The greatness of (a scholar's) wisdom is in no way belittled if in a later generation it is discovered that some of the things he maintained or accepted on the authority of others are unreliable. The same is true for Chazal in these areas... Imagine if a scholar such as Humboldt had lived in their times and had traveled to the ends of the world for his biological investigations. If upon his return he would report that in some distant land there is a humanoid creature growing from the ground or that he had found mice that had been generated from the soil and had in fact seen a mouse that was half earth and half flesh and his report was accepted by the world as true, wouldn’t we expect the Sages to discuss the Torah aspects that apply to these instances? What laws of defilement and decontamination apply to these creatures? Or would we expect them to go on long journeys to find out whether what the world has accepted is really true? And if, as we see things today, these instances are considered fiction, can the Sages be blamed for ideas that were accepted by the naturalists of their times? And this is what really happened. These statements are to be found in the works of Pliny, who lived in Rome at the time the Second Temple was destroyed, and who collected in his books on nature all that was well known and accepted in his day.
There is no such creature as a mouse that grows from dirt. But it is perfectly reasonable for Chazal to have believed in such a creature, just as people today believe in duck-billed platypuses and other creatures that they have never seen.
Rabbi Moshe Meiselman, however, in his book Torah, Chazal and Science, has a different take on the matter.
You see, Rabbi Meiselman is caught in a difficult situation. On the one hand, he insists, as a matter of dogma, that whenever Chazal make a definitive statement about the natural world, it must be true, and to say otherwise is heresy. On the other hand, he believes that science has proven that spontaneous generation never occurs (though his basis for this is very unclear, due to his free dismissal of science in other areas). So, in this case, he is forced to making the astonishing claim that Chazal themselves never actually believed in the existence of the mud-mouse!
What of the Mishnah discussing its halachos? Rabbi Meiselman claims that Chazal were "merely familiar with the persistent rumors" about the mud-mouse, and wished to clarify its halachic status. But "they made no definitive statement" that this creature exists. That's true; still, it is most reasonable to say that Chazal presumed that such a creature did indeed exist. The Rishonim and Acharonim, based on this Mishnah and the discussions in the Gemara, understood that Chazal were attesting to the existence of such a creature. But Rabbi Meiselman, as is his style, claims that the "accepted understanding" (i.e. mesorah) regarding this Gemara is wrong.
But what about the Gemara, in which Rabbi Ami tells a heretic, who does not believe in the viability of the resurrection of the dead, to "Go out to the valley and see the mud-mouse"? Amazingly, Rabbi Meiselman still insists that Rabbi Ami was making no attestation as the existence of the mud-mouse. Instead, he was saying "Since you believe that mice grow from dirt, why shouldn't you believe in techiyas hameisim." Notwithstanding the fact that Chazal often consciously rebuffed heretics with weak arguments, or according to their own, mistaken understanding of pesukim, it is extraordinarily unreasonable to explain this case in such a way - Rabbi Ami actually told him to go and see it! Furthermore, Rabbi Ami precedes and follows his mouse-argument with other scientific arguments that are based on actual realities. Yet Rabbi Meiselman presents his explanation, which goes against the plain meaning of the words, the surrounding context, and the traditional understanding, as the "likely" explanation of the Gemara!
But there is an even more blatant proof that Chazal believed in the existence of the mud-mouse. It's from the third source in Chazal discussing this creature - and it's a source that Rabbi Meiselman entirely neglects to mention. The Gemara and Midrash explain that an exegesis from a Scriptural verse is used to deduce that such a creature transmits spiritual impurity:
"I might think that a swarming creature causes impurity, but a mouse that is half flesh and half earth, which does not reproduce, does not cause impurity. But it is logical: The rat causes impurity and the mouse causes impurity; just as “rat” is as its meaning, so too “mouse” is as its meaning (and thus a mouse that is half flesh and half earth would transmit impurity). Yet alternatively, one could say, just as the rat procreates, so too the mouse referred to is one that procreates, which excludes a mouse that is half flesh and half earth and does not procreate! Therefore it teaches us, “[And this is impure for you] amongst the swarming creatures (basheretz) [which swarms on the land]”—to include the mouse that is half flesh and half earth, that one who touches the flesh becomes impure and if he touches the earth he remains pure." (Midrash Sifra, parashas Shemini 5:6; Talmud, Chullin 127a)Chazal actually had a derashah from the Torah specifically for the mud-mouse! Now, while some people are comfortable in saying that Chazal's drashos were their own inventions, and could have a mistaken basis, I'm pretty sure that Rabbi Meiselman does not fall into that category. Furthermore, in the prologue to the book, Rabbi Meiselman insists that even in cases where Chazal make mistakes in Torah, we do not have the right to point it out. It's no wonder that Rabbi Meiselman omitted this Gemara from his chapter on the earth-mouse - there's no way that he can quote it and maintain his approach.
(As an aside, the Gemara in Chullin, which presents the mud-mouse as an opposite case to para v'rava, shows that "ain para v'rava" with regard to lice refers to spontaneous generation, in contrast to the strained apologetics of Dr Betech and Rabbi Meiselman.")
It is ironic that at the end of the chapter, Rabbi Meiselman has some weasel words about how he "makes no claim" that his approach is "definitely the correct one" and the correct approach "may be different altogether." He's made it clear that spontaneous generation of mice does not happen, and he's made it clear that to believe that Chazal made a false attestation is heresy. So which different approach is he allowing room for?
What of Rav Hirsch? Well, as noted in an earlier post, despite Rabbi Meiselman's presentation of his book as a definitive guide to Torah and science, and Rav Hirsch's essay being the most substantial pre-20th century treatment of this topic, Rabbi Meiselman omits any mention of Rav Hirsch's essay. Presumably this is because, according to the dogmas that Rabbi Meiselman sets down and claims to be based on tradition, Rav Hirsch's essay is heresy.
Chazal discussed the halachos of the mud-mouse. They had a specific drashah from the Torah to refer to the mud-mouse. They told heretics to go and look at the mud-mouse. It's unreasonable in the extreme to claim that Chazal were not convinced that such a creature exists. Yet this is what Rabbi Meiselman insists upon. And he further insists that if you agree with him that there is no such thing as spontaneous generation, then you are committing heresy if you accept the view of all the Rishonim and Acharonim who disagree with his understanding of the Gemara, and who explain that Chazal were indeed attesting to such a creature!
Perhaps even more disturbing is how in order to try to pull this off, Rabbi Meiselman omits any mention of the crucial Gemara about a derashah for the mud-mouse. Even more ironically, in the conclusion of the book (p. 673), where Rabbi Meiselman repeats why only a person such as himself is qualified to write on these topics, he says that it must be dealt with by "sincere and qualified scholars, interested only in truth." Is omitting crucial Gemaras and prominent Acharonim, not to mention bending over backwards and engaging in tortuous apologetics to avoid the straightforward meaning of the Gemara that was accepted by all the Rishonim and Acharonim, the sign of a sincere and qualified scholar who is interested only in truth?!