1) AN EGG FOUND IN THE NEST ON THE MORNING OF YOM TOV
QUESTION: Rebbi Yosi ben Shaul rules that if one checked the chicken's nest for eggs before Yom Tov and found none, and on the morning of Yom Tov he finds an egg in the nest immediately before dawn, the egg is prohibited. The Gemara explains that Rebbi Yosi ben Shaul refers to a case in which there is no rooster in the vicinity, and thus the egg must have been formed from the heat of the ground ("Safna me'Ar'a") and was laid at night, on Yom Tov.
The Gemara asks that if there is no rooster nearby, then even if one did not check the nest before Yom Tov the egg should be prohibited because it may have been laid at night on Yom Tov. The Gemara answers that when he did not check the nest before Yom Tov, he must assume that the egg was laid during the day before Yom Tov, and thus it is permitted.
Why, in a case of doubt, does one assume that the egg was laid before Yom Tov? Since the Gemara is discussing a case in which there is no rooster nearby, there is a possibility that the egg was laid at night on Yom Tov. The egg should be prohibited due to a doubt about when it was laid (since it is a "Davar she'Yesh Lo Matirin").
(a) TOSFOS (DH Ki Lo Badak) answers that most eggs are laid during the daytime (even if they are "Safna me'Ar'a"), and therefore one does not need to take into consideration the small chance that it was laid at night unless he knows for certain that the chicken coop contained no eggs before Yom Tov. This is also the approach of RASHI (DH Eima) and other Rishonim.
This answer is problematic, however, because the Gemara earlier (4a) teaches that even though most of the eggs in a mixture are permitted, the entire mixture is prohibited because a "Davar she'Yesh Lo Matirin" is not Batel. Here, too, the egg should not be permitted merely because most eggs are laid during the day.
The answer to this question is that the principle of "Davar she'Yesh Lo Matirin" prohibits the item only when it is known for certain that at least one item in the group is forbidden ("Ischazek Isura") and now a doubt has arisen which one it is. (For example, the forbidden item fell into a mixture with more Heter than Isur.) However, if there is a "Rov" (majority) of permitted items in the mixture, and the item in doubt was never known to be certainly forbidden (it was only a Safek), then the mixture is permitted and the principle of "Davar she'Yesh Lo Matirin" does not prohibit it. (RE'AH, RAN)
Alternatively, in this case it is not merely a Rov which says that the egg was laid during the day and thus should be permitted. Rather, it is a naturally-occurring process ("eggs are normally laid by day"). Such an established Rov may be applied to prove that the egg was laid during the day.
(b) The RIF omits the Halachah of Rebbi Yosi ben Shaul who says that when there is no rooster nearby, and one checked the nest before Yom Tov, the egg found there on Yom Tov morning is prohibited. The words of RABEINU YEHONASAN MI'LUNIL imply that he understands, according to the Rif, that even if one did not check the nest before Yom Tov there is still a doubt about when the egg was laid, and it is prohibited because of that Safek (in contrast to the view of Tosfos).
However, the Gemara clearly states that if one did not check the nest before Yom Tov the egg is permitted. How does the Rif explain the Gemara?
The Rif learns that the Gemara is in accordance with the opinion of Rav Papa (3b) who maintains that a doubtful "Davar she'Yesh Lo Matirin" is permitted in the case of a Safek d'Rabanan, in contrast to the opinion of Rav Ashi (4a) who prohibits the item in such a case. Since the Halachah follows the opinion of Rav Ashi in the case of a Safek d'Rabanan which is a "Davar she'Yesh Lo Matirin," the egg in this case, too, is prohibited.
This also seems to be the opinion of the RAMBAM, as the TZELACH (7b) points out.