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I used 'in ways' for 'how' in the following sentence. Is this correct? I appreciate it if you provide other examples using 'in ways'.

In this view, imagination can be utilized to imagine universe both “in ways it is” and “in ways it is not”.

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You're missing the word the in front of universe, but aside from that this is correct.

In this view, imagination can be utilized to imagine the universe both "in ways it is" and "in ways it is not".

Now, that doesn't mean that in ways and how are interchangeable and have the same meaning; they're not.

When you use how, you're talking about one perception of the universe in each case. How is saying there's "the way it is" and "the way it isn't". One way it is, one way it's not.

When you say in ways, plural, you're referring to multiple imagined ways in each scenario. "These are the different ways we can look at the universe, and they're true" and "These are the different ways we can make things up about the universe, and it's not really this way". So plurality is the main difference.

As for other sentences using in ways, here are a few off the top of my head:

In many ways, John is smarter than Mary.

They have contributed to the project in various ways.

He wants to be involved in other ways.

As I tried to think of examples, it occurred to me that in ways is rarely used without a word in the middle. It works in your example because it's a short descriptive phrase, but I think the in could (and possibly should) be removed from the part in quotes. That is:

In this view, imagination can be utilized to imagine the universe in both "ways it is" and "ways it is not".

Note how the "is" was removed from the second quoted portion (it carries over to both quotes), and how I switched the order of in and both (though that's a stylistic thing, either way is correct).

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