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This is a short story I read on the Internet, probably Project Gutenberg, in the last 15 years. It's likely to be much older - '60s maybe.

Humanity was at war with an alien race. The aliens had self-guiding space mines with some rudimentary intelligence, I think they were said to be organic. The mines' intelligence made it hard for computers to predict their movements. In desperation, a researcher suggested wiring human brains directly into battleships. A retired professor volunteered for the process and his brain was removed and placed in an experimental ship. The professor then kidnapped the researcher along with his ex-wife, and used most of the ship's fuel to take them to a distant, uninhabited planet. His plan was for them to found a new race and have another go at human civilisation, with the professor as an advisor for as long as his brain survived.

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"Mr. Spaceship" by Philip K. Dick

The story is set in the distant future, where humanity is at war with "Yuks", an alien life form which does not use mechanical spaceships nor constructions but instead relies on life forms to power their technology. The war has been going on for a long time and humanity has not been able to come up with a solution against the life-form based ships and mines that the Yuks use. One day a team of researchers led by Philip Kramer decide to build a spaceship which is powered by a human brain and they find the ideal candidate in Kramer's old professor, a dying man who volunteers to donate his brain to the project.

The spaceship is built and on the first test run into outer space the team discovers that the professor made some changes to the ship, giving him—or rather, his brain—full control over the entire ship. Sensing trouble, the team flees the empty ship being piloted by the professor and evacuate into outer space. Later, the spaceship returns and kidnaps Kramer and his wife. On board the ship, the professor's brain informs them that they will be looking for a new planet to colonize to try and start a new and better world. The professor decides on this colonization because he sees no hope in humanity and what he feels it has become: a species which desires, above all else, war.

An excerpt from the Project Gutenberg copy regarding the living mines:

“Mine is very simple. These creatures are superior to any mechanical system, but only because they’re alive. Almost any other life-form could compete with them, any higher life-form. If the yuks can put out living mines to protect their planets, we ought to be able to harness some of our own life-forms in a similar way. Let’s make use of the same weapon ourselves.”

Found with a search for site:gutenberg.org mines brain spaceship

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    Thanks, quick work. I searched for various combinations of "mine" and "brain ship" but didn't think of a site-specific search. Mar 28, 2023 at 13:44
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    @PastychomperthanksMonica: It's a handy trick. I often do similar searches for goodreads.com, amazon.com, and archive.org.
    – FuzzyBoots
    Mar 28, 2023 at 13:44
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    @FuzzyBoots related - you can do image searches the same way. identify bmx site:bicycles.stackexchange.com is a good adjacent to SE's own text searches.
    – Criggie
    Mar 30, 2023 at 1:26

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