
The importance of neutral null for understanding evolution - jonathansizz
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180405/
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macawfish
Evolutionary theory is uncannily similar to the Hebrew tetragrammaton, which
is often translated into English as "I am that I am". But digging in, you will
find that it is the verb "to be" in both perfect (now) and imperfect
(past/future) tenses.

It means something like "That which is now in a way consistent with that which
has been and will be". To me, that's evolution.

This is a reconciliation of philosophy and spirituality that I have found deep
joy and peace in. I was raised Christian, and while I was never pressured to
be creationist, neo-Darwinism left such a bad taste in my mouth that at a
young, naive age, I embraced creationism as a way to rationalize things that
my heart knew to be true.

But by the end of high school, I had come to terms with the beauty and depth
of evolutionary theory. Thanks to more ecological versions of evolutionary
theory, such as symbiogenesis, evolutionary understanding has since then
become a cornerstone of my spirituality.

As an artist and musician, I also appreciate the ' _creativity_ ' embedded in
the process of evolution. Evolution says "give it a try". If it doesn't work,
it tries something new. Once in a while, something sticks; it survives its own
context some way or another. Other forms die out, like snapshots of some
greater metamorphosis. We are lucky to witness them!

~~~
Retric
It sounds like you are reading to deeply into things that have simpler
explanations. Which is the point of the article, sometimes there is no real
explanation other than it just happened that way. Sort of like how driving on
the left or right side of the road started as a competently arbitrary choice,
but now the rules are generally fixed in a given area.

However, I might not be getting your point.

~~~
macawfish
Okay, I've definitely been "guilty" of reading deeply into things that have
simple explanations. That's cause I'm curious and I love trying to understand
things! Whether or not I've dug "too deep" is feeling pretty close to a value
judgement of something that's totally relative to one's point of view. So I'll
leave that alone.

> However, I might not be getting your point.

If you weren't, it wasn't your fault, it's more because I was being a little
too tacit.

The reason for my comment was to point out a remarkable similarity between two
spiritual/philosophical frameworks that have been painted as diametrically
opposed, and whose adherents are often cast as irreconcilable enemies. I grew
up with both of these influences each in their own strong ways, and struggled
to integrate them within myself. I'm grateful that I've been able to at all.
Some people end up feeling spit out and bitter.

My point is that the Hebrew word for god is essentially "I am cause I can be".
Which is pretty close to "it is what it is". It's a very existential kind of
character, but pretty simple. It's kinda like that question recently posted on
hacker news, why does anything exist? The answer here being "because it can,
that's why".

I'm not advocating that you or anyone adopt my spiritual worldview, just
sharing my perspective. Actually, my journey has been to let go of the baggage
of institutionalized Christianity. But I've chosen not to 'throw the baby out
with the bathwater'. I still believe that traditional myths and stories,
including my own, are beautiful and interesting.

As far as the article goes, I actually take issue with the presented dichotomy
between "function" and "no function", because to me, every DNA
sequence/expression, or lack-thereof, has _some_ implication, however nuanced.
Whether or not that implication counts as "functional" or not is often beyond
the capabilities of our time machines and is philosophically up for
discussion. As far as evolution is concerned, and here's where I agree with
the article, whether or not something counts as "functional" is beside the
point. The point is that if something survived, it did so because nothing was
stopping it. Or as you say because "it just happened that way", kinda like
those "extra" notes in a jazz solo.

~~~
Pigo
This is often a tight-rope conversation in public. I live close to Creation
Museum, and regularly have to stop myself from verbally accosting my family
for occasionally wanting to "just check it out". I'll die before I give that
monument to ignorance my money. But every once in awhile I dare to walk the
tight-rope when it's brought up on social media or in conversation. People
come armed with points they want to fire off when the debate is on, they don't
like curve balls that derail their momentum. When I try to share my view of
evolution as a remarkably brilliant plan for life that formed a conscious mind
all the way from a few molecules rolling into place, one side has their head
buried in how and the other why. If there's something greater than us in this
universe, a master clocksmith setting events in motion, watching from outside
time, I find it disrespectful to deny and mock it's work. It also seems
studying and understanding it's work to be one of the greatest endeavors a
person could put themselves to. If I'm wrong, and all existence is
happenstance, then I hope my silly view of the world didn't hurt anyone.

------
amitprayal
Then how can we account for butterflies that mimic wing coloration Of toxic
counterparts to ward off birds.Evolution is not blind, we just have not
figured out the feedback mechanism yet, most likely its some kind of genetic
memory.

~~~
erelde
$living_thing with $property (wing coloration) _isn 't_ dead before
reproduction happens, $property _may_ be kept in the offsprings.

$living_thing with $property (wing coloration) _is_ dead before reproduction
happens, $property _may not_ be transmitted to the offsprings.

It's a simple enough concept at its core. Then comes the complications of
mutations, random this and that.

~~~
talideon
And further, I'd point at the observed evolution of the Peppered Moth in
response to evolutionary pressures during the industrial revolution:
[https://en.wikipedia.org/wiki/Peppered_moth_evolution](https://en.wikipedia.org/wiki/Peppered_moth_evolution)

------
mcguire
" _And the proper null hypothesis posits that it is a result of neutral
evolution: that is, it survives by sheer chance provided that it is not
deleterious enough to be efficiently purged by purifying selection._ "

This is news?

And I claim precedence on the phrase "just so story" for those things
biologists have been spouting for decades.

~~~
azakai
Yes, but it is a nuance in a specialized field, so it might seem "obvious" to
outsiders.

The article does give the background here - there are multiple positions
within evolutionary biology. All accept natural selection, of course, but the
fine details matter too. In particular here the question is a decades long
debate that Gould&Lewontin headed, saying that not all apparently-useful
adaptations evolved, some are "spandrels" that arose for other reasons.

The article mentions other reasons to suspect that things that seem useful did
not evolve, such as the surprising effect of drift in multicellular organisms
(us) vs single-celled organisms. In the latter, selection affects each
nucleotide of DNA. In the former, selection must be powerful enough to
overcome noise, otherwise it is ineffective - which seems surprising, as this
is averaged over many individuals over much time. The surprising thing is that
this effect is, it turns out, non-linear.

~~~
jonathansizz
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.

~~~
spacehacker
In this talk touches upon an interesting hypothesis that the purpose of junk
DNA might be _evolvability_ :
[https://www.youtube.com/watch?v=ZcD_L6_iBLU](https://www.youtube.com/watch?v=ZcD_L6_iBLU)

The idea is basically that junk DNA contains a memory in shape of a
distributed representation of the past of the organism and its environment,
akin to how neural networks encode information. It basically provides a basis
for fast adaptability by introducing noise into the gene expression and
morphogenesis process so as to have more versatility and robustness to explore
alternatives (very similar to dropout in neural networks).

~~~
jonathansizz
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)?

~~~
spacehacker
But the null-hypothesis remains that it is junk. The hypothesis is that it is
not junk, borrowing evidence from neural networks in which (1) things that
look like noise are actually distributed representations and (2) in which
noise improves robustness and facilitates exploration. This evidence is
possibly transferable because both processes, neural network training and
evolution can be formalized as a high-dimensional optimization problem (one
being informed by gradient information while the other just randomly mutates
and exploits ensemble effects of recombination).

------
teapejon
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.

