Org Mode After Sentience

1) Different languages form connections in different areas of the brain. Scientifically observed. (Though the earier you learn multiple languages, the more those two areas will bleed together...)
Therefore, as the alien brain is undoubtedly different from ours, their approach to language will be somewhat different. Actually, human languages are approached differently - we have sign language, which uses the hands, as well as romance (latin derived) languages. The Fon language, which I've just been reading about for my humanities class, is tonal. This means that if you say "Lala" and your voice goes up, it's a different word from "LaLA," where your voice could go down on the second or just stay exactly the same. Basically, there's a lot of stuff potential in spoken languages that we can't necessarily translate into English, spanish, Thai, Check... you get the picture.

Rebuttal no. 1: Any species developing a written language will find ways to deal with that - accent marks, punctuation, and the like.
Re-rebuttal: that takes much longer than you'd think. The Romans didn't even have punctuation - that, plus syntax, was added slowly to latin to make it palatable to the locals. This resulted in Italian, Spanish, French, Portugese, and english, as well as, periphereally, Catalan. (Any one who knows that there were originally far too many spanish dialects, that have mostly been superseeded by Castillian spanish, you get webcookies.)

2) Semantics. They are not necessarily a part of the sentence. For example, classical latin classes nouns into various declensions, which all have different endings, which are supposed to tell you their relation to each other.
Semantics is really, really important in English. For example, the sentences "Annabel looked at the dog," and "The dog looked at Annabel," mean different things in English, due only to the order in which words are placed. A Latin-speaking Roman wouldn't be paying any attention to the word order: his sentence could be, "Annabella cainem verat," or "Cainem verat Annabella" or "Annabella verat cainem" or "Cainem Annabella verat," and it would make no difference to him. In addition, he wouldn't bother punctuating, nor would your Ancient Egyptian, Greek or Mayan.
Alien Semantics, as a result of their having a potentially dissimilar linguistic logic, would necessarily be unusual from any terran standpoint.

Rebuttal no. 2: Latin is a dead language. It was too difficult to learn. Similar languages will die out, right?
Re-rebuttal: Latin was the language of science, religion, the universe and everything from before year 0 to well into the 17th and 18th centuries. English has only been a common world language since the early 1700's, during the brittish empire.

3)Writing, records, and the rest. Though it's been discussed in other threads, writing systems are hugely complicated. The Arabic characters that most of us are using here are on the relatively simple end: on the other end, we have Chinese and Japanese characters, Egyptian Heiroglyphs (which were so complicated that they needed three seperate sets) the Mayan Syllabic alphabet, and the Incan predilection of recording all transactions in colored knots.
Just to show you how complicated this could get, imagine encoding accent marks, tonal inflections, semantics, or body language in a series of knots.

Rebuttal no 3: Err, what does this have to do with conversations again?
re-rebuttal: Everything. Intra-species communications will necesarily work - but ask any "alien" to decode them, and you have a psychological issue. Aliens are "other" and their minds will not necessarily work the same way as ours. At the risk of copying sciocont, I will call this the "Manifesto of dissimilarity."

4)Speech organs. (Or the lack thereof.)We have vocal cords - it was to our ancestors' advantage to be able to make noise long before speech was ever invented, as evidenced by vocal cords in terrestrial animals. However, what if you were a fish? Sound transmits differently in different atmospheres or liquids, so there could potentially be organisms where there was no advantage, or even point, to auditory/vocal communications. Sign language is the most obvious alternative, but it's really a replacement. Why burden your valuable opposable thumbs with the task of communicating all the time?
Other modes of communication could be:
Visual. Color displays, such as those by octopi. Now, we don't understand all the colorations of octopi, but their chromatophores are versatile enough for them to be used as an effective language communicator. They would probably operate in units of color that, combined like the phonemes of language, would sum up to units of meaning.
Chemical. We wouldn't see this going on, but pheremones and other chemical communications go on every day. This includes both the animal-centric smell and the chemicals released by plant "communications."

Anything could be used in place of "speech," but it would have to be both long-range and capable of innumerable nuances.

So, to sum up all my problems with "translatable" alien conversations, think of trying to turn any combination of the above into an understandable english sentence. (This is, personally, why I don't think we'll ever have any problems with Seti - there's no way we'd ever be able to distinguish "we come in peace" from "take us to your leader," and that's assuming that alien intelligence even communicates auditorially and uses radio waves to do so.)