Panmere

From arXiv, a paper entitled “Stokesian jellyfish: Viscous locomotion of bilayer vesicles” [1] that I think Rashevsky would have approved of. The abstract:

Motivated by recent advances in vesicle engineering, we consider theoretically the locomotion of shape-changing bilayer vesicles at low Reynolds number. By modulating their volume and membrane composition, the vesicles can be made to change shape quasi-statically in thermal equilibrium. When the control parameters are tuned appropriately to yield periodic shape changes which are not time-reversible, the result is a net swimming motion over one cycle of shape deformation. For two classical vesicle models (spontaneous curvature and bilayer coupling), we determine numerically the sequence of vesicle shapes through an enthalpy minimization, as well as the fluid-body interactions by solving a boundary integral  formulation of the Stokes equations. For both models, net locomotion can be obtained either by continuously modulating fore-aft asymmetric vesicle shapes, or by crossing a continuous shape-transition region and alternating between fore-aft asymmetric and fore-aft symmetric shapes. The obtained hydrodynamic efficiencies are similar to that of other low Reynolds number biological swimmers, and suggest that shape-changing vesicles might provide an alternative to flagella-based synthetic microswimmers.

References

[1] Evans, A., Spagnolie, S., Lauga, E. 2010. “Stokesian jellyfish: Viscous locomotion of bilayer vesicles”. arXiv:1002.1420v1

From Popular Science and Wired, DARPA is budgeting six million dollars on a rather frightening program called “BioDesign” [1]:

BioDesign is a new intellectual approach to biological functionality. The intrinsic concept is that by using gained knowledge of biological processes in combination with biotechnology and synthetic chemical technology, humans can employ system engineering methods to originate novel beneficial processes. BioDesign eliminates the randomness of natural evolutionary advancement primarily by advanced genetic engineering and molecular biology technologies to produce the intended biological effect. This thrust area includes designed molecular responses that increase resistance to cellular death signals and improved computational methods for prediction of function based solely on sequence and structure of proteins produced by synthetic biological systems. Development of technologies to genetically tag and/or lock synthesized molecules would provide methods for identifying the origin and source of synthetic biologicals (e.g., genes or proteins) allowing for traceability and prevention of manipulation (“tamper proof” synthetic biological).

FY 2011 Base Plans:
- Demonstrate computation protein conformation algorithms that model one residue per minute with 99.5% accuracy for every one kilodalton of mass regardless of protein class.
- Develop conformation prediction algorithms for biomimetic polymers and biological-nonbiological hybrids involving unnatural amino acids or inorganic materials.
- Demonstrate a robust understanding of the collective mechanisms that contribute to cell death.
- Identify and initiate strategies that would enable a new generation of regenerative cells that could ultimately be programmed to live indefinitely until needed for an injury repair or therapeutic application.
- Develop genetically encoded locks to create “tamper proof” DNA and protect commercial applications.
- Develop strategies to create a synthetic organism “self-destruct” option to be implemented upon nefarious removal of organism.
- Permanently append a synthetic organism’s genome and prevent foul play by tracking organism use and history, similar to a traceable serial number on a handgun.

So, as I read their Base Plans, it appears that in the next year DARPA will:

• Solve the protein-folding problem

• Solve the folding problem for entirely new classes of materials

• Solve the senescence problem

• Create synthetic life

• Create synthetic life that is a proof against evolutionary processes via unprecedented genomic stability

• Create synthetic life that is a proof against biological adaptivity and will instead self-destruct

What will they do with all their free time?

References

[1] 2010. DARPA, Department of Defense, Fiscal Year 2011 President’s Budget. PDF (pp.264-265)

From March’s Notices of the AMS, Chaim Goodman-Strauss authors an article, “Can’t Decide? Undecide!” [1], on the ubiquity of undecidability in mathematics.

References

[1] Goodman-Strauss,C. 2010. “Can’t Decide? Undecide!”. Notices of the AMS. Vol 57:3.

Robert Rosen’s anticipatory systems are the focus of the first in a series of thematic issues of the International Journal of General Systems [1], as noted by George Klir in the issue editorial:

The primary distinction is that thematic issues are invited and written by one author or, possibly, by one team of authors. The purpose of publishing each of these thematic issues is not only to stimulate interest in the covered area, but also to convey a message that this area is central to the aims of the journal, thus encouraging submission of papers contributing to it.

This is the first thematic issue. It is devoted to anticipatory systems and its author, Mihai Nadin, is one of the most distinguished contributors to this area. While the idea was introduced in two papers published by Robert Rosen in 1974 in the first volume of this journal, virtually nothing on anticipatory systems has been covered in the following 37 volumes. It is, thus, timely to report on the tremendous developments since those early papers and express in this way the ongoing interest of the International Journal of General Systems in this important area. It is my hope that this thematic issue will stimulate the basic and applied research in anticipatory systems and, at the same time, encourage researchers working in the area to submit papers describing their work to this journal. Finally, I would like to express my gratitude to Professor Mihai Nadin for accepting my invitation and preparing, within a relatively short time, this interesting and comprehensive overview of the rapidly growing area of anticipatory systems.

The issue features a paper by Mihai Nadin, “Anticipation and dynamics: Rosen’s anticipation in the perspective of time” [2].

* Notably, the issue is currently free to download.

* In addition, it appears that Taylor & Francis have made access to issues of the International Journal of General Systems and the International Journal of System Science available for free, for at least this month. So, do a sitewide search for “Robert Rosen” as the Author Name and download his papers now!

References

[1] International Journal of General Systems, Volume 39 Issue 1 2010.

[2] Nadin, M. 2010. “Anticipation and dynamics: Rosen’s anticipation in the perspective of time“. IJGS 39(1):3-33. DOI: 10.1080/03081070903453685.

The folks at the n-Category Café have been discussing the possible relationships between time and category structure. For example, these comments from John Baez on the post “Kan Lifts”:

Why is Set so different than Set^op? It’s because the morphisms are functions: relations that can be many-to-one, but not one-to-many.

Why do many-to-one but not one-to-many relations get singled out for single treatment and dubbed ‘functions’? Because functions are supposed to be ‘deterministic’: the cause must determine the effect. We don’t care if the effect fails to determine the cause.

Why does our customary concept of determinism have this asymmetry built in? Well, we see it a lot in ordinary life. It’s often (though not always) true that the initial state of an experiment determines the final outcome. But it’s much less common for the final outcome to determine the initial state… at least, not in an easily visible way.

For example, take a heat distribution and run it forwards to equilibrium. We always get the same equilibrium, regardless of the initial conditions.

This asymmetry is built into equations like the heat equation, but it seems absent from the fundamental laws of physics — so far, anyway. This leads to a big puzzle: “why is there this ‘arrow of time’?”

Nobody knows the answer, except “that’s how this universe is: there’s a low-entropy big bang in the past, and a high-entropy expansion in the future, as far as we can see.”

So, the beautiful time-symmetric formalism of quantum theory, so nicely modelled by the dagger-categories we’ve learned to love, is far removed from common experience, where functions rule the roost.

See also the recent post “The Arrow of Time in Cat“.

Because in the encyclopedia of nature, wheels are rarely mentioned.