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This is a part of the paper "THE PERCEPTRON: A PROBABILISTIC MODEL FOR INFORMATION STORAGE AND ORGANIZATION IN THE BRAIN"

The first of these questions is in the province of sensory physiology, and is the only one for which appreciable understanding has been achieved. This article will be concerned primarily with the second and third questions, which are still subject to a vast amount of speculation, and where the few relevant facts currently supplied by neurophysiology have not yet been integrated into an acceptable theory.

Where "be subject to" seems to indicate the author is complaining the 'vast amount of speculation', and suggesting integrate the few relevant facts into an acceptable theory.

Am I misunderstanding this?

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"...are still subject to" in no way carries a connotation that the author is complaining. In fact, it is carefully neutral in tone, as is appropriate for a scientific article.

Likewise, the phrase that follows the "and" does not "suggest [integration] of the few relevant facts into an acceptable theory", but implies that this is will be the subject of part of the paper.

"This article will be concerned primarily with the second and third questions, which are still subject to a vast amount of speculation, and where the few relevant facts currently supplied by neurophysiology have not yet been integrated into an acceptable theory."

Paraphrasing,

  1. "The second and third questions are part of the topic of this article."
  2. "The second and third questions have not been answered and are still thought about."
  3. "We know some facts that might help us answer these questions, but those facts have not been organized into a theory."

The tone and connotations of 1), 2) and 3) closely summarize the author's.

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When you look up the synonyms of "be subject to",,

considering the following text after the "be subject to",

a vast amount of speculation, and where the few relevant facts currently supplied by neurophysiology have not yet been integrated into an acceptable theory.

it would be natural to guess that the OP's question is related with synonyms such as "depend on", "related with". No complaint is suggested, "suggestion" may be.

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