The importance of neutral null for understanding evolution

Okay, but the article is mostly not about adaptations or phenotypes, it's about evolution in its broadest sense: changes in the sequences of genomes. Most of these changes have no effect on phenotype; others have effects which may not be adaptive.

Junk DNA is real, although it also serves as a broad canvas on which selection can subsequently act. Pervasive transcription doesn't mean pervasive genomic adaptation.

A significant number (perhaps even a majority) of biologists seem to hold views akin to a naive adaptationist outlook, which demonstrably leads them astray in their interpretation of data. The proportion of the educated public holding these views is even higher. Richard Dawkins has a lot to answer for.

Above all, a simplistic adaptationist view of evolution is not only inaccurate, ignoring the last half-century of developments in the field of population genetics, but also misses a lot of the (often subtle) detail that makes evolutionary biology so interesting.

If I'm understanding you correctly, you're saying that evolution is a tautological collapse of the "why" in "why do we exist".

Let me explain: evolution is a massive, groping search in the ultrahigh dimensional space of possible organisms, one that is solving for fitness by literally obliterating less fit entities from existence. So fitness is actually just "what is good at existing", which, given enough iterations, will determine what actually exists anyway.

So now we can simply substitute in the answer to the question "why do we exist?": We exist because we evolved, which is like saying, we exist because we are fit, which is like saying, we exist because we exist. And that explanational ouroboros sort of levitates before us, a silent, immutable feature of the universe: we are here because we exist, because we exist, because...

And it's so easy for us to make that small, seductive step to saying that our existence is therefore inevitable. But I think that's a mistake. The tautology doesn't answer the why question; it annihilates it, dissolving the teleological question into its mechanistic refutation: WE. ARE. HERE.

Everything in creation is necessary, we just might not have need of it immediately.

Based on what you've done here there is a some unnecessary.

You're looking for purpose, but as the article states at the outset, don't ask 'what is this for'; ask 'how has this sequence evolved?'.

90% of our genome is unconserved, meaning that it is not under selection. Most of this consists of dead viruses and mobile elements. Such DNA was present for its own purposes while it was active but is long since dead. A tiny proportion of this junk is later co-opted by the host organism.

The null hypothesis is that junk DNA is junk. It survives in the genomes of species with small effective population size because its selection coefficient is too small for it to be purged.

The alternative hypothesis you gave would need evidence to support it, otherwise it's another 'just so' story. Ask yourself, if this junk is beneficial for adaptation as you hypothesize, why don't bacteria have any? More broadly, why is the amount of junk DNA indirectly proportional to the effective population size (as the null hypothesis predicts)?