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In the normal function of the kidney, the bloodstream is near emptied of fluids as it moves through the glomerulus, in which glomerular filtrate is formed.

As it proceeds through the Nephron, a significant amount of this material is returned to the bloodstream, and only a comparatively timy amount goes into the urine.

Why, in evoultionary terms, is it not more favourable energetically to remove only the small number of molecules, perhaph using specialised channels made of protein and activated only by a certain molecules which need removing, at a potentially huge energy saving?

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Probably because it's easier to retain what the body wants than get rid of what the body doesn't want.

What does your body want to keep from your Urine? Pretty much water and selective ions (Cl-, K+, Na+, Ca+2, etc.). Maybe a few other things, depending on how healthy you are.

Now, what does your body want to get rid of in your Urine? Well, anything it can't get rid of in your solid waste. That includes pretty much anything water soluble that could harm you, whether it's Urea, chelating agents for heavy metals, ions your body doesn't want (excess minerals), excess vitamins, sugars (to maintain insulin levels), hormones, liver byproducts, and whatever dark horrors mother nature is concocting for us in the forms of virii or whatever else.

That's just the beginning of the list, but already you should start to see the impracticality of having active transport or coupled transport for everything. The list of transmembrane proteins needed to ferry all of the items your body wants to get rid of is a lot longer than the list of transmembrane proteins needed to keep what the body needs.

Then you have the "unknowns" - whatever else your body hasn't encountered yet, but will still be water-soluble. If the body required some sort of transport across membranes for everything it didn't want, then it would need to adapt to every single new compound it encounters. Given the relatively slow generation periods for humans, if a new compound turned out to be significantly fatal then the slow adaptation could spell disaster for any small populations and create serial bottlenecking events.

So, while it may not be energetically favorable to let water and ions pass into the Nephron and subsequent tubules to be reclaimed, Evolutionarily speaking it's probably strongly selected for. We may expend a lot of energy reclaiming water against its concentration gradient, along with whatever else we want from Urine, but at the same time we get rid of everything else we don't need that's filtered through the glomerulus. It doesn't matter what the "everything else" is - but we know we don't need it, and that's the big key.

With my current level of knowledge (B.S. - Biology) this is the best explanation I could think of, but I haven't read any specific papers nor heard any particular theories on why the kidney's components act as they do.

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This is a great answer. Usually biological arguments based only on logic are a little questionable, but you make a very persuasive argument that the alternative arrangement is just not feasible. –  octern Nov 18 '12 at 19:14
    
I've spent a while thinking about this, but it makes a lot of sense, and before I read this answer, I was thinking along similar lines. With the time that changes due to natural selection take, it must make sense to remove everything that isn't exactly what it needs, so newly synthesised or evolved poisons can still be removed, even without the body knowing their sturcuture. –  Matthew Higgins Dec 15 '12 at 14:02
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I would argue from an evolutionary perspective: not all kidneys are created equal. The mammalian kidney has a long evolutionary history and potentially a lot of phylogenetic inertia. Mammals do what they can with what they inherited from their ancestors.

The metanephric kidney, which is what mammals have, is thought to have evolved with the first amniotes (terrestrial, cleidoic-egg-laying tetrapods). However, the metanephros, from when the definitive metanephric kidney evolved, was (is) present in most fishes as well as amphibians. These groups live all or part of their lives in fresh water, so their tissues are hyperosmotic relative to the water. Their problem is not retaining water, but getting rid of all the water that enters their tissues via osmosis. (Marine bony fish have small, aglomerular kidneys.) They produce large volumes of urine, and their kidneys are set up to reclaim essential minerals, etc., as @MCM describes.

So the first amniotes, although now living on land, had a kidney that had evolved in conditions where water was in excess. It evolved for filtering large volumes and reclaiming minerals. Amniotes simply adapted it for a water-poor environment.

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