Interestingly, warm-blooded animals (including humans!) tend to have simple genomes compared to cold-blooded ones or similar complexity. It's just much easier to get repeatable results during development when you can do all the trickiest parts at fixed temperature, a human can use a single gene to achieve what a frog needs half a dozen for.

Humans outsource a lot to the microbiome. We have to add up all that too!

As far as we know, all complex organisms have an accompanying microbiome of commensurate species, even the most basic ones like marine sponges [1]. Plants nurture these symbionts in their roots while animals do it in their digestive tracts (mostly, both have surface microbes too that do various things too).

[1] https://www.nature.com/articles/s41396-020-0591-9

The reason for this is that chemical reaction rates are temperature dependent, and cold blooded animals need different systems of chemicals/proteins to keep them operating over significantly different temperatures.

I wonder to what degree the competitive advantage of being warm blooded consists of the smaller genome vs. more obvious advantages like ability to stay active in colder climates.

This is super interesting! Can you share more info/resources?

Moral of the story, if you notice you have to deal with a multitude of states, get out of that swamp first, get some foundations right and then iterate. Applies to both biology and coding.

On the other hand, the human body is super-reliant on very nearly exact temperature regulation. A few degrees can kill us easily. Cold blooded systems are substantially less reliant on pristine conditions.

Warm blooded systems though can power high energy activities like maintaining a large brain, which could figure out how to get warm.

A few degrees can kill a human only in theory, in practice a human would wear a jacket or seek shade.

Octopi are cold blooded and smart

But they live in a fairly constant temperature environment compared to a land reptile for example.

Update: they do some funky stuff https://www.sciencedaily.com/releases/2023/06/230608120915.h...

> The octopuses achieve this by editing their RNA, the messenger molecule between DNA and proteins.

Lesson number two: if you cannot avoid dealing with multiple states, consider monkey patching. The result might resemble an eldritch horror, but at least it will work.

No wonder they die so young

A few degrees kills many, many people every year. I didn't say a few environmental degrees, I said a few degrees of regulated temperature. All it takes is a tiny little virus to make your immune system eat itself and kill you with your own heat. That's a very good example of a system that is highly reliant on the right environment to operate properly.

So, expressing your genes at 37°C is a bit like running your code from Docker image?

"Well, it runs on my machine" - some small mammal, ca. 50 million years ago

So, indication of advanced evolution: outsourcing some of our development to other lifeforms (e.g. microbiomes)

I wonder if someone would take human DNA and all the necessary bits and cloned one on another planet completely alien to Earth: would that human being have a bad time because of the missing microbiomes or will they somehow grow their own (I'm thinking gut bacteria and microbiomes and so on)?

A lot of research is performed on “axenic” mice — mice without any biome.

I do not think this is generally true. Do you have a citation?

Endothermy vs ectothermy is much more about aerobic vs anaerobic metabolism.

Endotherms can sustain high levels of physical activity for hours and days. An ectotherm is lucky to go one minute.

Nick Lane’s fabulous book:

“Power, Sex, Suicide: Mitochondria and the Meaning of Life” is the right place to start.

We touched on polyploidy in genetics of course but I don't recall anything that was particularly salient insofar as resistances. In humans xploidy typically results in either excessive protein expression or compromised (≤50%) protein expression - in many cases this is fatal or seriously damaging in terms of fertility/development. There are exceptions, for instance the mammalian liver has polyploidal cells.

But plants are way different in terms of habit, think about evolving to sit in the same place for a hundred years...

These for example could have epigenetic crosstalk between their environment (epiphytic nature) and their hosts. E.g. a special chromosome for birch vs oak. Or drought vs monsoon. Given the endpoint of the species is purportedly 350mn years it stands to reason that a highly specialized and nuanced system of regulatory pathways may have emerged. Sequence data and genomics would be revelatory.

It wouldn't surprise me if there was specialized information per-host which was regulated by signal produced by the host, I think this would explain redundancy pretty well. Different epigenetic pathways operating on different x¹ chromosomes yielding differential response to discrete small molecules/proteins/hormones produced by host species which prove beneficial in the looong run. This could have a whole cascade of effects or just subtle SNP differences which yield fitness enhancements. Essentially each one being a subroutine for each host case producing local optimums.

But I'm just a scrubby undergrad so with a grain of salt. There's probably many other more reasonable explanations, it's biology, biology seeks to find exceptions to every rule by its nature.

Weird, since ferns’ fractal growth plan lends itself so well to simple recursion.

Maybe most of the genome is just a long comment explaining why they can’t use recursion.

Or maybe the simple growth plan allowed it to accumulate lots of cruft that’s basically doing nothing

We used to think huge amounts of our own genome didn't do anything.

But it is true that huge amounts of our genome don't do anything. There are sequences where the same letter or string repeats thousands of times. There are many copies of things that have accumulated mutations that make them non-functional.

The idea that repeated sequences in certain genomes are non-functional or 'junk' is questionable, as they provide additional encapsulation to chromosomes with cell nuclei (a sort of fault tolerance).[0]

[0]: https://www.sciencedirect.com/science/article/pii/S108495212...

Computer architectures sometimes necessitate no-ops under certain circumstances to facilitate functionality. Even though they're no-ops, they're not useless. To the contrary, they have very specific and required uses, which is why they exist.

Evolution works on integrated systems, not parts. Which goes a long way toward explaining why life doesn't seem to have any single-use components - everything serves multiple purposes. We just don't understand them all yet.

That hasn't changed. It's still ~90% junk.

  Total Essential/Functional (so far) = 8.7%
  Total Junk (so far) = 65%
  Unknown (probably mostly junk) = 26.3%

  https://sandwalk.blogspot.com/2011/05/whats-in-your-genome.html
  https://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html

There's a reason for everything.

There is a reason for all the junk in my drawer, but it is still junk.

In cases like this why don’t they try grow a fern that only has genes with an identified purpose and go from there?

Biology only cares about elegance when it substantially contributes to fitness, otherwise entropy is the natural way of things!

Natural selection leaving review comments: lgtm

:shipit: haha

It’s my (very simplistic and layperson) understanding that the size of an organism’s genome is more correlated to how long it has been evolving, rather than any specific complexity of the organism. Since ferns are one of the oldest organisms known to science, it makes sense that their genome would be relatively large.

I don’t remember when/where I heard this, it may very well be BS.

It's an active area of research but there's no consensus on why this happens other than hand wavy evolutionary biology stuff. The most interesting mechanism is paleopolyploidy [1] where the whole genome of the organism is doubled due to hybridization or DNA replication errors and from that point on the duplicates start diverging. It has occurred at least once in most flowering plants and it must have happened several times with this fern. Normally after this kind of event, the genome is paired down and duplicate genes are "silenced" in a process called diploidization [2] but if there are a bunch of transposable element, they might differentiate the copies enough to keep them before the process completes.

[1] https://en.wikipedia.org/wiki/Paleopolyploidy

[2] https://en.wikipedia.org/wiki/Diploidization

There’s a recent veritasium video on jumping spiders. Turns out some of them evolved red colour eyesight in multiple independent ways, one example involves replicating a green colour vision gene and then mutation, another one adding a filter on top of green colour receptors, forcing neurons to activate on red instead!

Well it makes perfect sense, after all you have to water plants. So, they can’t be DRY.

Thanks, I need a LOL moment today and you gave it to me! Good thing I didn't soil myself in the process...

Unimportant, but "pared" down, not "paired".

Life...uhhh....finds a way

- Jurassic Park

It is common for human cancers to be polyploid after accumulate whole genome doublings (WGD), where a tumour cells goes from being approximately diploid to tetraploid. Different tumour types have higher rates of WGD, for example, glioblastoma, ovarian cancer, and pancreatic adenocarcinoma. But what usually happens is that the tumour loses parts of the doubled genome to reach a ploidy (average copy number across the genome) of 3-4ish.

> there's no consensus on why this happens other than hand wavy evolutionary biology stuff

This reminds me of a comment about chess - there may be certain abstractions, lines/strategic patterns with meaningful relations "in the big", but in the small, like with endgame tablebases, small differences in state have an effect on the outcome of the system that is difficult to explain/predict because it seems to be random.

Like looking into an extremely compact fractal phase space instead of more predictable/seemingly geometrical ones.

This is like template metaprogramming :)

You're confusing the difference between macros and functions, only functions fully avoid duplication (except when they are inlined!)

Macros are expanded into text by the preprocessor. Templates are expanded by the compiler instead.

Real macros (lisp-style not C-style) are more like template metaprogramming, too. It's not clear which source language GP comment is referring to.

Actually c++ later seems to evolve a similar way : see part 2 of 4 of this series : https://deque.blog/2017/05/09/lisp-meta-programming-for-c-de...

Plants are tolerant of gene duplication, possibly related to the fact that their stem cells are permanently active (which is why you can take a branch tip and get it to grow into a whole plant, quite unlike the efforts needed to clone Dolly the sheep). Their development is thus remarkably plastic (so you can get trees at the snowline that look like small shrubs, while the same species grows into tall straight trees a few thousand feet lower). In contrast, gene duplication at a large scale in any animal would probably fundamentally mess up body plan development in non-survivable ways.

Plants might be under active selection for gene duplication since it does allow rapid evolution and facilitates spread into new environments:

Evolution of Gene Duplication in Plants (2016) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972278/

> In contrast, gene duplication at a large scale in any animal would probably fundamentally mess up body plan development in non-survivable ways.

While unusual, polyploidy in mammals is survivable, there's a species which is tetraploid:

https://en.wikipedia.org/wiki/Plains_viscacha_rat

The wiki exaggerates the degree to which this claim is controversial, fwiw. Better than the alternative, probably.

Plants are considerably simpler than animals so they tolerate a lot more genetic nonsense. Crazy things like duplications which would simply result in non viable animals most often don’t have nearly the harmful effects in some plants so they survive and aren’t nearly so aggressively pruned out by evolution.

Without plant based life, there are no humans, so we are technically using those genes.

Until a better story emerges, I'm imagining that fern mode is just what we see when it is dormant. Perhaps if we prod it in the right way it will wake up and show us its true colors.

Love this! Like when we accidentally discovered the axolotl can turn into a salamander if you stress it enough.

one theory is it is anti-viral. can't infect a gene you can't find because it is a needle in haystack

Perhaps they need that code to deal with the extreme environmental changes day to day due to being in a fixed location.

It makes sense to me. If you can't move (or can't move much) there'll be less variety in what you can take in, and some simple strategies for dealing with stressor don't work, so there is more need to be able to synthesise a wider variety of things.

If we count evolution as amount of genes evolved in the genotype, onions are five times more evolved than us.

But lot of this consists into redundant copies of the same information and another big chunk is included garbage borrowed from attackers. This fern could have a lot of things trying to finish it, an a lot of time to think about the problem. And of course could be also an hybrid or an hybrid of several hybrids.