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As the old joke goes, "God must have been a civil engineer. Who else would put a waste facility straight through a recreational area?"

But maybe it wasn't God. Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?

To be clear, I'm not asking why isn't it elsewhere. I'm asking where the original "design" came from that spread everywhere.

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Yes, there is.

In order to reproduce, material has to leave one organism and enter another and, in species with internal fertilisation, the eggs need to leave later. Think back to a worm-like organism: it's basically a tube with an opening at either end, those two openings are the easy options for where you can locate your reproductive transfer (and possibly egg-laying). Positioning it at the head end has obvious drawbacks in terms of accidentally consumption, so that leaves positioning it at the excretion end.

Once evolved, there is no compelling reason to fundamentally alter this bodyplan, particularly as other animals show little or no sign of sharing our revulsion at bodily excretions.

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Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?

Because it works.

Evolution doesn't grow things or remove things because they might be funky or useful, Evolution is dictated by the survivability of organisms. If a change helps an organism survive to pass on its genes, it's kept. If it doesn't, it's eliminated from the gene pool over time. As long as a change doesn't significantly help or harm, it can be kept for hundreds, thousands, even millions of generations.

Evolutionarily speaking they are where they are because we're mammals that were formally quadripeds that became bipeds. The stereotypical quadripedal design has the reproductive organs located near the pelvis. Probably because they're best protected there. Powerful hind limbs for kicking, and nasty teeth and claws up front. It also gives easy access for mating, which is pretty important if you want to continue the species. On quadripeds it could be pretty darn awkward if the genitalia were located near the ribcage

Really, you could come up with a lot of reasons why the organs are located where they are. There are a lot of advantages, and a lot of disadvantages, but in the end the simplest explanation is going to be "Because we can survive with them there." The advantages have outweighed the disadvantages for our species' history thus far, and until that changes they'll probably just stay where they are.

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your middle paragraph explains why the reproductive system is located where it is. But why is the urinary system located here as well, not say on the abdomen of the quadruped. –  Mew Jan 14 '13 at 23:40
    
@Chris Could you clarify? The kidneys and bladder are located within the abdomen of quadrupeds (and us). –  MCM Jan 15 '13 at 1:52
    
Yes I meant urinary duct, not system, which is located where the reproductive system is. That is, why are these located in the same spot as each other. Your second paragraph explained for the reproductive system, but not the urinary duct. –  Mew Jan 15 '13 at 2:34
    
Nice job giving an answer that avoids the pitfalls of naive adaptationism. The presence of a trait doesn't mean it's a good idea, just that it's not bad enough to kill anyone (and/or kill their chances at reproducing). –  octern Jan 15 '13 at 16:13
    
I was asking where it came from in the first place, not why it didn't change. –  Joe Z. Jan 29 '13 at 14:01
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The reason lies within our wormy chordate ancestors - an orifice used to eliminate waste can also function as an orifice to eject eggs. My vertebrate zoology is a little bit rusty so I would suggest picking up any first-course book on the subject, most of them cover the evolution of urinary/reproductive organs extensively.

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I actually like this answer best - the body plan is ancient and mostly hasn't changed... –  shigeta Jan 16 '13 at 16:36
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Human body has three channels for excretion of substances, one for each of the three physical phases of matter: lungs for gaseous substances, such as CO2, anus for solid substances such as feces and urinal channel for liquid substances.

It turned out that sperm is liquid, so it uses the same channel as liquid urine.

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Excretion of substances is a great reason for them to exist, but not for their positioning. Just because sperm is a liquid isn't a great reason for the penis to be located between the legs. –  MCM Jan 10 '13 at 3:00
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Anixx, one word - beans. –  Noam N. Kremen Jan 12 '13 at 21:59
    
@MCM, the question doesn't ask why the penis is located between the legs, but rather asks why the urinary duct is close to the reproductive organs. Anixx is trying to say that it is more efficient to utilize the one pipe for both liquids, just as we use our lungs to both breathe in oxygen, and expel carbon dioxide, rather than have two separate systems. –  Mew Jan 14 '13 at 23:37
    
@Chris - I understand your point, but my critique was that there are pretty common examples of organisms that don't put the excretion of phases of matter together, so I didn't find Anixx's argument as full as it could be. –  MCM Jan 15 '13 at 1:54
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