Self-Organizing systems discussion:

[kirkulator]

Hello, I was reading into self-organizing systems and I decided to post on a curiosity that i stumbled over because members here know more about this topic than I do. So if any of you will, give me some insights. [I am an undergraduate math student]

I read that studies suggest that through natural selection, we evolve to have mechanisms controlled by algorithms [encoded in the genome] and that through self organizing processes, these algorithms may possibly generate the enormous capacity seen in biological systems. Does this hint towards technology some day becoming just as complex as a biological being such as a human? I mean, does it give some credibility to that possibility because we've seen man-made things self organize.

Thanks!
Amanda

 

[Evo]

because we've seen man-made things self organize.

Please explain what you mean by self organize.

 

[kirkulator]

self-organizing systems are physical and biological systems in which pattern and structure at the global level arises solely from interactions among the lower-level components of the system. the systems components are executed using only local information, without reference to the global patterns.

 

[Ygggdrasil]

I think that viruses may be good model systems for the type of biophysical studies required to understand some of the principles underlying self-organization and self-assembly in biological systems. Although viruses are complex biological systems, they are simple enough that they can potentially be understood as simply chemical systems.

There are, of course, other areas in biology that study self-organization such as work done studying the role of reaction-diffusion systems in spatial pattern formation during development.

The following thread, especially some of the later posts, has an interesting discussion of self-organization in the context of viruses. I'll give a link to http://www.pnas.org/content/suppl/2007/12/05/0709489104.DC1/09489Movie1.mov http://www.pnas.org/content/suppl/2007/12/05/0709489104.DC1/09489Movie2.mov from a paper that I cited in the thread showing a macroscopic model of poliovirus capsid assembly:

Olson, Hu, and Keinan. (2007) Chemical mimicry of viral capsid self-assembly. Proc. Natl. Acad. Sci. USA 104: 20731-20736. http://dx.doi.org/10.1073/pnas.0709489104.

 

[Pythagorean]

a low-parameter self-organizing system:

https://www.youtube.com/watch?v=KPP-4-LEHXQ

 

[Ryan_m_b]

Hello, I was reading into self-organizing systems and I decided to post on a curiosity that i stumbled over because members here know more about this topic than I do. So if any of you will, give me some insights. [I am an undergraduate math student]

This looks to be a hard OP to answer because of an unfamiliarity with terms. Perhaps if you could define and describe some of the terms you are using people would find it easier to answer.

I read that studies suggest that through natural selection, we evolve to have mechanisms controlled by algorithms [encoded in the genome] and that through self organizing processes, these algorithms may possibly generate the enormous capacity seen in biological systems.

We have an introduction to evolution you might like to read. Whilst my mathematics doesn't extend beyond school I don't think this is correct to say. DNA contains genes; sequences that code for RNA (the vast majority of which are then converted to protein) and sequences that through processes such as protein binding regulate these genes as either on or off. Proteins are the molecular tools of biology and help establish a metabolism; a myriad of self regulating chemical interactions essential for life. The whole process is contextual on on the local environment.

Does this hint towards technology some day becoming just as complex as a biological being such as a human? I mean, does it give some credibility to that possibility because we've seen man-made things self organize.

The difference between technological artefacts and living things is that living things reproduce with variation under environmental attrition i.e. they evolve. Whether or not technological artefacts one day become more complex than living organisms will depend on whether or not people figure out how to do it.

self-organizing systems are physical and biological systems in which pattern and structure at the global level arises solely from interactions among the lower-level components of the system. the systems components are executed using only local information, without reference to the global patterns.

If I'm reading this correctly then no this does not apply to biology as global, long-range effects feed back to the local level in organisms.

 

[jackmell]

I read that studies suggest that through natural selection, we evolve to have mechanisms controlled by algorithms [encoded in the genome] and that through self organizing processes, these algorithms may possibly generate the enormous capacity seen in biological systems.

You mind giving the source for that statement? I think I see what you mean though and would re-phrase is as "we evolved mechanisms controlled by (non-linear) dynamics encoded in the biochemistry of genetics and through emergence and non-linear effects, these dynamics generated the enormous diversity seen in biology." You a math major huh? Well there you go. Now you livin' in the big house.

 

[D H]

Please explain what you mean by self organize.

Have you ever taken a long drive, city to city or longer? You'll be driving along on a fairly empty road and suddenly come up against a herd of relatively slow moving cars. Negotiating through that herd can be challenging. Once through it, you'll have a nice, long stretch until you come up to the next herd.

And that's on an open road. Things get even tenser when traffic density increases. Traffic jams occur when the freeway loses a lane. That makes sense. But what about traffic jams that just seem to appear out of nowhere? Even weirder, what explains traffic jams that arise where a freeway adds a lane? Those herds of cars, those traffic jams, and many other traffic behaviors are explained by examining traffic as a self organizing system.

Self organizing systems have been a hot topic in dynamic systems theory for quite some time now. It has been used to describe traffic flow, the behavior of a flock of birds, some aspects of cognitive development in children, and a whole host of other complex behaviors.

 

[jackmell]

Self organizing systems have been a hot topic in dynamic systems theory for quite some time now. It has been used to describe traffic flow, the behavior of a flock of birds, some aspects of cognitive development in children, and a whole host of other complex behaviors.

Termites. Don't forget the termites: they really don't know what they're building. Nevertheless, the marvelous clay cathedrals emerge by virtue of the the non-linear dynamics of mud, termite, and pheromone. Interestingly, these termite dynamics can be somewhat modeled by a coupled set of non-linear PDEs. This is explained in "Self-Organization in Biological Systems", by Camazine, et.al. It's all in the dynamics of the interactions and so independent of the particular substrate instantiating the phenomenon so to answer the second question of the OP, I would argue yes: If man-made technology can reach the same level of (non-linear) complexity as biological systems, for example in AI, then by the intrinsic dynamics alone, self-organizing factors such as non-linear dynamics and emergence could create the same level (complexity) of phenomenon we see in biology such as a self-aware consciousness.

 

[atyy]

While we're still at the definitional stage here, let's ask for a second definition: what is complexity?

Personally, I always wish my technology to feel simpler and simpler. I'm not sure that's true for technology, but it seems true for some parts of science where we explain more and more with less and less.

Human beings and their technology are subject to natural selection. But what does natural selection maximize?
Some sort of fitness: http://www.ncbi.nlm.nih.gov/pubmed/19474791, http://www.ncbi.nlm.nih.gov/pubmed/20740005?
Some sort of information: http://www.ncbi.nlm.nih.gov/pubmed/16123265, http://arxiv.org/abs/0901.3742?
Or both, depending on how one views it?

 

[Pythagorean]

Here are some examples of self-organization in biology provided by wiki

1. spontaneous folding of proteins and other biomacromolecules
2. formation of lipid bilayer membranes
3. homeostasis (the self-maintaining nature of systems from the cell to the whole organism)
4. pattern formation and morphogenesis, or how the living organism develops and grows. See also embryology.
5. the coordination of human movement, e.g. seminal studies of bimanual coordination by Kelso
6. the creation of structures by social animals, such as social insects (bees, ants, termites), and many mammals
7. flocking behaviour (such as the formation of flocks by birds, schools of fish, etc.)
8. the origin of life itself from self-organizing chemical systems, in the theories of hypercycles and autocatalytic networks
9. the organization of Earth's biosphere in a way that is broadly conducive to life (according to the controversial Gaia hypothesis)

http://en.wikipedia.org/wiki/Self-organization#Self-organization_in_biology

Personally, I think abiogenesis is one of the most striking examples of self organization in the whole universe

 

[kirkulator]

Hey guys: this is a source where i extracted my statement on algorithms encoded in the genome:

http://web.mac.com/camazine/Camazine/Self-organization_files/Self-organization.pdf

May i remind you that this is extremely hypothetical! Thank you all so much for the insights and the links, I am learning a lot more about this topic getting prospective from all of you!
: )
- Amanda
Ps: yes, i am graduating next year with a major in pure mathematics and a minor in computer science though i have a strong interest in nearly all science fields and philosophy for that matter.

 

[Ophiolite]

I recommend the extensive work of Stuart Kaufmann. He has been pursuing some fascinating concepts in self-organisation and emergent properties related to abiogenesis and biological evolution. He has a number of excellent published books which have garnered praise from Nobel laureates and the likes of Stehpen Gould. If his ideas are wrong they are wrong in a gloriously elegant, inventive and original way.

 

[Noko]

I recommend the extensive work of Stuart Kaufmann. He has been pursuing some fascinating concepts in self-organisation and emergent properties related to abiogenesis and biological evolution. He has a number of excellent published books which have garnered praise from Nobel laureates and the likes of Stehpen Gould. If his ideas are wrong they are wrong in a gloriously elegant, inventive and original way.

Stuart Kaufmann is a treat when it comes to complex systems. In Reinventing The Sacred he mentions something that keeps me thinking well into the night,

The number of possible combinations of activities of these genes is 2^2,500 or about 10⁷⁵⁰. There are only an estimated 10⁸⁰ particles in the known universe, which means that the number of possible states of our regulating genes is enormously, vastly larger than the number of particles in the universe. If we add in our structural genes, there are 2^25,000 or about 10^7,500 states. The universe is about 10¹⁷ seconds old. It takes a few minutes to an hour for genes to turn on or off. Even if we were a thousand times as old as the universe, there is not time enough for our regulatory network to "visit" even a tiny fraction of its possible states. And remember, we are still assuming genes are as simple as light bulbs, with no states but "on" or "off".