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The importance of neutral null for understanding evolution (nih.gov)
95 points by jonathansizz on Jan 16, 2017 | hide | past | favorite | 32 comments

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!

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.

> evolution is a massive, groping search

It's not a search. There is no goal, no searcher, and nothing to find. The word evolution was chosen deliberately in its meaning of a dynamical system moving through state space. Not searching: just evolving.

In a banal sense, it's correct to say that there's no searcher, no goal to evolution. As far as we know, "natural selection" isn't "real" in the sense that electromagnetism is "real"; natural selection is just a staggeringly convenient shorthand that refers to the multitude of ways organisms can die. But if we go further, and think of evolution as a mere random walk through state space, we've suddenly lost all explanatory power. The independent emergence of echolocation in whales and bats, for instance, becomes a brute mystery.

Evolution only makes sense if we think of it as as some kind of massively parallel Monte Carlo that's weighted to explore regions of the state space with high fitness. So it's perfectly valid to talk, as biologist do, of selection pressures and directional selection, because- and here we've come full circle- there is a goal to evolution: to exist.

And, to exist with a minimum of fuss. Why do people get cancer, or get feeble when old? Well, if the organism can reproduce and support their offspring well enough, given the eco-niche and available calories etc, then they are Fit. So, just enough avoiding cancer to work out in the end.

Kind of like the space program, where everything is made by the lowest bidder.

While Evolution clearly doesn't have any "goal" I wonder if we can say that it directs to the goal that is constantly changing (that is, a goal only known once some organism is there)?

No, you can't. There is no look ahead at all. No gradients are available to measure. Without looking ahead, the notion of a goal is meaningless.

It's a random walk with probabilities changing from 1 generation to the next based on surviving geno/phenotypes.

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.

"Reading too deeply into things that have simpler explanations" is a hallmark of Kabbalah, which it sounds like the op has read into. Also, acid trips.

I haven't studied Kabbalah, nor have I tripped on acid. I studied folk Christian mysticism, as passed to me from my grandfather (oral tradition). I also used the internet and other resources to dig into the language and history.

You may find both interesting! And I hope that my comment didn't/doesn't seem accusatory, I'm coming from a similar spiritual standpoint myself.

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.

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.

I think you would enjoy listening Jordan B. Peterson's comments on the links between evolution and the stories of the Bible. It is very interesting.

https://en.wikipedia.org/wiki/Jordan_Peterson https://www.youtube.com/user/JordanPetersonVideos http://jordanbpeterson.com/2016/12/podcast/

> 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.

Could you elaborate on why you see that as reflecting evolution? To me, being consistent with past and future means stasis and would preclude the evolution of such diverse lifeforms as we see today.

If you have not read it, you might be interested in John Walton's The Lost World of Genesis 1

there is no purpose in biology, there just is

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.

$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.

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

The article isn't saying there is no adaptation; obviously there is and we have evidence for much of it. But where we don't have evidence, we need to assume a null hypothesis of no selection. This might sound obvious to outsiders, but unfortunately it often needs to be pointed out to many biologists (who of course should know better).

> Evolution is not blind

what is your evidence for this claim?

when you say "how can we account for butterflies that mimic wing coloration Of toxic counterparts to ward off birds" there's no reason to suppose the development of that would need to be directed.

The ones with wings that didn't mimic died more.

"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.

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.

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.

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

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).

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)?

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).

"Just So Story" has been used frequently in debates within evolutionary biology and other areas of scientific debate. There's even a Wikipedia page about this usage: https://en.wikipedia.org/wiki/Just-so_story

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.

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