Brad!
Have you posted in the clam forum at RC yet? I did and got nothing useful out of it, but maybe since you have PICTURES it will trigger some responses.
It seems to me this is part of the byssal gland. As to why it would do this, is completely beyond my speculations. The only thing I can think of, is that I had had some uncontrolled temp spikes a few weeks prior, and I subjectively felt that ever after since that, that the clam had not been expanding its mantle as much as it was prior to the spike. But why would this lead to the gland sticking out the inhalant siphon, and why would this happen a few weeks later (as opposed to right away)?
Or is it the byssal gland, maybe it is something else.
At any rate I was at a complete loss ... I did not know what to do, so I left it alone, continued feeding DT's, etc. But unfortunately, one day, poof, it was gone. So leaving it alone wasn't good enough ... There were no clues the day before that it was out to blink out (other than the lack of expansion for the few weeks prior). Just a nasty surprise one morning. :(
Good luck. And if you find anything out, please let me know too. I really, really would like to know the cause of this phenomenon..
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