The fact that native speakers of a single language disagree on the validity of certain utterances does not invalidate the concept of Universal Grammar. No two individuals learn their native languages in exactly the same way. The language that they pick up is shaped by their unique experiences with other people using the language, so it is unlikely that any two individuals have the exact same "instance" of the language (a more technical way to put this is that everyone has their own ideolect), and thus may differ in the judgements on whether particular utterances in that language are valid.
Even though individuals may speak the same language, because the concept of this language in each of their heads may differ slightly due to their individual experiences, one could say that a few of their parameters differ. If groups of individuals are separated from one another, these parameters can end up diverging between populations, leading to differing dialects and even separate languages over longer periods of time.
From reading the Ars Technica piece (I don't have access to the original Nature article), it seems like they've shown that language features are highly dependent on lineage, but I don't see how this result is incompatible with the concept of Universal Grammar. Because a language has to be relearned by every individual born into the language environment, there is a lot imperfect copying going on, leading to individuals having slightly different parameters of their Universal Grammars. There is a direct biological analogy here: imperfect copying of DNA leads to mutations which can lead to speciation over time. The values of the DNA base pairs are the parameters, but the mechanism by which the DNA is translated into proteins by every individual is still the same. This mechanism is analogous to Universal Grammar translating parameters into the actual spoken language.
It is true that Universal Grammar tends to look at statistical occurrences of features across languages in order to deduce universal statements about them. This is the weakest part of the theory, because the absence of a feature across all languages does not necessarily mean that such a feature cannot arise, nor does the presence of a feature across all languages necessarily mean that it must always be present. Perhaps one of the worst results of language extinction is the fact that there will be fewer data sets to test proposed language universals against.
To address your other assertion, the concept of Universal Grammar does not only apply to syntax. For instance, there are phonological universals, which are deduced based on phonotactics of known languages. For example, all known languages have at the very least the minimal vowel system of three vowels /i a u/ or slight variations thereof.
"...Because a language has to be relearned by every individual born into the language environment, there is a lot imperfect copying going on, leading to individuals having slightly different parameters of their Universal Grammars."
My point with respect to the parameters notion is that the more closely we examine every aspect of language, the finer the distinctions we discover. At some point, the number of necessary "learned parameters" grows so large that it's like claiming that all books are the same except for the character parameters. The characters ARE the book, with some near-universal exceptions such as paper and binding, and the learned language parameters ARE the language, with some near-universal exceptions that are general cognitive properties of human brain architecture that apply to much more than just language.
Just because the parameters may be diverse does not mean the rules need to be just as diverse. If I may use the biological analogy again, despite the myriad combinations of DNA base pairs, they are all still translated by a universal genetic code that's simple enough to describe in one table (http://en.wikipedia.org/wiki/DNA_codon_table ). I'm fully aware that a description of Universal Grammar would likely be more complex than this though.
The collection of language parameters in a person's head is not the language itself, just like the DNA of an individual is not the species itself. It's the translation of those parameters by a shared mechanism that gives rise to the spoken language. This is where I think your book analogy falls through.
Even though individuals may speak the same language, because the concept of this language in each of their heads may differ slightly due to their individual experiences, one could say that a few of their parameters differ. If groups of individuals are separated from one another, these parameters can end up diverging between populations, leading to differing dialects and even separate languages over longer periods of time.
From reading the Ars Technica piece (I don't have access to the original Nature article), it seems like they've shown that language features are highly dependent on lineage, but I don't see how this result is incompatible with the concept of Universal Grammar. Because a language has to be relearned by every individual born into the language environment, there is a lot imperfect copying going on, leading to individuals having slightly different parameters of their Universal Grammars. There is a direct biological analogy here: imperfect copying of DNA leads to mutations which can lead to speciation over time. The values of the DNA base pairs are the parameters, but the mechanism by which the DNA is translated into proteins by every individual is still the same. This mechanism is analogous to Universal Grammar translating parameters into the actual spoken language.
It is true that Universal Grammar tends to look at statistical occurrences of features across languages in order to deduce universal statements about them. This is the weakest part of the theory, because the absence of a feature across all languages does not necessarily mean that such a feature cannot arise, nor does the presence of a feature across all languages necessarily mean that it must always be present. Perhaps one of the worst results of language extinction is the fact that there will be fewer data sets to test proposed language universals against.
To address your other assertion, the concept of Universal Grammar does not only apply to syntax. For instance, there are phonological universals, which are deduced based on phonotactics of known languages. For example, all known languages have at the very least the minimal vowel system of three vowels /i a u/ or slight variations thereof.