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You should be able to remove the Transcendent Thought tech from the game as follows:
- Make a backup copy of Alpha(x).txt in case something goes wrong.
- Open Alpha(x).txt in a text editor such as Notepad.
- In the #TECHNOLOGY section, locate the line Transcendent Thought, TranT, 0, 2, 0, 0, Thresh, ConSing, 000000000.
- Change the entries of Thresh and ConSing both to Disable and save the file.
I tested this procedure and it definitely removes Transcendent Thought from the game. However, I don't know what will happen after you research all available techs. Probably the game will crash or freeze. Do you have a reason for continuing to play long after you could have transcended or won by some other means?