Hairballs

Network visualizations are notoriously difficult to interpret. Their canonical representation in a visual form has earned the moniker hairball, and you can probably guess why. If you are unfamiliar with the hairball, or doubt their prevalence in biological sicences, explore what is always a good source of network hairballs: study of yeast and systems biology.

You can already guess that nothing with the name hairball can truly be useful. In general, they are not. These views are at best accidentally informative, and cannot be relied upon to consistently reveal meaningful patterns.

Conventional network visualization is unsuitable for visual analytics of large networks. So-called hairballs earn their moniker by becoming impenetrably complex as your network grows. They are least effective when visualization is most needed — for large networks.

Hairballs turn complex data into visualizations that are just as complex, or even more so. Hairballs can even seduce us to believe that they carry a high information value. But, just because they look complex does not mean that they can communicate complex information. Hairballs are the junk food of network visualization — they have very low nutritional value, leaving the user hungry.

In a hairball, data is subordinate to layout — node and edge positions and lengths depend as much on the layout algorithm (of which there are many), as on the data. The effect of layout rules is difficult to predict, making direct comparisons of these visualizations impossible. For example, imagine trying to compare two scatter plots in which the ordinality of the scales were altered (e.g. x = 1, 2, 3, … in one and x = 3, 1, 2, … in the other).

As a result, a great deal of detail about the structure of a network is irretrievably lost in a hairball and any emergent patterns may be either real (reflected in the data) or accidental (artefact of the layout). Importantly, there is no aesthetic magic sauce added to the layout. If the layout shows a pattern, you can be sure it is due to structure in the underlying data and not on the layout algorithm’s interpretation of how the data should be shown.”
http://www.hiveplot.net

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Stalling for the future

“It is interesting to me to recall that the first meeting I attended after returning a few  years ago was about trying to get a community decision approved in view of the lack of a sufficient number of votes, which is the issue of the mandate at present. Meanwhile the mandate goes on in effect without a formal approval. Similarly, your need to get so many signatures for a vote on entry policy reform can be stalled in various ways, while you run out of steam and everyone forgets about the issue. Meanwhile the policies of the existing bureaucracy go on in effect, without serious challenge, as they must in order to maintain the status quo, even though a series of recent platforms has strongly voiced the need for systemic change. For it is the era of the financial status quo, and the required over-planning to achieve it, here as everywhere in the world. The era of reform can be deferred for a long time, simply by virtue of the principle of socio-economic inertia. The philosopher Whitehead once said that ‘evil’ is simply resistance to change. Here we might just call it stalling for the future.

Rod Hemsell

Ir contra la especie

“Continuarán las guerras y por tanto los fanatismos hasta que tal vez la misma naturaleza lo llame al orden y haga inviable nuestras civilizaciones. Tal vez nuestra visión es demasiado cruda, sin piedad y vemos al hombre como una criatura única, la única que hay arriba de la tierra capaz de ir contra su propia especie. Vuelvo a repetir, porque algunos llaman la crisis ecológica del planeta, es consecuencia del triunfo avasallante de la ambición humana. Ese es nuestro triunfo, también nuestra derrota, porque tenemos impotencia política de encuadrarnos en una nueva época. Y hemos contribuido a construir y no nos damos cuenta.

¿Por qué digo esto? Son datos nada más. Lo cierto es que la población se cuadriplicó y el PBI creció por lo menos veinte veces en el último siglo. Desde 1990 aproximadamente cada seis años se duplica el comercio mundial. Podíamos seguir anotando datos que establecen la marcha de la globalización. ¿Qué nos está pasando? Entramos en otra época aceleradamente pero con políticos, atavíos culturales, partidos, y jóvenes, todos viejos ante la pavorosa acumulación de cambios que ni siquiera podemos registrar. No podemos manejar la globalización, porque nuestro pensamiento no es global. No sabemos si es una limitante cultural o estamos llegando a los límites biológicos.

(…)

El hombre puede llevar la agricultura al mar. El hombre puede crear vegetales que vivan con agua salada. La fuerza de la humanidad se concentra en lo esencial. Es inconmensurable. Allí están las más portentosas fuentes de energía. ¿Qué sabemos de la fotosíntesis?, casi nada. La energía en el mundo sobra si trabajamos para usarla con ella. Es posible arrancar de cuajo toda la indigencia del planeta. Es posible crear estabilidad y será posible a generaciones venideras, si logran empezar a razonar como especie y no solo como individuo, llevar la vida a la galaxia y seguir con ese sueño conquistador que llevamos en nuestra genética los seres humanos.

Pero para que todos esos sueños sean posibles, necesitamos gobernarnos a nosotros mismos o sucumbiremos porque no somos capaces de estar a la altura de la civilización que en los hechos fuimos desarrollando.

Este es nuestro dilema. No nos entretengamos solos remendando consecuencias. Pensemos en las causas de fondo, en la civilización del despilfarro, en la civilización del use-tire que lo que está tirando es tiempo de vida humana malgastado, derrochando cuestiones inútiles. Piensen que la vida humana es un milagro. Que estamos vivos por milagro y nada vale más que la vida. Y que nuestro deber biológico es por encima de todas las cosas respetar la vida e impulsarla, cuidarla, procrearla y entender que la especie es nuestro nosotros.

Gracias.”

Jose Mujica

Meditation II

“From this I should conclude that I knew the wax by means of vision and not simply by the intuition of the mind; unless by chance I remember that, when looking from a window and saying I see men who pass in the street, I really do not see them, but infer that what I see is men, just as I say that I see wax. And yet what do I see from the window but hats and coats which may cover automatic machines? Yet I judge there to be men. And similarly solely by the faculty of judgment which rests in my mind, I comprehend that which I believed I saw with my eyes.

Descartes

The Ideal Opposites

“The world is thus faced by the paradox that, at least in its higher actualities, it craves for novelty and yet is haunted by terror at the loss of the past, with its familiarities and its loved ones. It seeks escape from time in its character of ‘perpetually perishing’. Part of the joy of the new years is the hope of the old round of seasons, with their stable facts -of friendship, love, and old association. Yet conjointly with this terror, the present as mere unrelieved preservation of the past assumes the character of a horror of the past, rejection of it, revolt:

To die be given, or attain,
Fierce work it were to do again.

(…) is the question whether the process of the temporal world passes into the formation of other actualities, bound together in an order in which novelty does not mean loss.

The ultimate evil in the temporal world is deeper than any specific evil. It lies in the fact that the past fades, that time is a ‘perpetual perishing’. Objectification involves elimination. The present fact has not the past fact with it in any full immediacy. The process of time veils the past below distinctive feeling. There is a unison of becoming among things in the present. What should there not be novelty without loss of this direct unison of immediacy amongst things?”

Alfred North Whitehead

The illusion of action

“Agitation, haste, restlessnes lead nowhere. It is foam on the sea; it is a great fuzz that stops with itself. Men have a feeling that if they are not all the time running about and bursting into fits of feversih activity, they are doing nothing. It is an illusion to think that all these so-called movements change things. It is merely taking a cup and beating the water in it; the water is moved about, but it is not changed for all your beating. This illusion of action is one of the greatest illusions of human nature. It hurts progress because it brings on you the necessity of rushing always into some excited movement. If you could only perceive the illusion and see how useless it all is, how it changes nothing! Nowhere can you achieve anything by it. Those who are thus rushing about are the tools of forces that make them dance for their own amusement. And they are not forces of the best quality either.

 

Whatever has been done in the world has been done by the very few who can stand outside the action in silence; for it is they who are the instruments of the Divine Power. They are dynamic agents, conscious instruments; they bring down the forces that change the world. Things can be done in that way, not by a restless activity. In peace, in silence and in quietness the world was built, it is in peace and silence and quietness that it must be done. It is ignorance to believe that you must run from morning to night and labour at all sorts of futile things in order to do something for the world.”

 

The Mother

Physics and Philosophy

“We can say that physics is a part of science and as such aims at a description and understanding of nature. Any kind of understanding, scientific or not, depends on our language, on the communication of ideas. Every description of phenomena, of experiments and their results, rests upon language as the only means of communication. The words of this language represent the concepts of daily life, which in the scientific language of physics may be refined to the concepts of classical physics. These concepts are the only tools for an unambiguous communication about events, about the setting up of experiments, and about their results. If therefore the atomic physicist is asked to give a description of what really happens in his experiments, the words “description” and “really” and “happens” can only refer to the concepts of daily life or of classical physics. As soon as the physicist gave up this basis he would lose the means of unambiguous communication and could not continue in his science. Therefore, any statement about what has “actually happened” is a statement in terms of the classical concepts and — because of thermodynamics and of the uncertainty relations — by its very nature incomplete with respect to the details of the atomic events involved. The demand to “describe what happens” in the quantum-theoretical process between two successive observations is a contradiction in adjecto, since the word “describe” refers to the use of the classical concepts, while these concepts cannot be applied in the space between the observations; they can only be applied at the points of observation.”

Werner Heisenberg

El mecanicismo

“El mecanicismo puede ser definido como la teoría que afirma que no existen cualidades de los cuerpos que pertenezcan realmente a ellos -las cualidades sensibles son sólo afecciones del sujeto que las percibe-, mientras que todos los comportamientos derivan de sus figuras geométricas y de su movimiento local. No existen, por tanto, formas substanciales ni accidentales. La materia es definida únicamente en función de su característica constitutiva, la extensión, y, en cuanto al movimiento, no hay otro que el movimiento según la cantidad de espacio recorrido.

La diferencia entre naturaleza y arte es, pues sólo de tamaño…

¿Es el mecanicismo filosofía de la naturaleza o solamente una metodología científica?

También el atomismo es, en cierto modo, un mecanicismo en el sentido de que sólo acepta el movimiento local y no hay en esta filosofía ninguna alteración en la substancia corpórea, esto es, en este caso, en el átomo.

El mecanicismo no podrá ser nunca un modelo suficiente para explicar su comportamiento [el de los seres vivos]. La interacción entre el todo y sus partes que se observa en los vivientes supera, de raíz, las posibilidades de toda explicación mecánica.

Hay que distinguir, pues, entre el mecanicismo y la matematización de lo físico. Mientras lo segundo es un método de abordar la realidad natural (…), lo primero, el mecanicismo, ha de ser definido como aquella teoría que sostiene que la matematización de lo real es la metafísica de la naturaleza y, aún en muchos casos, toda la metafísica.”

Petit & Prevosti

 

O mundo do tempo

“O azul é fundo e denso, em si está contida a lógica desconhecida deste lugar. Mergulhar aí pode ser perigoso.

Os habitante do mundo do tempo, essa terra colorida só se aventuram nesse lugar quando já são velhos e muito maduros.

As outras cores são para ser navegadas ao sabor da vida, da verdade ou do medo. De um modo geral, os habitantes do mundo do tempo gostam mais da zona do verde. Dizem ser mais estável, mais amena.

No entanto, a grande ocupação deste povo é tentar descobrir como as cores da sua terra podem fundir-se em vez de viver separadamente.”

Sara Anjo


TSplant