All that stuff you read came from one study done from lab rats. I don't see any mention of how much exposure (in grams, or however they want to do it) the rats had to ingest to produce deformities.
Also, it's like there's ONE research article from a lab... no follow ups, no other real subsequent labwork done to confirm this claim.
Despite the article, it's well known that what happens with rats in a controlled setting doesn't necessarily transfer to how it will happen with humans. We don't live in controlled settings, and we certainly don't have the physiology of rats. So I am always a bit skeptical of such a study unless backed by human trials. With all the people that use nalgene bottles, you'd think they would have compiled enough data to confirm what they found happens with rats by now.
Remember in the late 70s/early 80s when people panicked because some study said Orbit gum caused cancer in mice? In a panic, store owners removed the gum from the shelves, and people stopped buying a very popular gum. Later, subsequent studies showed that it had no effect on humans.
I really think nalgene bottles are fine- nalgene has been around for many many years. I remember using nalgene bottles in chemistry class in the 80s. They used to make eyewash stations used by medical facilities worldwide. If there really was a problem with nalgene bottles by now, they would have certainly been exposed by many research studies by now.
I like my nalgene bottles, btw.