Knots in the leash

I have a box on the floor where I toss my dogs' leashes when I'm done walking them. More frequently than I would expect, when I take out a leash, it has a knot in it.

Once it is in a knot, it takes concentrated intelligent effort to untie it. If leashes having knots were just bouncing around in a cell like molecules do, they would, on their own, untie less frequently than they form knots (assuming there were no molecular forces tending to prevent knots from forming).

Knots, once tied, are stable. They tend to persist. You don't need God or angels to explain this behavior.

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Protein molecules are usually polypeptides, meaning, they are a long chain of amino acid molecules strung together (like pearls on a necklace); sometimes as many as 27,000 amino acids long.

Due to various kinds of molecular forces, proteins fold up into a shape specific to each kind protein. This shape is essential for the protein to perform its function in the cell (just like the shape of a coffee cup is essential).

And ditto for all other kinds of molecules in the cell; they all have characteristics which are essential for their proper functioning — shape, electronic forces, size, mass, etc.

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The knot in the leash is a good metaphor for how evolution works. I randomly toss the leash into the box, and aspects of its shape results in knots when I retrieve it. The knot is inherently stable.

In evolution, many many kinds of molecules are bouncing around inside the cell. DNA molecules are inherently stable, but changes to them can sometimes occur — mutations. These mutations are sometimes stable also.

Then, the DNA is used to create a new individual organism via reproduction, and it develops using this new DNA. Usually the results are unfavorable, and the organism doesn't develop properly and dies. But sometimes the organism survives this.

Once "in the wild", competing with other creatures of the same as well as different species, the inherent characteristics of the effects of this new DNA gets tested. Usually it is harmful or has no effect. But occasionally the effect is beneficial and the organism is better able to reproduce and to pass along the new DNA.