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Nega'im 5:1 teaches that all cases of doubtful nega'im are to be ruled pure, with two exceptions:

  1. A case where it is unclear whether white hairs in a nega' appeared before or after the nega' itself.

  2. A case where a nega' was quarantined and appeared larger one week later, and it is unclear whether it is in fact the original nega' that has expanded, or it is actually a wholly new nega'.

What is the basis for the general principle? And why are the two exceptional cases different?

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In short, the rational is the rules of Chazaka. My answer is based on the Rash Negayim 4.11.

See Nazir 65b

MISHNA: Any case of uncertainty with regard to leprous sores is initially deemed pure until it is established that it is a case of ritual impurity. Once it has been determined to be a case of impurity, uncertainty concerning it is deemed impure. GEMARA: The Gemara asks: From where are these matters derived? Rav Yehuda said that Rav said: The verse states: “This is the law of the plague of leprosy…to pronounce it pure or to pronounce it impure” (Leviticus 13:59). Since the verse opened with purity first, this teaches that any case of uncertainty concerning leprous sores is deemed pure. The Gemara asks: If so, if the halakha is based on this verse, then even once it has been determined to be a case of impurity, uncertainty concerning it should be deemed pure as well, as this interpretation of the verse should apply to all cases of uncertainty with regard to leprosy (Tosfot explains in name of Rabenu Tam the Kushia of the Gemara: If it has been determined to be a case of purity, we don't need the verse, the Hezkat Tahara is sufficient. The Rash in Negayim 4.11 has an other pshat. He understands that the words of the Gemara משנזקק לטומאה reffer to Mishna Negayim 5. 4-5. Indeed, these Mishna in Nazir is taught also in Negayim, but there, the rule is followed by two examples. And the Rash adds that in Torat Kohanim the Tana explains the two cases thanks to two verses in parasha of Negayim. So, the Gemara addresses here a case of two sores, one of them enlarged and needs to be impure because of the פשיון, enlargement. But we don't know which of the two. Thanks to the verse ואמא הכהן אותו, we know that the Cohen can make impure a specific sore. So we don't need the verse of Rav Yehuda. So the Gemara says that the verse needs to address the second case, of two sores that enlarged and then shortened. But one of them is is still greater than it's initial size. We know thanks to the verse וטהרו הכהן that the doubtful sore remains impure. Thus, the verse of Rabbi Yehuda cannot make it pure).

Rather, when this statement, that Rav Yehuda said that Rav said, was stated, it was stated with regard to the following dispute in a mishna concerning an uncertain leprous sore (Nega’im 4:11): If the snow-white leprous sore [baheret], which is one sign of leprosy, preceded the white hair, which is another sign, he is impure. This halakha is stated in the Torah (see Leviticus 13:3). And if the white hair preceded the baheret he is pure, as this is not considered a sign of impurity. If there is uncertainty as to which came first, he is impure. And Rabbi Yehoshua said: Keiha. The Gemara asks: What is the meaning of keiha? Rav Yehuda said: Rabbi Yehoshua pronounced the matter unsolvable and ruled it is pure (Tosfot in Nidda 19a explains that the natural course of the disease is tha the skin became white first and further the hair becomes white, this is against the Chezkat Tahara and this leads Tana Kama to say he is impure, but Rabbi Yehoshua, according to Rav Yehuda learns from the verse that the Chezkat Tahara is not altered, but Rabenu Tam explains that they tell about a man who was Tame (1). And the Rash says that the man was not impure, but because the first חצי גריס was here without white hair, we are almost sure that the second חצי גריס too was already here before the hair became white.). The Gemara further asks: And perhaps this means that he pronounced the matter unsolvable and ruled it is impure (Tosfot explains that perhaps Rabbi Yehoshua is more stringent than Tana Kama, Tana Kama rules that is Tame from Safek and Rabbi Yehoshua Tame Surely)? Rav Yehuda said that Rav said: The verse states: “To pronounce it pure or to pronounce it impure” (Leviticus 13:59); since the verse opened with purity first, any case of uncertainty concerning leprous sores is deemed pure.

(1): See the Rash in Mishna 4.11. following the pshat of Rabenu Tam in Gemara, the answer is that in the case of the Machloket rabanan and Rabbi Yehoshua we have no Chezkat tahara. The man was muchlat because of a previous nega. This explains why rabanan make him impure and why Rabbi Yehoshua needs a verse to make him pure. This man has already a first nega which was muchlat, and then, a second nega appeared. The rule is that the Cohen will not see the second nega until the first nega recovered. So, now the first nega recovered and he looks at the second nega. For this second nega we are dubitative, the white he was here before the nega or after. Rabanan rule the safek as impure, Rabbi Yehoshua rules it as pure. The reasoning of Rabbi Yehoshua is Chezkat haguf against Chezkat tumea. Both are chazakot demeyikara.

Now we can read the Mishna, thanks to the Rash in the previous Mishna..

כל ספק נגעים טהור וכולי עלמא every doubt in negayim is pure, everybody agrees to this rule because of the Chezkat tahara,

חוץ מזה דפליגי except for the case of the previous Mishna, in which there is a disagreement between Tanayim.

For this there are three opinions in the Rash. The Mishna is against Rabbi Yehoshua.

  1. Rabbenu Tam explanation. A man was impure because of a first sore, he was muchlat. In the meantime, a second sore appeared. For this second sore there is a doubt if the haire whitened before the sore appeared (and is not a sign of impurity), or afterwards (and is a sign of impurity). We have no prior Chezkat Tahara.

  2. Tosfot in Nidda 19a explains that there is a sore with white hair and we don't know if the sore appeared because the hair became white (and there is impurity). Since the general course of the illness is that the becomes white because of the sore, we have a chazaka against the chezkat Tahara. And the sore is impure.

  3. The Rash explains that there was formerly a sore of an half gris surface, without hair, further, a second sore of an half gris surface appeared. Since the first sore didn't appear upon a white hair, we say that similarely the second sore didn't apperar upon a white hair, but after the white hair.

עוד אחר and an other case in which Rabbi Yehoshua agrees because there isn't Chezkat haguf because there was already a sore kegris and Chazaka it's the same sore we see now, the presence of an other sore is not אתחזק, and we think that the same sore is enlarged. The metsora is muchlat. This is different from Mishna 4 because there we have an other sore from the beginning.

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I think it is because of the general rule of Chazokah - when all things are equal then a person retains his former status. In this case, he remains a non-Metzorah.

The 2 exceptions are exceptions because there's a Pasuk for each one that makes not all things equal.

I think the Yachin on this Mishnah hints/says this:

כל ספק נגעים טהור: אליבא דכולי עלמא היכא דליכא חזקה לטהרה ולטומאה:‏

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