This title is quite misleading: Beings Not Made for Space – NYTimes.com.
Human beings are also not made for living on the sea but we’ve learned how to do it for indefinite periods. We are learning how to live in space as well. For example, the degradation of bone density has long been a serious problem but has indicated in the article is now largely preventable with improved exercise and nutrition regimes.
The eye issue mentioned in the article has only recently started to receive serious research attention and already there are signs that it might be solvable with simple nutritional anti-oxidants: Orbital Samples With Sight-Saving Potential – NASA.
Note that living in space and living in microgravity are not synonymous. I don’t know of any space settlement advocate who has promoted long term residency in microgravity. As the article hints at, habitats in space can rotate to provide spin gravity, which can reduce or eliminate the effects of microgravity. The large wheel-shaped space station seen in the movie 2001: A Space Odyssey is the iconic approach to this.
2001: A Space Odyssey film poster
For long distance transports, a centrifuge could be added to provide some fraction of a G, which should be sufficient to prevent or ameliorate microgravity problems. A recent version of such a vehicle is the Nautilus-X concept, which was designed by Mark Holderman and Edward Henderson of NASA Johnson Space Center. If NASA was not wasting vast amounts of money on SLS/Orion, in-space infrastructure systems like this could be under development today.
Nautilus-X concept for in-space transport.
Radiation protection requires shielding, not magic. Habitats on the Moon or Mars are easily shielded with regolith. In-space transports may not get radiation levels down to that of the earth at sea level but a lot can be done by surrounding living areas with all the water, foodstuffs, equipment, propellants, waste, etc that are coming along on the trip as well. Space transports should be designed from the start with radiation exposure reduction has a key goal. Eventually, material shielding may be supplemented with magnetic shielding as well.
People are almost certainly going to live in space permanently at some point. The human spaceflight programs of today are learning how to make that happen.
See the HobbySpace Living in Space section for lots of resources on the microgravity health effects, radiation shielding, etc.
Update Jan.31.14: Some comments about this post: Beings Making Space Livable – Transterrestrial Musings