited the first realms of knowledge. today we continue our journey.

as molecules grow and interact, they develop strange shapes, this is, they become spatially arranged. like the water molecule, proteins for example are nothing more than very big molecules, exhibiting strange shapes. as molecules become bigger, their interactions become more complex. an example of this is a catalyst. we can see it as a special harbor of sorts. imagine you are learning to sail. you can try it in a big open ocean, plagued by storms, or you can try it in a safe harbor where the waves are not too high. a catalyst is a molecule that, for its simple properties, facilitates the reaction of other molecules.

let’s think about it for a second. different molecules can interact with each other, and their own properties (in this case spatial) can affect other molecules profoundly. note that a catalyst exists anyway, independent of whether it will ever affect other molecules or not. but for the other molecules the difference can be dramatic.

for example, though not very scientifically correct, would be using anti freeze in your car’s radiator. the anti freeze itself is just a molecule that does very little alone. but if mixed with water, it will lower its freezing temperature. this can be very important if you are trying to get to work and your car is frozen. so a tiny molecule sometimes can make a big difference.

one of these cases is life. it might be arguable whether certain moving molecules are “alive”, but as soon as molecules get big enough, they start doing work. the same work we talked about before, the one we can measure. an example of this work would be the work of the contents of a cell to assemble molecules. these are just like tiny robots. if a molecule can do work, and another can use the work to create other molecules, we can have molecular evolution.

i won’t try to explain how this works, i’m sure many experts would be better at it. but one thing i can say is that as information increases, so do these unintended consequences. the bigger and more arranged a molecule is, the more likely it can do work on others for example. so after many many years of molecular evolution, a good set of working producing molecules got together in things we call cells, . cells themselves are a multitude to explore, but what i am interested in is how to save and retrieve them, or, how to quantify them in terms of information.

it is common to say DNA (one of the in cells) is the script for life. i disagree. as the analogies i used before, it is not enough to store the alphabet, it is necessary to store the agents that can work with it (like the painter and the painting, or kolmogorov complexity). this would be a contribution of computer scientists that is overlooked. just read this interview of richard stallman (founder of the GNU free software movement), and how profound it is (search for quaternary).

DNA is a quaternary program that runs on a cell computer. to accurately describe a cell system, we need all the information of the DNA, but also the information of the computer it runs on. all the proteins, all the structure, all the constraints. DNA might be a key, but alone it is worthless.

so we have a new layer of agents. we have the laws that govern things both in groups and alone (laws), and we now have things that can do work independently. the why is easy, it is part of their properties, these small machines are just like elaborate catalysts, mindless automatons. but they function as new laws for bigger systems.

but more essential to them is the fact that their activity adds to the structure of their surrounding world. like the boy picking up pebbles to draw a circle, these molecules take in simpler forms of matter and energy and convert them in more arranged forms thereof. information must include not only the “actg” letters, but also all the machinery required. so to quantify a cell, we would have to quantify everything.

how much information are we talking about? i am leaving quantification for later. but if we survey all the constituents of a cell, which themselves are thousands, and if we compute how unlikely it is that they are all together versus apart, we can quickly realize that the information stored there is no short than a universally big number. note that physical information is not computing the “actg” unique sequence in bits, that is computational ignorance. that is not physical information, that is information we perceive as high level, us being humans. the real information includes all constituents and their structure. the names, as we’ll see soon, are a human illusion.

already we begin to see tiny minds at work. the molecules that move molecules around, following some anti-entropic imperative. that ensemble then, using the same rules, clusters itself in groups, becoming what we call organisms: . some of these will be specified, where large groups of similar cells can be called organs, systems, and so on. all these abstractions, as we’ve been saying, are just encapsulating names for things, since things themselves require no layers whatsoever.

so we continued our journey into the realms of the biochemist and now the biologist. to biologists, evolution and replication is about organisms. to a biochemist, it might be just about replication of certain molecules. either way, they are expressions of how entropy can locally be reversed, and slowly, we build up our complexity. soon, we will come full circle.

we were at the regular bagpiper meetings in lisbon’s downtown area (terreiro do gaiteiro). free entry, cheap booze, and anyone can get up and play anything, anytime, with anyone else. we did some videos, and i got to play some simple tunes with other bagpipers and drummers. it was a privilege to play with some of the people there. so this time here’s just a collection of clips for a change.

on one of them you can see some old dance called “repasseado”. after a while (and some drinks) a lot of people started spontaneously dancing these old dances.

credits on the video to nebulax

6 out of 26 guests have left _42 creeped out (23%, or a bit over one out of five). we may have underestimated the importance of a couch description. our couch is significantly better than the two previous ones. we also chose a more artistic description, because we are working actively on design and engineering projects all the time.

the problem, it seems, is the same old problem about people. people describe themselves as what they want to be, not as what they are. close minded people will invariably say they are open minded. racist people will say they “love multiculturalism”. intolerant people will rave about how tolerant they are. to quote bukowski,

and the best at murder are those who preach against it

and the best at hate are those who preach love

and the best at war finally are those who preach peace

those who preach god, need god

those who preach peace do not have peace

those who preach peace do not have love

full quote here, ironically the second post on the e8 blog.

the real honesty comes from acknowledging our own hypocrisy and fragility. to know that we are all fuckups in a way or another. this is an instinctive natural behavior very common in travelers, since they are very dependent on others. but that is disappearing from cs too.

the problem here is that couchsurfing is slowly changing. the average social class of our guests has been going up (again, maybe due to a more “clean” description). with it, the disgust faces, the awkward moments, and the people leaving when we are not there.

so we changed the description again, to something scary, like it was with SPCC and e8. this means we will be biasing our data heavily, but that also means we won’t have to put up with arrogance and narrow-mindedness veiled as fragility or generosity.

we are a bit tired of guests saying they are leaving because they are sick when they are disgusted. that they are leaving because they found a friend when they just don’t want to make friends. that they are leaving to make room for others, when what they need is more space for themselves.

once we get to minds (i know, i’ve been saying this a lot), it should become clear how this happens so much. for now, let’s just hope being scary brings us less awkwardness.

some asturian pipes this time.

we are living exceptional times now. i was wrong. most cables being released now are impressive. i can’t wait for the rest. the us funding coups, corruption, corporate terrorism. the good stuff is here. which turns our simplified picture into a richer one. i’m no longer skeptic of wikileaks and its mission. they are showing us the truth we’ve suspected all along, and we’re reading it early enough that we can prosecute the criminals. whether we will be able to, is the big question.

hacking these days says little about what it was initially. hacking is no more than exploiting fragilities of information systems. phreaking on the other hand is the human kind of exploiting of fragilities. for example, you could use some unknown software failure to access some internal website, or you could call the company, emulate some voice tone and professional vocabulary and request the same information. one exploits machines, the other exploits humans.

old school hackers like assange are highly knowledgeable of both. the key aspect of wikileaks is that it isn’t neither humanly nor politically naive. in fact, it follows a very elaborate philosophy, though somewhat lacking in questioning pillars of the establishment.

still, the wikileaks movement might still be phreaked. assange was phreaked because of his own vulnerabilities (narcissism and women). states and secret agencies are very cunning in this kind of hacking, and have spun it very well. then, there is the simple fact that the whole movement might be used as a reichtag event to justify new laws. these will obviously run while the fires are going on, so nobody can see them come through.

i tend to favor incompetence over conspiracies, since they are indistinguishable in practice, and the first seems to be simpler and more in line with human nature. the de facto events tend to be the same, irregardless of whether there is some unseen hand behind it or not. like i was arguing before about planned obsoletion, it happens both by planned decisions and pure managerial incompetence. for the consumer, they are indistinguishable.

so now we are seeing the typical disaster / ransack human reactive mindset. states are reacting any way they can (the same states that preached openness), by trying to spin this nightmare in their favor. they were incredibly incompetent in protecting their secrets, so to protect them they must conjure up any kind of elaborate reaction. if it does come through, it will be indifferent whether this was planned or not. in practice, rights are lost anyway.

meanwhile, the cyber troops are banding up and now we have a real battlefield. the internet empowered the citizens, and anyone can download a ddos software and use it. so damaging big companies is possible (just read about the 16 year old arrested in holland this week for doing ddos attacks). if a state is afraid of children, we can’t even begin to rationalize how this will play out.

something will have to give. on one hand, the naive and suddenly empowered anonymous citizens, with a leader to look up to with clear ideals and philosophy (though little dissent from the mainstream political culture). on the other hand, the status quo, the powerful rulers of the planet, feeling threatened for the first time.

so it can easily go one way or the other. my guess is that there will be strong crackdown on dissidents and we’ll lose some internet rights along the way. only time will tell.

from the core definition we started with, we will now begin our journey into complexity. to avoid issues with things we don’t know much about (i.e., smaller than atoms), i will begin from the layer onwards. why? considering the model is fractal itself, we can define , where is a sub element of an atom, thus avoiding many issues things of lower layers have. note that the properties of the things we will be dealing with may be broken down, as we noted above, into smaller parts, explained by the constituents for .

so we can either say there are macroscopic properties of such as mass, electronegativity and so on, or we can say the properties of come from the properties of . for example, we could say electronegativity has to do with the balance of positive and negative charges in an atom (a property of its constituents), or we can just say an atom has electronegativity as one of its properties. what we are doing is encapsulating questions into a bigger layer of abstraction, so we can work using only our small brains.

so it’s exactly what i’m doing, and why these terms i’ll be using can be broken down, but won’t. for the sake of validity, any thing has sub things, so if anyone wants to expand any definition to core terms they can do so.

so let’s see how simple laws can quickly show that the whole can be more than the sum of the parts.

let’s say we have water molecules. water molecules are a thing whose constituents are atoms (from layer ). so where m means the “molecule” layer. to specify it completely, we would choose . i will avoid breaking each one of these down but it could be easily done: . this expansion, even though it’s for water alone, already would lead to a lot of unnecessary text. if we also add temperature constraints, isotopes, and so on, we would quickly run into in-computability again.

so one of the properties of the water molecule is that one of its constituents, hydrogen, tends to lose most of its electrons against the stronger oxygen. this leads to a water molecule that is charged in space (see picture). an atom alone is neutral, but when they band up together and create bonds, electrons flow and this leads to spatial charge. so even though the parts are “neutral” alone, the whole isn’t.

so consequence of the differences of its constituents, the whole (water) has a property that isn’t easily understood from the properties of its constituents, unless they are put together and interact.

so to formalize this, we would say we have both the properties of oxygen and hydrogen alone (their charge, their mass, etc), and the properties of oxygen and hydrogen together (how their different masses and charges lead to change in both of them).

this means that our formula for water would seem incomplete at the lever we’re working on. . the fact that they are bounded has led to extra properties that were, even though explainable, not obvious.

this is where reductionists will say “yes, but the bonds are explainable by the laws that govern atoms themselves”, and it is correct. if i break down the higher level definitions, i will see that isn’t really separate from the properties of , rather it is just a property of when the two are together. on the contrary, emergents would claim that this property cannot be seen by the things alone, but only when the whole is created, which leads to emergence.

my answer is that these two claims are compatible. a thing alone is not a thing with another thing. like the two atoms, they bond naturally, therefore they are not entirely separate entities, with independent laws. their laws are generic enough to affect them and others irregardless of what type of atom it is.

a bond exists because the atoms allow for it, but is only possible when two or more are present. we will see this pattern in all layers of abstraction. some characteristics of laws (or properties of things) are only possible when their minimum quantity (as we defined it previously as the core mathematical concept) exists.

so the water molecule itself, as it turns out, also has charge itself (or a dipole), and its hydrogen atoms are somewhat naked versus the highly negative oxygen. what happens when we have a lot of water molecules together? is the law of charge attraction still valid as it was for atoms? as it turns out, yes. this law (the electric force between charges, part of the “physical laws” layer) requires the thing charge and the thing distance as its core properties. so atoms have charge, but apparently molecules have a kind of charge too, and the same with distance. so the law of electric force applies too. let’s formalize this.

, where is, in this case, Coulomb’s law, and becomes and becomes . charge is there on both cases. but what is distance? distance is another law (this time from the realm of mathematics).

. this brings us a lot of interesting questions, but for now, let’s accept that distance is defined for two things with the single property position. note that it is arguable that position exists when there is no comparison to it, so it might be an illusionary property.

does hydrogen have position and charge? check

does oxygen have position and charge? check

do we have enough of them and are they close enough that they bond? check

the law can be applied. if it is, we have water now

does water have position? check

does water have some kind of charge? check

the law can be applied. we have water interacting with water now. a thing called hydrogen bonds appears for example, which is a property of water in groups, but not a property of water alone.

we slowly moved from the same law applying to atoms (and its constituents) to that law being applied to groups of atoms (molecules) and then the same law applying to molecules between themselves to form clusters of molecules. there are many examples of this in nature.

note that the only reason why this was possible was because:

• there are some invisible things in our universe (laws) that require very little properties to be applicable (like the electric force for anything with charge and distance), in essence, they are layer blind;
• there are things with the said properties so they are affected by these laws;
• there are things that when together with other things, have properties themselves also subject to the same laws, that were undefined for things alone (e.g., bonds).

this is only possible because some of the core things (laws) are layer blind. there is no semantics on charge. it behaves the same way for a molecule and an atom, or an electron and a proton, or the two terminals on a battery. this is what the standard model worries about, and what urges the physicists to claim everything can be explained by simple math. this is one of my favorite deepities, because even though it might be true, it is deeply false, since it explains the behavior of fragmented parts, oblivious of how hard it is to compute any interaction of two or more elements, no matter how simple (see the three body problem for example).

in this sense, we can see how nature itself speaks beyond abstraction, in a more essential manner. this follows the occam’s razor principle for the most part. why have two laws for layers, when the same can be used. occam’s razor is a natural consequence of a natural world with no semantics, no distinction of molecule or atom. in essence, a mindless world with random laws and consequences thereof.

the fact that we understand them, with our tiny brains, is a bit of a mystery. but we can easily see how we live in a world with simple laws but complex interactions. our complexity does not come from formal semantic differences. it comes from the simple excess quantity of things (in our planet at least).

the fractal nature of things exists solely because we have minds that require abstraction. as we saw from this example, abstraction is something we create in mind, because not even the basic laws of the universe seem any different between layers. pattern finding is something we do every day as humans, for survival. but it is also why we are so easily deceived by simple math versus the overwhelming torrent of random events that we swim in.

our journey will now continue on to bigger complexities. we started with the realm of the mathematician, then the physicist, now the chemist. we will visit many trades on our way. i’ll meet you there.