To recapitulate thoughts not sent.
A fair amount of biology is composed of phenomenological studies. These are observations at a relatively gross scale as compared to a molecular and biochemical level that isolate and characterize some feature or behavior, typically of a physiological sort. The phenomenon are then modeled and further observations, tests, and simulations are conducted to verify the accuracy of the model. Assuming all these reviews are completed, the model is then used as a map of sorts to go looking for the underlying cellular, molecular, and bio-chemical structures that could potentially give rise to the phenomenological observations and the model.
The problem is that a fair number of these models and their phenomenological support fail, when looking for the underlying processes and structures that should be present.
A particularly good example concerns biological rhythms and biological clocks. Organisms perform a temporal orientation in relation to their own processes: metabolism, respiration, growth, reproduction; and in relation to external environmental periodic changes: in light, temperature, food, pH, salinity, water, etc. Despite all these phenomenon and some extremely sophisticated and beautiful models, at the end of the day, we know almost nothing about how biology measures time.
"Many important biological rhythms occur on cycles longer that 24 hours. Annual cycles of breeding, hibernation, and migration are examples of behaviors that occur on a yearly cycle, so-called circannual behaviors. These behaviors seem to be largely timed by hormonal and other physiological changes that are keyed to exogenous factors such as day length. The degree to which endogenous biological clocks underlay circannual rhythms is not known...
The physiological mechanism of endogenous biological clocks is unknown, although there has been a great deal of study and speculation, most of it centered on regularly-occuring molecular interactions. The mechanism of the biological clock remains one of the most tantalizing puzzles in biology today." (Raven PH, Johnson GB, Biology, Mosby, 3rd ed, St.Louis, 1992, 1189p)
Probably the most interesting and extensive work done on biological clocks is from Arthur Winfree. For beautiful illustrations and a list of publications see his home pages:
Now there have been decades of work done on space orientation in animals and plants, but almost all of it is phenomenological--very much along the lines of the Nature letter. Some of the phenomenology models use some pretty awesome mathematics. However, there are few if any cellular or molecular level results that give a hint at how this orientation is accomplished. That doesn't mean that the best isn't full of talk about chemical signal transduction systems and the like. But once again, at the end of all the blah, blah, there is nada.
So, it occurred to me first of all if we can't explain how a corn plant grows straight up, a simple problem in space orientation*, then there is something profoundly wrong headed going on. (BTW there are corn varieties that refuse to grow up and insist on wondering around on the ground like crab grass--which proves directional growth is part of the genetic machinery.)
The only reason I can think of for these failures is that our automatic assumption that a phenomenon has to be localizable in a biological system is wrong. What we have observed and what we call a biological phenomenon might in reality be a relationship, an interaction with various environmental constants. Just looking at the biology side of the equation only gives half the picture, so that is why we can't find what we are looking for.
I got the article. Thanks for sending it.
I haven't done anymore than scan it quickly. But I seriously suspect this might be one of those phenomenological studies that fails to indicate the right place to go looking for a more tightly resolved structural explanation--like those missing biological clocks.
*Yes under all kinds of light regimes including omni directional, low
radiance infrared, green, blue, and total darkness--although they don't last
long in some of these. And, their roots will find where down is no matter how
you try to confuse them. On the other hand you can screw up the root
system in slowly rotating wheels that use the equivalence relation
between gravitational and centripetal force. The primary root tracks
a force vector, but how is a mystery.