This is an interesting use of "manifold".
In mathematics, a manifold has a well-defined
meaning. The structure of a manifold
is encoded by a collection of charts that form an atlas. A chart is a mapping between the
manifold and a simple (euclidean) space, see
http://en.wikipedia.org/wiki/Manifold
If science is a manifold, then each science -
physics, chemistry, biology, psychology etc. - is a chart, and all sciences together form the
atlas of the manifold. Sunny Y. Auyang makes
this point in her book "Foundations of complex-system theories".

If understanding is a manifold, then each analogy is a chart, and all analogies together form the atlas of the manifold, see http://is.gd/22u44

Holt uses the term manifold in the sense of
an emergent property: a forest is an emergent
entity made of trees, plants, soil, etc. The
form of plants and trees can be described by fractal patterns. There are clearings and trails in the forest which can be described by patterns as well. Thus one can perhaps say if an emergent entity is a manifold, then each pattern is a chart, and all patterns together form the atlas of the manifold. This pattern could be a simple physical pattern, or a basic agent interaction pattern (http://is.gd/22uZ6) for an agent based system, for instance.

-J.

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