Scientific Notebook

May 16, 2012

Out of our heads

Filed under: Review — tsuresuregusa @ 1:31 pm

I just finished reading this morning Alva Noe’s book, Out of our heads. In it, Noe argues for an understanding of the mind which is not localized in the brain, but an extended phenomenon that includes the body, the brain and the environment. His conclusions imply that most of neuroscience today is plain and simply bullshit. Wouldn’t be the first time this happens in science (eg, Maxwell writing on aether for the 9th edition of the Britannica). The work goes in line with the position of Thompson and Varela, and against the line of Dennet and Dawkins.

What I miss in this work are the philosophical implications of this “new” understanding of the mind. Malabou tries to do something like this in her What should we do with out brains, but fails to understand the basic biology when following the aforementioned line of D&D. There is even a chapter in her book entitled “you are your synapses”. What Noe (and before him Varela) says is, “no, you are NOT your synapses.” For me, this kind of reductionism is equivalent to say “you are your electrons.”

To pursue the philosophical and political implications of our biology, of the way the mind is extended and not a discrete event that happens inside our brains is something that, to the best of my knowledge, remains Terra Incognita. 



Comodification of Science and Quantum Reality

Filed under: Review, Uncategorized — tsuresuregusa @ 12:58 pm

Tooday reading the news I found out that quantum states are “real” (M. F. Pusey, J. Barrett & T. Rudolph Nature Phys.; 2012). I like this formulation to determine what is a real property of a system: As the energy is a physical property of the system, different values of the energy E and E′ correspond to disjoint regions of phase space, hence the distributions μE(x,p) and μE(x,p) have disjoint supports.

The other finding of today was a paper on the commodification of science ( In the middle ages, universities where under the church dominance. There, knowledge was only passed through. (Remember Aquinas’ “creatura non potest creare”). With the new vision of the world that came with the scientific revolution, and the consequent changes on social structure (formation of nations, state and a capitalist economic system), the role of universities changed and included for the first time the creation of knowledge. Universities where places to search for the truth. Time passed, there was a world war, then another, and scientists moved from one continent to the other, where they ended up working on atomic bombs. (I consider this shift really important since it shifted from a national science, with journals in vernacular languages, to a global science and its lingua franca, English.) After the second world war the economic dominance of united stated imposed an economic worldview that supposedly will bring freedom to the world. The invisible hand of the market knows what’s best for the world. Scientist, since where a fundamental part of economic development, were greatly payed for their compliance to the economic logic, tenure track and payed world trips among others, so no scientific critic to economy was made. (Brilliant exceptions I now are these:

I don’t think that the commodification of science brings anything good. In fact, I think the opposite is true. Cf. the case of Chile and its educational system. Neither I think that a return to Humboldian (or worse, medieval) university is the answer.

A proper university must be something closer to its Latin etimological root, universitas magistrorum et scholarium, which roughly means “community of teachers and scholars.” This community cannot be bounded to national states, for the Truth that it searches belongs to Humanity, not to a country or a publishing group. A true university is thought beyond capital, nation and state, and the search for the truth and the fun associated with it are its motors. The difficulties associated with such an enterprise are tremendous, but humanity is famous for accomplishing the impossible.

May 9, 2012

Chiral structures in 3D ED simulations

Filed under: Research — tsuresuregusa @ 6:09 pm

I was reading this paper and asked myself if the same can happen with continuous potentials.

I’m using Dynamo with the following potential: ./bin/dynamod -m 16 –s1 1.3,-0.5:1.2,1.2:1.1,1:1.05,2:1,10:0.99,100 -d .66  -C 5 this mean a system of discontinuous potential with energies given by the pairs –s1 r,e, in units of particle radius, 1, and the system temperature, 1.

For denstities over .65 the system remains ordered while for lower densities the systems is fluid. For a smaller system (108 particles) I determined the transition density at 0.64370. For the current system I don’t know yet, but somewhere between .64 and .66

Snapshot of two system presenting crystal structure and liquid with density nu = 0.66 and 0.64, N = 500, E = -750. Color code represents the ID of the particle.


Filed under: Publications — tsuresuregusa @ 5:57 pm

Extended event driven molecular dynamics for simulating dense granular matter S.González, D. Risso and R. Soto, Eur. Phys. J. Special Topics,Volume 179, (2009)

An event driven algorithm for fractal cluster formation, S. Gonzalez, A. R. Thornton, and S. Luding,  in press, CPC 2010.

About me

Filed under: about — tsuresuregusa @ 5:50 pm

My work is mainly on computer simulations of granular matter. My thesis work is devoted to the study of the clustering phase diagram in free cooling gases with long range interactions, mixing a theoretical approach and event driven simulations. Currently I am also working on the mechanisms behind charge transfer in granular matter, and the role of cohesion on macroscopic properties of granular flows.

Since january 2011, I am collaborating with Marcus Bannerman from Thorsten Pöschel’s Group in the development of DynamO,  the first open-source Event-Driven code. You can get the code here:

Hello world!

Filed under: about — tsuresuregusa @ 5:44 pm

Nico has such a good idea that I copied it.  Let’s see how it goes.

Blog at