A number of people have asked me for my thoughts on the current Worm Controversy. I must confess that I have not studied this current episode in great detail. However, I have extensively studied a closely related topic - that of the Talmud's license to kill lice on Shabbos due to the belief that they spontaneously generate. I strongly urge anyone who has a desire to fully understand this topic to read the last chapter of my book Sacred Monsters. Meanwhile, here are the conclusions on the lice, and my thoughts regarding its ramifications for the worm controversy.
Chazal clearly believed that lice spontaneously generate. They described them as "not reproducing," and explicitly rejected the notion that they hatch from eggs.
Based on this, Chazal granted permission to kill lice on Shabbos.
We now know that lice do not spontaneously generate. There is no reason to believe that any lice ever spontaneously generated.
There were some authorities, such as R. Yitzchak Lampronti, who therefore recommended that one not kill lice on Shabbos.
Others, such as R. Dessler, suggested that Chazal were merely giving an explanation for a law whose reason has been lost in antiquity (but there seems to be little basis for this).
Another approach is taken by R. Yitzchak Herzog, and it is one which I personally believe to be the most appropriate, for a variety of reasons. R. Herzog says that even though Chazal did apparently base their permission on a mistaken understanding of the natural world, their ruling still holds true, due to their authority.
I realize that this last approach is hard for many people to understand, which is why I recommend that people read my book Sacred Monsters, which has a lengthy explanation of the reasoning behind it. Basically, as we see from several other areas of Torah, halachah has its own priorities and protocols involved in its determination, in which conforming to objective reality is only one factor and not the highest priority. Being an Orthodox Jew means accepting the halachic authority of Chazal, period.
But aside from the innate reasons for following Chazal's halachic rulings no matter what their basis, there are also consequences to doing otherwise that people do not appreciate. Once you say that we should change Chazal's rulings in accordance with our understanding of the world, there are going to be all kinds of halachos that people will argue should be changed; most people do not realize how explosive this Pandora's Box will be. And what about the ramifications for previous generations who observed Chazal's rulings? Changing halachic practice from that instructed by Chazal has the potential to fundamentally undermine Judaism.
Now on to the topic of the anistakis worms in fish. The Talmud permits certain worms found in the flesh of fish, because "mineh gavli." This means that they are generated from the flesh of the fish rather than being swallowed by the fish. (It does NOT mean that they "reached their recognizable form in the flesh of the fish".) It is abundantly clear that this is the meaning of the Gemara - first of all, from the context of the Gemara itself (which states that if worms were swallowed, they would only be found in the gut), and second, from the fact that such spontaneous generation was clearly absolutely normative belief for Chazal and there is no reason to suspect that they meant anything else.
As with lice, we know that this belief is mistaken. But as with lice, I would again concur with Rav Herzog (and R. Dessler, though not for his reason) that Chazal's ruling still holds true regardless. Claims that Chazal "weren't talking about the worms that we see" are unconvincing, to say the least. From what I understand, there is no convincing reason to believe that the physiology and life-cycle of these worms, or the way in which fish are processed, has changed (in a relevant way) since the Gemara/ Shulchan Aruch (although I am, of course, open to being corrected on this). And it is unreasonable to say that Chazal were referring to a different species altogether, and thereby entirely misleading everyone for centuries into believing that all worms found in the flesh of fish are permitted. The Shulchan Aruch likewise gives blanket permission for worms found in the flesh of fish. Chazal permitted such worms; for thousands of years, Jews have been eating such worms; thus, it is still permitted to each such worms.
To say otherwise is, in my view, opening a very dangerous can of worms.