The first tool for thinking is our human brain. Self evident, but so basic.
Ancients established philosophy as a discipline for channeling reasoned thought. From that, in loose descriptors, grew natural philosophy, grew the scientific method.
With all the power of algorithms and computers capable of crunching huge amounts of data, there is still nothing quite as good as the human brain for pattern recognition. And for all our abilities, we cannot know the details of the world, there is much too much, we know the world through recognizable, repeating/repeatable patterns.
That's where the scientific method comes in. It helps divide the durable, inherently trustworthy patterns from the spurious ones. I love the question, search, tease out fascinating details, make the next supposition, ask the next question way of examining data used in the scientific method.
Another tool for thinking of the world, though, is poetry. And I'm not talking just the pattern in form poetry. I'm talking about how a line carries a little surprise, in the words, their layered meaning, the single line, how the line spins into the strophe/stanza, how the stanza swirls together to a piece.
A physicist friend of mine recently spoke for about fifteen minutes about how the brain will create the notion of pattern around what is just chaotic nonsense, and he used as his illustration the spurious patterns we imagine we find in Lewis Carroll's poem Jaberwocky.
Oh, but wait. Take for example the second and third verses:
"Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
The frumious Bandersnatch!"
He took his vorpal sword in hand:
Long time the manxome foe he sought--
So rested he by the Tumtum tree
And stood awhile in thought.
If I take out the silly words and replace them by implied idea, reading context, we get advice from a father adressing his son (or any younger man) to beware this dangerous thing with "jaws that bite, ...claws that catch," and shun that thing whose very name sounds hazardous. And then, after a long time seeking the foe, father takes his sword and stands by a tree where he rests and thinks and gives his advice. And so goes the whole poem. What is a more known, familiar, very real-world and reliable pattern than for an elder to give advice, painting the picture of his own experience to back it up?
Carroll's own suggestions meaning and not-meaning imply some push-pull between providing interpretation vs. going even farther into intentional confusion, i.e., he suggested the poem be republished in reverse printing. The publisher told him it would be just too expensive. So Carroll is left with a standard English alphabet, and many interspersed meaningful, familiar words. So it is with so much of the back and forth between intuitive knowing and provable pattern.
What will scientists make, for example, of the four-letter alphabet of our DNA, and the "junk" they find there? I'd be willing to bet that the "junk" isn't, that it's just that we don't understand properly yet. I see a reality where the imagination of the poet and the rigor of the researcher following the scientific method, both, are useful to find a dependable answer to whatever questions we might think to ask the ocean sky.
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