Many of those who hold that Chazal never made mistakes in science, rather their science is part of Torah shebaal peh and was received at Har Sinai, explain seeming conflicts between torah and science by saying נשתנה הטבע, nature changed. IMHO, this is an untenable position for the following reasons.
1. They hold that all of Chazal's science is part of Torah. This means that when Chazal said that remedy x cures sickness y, that was part of Torah, it was received at Har Sinai. Why doesn't it work today? The world changed. This makes no sense. Torah preceded the world by 2000 years (Gemara Shabbos). Hashem created the world by looking into the Torah. How can you say that things in the Torah are no longer true? For over 4000 years remedy X cured Y, suddenly after the era of Torah Shebaal Peh ended the world changed so this stopped working and the torah became untrue, why would Hashem do such a thing? It makes Torah into a joke. Why would Hashem change the world so that Torah no longer reflects the world if the world was created based on Torah.
Even more then that, this seems to contradict the Rambam's principle of the immutability of Torah. Torah has now changed. It used to be that the Torah provided a rememdy for sickness Y, now it no longer does. It used to be that the Torah explained various natural phenomena, now it doesn't. In other words the Torah changed because it no longer reflects the physical world.
2. If Chazal had a kabbala (tradition) about science you would think that they would have had a kabbala that the world is going to change and that the science would no longer be true. נשתנה הטבע should also be part of Torah. After all, if you are going to claim that all of science is in Torah then this very important fact should be there as well. Yet, Chazal never even hint that the scientific pronouncements that they are making are only temporary. They didn't say that remedy X will only work for a limited time. they made a blanket statement that remedy X cures Y. It is clear that Chazal had no idea that נשתנה הטבע was going to happen, why not? If Torah included science it should have included נשתנה הטבע as well.
3. There is not a shred of evidence that נשתנה הטבע. Remember, the Geonim who lived only a few hundred years after the time of the gemara already stated that the cures of Chazal don't work, that is a very short time. Here are some examples of things where it is quite implausible to say that נשתנה הטבע.
a. The Gemara in Bava Basra (25a) states clearly that Chazal held that the Sun revolves around the Earth and that the Earth is surrounded by a roof that the sun goes out of at night (see Chazal and Mistakes in Science for more about this). It would be preposterous to claim that in the times of Chazal the Sun revolved around the Earth and went out a window but now נשתנה הטבע and the Earth revolves around the sun etc. Everyone can understand that such a change didn't happen.
b. The gemara seems to say that lice are born from spontaneous generation. again it is not plausible to think that in the times of Chazal there was spontaneous generation but in the last 1500 years it stopped
c. The gemara states that the mother contributes the blood to the baby (based on this some poskim didn't want to accept blood tests to establish paternity). It is implausible to think that the whole nature of human development changed after the time of chazal.
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In fact, I don't see a single torah science conflict where it is plausible to say נשתנה הטבע.
Based on the above, it is clear that נשתנה הטבע does not answer any contradictions, rather it is a copout, meaning that we have no answer. The real answer would seem to be like those Rishonim and Acharonim who hold that Chazal did not have a kabbala on science and therefore could make mistakes in science.
Update
I found a fascinating site השתנות הטבעים which has a long list of things where what Chazal say doesn't fit the scientific facts of today. If you look at the list (which is only partial) you will see that it is quite large. To believe that in all of these things נשתנה הטבע is quite a stretch for anyone. Here are just some of the changes related to the human body. You would have to believe that the human body changed drastically as
a. none of the remedies of chazal work
b. the things that Chazal say are dangerous are not (e.g. eating or cooking fish and meat together), and things tht Chazal say are good for you (rotting fish) are dangerous
c. Genetics changed (it was once a good thing to marry your niece)
d. all things about birth and a baby's development changed (see 7, 8 , or 9 month pregnancies), the position of babies when born, women don't get pregnant from the first sex act, etc.
e. all things related to hilcho nidda changed - until when a woman can give birth (60 if she gets married before 20), when does a women stop menstruating when pregnant, how long does a woman not menstruate after birth, the whole idea of וסתות and הרגשה
f. various halachos related to mila such as washing the baby on the third day, metzitza bpeh (which was considered to be necessary to ensure the safety of the baby).
g. the din of פצוע דכא
h. various foods/actions that are קשה לשכחה
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To say נשתנה הטבע on one of these maybe, on all of these (and this is just a drop in the bucket) is clearly ridiculous, there is absolutely no evidence that from the time of Chazal until the time of the Geonim/Rishonim, who pointed out many of these, (which is a few hundred years), or even modern times, there were wholescale changes in humanity such that all of these changes could have taken place.
Update 2
R' Feldman writes As the Leshem cited above says, if even regarding matters which are not related to halacha, the Sages say, sod Hashem liyerav, “G-d reveals the secrets of nature to those who fear him,” then certainly there must have been siyata dishmaya (Divine assistance) and even ruach hakodesh (a Divine spirit) assisting the Sages in their redaction of the Oral Law. It is therefore inconceivable, to these opinions, that G-d would have permitted falsities to have been transmitted as Torah She-be-al-peh and not have revealed His secrets to those who fear Him.
My response to this is that according to him it comes out Hashem transmitted information as Torah Shebaal Peh that then became untrue because Hashem changed nature. Is that any more conceivable? Is it any more conceivable that Hashem would reveal scientific facts in Torah and then change nature to invalidate that revealed Torah without telling Chazal (after all Chazal in their scientific pronouncements never even hint that things will change)?
In other words his argument falls apart because even according to him hashem did not reveal everything to chazal because bottom line, we have a gemara full of remedies that don't work. Using his logic, how could it be that hashem didn't reveal the secret that nature was going to change? How could he have allowed Chazal to put remedies and other scientific facts in the gemara that were going to change?
