One of the fascinating, exciting even suspenseful aspects of learning Gemara is how a detailed discussion on the minutiae of Jewish law can without notice transition into philosophical, historical or theological issues and transition right back without missing a beat. Each facet of the discussion is deemed no less or more important than the other. Theory and practice, law and story, philosophy and history, theology and science all blend in seamlessly finding their place in the sea of Talmud.
In our last posts (here and here) we discussed cases where there is confusion as to whom or even whether a person is married. It is for this reason that commitments of all kinds are undertaken in the presence of witnesses. "Witnesses were established only because of the liars." (Kiddushin 65b) While we can never be certain that witnesses are telling the truth - either due to nefarious motives or plain human frailty - the Torah establishes that the testimony of two witnesses is to be accepted. And while the testimony of one witness is not in and of itself enough to make a conviction it is enough to create an aura of doubt, which must be dispelled. 
Thus if one witness testifies that Reuven owes Shimon $100, Shimon must take an oath that such is not true. If he were unwilling to do so he would be forced to pay. In contrast to monetary law one witness has little impact in a potential capital case - as are all cases involving marriage and divorce.  For example in order to declare a woman forbidden to her husband due to infidelity we would require the testimony of two witnesses. Or maybe not! 
As we discussed in our last post if one believes something, say a piece of meat, to be forbidden then it is forbidden to him and he may not eat it despite the fact that according to the rules of evidence it is permitted and is in fact permitted to others. Similarly if a husband truly believes his wife to have been unfaithful he would be obligated to cease living with her (of course having a marriage reach a point where a husband might believe such is most tragic)[1].
But what of a case in which one witness testifies that the wife was unfaithful and the husband remains silent? Should such silence be interpreted as agreement based on the principle of stkiah khoda'ah, silence reflects acquiescence? If so the couple would be forbidden to each other. So argues Abaye. Rava, whose view we follow, disagrees asserting silence is just that and nothing else. Being impossible to refute the claim with 100% certainty, or feeling no need to respond to this ludicrous claim, there is only one witness and the couple remain permitted to each other. 
This is an important if sad discussion. What makes it rather mindboggling is what follows. The Gemara (Kiddushin 66a) relates how Yannai, one of the Hasmonean kings, upon return from a great military victory called "all the scholars of Israel" to celebrate in the Temple. Recalling the celebration of those few Jews who returned to build the Temple but could afford little besides vegetables and salt he feasted on the same. As Rashi notes this was a way to give thanks to G-d for granting them success and wealth. How beautiful! 

However "there was one person, a scoffer, evil heart and idolater and Elazar ben Poriah was his name" who told Yannai the rabbis are just paying lip service to you but do not accept you. 
Even if such were true it is irrelevant. And if relevant all the more reason not to tell the king. It is what we do not what we think that matters most, especially in our relations to our political leaders. The rabbis had learned from the tragic story of Kamtza and bar-Kamtza (Gittin 55b-56a) the importance of shalom malchut, of having peaceful and positive relations with those in power. 
Yannai curious as to this claim asked for some evidence. So this evil person told him to put on the tzizt, the headpiece worn by the high priest. He did so and all would have been fine - except there was "one elder and Yehuda the son of Gedidiya was his name" who said to Yannai, "Yannai the king, the crown of kingdom is a great honour, leave the crown of the priesthood for the children of Aaron." Being that the Hasmonean kings were kohanim his comment was at best undiplomatic. It is true that the Hasmoneans violated Judaism's insistence on separation of "church and state" - the monarchy in the hands of the tribe of Judah and the religious leadership in the domain of the tribe of Levi - but to question Yaanai's priesthood was a mistake, even if well intentioned[2]
As to why he did so the Gemara explains that there were rumours that "his mother was taken captive in Modiin" and Yannai the product of that union was not actually a kohen. The Gemara reports that they investigated and could not substantiate such rumours affirming Yaanai's status as a kohen
The story would have ended there if not for that evil one Elazar ben Poriah who said to the king that while a commoner might be expected to take such an 'insult' but you, a "king and high priest, is this your fate?" Yannai asked Elazar ben Poriah what he recommended to which he responded "kill them". Yannai's response to this piece of advice at first glance defies belief; "and what shall become of the Torah?" Murder was of little concern yet the fate of the Torah was! But such is the way of many. They view the killing of the "enemy" as justified and it presents no moral qualms. But Yannai saw himself as a good religious Jew and was concerned that if he kills all the Sages the Torah will come to an end too and perhaps for that reason alone he should keep them alive. 
This was a most insightful comment, the Torah cannot survive without those who teach, interpret and apply it to our lives. Elazar ben Poriah responded "behold it is rolled up and lying in the corner, whoever wants to learn can come and learn." This too is true - but only partially. Everyone can put in the effort to learn and where there is a will there is a way but nonetheless there are limits to what we can accomplish without mentors. "Rav Nachman the son of Yitzchak said: Immediately a whiff of heresy entered him. He should have responded such is true regarding the Written law, but what about the Oral law?" Not realizing that Torah would actually be endangered Yannai went and killed the Sages of Israel "and the world was desolate until Shimon ben Shetach came and returned the Torah to its pristine glory." Luckily - or let's say thank G-d - Shimon ben Shetach's sister was married to Yannai and she saved him, allowing Torah to be saved[3]

And why does this unbelievable story appear here? Because in analyzing the story Abaye tries to prove that the reason the rabbis thought Yannai was not a kohen is because there was one witness testifying to him being a product of his mother being raped. And the only reason the one witness was not accepted was because Yannai denied the charge. But had he remained quiet we would have accepted the testimony of the one witness. The Gemara goes on to reject this proof - in one line no less - as it continues with its legal discussion. 
For us this is astounding. Yet if one understands the precision and care with which the Gemara was edited it makes perfect sense[4]. There is a time and place for everything and the Gemara spends much time discussing and analyzing tragedies. But that was not the focus here. The Gemara was having a legal discussion and this story possibly shed life on that discussion. That is why it is here. But it is amazing the types of evidence that one might come across in a Talmudic discussion.    
[1] In a most fascinating (to say the least) teshuva the Noda BeYehuda (Or Chaim # 35) discusses the case of a yeshiva student who wanted to repent after having had an affair. In responding to his inquiry as to whether he is required (or even permitted) to ask mechila from the husband, one of the considerations the Noda BeYehuda raised was whether in his assessment the husband would believe him. Only in such a situation would there be any reason to consider doing such as only then would the question arise as to the couple remaining married to each other. At the same time the Mishna (Nedarim 90b) notes there are cases where we must suspect one is lying in order to get out of a marriage. 
[2] While he may have been the proximate cause of Yannai's action he quite correctly is not the one the Gemara castigates. Absent Elazar ben Poriah his words would have had no impact. Kind of like the batter who strikes out with the bases loaded to end a 10-7 game. The blame must go to the pitchers. 
[3] The Gemara in Brachot (48a) relates that one day after a meal Yannai needed someone to help with birchat hamazon. His wife said she could get helpr for him but he first had to promise he would not harm the one who would help, the helper being Shimon ben Shetach. Here is someone who had no compunction about killing hundreds, perhaps thousands of rabbis yet was concerned about benchingafter he ate. Sadly I have grown to understand how such is possible. 
[4] On the surface the discussions of the Gemara may appear rather random with many tangents - as happens in our own discussions. Such a reading however is erroneous. The Gemara's editing is a masterpiece of order and structure and even the tangents are precisely placed in their place.